diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 2936c4d..0000000 Binary files a/.DS_Store and /dev/null differ diff --git a/.gitignore b/.gitignore index 842e969..82a96fc 100644 --- a/.gitignore +++ b/.gitignore @@ -146,3 +146,7 @@ polyconf_examples/PMMA_* polytop_examples/data/ethylamine_dendrimer.* polytop_examples/data/four_arm_star.* polytop_examples/data/pei_linear_polymer.* + +# OS X nonsense + +.DS_store diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index 07ffcf5..b722986 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -1,31 +1,29 @@ -PolyConstruct +Getting Started with PolyConstruct =============== This page details how to get started with *PolyConstruct*. The design, testing, and validation of *PolyConstruct* is detailed in the manuscript *"PolyConstruct: adapting biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop"*, by -***Rangika Munaweera**, **Ada Quinn**, Luna Morrow, Richard A Morris, Megan L O’Mara* +**Rangika Munaweera**, **Ada Quinn**, Luna Morrow, Richard A Morris, and Megan L O’Mara* -Getting Started -=============== **Installing PolyConstruct:** -From your home directory, clone *PolyConstruct* from GitHub: +From your home directory, clone PolyConstruct from Git: .. code-block:: python cd ~ git clone https://github.com/OMaraLab/polyconstruct.git -Then navigate to `~/PolyConstruct`: +Then navigate to polyconstruct: .. code-block:: python cd polyconstruct -To setup an environment for *PolyConstruct*, run: +To setup an environment for polyconstruct, run: .. code-block:: python @@ -34,7 +32,7 @@ To setup an environment for *PolyConstruct*, run: pip install -r requirements.txt -Then, build the *PolyTop*, *PolyConf* and *PolyBuild* packages: +Then, build the PolyTop, PolyConf and PolyBuild packages: .. code-block:: python @@ -86,8 +84,8 @@ Monomer design For both *PolyBuild* and *PolyTop*, monomer parameters should include all monomer atoms that will be present in the simulation model of the final polymer, and dummy atoms correesponding to connectivity with adjacent monomers. The method for preparing monomer .itp depends on the choice of force field, and a number of suitable automated tools -exist for small molecule parameterization such as the `Automated Topology Builder `_, -`antechamber `_, and `LigParGen `_. +exist for small molecule parameterization such as the `Automated Topology Builder `, +`antechamber `, and `LigParGen https://zarbi.chem.yale.edu/ligpargen/`. Monomer coordinates and parameters used as inputs should be designed to reflect the state of the monomer in the mature polymer chain, rather than the isolated monomer molecule prior to polymerization. For example, @@ -98,8 +96,9 @@ and not the ammonium and carboxylate groups found in the precursor amino acids. Monomer parameters should be designed in a manner consistent with the desired force field. We recommend you do not combine monomer parameters from different force field families in a single polymer. + For *PolyConf* These coordinate files should represent a sensible monomer geometry as could be found in the final -polymer. These might be created using tools like `ChimeraX `_, with theoretical ideal bond lengths and +polymer. These might be created using tools like ChimeraX, with theoretical ideal bond lengths and angles, by geometry optimization, or generated by automated parameterization tools. Additionally, it is often convenient if the monomer is in a conformation where atoms corresponding to adjacent monomers are as far as possible from other atoms, and pointed away from other attachment points. @@ -112,8 +111,7 @@ Worked Examples PolyConf creates polymer coordinate files through the tiling and manipulation of monomer pdb files. There are several detailed examples of the use of PolyConf to create ensembles of starting -conformations for a series of increasingly complex polymer architectures. These are contained in the -*PolyConf* repository in the folder `polyconstruct/polyconf_examples/` contained in the +conformations for a series of increasingly complex polymer architectures. These are contained in the PolyConf repository in the folder 'polyconstruct/polyconf_examples/' contained in the Here is one simple example, showing the construction of a linear polyethylenimine 128-mer. @@ -190,31 +188,18 @@ Here is one simple example, showing the construction of a linear polyethylenimin # end of example script +**PolyBuild** +Example input itp files and the resulting rtp database entries are presented in the folder `polybuild_examples/RTP_entries` -**PolyTop** +RTP entries +**PolyTop** -.. note:: - The import path provided in the examples below is *different* to the path - in the examples contained within 'polyconstruct/data_paper_examples/', as - the path used to locate modules from within the package structure is - different. You must use the structure in the examples below for the module - import to be correctly resolved. Simple example - construction of a linear homopolymer: -.. note:: - Note that when more than one type of junction exists within a PolyTop polymer, - it is important that each junction type is given a unique name. In the case where - there exist multiple junctions in either molecule sharing the same name, the specific - junctions chosen will be randomly distributed among junctions with the same name, - allowing for stochastic extension of polymers. For repeatability it is therefore - necessary to use a consistent seed value (in python), and use PolyTop as a python - library rather than from the command line. If an exact structure is desired instead, - simply ensure that each junction type has a unique name that does not allow for any - discrepancy in exactly which junctions are joined and where. .. code-block:: python @@ -252,6 +237,9 @@ Simple example - construction of a linear homopolymer: Visualize.polymer(polymer,infer_bond_order=False).draw2D('data_paper_examples/pei_linear_polymer.png',(400,300)) +.. note:: + Note that when more than one type of junction exists within a PolyTop polymer, + it is important that each junction type is given a unique name. Complex example - construction of a 4-arm PEG star polymer from single monomeric units: @@ -266,9 +254,9 @@ Complex example - construction of a 4-arm PEG star polymer from single monomeric from polytop.Topology import Topology # Load in monomer topologies from ITP files - ethanol = Topology.from_ITP("data_paper_examples/extended_ethanol.itp") # main arm monomer - methane = Topology.from_ITP("data_paper_examples/extended_methane.itp") # terminal monomer - neopentane = Topology.from_ITP("data_paper_examples/extended_neopentane.itp") # central monomer + ethanol = Topology.from_ITP("polytop_examples/data/extended_ethanol.itp") # main arm monomer + methane = Topology.from_ITP("polytop_examples/data/extended_methane.itp") # terminal monomer + neopentane = Topology.from_ITP("polytop_examples/data/extended_neopentane.itp") # central monomer # Create junctions for each monomer with the bonding atom and then the leaving # atom specified, in that order, with a unique name. Note how each junction @@ -331,18 +319,16 @@ Complex example - construction of a 4-arm PEG star polymer from single monomeric four_polymer.topology.title = "four arm star polymer" # renames the ITP header and image # save the polymer to a file and visualise the structure with RDKit for an easy visual structure check - four_polymer.save_to_file('data_paper_examples/four_arm_star_overlapped_monomers.json') # text dump - four_polymer.topology.to_ITP('data_paper_examples/four_arm_star_overlapped_monomers.itp') - Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data_paper_examples/four_arm_star_overlapped_monomers.png',(400,300)) + four_polymer.save_to_file('polytop_examples/data/four_arm_star.json') # text dump + four_polymer.topology.to_ITP('polytop_examples/data/four_arm_star.itp') + Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('polytop_examples/data/four_arm_star.png',(800,600)) -All of the monomer ITP files used in the above two examples, and the resulting -polymer files, are also readily available at 'polyconstruct/data_paper_examples/'. +-------------------------------------------------------------------------------------- +Find the above and additional worked examples as executable Python scripts on the `PolyConstruct GitHub repository `_. --------------------------------------------------------------------------------------- +Examples for *PolyTop* are available at 'polyconstruct/polytop_examples/' + +Examples for *PolyConf* at 'polyconstruct/polyconf_examples/' -Find the above and additional worked examples as executable Python scripts or Jupyter -Notebooks on the `PolyConstruct GitHub repository `_. -Examples for PolyTop are available at 'polyconstruct/paper_worked_examples.ipynb' -and for PolyConf at 'polyconstruct/polyconf_examples/'; while instructions to -use the two PolyBuild scripts are included under the :ref:`PolyBuild` documentation. +Instructions to use *PolyBuild* are included under the :ref:`PolyBuild` documentation. diff --git a/polybuild/.DS_Store b/polybuild/.DS_Store deleted file mode 100644 index c44b6ff..0000000 Binary files a/polybuild/.DS_Store and /dev/null differ diff --git a/polybuild_examples/.DS_Store b/polybuild_examples/.DS_Store deleted file mode 100644 index c44b6ff..0000000 Binary files a/polybuild_examples/.DS_Store and /dev/null differ diff --git a/polytop_examples/data/ethylamine_dendrimer.itp b/polytop_examples/data/ethylamine_dendrimer.itp deleted file mode 100644 index 1865814..0000000 --- a/polytop_examples/data/ethylamine_dendrimer.itp +++ /dev/null @@ -1,1319 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -; This file was generated at 14:09 on 2024-12-06 by -; -; Automatic Topology Builder -; -; REVISION 2024-11-20 12:06:25 -;--------------------------------------------------------------------------------------------------------------------------- -; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark -; -; Institute : Molecular Dynamics group, -; School of Chemistry and Molecular Biosciences (SCMB), -; The University of Queensland, QLD 4072, Australia -; URL : https://atb.uq.edu.au -; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. -; An Automated force field Topology Builder (ATB) and repository: version 1.0. -; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. -; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. -; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. -; DOI:10.1021/acs.jctc.8b00768 -; -; Disclaimer : -; While every effort has been made to ensure the accuracy and validity of parameters provided below -; the assignment of parameters is being based on an automated procedure combining data provided by a -; given user as well as calculations performed using third party software. They are provided as a guide. -; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided -; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion -; and to perform additional validation tests for their specific application if required. Neither the authors -; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. -; -; Release notes and warnings: -; (1) The topology is based on a set of atomic coordinates and other data provided by the user after -; after quantum mechanical optimization of the structure using different levels of theory depending on -; the nature of the molecule. -; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. -; In these cases alternative type codes are provided at the end of the line. -; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral -; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" -; or "uncertain" in comments. -; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder -; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually -; before the file can be used. -;--------------------------------------------------------------------------------------------------------------------------- -; Input Structure : 6HTJ -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 1746623 -; ATB Topology Hash: f4741 -;--------------------------------------------------------------------------------------------------------------------------- -; Final Topology Generation was performed using: -; A B3LYP/6-31G* optimized geometry. -; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. -; Initial charges were estimated using the ESP method of Merz-Kollman. -; Final charges and charge groups were generated by method described in the ATB paper. -; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. -;--------------------------------------------------------------------------------------------------------------------------- -; -; - -[ moleculetype ] -6HTJ 3 -[ atoms ] - 1 NTer 1 6HTJ N2 1 -0.554160 14.0067 - 2 CPos 1 6HTJ C6 2 0.021840 12.0110 - 3 HC 1 6HTJ H13 3 0.078840 1.0080 - 4 HC 1 6HTJ H14 4 0.078840 1.0080 - 5 CPos 1 6HTJ C5 5 0.021840 12.0110 - 6 HC 1 6HTJ H11 6 0.078840 1.0080 - 7 HC 1 6HTJ H12 7 0.078840 1.0080 - 8 NTer 1 6HTJ N1 8 -0.554160 14.0067 - 9 CPos 2 BB6C C6 9 -0.138020 12.0110 - 10 HC 2 BB6C H13 10 0.115980 1.0080 - 11 HC 2 BB6C H14 11 0.115980 1.0080 - 12 CPos 2 BB6C C5 12 0.141980 12.0110 - 13 HC 2 BB6C H11 13 0.059980 1.0080 - 14 HC 2 BB6C H12 14 0.059980 1.0080 - 15 NTer 2 BB6C N1 15 -0.591020 14.0067 - 16 CPos 3 BB6C C6 16 -0.137720 12.0110 - 17 HC 3 BB6C H13 17 0.116280 1.0080 - 18 HC 3 BB6C H14 18 0.116280 1.0080 - 19 CPos 3 BB6C C5 19 0.142280 12.0110 - 20 HC 3 BB6C H11 20 0.060280 1.0080 - 21 HC 3 BB6C H12 21 0.060280 1.0080 - 22 NTer 3 BB6C N1 22 -0.590720 14.0067 - 23 CPos 4 BB6C C6 23 -0.137720 12.0110 - 24 HC 4 BB6C H13 24 0.116280 1.0080 - 25 HC 4 BB6C H14 25 0.116280 1.0080 - 26 CPos 4 BB6C C5 26 0.142280 12.0110 - 27 HC 4 BB6C H11 27 0.060280 1.0080 - 28 HC 4 BB6C H12 28 0.060280 1.0080 - 29 NTer 4 BB6C N1 29 -0.590720 14.0067 - 30 CPos 5 BB6C C6 30 -0.137266 12.0110 - 31 HC 5 BB6C H13 31 0.116734 1.0080 - 32 HC 5 BB6C H14 32 0.116734 1.0080 - 33 CPos 5 BB6C C5 33 0.142734 12.0110 - 34 HC 5 BB6C H11 34 0.060734 1.0080 - 35 HC 5 BB6C H12 35 0.060734 1.0080 - 36 NTer 5 BB6C N1 36 -0.590266 14.0067 - 37 CPos 6 BB6C C6 37 -0.136736 12.0110 - 38 HC 6 BB6C H13 38 0.117264 1.0080 - 39 HC 6 BB6C H14 39 0.117264 1.0080 - 40 CPos 6 BB6C C5 40 0.143264 12.0110 - 41 HC 6 BB6C H11 41 0.061264 1.0080 - 42 HC 6 BB6C H12 42 0.061264 1.0080 - 43 NTer 6 BB6C N1 43 -0.589736 14.0067 - 44 CPos 7 BB6C C6 44 -0.136786 12.0110 - 45 HC 7 BB6C H13 45 0.117214 1.0080 - 46 HC 7 BB6C H14 46 0.117214 1.0080 - 47 CPos 7 BB6C C5 47 0.143214 12.0110 - 48 HC 7 BB6C H11 48 0.061214 1.0080 - 49 HC 7 BB6C H12 49 0.061214 1.0080 - 50 NTer 7 BB6C N1 50 -0.589786 14.0067 - 51 CPos 8 BB6C C6 51 -0.136861 12.0110 - 52 HC 8 BB6C H13 52 0.117139 1.0080 - 53 HC 8 BB6C H14 53 0.117139 1.0080 - 54 CPos 8 BB6C C5 54 0.143139 12.0110 - 55 HC 8 BB6C H11 55 0.061139 1.0080 - 56 HC 8 BB6C H12 56 0.061139 1.0080 - 57 NTer 8 BB6C N1 57 -0.589861 14.0067 - 58 CPos 9 BB6C C6 58 -0.136736 12.0110 - 59 HC 9 BB6C H13 59 0.117264 1.0080 - 60 HC 9 BB6C H14 60 0.117264 1.0080 - 61 CPos 9 BB6C C5 61 0.143264 12.0110 - 62 HC 9 BB6C H11 62 0.061264 1.0080 - 63 HC 9 BB6C H12 63 0.061264 1.0080 - 64 NTer 9 BB6C N1 64 -0.589736 14.0067 - 65 CPos 10 BB6C C6 65 -0.136786 12.0110 - 66 HC 10 BB6C H13 66 0.117214 1.0080 - 67 HC 10 BB6C H14 67 0.117214 1.0080 - 68 CPos 10 BB6C C5 68 0.143214 12.0110 - 69 HC 10 BB6C H11 69 0.061214 1.0080 - 70 HC 10 BB6C H12 70 0.061214 1.0080 - 71 NTer 10 BB6C N1 71 -0.589786 14.0067 - 72 CPos 11 BB6C C6 72 -0.136861 12.0110 - 73 HC 11 BB6C H13 73 0.117139 1.0080 - 74 HC 11 BB6C H14 74 0.117139 1.0080 - 75 CPos 11 BB6C C5 75 0.143139 12.0110 - 76 HC 11 BB6C H11 76 0.061139 1.0080 - 77 HC 11 BB6C H12 77 0.061139 1.0080 - 78 NTer 11 BB6C N1 78 -0.589861 14.0067 - 79 CPos 12 BB6C C6 79 -0.136811 12.0110 - 80 HC 12 BB6C H13 80 0.117189 1.0080 - 81 HC 12 BB6C H14 81 0.117189 1.0080 - 82 CPos 12 BB6C C5 82 0.143189 12.0110 - 83 HC 12 BB6C H11 83 0.061189 1.0080 - 84 HC 12 BB6C H12 84 0.061189 1.0080 - 85 NTer 12 BB6C N1 85 -0.589811 14.0067 - 86 CPos 13 BB6C C6 86 -0.137307 12.0110 - 87 HC 13 BB6C H13 87 0.116693 1.0080 - 88 HC 13 BB6C H14 88 0.116693 1.0080 - 89 CPos 13 BB6C C5 89 0.142693 12.0110 - 90 HC 13 BB6C H11 90 0.060693 1.0080 - 91 HC 13 BB6C H12 91 0.060693 1.0080 - 92 NTer 13 BB6C N1 92 -0.590307 14.0067 - 93 HS14 14 PHGY H12 93 0.376960 1.0080 - 94 NPri 14 PHGY N2 94 -1.037040 14.0067 - 95 HS14 14 PHGY H11 95 0.376960 1.0080 - 96 CPos 14 PHGY C2 96 0.353960 12.0110 - 97 HC 14 PHGY H3 97 0.024960 1.0080 - 98 HC 14 PHGY H4 98 0.024960 1.0080 - 99 C 14 PHGY C1 99 -0.037040 12.0110 - 100 HC 14 PHGY H1 100 0.064960 1.0080 - 101 HC 14 PHGY H2 101 0.064960 1.0080 - 102 HS14 15 PHGY H12 102 0.377742 1.0080 - 103 NPri 15 PHGY N2 103 -1.036258 14.0067 - 104 HS14 15 PHGY H11 104 0.377742 1.0080 - 105 CPos 15 PHGY C2 105 0.354742 12.0110 - 106 HC 15 PHGY H3 106 0.025742 1.0080 - 107 HC 15 PHGY H4 107 0.025742 1.0080 - 108 C 15 PHGY C1 108 -0.036258 12.0110 - 109 HC 15 PHGY H1 109 0.065742 1.0080 - 110 HC 15 PHGY H2 110 0.065742 1.0080 - 111 HS14 16 PHGY H12 111 0.377761 1.0080 - 112 NPri 16 PHGY N2 112 -1.036239 14.0067 - 113 HS14 16 PHGY H11 113 0.377761 1.0080 - 114 CPos 16 PHGY C2 114 0.354761 12.0110 - 115 HC 16 PHGY H3 115 0.025761 1.0080 - 116 HC 16 PHGY H4 116 0.025761 1.0080 - 117 C 16 PHGY C1 117 -0.036239 12.0110 - 118 HC 16 PHGY H1 118 0.065761 1.0080 - 119 HC 16 PHGY H2 119 0.065761 1.0080 - 120 HS14 17 PHGY H12 120 0.377712 1.0080 - 121 NPri 17 PHGY N2 121 -1.036288 14.0067 - 122 HS14 17 PHGY H11 122 0.377712 1.0080 - 123 CPos 17 PHGY C2 123 0.354712 12.0110 - 124 HC 17 PHGY H3 124 0.025712 1.0080 - 125 HC 17 PHGY H4 125 0.025712 1.0080 - 126 C 17 PHGY C1 126 -0.036288 12.0110 - 127 HC 17 PHGY H1 127 0.065712 1.0080 - 128 HC 17 PHGY H2 128 0.065712 1.0080 - 129 HS14 18 PHGY H12 129 0.377663 1.0080 - 130 NPri 18 PHGY N2 130 -1.036337 14.0067 - 131 HS14 18 PHGY H11 131 0.377663 1.0080 - 132 CPos 18 PHGY C2 132 0.354663 12.0110 - 133 HC 18 PHGY H3 133 0.025663 1.0080 - 134 HC 18 PHGY H4 134 0.025663 1.0080 - 135 C 18 PHGY C1 135 -0.036337 12.0110 - 136 HC 18 PHGY H1 136 0.065663 1.0080 - 137 HC 18 PHGY H2 137 0.065663 1.0080 - 138 HS14 19 PHGY H12 138 0.377490 1.0080 - 139 NPri 19 PHGY N2 139 -1.036510 14.0067 - 140 HS14 19 PHGY H11 140 0.377490 1.0080 - 141 CPos 19 PHGY C2 141 0.354490 12.0110 - 142 HC 19 PHGY H3 142 0.025490 1.0080 - 143 HC 19 PHGY H4 143 0.025490 1.0080 - 144 C 19 PHGY C1 144 -0.036510 12.0110 - 145 HC 19 PHGY H1 145 0.065490 1.0080 - 146 HC 19 PHGY H2 146 0.065490 1.0080 - 147 HS14 20 PHGY H12 147 0.377490 1.0080 - 148 NPri 20 PHGY N2 148 -1.036510 14.0067 - 149 HS14 20 PHGY H11 149 0.377490 1.0080 - 150 CPos 20 PHGY C2 150 0.354490 12.0110 - 151 HC 20 PHGY H3 151 0.025490 1.0080 - 152 HC 20 PHGY H4 152 0.025490 1.0080 - 153 C 20 PHGY C1 153 -0.036510 12.0110 - 154 HC 20 PHGY H1 154 0.065490 1.0080 - 155 HC 20 PHGY H2 155 0.065490 1.0080 - 156 HS14 21 PHGY H12 156 0.377693 1.0080 - 157 NPri 21 PHGY N2 157 -1.036307 14.0067 - 158 HS14 21 PHGY H11 158 0.377693 1.0080 - 159 CPos 21 PHGY C2 159 0.354693 12.0110 - 160 HC 21 PHGY H3 160 0.025693 1.0080 - 161 HC 21 PHGY H4 161 0.025693 1.0080 - 162 C 21 PHGY C1 162 -0.036307 12.0110 - 163 HC 21 PHGY H1 163 0.065693 1.0080 - 164 HC 21 PHGY H2 164 0.065693 1.0080 - 165 HS14 22 PHGY H12 165 0.377722 1.0080 - 166 NPri 22 PHGY N2 166 -1.036278 14.0067 - 167 HS14 22 PHGY H11 167 0.377722 1.0080 - 168 CPos 22 PHGY C2 168 0.354722 12.0110 - 169 HC 22 PHGY H3 169 0.025722 1.0080 - 170 HC 22 PHGY H4 170 0.025722 1.0080 - 171 C 22 PHGY C1 171 -0.036278 12.0110 - 172 HC 22 PHGY H1 172 0.065722 1.0080 - 173 HC 22 PHGY H2 173 0.065722 1.0080 - 174 HS14 23 PHGY H12 174 0.377742 1.0080 - 175 NPri 23 PHGY N2 175 -1.036258 14.0067 - 176 HS14 23 PHGY H11 176 0.377742 1.0080 - 177 CPos 23 PHGY C2 177 0.354742 12.0110 - 178 HC 23 PHGY H3 178 0.025742 1.0080 - 179 HC 23 PHGY H4 179 0.025742 1.0080 - 180 C 23 PHGY C1 180 -0.036258 12.0110 - 181 HC 23 PHGY H1 181 0.065742 1.0080 - 182 HC 23 PHGY H2 182 0.065742 1.0080 - 183 HS14 24 PHGY H12 183 0.377732 1.0080 - 184 NPri 24 PHGY N2 184 -1.036268 14.0067 - 185 HS14 24 PHGY H11 185 0.377732 1.0080 - 186 CPos 24 PHGY C2 186 0.354732 12.0110 - 187 HC 24 PHGY H3 187 0.025732 1.0080 - 188 HC 24 PHGY H4 188 0.025732 1.0080 - 189 C 24 PHGY C1 189 -0.036268 12.0110 - 190 HC 24 PHGY H1 190 0.065732 1.0080 - 191 HC 24 PHGY H2 191 0.065732 1.0080 - 192 HS14 25 PHGY H12 192 0.377712 1.0080 - 193 NPri 25 PHGY N2 193 -1.036288 14.0067 - 194 HS14 25 PHGY H11 194 0.377712 1.0080 - 195 CPos 25 PHGY C2 195 0.354712 12.0110 - 196 HC 25 PHGY H3 196 0.025712 1.0080 - 197 HC 25 PHGY H4 197 0.025712 1.0080 - 198 C 25 PHGY C1 198 -0.036288 12.0110 - 199 HC 25 PHGY H1 199 0.065712 1.0080 - 200 HC 25 PHGY H2 200 0.065712 1.0080 - 201 HS14 26 PHGY H12 201 0.377742 1.0080 - 202 NPri 26 PHGY N2 202 -1.036258 14.0067 - 203 HS14 26 PHGY H11 203 0.377742 1.0080 - 204 CPos 26 PHGY C2 204 0.354742 12.0110 - 205 HC 26 PHGY H3 205 0.025742 1.0080 - 206 HC 26 PHGY H4 206 0.025742 1.0080 - 207 C 26 PHGY C1 207 -0.036258 12.0110 - 208 HC 26 PHGY H1 208 0.065742 1.0080 - 209 HC 26 PHGY H2 209 0.065742 1.0080 - 210 HS14 27 PHGY H12 210 0.377732 1.0080 - 211 NPri 27 PHGY N2 211 -1.036268 14.0067 - 212 HS14 27 PHGY H11 212 0.377732 1.0080 - 213 CPos 27 PHGY C2 213 0.354732 12.0110 - 214 HC 27 PHGY H3 214 0.025732 1.0080 - 215 HC 27 PHGY H4 215 0.025732 1.0080 - 216 C 27 PHGY C1 216 -0.036268 12.0110 - 217 HC 27 PHGY H1 217 0.065732 1.0080 - 218 HC 27 PHGY H2 218 0.065732 1.0080 - 219 HS14 28 PHGY H12 219 0.377510 1.0080 - 220 NPri 28 PHGY N2 220 -1.036490 14.0067 - 221 HS14 28 PHGY H11 221 0.377510 1.0080 - 222 CPos 28 PHGY C2 222 0.354510 12.0110 - 223 HC 28 PHGY H3 223 0.025510 1.0080 - 224 HC 28 PHGY H4 224 0.025510 1.0080 - 225 C 28 PHGY C1 225 -0.036490 12.0110 - 226 HC 28 PHGY H1 226 0.065510 1.0080 - 227 HC 28 PHGY H2 227 0.065510 1.0080 - 228 HS14 29 PHGY H12 228 0.375659 1.0080 - 229 NPri 29 PHGY N2 229 -1.038342 14.0067 - 230 HS14 29 PHGY H11 230 0.375659 1.0080 - 231 CPos 29 PHGY C2 231 0.352658 12.0110 - 232 HC 29 PHGY H3 232 0.023658 1.0080 - 233 HC 29 PHGY H4 233 0.023658 1.0080 - 234 C 29 PHGY C1 234 -0.038342 12.0110 - 235 HC 29 PHGY H1 235 0.063658 1.0080 - 236 HC 29 PHGY H2 236 0.063658 1.0080 - -[ bonds ] - 1 16 2 0.1470 8.7100e+06 - 1 9 2 0.1470 8.7100e+06 - 1 2 2 0.1470 8.7100e+06 - 2 5 2 0.1540 4.0057e+06 - 2 4 2 0.1090 1.2300e+07 - 2 3 2 0.1090 1.2300e+07 - 5 7 2 0.1090 1.2300e+07 - 5 8 2 0.1470 8.7100e+06 - 5 6 2 0.1090 1.2300e+07 - 8 30 2 0.1470 8.7100e+06 - 8 23 2 0.1470 8.7100e+06 - 9 11 2 0.1090 1.2300e+07 - 9 10 2 0.1090 1.2300e+07 - 9 12 2 0.1530 7.1500e+06 - 12 14 2 0.1090 1.2300e+07 - 12 13 2 0.1090 1.2300e+07 - 12 15 2 0.1470 8.7100e+06 - 15 72 2 0.1470 8.7100e+06 - 15 51 2 0.1470 8.7100e+06 - 16 19 2 0.1530 7.1500e+06 - 16 17 2 0.1090 1.2300e+07 - 16 18 2 0.1090 1.2300e+07 - 19 21 2 0.1090 1.2300e+07 - 19 20 2 0.1090 1.2300e+07 - 19 22 2 0.1470 8.7100e+06 - 22 86 2 0.1470 8.7100e+06 - 22 37 2 0.1470 8.7100e+06 - 23 26 2 0.1530 7.1500e+06 - 23 25 2 0.1090 1.2300e+07 - 23 24 2 0.1090 1.2300e+07 - 26 27 2 0.1090 1.2300e+07 - 26 28 2 0.1090 1.2300e+07 - 26 29 2 0.1470 8.7100e+06 - 29 58 2 0.1470 8.7100e+06 - 29 79 2 0.1470 8.7100e+06 - 30 31 2 0.1090 1.2300e+07 - 30 33 2 0.1530 7.1500e+06 - 30 32 2 0.1090 1.2300e+07 - 33 35 2 0.1090 1.2300e+07 - 33 34 2 0.1090 1.2300e+07 - 33 36 2 0.1470 8.7100e+06 - 36 65 2 0.1470 8.7100e+06 - 36 44 2 0.1470 8.7100e+06 - 37 39 2 0.1090 1.2300e+07 - 37 38 2 0.1090 1.2300e+07 - 37 40 2 0.1530 7.1500e+06 - 40 41 2 0.1090 1.2300e+07 - 40 43 2 0.1470 8.7100e+06 - 40 42 2 0.1090 1.2300e+07 - 43 117 2 0.1470 8.7100e+06 - 43 216 2 0.1470 8.7100e+06 - 44 47 2 0.1530 7.1500e+06 - 44 45 2 0.1090 1.2300e+07 - 44 46 2 0.1090 1.2300e+07 - 47 50 2 0.1470 8.7100e+06 - 47 49 2 0.1090 1.2300e+07 - 47 48 2 0.1090 1.2300e+07 - 50 171 2 0.1470 8.7100e+06 - 50 180 2 0.1470 8.7100e+06 - 51 53 2 0.1090 1.2300e+07 - 51 52 2 0.1090 1.2300e+07 - 51 54 2 0.1530 7.1500e+06 - 54 56 2 0.1090 1.2300e+07 - 54 55 2 0.1090 1.2300e+07 - 54 57 2 0.1470 8.7100e+06 - 57 99 2 0.1470 8.7100e+06 - 57 144 2 0.1470 8.7100e+06 - 58 61 2 0.1530 7.1500e+06 - 58 60 2 0.1090 1.2300e+07 - 58 59 2 0.1090 1.2300e+07 - 61 62 2 0.1090 1.2300e+07 - 61 64 2 0.1470 8.7100e+06 - 61 63 2 0.1090 1.2300e+07 - 64 126 2 0.1470 8.7100e+06 - 64 189 2 0.1470 8.7100e+06 - 65 66 2 0.1090 1.2300e+07 - 65 67 2 0.1090 1.2300e+07 - 65 68 2 0.1530 7.1500e+06 - 68 71 2 0.1470 8.7100e+06 - 68 70 2 0.1090 1.2300e+07 - 68 69 2 0.1090 1.2300e+07 - 71 108 2 0.1470 8.7100e+06 - 71 207 2 0.1470 8.7100e+06 - 72 73 2 0.1090 1.2300e+07 - 72 74 2 0.1090 1.2300e+07 - 72 75 2 0.1530 7.1500e+06 - 75 78 2 0.1470 8.7100e+06 - 75 77 2 0.1090 1.2300e+07 - 75 76 2 0.1090 1.2300e+07 - 78 135 2 0.1470 8.7100e+06 - 78 162 2 0.1470 8.7100e+06 - 79 82 2 0.1530 7.1500e+06 - 79 81 2 0.1090 1.2300e+07 - 79 80 2 0.1090 1.2300e+07 - 82 84 2 0.1090 1.2300e+07 - 82 85 2 0.1470 8.7100e+06 - 82 83 2 0.1090 1.2300e+07 - 85 225 2 0.1470 8.7100e+06 - 85 198 2 0.1470 8.7100e+06 - 86 87 2 0.1090 1.2300e+07 - 86 88 2 0.1090 1.2300e+07 - 86 89 2 0.1530 7.1500e+06 - 89 91 2 0.1090 1.2300e+07 - 89 90 2 0.1090 1.2300e+07 - 89 92 2 0.1470 8.7100e+06 - 92 153 2 0.1470 8.7100e+06 - 92 234 2 0.1470 8.7100e+06 - 93 94 2 0.1020 1.7782e+07 - 94 95 2 0.1020 1.7782e+07 - 94 96 2 0.1470 8.7100e+06 - 96 99 2 0.1530 7.1500e+06 - 96 97 2 0.1090 1.2300e+07 - 96 98 2 0.1090 1.2300e+07 - 99 100 2 0.1090 1.2300e+07 - 99 101 2 0.1090 1.2300e+07 - 102 103 2 0.1020 1.7782e+07 - 103 105 2 0.1470 8.7100e+06 - 103 104 2 0.1020 1.7782e+07 - 105 107 2 0.1090 1.2300e+07 - 105 108 2 0.1530 7.1500e+06 - 105 106 2 0.1090 1.2300e+07 - 108 109 2 0.1090 1.2300e+07 - 108 110 2 0.1090 1.2300e+07 - 111 112 2 0.1020 1.7782e+07 - 112 113 2 0.1020 1.7782e+07 - 112 114 2 0.1470 8.7100e+06 - 114 116 2 0.1090 1.2300e+07 - 114 117 2 0.1530 7.1500e+06 - 114 115 2 0.1090 1.2300e+07 - 117 118 2 0.1090 1.2300e+07 - 117 119 2 0.1090 1.2300e+07 - 120 121 2 0.1020 1.7782e+07 - 121 123 2 0.1470 8.7100e+06 - 121 122 2 0.1020 1.7782e+07 - 123 125 2 0.1090 1.2300e+07 - 123 126 2 0.1530 7.1500e+06 - 123 124 2 0.1090 1.2300e+07 - 126 128 2 0.1090 1.2300e+07 - 126 127 2 0.1090 1.2300e+07 - 129 130 2 0.1020 1.7782e+07 - 130 131 2 0.1020 1.7782e+07 - 130 132 2 0.1470 8.7100e+06 - 132 134 2 0.1090 1.2300e+07 - 132 135 2 0.1530 7.1500e+06 - 132 133 2 0.1090 1.2300e+07 - 135 137 2 0.1090 1.2300e+07 - 135 136 2 0.1090 1.2300e+07 - 138 139 2 0.1020 1.7782e+07 - 139 141 2 0.1470 8.7100e+06 - 139 140 2 0.1020 1.7782e+07 - 141 143 2 0.1090 1.2300e+07 - 141 142 2 0.1090 1.2300e+07 - 141 144 2 0.1530 7.1500e+06 - 144 145 2 0.1090 1.2300e+07 - 144 146 2 0.1090 1.2300e+07 - 147 148 2 0.1020 1.7782e+07 - 148 150 2 0.1470 8.7100e+06 - 148 149 2 0.1020 1.7782e+07 - 150 152 2 0.1090 1.2300e+07 - 150 153 2 0.1530 7.1500e+06 - 150 151 2 0.1090 1.2300e+07 - 153 155 2 0.1090 1.2300e+07 - 153 154 2 0.1090 1.2300e+07 - 156 157 2 0.1020 1.7782e+07 - 157 158 2 0.1020 1.7782e+07 - 157 159 2 0.1470 8.7100e+06 - 159 161 2 0.1090 1.2300e+07 - 159 162 2 0.1530 7.1500e+06 - 159 160 2 0.1090 1.2300e+07 - 162 164 2 0.1090 1.2300e+07 - 162 163 2 0.1090 1.2300e+07 - 165 166 2 0.1020 1.7782e+07 - 166 168 2 0.1470 8.7100e+06 - 166 167 2 0.1020 1.7782e+07 - 168 171 2 0.1530 7.1500e+06 - 168 170 2 0.1090 1.2300e+07 - 168 169 2 0.1090 1.2300e+07 - 171 172 2 0.1090 1.2300e+07 - 171 173 2 0.1090 1.2300e+07 - 174 175 2 0.1020 1.7782e+07 - 175 177 2 0.1470 8.7100e+06 - 175 176 2 0.1020 1.7782e+07 - 177 178 2 0.1090 1.2300e+07 - 177 179 2 0.1090 1.2300e+07 - 177 180 2 0.1530 7.1500e+06 - 180 182 2 0.1090 1.2300e+07 - 180 181 2 0.1090 1.2300e+07 - 183 184 2 0.1020 1.7782e+07 - 184 185 2 0.1020 1.7782e+07 - 184 186 2 0.1470 8.7100e+06 - 186 187 2 0.1090 1.2300e+07 - 186 188 2 0.1090 1.2300e+07 - 186 189 2 0.1530 7.1500e+06 - 189 191 2 0.1090 1.2300e+07 - 189 190 2 0.1090 1.2300e+07 - 192 193 2 0.1020 1.7782e+07 - 193 194 2 0.1020 1.7782e+07 - 193 195 2 0.1470 8.7100e+06 - 195 197 2 0.1090 1.2300e+07 - 195 198 2 0.1530 7.1500e+06 - 195 196 2 0.1090 1.2300e+07 - 198 200 2 0.1090 1.2300e+07 - 198 199 2 0.1090 1.2300e+07 - 201 202 2 0.1020 1.7782e+07 - 202 204 2 0.1470 8.7100e+06 - 202 203 2 0.1020 1.7782e+07 - 204 207 2 0.1530 7.1500e+06 - 204 206 2 0.1090 1.2300e+07 - 204 205 2 0.1090 1.2300e+07 - 207 209 2 0.1090 1.2300e+07 - 207 208 2 0.1090 1.2300e+07 - 210 211 2 0.1020 1.7782e+07 - 211 213 2 0.1470 8.7100e+06 - 211 212 2 0.1020 1.7782e+07 - 213 215 2 0.1090 1.2300e+07 - 213 216 2 0.1530 7.1500e+06 - 213 214 2 0.1090 1.2300e+07 - 216 218 2 0.1090 1.2300e+07 - 216 217 2 0.1090 1.2300e+07 - 219 220 2 0.1020 1.7782e+07 - 220 221 2 0.1020 1.7782e+07 - 220 222 2 0.1470 8.7100e+06 - 222 223 2 0.1090 1.2300e+07 - 222 225 2 0.1530 7.1500e+06 - 222 224 2 0.1090 1.2300e+07 - 225 226 2 0.1090 1.2300e+07 - 225 227 2 0.1090 1.2300e+07 - 228 229 2 0.1020 1.7782e+07 - 229 231 2 0.1470 8.7100e+06 - 229 230 2 0.1020 1.7782e+07 - 231 232 2 0.1090 1.2300e+07 - 231 234 2 0.1530 7.1500e+06 - 231 233 2 0.1090 1.2300e+07 - 234 235 2 0.1090 1.2300e+07 - 234 236 2 0.1090 1.2300e+07 - -[ pairs ] - 1 7 1 - 1 8 1 - 1 6 1 - 3 7 1 - 3 8 1 - 3 6 1 - 4 6 1 - 4 7 1 - 4 8 1 - 10 13 1 - 10 15 1 - 10 14 1 - 11 14 1 - 11 15 1 - 11 13 1 - 17 22 1 - 17 21 1 - 17 20 1 - 18 22 1 - 18 21 1 - 18 20 1 - 24 28 1 - 24 27 1 - 24 29 1 - 25 27 1 - 25 28 1 - 25 29 1 - 31 34 1 - 31 36 1 - 31 35 1 - 32 34 1 - 32 36 1 - 32 35 1 - 38 42 1 - 38 43 1 - 38 41 1 - 39 42 1 - 39 41 1 - 39 43 1 - 45 48 1 - 45 49 1 - 45 50 1 - 46 49 1 - 46 50 1 - 46 48 1 - 52 57 1 - 52 56 1 - 52 55 1 - 53 57 1 - 53 56 1 - 53 55 1 - 59 64 1 - 59 62 1 - 59 63 1 - 60 64 1 - 60 63 1 - 60 62 1 - 66 71 1 - 66 69 1 - 66 70 1 - 67 70 1 - 67 69 1 - 67 71 1 - 73 76 1 - 73 77 1 - 73 78 1 - 74 77 1 - 74 76 1 - 74 78 1 - 80 85 1 - 80 84 1 - 80 83 1 - 81 85 1 - 81 83 1 - 81 84 1 - 87 91 1 - 87 90 1 - 87 92 1 - 88 91 1 - 88 92 1 - 88 90 1 - 93 99 1 - 93 97 1 - 93 98 1 - 94 101 1 - 94 100 1 - 95 98 1 - 95 97 1 - 95 99 1 - 97 100 1 - 97 101 1 - 98 101 1 - 98 100 1 - 102 107 1 - 102 106 1 - 102 108 1 - 103 110 1 - 103 109 1 - 104 108 1 - 104 106 1 - 104 107 1 - 106 110 1 - 106 109 1 - 107 110 1 - 107 109 1 - 111 117 1 - 111 116 1 - 111 115 1 - 112 118 1 - 112 119 1 - 113 115 1 - 113 117 1 - 113 116 1 - 115 119 1 - 115 118 1 - 116 118 1 - 116 119 1 - 120 126 1 - 120 124 1 - 120 125 1 - 121 128 1 - 121 127 1 - 122 126 1 - 122 125 1 - 122 124 1 - 124 127 1 - 124 128 1 - 125 127 1 - 125 128 1 - 129 134 1 - 129 135 1 - 129 133 1 - 130 136 1 - 130 137 1 - 131 133 1 - 131 135 1 - 131 134 1 - 133 137 1 - 133 136 1 - 134 136 1 - 134 137 1 - 138 144 1 - 138 143 1 - 138 142 1 - 139 146 1 - 139 145 1 - 140 142 1 - 140 144 1 - 140 143 1 - 142 145 1 - 142 146 1 - 143 146 1 - 143 145 1 - 147 151 1 - 147 152 1 - 147 153 1 - 148 155 1 - 148 154 1 - 149 152 1 - 149 151 1 - 149 153 1 - 151 155 1 - 151 154 1 - 152 154 1 - 152 155 1 - 156 162 1 - 156 161 1 - 156 160 1 - 157 163 1 - 157 164 1 - 158 162 1 - 158 160 1 - 158 161 1 - 160 163 1 - 160 164 1 - 161 164 1 - 161 163 1 - 165 170 1 - 165 171 1 - 165 169 1 - 166 173 1 - 166 172 1 - 167 170 1 - 167 171 1 - 167 169 1 - 169 173 1 - 169 172 1 - 170 173 1 - 170 172 1 - 174 180 1 - 174 178 1 - 174 179 1 - 175 181 1 - 175 182 1 - 176 178 1 - 176 179 1 - 176 180 1 - 178 182 1 - 178 181 1 - 179 181 1 - 179 182 1 - 183 189 1 - 183 187 1 - 183 188 1 - 184 191 1 - 184 190 1 - 185 188 1 - 185 189 1 - 185 187 1 - 187 191 1 - 187 190 1 - 188 191 1 - 188 190 1 - 192 196 1 - 192 198 1 - 192 197 1 - 193 200 1 - 193 199 1 - 194 198 1 - 194 197 1 - 194 196 1 - 196 199 1 - 196 200 1 - 197 199 1 - 197 200 1 - 201 206 1 - 201 205 1 - 201 207 1 - 202 208 1 - 202 209 1 - 203 205 1 - 203 207 1 - 203 206 1 - 205 209 1 - 205 208 1 - 206 209 1 - 206 208 1 - 210 216 1 - 210 215 1 - 210 214 1 - 211 217 1 - 211 218 1 - 212 216 1 - 212 214 1 - 212 215 1 - 214 217 1 - 214 218 1 - 215 217 1 - 215 218 1 - 219 225 1 - 219 224 1 - 219 223 1 - 220 226 1 - 220 227 1 - 221 225 1 - 221 224 1 - 221 223 1 - 223 226 1 - 223 227 1 - 224 226 1 - 224 227 1 - 228 233 1 - 228 234 1 - 228 232 1 - 229 235 1 - 229 236 1 - 230 232 1 - 230 233 1 - 230 234 1 - 232 236 1 - 232 235 1 - 233 236 1 - 233 235 1 - -[ angles ] - 9 1 16 2 116.0000 6.2000e+02 - 2 1 16 2 116.0000 6.2000e+02 - 1 16 17 2 107.5700 4.8400e+02 - 1 16 18 2 107.5700 4.8400e+02 - 1 16 19 2 115.0000 6.1000e+02 - 1 9 12 2 115.0000 6.1000e+02 - 1 9 11 2 107.5700 4.8400e+02 - 1 9 10 2 107.5700 4.8400e+02 - 2 1 9 2 116.0000 6.2000e+02 - 1 2 3 2 111.3000 6.3200e+02 - 1 2 5 2 111.0000 5.3000e+02 - 1 2 4 2 111.3000 6.3200e+02 - 4 2 5 2 107.6000 5.0700e+02 - 2 5 7 2 107.6000 5.0700e+02 - 2 5 8 2 111.0000 5.3000e+02 - 3 2 5 2 107.6000 5.0700e+02 - 2 5 6 2 107.6000 5.0700e+02 - 3 2 4 2 106.7500 5.0300e+02 - 7 5 8 2 111.3000 6.3200e+02 - 6 5 7 2 106.7500 5.0300e+02 - 5 8 23 2 116.0000 6.2000e+02 - 5 8 30 2 116.0000 6.2000e+02 - 6 5 8 2 111.3000 6.3200e+02 - 8 30 32 2 107.5700 4.8400e+02 - 23 8 30 2 116.0000 6.2000e+02 - 8 30 33 2 115.0000 6.1000e+02 - 8 30 31 2 107.5700 4.8400e+02 - 8 23 25 2 107.5700 4.8400e+02 - 8 23 26 2 115.0000 6.1000e+02 - 8 23 24 2 107.5700 4.8400e+02 - 10 9 11 2 106.7500 5.0300e+02 - 11 9 12 2 108.5300 4.4300e+02 - 10 9 12 2 108.5300 4.4300e+02 - 9 12 15 2 111.0000 5.3000e+02 - 9 12 14 2 109.5000 4.4800e+02 - 9 12 13 2 109.5000 4.4800e+02 - 13 12 14 2 106.7500 5.0300e+02 - 14 12 15 2 108.0000 4.6500e+02 - 13 12 15 2 108.0000 4.6500e+02 - 12 15 72 2 116.0000 6.2000e+02 - 12 15 51 2 116.0000 6.2000e+02 - 51 15 72 2 116.0000 6.2000e+02 - 15 72 75 2 115.0000 6.1000e+02 - 15 72 73 2 107.5700 4.8400e+02 - 15 72 74 2 107.5700 4.8400e+02 - 15 51 54 2 115.0000 6.1000e+02 - 15 51 53 2 107.5700 4.8400e+02 - 15 51 52 2 107.5700 4.8400e+02 - 18 16 19 2 108.5300 4.4300e+02 - 17 16 19 2 108.5300 4.4300e+02 - 16 19 20 2 109.5000 4.4800e+02 - 16 19 22 2 111.0000 5.3000e+02 - 16 19 21 2 109.5000 4.4800e+02 - 17 16 18 2 106.7500 5.0300e+02 - 20 19 21 2 106.7500 5.0300e+02 - 21 19 22 2 108.0000 4.6500e+02 - 20 19 22 2 108.0000 4.6500e+02 - 19 22 86 2 116.0000 6.2000e+02 - 19 22 37 2 116.0000 6.2000e+02 - 37 22 86 2 116.0000 6.2000e+02 - 22 86 87 2 107.5700 4.8400e+02 - 22 86 88 2 107.5700 4.8400e+02 - 22 86 89 2 115.0000 6.1000e+02 - 22 37 38 2 107.5700 4.8400e+02 - 22 37 40 2 115.0000 6.1000e+02 - 22 37 39 2 107.5700 4.8400e+02 - 24 23 26 2 108.5300 4.4300e+02 - 25 23 26 2 108.5300 4.4300e+02 - 23 26 27 2 109.5000 4.4800e+02 - 23 26 29 2 111.0000 5.3000e+02 - 23 26 28 2 109.5000 4.4800e+02 - 24 23 25 2 106.7500 5.0300e+02 - 27 26 29 2 108.0000 4.6500e+02 - 27 26 28 2 106.7500 5.0300e+02 - 28 26 29 2 108.0000 4.6500e+02 - 26 29 79 2 116.0000 6.2000e+02 - 26 29 58 2 116.0000 6.2000e+02 - 29 58 59 2 107.5700 4.8400e+02 - 58 29 79 2 116.0000 6.2000e+02 - 29 58 61 2 115.0000 6.1000e+02 - 29 58 60 2 107.5700 4.8400e+02 - 29 79 81 2 107.5700 4.8400e+02 - 29 79 80 2 107.5700 4.8400e+02 - 29 79 82 2 115.0000 6.1000e+02 - 31 30 32 2 106.7500 5.0300e+02 - 31 30 33 2 108.5300 4.4300e+02 - 32 30 33 2 108.5300 4.4300e+02 - 30 33 34 2 109.5000 4.4800e+02 - 30 33 36 2 111.0000 5.3000e+02 - 30 33 35 2 109.5000 4.4800e+02 - 34 33 35 2 106.7500 5.0300e+02 - 35 33 36 2 108.0000 4.6500e+02 - 34 33 36 2 108.0000 4.6500e+02 - 33 36 44 2 116.0000 6.2000e+02 - 33 36 65 2 116.0000 6.2000e+02 - 36 65 67 2 107.5700 4.8400e+02 - 36 65 66 2 107.5700 4.8400e+02 - 44 36 65 2 116.0000 6.2000e+02 - 36 65 68 2 115.0000 6.1000e+02 - 36 44 46 2 107.5700 4.8400e+02 - 36 44 47 2 115.0000 6.1000e+02 - 36 44 45 2 107.5700 4.8400e+02 - 39 37 40 2 108.5300 4.4300e+02 - 38 37 39 2 106.7500 5.0300e+02 - 38 37 40 2 108.5300 4.4300e+02 - 37 40 41 2 109.5000 4.4800e+02 - 37 40 43 2 111.0000 5.3000e+02 - 37 40 42 2 109.5000 4.4800e+02 - 41 40 43 2 108.0000 4.6500e+02 - 41 40 42 2 106.7500 5.0300e+02 - 40 43 216 2 116.0000 6.2000e+02 - 42 40 43 2 108.0000 4.6500e+02 - 40 43 117 2 116.0000 6.2000e+02 - 117 43 216 2 116.0000 6.2000e+02 - 43 117 118 2 107.5700 4.8400e+02 - 43 117 114 2 115.0000 6.1000e+02 - 43 117 119 2 107.5700 4.8400e+02 - 43 216 217 2 107.5700 4.8400e+02 - 43 216 213 2 115.0000 6.1000e+02 - 43 216 218 2 107.5700 4.8400e+02 - 45 44 47 2 108.5300 4.4300e+02 - 44 47 48 2 109.5000 4.4800e+02 - 44 47 50 2 111.0000 5.3000e+02 - 44 47 49 2 109.5000 4.4800e+02 - 46 44 47 2 108.5300 4.4300e+02 - 45 44 46 2 106.7500 5.0300e+02 - 47 50 180 2 116.0000 6.2000e+02 - 48 47 50 2 108.0000 4.6500e+02 - 47 50 171 2 116.0000 6.2000e+02 - 49 47 50 2 108.0000 4.6500e+02 - 48 47 49 2 106.7500 5.0300e+02 - 50 171 173 2 107.5700 4.8400e+02 - 50 171 172 2 107.5700 4.8400e+02 - 50 171 168 2 115.0000 6.1000e+02 - 171 50 180 2 116.0000 6.2000e+02 - 50 180 182 2 107.5700 4.8400e+02 - 50 180 181 2 107.5700 4.8400e+02 - 50 180 177 2 115.0000 6.1000e+02 - 53 51 54 2 108.5300 4.4300e+02 - 52 51 53 2 106.7500 5.0300e+02 - 52 51 54 2 108.5300 4.4300e+02 - 51 54 55 2 109.5000 4.4800e+02 - 51 54 57 2 111.0000 5.3000e+02 - 51 54 56 2 109.5000 4.4800e+02 - 56 54 57 2 108.0000 4.6500e+02 - 55 54 56 2 106.7500 5.0300e+02 - 55 54 57 2 108.0000 4.6500e+02 - 54 57 144 2 116.0000 6.2000e+02 - 54 57 99 2 116.0000 6.2000e+02 - 57 99 101 2 107.5700 4.8400e+02 - 57 99 100 2 107.5700 4.8400e+02 - 57 99 96 2 115.0000 6.1000e+02 - 99 57 144 2 116.0000 6.2000e+02 - 57 144 146 2 107.5700 4.8400e+02 - 57 144 141 2 115.0000 6.1000e+02 - 57 144 145 2 107.5700 4.8400e+02 - 60 58 61 2 108.5300 4.4300e+02 - 58 61 63 2 109.5000 4.4800e+02 - 58 61 64 2 111.0000 5.3000e+02 - 58 61 62 2 109.5000 4.4800e+02 - 59 58 61 2 108.5300 4.4300e+02 - 59 58 60 2 106.7500 5.0300e+02 - 62 61 63 2 106.7500 5.0300e+02 - 62 61 64 2 108.0000 4.6500e+02 - 63 61 64 2 108.0000 4.6500e+02 - 61 64 126 2 116.0000 6.2000e+02 - 61 64 189 2 116.0000 6.2000e+02 - 126 64 189 2 116.0000 6.2000e+02 - 64 126 127 2 107.5700 4.8400e+02 - 64 126 123 2 115.0000 6.1000e+02 - 64 126 128 2 107.5700 4.8400e+02 - 64 189 190 2 107.5700 4.8400e+02 - 64 189 186 2 115.0000 6.1000e+02 - 64 189 191 2 107.5700 4.8400e+02 - 66 65 68 2 108.5300 4.4300e+02 - 66 65 67 2 106.7500 5.0300e+02 - 67 65 68 2 108.5300 4.4300e+02 - 65 68 70 2 109.5000 4.4800e+02 - 65 68 69 2 109.5000 4.4800e+02 - 65 68 71 2 111.0000 5.3000e+02 - 69 68 71 2 108.0000 4.6500e+02 - 68 71 108 2 116.0000 6.2000e+02 - 68 71 207 2 116.0000 6.2000e+02 - 70 68 71 2 108.0000 4.6500e+02 - 69 68 70 2 106.7500 5.0300e+02 - 108 71 207 2 116.0000 6.2000e+02 - 71 108 105 2 115.0000 6.1000e+02 - 71 108 109 2 107.5700 4.8400e+02 - 71 108 110 2 107.5700 4.8400e+02 - 71 207 209 2 107.5700 4.8400e+02 - 71 207 208 2 107.5700 4.8400e+02 - 71 207 204 2 115.0000 6.1000e+02 - 73 72 74 2 106.7500 5.0300e+02 - 73 72 75 2 108.5300 4.4300e+02 - 74 72 75 2 108.5300 4.4300e+02 - 72 75 77 2 109.5000 4.4800e+02 - 72 75 78 2 111.0000 5.3000e+02 - 72 75 76 2 109.5000 4.4800e+02 - 76 75 78 2 108.0000 4.6500e+02 - 77 75 78 2 108.0000 4.6500e+02 - 75 78 162 2 116.0000 6.2000e+02 - 75 78 135 2 116.0000 6.2000e+02 - 76 75 77 2 106.7500 5.0300e+02 - 135 78 162 2 116.0000 6.2000e+02 - 78 135 137 2 107.5700 4.8400e+02 - 78 135 136 2 107.5700 4.8400e+02 - 78 135 132 2 115.0000 6.1000e+02 - 78 162 164 2 107.5700 4.8400e+02 - 78 162 163 2 107.5700 4.8400e+02 - 78 162 159 2 115.0000 6.1000e+02 - 79 82 83 2 109.5000 4.4800e+02 - 80 79 82 2 108.5300 4.4300e+02 - 81 79 82 2 108.5300 4.4300e+02 - 79 82 84 2 109.5000 4.4800e+02 - 79 82 85 2 111.0000 5.3000e+02 - 80 79 81 2 106.7500 5.0300e+02 - 83 82 84 2 106.7500 5.0300e+02 - 84 82 85 2 108.0000 4.6500e+02 - 82 85 198 2 116.0000 6.2000e+02 - 83 82 85 2 108.0000 4.6500e+02 - 82 85 225 2 116.0000 6.2000e+02 - 85 225 227 2 107.5700 4.8400e+02 - 85 225 222 2 115.0000 6.1000e+02 - 85 225 226 2 107.5700 4.8400e+02 - 198 85 225 2 116.0000 6.2000e+02 - 85 198 199 2 107.5700 4.8400e+02 - 85 198 195 2 115.0000 6.1000e+02 - 85 198 200 2 107.5700 4.8400e+02 - 87 86 89 2 108.5300 4.4300e+02 - 87 86 88 2 106.7500 5.0300e+02 - 88 86 89 2 108.5300 4.4300e+02 - 86 89 90 2 109.5000 4.4800e+02 - 86 89 92 2 111.0000 5.3000e+02 - 86 89 91 2 109.5000 4.4800e+02 - 90 89 91 2 106.7500 5.0300e+02 - 91 89 92 2 108.0000 4.6500e+02 - 90 89 92 2 108.0000 4.6500e+02 - 89 92 153 2 116.0000 6.2000e+02 - 89 92 234 2 116.0000 6.2000e+02 - 92 153 150 2 115.0000 6.1000e+02 - 153 92 234 2 116.0000 6.2000e+02 - 92 153 155 2 107.5700 4.8400e+02 - 92 153 154 2 107.5700 4.8400e+02 - 92 234 236 2 107.5700 4.8400e+02 - 92 234 231 2 115.0000 6.1000e+02 - 92 234 235 2 107.5700 4.8400e+02 - 93 94 96 2 109.5000 4.2500e+02 - 93 94 95 2 104.0000 4.9000e+02 - 95 94 96 2 109.5000 4.2500e+02 - 94 96 99 2 115.0000 6.1000e+02 - 94 96 98 2 108.5300 4.4300e+02 - 94 96 97 2 108.5300 4.4300e+02 - 97 96 99 2 108.5300 4.4300e+02 - 98 96 99 2 108.5300 4.4300e+02 - 96 99 100 2 107.6000 5.0700e+02 - 96 99 101 2 107.6000 5.0700e+02 - 97 96 98 2 106.7500 5.0300e+02 - 100 99 101 2 106.7500 5.0300e+02 - 102 103 105 2 109.5000 4.2500e+02 - 102 103 104 2 104.0000 4.9000e+02 - 103 105 107 2 108.5300 4.4300e+02 - 104 103 105 2 109.5000 4.2500e+02 - 103 105 108 2 115.0000 6.1000e+02 - 103 105 106 2 108.5300 4.4300e+02 - 107 105 108 2 108.5300 4.4300e+02 - 106 105 107 2 106.7500 5.0300e+02 - 105 108 109 2 107.6000 5.0700e+02 - 106 105 108 2 108.5300 4.4300e+02 - 105 108 110 2 107.6000 5.0700e+02 - 109 108 110 2 106.7500 5.0300e+02 - 111 112 113 2 104.0000 4.9000e+02 - 111 112 114 2 109.5000 4.2500e+02 - 113 112 114 2 109.5000 4.2500e+02 - 112 114 116 2 108.5300 4.4300e+02 - 112 114 115 2 108.5300 4.4300e+02 - 112 114 117 2 115.0000 6.1000e+02 - 116 114 117 2 108.5300 4.4300e+02 - 115 114 116 2 106.7500 5.0300e+02 - 115 114 117 2 108.5300 4.4300e+02 - 114 117 119 2 107.6000 5.0700e+02 - 114 117 118 2 107.6000 5.0700e+02 - 118 117 119 2 106.7500 5.0300e+02 - 120 121 123 2 109.5000 4.2500e+02 - 120 121 122 2 104.0000 4.9000e+02 - 122 121 123 2 109.5000 4.2500e+02 - 121 123 126 2 115.0000 6.1000e+02 - 121 123 125 2 108.5300 4.4300e+02 - 121 123 124 2 108.5300 4.4300e+02 - 124 123 125 2 106.7500 5.0300e+02 - 125 123 126 2 108.5300 4.4300e+02 - 123 126 128 2 107.6000 5.0700e+02 - 124 123 126 2 108.5300 4.4300e+02 - 123 126 127 2 107.6000 5.0700e+02 - 127 126 128 2 106.7500 5.0300e+02 - 129 130 131 2 104.0000 4.9000e+02 - 129 130 132 2 109.5000 4.2500e+02 - 131 130 132 2 109.5000 4.2500e+02 - 130 132 133 2 108.5300 4.4300e+02 - 130 132 135 2 115.0000 6.1000e+02 - 130 132 134 2 108.5300 4.4300e+02 - 134 132 135 2 108.5300 4.4300e+02 - 133 132 134 2 106.7500 5.0300e+02 - 133 132 135 2 108.5300 4.4300e+02 - 132 135 136 2 107.6000 5.0700e+02 - 132 135 137 2 107.6000 5.0700e+02 - 136 135 137 2 106.7500 5.0300e+02 - 138 139 141 2 109.5000 4.2500e+02 - 138 139 140 2 104.0000 4.9000e+02 - 139 141 143 2 108.5300 4.4300e+02 - 139 141 144 2 115.0000 6.1000e+02 - 140 139 141 2 109.5000 4.2500e+02 - 139 141 142 2 108.5300 4.4300e+02 - 142 141 143 2 106.7500 5.0300e+02 - 143 141 144 2 108.5300 4.4300e+02 - 142 141 144 2 108.5300 4.4300e+02 - 141 144 146 2 107.6000 5.0700e+02 - 141 144 145 2 107.6000 5.0700e+02 - 145 144 146 2 106.7500 5.0300e+02 - 147 148 150 2 109.5000 4.2500e+02 - 147 148 149 2 104.0000 4.9000e+02 - 148 150 151 2 108.5300 4.4300e+02 - 148 150 152 2 108.5300 4.4300e+02 - 149 148 150 2 109.5000 4.2500e+02 - 148 150 153 2 115.0000 6.1000e+02 - 152 150 153 2 108.5300 4.4300e+02 - 151 150 152 2 106.7500 5.0300e+02 - 150 153 154 2 107.6000 5.0700e+02 - 151 150 153 2 108.5300 4.4300e+02 - 150 153 155 2 107.6000 5.0700e+02 - 154 153 155 2 106.7500 5.0300e+02 - 156 157 158 2 104.0000 4.9000e+02 - 156 157 159 2 109.5000 4.2500e+02 - 158 157 159 2 109.5000 4.2500e+02 - 157 159 161 2 108.5300 4.4300e+02 - 157 159 162 2 115.0000 6.1000e+02 - 157 159 160 2 108.5300 4.4300e+02 - 160 159 161 2 106.7500 5.0300e+02 - 161 159 162 2 108.5300 4.4300e+02 - 160 159 162 2 108.5300 4.4300e+02 - 159 162 164 2 107.6000 5.0700e+02 - 159 162 163 2 107.6000 5.0700e+02 - 163 162 164 2 106.7500 5.0300e+02 - 165 166 167 2 104.0000 4.9000e+02 - 165 166 168 2 109.5000 4.2500e+02 - 167 166 168 2 109.5000 4.2500e+02 - 166 168 170 2 108.5300 4.4300e+02 - 166 168 169 2 108.5300 4.4300e+02 - 166 168 171 2 115.0000 6.1000e+02 - 170 168 171 2 108.5300 4.4300e+02 - 168 171 172 2 107.6000 5.0700e+02 - 168 171 173 2 107.6000 5.0700e+02 - 169 168 171 2 108.5300 4.4300e+02 - 169 168 170 2 106.7500 5.0300e+02 - 172 171 173 2 106.7500 5.0300e+02 - 174 175 176 2 104.0000 4.9000e+02 - 174 175 177 2 109.5000 4.2500e+02 - 175 177 179 2 108.5300 4.4300e+02 - 175 177 180 2 115.0000 6.1000e+02 - 176 175 177 2 109.5000 4.2500e+02 - 175 177 178 2 108.5300 4.4300e+02 - 178 177 180 2 108.5300 4.4300e+02 - 178 177 179 2 106.7500 5.0300e+02 - 179 177 180 2 108.5300 4.4300e+02 - 177 180 181 2 107.6000 5.0700e+02 - 177 180 182 2 107.6000 5.0700e+02 - 181 180 182 2 106.7500 5.0300e+02 - 183 184 186 2 109.5000 4.2500e+02 - 183 184 185 2 104.0000 4.9000e+02 - 185 184 186 2 109.5000 4.2500e+02 - 184 186 188 2 108.5300 4.4300e+02 - 184 186 189 2 115.0000 6.1000e+02 - 184 186 187 2 108.5300 4.4300e+02 - 187 186 188 2 106.7500 5.0300e+02 - 187 186 189 2 108.5300 4.4300e+02 - 188 186 189 2 108.5300 4.4300e+02 - 186 189 190 2 107.6000 5.0700e+02 - 186 189 191 2 107.6000 5.0700e+02 - 190 189 191 2 106.7500 5.0300e+02 - 192 193 194 2 104.0000 4.9000e+02 - 192 193 195 2 109.5000 4.2500e+02 - 194 193 195 2 109.5000 4.2500e+02 - 193 195 196 2 108.5300 4.4300e+02 - 193 195 197 2 108.5300 4.4300e+02 - 193 195 198 2 115.0000 6.1000e+02 - 196 195 197 2 106.7500 5.0300e+02 - 197 195 198 2 108.5300 4.4300e+02 - 195 198 200 2 107.6000 5.0700e+02 - 195 198 199 2 107.6000 5.0700e+02 - 196 195 198 2 108.5300 4.4300e+02 - 199 198 200 2 106.7500 5.0300e+02 - 201 202 203 2 104.0000 4.9000e+02 - 201 202 204 2 109.5000 4.2500e+02 - 202 204 205 2 108.5300 4.4300e+02 - 203 202 204 2 109.5000 4.2500e+02 - 202 204 206 2 108.5300 4.4300e+02 - 202 204 207 2 115.0000 6.1000e+02 - 205 204 207 2 108.5300 4.4300e+02 - 204 207 208 2 107.6000 5.0700e+02 - 206 204 207 2 108.5300 4.4300e+02 - 204 207 209 2 107.6000 5.0700e+02 - 205 204 206 2 106.7500 5.0300e+02 - 208 207 209 2 106.7500 5.0300e+02 - 210 211 212 2 104.0000 4.9000e+02 - 210 211 213 2 109.5000 4.2500e+02 - 211 213 214 2 108.5300 4.4300e+02 - 212 211 213 2 109.5000 4.2500e+02 - 211 213 215 2 108.5300 4.4300e+02 - 211 213 216 2 115.0000 6.1000e+02 - 215 213 216 2 108.5300 4.4300e+02 - 214 213 215 2 106.7500 5.0300e+02 - 214 213 216 2 108.5300 4.4300e+02 - 213 216 217 2 107.6000 5.0700e+02 - 213 216 218 2 107.6000 5.0700e+02 - 217 216 218 2 106.7500 5.0300e+02 - 219 220 221 2 104.0000 4.9000e+02 - 219 220 222 2 109.5000 4.2500e+02 - 221 220 222 2 109.5000 4.2500e+02 - 220 222 225 2 115.0000 6.1000e+02 - 220 222 224 2 108.5300 4.4300e+02 - 220 222 223 2 108.5300 4.4300e+02 - 223 222 225 2 108.5300 4.4300e+02 - 223 222 224 2 106.7500 5.0300e+02 - 222 225 227 2 107.6000 5.0700e+02 - 222 225 226 2 107.6000 5.0700e+02 - 224 222 225 2 108.5300 4.4300e+02 - 226 225 227 2 106.7500 5.0300e+02 - 228 229 231 2 109.5000 4.2500e+02 - 228 229 230 2 104.0000 4.9000e+02 - 229 231 234 2 115.0000 6.1000e+02 - 230 229 231 2 109.5000 4.2500e+02 - 229 231 232 2 108.5300 4.4300e+02 - 229 231 233 2 108.5300 4.4300e+02 - 232 231 234 2 108.5300 4.4300e+02 - 232 231 233 2 106.7500 5.0300e+02 - 233 231 234 2 108.5300 4.4300e+02 - 231 234 235 2 107.6000 5.0700e+02 - 231 234 236 2 107.6000 5.0700e+02 - 235 234 236 2 106.7500 5.0300e+02 - -[ dihedrals ] - 16 1 2 5 1 0.0000 3.7700e+00 6 - 1 16 19 22 1 0.0000 5.9200e+00 3 - 1 9 12 15 1 0.0000 5.9200e+00 3 - 1 2 5 8 1 0.0000 5.9200e+00 3 - 2 5 8 23 1 180.0000 1.0000e+00 6 - 8 30 33 36 1 0.0000 5.9200e+00 3 - 8 23 26 29 1 0.0000 5.9200e+00 3 - 9 12 15 51 1 0.0000 3.7700e+00 6 - 15 72 75 78 1 0.0000 5.9200e+00 3 - 15 51 54 57 1 0.0000 5.9200e+00 3 - 16 19 22 37 1 0.0000 3.7700e+00 6 - 22 86 89 92 1 0.0000 5.9200e+00 3 - 22 37 40 43 1 0.0000 5.9200e+00 3 - 23 26 29 79 1 0.0000 3.7700e+00 6 - 29 58 61 64 1 0.0000 5.9200e+00 3 - 29 79 82 85 1 0.0000 5.9200e+00 3 - 30 33 36 65 1 0.0000 3.7700e+00 6 - 36 65 68 71 1 0.0000 5.9200e+00 3 - 36 44 47 50 1 0.0000 5.9200e+00 3 - 37 40 43 117 1 0.0000 3.7700e+00 6 - 112 114 117 43 1 0.0000 5.9200e+00 3 - 211 213 216 43 1 0.0000 5.9200e+00 3 - 44 47 50 171 1 0.0000 3.7700e+00 6 - 166 168 171 50 1 0.0000 5.9200e+00 3 - 175 177 180 50 1 0.0000 5.9200e+00 3 - 51 54 57 99 1 0.0000 3.7700e+00 6 - 94 96 99 57 1 0.0000 5.9200e+00 3 - 139 141 144 57 1 0.0000 5.9200e+00 3 - 58 61 64 189 1 0.0000 3.7700e+00 6 - 121 123 126 64 1 0.0000 5.9200e+00 3 - 184 186 189 64 1 0.0000 5.9200e+00 3 - 65 68 71 207 1 0.0000 3.7700e+00 6 - 103 105 108 71 1 0.0000 5.9200e+00 3 - 202 204 207 71 1 0.0000 5.9200e+00 3 - 72 75 78 135 1 0.0000 3.7700e+00 6 - 130 132 135 78 1 0.0000 5.9200e+00 3 - 157 159 162 78 1 0.0000 5.9200e+00 3 - 79 82 85 225 1 0.0000 3.7700e+00 6 - 220 222 225 85 1 0.0000 5.9200e+00 3 - 193 195 198 85 1 0.0000 5.9200e+00 3 - 86 89 92 153 1 0.0000 3.7700e+00 6 - 148 150 153 92 1 0.0000 5.9200e+00 3 - 229 231 234 92 1 0.0000 5.9200e+00 3 - 95 94 96 99 1 180.0000 1.0000e+00 6 - 104 103 105 108 1 180.0000 1.0000e+00 6 - 113 112 114 117 1 180.0000 1.0000e+00 6 - 122 121 123 126 1 180.0000 1.0000e+00 6 - 131 130 132 135 1 180.0000 1.0000e+00 6 - 140 139 141 144 1 180.0000 1.0000e+00 6 - 149 148 150 153 1 180.0000 1.0000e+00 6 - 158 157 159 162 1 180.0000 1.0000e+00 6 - 167 166 168 171 1 180.0000 1.0000e+00 6 - 176 175 177 180 1 180.0000 1.0000e+00 6 - 185 184 186 189 1 180.0000 1.0000e+00 6 - 194 193 195 198 1 180.0000 1.0000e+00 6 - 203 202 204 207 1 180.0000 1.0000e+00 6 - 212 211 213 216 1 180.0000 1.0000e+00 6 - 221 220 222 225 1 180.0000 1.0000e+00 6 - 230 229 231 234 1 180.0000 1.0000e+00 6 - -[ exclusions ] diff --git a/polytop_examples/data/ethylamine_dendrimer.json b/polytop_examples/data/ethylamine_dendrimer.json deleted file mode 100644 index ba4a9ec..0000000 --- a/polytop_examples/data/ethylamine_dendrimer.json +++ /dev/null @@ -1 +0,0 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C6", "charge_group_num": 16, "partial_charge": 0.021840000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H13", "charge_group_num": 17, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H14", "charge_group_num": 18, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C5", "charge_group_num": 19, "partial_charge": 0.021840000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H11", "charge_group_num": 20, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "H12", "charge_group_num": 21, "partial_charge": 0.07884, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "CPos", "residue_id": 2, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13802, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11598, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11598, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "CPos", "residue_id": 2, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14198000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.05998, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "HC", "residue_id": 2, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.05998, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "NTer", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "N2", "charge_group_num": 8, "partial_charge": -0.5541600000000001, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "CPos", "residue_id": 3, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13772, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11628000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11628000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 17, "atom_type": "CPos", "residue_id": 3, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14228000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 18, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06028000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 19, "atom_type": "HC", "residue_id": 3, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06028000000000001, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 20, "atom_type": "CPos", "residue_id": 4, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13772, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 21, "atom_type": "HC", "residue_id": 4, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11628, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 22, "atom_type": "HC", "residue_id": 4, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11628, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 23, "atom_type": "CPos", "residue_id": 4, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14228000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 24, "atom_type": "HC", "residue_id": 4, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06028, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 25, "atom_type": "HC", "residue_id": 4, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06028, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 26, "atom_type": "NTer", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "N1", "charge_group_num": 22, "partial_charge": -0.5541600000000001, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 27, "atom_type": "CPos", "residue_id": 5, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.1372657142857143, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 28, "atom_type": "HC", "residue_id": 5, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11673428571428572, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 29, "atom_type": "HC", "residue_id": 5, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11673428571428572, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 30, "atom_type": "CPos", "residue_id": 5, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14273428571428573, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 31, "atom_type": "HC", "residue_id": 5, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06073428571428571, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 32, "atom_type": "HC", "residue_id": 5, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06073428571428571, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 33, "atom_type": "CPos", "residue_id": 6, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.1367357142857143, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 34, "atom_type": "HC", "residue_id": 6, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11726428571428574, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 35, "atom_type": "HC", "residue_id": 6, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11726428571428574, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 36, "atom_type": "CPos", "residue_id": 6, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14326428571428573, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 37, "atom_type": "HC", "residue_id": 6, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06126428571428572, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 38, "atom_type": "HC", "residue_id": 6, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06126428571428572, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 39, "atom_type": "CPos", "residue_id": 7, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13678571428571432, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 40, "atom_type": "HC", "residue_id": 7, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11721428571428572, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 41, "atom_type": "HC", "residue_id": 7, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11721428571428572, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 42, "atom_type": "CPos", "residue_id": 7, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.1432142857142857, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 43, "atom_type": "HC", "residue_id": 7, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.0612142857142857, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 44, "atom_type": "HC", "residue_id": 7, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.0612142857142857, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 45, "atom_type": "CPos", "residue_id": 8, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13686142857142858, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 46, "atom_type": "HC", "residue_id": 8, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11713857142857144, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 47, "atom_type": "HC", "residue_id": 8, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11713857142857144, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 48, "atom_type": "CPos", "residue_id": 8, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14313857142857145, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 49, "atom_type": "HC", "residue_id": 8, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06113857142857143, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 50, "atom_type": "HC", "residue_id": 8, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06113857142857143, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 51, "atom_type": "CPos", "residue_id": 9, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.13673571428571427, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 52, "atom_type": "HC", "residue_id": 9, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11726428571428575, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 53, "atom_type": "HC", "residue_id": 9, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11726428571428575, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 54, "atom_type": "CPos", "residue_id": 9, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14326428571428576, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 55, "atom_type": "HC", "residue_id": 9, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06126428571428575, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 56, "atom_type": "HC", "residue_id": 9, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06126428571428575, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 57, "atom_type": "NTer", "residue_id": 5, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5902657142857142, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 58, "atom_type": "CPos", "residue_id": 10, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.1367857142857143, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 59, "atom_type": "HC", "residue_id": 10, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11721428571428573, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 60, "atom_type": "HC", "residue_id": 10, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11721428571428573, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 61, "atom_type": "CPos", "residue_id": 10, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14321428571428574, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 62, "atom_type": "HC", "residue_id": 10, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.061214285714285735, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 63, "atom_type": "HC", "residue_id": 10, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.061214285714285735, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 64, "atom_type": "NTer", "residue_id": 2, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.59102, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 65, "atom_type": "CPos", "residue_id": 11, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.1368614285714286, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 66, "atom_type": "HC", "residue_id": 11, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11713857142857141, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 67, "atom_type": "HC", "residue_id": 11, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11713857142857141, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 68, "atom_type": "CPos", "residue_id": 11, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14313857142857142, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 69, "atom_type": "HC", "residue_id": 11, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06113857142857142, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 70, "atom_type": "HC", "residue_id": 11, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06113857142857142, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 71, "atom_type": "NTer", "residue_id": 4, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5907199999999999, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 72, "atom_type": "CPos", "residue_id": 12, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.1368114285714286, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 73, "atom_type": "HC", "residue_id": 12, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11718857142857142, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 74, "atom_type": "HC", "residue_id": 12, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11718857142857142, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 75, "atom_type": "CPos", "residue_id": 12, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14318857142857142, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 76, "atom_type": "HC", "residue_id": 12, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06118857142857141, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 77, "atom_type": "HC", "residue_id": 12, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06118857142857141, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 78, "atom_type": "NTer", "residue_id": 3, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5907199999999999, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 79, "atom_type": "CPos", "residue_id": 13, "residue_name": "BB6C", "atom_name": "C6", "charge_group_num": 10, "partial_charge": -0.1373067142857143, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 80, "atom_type": "HC", "residue_id": 13, "residue_name": "BB6C", "atom_name": "H13", "charge_group_num": 11, "partial_charge": 0.11669328571428571, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 81, "atom_type": "HC", "residue_id": 13, "residue_name": "BB6C", "atom_name": "H14", "charge_group_num": 12, "partial_charge": 0.11669328571428571, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 82, "atom_type": "CPos", "residue_id": 13, "residue_name": "BB6C", "atom_name": "C5", "charge_group_num": 13, "partial_charge": 0.14269328571428572, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 83, "atom_type": "HC", "residue_id": 13, "residue_name": "BB6C", "atom_name": "H11", "charge_group_num": 14, "partial_charge": 0.06069328571428571, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 84, "atom_type": "HC", "residue_id": 13, "residue_name": "BB6C", "atom_name": "H12", "charge_group_num": 15, "partial_charge": 0.06069328571428571, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 86, "atom_type": "HS14", "residue_id": 14, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3769601111111112, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 87, "atom_type": "NPri", "residue_id": 14, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.037039888888889, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 88, "atom_type": "HS14", "residue_id": 14, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3769601111111112, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 89, "atom_type": "CPos", "residue_id": 14, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3539601111111112, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 90, "atom_type": "HC", "residue_id": 14, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.024960111111111166, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 91, "atom_type": "HC", "residue_id": 14, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.024960111111111166, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 92, "atom_type": "C", "residue_id": 14, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03703988888888883, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 93, "atom_type": "HC", "residue_id": 14, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06496011111111116, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 94, "atom_type": "HC", "residue_id": 14, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06496011111111116, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 95, "atom_type": "HS14", "residue_id": 15, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37774166666666686, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 96, "atom_type": "NPri", "residue_id": 15, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362583333333333, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 97, "atom_type": "HS14", "residue_id": 15, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37774166666666686, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 98, "atom_type": "CPos", "residue_id": 15, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35474166666666684, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 99, "atom_type": "HC", "residue_id": 15, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.02574166666666683, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 100, "atom_type": "HC", "residue_id": 15, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.02574166666666683, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 101, "atom_type": "C", "residue_id": 15, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03625833333333317, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 102, "atom_type": "HC", "residue_id": 15, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06574166666666682, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 103, "atom_type": "HC", "residue_id": 15, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06574166666666682, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 104, "atom_type": "HS14", "residue_id": 16, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37776111111111127, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 105, "atom_type": "NPri", "residue_id": 16, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362388888888887, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 106, "atom_type": "HS14", "residue_id": 16, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37776111111111127, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 107, "atom_type": "CPos", "residue_id": 16, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35476111111111125, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 108, "atom_type": "HC", "residue_id": 16, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025761111111111266, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 109, "atom_type": "HC", "residue_id": 16, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025761111111111266, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 110, "atom_type": "C", "residue_id": 16, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03623888888888873, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 111, "atom_type": "HC", "residue_id": 16, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06576111111111126, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 112, "atom_type": "HC", "residue_id": 16, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06576111111111126, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 113, "atom_type": "HS14", "residue_id": 17, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3777122222222221, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 114, "atom_type": "NPri", "residue_id": 17, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.036287777777778, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 115, "atom_type": "HS14", "residue_id": 17, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3777122222222221, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 116, "atom_type": "CPos", "residue_id": 17, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3547122222222221, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 117, "atom_type": "HC", "residue_id": 17, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025712222222222136, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 118, "atom_type": "HC", "residue_id": 17, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025712222222222136, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 119, "atom_type": "C", "residue_id": 17, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03628777777777786, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 120, "atom_type": "HC", "residue_id": 17, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06571222222222213, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 121, "atom_type": "HC", "residue_id": 17, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06571222222222213, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 122, "atom_type": "HS14", "residue_id": 18, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37766333333333324, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 123, "atom_type": "NPri", "residue_id": 18, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.036336666666667, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 124, "atom_type": "HS14", "residue_id": 18, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37766333333333324, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 125, "atom_type": "CPos", "residue_id": 18, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3546633333333332, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 126, "atom_type": "HC", "residue_id": 18, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025663333333333236, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 127, "atom_type": "HC", "residue_id": 18, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025663333333333236, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 128, "atom_type": "C", "residue_id": 18, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03633666666666677, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 129, "atom_type": "HC", "residue_id": 18, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06566333333333324, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 130, "atom_type": "HC", "residue_id": 18, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06566333333333324, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 131, "atom_type": "HS14", "residue_id": 19, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3774901666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 132, "atom_type": "NPri", "residue_id": 19, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0365098333333334, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 133, "atom_type": "HS14", "residue_id": 19, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3774901666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 134, "atom_type": "CPos", "residue_id": 19, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35449016666666666, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 135, "atom_type": "HC", "residue_id": 19, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025490166666666685, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 136, "atom_type": "HC", "residue_id": 19, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025490166666666685, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 137, "atom_type": "C", "residue_id": 19, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03650983333333332, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 138, "atom_type": "HC", "residue_id": 19, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.0654901666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 139, "atom_type": "HC", "residue_id": 19, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.0654901666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 140, "atom_type": "NTer", "residue_id": 8, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5898614285714285, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 141, "atom_type": "HS14", "residue_id": 20, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3774901666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 142, "atom_type": "NPri", "residue_id": 20, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0365098333333334, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 143, "atom_type": "HS14", "residue_id": 20, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3774901666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 144, "atom_type": "CPos", "residue_id": 20, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3544901666666666, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 145, "atom_type": "HC", "residue_id": 20, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025490166666666644, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 146, "atom_type": "HC", "residue_id": 20, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025490166666666644, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 147, "atom_type": "C", "residue_id": 20, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03650983333333336, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 148, "atom_type": "HC", "residue_id": 20, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06549016666666664, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 149, "atom_type": "HC", "residue_id": 20, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06549016666666664, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 151, "atom_type": "HS14", "residue_id": 21, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3776927777777777, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 152, "atom_type": "NPri", "residue_id": 21, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0363072222222223, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 153, "atom_type": "HS14", "residue_id": 21, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3776927777777777, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 154, "atom_type": "CPos", "residue_id": 21, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3546927777777777, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 155, "atom_type": "HC", "residue_id": 21, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.02569277777777772, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 156, "atom_type": "HC", "residue_id": 21, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.02569277777777772, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 157, "atom_type": "C", "residue_id": 21, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03630722222222228, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 158, "atom_type": "HC", "residue_id": 21, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06569277777777771, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 159, "atom_type": "HC", "residue_id": 21, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06569277777777771, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 160, "atom_type": "NTer", "residue_id": 11, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5898614285714286, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 161, "atom_type": "HS14", "residue_id": 22, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37772222222222207, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 162, "atom_type": "NPri", "residue_id": 22, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362777777777779, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 163, "atom_type": "HS14", "residue_id": 22, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37772222222222207, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 164, "atom_type": "CPos", "residue_id": 22, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35472222222222205, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 165, "atom_type": "HC", "residue_id": 22, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.02572222222222209, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 166, "atom_type": "HC", "residue_id": 22, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.02572222222222209, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 167, "atom_type": "C", "residue_id": 22, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03627777777777791, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 168, "atom_type": "HC", "residue_id": 22, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06572222222222208, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 169, "atom_type": "HC", "residue_id": 22, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06572222222222208, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 170, "atom_type": "HS14", "residue_id": 23, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37774166666666664, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 171, "atom_type": "NPri", "residue_id": 23, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362583333333333, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 172, "atom_type": "HS14", "residue_id": 23, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37774166666666664, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 173, "atom_type": "CPos", "residue_id": 23, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3547416666666666, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 174, "atom_type": "HC", "residue_id": 23, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025741666666666663, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 175, "atom_type": "HC", "residue_id": 23, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025741666666666663, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 176, "atom_type": "C", "residue_id": 23, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03625833333333334, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 177, "atom_type": "HC", "residue_id": 23, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06574166666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 178, "atom_type": "HC", "residue_id": 23, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06574166666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 179, "atom_type": "NTer", "residue_id": 7, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5897857142857144, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 180, "atom_type": "HS14", "residue_id": 24, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37773166666666663, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 181, "atom_type": "NPri", "residue_id": 24, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362683333333333, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 182, "atom_type": "HS14", "residue_id": 24, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37773166666666663, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 183, "atom_type": "CPos", "residue_id": 24, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3547316666666666, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 184, "atom_type": "HC", "residue_id": 24, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025731666666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 185, "atom_type": "HC", "residue_id": 24, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025731666666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 186, "atom_type": "C", "residue_id": 24, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03626833333333334, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 187, "atom_type": "HC", "residue_id": 24, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06573166666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 188, "atom_type": "HC", "residue_id": 24, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06573166666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 189, "atom_type": "NTer", "residue_id": 9, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5897357142857141, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 190, "atom_type": "HS14", "residue_id": 25, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37771222222222217, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 191, "atom_type": "NPri", "residue_id": 25, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.036287777777778, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 192, "atom_type": "HS14", "residue_id": 25, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37771222222222217, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 193, "atom_type": "CPos", "residue_id": 25, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35471222222222215, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 194, "atom_type": "HC", "residue_id": 25, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.02571222222222216, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 195, "atom_type": "HC", "residue_id": 25, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.02571222222222216, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 196, "atom_type": "C", "residue_id": 25, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03628777777777784, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 197, "atom_type": "HC", "residue_id": 25, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06571222222222216, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 198, "atom_type": "HC", "residue_id": 25, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06571222222222216, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 199, "atom_type": "HS14", "residue_id": 26, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.37774166666666675, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 200, "atom_type": "NPri", "residue_id": 26, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362583333333333, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 201, "atom_type": "HS14", "residue_id": 26, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.37774166666666675, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 202, "atom_type": "CPos", "residue_id": 26, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35474166666666673, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 203, "atom_type": "HC", "residue_id": 26, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025741666666666742, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 204, "atom_type": "HC", "residue_id": 26, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025741666666666742, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 205, "atom_type": "C", "residue_id": 26, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03625833333333326, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 206, "atom_type": "HC", "residue_id": 26, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06574166666666674, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 207, "atom_type": "HC", "residue_id": 26, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06574166666666674, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 208, "atom_type": "NTer", "residue_id": 10, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5897857142857142, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 209, "atom_type": "HS14", "residue_id": 27, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3777316666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 210, "atom_type": "NPri", "residue_id": 27, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0362683333333333, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 211, "atom_type": "HS14", "residue_id": 27, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3777316666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 212, "atom_type": "CPos", "residue_id": 27, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35473166666666656, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 213, "atom_type": "HC", "residue_id": 27, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025731666666666597, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 214, "atom_type": "HC", "residue_id": 27, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025731666666666597, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 215, "atom_type": "C", "residue_id": 27, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.0362683333333334, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 216, "atom_type": "HC", "residue_id": 27, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06573166666666659, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 217, "atom_type": "HC", "residue_id": 27, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06573166666666659, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 218, "atom_type": "NTer", "residue_id": 6, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5897357142857143, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 219, "atom_type": "HS14", "residue_id": 28, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.377509611111111, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 220, "atom_type": "NPri", "residue_id": 28, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.036490388888889, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 221, "atom_type": "HS14", "residue_id": 28, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.377509611111111, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 222, "atom_type": "CPos", "residue_id": 28, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.35450961111111096, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 223, "atom_type": "HC", "residue_id": 28, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.025509611111110966, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 224, "atom_type": "HC", "residue_id": 28, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.025509611111110966, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 225, "atom_type": "C", "residue_id": 28, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03649038888888903, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 226, "atom_type": "HC", "residue_id": 28, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06550961111111096, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 227, "atom_type": "HC", "residue_id": 28, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06550961111111096, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 228, "atom_type": "NTer", "residue_id": 12, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5898114285714287, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 229, "atom_type": "HS14", "residue_id": 29, "residue_name": "PHGY", "atom_name": "H12", "charge_group_num": 1, "partial_charge": 0.3756585, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 230, "atom_type": "NPri", "residue_id": 29, "residue_name": "PHGY", "atom_name": "N2", "charge_group_num": 2, "partial_charge": -1.0383415, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 231, "atom_type": "HS14", "residue_id": 29, "residue_name": "PHGY", "atom_name": "H11", "charge_group_num": 3, "partial_charge": 0.3756585, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 232, "atom_type": "CPos", "residue_id": 29, "residue_name": "PHGY", "atom_name": "C2", "charge_group_num": 4, "partial_charge": 0.3526585, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 233, "atom_type": "HC", "residue_id": 29, "residue_name": "PHGY", "atom_name": "H3", "charge_group_num": 5, "partial_charge": 0.023658499999999992, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 234, "atom_type": "HC", "residue_id": 29, "residue_name": "PHGY", "atom_name": "H4", "charge_group_num": 6, "partial_charge": 0.023658499999999992, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 235, "atom_type": "C", "residue_id": 29, "residue_name": "PHGY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": -0.03834150000000001, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 236, "atom_type": "HC", "residue_id": 29, "residue_name": "PHGY", "atom_name": "H1", "charge_group_num": 8, "partial_charge": 0.06365849999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 237, "atom_type": "HC", "residue_id": 29, "residue_name": "PHGY", "atom_name": "H2", "charge_group_num": 9, "partial_charge": 0.06365849999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 150, "atom_type": "NTer", "residue_id": 13, "residue_name": "BB6C", "atom_name": "N1", "charge_group_num": 16, "partial_charge": -0.5903067142857144, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}], "bonds": [{"atom_a": 1, "atom_b": 4, "bond_type": 2, "bond_length": 0.154, "force_constant": 4005700.0, "order": 1}, {"atom_a": 1, "atom_b": 3, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 13, "atom_b": 1, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 1, "atom_b": 2, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 4, "atom_b": 6, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 4, "atom_b": 26, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 4, "atom_b": 5, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 7, "atom_b": 9, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 7, "atom_b": 8, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 7, "atom_b": 10, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 13, "atom_b": 7, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 10, "atom_b": 12, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 10, "atom_b": 11, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 10, "atom_b": 64, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 13, "atom_b": 14, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 14, "atom_b": 17, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 14, "atom_b": 15, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 14, "atom_b": 16, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 17, "atom_b": 19, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 17, "atom_b": 18, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 17, "atom_b": 78, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 20, "atom_b": 23, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 26, "atom_b": 20, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 20, "atom_b": 22, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 20, "atom_b": 21, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 23, "atom_b": 24, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 23, "atom_b": 25, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 23, "atom_b": 71, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 26, "atom_b": 27, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 27, "atom_b": 28, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 27, "atom_b": 30, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 27, "atom_b": 29, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 30, "atom_b": 32, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 30, "atom_b": 31, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 30, "atom_b": 57, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 33, "atom_b": 35, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 78, "atom_b": 33, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 33, "atom_b": 34, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 33, "atom_b": 36, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 36, "atom_b": 37, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 36, "atom_b": 218, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 36, "atom_b": 38, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 39, "atom_b": 42, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 39, "atom_b": 40, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 57, "atom_b": 39, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 39, "atom_b": 41, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 42, "atom_b": 179, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 42, "atom_b": 44, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 42, "atom_b": 43, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 45, "atom_b": 47, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 45, "atom_b": 46, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 45, "atom_b": 48, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 64, "atom_b": 45, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 48, "atom_b": 50, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 48, "atom_b": 49, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 48, "atom_b": 140, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 51, "atom_b": 54, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 51, "atom_b": 53, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 51, "atom_b": 52, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 71, "atom_b": 51, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 54, "atom_b": 55, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 54, "atom_b": 189, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 54, "atom_b": 56, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 57, "atom_b": 58, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 58, "atom_b": 59, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 58, "atom_b": 60, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 58, "atom_b": 61, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 61, "atom_b": 208, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 61, "atom_b": 63, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 61, "atom_b": 62, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 64, "atom_b": 65, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 65, "atom_b": 66, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 65, "atom_b": 67, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 65, "atom_b": 68, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 68, "atom_b": 160, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 68, "atom_b": 70, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 68, "atom_b": 69, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 71, "atom_b": 72, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 72, "atom_b": 75, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 72, "atom_b": 74, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 72, "atom_b": 73, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 75, "atom_b": 77, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 75, "atom_b": 228, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 75, "atom_b": 76, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 78, "atom_b": 79, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 79, "atom_b": 80, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 79, "atom_b": 81, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 79, "atom_b": 82, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 82, "atom_b": 84, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 82, "atom_b": 83, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 82, "atom_b": 150, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 86, "atom_b": 87, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 87, "atom_b": 88, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 87, "atom_b": 89, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 89, "atom_b": 92, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 89, "atom_b": 90, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 89, "atom_b": 91, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 140, "atom_b": 92, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 92, "atom_b": 93, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 92, "atom_b": 94, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 95, "atom_b": 96, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 96, "atom_b": 98, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 96, "atom_b": 97, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 98, "atom_b": 100, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 98, "atom_b": 101, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 98, "atom_b": 99, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 208, "atom_b": 101, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 101, "atom_b": 102, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 101, "atom_b": 103, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 104, "atom_b": 105, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 105, "atom_b": 106, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 105, "atom_b": 107, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 107, "atom_b": 109, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 107, "atom_b": 110, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 107, "atom_b": 108, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 218, "atom_b": 110, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 110, "atom_b": 111, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 110, "atom_b": 112, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 113, "atom_b": 114, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 114, "atom_b": 116, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 114, "atom_b": 115, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 116, "atom_b": 118, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 116, "atom_b": 119, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 116, "atom_b": 117, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 119, "atom_b": 121, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 189, "atom_b": 119, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 119, "atom_b": 120, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 122, "atom_b": 123, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 123, "atom_b": 124, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 123, "atom_b": 125, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 125, "atom_b": 127, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 125, "atom_b": 128, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 125, "atom_b": 126, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 128, "atom_b": 130, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 160, "atom_b": 128, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 128, "atom_b": 129, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 131, "atom_b": 132, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 132, "atom_b": 134, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 132, "atom_b": 133, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 134, "atom_b": 136, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 134, "atom_b": 135, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 134, "atom_b": 137, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 137, "atom_b": 138, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 137, "atom_b": 139, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 140, "atom_b": 137, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 141, "atom_b": 142, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 142, "atom_b": 144, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 142, "atom_b": 143, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 144, "atom_b": 146, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 144, "atom_b": 147, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 144, "atom_b": 145, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 147, "atom_b": 149, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 150, "atom_b": 147, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 147, "atom_b": 148, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 151, "atom_b": 152, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 152, "atom_b": 153, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 152, "atom_b": 154, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 154, "atom_b": 156, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 154, "atom_b": 157, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 154, "atom_b": 155, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 157, "atom_b": 159, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 157, "atom_b": 158, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 160, "atom_b": 157, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 161, "atom_b": 162, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 162, "atom_b": 164, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 162, "atom_b": 163, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 164, "atom_b": 167, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 164, "atom_b": 166, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 164, "atom_b": 165, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 167, "atom_b": 168, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 179, "atom_b": 167, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 167, "atom_b": 169, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 170, "atom_b": 171, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 171, "atom_b": 173, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 171, "atom_b": 172, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 173, "atom_b": 174, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 173, "atom_b": 175, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 173, "atom_b": 176, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 179, "atom_b": 176, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 176, "atom_b": 178, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 176, "atom_b": 177, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 180, "atom_b": 181, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 181, "atom_b": 182, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 181, "atom_b": 183, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 183, "atom_b": 184, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 183, "atom_b": 185, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 183, "atom_b": 186, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 186, "atom_b": 188, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 186, "atom_b": 187, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 189, "atom_b": 186, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 190, "atom_b": 191, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 191, "atom_b": 192, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 191, "atom_b": 193, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 193, "atom_b": 195, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 193, "atom_b": 196, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 193, "atom_b": 194, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 196, "atom_b": 198, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 228, "atom_b": 196, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 196, "atom_b": 197, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 199, "atom_b": 200, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 200, "atom_b": 202, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 200, "atom_b": 201, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 202, "atom_b": 205, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 202, "atom_b": 204, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 202, "atom_b": 203, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 205, "atom_b": 207, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 205, "atom_b": 206, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 208, "atom_b": 205, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 209, "atom_b": 210, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 210, "atom_b": 212, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 210, "atom_b": 211, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 212, "atom_b": 214, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 212, "atom_b": 215, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 212, "atom_b": 213, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 215, "atom_b": 217, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 218, "atom_b": 215, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 215, "atom_b": 216, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 219, "atom_b": 220, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 220, "atom_b": 221, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 220, "atom_b": 222, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 222, "atom_b": 223, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 222, "atom_b": 225, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 222, "atom_b": 224, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 228, "atom_b": 225, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 225, "atom_b": 226, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 225, "atom_b": 227, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 229, "atom_b": 230, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 230, "atom_b": 232, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 230, "atom_b": 231, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 232, "atom_b": 233, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 232, "atom_b": 235, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 232, "atom_b": 234, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 150, "atom_b": 235, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 235, "atom_b": 236, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 235, "atom_b": 237, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}], "angles": [{"atom_a": 3, "atom_b": 1, "atom_c": 4, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 1, "atom_b": 4, "atom_c": 6, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 1, "atom_b": 4, "atom_c": 26, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 13, "atom_b": 1, "atom_c": 4, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 2, "atom_b": 1, "atom_c": 4, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 1, "atom_b": 4, "atom_c": 5, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 13, "atom_b": 1, "atom_c": 3, "angle_type": 2, "angle_value": 111.3, "force_constant": 632.0}, {"atom_a": 2, "atom_b": 1, "atom_c": 3, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 13, "atom_b": 1, "atom_c": 2, "angle_type": 2, "angle_value": 111.3, "force_constant": 632.0}, {"atom_a": 1, "atom_b": 13, "atom_c": 7, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 1, "atom_b": 13, "atom_c": 14, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 6, "atom_b": 4, "atom_c": 26, "angle_type": 2, "angle_value": 111.3, "force_constant": 632.0}, {"atom_a": 5, "atom_b": 4, "atom_c": 6, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 4, "atom_b": 26, "atom_c": 20, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 4, "atom_b": 26, "atom_c": 27, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 5, "atom_b": 4, "atom_c": 26, "angle_type": 2, "angle_value": 111.3, "force_constant": 632.0}, {"atom_a": 8, "atom_b": 7, "atom_c": 9, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 9, "atom_b": 7, "atom_c": 10, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 13, "atom_b": 7, "atom_c": 9, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 13, "atom_b": 7, "atom_c": 8, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 8, "atom_b": 7, "atom_c": 10, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 13, "atom_b": 7, "atom_c": 10, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 7, "atom_b": 10, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 7, "atom_b": 10, "atom_c": 12, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 7, "atom_b": 10, "atom_c": 11, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 7, "atom_b": 13, "atom_c": 14, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 11, "atom_b": 10, "atom_c": 12, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 12, "atom_b": 10, "atom_c": 64, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 11, "atom_b": 10, "atom_c": 64, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 10, "atom_b": 64, "atom_c": 65, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 10, "atom_b": 64, "atom_c": 45, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 13, "atom_b": 14, "atom_c": 15, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 13, "atom_b": 14, "atom_c": 16, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 13, "atom_b": 14, "atom_c": 17, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 16, "atom_b": 14, "atom_c": 17, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 15, "atom_b": 14, "atom_c": 17, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 14, "atom_b": 17, "atom_c": 18, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 14, "atom_b": 17, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 14, "atom_b": 17, "atom_c": 19, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 15, "atom_b": 14, "atom_c": 16, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 18, "atom_b": 17, "atom_c": 19, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 19, "atom_b": 17, "atom_c": 78, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 18, "atom_b": 17, "atom_c": 78, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 17, "atom_b": 78, "atom_c": 79, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 17, "atom_b": 78, "atom_c": 33, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 21, "atom_b": 20, "atom_c": 23, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 22, "atom_b": 20, "atom_c": 23, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 20, "atom_b": 23, "atom_c": 24, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 20, "atom_b": 23, "atom_c": 71, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 26, "atom_b": 20, "atom_c": 23, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 20, "atom_b": 23, "atom_c": 25, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 20, "atom_b": 26, "atom_c": 27, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 26, "atom_b": 20, "atom_c": 22, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 26, "atom_b": 20, "atom_c": 21, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 21, "atom_b": 20, "atom_c": 22, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 24, "atom_b": 23, "atom_c": 71, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 24, "atom_b": 23, "atom_c": 25, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 25, "atom_b": 23, "atom_c": 71, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 23, "atom_b": 71, "atom_c": 72, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 23, "atom_b": 71, "atom_c": 51, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 26, "atom_b": 27, "atom_c": 29, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 26, "atom_b": 27, "atom_c": 30, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 26, "atom_b": 27, "atom_c": 28, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 28, "atom_b": 27, "atom_c": 29, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 28, "atom_b": 27, "atom_c": 30, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 29, "atom_b": 27, "atom_c": 30, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 27, "atom_b": 30, "atom_c": 31, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 27, "atom_b": 30, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 27, "atom_b": 30, "atom_c": 32, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 31, "atom_b": 30, "atom_c": 32, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 32, "atom_b": 30, "atom_c": 57, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 31, "atom_b": 30, "atom_c": 57, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 30, "atom_b": 57, "atom_c": 39, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 30, "atom_b": 57, "atom_c": 58, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 35, "atom_b": 33, "atom_c": 36, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 78, "atom_b": 33, "atom_c": 35, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 34, "atom_b": 33, "atom_c": 35, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 33, "atom_b": 78, "atom_c": 79, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 78, "atom_b": 33, "atom_c": 34, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 78, "atom_b": 33, "atom_c": 36, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 34, "atom_b": 33, "atom_c": 36, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 33, "atom_b": 36, "atom_c": 37, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 33, "atom_b": 36, "atom_c": 218, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 33, "atom_b": 36, "atom_c": 38, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 37, "atom_b": 36, "atom_c": 218, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 37, "atom_b": 36, "atom_c": 38, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 36, "atom_b": 218, "atom_c": 215, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 38, "atom_b": 36, "atom_c": 218, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 36, "atom_b": 218, "atom_c": 110, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 57, "atom_b": 39, "atom_c": 42, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 40, "atom_b": 39, "atom_c": 42, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 39, "atom_b": 42, "atom_c": 43, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 39, "atom_b": 42, "atom_c": 179, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 39, "atom_b": 42, "atom_c": 44, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 41, "atom_b": 39, "atom_c": 42, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 40, "atom_b": 39, "atom_c": 41, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 57, "atom_b": 39, "atom_c": 40, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 57, "atom_b": 39, "atom_c": 41, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 39, "atom_b": 57, "atom_c": 58, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 42, "atom_b": 179, "atom_c": 176, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 43, "atom_b": 42, "atom_c": 179, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 42, "atom_b": 179, "atom_c": 167, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 44, "atom_b": 42, "atom_c": 179, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 43, "atom_b": 42, "atom_c": 44, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 47, "atom_b": 45, "atom_c": 48, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 64, "atom_b": 45, "atom_c": 47, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 46, "atom_b": 45, "atom_c": 47, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 46, "atom_b": 45, "atom_c": 48, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 64, "atom_b": 45, "atom_c": 46, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 45, "atom_b": 48, "atom_c": 49, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 64, "atom_b": 45, "atom_c": 48, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 45, "atom_b": 48, "atom_c": 140, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 45, "atom_b": 48, "atom_c": 50, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 45, "atom_b": 64, "atom_c": 65, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 50, "atom_b": 48, "atom_c": 140, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 49, "atom_b": 48, "atom_c": 50, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 49, "atom_b": 48, "atom_c": 140, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 48, "atom_b": 140, "atom_c": 137, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 48, "atom_b": 140, "atom_c": 92, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 53, "atom_b": 51, "atom_c": 54, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 51, "atom_b": 54, "atom_c": 56, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 71, "atom_b": 51, "atom_c": 54, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 51, "atom_b": 54, "atom_c": 189, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 51, "atom_b": 54, "atom_c": 55, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 52, "atom_b": 51, "atom_c": 54, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 71, "atom_b": 51, "atom_c": 53, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 52, "atom_b": 51, "atom_c": 53, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 71, "atom_b": 51, "atom_c": 52, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 51, "atom_b": 71, "atom_c": 72, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 55, "atom_b": 54, "atom_c": 56, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 55, "atom_b": 54, "atom_c": 189, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 56, "atom_b": 54, "atom_c": 189, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 54, "atom_b": 189, "atom_c": 119, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 54, "atom_b": 189, "atom_c": 186, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 57, "atom_b": 58, "atom_c": 60, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 57, "atom_b": 58, "atom_c": 59, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 57, "atom_b": 58, "atom_c": 61, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 59, "atom_b": 58, "atom_c": 61, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 59, "atom_b": 58, "atom_c": 60, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 60, "atom_b": 58, "atom_c": 61, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 58, "atom_b": 61, "atom_c": 63, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 58, "atom_b": 61, "atom_c": 62, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 58, "atom_b": 61, "atom_c": 208, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 62, "atom_b": 61, "atom_c": 208, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 61, "atom_b": 208, "atom_c": 101, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 61, "atom_b": 208, "atom_c": 205, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 63, "atom_b": 61, "atom_c": 208, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 62, "atom_b": 61, "atom_c": 63, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 64, "atom_b": 65, "atom_c": 68, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 64, "atom_b": 65, "atom_c": 66, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 64, "atom_b": 65, "atom_c": 67, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 66, "atom_b": 65, "atom_c": 67, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 66, "atom_b": 65, "atom_c": 68, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 67, "atom_b": 65, "atom_c": 68, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 65, "atom_b": 68, "atom_c": 70, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 65, "atom_b": 68, "atom_c": 160, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 65, "atom_b": 68, "atom_c": 69, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 69, "atom_b": 68, "atom_c": 160, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 70, "atom_b": 68, "atom_c": 160, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 68, "atom_b": 160, "atom_c": 157, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 68, "atom_b": 160, "atom_c": 128, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 69, "atom_b": 68, "atom_c": 70, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 71, "atom_b": 72, "atom_c": 74, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 71, "atom_b": 72, "atom_c": 73, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 71, "atom_b": 72, "atom_c": 75, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 72, "atom_b": 75, "atom_c": 76, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 73, "atom_b": 72, "atom_c": 75, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 74, "atom_b": 72, "atom_c": 75, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 72, "atom_b": 75, "atom_c": 77, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 72, "atom_b": 75, "atom_c": 228, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 73, "atom_b": 72, "atom_c": 74, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 76, "atom_b": 75, "atom_c": 77, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 77, "atom_b": 75, "atom_c": 228, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 75, "atom_b": 228, "atom_c": 196, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 76, "atom_b": 75, "atom_c": 228, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 75, "atom_b": 228, "atom_c": 225, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 78, "atom_b": 79, "atom_c": 80, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 78, "atom_b": 79, "atom_c": 81, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 78, "atom_b": 79, "atom_c": 82, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 80, "atom_b": 79, "atom_c": 82, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 80, "atom_b": 79, "atom_c": 81, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 81, "atom_b": 79, "atom_c": 82, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 79, "atom_b": 82, "atom_c": 83, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 79, "atom_b": 82, "atom_c": 150, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 79, "atom_b": 82, "atom_c": 84, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 83, "atom_b": 82, "atom_c": 84, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 84, "atom_b": 82, "atom_c": 150, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 83, "atom_b": 82, "atom_c": 150, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 82, "atom_b": 150, "atom_c": 147, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 82, "atom_b": 150, "atom_c": 235, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 86, "atom_b": 87, "atom_c": 89, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 86, "atom_b": 87, "atom_c": 88, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 88, "atom_b": 87, "atom_c": 89, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 87, "atom_b": 89, "atom_c": 92, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 87, "atom_b": 89, "atom_c": 91, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 87, "atom_b": 89, "atom_c": 90, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 90, "atom_b": 89, "atom_c": 92, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 91, "atom_b": 89, "atom_c": 92, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 89, "atom_b": 92, "atom_c": 93, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 140, "atom_b": 92, "atom_c": 89, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 89, "atom_b": 92, "atom_c": 94, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 90, "atom_b": 89, "atom_c": 91, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 140, "atom_b": 92, "atom_c": 94, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 140, "atom_b": 92, "atom_c": 93, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 92, "atom_b": 140, "atom_c": 137, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 93, "atom_b": 92, "atom_c": 94, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 95, "atom_b": 96, "atom_c": 98, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 95, "atom_b": 96, "atom_c": 97, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 96, "atom_b": 98, "atom_c": 100, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 97, "atom_b": 96, "atom_c": 98, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 96, "atom_b": 98, "atom_c": 101, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 96, "atom_b": 98, "atom_c": 99, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 100, "atom_b": 98, "atom_c": 101, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 99, "atom_b": 98, "atom_c": 100, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 98, "atom_b": 101, "atom_c": 102, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 99, "atom_b": 98, "atom_c": 101, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 208, "atom_b": 101, "atom_c": 98, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 98, "atom_b": 101, "atom_c": 103, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 101, "atom_b": 208, "atom_c": 205, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 208, "atom_b": 101, "atom_c": 102, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 208, "atom_b": 101, "atom_c": 103, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 102, "atom_b": 101, "atom_c": 103, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 104, "atom_b": 105, "atom_c": 106, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 104, "atom_b": 105, "atom_c": 107, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 106, "atom_b": 105, "atom_c": 107, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 105, "atom_b": 107, "atom_c": 109, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 105, "atom_b": 107, "atom_c": 108, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 105, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 109, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 108, "atom_b": 107, "atom_c": 109, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 108, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 218, "atom_b": 110, "atom_c": 107, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 107, "atom_b": 110, "atom_c": 112, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 107, "atom_b": 110, "atom_c": 111, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 110, "atom_b": 218, "atom_c": 215, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 218, "atom_b": 110, "atom_c": 111, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 218, "atom_b": 110, "atom_c": 112, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 111, "atom_b": 110, "atom_c": 112, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 113, "atom_b": 114, "atom_c": 116, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 113, "atom_b": 114, "atom_c": 115, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 115, "atom_b": 114, "atom_c": 116, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 114, "atom_b": 116, "atom_c": 119, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 114, "atom_b": 116, "atom_c": 118, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 114, "atom_b": 116, "atom_c": 117, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 117, "atom_b": 116, "atom_c": 118, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 118, "atom_b": 116, "atom_c": 119, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 116, "atom_b": 119, "atom_c": 121, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 117, "atom_b": 116, "atom_c": 119, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 189, "atom_b": 119, "atom_c": 116, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 116, "atom_b": 119, "atom_c": 120, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 120, "atom_b": 119, "atom_c": 121, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 189, "atom_b": 119, "atom_c": 121, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 119, "atom_b": 189, "atom_c": 186, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 189, "atom_b": 119, "atom_c": 120, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 122, "atom_b": 123, "atom_c": 124, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 122, "atom_b": 123, "atom_c": 125, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 124, "atom_b": 123, "atom_c": 125, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 123, "atom_b": 125, "atom_c": 126, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 123, "atom_b": 125, "atom_c": 128, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 123, "atom_b": 125, "atom_c": 127, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 127, "atom_b": 125, "atom_c": 128, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 126, "atom_b": 125, "atom_c": 127, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 126, "atom_b": 125, "atom_c": 128, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 125, "atom_b": 128, "atom_c": 129, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 160, "atom_b": 128, "atom_c": 125, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 125, "atom_b": 128, "atom_c": 130, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 129, "atom_b": 128, "atom_c": 130, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 160, "atom_b": 128, "atom_c": 130, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 128, "atom_b": 160, "atom_c": 157, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 160, "atom_b": 128, "atom_c": 129, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 131, "atom_b": 132, "atom_c": 134, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 131, "atom_b": 132, "atom_c": 133, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 132, "atom_b": 134, "atom_c": 136, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 132, "atom_b": 134, "atom_c": 137, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 133, "atom_b": 132, "atom_c": 134, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 132, "atom_b": 134, "atom_c": 135, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 135, "atom_b": 134, "atom_c": 136, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 136, "atom_b": 134, "atom_c": 137, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 135, "atom_b": 134, "atom_c": 137, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 134, "atom_b": 137, "atom_c": 139, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 134, "atom_b": 137, "atom_c": 138, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 140, "atom_b": 137, "atom_c": 134, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 138, "atom_b": 137, "atom_c": 139, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 140, "atom_b": 137, "atom_c": 138, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 140, "atom_b": 137, "atom_c": 139, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 141, "atom_b": 142, "atom_c": 144, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 141, "atom_b": 142, "atom_c": 143, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 142, "atom_b": 144, "atom_c": 145, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 142, "atom_b": 144, "atom_c": 146, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 143, "atom_b": 142, "atom_c": 144, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 142, "atom_b": 144, "atom_c": 147, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 146, "atom_b": 144, "atom_c": 147, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 145, "atom_b": 144, "atom_c": 146, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 144, "atom_b": 147, "atom_c": 148, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 150, "atom_b": 147, "atom_c": 144, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 145, "atom_b": 144, "atom_c": 147, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 144, "atom_b": 147, "atom_c": 149, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 148, "atom_b": 147, "atom_c": 149, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 150, "atom_b": 147, "atom_c": 149, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 147, "atom_b": 150, "atom_c": 235, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 150, "atom_b": 147, "atom_c": 148, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 151, "atom_b": 152, "atom_c": 153, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 151, "atom_b": 152, "atom_c": 154, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 153, "atom_b": 152, "atom_c": 154, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 152, "atom_b": 154, "atom_c": 156, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 152, "atom_b": 154, "atom_c": 157, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 152, "atom_b": 154, "atom_c": 155, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 155, "atom_b": 154, "atom_c": 156, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 156, "atom_b": 154, "atom_c": 157, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 155, "atom_b": 154, "atom_c": 157, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 154, "atom_b": 157, "atom_c": 159, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 154, "atom_b": 157, "atom_c": 158, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 160, "atom_b": 157, "atom_c": 154, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 160, "atom_b": 157, "atom_c": 159, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 158, "atom_b": 157, "atom_c": 159, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 160, "atom_b": 157, "atom_c": 158, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 161, "atom_b": 162, "atom_c": 163, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 161, "atom_b": 162, "atom_c": 164, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 163, "atom_b": 162, "atom_c": 164, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 162, "atom_b": 164, "atom_c": 166, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 162, "atom_b": 164, "atom_c": 165, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 162, "atom_b": 164, "atom_c": 167, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 166, "atom_b": 164, "atom_c": 167, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 164, "atom_b": 167, "atom_c": 168, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 164, "atom_b": 167, "atom_c": 169, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 179, "atom_b": 167, "atom_c": 164, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 165, "atom_b": 164, "atom_c": 167, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 165, "atom_b": 164, "atom_c": 166, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 168, "atom_b": 167, "atom_c": 169, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 179, "atom_b": 167, "atom_c": 168, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 179, "atom_b": 167, "atom_c": 169, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 167, "atom_b": 179, "atom_c": 176, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 170, "atom_b": 171, "atom_c": 172, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 170, "atom_b": 171, "atom_c": 173, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 171, "atom_b": 173, "atom_c": 175, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 171, "atom_b": 173, "atom_c": 176, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 172, "atom_b": 171, "atom_c": 173, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 171, "atom_b": 173, "atom_c": 174, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 174, "atom_b": 173, "atom_c": 176, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 174, "atom_b": 173, "atom_c": 175, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 175, "atom_b": 173, "atom_c": 176, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 173, "atom_b": 176, "atom_c": 177, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 173, "atom_b": 176, "atom_c": 178, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 179, "atom_b": 176, "atom_c": 173, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 179, "atom_b": 176, "atom_c": 178, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 179, "atom_b": 176, "atom_c": 177, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 177, "atom_b": 176, "atom_c": 178, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 180, "atom_b": 181, "atom_c": 183, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 180, "atom_b": 181, "atom_c": 182, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 182, "atom_b": 181, "atom_c": 183, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 181, "atom_b": 183, "atom_c": 185, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 181, "atom_b": 183, "atom_c": 186, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 181, "atom_b": 183, "atom_c": 184, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 184, "atom_b": 183, "atom_c": 185, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 184, "atom_b": 183, "atom_c": 186, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 185, "atom_b": 183, "atom_c": 186, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 183, "atom_b": 186, "atom_c": 187, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 183, "atom_b": 186, "atom_c": 188, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 189, "atom_b": 186, "atom_c": 183, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 187, "atom_b": 186, "atom_c": 188, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 189, "atom_b": 186, "atom_c": 188, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 189, "atom_b": 186, "atom_c": 187, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 190, "atom_b": 191, "atom_c": 192, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 190, "atom_b": 191, "atom_c": 193, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 192, "atom_b": 191, "atom_c": 193, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 191, "atom_b": 193, "atom_c": 194, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 191, "atom_b": 193, "atom_c": 195, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 191, "atom_b": 193, "atom_c": 196, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 194, "atom_b": 193, "atom_c": 195, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 195, "atom_b": 193, "atom_c": 196, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 193, "atom_b": 196, "atom_c": 198, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 193, "atom_b": 196, "atom_c": 197, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 228, "atom_b": 196, "atom_c": 193, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 194, "atom_b": 193, "atom_c": 196, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 228, "atom_b": 196, "atom_c": 198, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 197, "atom_b": 196, "atom_c": 198, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 228, "atom_b": 196, "atom_c": 197, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 196, "atom_b": 228, "atom_c": 225, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 199, "atom_b": 200, "atom_c": 201, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 199, "atom_b": 200, "atom_c": 202, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 200, "atom_b": 202, "atom_c": 203, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 201, "atom_b": 200, "atom_c": 202, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 200, "atom_b": 202, "atom_c": 204, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 200, "atom_b": 202, "atom_c": 205, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 203, "atom_b": 202, "atom_c": 205, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 202, "atom_b": 205, "atom_c": 206, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 204, "atom_b": 202, "atom_c": 205, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 208, "atom_b": 205, "atom_c": 202, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 202, "atom_b": 205, "atom_c": 207, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 203, "atom_b": 202, "atom_c": 204, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 206, "atom_b": 205, "atom_c": 207, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 208, "atom_b": 205, "atom_c": 207, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 208, "atom_b": 205, "atom_c": 206, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 209, "atom_b": 210, "atom_c": 211, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 209, "atom_b": 210, "atom_c": 212, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 210, "atom_b": 212, "atom_c": 213, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 211, "atom_b": 210, "atom_c": 212, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 210, "atom_b": 212, "atom_c": 214, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 210, "atom_b": 212, "atom_c": 215, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 214, "atom_b": 212, "atom_c": 215, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 213, "atom_b": 212, "atom_c": 214, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 213, "atom_b": 212, "atom_c": 215, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 212, "atom_b": 215, "atom_c": 216, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 212, "atom_b": 215, "atom_c": 217, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 218, "atom_b": 215, "atom_c": 212, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 216, "atom_b": 215, "atom_c": 217, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 218, "atom_b": 215, "atom_c": 217, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 218, "atom_b": 215, "atom_c": 216, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 219, "atom_b": 220, "atom_c": 221, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 219, "atom_b": 220, "atom_c": 222, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 221, "atom_b": 220, "atom_c": 222, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 220, "atom_b": 222, "atom_c": 225, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 220, "atom_b": 222, "atom_c": 224, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 220, "atom_b": 222, "atom_c": 223, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 223, "atom_b": 222, "atom_c": 225, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 223, "atom_b": 222, "atom_c": 224, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 222, "atom_b": 225, "atom_c": 227, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 222, "atom_b": 225, "atom_c": 226, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 228, "atom_b": 225, "atom_c": 222, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 224, "atom_b": 222, "atom_c": 225, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 228, "atom_b": 225, "atom_c": 227, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 228, "atom_b": 225, "atom_c": 226, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 226, "atom_b": 225, "atom_c": 227, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 229, "atom_b": 230, "atom_c": 232, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 229, "atom_b": 230, "atom_c": 231, "angle_type": 2, "angle_value": 104.0, "force_constant": 490.0}, {"atom_a": 230, "atom_b": 232, "atom_c": 235, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 231, "atom_b": 230, "atom_c": 232, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 230, "atom_b": 232, "atom_c": 233, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 230, "atom_b": 232, "atom_c": 234, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 233, "atom_b": 232, "atom_c": 235, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 233, "atom_b": 232, "atom_c": 234, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 234, "atom_b": 232, "atom_c": 235, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 232, "atom_b": 235, "atom_c": 236, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 150, "atom_b": 235, "atom_c": 232, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 232, "atom_b": 235, "atom_c": 237, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 150, "atom_b": 235, "atom_c": 237, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 150, "atom_b": 235, "atom_c": 236, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 236, "atom_b": 235, "atom_c": 237, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}], "dihedrals": [{"atom_a": 1, "atom_b": 4, "atom_c": 26, "atom_d": 20, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 13, "atom_b": 1, "atom_c": 4, "atom_d": 26, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 14, "atom_b": 13, "atom_c": 1, "atom_d": 4, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 13, "atom_b": 7, "atom_c": 10, "atom_d": 64, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 7, "atom_b": 10, "atom_c": 64, "atom_d": 45, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 13, "atom_b": 14, "atom_c": 17, "atom_d": 78, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 14, "atom_b": 17, "atom_c": 78, "atom_d": 33, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 26, "atom_b": 20, "atom_c": 23, "atom_d": 71, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 20, "atom_b": 23, "atom_c": 71, "atom_d": 72, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 26, "atom_b": 27, "atom_c": 30, "atom_d": 57, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 27, "atom_b": 30, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 78, "atom_b": 33, "atom_c": 36, "atom_d": 218, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 33, "atom_b": 36, "atom_c": 218, "atom_d": 110, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 57, "atom_b": 39, "atom_c": 42, "atom_d": 179, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 39, "atom_b": 42, "atom_c": 179, "atom_d": 167, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 64, "atom_b": 45, "atom_c": 48, "atom_d": 140, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 45, "atom_b": 48, "atom_c": 140, "atom_d": 92, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 71, "atom_b": 51, "atom_c": 54, "atom_d": 189, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 51, "atom_b": 54, "atom_c": 189, "atom_d": 186, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 57, "atom_b": 58, "atom_c": 61, "atom_d": 208, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 58, "atom_b": 61, "atom_c": 208, "atom_d": 205, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 64, "atom_b": 65, "atom_c": 68, "atom_d": 160, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 68, "atom_c": 160, "atom_d": 128, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 71, "atom_b": 72, "atom_c": 75, "atom_d": 228, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 72, "atom_b": 75, "atom_c": 228, "atom_d": 225, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 78, "atom_b": 79, "atom_c": 82, "atom_d": 150, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 82, "atom_c": 150, "atom_d": 147, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 3.77, "multiplicity": 6, "constants": []}, {"atom_a": 88, "atom_b": 87, "atom_c": 89, "atom_d": 92, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 87, "atom_b": 89, "atom_c": 92, "atom_d": 140, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 97, "atom_b": 96, "atom_c": 98, "atom_d": 101, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 96, "atom_b": 98, "atom_c": 101, "atom_d": 208, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 106, "atom_b": 105, "atom_c": 107, "atom_d": 110, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 105, "atom_b": 107, "atom_c": 110, "atom_d": 218, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 115, "atom_b": 114, "atom_c": 116, "atom_d": 119, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 114, "atom_b": 116, "atom_c": 119, "atom_d": 189, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 124, "atom_b": 123, "atom_c": 125, "atom_d": 128, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 123, "atom_b": 125, "atom_c": 128, "atom_d": 160, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 133, "atom_b": 132, "atom_c": 134, "atom_d": 137, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 132, "atom_b": 134, "atom_c": 137, "atom_d": 140, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 143, "atom_b": 142, "atom_c": 144, "atom_d": 147, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 142, "atom_b": 144, "atom_c": 147, "atom_d": 150, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 153, "atom_b": 152, "atom_c": 154, "atom_d": 157, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 152, "atom_b": 154, "atom_c": 157, "atom_d": 160, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 163, "atom_b": 162, "atom_c": 164, "atom_d": 167, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 162, "atom_b": 164, "atom_c": 167, "atom_d": 179, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 172, "atom_b": 171, "atom_c": 173, "atom_d": 176, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 171, "atom_b": 173, "atom_c": 176, "atom_d": 179, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 182, "atom_b": 181, "atom_c": 183, "atom_d": 186, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 181, "atom_b": 183, "atom_c": 186, "atom_d": 189, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 192, "atom_b": 191, "atom_c": 193, "atom_d": 196, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 191, "atom_b": 193, "atom_c": 196, "atom_d": 228, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 201, "atom_b": 200, "atom_c": 202, "atom_d": 205, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 200, "atom_b": 202, "atom_c": 205, "atom_d": 208, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 211, "atom_b": 210, "atom_c": 212, "atom_d": 215, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 210, "atom_b": 212, "atom_c": 215, "atom_d": 218, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 221, "atom_b": 220, "atom_c": 222, "atom_d": 225, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 220, "atom_b": 222, "atom_c": 225, "atom_d": 228, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 231, "atom_b": 230, "atom_c": 232, "atom_d": 235, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 230, "atom_b": 232, "atom_c": 235, "atom_d": 150, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 2, "atom_b": 26, "pair_type": 1}, {"atom_a": 2, "atom_b": 5, "pair_type": 1}, {"atom_a": 3, "atom_b": 5, "pair_type": 1}, {"atom_a": 3, "atom_b": 6, "pair_type": 1}, {"atom_a": 3, "atom_b": 26, "pair_type": 1}, {"atom_a": 13, "atom_b": 5, "pair_type": 1}, {"atom_a": 13, "atom_b": 6, "pair_type": 1}, {"atom_a": 8, "atom_b": 11, "pair_type": 1}, {"atom_a": 8, "atom_b": 64, "pair_type": 1}, {"atom_a": 8, "atom_b": 12, "pair_type": 1}, {"atom_a": 9, "atom_b": 12, "pair_type": 1}, {"atom_a": 9, "atom_b": 64, "pair_type": 1}, {"atom_a": 9, "atom_b": 11, "pair_type": 1}, {"atom_a": 13, "atom_b": 26, "pair_type": 1}, {"atom_a": 15, "atom_b": 78, "pair_type": 1}, {"atom_a": 15, "atom_b": 19, "pair_type": 1}, {"atom_a": 15, "atom_b": 18, "pair_type": 1}, {"atom_a": 16, "atom_b": 78, "pair_type": 1}, {"atom_a": 16, "atom_b": 19, "pair_type": 1}, {"atom_a": 16, "atom_b": 18, "pair_type": 1}, {"atom_a": 21, "atom_b": 25, "pair_type": 1}, {"atom_a": 21, "atom_b": 24, "pair_type": 1}, {"atom_a": 21, "atom_b": 71, "pair_type": 1}, {"atom_a": 22, "atom_b": 24, "pair_type": 1}, {"atom_a": 22, "atom_b": 25, "pair_type": 1}, {"atom_a": 22, "atom_b": 71, "pair_type": 1}, {"atom_a": 28, "atom_b": 31, "pair_type": 1}, {"atom_a": 28, "atom_b": 57, "pair_type": 1}, {"atom_a": 28, "atom_b": 32, "pair_type": 1}, {"atom_a": 29, "atom_b": 31, "pair_type": 1}, {"atom_a": 29, "atom_b": 57, "pair_type": 1}, {"atom_a": 29, "atom_b": 32, "pair_type": 1}, {"atom_a": 34, "atom_b": 38, "pair_type": 1}, {"atom_a": 34, "atom_b": 218, "pair_type": 1}, {"atom_a": 34, "atom_b": 37, "pair_type": 1}, {"atom_a": 35, "atom_b": 38, "pair_type": 1}, {"atom_a": 35, "atom_b": 37, "pair_type": 1}, {"atom_a": 35, "atom_b": 218, "pair_type": 1}, {"atom_a": 40, "atom_b": 43, "pair_type": 1}, {"atom_a": 40, "atom_b": 44, "pair_type": 1}, {"atom_a": 40, "atom_b": 179, "pair_type": 1}, {"atom_a": 41, "atom_b": 44, "pair_type": 1}, {"atom_a": 41, "atom_b": 179, "pair_type": 1}, {"atom_a": 41, "atom_b": 43, "pair_type": 1}, {"atom_a": 46, "atom_b": 140, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 47, "atom_b": 140, "pair_type": 1}, {"atom_a": 47, "atom_b": 50, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 52, "atom_b": 189, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 189, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 59, "atom_b": 208, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 60, "atom_b": 208, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 66, "atom_b": 160, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 160, "pair_type": 1}, {"atom_a": 73, "atom_b": 228, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 228, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 150, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 150, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 86, "atom_b": 92, "pair_type": 1}, {"atom_a": 86, "atom_b": 90, "pair_type": 1}, {"atom_a": 86, "atom_b": 91, "pair_type": 1}, {"atom_a": 87, "atom_b": 94, "pair_type": 1}, {"atom_a": 87, "atom_b": 93, "pair_type": 1}, {"atom_a": 88, "atom_b": 91, "pair_type": 1}, {"atom_a": 88, "atom_b": 90, "pair_type": 1}, {"atom_a": 88, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 91, "atom_b": 94, "pair_type": 1}, {"atom_a": 91, "atom_b": 93, "pair_type": 1}, {"atom_a": 95, "atom_b": 100, "pair_type": 1}, {"atom_a": 95, "atom_b": 99, "pair_type": 1}, {"atom_a": 95, "atom_b": 101, "pair_type": 1}, {"atom_a": 96, "atom_b": 103, "pair_type": 1}, {"atom_a": 96, "atom_b": 102, "pair_type": 1}, {"atom_a": 97, "atom_b": 101, "pair_type": 1}, {"atom_a": 97, "atom_b": 99, "pair_type": 1}, {"atom_a": 97, "atom_b": 100, "pair_type": 1}, {"atom_a": 99, "atom_b": 103, "pair_type": 1}, {"atom_a": 99, "atom_b": 102, "pair_type": 1}, {"atom_a": 100, "atom_b": 103, "pair_type": 1}, {"atom_a": 100, "atom_b": 102, "pair_type": 1}, {"atom_a": 104, "atom_b": 110, "pair_type": 1}, {"atom_a": 104, "atom_b": 109, "pair_type": 1}, {"atom_a": 104, "atom_b": 108, "pair_type": 1}, {"atom_a": 105, "atom_b": 111, "pair_type": 1}, {"atom_a": 105, "atom_b": 112, "pair_type": 1}, {"atom_a": 106, "atom_b": 108, "pair_type": 1}, {"atom_a": 106, "atom_b": 110, "pair_type": 1}, {"atom_a": 106, "atom_b": 109, "pair_type": 1}, {"atom_a": 108, "atom_b": 112, "pair_type": 1}, {"atom_a": 108, "atom_b": 111, "pair_type": 1}, {"atom_a": 109, "atom_b": 111, "pair_type": 1}, {"atom_a": 109, "atom_b": 112, "pair_type": 1}, {"atom_a": 113, "atom_b": 119, "pair_type": 1}, {"atom_a": 113, "atom_b": 117, "pair_type": 1}, {"atom_a": 113, "atom_b": 118, "pair_type": 1}, {"atom_a": 114, "atom_b": 121, "pair_type": 1}, {"atom_a": 114, "atom_b": 120, "pair_type": 1}, {"atom_a": 115, "atom_b": 119, "pair_type": 1}, {"atom_a": 115, "atom_b": 118, "pair_type": 1}, {"atom_a": 115, "atom_b": 117, "pair_type": 1}, {"atom_a": 117, "atom_b": 120, "pair_type": 1}, {"atom_a": 117, "atom_b": 121, "pair_type": 1}, {"atom_a": 118, "atom_b": 120, "pair_type": 1}, {"atom_a": 118, "atom_b": 121, "pair_type": 1}, {"atom_a": 122, "atom_b": 127, "pair_type": 1}, {"atom_a": 122, "atom_b": 128, "pair_type": 1}, {"atom_a": 122, "atom_b": 126, "pair_type": 1}, {"atom_a": 123, "atom_b": 129, "pair_type": 1}, {"atom_a": 123, "atom_b": 130, "pair_type": 1}, {"atom_a": 124, "atom_b": 126, "pair_type": 1}, {"atom_a": 124, "atom_b": 128, "pair_type": 1}, {"atom_a": 124, "atom_b": 127, "pair_type": 1}, {"atom_a": 126, "atom_b": 130, "pair_type": 1}, {"atom_a": 126, "atom_b": 129, "pair_type": 1}, {"atom_a": 127, "atom_b": 129, "pair_type": 1}, {"atom_a": 127, "atom_b": 130, "pair_type": 1}, {"atom_a": 131, "atom_b": 137, "pair_type": 1}, {"atom_a": 131, "atom_b": 136, "pair_type": 1}, {"atom_a": 131, "atom_b": 135, "pair_type": 1}, {"atom_a": 132, "atom_b": 139, "pair_type": 1}, {"atom_a": 132, "atom_b": 138, "pair_type": 1}, {"atom_a": 133, "atom_b": 135, "pair_type": 1}, {"atom_a": 133, "atom_b": 137, "pair_type": 1}, {"atom_a": 133, "atom_b": 136, "pair_type": 1}, {"atom_a": 135, "atom_b": 138, "pair_type": 1}, {"atom_a": 135, "atom_b": 139, "pair_type": 1}, {"atom_a": 136, "atom_b": 139, "pair_type": 1}, {"atom_a": 136, "atom_b": 138, "pair_type": 1}, {"atom_a": 141, "atom_b": 145, "pair_type": 1}, {"atom_a": 141, "atom_b": 146, "pair_type": 1}, {"atom_a": 141, "atom_b": 147, "pair_type": 1}, {"atom_a": 142, "atom_b": 149, "pair_type": 1}, {"atom_a": 142, "atom_b": 148, "pair_type": 1}, {"atom_a": 143, "atom_b": 146, "pair_type": 1}, {"atom_a": 143, "atom_b": 145, "pair_type": 1}, {"atom_a": 143, "atom_b": 147, "pair_type": 1}, {"atom_a": 145, "atom_b": 149, "pair_type": 1}, {"atom_a": 145, "atom_b": 148, "pair_type": 1}, {"atom_a": 146, "atom_b": 148, "pair_type": 1}, {"atom_a": 146, "atom_b": 149, "pair_type": 1}, {"atom_a": 151, "atom_b": 157, "pair_type": 1}, {"atom_a": 151, "atom_b": 156, "pair_type": 1}, {"atom_a": 151, "atom_b": 155, "pair_type": 1}, {"atom_a": 152, "atom_b": 158, "pair_type": 1}, {"atom_a": 152, "atom_b": 159, "pair_type": 1}, {"atom_a": 153, "atom_b": 157, "pair_type": 1}, {"atom_a": 153, "atom_b": 155, "pair_type": 1}, {"atom_a": 153, "atom_b": 156, "pair_type": 1}, {"atom_a": 155, "atom_b": 158, "pair_type": 1}, {"atom_a": 155, "atom_b": 159, "pair_type": 1}, {"atom_a": 156, "atom_b": 159, "pair_type": 1}, {"atom_a": 156, "atom_b": 158, "pair_type": 1}, {"atom_a": 161, "atom_b": 166, "pair_type": 1}, {"atom_a": 161, "atom_b": 167, "pair_type": 1}, {"atom_a": 161, "atom_b": 165, "pair_type": 1}, {"atom_a": 162, "atom_b": 169, "pair_type": 1}, {"atom_a": 162, "atom_b": 168, "pair_type": 1}, {"atom_a": 163, "atom_b": 166, "pair_type": 1}, {"atom_a": 163, "atom_b": 167, "pair_type": 1}, {"atom_a": 163, "atom_b": 165, "pair_type": 1}, {"atom_a": 165, "atom_b": 169, "pair_type": 1}, {"atom_a": 165, "atom_b": 168, "pair_type": 1}, {"atom_a": 166, "atom_b": 169, "pair_type": 1}, {"atom_a": 166, "atom_b": 168, "pair_type": 1}, {"atom_a": 170, "atom_b": 176, "pair_type": 1}, {"atom_a": 170, "atom_b": 174, "pair_type": 1}, {"atom_a": 170, "atom_b": 175, "pair_type": 1}, {"atom_a": 171, "atom_b": 177, "pair_type": 1}, {"atom_a": 171, "atom_b": 178, "pair_type": 1}, {"atom_a": 172, "atom_b": 174, "pair_type": 1}, {"atom_a": 172, "atom_b": 175, "pair_type": 1}, {"atom_a": 172, "atom_b": 176, "pair_type": 1}, {"atom_a": 174, "atom_b": 178, "pair_type": 1}, {"atom_a": 174, "atom_b": 177, "pair_type": 1}, {"atom_a": 175, "atom_b": 177, "pair_type": 1}, {"atom_a": 175, "atom_b": 178, "pair_type": 1}, {"atom_a": 180, "atom_b": 186, "pair_type": 1}, {"atom_a": 180, "atom_b": 184, "pair_type": 1}, {"atom_a": 180, "atom_b": 185, "pair_type": 1}, {"atom_a": 181, "atom_b": 188, "pair_type": 1}, {"atom_a": 181, "atom_b": 187, "pair_type": 1}, {"atom_a": 182, "atom_b": 185, "pair_type": 1}, {"atom_a": 182, "atom_b": 186, "pair_type": 1}, {"atom_a": 182, "atom_b": 184, "pair_type": 1}, {"atom_a": 184, "atom_b": 188, "pair_type": 1}, {"atom_a": 184, "atom_b": 187, "pair_type": 1}, {"atom_a": 185, "atom_b": 188, "pair_type": 1}, {"atom_a": 185, "atom_b": 187, "pair_type": 1}, {"atom_a": 190, "atom_b": 194, "pair_type": 1}, {"atom_a": 190, "atom_b": 196, "pair_type": 1}, {"atom_a": 190, "atom_b": 195, "pair_type": 1}, {"atom_a": 191, "atom_b": 198, "pair_type": 1}, {"atom_a": 191, "atom_b": 197, "pair_type": 1}, {"atom_a": 192, "atom_b": 196, "pair_type": 1}, {"atom_a": 192, "atom_b": 195, "pair_type": 1}, {"atom_a": 192, "atom_b": 194, "pair_type": 1}, {"atom_a": 194, "atom_b": 197, "pair_type": 1}, {"atom_a": 194, "atom_b": 198, "pair_type": 1}, {"atom_a": 195, "atom_b": 197, "pair_type": 1}, {"atom_a": 195, "atom_b": 198, "pair_type": 1}, {"atom_a": 199, "atom_b": 204, "pair_type": 1}, {"atom_a": 199, "atom_b": 203, "pair_type": 1}, {"atom_a": 199, "atom_b": 205, "pair_type": 1}, {"atom_a": 200, "atom_b": 206, "pair_type": 1}, {"atom_a": 200, "atom_b": 207, "pair_type": 1}, {"atom_a": 201, "atom_b": 203, "pair_type": 1}, {"atom_a": 201, "atom_b": 205, "pair_type": 1}, {"atom_a": 201, "atom_b": 204, "pair_type": 1}, {"atom_a": 203, "atom_b": 207, "pair_type": 1}, {"atom_a": 203, "atom_b": 206, "pair_type": 1}, {"atom_a": 204, "atom_b": 207, "pair_type": 1}, {"atom_a": 204, "atom_b": 206, "pair_type": 1}, {"atom_a": 209, "atom_b": 215, "pair_type": 1}, {"atom_a": 209, "atom_b": 214, "pair_type": 1}, {"atom_a": 209, "atom_b": 213, "pair_type": 1}, {"atom_a": 210, "atom_b": 216, "pair_type": 1}, {"atom_a": 210, "atom_b": 217, "pair_type": 1}, {"atom_a": 211, "atom_b": 215, "pair_type": 1}, {"atom_a": 211, "atom_b": 213, "pair_type": 1}, {"atom_a": 211, "atom_b": 214, "pair_type": 1}, {"atom_a": 213, "atom_b": 216, "pair_type": 1}, {"atom_a": 213, "atom_b": 217, "pair_type": 1}, {"atom_a": 214, "atom_b": 216, "pair_type": 1}, {"atom_a": 214, "atom_b": 217, "pair_type": 1}, {"atom_a": 219, "atom_b": 225, "pair_type": 1}, {"atom_a": 219, "atom_b": 224, "pair_type": 1}, {"atom_a": 219, "atom_b": 223, "pair_type": 1}, {"atom_a": 220, "atom_b": 226, "pair_type": 1}, {"atom_a": 220, "atom_b": 227, "pair_type": 1}, {"atom_a": 221, "atom_b": 225, "pair_type": 1}, {"atom_a": 221, "atom_b": 224, "pair_type": 1}, {"atom_a": 221, "atom_b": 223, "pair_type": 1}, {"atom_a": 223, "atom_b": 226, "pair_type": 1}, {"atom_a": 223, "atom_b": 227, "pair_type": 1}, {"atom_a": 224, "atom_b": 226, "pair_type": 1}, {"atom_a": 224, "atom_b": 227, "pair_type": 1}, {"atom_a": 229, "atom_b": 234, "pair_type": 1}, {"atom_a": 229, "atom_b": 235, "pair_type": 1}, {"atom_a": 229, "atom_b": 233, "pair_type": 1}, {"atom_a": 230, "atom_b": 236, "pair_type": 1}, {"atom_a": 230, "atom_b": 237, "pair_type": 1}, {"atom_a": 231, "atom_b": 233, "pair_type": 1}, {"atom_a": 231, "atom_b": 234, "pair_type": 1}, {"atom_a": 231, "atom_b": 235, "pair_type": 1}, {"atom_a": 233, "atom_b": 237, "pair_type": 1}, {"atom_a": 233, "atom_b": 236, "pair_type": 1}, {"atom_a": 234, "atom_b": 237, "pair_type": 1}, {"atom_a": 234, "atom_b": 236, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:09 on 2024-12-06 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 6HTJ", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1746623", "; ATB Topology Hash: f4741", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "6HTJ", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/polytop_examples/data/ethylamine_dendrimer.png b/polytop_examples/data/ethylamine_dendrimer.png deleted file mode 100644 index 400fd91..0000000 Binary files a/polytop_examples/data/ethylamine_dendrimer.png and /dev/null differ diff --git a/polytop_examples/data/four_arm_star.itp b/polytop_examples/data/four_arm_star.itp deleted file mode 100644 index 4fa0280..0000000 --- a/polytop_examples/data/four_arm_star.itp +++ /dev/null @@ -1,637 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; four arm star polymer -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Pentaerythritol -; -; This file was generated at 13:37 on 2024-11-22 by -; -; Automatic Topology Builder -; -; REVISION 2024-11-20 12:06:25 -;--------------------------------------------------------------------------------------------------------------------------- -; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark -; -; Institute : Molecular Dynamics group, -; School of Chemistry and Molecular Biosciences (SCMB), -; The University of Queensland, QLD 4072, Australia -; URL : https://atb.uq.edu.au -; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. -; An Automated force field Topology Builder (ATB) and repository: version 1.0. -; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. -; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. -; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. -; DOI:10.1021/acs.jctc.8b00768 -; -; Disclaimer : -; While every effort has been made to ensure the accuracy and validity of parameters provided below -; the assignment of parameters is being based on an automated procedure combining data provided by a -; given user as well as calculations performed using third party software. They are provided as a guide. -; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided -; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion -; and to perform additional validation tests for their specific application if required. Neither the authors -; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. -; -; Release notes and warnings: -; (1) The topology is based on a set of atomic coordinates and other data provided by the user after -; after quantum mechanical optimization of the structure using different levels of theory depending on -; the nature of the molecule. -; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. -; In these cases alternative type codes are provided at the end of the line. -; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral -; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" -; or "uncertain" in comments. -; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder -; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually -; before the file can be used. -;--------------------------------------------------------------------------------------------------------------------------- -; Input Structure : 8WDY -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 39051 -; ATB Topology Hash: 07f0b -;--------------------------------------------------------------------------------------------------------------------------- -; Final Topology Generation was performed using: -; A B3LYP/6-31G* optimized geometry. -; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. -; Initial charges were estimated using the ESP method of Merz-Kollman. -; Final charges and charge groups were generated by method described in the ATB paper. -; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. -;--------------------------------------------------------------------------------------------------------------------------- -; -; - -[ moleculetype ] -8WDY 3 -[ atoms ] - 1 CPos 1 8WDY C5 1 0.231500 12.0110 - 2 HC 1 8WDY H10 2 0.010500 1.0080 - 3 HC 1 8WDY H11 3 0.010500 1.0080 - 4 C 1 8WDY C2 4 -0.014500 12.0110 - 5 CPos 1 8WDY C1 5 0.231500 12.0110 - 6 HC 1 8WDY H2 6 0.010500 1.0080 - 7 HC 1 8WDY H3 7 0.010500 1.0080 - 8 CPos 1 8WDY C3 8 0.231500 12.0110 - 9 HC 1 8WDY H4 9 0.010500 1.0080 - 10 HC 1 8WDY H5 10 0.010500 1.0080 - 11 CPos 1 8WDY C4 11 0.231500 12.0110 - 12 HC 1 8WDY H7 12 0.010500 1.0080 - 13 HC 1 8WDY H8 13 0.010500 1.0080 - 14 CPos 2 4Y3B C3 14 0.212333 12.0110 - 15 HC 2 4Y3B H6 15 0.006333 1.0080 - 16 HC 2 4Y3B H7 16 0.006333 1.0080 - 17 CPos 2 4Y3B C2 17 0.167333 12.0110 - 18 HC 2 4Y3B H4 18 0.036333 1.0080 - 19 HC 2 4Y3B H5 19 0.036333 1.0080 - 20 OE 2 4Y3B O1 20 -0.440667 15.9994 - 21 CPos 3 4Y3B C3 21 0.210667 12.0110 - 22 HC 3 4Y3B H6 22 0.004667 1.0080 - 23 HC 3 4Y3B H7 23 0.004667 1.0080 - 24 CPos 3 4Y3B C2 24 0.165667 12.0110 - 25 HC 3 4Y3B H4 25 0.034667 1.0080 - 26 HC 3 4Y3B H5 26 0.034667 1.0080 - 27 OE 3 4Y3B O1 27 -0.442333 15.9994 - 28 CPos 4 4Y3B C3 28 0.210667 12.0110 - 29 HC 4 4Y3B H6 29 0.004667 1.0080 - 30 HC 4 4Y3B H7 30 0.004667 1.0080 - 31 CPos 4 4Y3B C2 31 0.165667 12.0110 - 32 HC 4 4Y3B H4 32 0.034667 1.0080 - 33 HC 4 4Y3B H5 33 0.034667 1.0080 - 34 OE 4 4Y3B O1 34 -0.442333 15.9994 - 35 CPos 5 4Y3B C3 35 0.210148 12.0110 - 36 HC 5 4Y3B H6 36 0.004148 1.0080 - 37 HC 5 4Y3B H7 37 0.004148 1.0080 - 38 CPos 5 4Y3B C2 38 0.165148 12.0110 - 39 HC 5 4Y3B H4 39 0.034148 1.0080 - 40 HC 5 4Y3B H5 40 0.034148 1.0080 - 41 OE 5 4Y3B O1 41 -0.442852 15.9994 - 42 CPos 6 4Y3B C3 42 0.209444 12.0110 - 43 HC 6 4Y3B H6 43 0.003444 1.0080 - 44 HC 6 4Y3B H7 44 0.003444 1.0080 - 45 CPos 6 4Y3B C2 45 0.164444 12.0110 - 46 HC 6 4Y3B H4 46 0.033444 1.0080 - 47 HC 6 4Y3B H5 47 0.033444 1.0080 - 48 OE 6 4Y3B O1 48 -0.443556 15.9994 - 49 CPos 7 4Y3B C3 49 0.209259 12.0110 - 50 HC 7 4Y3B H6 50 0.003259 1.0080 - 51 HC 7 4Y3B H7 51 0.003259 1.0080 - 52 CPos 7 4Y3B C2 52 0.164259 12.0110 - 53 HC 7 4Y3B H4 53 0.033259 1.0080 - 54 HC 7 4Y3B H5 54 0.033259 1.0080 - 55 OE 7 4Y3B O1 55 -0.443741 15.9994 - 56 CPos 8 4Y3B C3 56 0.209202 12.0110 - 57 HC 8 4Y3B H6 57 0.003202 1.0080 - 58 HC 8 4Y3B H7 58 0.003202 1.0080 - 59 CPos 8 4Y3B C2 59 0.164202 12.0110 - 60 HC 8 4Y3B H4 60 0.033202 1.0080 - 61 HC 8 4Y3B H5 61 0.033202 1.0080 - 62 OE 8 4Y3B O1 62 -0.443798 15.9994 - 63 CPos 9 4Y3B C3 63 0.209066 12.0110 - 64 HC 9 4Y3B H6 64 0.003066 1.0080 - 65 HC 9 4Y3B H7 65 0.003066 1.0080 - 66 CPos 9 4Y3B C2 66 0.164066 12.0110 - 67 HC 9 4Y3B H4 67 0.033066 1.0080 - 68 HC 9 4Y3B H5 68 0.033066 1.0080 - 69 OE 9 4Y3B O1 69 -0.443934 15.9994 - 70 CPos 10 4Y3B C3 70 0.208967 12.0110 - 71 HC 10 4Y3B H6 71 0.002967 1.0080 - 72 HC 10 4Y3B H7 72 0.002967 1.0080 - 73 CPos 10 4Y3B C2 73 0.163967 12.0110 - 74 HC 10 4Y3B H4 74 0.032967 1.0080 - 75 HC 10 4Y3B H5 75 0.032967 1.0080 - 76 OE 10 4Y3B O1 76 -0.444033 15.9994 - 77 CPos 11 4Y3B C3 77 0.208940 12.0110 - 78 HC 11 4Y3B H6 78 0.002940 1.0080 - 79 HC 11 4Y3B H7 79 0.002940 1.0080 - 80 CPos 11 4Y3B C2 80 0.163940 12.0110 - 81 HC 11 4Y3B H4 81 0.032940 1.0080 - 82 HC 11 4Y3B H5 82 0.032940 1.0080 - 83 OE 11 4Y3B O1 83 -0.444060 15.9994 - 84 CPos 12 4Y3B C3 84 0.208919 12.0110 - 85 HC 12 4Y3B H6 85 0.002919 1.0080 - 86 HC 12 4Y3B H7 86 0.002919 1.0080 - 87 CPos 12 4Y3B C2 87 0.163919 12.0110 - 88 HC 12 4Y3B H4 88 0.032919 1.0080 - 89 HC 12 4Y3B H5 89 0.032919 1.0080 - 90 OE 12 4Y3B O1 90 -0.444081 15.9994 - 91 CPos 13 4Y3B C3 91 0.174485 12.0110 - 92 HC 13 4Y3B H6 92 -0.031515 1.0080 - 93 HC 13 4Y3B H7 93 -0.031515 1.0080 - 94 CPos 13 4Y3B C2 94 0.129485 12.0110 - 95 HC 13 4Y3B H4 95 -0.001515 1.0080 - 96 HC 13 4Y3B H5 96 -0.001515 1.0080 - 97 OE 13 4Y3B O1 97 -0.478515 15.9994 - 98 CPos 14 45ZJ C1 98 0.071393 12.0110 - 99 HC 14 45ZJ H1 99 -0.083607 1.0080 - 100 HC 14 45ZJ H2 100 -0.083607 1.0080 - 101 HC 14 45ZJ H3 101 -0.083607 1.0080 - 102 CPos 15 45ZJ C1 102 0.046715 12.0110 - 103 HC 15 45ZJ H1 103 -0.108285 1.0080 - 104 HC 15 45ZJ H2 104 -0.108285 1.0080 - 105 HC 15 45ZJ H3 105 -0.108285 1.0080 - 106 CPos 16 45ZJ C1 106 0.038101 12.0110 - 107 HC 16 45ZJ H1 107 -0.116899 1.0080 - 108 HC 16 45ZJ H2 108 -0.116899 1.0080 - 109 HC 16 45ZJ H3 109 -0.116899 1.0080 - 110 CPos 17 45ZJ C1 110 0.102246 12.0110 - 111 HC 17 45ZJ H1 111 -0.052754 1.0080 - 112 HC 17 45ZJ H2 112 -0.052754 1.0080 - 113 HC 17 45ZJ H3 113 -0.052754 1.0080 - -[ bonds ] - 1 3 2 0.1090 1.2300e+07 - 1 41 2 0.1430 8.1800e+06 - 1 4 2 0.1540 4.0057e+06 - 1 2 2 0.1090 1.2300e+07 - 4 5 2 0.1540 4.0057e+06 - 4 8 2 0.1540 4.0057e+06 - 4 11 2 0.1540 4.0057e+06 - 5 20 2 0.1430 8.1800e+06 - 5 7 2 0.1090 1.2300e+07 - 5 6 2 0.1090 1.2300e+07 - 8 10 2 0.1090 1.2300e+07 - 8 27 2 0.1430 8.1800e+06 - 8 9 2 0.1090 1.2300e+07 - 11 12 2 0.1090 1.2300e+07 - 11 13 2 0.1090 1.2300e+07 - 11 34 2 0.1430 8.1800e+06 - 14 15 2 0.1090 1.2300e+07 - 14 16 2 0.1090 1.2300e+07 - 14 17 2 0.1530 7.1500e+06 - 14 48 2 0.1430 8.1800e+06 - 17 20 2 0.1430 8.1800e+06 - 17 18 2 0.1090 1.2300e+07 - 17 19 2 0.1090 1.2300e+07 - 21 23 2 0.1090 1.2300e+07 - 21 24 2 0.1530 7.1500e+06 - 21 55 2 0.1430 8.1800e+06 - 21 22 2 0.1090 1.2300e+07 - 24 26 2 0.1090 1.2300e+07 - 24 27 2 0.1430 8.1800e+06 - 24 25 2 0.1090 1.2300e+07 - 28 31 2 0.1530 7.1500e+06 - 28 29 2 0.1090 1.2300e+07 - 28 30 2 0.1090 1.2300e+07 - 28 62 2 0.1430 8.1800e+06 - 31 34 2 0.1430 8.1800e+06 - 31 33 2 0.1090 1.2300e+07 - 31 32 2 0.1090 1.2300e+07 - 35 37 2 0.1090 1.2300e+07 - 35 36 2 0.1090 1.2300e+07 - 35 69 2 0.1430 8.1800e+06 - 35 38 2 0.1530 7.1500e+06 - 38 40 2 0.1090 1.2300e+07 - 38 41 2 0.1430 8.1800e+06 - 38 39 2 0.1090 1.2300e+07 - 42 43 2 0.1090 1.2300e+07 - 42 44 2 0.1090 1.2300e+07 - 42 45 2 0.1530 7.1500e+06 - 42 76 2 0.1430 8.1800e+06 - 45 48 2 0.1430 8.1800e+06 - 45 46 2 0.1090 1.2300e+07 - 45 47 2 0.1090 1.2300e+07 - 49 52 2 0.1530 7.1500e+06 - 49 51 2 0.1090 1.2300e+07 - 49 50 2 0.1090 1.2300e+07 - 49 83 2 0.1430 8.1800e+06 - 52 53 2 0.1090 1.2300e+07 - 52 55 2 0.1430 8.1800e+06 - 52 54 2 0.1090 1.2300e+07 - 56 90 2 0.1430 8.1800e+06 - 56 58 2 0.1090 1.2300e+07 - 56 59 2 0.1530 7.1500e+06 - 56 57 2 0.1090 1.2300e+07 - 59 60 2 0.1090 1.2300e+07 - 59 61 2 0.1090 1.2300e+07 - 59 62 2 0.1430 8.1800e+06 - 63 97 2 0.1430 8.1800e+06 - 63 65 2 0.1090 1.2300e+07 - 63 66 2 0.1530 7.1500e+06 - 63 64 2 0.1090 1.2300e+07 - 66 68 2 0.1090 1.2300e+07 - 66 69 2 0.1430 8.1800e+06 - 66 67 2 0.1090 1.2300e+07 - 70 71 2 0.1090 1.2300e+07 - 70 72 2 0.1090 1.2300e+07 - 70 98 2 0.1430 8.1800e+06 - 70 73 2 0.1530 7.1500e+06 - 73 76 2 0.1430 8.1800e+06 - 73 74 2 0.1090 1.2300e+07 - 73 75 2 0.1090 1.2300e+07 - 77 102 2 0.1430 8.1800e+06 - 77 79 2 0.1090 1.2300e+07 - 77 80 2 0.1530 7.1500e+06 - 77 78 2 0.1090 1.2300e+07 - 80 82 2 0.1090 1.2300e+07 - 80 83 2 0.1430 8.1800e+06 - 80 81 2 0.1090 1.2300e+07 - 84 106 2 0.1430 8.1800e+06 - 84 85 2 0.1090 1.2300e+07 - 84 86 2 0.1090 1.2300e+07 - 84 87 2 0.1530 7.1500e+06 - 87 89 2 0.1090 1.2300e+07 - 87 90 2 0.1430 8.1800e+06 - 87 88 2 0.1090 1.2300e+07 - 91 94 2 0.1530 7.1500e+06 - 91 110 2 0.1430 8.1800e+06 - 91 92 2 0.1090 1.2300e+07 - 91 93 2 0.1090 1.2300e+07 - 94 96 2 0.1090 1.2300e+07 - 94 95 2 0.1090 1.2300e+07 - 94 97 2 0.1430 8.1800e+06 - 98 99 2 0.1090 1.2300e+07 - 98 101 2 0.1090 1.2300e+07 - 98 100 2 0.1090 1.2300e+07 - 102 104 2 0.1090 1.2300e+07 - 102 103 2 0.1090 1.2300e+07 - 102 105 2 0.1090 1.2300e+07 - 106 107 2 0.1090 1.2300e+07 - 106 109 2 0.1090 1.2300e+07 - 106 108 2 0.1090 1.2300e+07 - 110 113 2 0.1090 1.2300e+07 - 110 111 2 0.1090 1.2300e+07 - 110 112 2 0.1090 1.2300e+07 - -[ pairs ] - 1 12 1 - 1 13 1 - 1 6 1 - 1 10 1 - 1 7 1 - 1 9 1 - 2 8 1 - 2 5 1 - 2 11 1 - 3 11 1 - 3 5 1 - 3 8 1 - 5 9 1 - 5 12 1 - 5 10 1 - 5 13 1 - 6 8 1 - 6 11 1 - 7 8 1 - 7 11 1 - 8 12 1 - 8 13 1 - 9 11 1 - 10 11 1 - 15 18 1 - 15 20 1 - 15 19 1 - 16 18 1 - 16 20 1 - 16 19 1 - 22 26 1 - 22 27 1 - 22 25 1 - 23 26 1 - 23 27 1 - 23 25 1 - 29 34 1 - 29 32 1 - 29 33 1 - 30 33 1 - 30 32 1 - 30 34 1 - 36 40 1 - 36 41 1 - 36 39 1 - 37 40 1 - 37 39 1 - 37 41 1 - 43 47 1 - 43 46 1 - 43 48 1 - 44 46 1 - 44 47 1 - 44 48 1 - 50 55 1 - 50 53 1 - 50 54 1 - 51 54 1 - 51 55 1 - 51 53 1 - 57 61 1 - 57 60 1 - 57 62 1 - 58 61 1 - 58 62 1 - 58 60 1 - 64 68 1 - 64 67 1 - 64 69 1 - 65 67 1 - 65 68 1 - 65 69 1 - 71 75 1 - 71 76 1 - 71 74 1 - 72 76 1 - 72 75 1 - 72 74 1 - 78 81 1 - 78 82 1 - 78 83 1 - 79 82 1 - 79 81 1 - 79 83 1 - 85 88 1 - 85 89 1 - 85 90 1 - 86 89 1 - 86 88 1 - 86 90 1 - 92 95 1 - 92 97 1 - 92 96 1 - 93 97 1 - 93 95 1 - 93 96 1 - -[ angles ] - 2 1 3 2 107.5700 4.8400e+02 - 3 1 4 2 109.5000 4.4800e+02 - 3 1 41 2 109.6000 4.5000e+02 - 1 41 38 2 109.5000 4.5000e+02 - 2 1 41 2 109.6000 4.5000e+02 - 4 1 41 2 115.0000 6.1000e+02 - 1 4 5 2 109.5000 5.2000e+02 - 2 1 4 2 109.5000 4.4800e+02 - 1 4 11 2 109.5000 5.2000e+02 - 1 4 8 2 109.5000 5.2000e+02 - 5 4 8 2 109.5000 5.2000e+02 - 5 4 11 2 109.5000 5.2000e+02 - 4 5 6 2 109.5000 4.4800e+02 - 4 5 20 2 115.0000 6.1000e+02 - 4 5 7 2 109.5000 4.4800e+02 - 8 4 11 2 109.5000 5.2000e+02 - 4 8 10 2 109.5000 4.4800e+02 - 4 8 27 2 115.0000 6.1000e+02 - 4 8 9 2 109.5000 4.4800e+02 - 4 11 13 2 109.5000 4.4800e+02 - 4 11 12 2 109.5000 4.4800e+02 - 4 11 34 2 115.0000 6.1000e+02 - 7 5 20 2 109.6000 4.5000e+02 - 6 5 20 2 109.6000 4.5000e+02 - 5 20 17 2 109.5000 4.5000e+02 - 6 5 7 2 107.5700 4.8400e+02 - 9 8 10 2 107.5700 4.8400e+02 - 10 8 27 2 109.6000 4.5000e+02 - 8 27 24 2 109.5000 4.5000e+02 - 9 8 27 2 109.6000 4.5000e+02 - 12 11 13 2 107.5700 4.8400e+02 - 12 11 34 2 109.6000 4.5000e+02 - 13 11 34 2 109.6000 4.5000e+02 - 11 34 31 2 109.5000 4.5000e+02 - 15 14 16 2 107.6000 5.0700e+02 - 15 14 17 2 110.3000 5.2400e+02 - 15 14 48 2 111.0000 5.3000e+02 - 16 14 48 2 111.0000 5.3000e+02 - 16 14 17 2 110.3000 5.2400e+02 - 17 14 48 2 109.5000 5.2000e+02 - 14 17 18 2 109.6000 4.5000e+02 - 14 17 19 2 109.6000 4.5000e+02 - 14 17 20 2 111.0000 5.3000e+02 - 14 48 45 2 109.5000 4.5000e+02 - 18 17 20 2 111.0000 5.3000e+02 - 19 17 20 2 111.0000 5.3000e+02 - 18 17 19 2 108.0000 4.6500e+02 - 22 21 23 2 107.6000 5.0700e+02 - 23 21 24 2 110.3000 5.2400e+02 - 23 21 55 2 111.0000 5.3000e+02 - 24 21 55 2 109.5000 5.2000e+02 - 21 24 25 2 109.6000 4.5000e+02 - 21 24 26 2 109.6000 4.5000e+02 - 21 24 27 2 111.0000 5.3000e+02 - 22 21 24 2 110.3000 5.2400e+02 - 21 55 52 2 109.5000 4.5000e+02 - 22 21 55 2 111.0000 5.3000e+02 - 25 24 26 2 108.0000 4.6500e+02 - 26 24 27 2 111.0000 5.3000e+02 - 25 24 27 2 111.0000 5.3000e+02 - 29 28 31 2 110.3000 5.2400e+02 - 28 31 32 2 109.6000 4.5000e+02 - 28 31 34 2 111.0000 5.3000e+02 - 31 28 62 2 109.5000 5.2000e+02 - 30 28 31 2 110.3000 5.2400e+02 - 28 31 33 2 109.6000 4.5000e+02 - 29 28 30 2 107.6000 5.0700e+02 - 29 28 62 2 111.0000 5.3000e+02 - 30 28 62 2 111.0000 5.3000e+02 - 28 62 59 2 109.5000 4.5000e+02 - 32 31 34 2 111.0000 5.3000e+02 - 33 31 34 2 111.0000 5.3000e+02 - 32 31 33 2 108.0000 4.6500e+02 - 36 35 37 2 107.6000 5.0700e+02 - 37 35 69 2 111.0000 5.3000e+02 - 37 35 38 2 110.3000 5.2400e+02 - 36 35 38 2 110.3000 5.2400e+02 - 36 35 69 2 111.0000 5.3000e+02 - 35 69 66 2 109.5000 4.5000e+02 - 38 35 69 2 109.5000 5.2000e+02 - 35 38 39 2 109.6000 4.5000e+02 - 35 38 40 2 109.6000 4.5000e+02 - 35 38 41 2 111.0000 5.3000e+02 - 39 38 40 2 108.0000 4.6500e+02 - 40 38 41 2 111.0000 5.3000e+02 - 39 38 41 2 111.0000 5.3000e+02 - 43 42 44 2 107.6000 5.0700e+02 - 43 42 45 2 110.3000 5.2400e+02 - 43 42 76 2 111.0000 5.3000e+02 - 44 42 76 2 111.0000 5.3000e+02 - 44 42 45 2 110.3000 5.2400e+02 - 45 42 76 2 109.5000 5.2000e+02 - 42 45 46 2 109.6000 4.5000e+02 - 42 45 47 2 109.6000 4.5000e+02 - 42 45 48 2 111.0000 5.3000e+02 - 42 76 73 2 109.5000 4.5000e+02 - 47 45 48 2 111.0000 5.3000e+02 - 46 45 48 2 111.0000 5.3000e+02 - 46 45 47 2 108.0000 4.6500e+02 - 51 49 52 2 110.3000 5.2400e+02 - 50 49 52 2 110.3000 5.2400e+02 - 49 52 53 2 109.6000 4.5000e+02 - 49 52 55 2 111.0000 5.3000e+02 - 52 49 83 2 109.5000 5.2000e+02 - 49 52 54 2 109.6000 4.5000e+02 - 50 49 51 2 107.6000 5.0700e+02 - 51 49 83 2 111.0000 5.3000e+02 - 50 49 83 2 111.0000 5.3000e+02 - 49 83 80 2 109.5000 4.5000e+02 - 53 52 55 2 111.0000 5.3000e+02 - 53 52 54 2 108.0000 4.6500e+02 - 54 52 55 2 111.0000 5.3000e+02 - 59 56 90 2 109.5000 5.2000e+02 - 58 56 90 2 111.0000 5.3000e+02 - 56 90 87 2 109.5000 4.5000e+02 - 57 56 90 2 111.0000 5.3000e+02 - 58 56 59 2 110.3000 5.2400e+02 - 57 56 58 2 107.6000 5.0700e+02 - 56 59 60 2 109.6000 4.5000e+02 - 56 59 61 2 109.6000 4.5000e+02 - 56 59 62 2 111.0000 5.3000e+02 - 57 56 59 2 110.3000 5.2400e+02 - 60 59 61 2 108.0000 4.6500e+02 - 60 59 62 2 111.0000 5.3000e+02 - 61 59 62 2 111.0000 5.3000e+02 - 66 63 97 2 109.5000 5.2000e+02 - 65 63 97 2 111.0000 5.3000e+02 - 64 63 97 2 111.0000 5.3000e+02 - 63 97 94 2 109.5000 4.5000e+02 - 64 63 65 2 107.6000 5.0700e+02 - 65 63 66 2 110.3000 5.2400e+02 - 63 66 67 2 109.6000 4.5000e+02 - 63 66 68 2 109.6000 4.5000e+02 - 63 66 69 2 111.0000 5.3000e+02 - 64 63 66 2 110.3000 5.2400e+02 - 68 66 69 2 111.0000 5.3000e+02 - 67 66 68 2 108.0000 4.6500e+02 - 67 66 69 2 111.0000 5.3000e+02 - 71 70 72 2 107.6000 5.0700e+02 - 71 70 73 2 110.3000 5.2400e+02 - 71 70 98 2 111.0000 5.3000e+02 - 72 70 98 2 111.0000 5.3000e+02 - 72 70 73 2 110.3000 5.2400e+02 - 70 98 101 2 106.7500 5.0300e+02 - 70 98 99 2 106.7500 5.0300e+02 - 73 70 98 2 109.5000 5.2000e+02 - 70 98 100 2 106.7500 5.0300e+02 - 70 73 75 2 109.6000 4.5000e+02 - 70 73 76 2 111.0000 5.3000e+02 - 70 73 74 2 109.6000 4.5000e+02 - 75 73 76 2 111.0000 5.3000e+02 - 74 73 76 2 111.0000 5.3000e+02 - 74 73 75 2 108.0000 4.6500e+02 - 78 77 102 2 111.0000 5.3000e+02 - 79 77 102 2 111.0000 5.3000e+02 - 77 102 104 2 106.7500 5.0300e+02 - 80 77 102 2 109.5000 5.2000e+02 - 77 102 103 2 106.7500 5.0300e+02 - 77 102 105 2 106.7500 5.0300e+02 - 78 77 79 2 107.6000 5.0700e+02 - 79 77 80 2 110.3000 5.2400e+02 - 77 80 81 2 109.6000 4.5000e+02 - 77 80 82 2 109.6000 4.5000e+02 - 77 80 83 2 111.0000 5.3000e+02 - 78 77 80 2 110.3000 5.2400e+02 - 82 80 83 2 111.0000 5.3000e+02 - 81 80 82 2 108.0000 4.6500e+02 - 81 80 83 2 111.0000 5.3000e+02 - 84 106 107 2 106.7500 5.0300e+02 - 84 106 109 2 106.7500 5.0300e+02 - 87 84 106 2 109.5000 5.2000e+02 - 85 84 106 2 111.0000 5.3000e+02 - 84 106 108 2 106.7500 5.0300e+02 - 86 84 106 2 111.0000 5.3000e+02 - 85 84 86 2 107.6000 5.0700e+02 - 85 84 87 2 110.3000 5.2400e+02 - 86 84 87 2 110.3000 5.2400e+02 - 84 87 88 2 109.6000 4.5000e+02 - 84 87 89 2 109.6000 4.5000e+02 - 84 87 90 2 111.0000 5.3000e+02 - 88 87 89 2 108.0000 4.6500e+02 - 89 87 90 2 111.0000 5.3000e+02 - 88 87 90 2 111.0000 5.3000e+02 - 91 94 95 2 109.6000 4.5000e+02 - 94 91 110 2 109.5000 5.2000e+02 - 92 91 94 2 110.3000 5.2400e+02 - 91 94 96 2 109.6000 4.5000e+02 - 91 94 97 2 111.0000 5.3000e+02 - 93 91 94 2 110.3000 5.2400e+02 - 92 91 110 2 111.0000 5.3000e+02 - 91 110 112 2 106.7500 5.0300e+02 - 91 110 111 2 106.7500 5.0300e+02 - 93 91 110 2 111.0000 5.3000e+02 - 91 110 113 2 106.7500 5.0300e+02 - 92 91 93 2 107.6000 5.0700e+02 - 96 94 97 2 111.0000 5.3000e+02 - 95 94 96 2 108.0000 4.6500e+02 - 95 94 97 2 111.0000 5.3000e+02 - 99 98 101 2 108.5300 4.4300e+02 - 99 98 100 2 108.5300 4.4300e+02 - 100 98 101 2 108.5300 4.4300e+02 - 103 102 104 2 108.5300 4.4300e+02 - 104 102 105 2 108.5300 4.4300e+02 - 103 102 105 2 108.5300 4.4300e+02 - 107 106 108 2 108.5300 4.4300e+02 - 107 106 109 2 108.5300 4.4300e+02 - 108 106 109 2 108.5300 4.4300e+02 - 112 110 113 2 108.5300 4.4300e+02 - 111 110 113 2 108.5300 4.4300e+02 - 111 110 112 2 108.5300 4.4300e+02 - -[ dihedrals ] - 35 38 41 1 1 0.0000 1.2600e+00 3 - 41 1 4 5 1 0.0000 5.9200e+00 3 - 5 4 8 27 1 0.0000 5.9200e+00 3 - 8 4 5 20 1 0.0000 5.9200e+00 3 - 5 4 11 34 1 0.0000 5.9200e+00 3 - 14 17 20 5 1 0.0000 1.2600e+00 3 - 21 24 27 8 1 0.0000 1.2600e+00 3 - 28 31 34 11 1 0.0000 1.2600e+00 3 - 48 14 17 20 1 0.0000 5.9200e+00 3 - 42 45 48 14 1 0.0000 1.2600e+00 3 - 55 21 24 27 1 0.0000 5.9200e+00 3 - 49 52 55 21 1 0.0000 1.2600e+00 3 - 62 28 31 34 1 0.0000 5.9200e+00 3 - 56 59 62 28 1 0.0000 1.2600e+00 3 - 63 66 69 35 1 0.0000 1.2600e+00 3 - 69 35 38 41 1 0.0000 5.9200e+00 3 - 76 42 45 48 1 0.0000 5.9200e+00 3 - 70 73 76 42 1 0.0000 1.2600e+00 3 - 83 49 52 55 1 0.0000 5.9200e+00 3 - 77 80 83 49 1 0.0000 1.2600e+00 3 - 90 56 59 62 1 0.0000 5.9200e+00 3 - 84 87 90 56 1 0.0000 1.2600e+00 3 - 97 63 66 69 1 0.0000 5.9200e+00 3 - 91 94 97 63 1 0.0000 1.2600e+00 3 - 98 70 73 76 1 0.0000 5.9200e+00 3 - 102 77 80 83 1 0.0000 5.9200e+00 3 - 106 84 87 90 1 0.0000 5.9200e+00 3 - 110 91 94 97 1 0.0000 5.9200e+00 3 - -[ exclusions ] diff --git a/polytop_examples/data/four_arm_star.json b/polytop_examples/data/four_arm_star.json deleted file mode 100644 index c4bbe59..0000000 --- a/polytop_examples/data/four_arm_star.json +++ /dev/null @@ -1 +0,0 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H10", "charge_group_num": 4, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H11", "charge_group_num": 5, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "C", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C2", "charge_group_num": 6, "partial_charge": -0.014500000000000002, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H2", "charge_group_num": 8, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H3", "charge_group_num": 9, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H4", "charge_group_num": 13, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H5", "charge_group_num": 14, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H7", "charge_group_num": 18, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "HC", "residue_id": 1, "residue_name": "8WDY", "atom_name": "H8", "charge_group_num": 19, "partial_charge": 0.010499999999999999, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0063333333333333375, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CPos", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16733333333333333, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.036333333333333336, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "HC", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.036333333333333336, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "OE", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.44066666666666665, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "CPos", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C1", "charge_group_num": 7, "partial_charge": 0.2315, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 17, "atom_type": "HC", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.004666666666666675, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 18, "atom_type": "HC", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.004666666666666675, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 19, "atom_type": "CPos", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16566666666666668, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 20, "atom_type": "HC", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03466666666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 21, "atom_type": "HC", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03466666666666667, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 22, "atom_type": "OE", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4423333333333333, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 23, "atom_type": "CPos", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C3", "charge_group_num": 12, "partial_charge": 0.2315, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 24, "atom_type": "HC", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.004666666666666664, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 25, "atom_type": "HC", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.004666666666666664, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 26, "atom_type": "CPos", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16566666666666666, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 27, "atom_type": "HC", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03466666666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 28, "atom_type": "HC", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03466666666666666, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 29, "atom_type": "OE", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4423333333333333, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 30, "atom_type": "CPos", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C4", "charge_group_num": 17, "partial_charge": 0.2315, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 31, "atom_type": "HC", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.004148148148148155, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 32, "atom_type": "HC", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.004148148148148155, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 33, "atom_type": "CPos", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16514814814814813, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 34, "atom_type": "HC", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03414814814814815, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 35, "atom_type": "HC", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03414814814814815, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 36, "atom_type": "OE", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.44285185185185183, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 37, "atom_type": "CPos", "residue_id": 1, "residue_name": "8WDY", "atom_name": "C5", "charge_group_num": 3, "partial_charge": 0.2315, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 38, "atom_type": "HC", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0034444444444444583, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 39, "atom_type": "HC", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0034444444444444583, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 40, "atom_type": "CPos", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16444444444444445, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 41, "atom_type": "HC", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03344444444444446, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 42, "atom_type": "HC", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03344444444444446, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 43, "atom_type": "OE", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.44355555555555554, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 44, "atom_type": "CPos", "residue_id": 2, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.21233333333333335, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 45, "atom_type": "HC", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0032592592592592708, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 46, "atom_type": "HC", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0032592592592592708, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 47, "atom_type": "CPos", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16425925925925927, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 48, "atom_type": "HC", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.033259259259259266, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 49, "atom_type": "HC", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.033259259259259266, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 50, "atom_type": "OE", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4437407407407407, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 51, "atom_type": "CPos", "residue_id": 3, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.2106666666666667, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 52, "atom_type": "HC", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0032016460905350003, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 53, "atom_type": "HC", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0032016460905350003, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 54, "atom_type": "CPos", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.164201646090535, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 55, "atom_type": "HC", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.033201646090535, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 56, "atom_type": "HC", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.033201646090535, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 57, "atom_type": "OE", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.443798353909465, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 58, "atom_type": "CPos", "residue_id": 4, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.21066666666666667, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 59, "atom_type": "HC", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0030658436213991886, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 60, "atom_type": "HC", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0030658436213991886, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 61, "atom_type": "CPos", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.1640658436213992, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 62, "atom_type": "HC", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03306584362139919, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 63, "atom_type": "HC", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03306584362139919, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 64, "atom_type": "OE", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4439341563786008, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 65, "atom_type": "CPos", "residue_id": 5, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.21014814814814814, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 66, "atom_type": "HC", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.002967078189300418, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 67, "atom_type": "HC", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.002967078189300418, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 68, "atom_type": "CPos", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16396707818930042, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 69, "atom_type": "HC", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03296707818930042, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 70, "atom_type": "HC", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03296707818930042, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 71, "atom_type": "OE", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4440329218106996, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 72, "atom_type": "CPos", "residue_id": 6, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.20944444444444446, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 73, "atom_type": "HC", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.002940100594421591, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 74, "atom_type": "HC", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.002940100594421591, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 75, "atom_type": "CPos", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.1639401005944216, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 76, "atom_type": "HC", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03294010059442159, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 77, "atom_type": "HC", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03294010059442159, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 78, "atom_type": "OE", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.44405989940557844, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 79, "atom_type": "CPos", "residue_id": 7, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.20925925925925928, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 80, "atom_type": "HC", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": 0.0029186099679926825, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 81, "atom_type": "HC", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": 0.0029186099679926825, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 82, "atom_type": "CPos", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.16391860996799268, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 83, "atom_type": "HC", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": 0.03291860996799268, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 84, "atom_type": "HC", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": 0.03291860996799268, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 85, "atom_type": "OE", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4440813900320073, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 86, "atom_type": "CPos", "residue_id": 8, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.20920164609053502, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 89, "atom_type": "HC", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "H6", "charge_group_num": 4, "partial_charge": -0.03151484295311456, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 90, "atom_type": "HC", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "H7", "charge_group_num": 5, "partial_charge": -0.03151484295311456, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 91, "atom_type": "CPos", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "C2", "charge_group_num": 6, "partial_charge": 0.12948515704688543, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 92, "atom_type": "HC", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "H4", "charge_group_num": 7, "partial_charge": -0.0015148429531145619, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 93, "atom_type": "HC", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "H5", "charge_group_num": 8, "partial_charge": -0.0015148429531145619, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 94, "atom_type": "OE", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "O1", "charge_group_num": 9, "partial_charge": -0.4785148429531145, "mass": 15.9994, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 95, "atom_type": "CPos", "residue_id": 9, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.2090658436213992, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 96, "atom_type": "CPos", "residue_id": 10, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.20896707818930044, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 97, "atom_type": "CPos", "residue_id": 14, "residue_name": "45ZJ", "atom_name": "C1", "charge_group_num": 3, "partial_charge": 0.07139342179311316, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 98, "atom_type": "HC", "residue_id": 14, "residue_name": "45ZJ", "atom_name": "H1", "charge_group_num": 4, "partial_charge": -0.08360657820688684, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 99, "atom_type": "HC", "residue_id": 14, "residue_name": "45ZJ", "atom_name": "H2", "charge_group_num": 5, "partial_charge": -0.08360657820688684, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 100, "atom_type": "HC", "residue_id": 14, "residue_name": "45ZJ", "atom_name": "H3", "charge_group_num": 6, "partial_charge": -0.08360657820688684, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 101, "atom_type": "CPos", "residue_id": 11, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.2089401005944216, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 102, "atom_type": "CPos", "residue_id": 15, "residue_name": "45ZJ", "atom_name": "C1", "charge_group_num": 3, "partial_charge": 0.04671467764060355, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 103, "atom_type": "HC", "residue_id": 15, "residue_name": "45ZJ", "atom_name": "H1", "charge_group_num": 4, "partial_charge": -0.10828532235939643, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 104, "atom_type": "HC", "residue_id": 15, "residue_name": "45ZJ", "atom_name": "H2", "charge_group_num": 5, "partial_charge": -0.10828532235939643, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 105, "atom_type": "HC", "residue_id": 15, "residue_name": "45ZJ", "atom_name": "H3", "charge_group_num": 6, "partial_charge": -0.10828532235939643, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 106, "atom_type": "CPos", "residue_id": 12, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.2089186099679927, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 107, "atom_type": "CPos", "residue_id": 16, "residue_name": "45ZJ", "atom_name": "C1", "charge_group_num": 3, "partial_charge": 0.03810094175371949, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 108, "atom_type": "HC", "residue_id": 16, "residue_name": "45ZJ", "atom_name": "H1", "charge_group_num": 4, "partial_charge": -0.1168990582462805, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 109, "atom_type": "HC", "residue_id": 16, "residue_name": "45ZJ", "atom_name": "H2", "charge_group_num": 5, "partial_charge": -0.1168990582462805, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 110, "atom_type": "HC", "residue_id": 16, "residue_name": "45ZJ", "atom_name": "H3", "charge_group_num": 6, "partial_charge": -0.1168990582462805, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 88, "atom_type": "CPos", "residue_id": 13, "residue_name": "4Y3B", "atom_name": "C3", "charge_group_num": 3, "partial_charge": 0.17448515704688544, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 112, "atom_type": "CPos", "residue_id": 17, "residue_name": "45ZJ", "atom_name": "C1", "charge_group_num": 3, "partial_charge": 0.10224628926172133, "mass": 12.011, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 113, "atom_type": "HC", "residue_id": 17, "residue_name": "45ZJ", "atom_name": "H1", "charge_group_num": 4, "partial_charge": -0.052753710738278656, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 114, "atom_type": "HC", "residue_id": 17, "residue_name": "45ZJ", "atom_name": "H2", "charge_group_num": 5, "partial_charge": -0.052753710738278656, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 115, "atom_type": "HC", "residue_id": 17, "residue_name": "45ZJ", "atom_name": "H3", "charge_group_num": 6, "partial_charge": -0.052753710738278656, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}], "bonds": [{"atom_a": 37, "atom_b": 1, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 37, "atom_b": 2, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 37, "atom_b": 3, "bond_type": 2, "bond_length": 0.154, "force_constant": 4005700.0, "order": 1}, {"atom_a": 3, "atom_b": 16, "bond_type": 2, "bond_length": 0.154, "force_constant": 4005700.0, "order": 1}, {"atom_a": 3, "atom_b": 23, "bond_type": 2, "bond_length": 0.154, "force_constant": 4005700.0, "order": 1}, {"atom_a": 3, "atom_b": 30, "bond_type": 2, "bond_length": 0.154, "force_constant": 4005700.0, "order": 1}, {"atom_a": 16, "atom_b": 4, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 16, "atom_b": 5, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 23, "atom_b": 6, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 23, "atom_b": 7, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 30, "atom_b": 8, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 30, "atom_b": 9, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 44, "atom_b": 10, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 44, "atom_b": 11, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 12, "atom_b": 15, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 12, "atom_b": 13, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 44, "atom_b": 12, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 12, "atom_b": 14, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 16, "atom_b": 15, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 51, "atom_b": 17, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 51, "atom_b": 18, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 19, "atom_b": 21, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 51, "atom_b": 19, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 19, "atom_b": 22, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 19, "atom_b": 20, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 23, "atom_b": 22, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 58, "atom_b": 24, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 58, "atom_b": 25, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 58, "atom_b": 26, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 26, "atom_b": 29, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 26, "atom_b": 28, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 26, "atom_b": 27, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 30, "atom_b": 29, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 65, "atom_b": 31, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 65, "atom_b": 32, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 33, "atom_b": 35, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 33, "atom_b": 36, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 33, "atom_b": 34, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 65, "atom_b": 33, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 37, "atom_b": 36, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 72, "atom_b": 38, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 72, "atom_b": 39, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 40, "atom_b": 43, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 40, "atom_b": 41, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 72, "atom_b": 40, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 40, "atom_b": 42, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 44, "atom_b": 43, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 79, "atom_b": 45, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 79, "atom_b": 46, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 47, "atom_b": 48, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 79, "atom_b": 47, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 47, "atom_b": 50, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 47, "atom_b": 49, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 51, "atom_b": 50, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 86, "atom_b": 52, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 86, "atom_b": 53, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 54, "atom_b": 55, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 54, "atom_b": 56, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 86, "atom_b": 54, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 54, "atom_b": 57, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 58, "atom_b": 57, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 95, "atom_b": 59, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 95, "atom_b": 60, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 61, "atom_b": 63, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 61, "atom_b": 64, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 61, "atom_b": 62, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 95, "atom_b": 61, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 65, "atom_b": 64, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 96, "atom_b": 66, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 96, "atom_b": 67, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 68, "atom_b": 71, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 96, "atom_b": 68, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 68, "atom_b": 69, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 68, "atom_b": 70, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 72, "atom_b": 71, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 101, "atom_b": 73, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 101, "atom_b": 74, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 75, "atom_b": 77, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 75, "atom_b": 78, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 75, "atom_b": 76, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 101, "atom_b": 75, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 79, "atom_b": 78, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 106, "atom_b": 80, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 106, "atom_b": 81, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 82, "atom_b": 84, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 106, "atom_b": 82, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 82, "atom_b": 85, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 82, "atom_b": 83, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 86, "atom_b": 85, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 88, "atom_b": 89, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 88, "atom_b": 90, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 88, "atom_b": 91, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 91, "atom_b": 93, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 91, "atom_b": 92, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 91, "atom_b": 94, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 95, "atom_b": 94, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 96, "atom_b": 97, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 97, "atom_b": 98, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 97, "atom_b": 100, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 97, "atom_b": 99, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 101, "atom_b": 102, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 102, "atom_b": 104, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 102, "atom_b": 103, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 102, "atom_b": 105, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 106, "atom_b": 107, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 107, "atom_b": 108, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 107, "atom_b": 110, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 107, "atom_b": 109, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 88, "atom_b": 112, "bond_type": 2, "bond_length": 0.143, "force_constant": 8180000.0, "order": 1}, {"atom_a": 112, "atom_b": 115, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 112, "atom_b": 113, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}, {"atom_a": 112, "atom_b": 114, "bond_type": 2, "bond_length": 0.109, "force_constant": 12300000.0, "order": 1}], "angles": [{"atom_a": 1, "atom_b": 37, "atom_c": 2, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 1, "atom_b": 37, "atom_c": 3, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 1, "atom_b": 37, "atom_c": 36, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 2, "atom_b": 37, "atom_c": 3, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 2, "atom_b": 37, "atom_c": 36, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 37, "atom_b": 3, "atom_c": 16, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 3, "atom_b": 37, "atom_c": 36, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 37, "atom_b": 3, "atom_c": 30, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 37, "atom_b": 3, "atom_c": 23, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 16, "atom_b": 3, "atom_c": 23, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 16, "atom_b": 3, "atom_c": 30, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 3, "atom_b": 16, "atom_c": 4, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 3, "atom_b": 16, "atom_c": 15, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 3, "atom_b": 16, "atom_c": 5, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 23, "atom_b": 3, "atom_c": 30, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 3, "atom_b": 23, "atom_c": 7, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 3, "atom_b": 23, "atom_c": 22, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 3, "atom_b": 23, "atom_c": 6, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 3, "atom_b": 30, "atom_c": 9, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 3, "atom_b": 30, "atom_c": 8, "angle_type": 2, "angle_value": 109.5, "force_constant": 448.0}, {"atom_a": 3, "atom_b": 30, "atom_c": 29, "angle_type": 2, "angle_value": 115.0, "force_constant": 610.0}, {"atom_a": 4, "atom_b": 16, "atom_c": 5, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 4, "atom_b": 16, "atom_c": 15, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 5, "atom_b": 16, "atom_c": 15, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 6, "atom_b": 23, "atom_c": 7, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 6, "atom_b": 23, "atom_c": 22, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 7, "atom_b": 23, "atom_c": 22, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 8, "atom_b": 30, "atom_c": 9, "angle_type": 2, "angle_value": 107.57, "force_constant": 484.0}, {"atom_a": 8, "atom_b": 30, "atom_c": 29, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 9, "atom_b": 30, "atom_c": 29, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 10, "atom_b": 44, "atom_c": 11, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 10, "atom_b": 44, "atom_c": 12, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 10, "atom_b": 44, "atom_c": 43, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 11, "atom_b": 44, "atom_c": 43, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 11, "atom_b": 44, "atom_c": 12, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 13, "atom_b": 12, "atom_c": 15, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 16, "atom_b": 15, "atom_c": 12, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 44, "atom_b": 12, "atom_c": 15, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 14, "atom_b": 12, "atom_c": 15, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 44, "atom_b": 12, "atom_c": 13, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 13, "atom_b": 12, "atom_c": 14, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 12, "atom_b": 44, "atom_c": 43, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 44, "atom_b": 12, "atom_c": 14, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 17, "atom_b": 51, "atom_c": 18, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 17, "atom_b": 51, "atom_c": 50, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 17, "atom_b": 51, "atom_c": 19, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 18, "atom_b": 51, "atom_c": 19, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 18, "atom_b": 51, "atom_c": 50, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 20, "atom_b": 19, "atom_c": 21, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 51, "atom_b": 19, "atom_c": 21, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 21, "atom_b": 19, "atom_c": 22, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 19, "atom_b": 51, "atom_c": 50, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 51, "atom_b": 19, "atom_c": 20, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 51, "atom_b": 19, "atom_c": 22, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 23, "atom_b": 22, "atom_c": 19, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 20, "atom_b": 19, "atom_c": 22, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 24, "atom_b": 58, "atom_c": 25, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 24, "atom_b": 58, "atom_c": 26, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 24, "atom_b": 58, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 25, "atom_b": 58, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 25, "atom_b": 58, "atom_c": 26, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 58, "atom_b": 26, "atom_c": 27, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 58, "atom_b": 26, "atom_c": 29, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 26, "atom_b": 58, "atom_c": 57, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 58, "atom_b": 26, "atom_c": 28, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 27, "atom_b": 26, "atom_c": 29, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 28, "atom_b": 26, "atom_c": 29, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 30, "atom_b": 29, "atom_c": 26, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 27, "atom_b": 26, "atom_c": 28, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 31, "atom_b": 65, "atom_c": 32, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 31, "atom_b": 65, "atom_c": 33, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 31, "atom_b": 65, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 32, "atom_b": 65, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 32, "atom_b": 65, "atom_c": 33, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 65, "atom_b": 33, "atom_c": 35, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 34, "atom_b": 33, "atom_c": 35, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 35, "atom_b": 33, "atom_c": 36, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 65, "atom_b": 33, "atom_c": 36, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 34, "atom_b": 33, "atom_c": 36, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 37, "atom_b": 36, "atom_c": 33, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 65, "atom_b": 33, "atom_c": 34, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 33, "atom_b": 65, "atom_c": 64, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 38, "atom_b": 72, "atom_c": 39, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 38, "atom_b": 72, "atom_c": 40, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 38, "atom_b": 72, "atom_c": 71, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 39, "atom_b": 72, "atom_c": 71, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 39, "atom_b": 72, "atom_c": 40, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 42, "atom_b": 40, "atom_c": 43, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 44, "atom_b": 43, "atom_c": 40, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 41, "atom_b": 40, "atom_c": 43, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 72, "atom_b": 40, "atom_c": 43, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 72, "atom_b": 40, "atom_c": 41, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 41, "atom_b": 40, "atom_c": 42, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 40, "atom_b": 72, "atom_c": 71, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 72, "atom_b": 40, "atom_c": 42, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 45, "atom_b": 79, "atom_c": 46, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 45, "atom_b": 79, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 45, "atom_b": 79, "atom_c": 47, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 46, "atom_b": 79, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 46, "atom_b": 79, "atom_c": 47, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 79, "atom_b": 47, "atom_c": 48, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 48, "atom_b": 47, "atom_c": 50, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 48, "atom_b": 47, "atom_c": 49, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 79, "atom_b": 47, "atom_c": 50, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 47, "atom_b": 79, "atom_c": 78, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 79, "atom_b": 47, "atom_c": 49, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 51, "atom_b": 50, "atom_c": 47, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 49, "atom_b": 47, "atom_c": 50, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 52, "atom_b": 86, "atom_c": 54, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 52, "atom_b": 86, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 52, "atom_b": 86, "atom_c": 53, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 53, "atom_b": 86, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 53, "atom_b": 86, "atom_c": 54, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 55, "atom_b": 54, "atom_c": 56, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 86, "atom_b": 54, "atom_c": 55, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 55, "atom_b": 54, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 86, "atom_b": 54, "atom_c": 56, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 56, "atom_b": 54, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 54, "atom_b": 86, "atom_c": 85, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 86, "atom_b": 54, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 58, "atom_b": 57, "atom_c": 54, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 59, "atom_b": 95, "atom_c": 60, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 59, "atom_b": 95, "atom_c": 61, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 59, "atom_b": 95, "atom_c": 94, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 60, "atom_b": 95, "atom_c": 94, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 60, "atom_b": 95, "atom_c": 61, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 63, "atom_b": 61, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 95, "atom_b": 61, "atom_c": 63, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 62, "atom_b": 61, "atom_c": 63, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 62, "atom_b": 61, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 95, "atom_b": 61, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 65, "atom_b": 64, "atom_c": 61, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 95, "atom_b": 61, "atom_c": 62, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 61, "atom_b": 95, "atom_c": 94, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 66, "atom_b": 96, "atom_c": 67, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 66, "atom_b": 96, "atom_c": 68, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 66, "atom_b": 96, "atom_c": 97, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 67, "atom_b": 96, "atom_c": 97, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 67, "atom_b": 96, "atom_c": 68, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 70, "atom_b": 68, "atom_c": 71, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 72, "atom_b": 71, "atom_c": 68, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 96, "atom_b": 68, "atom_c": 71, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 69, "atom_b": 68, "atom_c": 71, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 96, "atom_b": 68, "atom_c": 70, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 68, "atom_b": 96, "atom_c": 97, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 96, "atom_b": 68, "atom_c": 69, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 69, "atom_b": 68, "atom_c": 70, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 73, "atom_b": 101, "atom_c": 74, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 73, "atom_b": 101, "atom_c": 102, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 73, "atom_b": 101, "atom_c": 75, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 74, "atom_b": 101, "atom_c": 75, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 74, "atom_b": 101, "atom_c": 102, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 77, "atom_b": 75, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 101, "atom_b": 75, "atom_c": 77, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 76, "atom_b": 75, "atom_c": 77, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 76, "atom_b": 75, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 79, "atom_b": 78, "atom_c": 75, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 101, "atom_b": 75, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 101, "atom_b": 75, "atom_c": 76, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 75, "atom_b": 101, "atom_c": 102, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 80, "atom_b": 106, "atom_c": 107, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 80, "atom_b": 106, "atom_c": 81, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 80, "atom_b": 106, "atom_c": 82, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 81, "atom_b": 106, "atom_c": 82, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 81, "atom_b": 106, "atom_c": 107, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 83, "atom_b": 82, "atom_c": 84, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 106, "atom_b": 82, "atom_c": 84, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 84, "atom_b": 82, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 82, "atom_b": 106, "atom_c": 107, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 106, "atom_b": 82, "atom_c": 83, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 106, "atom_b": 82, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 83, "atom_b": 82, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 86, "atom_b": 85, "atom_c": 82, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 89, "atom_b": 88, "atom_c": 112, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 89, "atom_b": 88, "atom_c": 90, "angle_type": 2, "angle_value": 107.6, "force_constant": 507.0}, {"atom_a": 89, "atom_b": 88, "atom_c": 91, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 90, "atom_b": 88, "atom_c": 91, "angle_type": 2, "angle_value": 110.3, "force_constant": 524.0}, {"atom_a": 90, "atom_b": 88, "atom_c": 112, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 88, "atom_b": 91, "atom_c": 92, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 91, "atom_b": 88, "atom_c": 112, "angle_type": 2, "angle_value": 109.5, "force_constant": 520.0}, {"atom_a": 88, "atom_b": 91, "atom_c": 93, "angle_type": 2, "angle_value": 109.6, "force_constant": 450.0}, {"atom_a": 88, "atom_b": 91, "atom_c": 94, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 93, "atom_b": 91, "atom_c": 94, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 92, "atom_b": 91, "atom_c": 93, "angle_type": 2, "angle_value": 108.0, "force_constant": 465.0}, {"atom_a": 92, "atom_b": 91, "atom_c": 94, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 95, "atom_b": 94, "atom_c": 91, "angle_type": 2, "angle_value": 109.5, "force_constant": 450.0}, {"atom_a": 96, "atom_b": 97, "atom_c": 100, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 96, "atom_b": 97, "atom_c": 98, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 96, "atom_b": 97, "atom_c": 99, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 98, "atom_b": 97, "atom_c": 100, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 98, "atom_b": 97, "atom_c": 99, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 99, "atom_b": 97, "atom_c": 100, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 101, "atom_b": 102, "atom_c": 104, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 101, "atom_b": 102, "atom_c": 103, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 101, "atom_b": 102, "atom_c": 105, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 103, "atom_b": 102, "atom_c": 104, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 104, "atom_b": 102, "atom_c": 105, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 103, "atom_b": 102, "atom_c": 105, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 106, "atom_b": 107, "atom_c": 108, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 106, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 106, "atom_b": 107, "atom_c": 109, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 108, "atom_b": 107, "atom_c": 109, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 108, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 109, "atom_b": 107, "atom_c": 110, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 88, "atom_b": 112, "atom_c": 114, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 88, "atom_b": 112, "atom_c": 113, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 88, "atom_b": 112, "atom_c": 115, "angle_type": 2, "angle_value": 106.75, "force_constant": 503.0}, {"atom_a": 114, "atom_b": 112, "atom_c": 115, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 113, "atom_b": 112, "atom_c": 115, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}, {"atom_a": 113, "atom_b": 112, "atom_c": 114, "angle_type": 2, "angle_value": 108.53, "force_constant": 443.0}], "dihedrals": [{"atom_a": 36, "atom_b": 37, "atom_c": 3, "atom_d": 16, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 16, "atom_b": 3, "atom_c": 23, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 23, "atom_b": 3, "atom_c": 16, "atom_d": 15, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 16, "atom_b": 3, "atom_c": 30, "atom_d": 29, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 44, "atom_b": 12, "atom_c": 15, "atom_d": 16, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 43, "atom_b": 44, "atom_c": 12, "atom_d": 15, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 50, "atom_b": 51, "atom_c": 19, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 51, "atom_b": 19, "atom_c": 22, "atom_d": 23, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 58, "atom_b": 26, "atom_c": 29, "atom_d": 30, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 57, "atom_b": 58, "atom_c": 26, "atom_d": 29, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 33, "atom_c": 36, "atom_d": 37, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 64, "atom_b": 65, "atom_c": 33, "atom_d": 36, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 72, "atom_b": 40, "atom_c": 43, "atom_d": 44, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 71, "atom_b": 72, "atom_c": 40, "atom_d": 43, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 47, "atom_c": 50, "atom_d": 51, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 78, "atom_b": 79, "atom_c": 47, "atom_d": 50, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 85, "atom_b": 86, "atom_c": 54, "atom_d": 57, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 54, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 94, "atom_b": 95, "atom_c": 61, "atom_d": 64, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 95, "atom_b": 61, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 96, "atom_b": 68, "atom_c": 71, "atom_d": 72, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 97, "atom_b": 96, "atom_c": 68, "atom_d": 71, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 101, "atom_b": 75, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 102, "atom_b": 101, "atom_c": 75, "atom_d": 78, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 107, "atom_b": 106, "atom_c": 82, "atom_d": 85, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 106, "atom_b": 82, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 112, "atom_b": 88, "atom_c": 91, "atom_d": 94, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 88, "atom_b": 91, "atom_c": 94, "atom_d": 95, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 23, "pair_type": 1}, {"atom_a": 1, "atom_b": 16, "pair_type": 1}, {"atom_a": 1, "atom_b": 30, "pair_type": 1}, {"atom_a": 2, "atom_b": 30, "pair_type": 1}, {"atom_a": 2, "atom_b": 16, "pair_type": 1}, {"atom_a": 2, "atom_b": 23, "pair_type": 1}, {"atom_a": 4, "atom_b": 23, "pair_type": 1}, {"atom_a": 4, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 4, "pair_type": 1}, {"atom_a": 5, "atom_b": 23, "pair_type": 1}, {"atom_a": 5, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 5, "pair_type": 1}, {"atom_a": 37, "atom_b": 6, "pair_type": 1}, {"atom_a": 16, "atom_b": 6, "pair_type": 1}, {"atom_a": 6, "atom_b": 30, "pair_type": 1}, {"atom_a": 16, "atom_b": 7, "pair_type": 1}, {"atom_a": 37, "atom_b": 7, "pair_type": 1}, {"atom_a": 7, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 8, "pair_type": 1}, {"atom_a": 23, "atom_b": 8, "pair_type": 1}, {"atom_a": 16, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 9, "pair_type": 1}, {"atom_a": 23, "atom_b": 9, "pair_type": 1}, {"atom_a": 16, "atom_b": 9, "pair_type": 1}, {"atom_a": 10, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 10, "atom_b": 14, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 11, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 14, "pair_type": 1}, {"atom_a": 17, "atom_b": 21, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 17, "atom_b": 20, "pair_type": 1}, {"atom_a": 18, "atom_b": 21, "pair_type": 1}, {"atom_a": 18, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 24, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 25, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 35, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 31, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 35, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 36, "pair_type": 1}, {"atom_a": 38, "atom_b": 42, "pair_type": 1}, {"atom_a": 38, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 39, "atom_b": 42, "pair_type": 1}, {"atom_a": 39, "atom_b": 43, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 45, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 64, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 78, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/polytop_examples/data/four_arm_star.png b/polytop_examples/data/four_arm_star.png deleted file mode 100644 index f5beba2..0000000 Binary files a/polytop_examples/data/four_arm_star.png and /dev/null differ diff --git a/polytop_examples/data/pei_linear_polymer.itp b/polytop_examples/data/pei_linear_polymer.itp deleted file mode 100644 index 9e6bc1d..0000000 --- a/polytop_examples/data/pei_linear_polymer.itp +++ /dev/null @@ -1,419 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; pei polymer -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -; This file was generated at 14:05 on 2024-12-13 by -; -; Automatic Topology Builder -; -; REVISION 2024-11-20 12:06:25 -;--------------------------------------------------------------------------------------------------------------------------- -; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark -; -; Institute : Molecular Dynamics group, -; School of Chemistry and Molecular Biosciences (SCMB), -; The University of Queensland, QLD 4072, Australia -; URL : https://atb.uq.edu.au -; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. -; An Automated force field Topology Builder (ATB) and repository: version 1.0. -; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. -; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. -; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. -; DOI:10.1021/acs.jctc.8b00768 -; -; Disclaimer : -; While every effort has been made to ensure the accuracy and validity of parameters provided below -; the assignment of parameters is being based on an automated procedure combining data provided by a -; given user as well as calculations performed using third party software. They are provided as a guide. -; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided -; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion -; and to perform additional validation tests for their specific application if required. Neither the authors -; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. -; -; Release notes and warnings: -; (1) The topology is based on a set of atomic coordinates and other data provided by the user after -; after quantum mechanical optimization of the structure using different levels of theory depending on -; the nature of the molecule. -; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. -; In these cases alternative type codes are provided at the end of the line. -; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral -; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" -; or "uncertain" in comments. -; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder -; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually -; before the file can be used. -;--------------------------------------------------------------------------------------------------------------------------- -; Input Structure : LHCU -; Output : UNITED ATOM topology -; Use in conjunction with the corresponding united atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 1707355 -; ATB Topology Hash: f968d -;--------------------------------------------------------------------------------------------------------------------------- -; Final Topology Generation was performed using: -; A B3LYP/6-31G* optimized geometry. -; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. -; Initial charges were estimated using the ESP method of Merz-Kollman. -; Final charges and charge groups were generated by method described in the ATB paper. -; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. -;--------------------------------------------------------------------------------------------------------------------------- -; -; - -[ moleculetype ] -LHCU 3 -[ atoms ] - 1 NOpt 1 LHCU N71 1 -0.698385 14.0067 - 2 HS14 1 LHCU H72 2 0.291615 1.0080 - 3 CH2 1 LHCU C61 3 0.197615 14.0270 - 4 CH2 1 LHCU C5 4 0.212615 14.0270 - 5 NOpt 1 LHCU N7 5 -0.711385 14.0067 - 6 HS14 1 LHCU H21 6 0.305615 1.0080 - 7 CH3 1 LHCU C6 7 0.197615 15.0350 - 8 NOpt 2 LHCU N71 8 -0.698962 14.0067 - 9 HS14 2 LHCU H72 9 0.291038 1.0080 - 10 CH2 2 LHCU C61 10 0.197038 14.0270 - 11 CH2 2 LHCU C5 11 0.212038 14.0270 - 12 NOpt 3 LHCU N71 12 -0.699192 14.0067 - 13 HS14 3 LHCU H72 13 0.290808 1.0080 - 14 CH2 3 LHCU C61 14 0.196808 14.0270 - 15 CH2 3 LHCU C5 15 0.211808 14.0270 - 16 NOpt 4 LHCU N71 16 -0.699238 14.0067 - 17 HS14 4 LHCU H72 17 0.290762 1.0080 - 18 CH2 4 LHCU C61 18 0.196762 14.0270 - 19 CH2 4 LHCU C5 19 0.211762 14.0270 - 20 NOpt 5 LHCU N71 20 -0.699248 14.0067 - 21 HS14 5 LHCU H72 21 0.290752 1.0080 - 22 CH2 5 LHCU C61 22 0.196752 14.0270 - 23 CH2 5 LHCU C5 23 0.211752 14.0270 - 24 NOpt 6 LHCU N71 24 -0.699250 14.0067 - 25 HS14 6 LHCU H72 25 0.290750 1.0080 - 26 CH2 6 LHCU C61 26 0.196750 14.0270 - 27 CH2 6 LHCU C5 27 0.211750 14.0270 - 28 NOpt 7 LHCU N71 28 -0.699250 14.0067 - 29 HS14 7 LHCU H72 29 0.290750 1.0080 - 30 CH2 7 LHCU C61 30 0.196750 14.0270 - 31 CH2 7 LHCU C5 31 0.211750 14.0270 - 32 NOpt 8 LHCU N71 32 -0.699250 14.0067 - 33 HS14 8 LHCU H72 33 0.290750 1.0080 - 34 CH2 8 LHCU C61 34 0.196750 14.0270 - 35 CH2 8 LHCU C5 35 0.211750 14.0270 - 36 NOpt 9 LHCU N71 36 -0.699250 14.0067 - 37 HS14 9 LHCU H72 37 0.290750 1.0080 - 38 CH2 9 LHCU C61 38 0.196750 14.0270 - 39 CH2 9 LHCU C5 39 0.211750 14.0270 - 40 NOpt 10 LHCU N71 40 -0.699250 14.0067 - 41 HS14 10 LHCU H72 41 0.290750 1.0080 - 42 CH2 10 LHCU C61 42 0.196750 14.0270 - 43 CH2 10 LHCU C5 43 0.211750 14.0270 - 44 NOpt 11 LHCU N71 44 -0.699250 14.0067 - 45 HS14 11 LHCU H72 45 0.290750 1.0080 - 46 CH2 11 LHCU C61 46 0.196750 14.0270 - 47 CH2 11 LHCU C5 47 0.211750 14.0270 - 48 NOpt 12 LHCU N71 48 -0.699250 14.0067 - 49 HS14 12 LHCU H72 49 0.290750 1.0080 - 50 CH2 12 LHCU C61 50 0.196750 14.0270 - 51 CH2 12 LHCU C5 51 0.211750 14.0270 - 52 NOpt 13 LHCU N71 52 -0.699250 14.0067 - 53 HS14 13 LHCU H72 53 0.290750 1.0080 - 54 CH2 13 LHCU C61 54 0.196750 14.0270 - 55 CH2 13 LHCU C5 55 0.211750 14.0270 - 56 NOpt 14 LHCU N71 56 -0.699250 14.0067 - 57 HS14 14 LHCU H72 57 0.290750 1.0080 - 58 CH2 14 LHCU C61 58 0.196750 14.0270 - 59 CH2 14 LHCU C5 59 0.211750 14.0270 - 60 NOpt 15 LHCU N71 60 -0.699250 14.0067 - 61 HS14 15 LHCU H72 61 0.290750 1.0080 - 62 CH2 15 LHCU C61 62 0.196750 14.0270 - 63 CH2 15 LHCU C5 63 0.211750 14.0270 - 64 NOpt 16 LHCU N71 64 -0.699250 14.0067 - 65 HS14 16 LHCU H72 65 0.290750 1.0080 - 66 CH2 16 LHCU C61 66 0.196750 14.0270 - 67 CH2 16 LHCU C5 67 0.211750 14.0270 - 68 NOpt 17 LHCU N71 68 -0.699250 14.0067 - 69 HS14 17 LHCU H72 69 0.290750 1.0080 - 70 CH2 17 LHCU C61 70 0.196750 14.0270 - 71 CH2 17 LHCU C5 71 0.211750 14.0270 - 72 NOpt 18 LHCU N71 72 -0.699250 14.0067 - 73 HS14 18 LHCU H72 73 0.290750 1.0080 - 74 CH2 18 LHCU C61 74 0.196750 14.0270 - 75 CH2 18 LHCU C5 75 0.211750 14.0270 - 76 NOpt 19 LHCU N71 76 -0.699250 14.0067 - 77 HS14 19 LHCU H72 77 0.290750 1.0080 - 78 CH2 19 LHCU C61 78 0.196750 14.0270 - 79 CH2 19 LHCU C5 79 0.211750 14.0270 - 80 CH3 20 LHCU C62 80 0.000375 15.0350 - 81 CH2 20 LHCU C51 81 0.200375 14.0270 - 82 NOpt 20 LHCU N71 82 -0.698625 14.0067 - 83 HS14 20 LHCU H72 83 0.291375 1.0080 - 84 CH2 20 LHCU C61 84 0.197375 14.0270 - 85 CH2 20 LHCU C5 85 0.212375 14.0270 - -[ bonds ] - 1 2 2 0.1020 1.7782e+07 - 1 11 2 0.1470 8.7100e+06 - 1 3 2 0.1470 8.7100e+06 - 3 4 2 0.1530 7.1500e+06 - 4 5 2 0.1470 8.7100e+06 - 5 6 2 0.1020 1.7782e+07 - 5 7 2 0.1470 8.7100e+06 - 8 15 2 0.1470 8.7100e+06 - 8 9 2 0.1020 1.7782e+07 - 8 10 2 0.1470 8.7100e+06 - 10 11 2 0.1530 7.1500e+06 - 12 13 2 0.1020 1.7782e+07 - 12 19 2 0.1470 8.7100e+06 - 12 14 2 0.1470 8.7100e+06 - 14 15 2 0.1530 7.1500e+06 - 16 23 2 0.1470 8.7100e+06 - 16 17 2 0.1020 1.7782e+07 - 16 18 2 0.1470 8.7100e+06 - 18 19 2 0.1530 7.1500e+06 - 20 21 2 0.1020 1.7782e+07 - 20 22 2 0.1470 8.7100e+06 - 20 27 2 0.1470 8.7100e+06 - 22 23 2 0.1530 7.1500e+06 - 24 26 2 0.1470 8.7100e+06 - 24 25 2 0.1020 1.7782e+07 - 24 31 2 0.1470 8.7100e+06 - 26 27 2 0.1530 7.1500e+06 - 28 35 2 0.1470 8.7100e+06 - 28 30 2 0.1470 8.7100e+06 - 28 29 2 0.1020 1.7782e+07 - 30 31 2 0.1530 7.1500e+06 - 32 34 2 0.1470 8.7100e+06 - 32 39 2 0.1470 8.7100e+06 - 32 33 2 0.1020 1.7782e+07 - 34 35 2 0.1530 7.1500e+06 - 36 37 2 0.1020 1.7782e+07 - 36 43 2 0.1470 8.7100e+06 - 36 38 2 0.1470 8.7100e+06 - 38 39 2 0.1530 7.1500e+06 - 40 42 2 0.1470 8.7100e+06 - 40 41 2 0.1020 1.7782e+07 - 40 47 2 0.1470 8.7100e+06 - 42 43 2 0.1530 7.1500e+06 - 44 45 2 0.1020 1.7782e+07 - 44 51 2 0.1470 8.7100e+06 - 44 46 2 0.1470 8.7100e+06 - 46 47 2 0.1530 7.1500e+06 - 48 55 2 0.1470 8.7100e+06 - 48 50 2 0.1470 8.7100e+06 - 48 49 2 0.1020 1.7782e+07 - 50 51 2 0.1530 7.1500e+06 - 52 53 2 0.1020 1.7782e+07 - 52 59 2 0.1470 8.7100e+06 - 52 54 2 0.1470 8.7100e+06 - 54 55 2 0.1530 7.1500e+06 - 56 58 2 0.1470 8.7100e+06 - 56 63 2 0.1470 8.7100e+06 - 56 57 2 0.1020 1.7782e+07 - 58 59 2 0.1530 7.1500e+06 - 60 62 2 0.1470 8.7100e+06 - 60 61 2 0.1020 1.7782e+07 - 60 67 2 0.1470 8.7100e+06 - 62 63 2 0.1530 7.1500e+06 - 64 71 2 0.1470 8.7100e+06 - 64 66 2 0.1470 8.7100e+06 - 64 65 2 0.1020 1.7782e+07 - 66 67 2 0.1530 7.1500e+06 - 68 70 2 0.1470 8.7100e+06 - 68 75 2 0.1470 8.7100e+06 - 68 69 2 0.1020 1.7782e+07 - 70 71 2 0.1530 7.1500e+06 - 72 74 2 0.1470 8.7100e+06 - 72 79 2 0.1470 8.7100e+06 - 72 73 2 0.1020 1.7782e+07 - 74 75 2 0.1530 7.1500e+06 - 76 85 2 0.1470 8.7100e+06 - 76 77 2 0.1020 1.7782e+07 - 76 78 2 0.1470 8.7100e+06 - 78 79 2 0.1530 7.1500e+06 - 80 81 2 0.1530 7.1500e+06 - 81 82 2 0.1470 8.7100e+06 - 82 84 2 0.1470 8.7100e+06 - 82 83 2 0.1020 1.7782e+07 - 84 85 2 0.1530 7.1500e+06 - -[ pairs ] - 1 5 1 - 2 4 1 - 3 7 1 - 3 6 1 - 9 11 1 - 13 15 1 - 17 19 1 - 21 23 1 - 25 27 1 - 29 31 1 - 33 35 1 - 37 39 1 - 41 43 1 - 45 47 1 - 49 51 1 - 53 55 1 - 57 59 1 - 61 63 1 - 65 67 1 - 69 71 1 - 73 75 1 - 77 79 1 - 80 84 1 - 80 83 1 - 81 85 1 - 83 85 1 - -[ angles ] - 2 1 11 2 109.5000 4.2500e+02 - 2 1 3 2 109.5000 4.2500e+02 - 1 11 10 2 111.0000 5.3000e+02 - 3 1 11 2 116.0000 6.2000e+02 - 1 3 4 2 111.0000 5.3000e+02 - 3 4 5 2 111.0000 5.3000e+02 - 4 5 6 2 109.5000 4.2500e+02 - 4 5 7 2 116.0000 6.2000e+02 - 6 5 7 2 109.5000 4.2500e+02 - 8 15 14 2 111.0000 5.3000e+02 - 10 8 15 2 116.0000 6.2000e+02 - 9 8 15 2 109.5000 4.2500e+02 - 9 8 10 2 109.5000 4.2500e+02 - 8 10 11 2 111.0000 5.3000e+02 - 13 12 19 2 109.5000 4.2500e+02 - 13 12 14 2 109.5000 4.2500e+02 - 14 12 19 2 116.0000 6.2000e+02 - 12 19 18 2 111.0000 5.3000e+02 - 12 14 15 2 111.0000 5.3000e+02 - 17 16 23 2 109.5000 4.2500e+02 - 18 16 23 2 116.0000 6.2000e+02 - 16 23 22 2 111.0000 5.3000e+02 - 17 16 18 2 109.5000 4.2500e+02 - 16 18 19 2 111.0000 5.3000e+02 - 21 20 27 2 109.5000 4.2500e+02 - 21 20 22 2 109.5000 4.2500e+02 - 22 20 27 2 116.0000 6.2000e+02 - 20 22 23 2 111.0000 5.3000e+02 - 20 27 26 2 111.0000 5.3000e+02 - 24 26 27 2 111.0000 5.3000e+02 - 25 24 26 2 109.5000 4.2500e+02 - 26 24 31 2 116.0000 6.2000e+02 - 25 24 31 2 109.5000 4.2500e+02 - 24 31 30 2 111.0000 5.3000e+02 - 28 35 34 2 111.0000 5.3000e+02 - 30 28 35 2 116.0000 6.2000e+02 - 29 28 35 2 109.5000 4.2500e+02 - 28 30 31 2 111.0000 5.3000e+02 - 29 28 30 2 109.5000 4.2500e+02 - 33 32 34 2 109.5000 4.2500e+02 - 34 32 39 2 116.0000 6.2000e+02 - 32 34 35 2 111.0000 5.3000e+02 - 33 32 39 2 109.5000 4.2500e+02 - 32 39 38 2 111.0000 5.3000e+02 - 37 36 38 2 109.5000 4.2500e+02 - 37 36 43 2 109.5000 4.2500e+02 - 36 43 42 2 111.0000 5.3000e+02 - 38 36 43 2 116.0000 6.2000e+02 - 36 38 39 2 111.0000 5.3000e+02 - 42 40 47 2 116.0000 6.2000e+02 - 40 42 43 2 111.0000 5.3000e+02 - 41 40 42 2 109.5000 4.2500e+02 - 41 40 47 2 109.5000 4.2500e+02 - 40 47 46 2 111.0000 5.3000e+02 - 45 44 46 2 109.5000 4.2500e+02 - 45 44 51 2 109.5000 4.2500e+02 - 46 44 51 2 116.0000 6.2000e+02 - 44 51 50 2 111.0000 5.3000e+02 - 44 46 47 2 111.0000 5.3000e+02 - 50 48 55 2 116.0000 6.2000e+02 - 48 55 54 2 111.0000 5.3000e+02 - 49 48 55 2 109.5000 4.2500e+02 - 49 48 50 2 109.5000 4.2500e+02 - 48 50 51 2 111.0000 5.3000e+02 - 53 52 54 2 109.5000 4.2500e+02 - 53 52 59 2 109.5000 4.2500e+02 - 54 52 59 2 116.0000 6.2000e+02 - 52 59 58 2 111.0000 5.3000e+02 - 52 54 55 2 111.0000 5.3000e+02 - 56 58 59 2 111.0000 5.3000e+02 - 58 56 63 2 116.0000 6.2000e+02 - 57 56 58 2 109.5000 4.2500e+02 - 56 63 62 2 111.0000 5.3000e+02 - 57 56 63 2 109.5000 4.2500e+02 - 60 62 63 2 111.0000 5.3000e+02 - 62 60 67 2 116.0000 6.2000e+02 - 61 60 62 2 109.5000 4.2500e+02 - 61 60 67 2 109.5000 4.2500e+02 - 60 67 66 2 111.0000 5.3000e+02 - 64 71 70 2 111.0000 5.3000e+02 - 66 64 71 2 116.0000 6.2000e+02 - 65 64 71 2 109.5000 4.2500e+02 - 64 66 67 2 111.0000 5.3000e+02 - 65 64 66 2 109.5000 4.2500e+02 - 70 68 75 2 116.0000 6.2000e+02 - 69 68 70 2 109.5000 4.2500e+02 - 68 70 71 2 111.0000 5.3000e+02 - 68 75 74 2 111.0000 5.3000e+02 - 69 68 75 2 109.5000 4.2500e+02 - 73 72 74 2 109.5000 4.2500e+02 - 74 72 79 2 116.0000 6.2000e+02 - 72 74 75 2 111.0000 5.3000e+02 - 73 72 79 2 109.5000 4.2500e+02 - 72 79 78 2 111.0000 5.3000e+02 - 78 76 85 2 116.0000 6.2000e+02 - 77 76 85 2 109.5000 4.2500e+02 - 76 85 84 2 111.0000 5.3000e+02 - 77 76 78 2 109.5000 4.2500e+02 - 76 78 79 2 111.0000 5.3000e+02 - 80 81 82 2 111.0000 5.3000e+02 - 81 82 83 2 109.5000 4.2500e+02 - 81 82 84 2 116.0000 6.2000e+02 - 82 84 85 2 111.0000 5.3000e+02 - 83 82 84 2 109.5000 4.2500e+02 - -[ dihedrals ] - 8 10 11 1 1 0.0000 5.9200e+00 3 - 11 1 3 4 1 180.0000 1.0000e+00 6 - 1 3 4 5 1 0.0000 5.9200e+00 3 - 3 4 5 7 1 180.0000 1.0000e+00 6 - 12 14 15 8 1 0.0000 5.9200e+00 3 - 15 8 10 11 1 180.0000 1.0000e+00 6 - 19 12 14 15 1 180.0000 1.0000e+00 6 - 16 18 19 12 1 0.0000 5.9200e+00 3 - 23 16 18 19 1 180.0000 1.0000e+00 6 - 20 22 23 16 1 0.0000 5.9200e+00 3 - 27 20 22 23 1 180.0000 1.0000e+00 6 - 24 26 27 20 1 0.0000 5.9200e+00 3 - 31 24 26 27 1 180.0000 1.0000e+00 6 - 28 30 31 24 1 0.0000 5.9200e+00 3 - 32 34 35 28 1 0.0000 5.9200e+00 3 - 35 28 30 31 1 180.0000 1.0000e+00 6 - 39 32 34 35 1 180.0000 1.0000e+00 6 - 36 38 39 32 1 0.0000 5.9200e+00 3 - 40 42 43 36 1 0.0000 5.9200e+00 3 - 43 36 38 39 1 180.0000 1.0000e+00 6 - 47 40 42 43 1 180.0000 1.0000e+00 6 - 44 46 47 40 1 0.0000 5.9200e+00 3 - 51 44 46 47 1 180.0000 1.0000e+00 6 - 48 50 51 44 1 0.0000 5.9200e+00 3 - 55 48 50 51 1 180.0000 1.0000e+00 6 - 52 54 55 48 1 0.0000 5.9200e+00 3 - 59 52 54 55 1 180.0000 1.0000e+00 6 - 56 58 59 52 1 0.0000 5.9200e+00 3 - 63 56 58 59 1 180.0000 1.0000e+00 6 - 60 62 63 56 1 0.0000 5.9200e+00 3 - 67 60 62 63 1 180.0000 1.0000e+00 6 - 64 66 67 60 1 0.0000 5.9200e+00 3 - 68 70 71 64 1 0.0000 5.9200e+00 3 - 71 64 66 67 1 180.0000 1.0000e+00 6 - 75 68 70 71 1 180.0000 1.0000e+00 6 - 72 74 75 68 1 0.0000 5.9200e+00 3 - 79 72 74 75 1 180.0000 1.0000e+00 6 - 76 78 79 72 1 0.0000 5.9200e+00 3 - 85 76 78 79 1 180.0000 1.0000e+00 6 - 82 84 85 76 1 0.0000 5.9200e+00 3 - 80 81 82 84 1 180.0000 1.0000e+00 6 - 81 82 84 85 1 180.0000 1.0000e+00 6 - -[ exclusions ] diff --git a/polytop_examples/data/pei_linear_polymer.json b/polytop_examples/data/pei_linear_polymer.json deleted file mode 100644 index 1c1dd5b..0000000 --- a/polytop_examples/data/pei_linear_polymer.json +++ /dev/null @@ -1 +0,0 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2916153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 2, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19761538461538464, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 3, "atom_type": "CH2", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21261538461538462, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 4, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N7", "charge_group_num": 7, "partial_charge": -0.7113846153846153, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 5, "atom_type": "HS14", "residue_id": 1, "residue_name": "LHCU", "atom_name": "H21", "charge_group_num": 8, "partial_charge": 0.3056153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 6, "atom_type": "CH3", "residue_id": 1, "residue_name": "LHCU", "atom_name": "C6", "charge_group_num": 9, "partial_charge": 0.19761538461538464, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 7, "atom_type": "HS14", "residue_id": 2, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2910384615384616, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 8, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19703846153846158, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 9, "atom_type": "CH2", "residue_id": 2, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21203846153846156, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 10, "atom_type": "NOpt", "residue_id": 1, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6983846153846153, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 11, "atom_type": "HS14", "residue_id": 3, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2908076923076923, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 12, "atom_type": "CH2", "residue_id": 3, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19680769230769235, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 13, "atom_type": "CH2", "residue_id": 3, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21180769230769234, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 14, "atom_type": "NOpt", "residue_id": 2, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6989615384615383, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 15, "atom_type": "HS14", "residue_id": 4, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29076153846153846, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 16, "atom_type": "CH2", "residue_id": 4, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.1967615384615385, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 17, "atom_type": "CH2", "residue_id": 4, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21176153846153847, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 18, "atom_type": "NOpt", "residue_id": 3, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6991923076923076, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 19, "atom_type": "HS14", "residue_id": 5, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907523076923077, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 20, "atom_type": "CH2", "residue_id": 5, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675230769230773, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 21, "atom_type": "CH2", "residue_id": 5, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2117523076923077, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 22, "atom_type": "NOpt", "residue_id": 4, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992384615384615, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 23, "atom_type": "HS14", "residue_id": 6, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907504615384615, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 24, "atom_type": "CH2", "residue_id": 6, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675046153846157, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 25, "atom_type": "CH2", "residue_id": 6, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175046153846155, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 26, "atom_type": "NOpt", "residue_id": 5, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992476923076922, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 27, "atom_type": "HS14", "residue_id": 7, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500923076923, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 28, "atom_type": "CH2", "residue_id": 7, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.1967500923076923, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 29, "atom_type": "CH2", "residue_id": 7, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2117500923076923, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 30, "atom_type": "NOpt", "residue_id": 6, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992495384615384, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 31, "atom_type": "HS14", "residue_id": 8, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500184615384, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 32, "atom_type": "CH2", "residue_id": 8, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675001846153845, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 33, "atom_type": "CH2", "residue_id": 8, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175001846153843, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 34, "atom_type": "NOpt", "residue_id": 7, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499076923077, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 35, "atom_type": "HS14", "residue_id": 9, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500036923077, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 36, "atom_type": "CH2", "residue_id": 9, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.1967500036923077, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 37, "atom_type": "CH2", "residue_id": 9, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000369230768, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 38, "atom_type": "NOpt", "residue_id": 8, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499815384615, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 39, "atom_type": "HS14", "residue_id": 10, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500007384615, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 40, "atom_type": "CH2", "residue_id": 10, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000073846155, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 41, "atom_type": "CH2", "residue_id": 10, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000073846154, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 42, "atom_type": "NOpt", "residue_id": 9, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499963076922, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 43, "atom_type": "HS14", "residue_id": 11, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29075000014769226, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 44, "atom_type": "CH2", "residue_id": 11, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000014769234, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 45, "atom_type": "CH2", "residue_id": 11, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000014769232, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 46, "atom_type": "NOpt", "residue_id": 10, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499992615384, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 47, "atom_type": "HS14", "residue_id": 12, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500000295385, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 48, "atom_type": "CH2", "residue_id": 12, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000002953852, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 49, "atom_type": "CH2", "residue_id": 12, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2117500000295385, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 50, "atom_type": "NOpt", "residue_id": 11, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499998523076, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 51, "atom_type": "HS14", "residue_id": 13, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500000059077, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 52, "atom_type": "CH2", "residue_id": 13, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000000590775, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 53, "atom_type": "CH2", "residue_id": 13, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000000590774, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 54, "atom_type": "NOpt", "residue_id": 12, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999704614, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 55, "atom_type": "HS14", "residue_id": 14, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29075000000118156, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 56, "atom_type": "CH2", "residue_id": 14, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000000118162, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 57, "atom_type": "CH2", "residue_id": 14, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2117500000011816, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 58, "atom_type": "NOpt", "residue_id": 13, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999940922, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 59, "atom_type": "HS14", "residue_id": 15, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500000002363, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 60, "atom_type": "CH2", "residue_id": 15, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000000023637, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 61, "atom_type": "CH2", "residue_id": 15, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000000023636, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 62, "atom_type": "NOpt", "residue_id": 14, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999988183, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 63, "atom_type": "HS14", "residue_id": 16, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29075000000004725, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 64, "atom_type": "CH2", "residue_id": 16, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000000004728, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 65, "atom_type": "CH2", "residue_id": 16, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000000004726, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 66, "atom_type": "NOpt", "residue_id": 15, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999997636, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 67, "atom_type": "HS14", "residue_id": 17, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500000000095, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 68, "atom_type": "CH2", "residue_id": 17, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.1967500000000095, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 69, "atom_type": "CH2", "residue_id": 17, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2117500000000095, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 70, "atom_type": "NOpt", "residue_id": 16, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999999526, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 71, "atom_type": "HS14", "residue_id": 18, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29075000000000195, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 72, "atom_type": "CH2", "residue_id": 18, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000000000198, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 73, "atom_type": "CH2", "residue_id": 18, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21175000000000196, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 74, "atom_type": "NOpt", "residue_id": 17, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999999905, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 77, "atom_type": "HS14", "residue_id": 19, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.2907500000000004, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 78, "atom_type": "CH2", "residue_id": 19, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19675000000000042, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 79, "atom_type": "CH2", "residue_id": 19, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.2117500000000004, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 80, "atom_type": "NOpt", "residue_id": 18, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.699249999999998, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 81, "atom_type": "CH3", "residue_id": 20, "residue_name": "LHCU", "atom_name": "C62", "charge_group_num": 1, "partial_charge": 0.0003750000000000799, "mass": 15.035, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 82, "atom_type": "CH2", "residue_id": 20, "residue_name": "LHCU", "atom_name": "C51", "charge_group_num": 2, "partial_charge": 0.20037500000000008, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 83, "atom_type": "NOpt", "residue_id": 20, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6986249999999998, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 84, "atom_type": "HS14", "residue_id": 20, "residue_name": "LHCU", "atom_name": "H72", "charge_group_num": 4, "partial_charge": 0.29137500000000005, "mass": 1.008, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 85, "atom_type": "CH2", "residue_id": 20, "residue_name": "LHCU", "atom_name": "C61", "charge_group_num": 5, "partial_charge": 0.19737500000000008, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 86, "atom_type": "CH2", "residue_id": 20, "residue_name": "LHCU", "atom_name": "C5", "charge_group_num": 6, "partial_charge": 0.21237500000000006, "mass": 14.027, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}, {"atom_id": 76, "atom_type": "NOpt", "residue_id": 19, "residue_name": "LHCU", "atom_name": "N71", "charge_group_num": 3, "partial_charge": -0.6992499999999995, "mass": 14.0067, "x": 0.0, "y": 0.0, "z": 0.0, "formerly": null}], "bonds": [{"atom_a": 10, "atom_b": 1, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 2, "atom_b": 3, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 10, "atom_b": 2, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 3, "atom_b": 4, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 4, "atom_b": 5, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 4, "atom_b": 6, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 14, "atom_b": 7, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 14, "atom_b": 8, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 8, "atom_b": 9, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 10, "atom_b": 9, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 18, "atom_b": 11, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 18, "atom_b": 12, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 12, "atom_b": 13, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 14, "atom_b": 13, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 22, "atom_b": 15, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 16, "atom_b": 17, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 22, "atom_b": 16, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 18, "atom_b": 17, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 26, "atom_b": 19, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 20, "atom_b": 21, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 26, "atom_b": 20, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 22, "atom_b": 21, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 30, "atom_b": 23, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 24, "atom_b": 25, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 30, "atom_b": 24, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 26, "atom_b": 25, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 34, "atom_b": 27, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 28, "atom_b": 29, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 34, "atom_b": 28, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 30, "atom_b": 29, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 38, "atom_b": 31, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 32, "atom_b": 33, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 38, "atom_b": 32, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 34, "atom_b": 33, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 42, "atom_b": 35, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 42, "atom_b": 36, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 36, "atom_b": 37, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 38, "atom_b": 37, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 46, "atom_b": 39, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 40, "atom_b": 41, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 46, "atom_b": 40, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 42, "atom_b": 41, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 50, "atom_b": 43, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 50, "atom_b": 44, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 44, "atom_b": 45, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 46, "atom_b": 45, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 54, "atom_b": 47, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 54, "atom_b": 48, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 48, "atom_b": 49, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 50, "atom_b": 49, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 58, "atom_b": 51, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 58, "atom_b": 52, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 52, "atom_b": 53, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 54, "atom_b": 53, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 62, "atom_b": 55, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 56, "atom_b": 57, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 62, "atom_b": 56, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 58, "atom_b": 57, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 66, "atom_b": 59, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 66, "atom_b": 60, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 60, "atom_b": 61, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 62, "atom_b": 61, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 70, "atom_b": 63, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 70, "atom_b": 64, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 64, "atom_b": 65, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 66, "atom_b": 65, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 74, "atom_b": 67, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 74, "atom_b": 68, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 68, "atom_b": 69, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 70, "atom_b": 69, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 80, "atom_b": 71, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 80, "atom_b": 72, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 72, "atom_b": 73, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 74, "atom_b": 73, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 76, "atom_b": 77, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 76, "atom_b": 78, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 78, "atom_b": 79, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 80, "atom_b": 79, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 81, "atom_b": 82, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 82, "atom_b": 83, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 83, "atom_b": 85, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}, {"atom_a": 83, "atom_b": 84, "bond_type": 2, "bond_length": 0.102, "force_constant": 17782000.0, "order": 1}, {"atom_a": 85, "atom_b": 86, "bond_type": 2, "bond_length": 0.153, "force_constant": 7150000.0, "order": 1}, {"atom_a": 76, "atom_b": 86, "bond_type": 2, "bond_length": 0.147, "force_constant": 8710000.0, "order": 1}], "angles": [{"atom_a": 1, "atom_b": 10, "atom_c": 9, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 1, "atom_b": 10, "atom_c": 2, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 2, "atom_b": 3, "atom_c": 4, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 10, "atom_b": 2, "atom_c": 3, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 2, "atom_b": 10, "atom_c": 9, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 3, "atom_b": 4, "atom_c": 5, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 3, "atom_b": 4, "atom_c": 6, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 5, "atom_b": 4, "atom_c": 6, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 7, "atom_b": 14, "atom_c": 8, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 7, "atom_b": 14, "atom_c": 13, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 8, "atom_b": 14, "atom_c": 13, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 14, "atom_b": 8, "atom_c": 9, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 10, "atom_b": 9, "atom_c": 8, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 11, "atom_b": 18, "atom_c": 17, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 11, "atom_b": 18, "atom_c": 12, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 12, "atom_b": 18, "atom_c": 17, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 18, "atom_b": 12, "atom_c": 13, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 14, "atom_b": 13, "atom_c": 12, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 15, "atom_b": 22, "atom_c": 16, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 15, "atom_b": 22, "atom_c": 21, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 22, "atom_b": 16, "atom_c": 17, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 18, "atom_b": 17, "atom_c": 16, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 16, "atom_b": 22, "atom_c": 21, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 19, "atom_b": 26, "atom_c": 25, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 19, "atom_b": 26, "atom_c": 20, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 22, "atom_b": 21, "atom_c": 20, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 26, "atom_b": 20, "atom_c": 21, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 20, "atom_b": 26, "atom_c": 25, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 23, "atom_b": 30, "atom_c": 24, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 23, "atom_b": 30, "atom_c": 29, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 30, "atom_b": 24, "atom_c": 25, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 26, "atom_b": 25, "atom_c": 24, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 24, "atom_b": 30, "atom_c": 29, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 27, "atom_b": 34, "atom_c": 28, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 27, "atom_b": 34, "atom_c": 33, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 34, "atom_b": 28, "atom_c": 29, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 30, "atom_b": 29, "atom_c": 28, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 28, "atom_b": 34, "atom_c": 33, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 31, "atom_b": 38, "atom_c": 32, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 31, "atom_b": 38, "atom_c": 37, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 34, "atom_b": 33, "atom_c": 32, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 38, "atom_b": 32, "atom_c": 33, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 32, "atom_b": 38, "atom_c": 37, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 35, "atom_b": 42, "atom_c": 36, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 35, "atom_b": 42, "atom_c": 41, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 42, "atom_b": 36, "atom_c": 37, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 36, "atom_b": 42, "atom_c": 41, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 38, "atom_b": 37, "atom_c": 36, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 39, "atom_b": 46, "atom_c": 45, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 39, "atom_b": 46, "atom_c": 40, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 42, "atom_b": 41, "atom_c": 40, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 46, "atom_b": 40, "atom_c": 41, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 40, "atom_b": 46, "atom_c": 45, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 43, "atom_b": 50, "atom_c": 44, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 43, "atom_b": 50, "atom_c": 49, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 50, "atom_b": 44, "atom_c": 45, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 44, "atom_b": 50, "atom_c": 49, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 46, "atom_b": 45, "atom_c": 44, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 47, "atom_b": 54, "atom_c": 48, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 47, "atom_b": 54, "atom_c": 53, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 48, "atom_b": 54, "atom_c": 53, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 54, "atom_b": 48, "atom_c": 49, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 50, "atom_b": 49, "atom_c": 48, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 51, "atom_b": 58, "atom_c": 52, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 51, "atom_b": 58, "atom_c": 57, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 58, "atom_b": 52, "atom_c": 53, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 52, "atom_b": 58, "atom_c": 57, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 54, "atom_b": 53, "atom_c": 52, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 55, "atom_b": 62, "atom_c": 61, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 55, "atom_b": 62, "atom_c": 56, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 62, "atom_b": 56, "atom_c": 57, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 58, "atom_b": 57, "atom_c": 56, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 56, "atom_b": 62, "atom_c": 61, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 59, "atom_b": 66, "atom_c": 65, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 59, "atom_b": 66, "atom_c": 60, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 66, "atom_b": 60, "atom_c": 61, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 60, "atom_b": 66, "atom_c": 65, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 62, "atom_b": 61, "atom_c": 60, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 63, "atom_b": 70, "atom_c": 64, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 63, "atom_b": 70, "atom_c": 69, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 70, "atom_b": 64, "atom_c": 65, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 64, "atom_b": 70, "atom_c": 69, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 66, "atom_b": 65, "atom_c": 64, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 67, "atom_b": 74, "atom_c": 73, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 67, "atom_b": 74, "atom_c": 68, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 68, "atom_b": 74, "atom_c": 73, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 74, "atom_b": 68, "atom_c": 69, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 70, "atom_b": 69, "atom_c": 68, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 71, "atom_b": 80, "atom_c": 72, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 71, "atom_b": 80, "atom_c": 79, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 72, "atom_b": 80, "atom_c": 79, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 80, "atom_b": 72, "atom_c": 73, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 74, "atom_b": 73, "atom_c": 72, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 77, "atom_b": 76, "atom_c": 86, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 77, "atom_b": 76, "atom_c": 78, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 78, "atom_b": 76, "atom_c": 86, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 76, "atom_b": 78, "atom_c": 79, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 80, "atom_b": 79, "atom_c": 78, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 81, "atom_b": 82, "atom_c": 83, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 82, "atom_b": 83, "atom_c": 84, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 82, "atom_b": 83, "atom_c": 85, "angle_type": 2, "angle_value": 116.0, "force_constant": 620.0}, {"atom_a": 83, "atom_b": 85, "atom_c": 86, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}, {"atom_a": 84, "atom_b": 83, "atom_c": 85, "angle_type": 2, "angle_value": 109.5, "force_constant": 425.0}, {"atom_a": 76, "atom_b": 86, "atom_c": 85, "angle_type": 2, "angle_value": 111.0, "force_constant": 530.0}], "dihedrals": [{"atom_a": 10, "atom_b": 2, "atom_c": 3, "atom_d": 4, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 2, "atom_b": 3, "atom_c": 4, "atom_d": 6, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 9, "atom_b": 10, "atom_c": 2, "atom_d": 3, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 13, "atom_b": 14, "atom_c": 8, "atom_d": 9, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 14, "atom_b": 8, "atom_c": 9, "atom_d": 10, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 17, "atom_b": 18, "atom_c": 12, "atom_d": 13, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 18, "atom_b": 12, "atom_c": 13, "atom_d": 14, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 22, "atom_b": 16, "atom_c": 17, "atom_d": 18, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 21, "atom_b": 22, "atom_c": 16, "atom_d": 17, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 26, "atom_b": 20, "atom_c": 21, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 25, "atom_b": 26, "atom_c": 20, "atom_d": 21, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 30, "atom_b": 24, "atom_c": 25, "atom_d": 26, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 29, "atom_b": 30, "atom_c": 24, "atom_d": 25, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 33, "atom_b": 34, "atom_c": 28, "atom_d": 29, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 34, "atom_b": 28, "atom_c": 29, "atom_d": 30, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 38, "atom_b": 32, "atom_c": 33, "atom_d": 34, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 37, "atom_b": 38, "atom_c": 32, "atom_d": 33, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 42, "atom_b": 36, "atom_c": 37, "atom_d": 38, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 41, "atom_b": 42, "atom_c": 36, "atom_d": 37, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 46, "atom_b": 40, "atom_c": 41, "atom_d": 42, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 45, "atom_b": 46, "atom_c": 40, "atom_d": 41, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 50, "atom_b": 44, "atom_c": 45, "atom_d": 46, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 49, "atom_b": 50, "atom_c": 44, "atom_d": 45, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 53, "atom_b": 54, "atom_c": 48, "atom_d": 49, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 54, "atom_b": 48, "atom_c": 49, "atom_d": 50, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 57, "atom_b": 58, "atom_c": 52, "atom_d": 53, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 58, "atom_b": 52, "atom_c": 53, "atom_d": 54, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 61, "atom_b": 62, "atom_c": 56, "atom_d": 57, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 62, "atom_b": 56, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 66, "atom_b": 60, "atom_c": 61, "atom_d": 62, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 66, "atom_c": 60, "atom_d": 61, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 70, "atom_b": 64, "atom_c": 65, "atom_d": 66, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 69, "atom_b": 70, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 73, "atom_b": 74, "atom_c": 68, "atom_d": 69, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 74, "atom_b": 68, "atom_c": 69, "atom_d": 70, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 80, "atom_c": 72, "atom_d": 73, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 80, "atom_b": 72, "atom_c": 73, "atom_d": 74, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 76, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 76, "atom_b": 78, "atom_c": 79, "atom_d": 80, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 81, "atom_b": 82, "atom_c": 83, "atom_d": 85, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 82, "atom_b": 83, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 83, "atom_b": 85, "atom_c": 86, "atom_d": 76, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 3, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 2, "atom_b": 5, "pair_type": 1}, {"atom_a": 10, "atom_b": 4, "pair_type": 1}, {"atom_a": 7, "atom_b": 9, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 15, "atom_b": 17, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 25, "pair_type": 1}, {"atom_a": 27, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 33, "pair_type": 1}, {"atom_a": 35, "atom_b": 37, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 43, "atom_b": 45, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 53, "pair_type": 1}, {"atom_a": 55, "atom_b": 57, "pair_type": 1}, {"atom_a": 59, "atom_b": 61, "pair_type": 1}, {"atom_a": 63, "atom_b": 65, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 71, "atom_b": 73, "pair_type": 1}, {"atom_a": 77, "atom_b": 79, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 82, "atom_b": 86, "pair_type": 1}, {"atom_a": 84, "atom_b": 86, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C5", "residue_atom": "N7"}, {"name": "from", "monomer_atom": "N71", "residue_atom": "C51"}]} \ No newline at end of file diff --git a/polytop_examples/data/pei_linear_polymer.png b/polytop_examples/data/pei_linear_polymer.png deleted file mode 100644 index 6fff54d..0000000 Binary files a/polytop_examples/data/pei_linear_polymer.png and /dev/null differ