# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 08:43:32 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: (2Z)-6-O-hexadecanoyl-L-threo-hex-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(=O)OC[C@H](O)[C@@H](O)\C(O)=C(O)/C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PVC  PVC  '(2Z)-6-O-hexadecanoyl-L-threo-hex-2-enonic acid'  ligand  70  30  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PVC
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PVC  CP1   C  C     0   0.608   -2.7398  -0.1094   1.0516
 PVC  OP    O  O     0  -0.452   -2.7483  -0.3311   2.2365
 PVC  CP2   C  CH2   0  -0.584   -1.5158  -0.0876   0.1776
 PVC  CP3   C  CH2   0  -0.418   -0.2101  -0.1807   0.9506
 PVC  CP4   C  CH2   0  -0.416    1.0005  -0.1579   0.0253
 PVC  CP5   C  CH2   0  -0.413    2.3215  -0.2146   0.7816
 PVC  CP6   C  CH2   0  -0.412    3.5396  -0.1949  -0.1337
 PVC  CP7   C  CH2   0  -0.412    4.8602  -0.2089   0.6259
 PVC  CP8   C  CH2   0  -0.412    6.0808  -0.1875  -0.2861
 PVC  CP9   C  CH2   0  -0.412    7.4001  -0.1664   0.4756
 PVC  CPA   C  CH2   0  -0.412    8.6217  -0.1442  -0.4351
 PVC  CPB   C  CH2   0  -0.412    9.9402  -0.1004   0.3269
 PVC  CPC   C  CH2   0  -0.412   11.1615  -0.0776  -0.5842
 PVC  CPD   C  CH2   0  -0.412   12.4806  -0.0253   0.1765
 PVC  CC6   C  CH2   0  -0.196   -5.0874   0.1545   1.0476
 PVC  CC5   C  CH1   0  -0.031   -6.1548   0.5785   0.0539
 PVC  CC4   C  CH1   0  -0.084   -7.5486   0.4444   0.6977
 PVC  CC3   C  C     0   0.360   -8.6174   0.8157  -0.3089
 PVC  CC2   C  C     0   0.052   -9.1618   0.0451  -1.2774
 PVC  CC1   C  C     0   0.460   -8.9408  -1.3737  -1.5529
 PVC  O2    O  OH1   0  -0.659  -10.0269   0.6789  -2.1368
 PVC  O3    O  OH1   0  -0.602   -8.9839   2.0915  -0.1967
 PVC  O4    O  OH1   0  -0.654   -7.6751   1.1981   1.8755
 PVC  O5    O  OH1   0  -0.656   -5.9267   1.8638  -0.4654
 PVC  O6    O  O2    0  -0.461   -3.8423   0.1396   0.3507
 PVC  OC1   O  O     0  -0.462   -9.5686  -1.9687  -2.4006
 PVC  OC2   O  OH1   0  -0.604   -8.0117  -1.9549  -0.8010
 PVC  CPE   C  CH2   0  -0.406   13.7003  -0.0021  -0.7365
 PVC  CPF   C  CH2   0  -0.419   15.0221   0.0465   0.0204
 PVC  CPG   C  CH3   0  -0.663   16.2304   0.0698  -0.9059
 PVC  HP21  H  HCH2  0   0.276   -1.5990  -0.9182  -0.5323
 PVC  HP22  H  HCH2  0   0.270   -1.5393   0.8204  -0.4324
 PVC  HP31  H  HCH2  0   0.224   -0.1393   0.6503   1.6578
 PVC  HP32  H  HCH2  0   0.225   -0.1937  -1.0967   1.5469
 PVC  HP41  H  HCH2  0   0.213    0.9419  -0.9998  -0.6733
 PVC  HP42  H  HCH2  0   0.212    0.9738   0.7488  -0.5893
 PVC  HP51  H  HCH2  0   0.208    2.3774   0.6319   1.4751
 PVC  HP52  H  HCH2  0   0.209    2.3480  -1.1169   1.4028
 PVC  HP61  H  HCH2  0   0.208    3.4989  -1.0548  -0.8117
 PVC  HP62  H  HCH2  0   0.207    3.4986   0.6953  -0.7716
 PVC  HP71  H  HCH2  0   0.206    4.8983   0.6540   1.3005
 PVC  HP72  H  HCH2  0   0.207    4.9023  -1.0960   1.2680
 PVC  HP81  H  HCH2  0   0.207    6.0555  -1.0608  -0.9476
 PVC  HP82  H  HCH2  0   0.206    6.0272   0.6893  -0.9416
 PVC  HP91  H  HCH2  0   0.206    7.4240   0.7094   1.1341
 PVC  HP92  H  HCH2  0   0.206    7.4546  -1.0407   1.1342
 PVC  HPA1  H  HCH2  0   0.206    8.6059  -1.0264  -1.0852
 PVC  HPA2  H  HCH2  0   0.206    8.5595   0.7231  -1.1023
 PVC  HPB1  H  HCH2  0   0.206    9.9554   0.7832   0.9751
 PVC  HPB2  H  HCH2  0   0.206   10.0032  -0.9663   0.9957
 PVC  HPC1  H  HCH2  0   0.206   11.1490  -0.9633  -1.2295
 PVC  HPC2  H  HCH2  0   0.206   11.0953   0.7858  -1.2560
 PVC  HPD1  H  HCH2  0   0.206   12.4933   0.8608   0.8214
 PVC  HPD2  H  HCH2  0   0.206   12.5473  -0.8886   0.8482
 PVC  HC61  H  HCH2  0   0.244   -5.0409   0.8463   1.8927
 PVC  HC62  H  HCH2  0   0.246   -5.3144  -0.8404   1.4394
 PVC  HC5   H  HCH1  0   0.261   -6.1253  -0.1029  -0.8005
 PVC  HC4   H  HCH1  0   0.280   -7.6801  -0.5934   0.9986
 PVC  H2    H  HOH1  0   0.472  -10.8729   0.2154  -2.1556
 PVC  H3    H  HOH1  0   0.481   -9.6612   2.2929  -0.8605
 PVC  H4    H  HOH1  0   0.450   -7.6949   2.1384   1.6666
 PVC  H5    H  HOH1  0   0.449   -5.7530   2.4813   0.2535
 PVC  HC2   H  HOH1  0   0.488   -7.9525  -2.8957  -1.0247
 PVC  HPE1  H  HCH2  0   0.205   13.6864  -0.8868  -1.3834
 PVC  HPE2  H  HCH2  0   0.205   13.6350   0.8623  -1.4072
 PVC  HPF1  H  HCH2  0   0.210   15.0371   0.9297   0.6669
 PVC  HPF2  H  HCH2  0   0.210   15.0880  -0.8180   0.6887
 PVC  HPG1  H  HCH3  0   0.225   17.1669   0.0997  -0.3477
 PVC  HPG2  H  HCH3  0   0.215   16.2536  -0.8167  -1.5425
 PVC  HPG3  H  HCH3  0   0.216   16.2070   0.9437  -1.5596

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PVC  CP1  OP    double  1.205  0.020  1.205
 PVC  CP1  CP2   single  1.504  0.020  1.504
 PVC  CP1  O6    single  1.330  0.020  1.330
 PVC  CP2  CP3   single  1.520  0.020  1.520
 PVC  CP2  HP21  single  0.970  0.020  1.090
 PVC  CP2  HP22  single  0.970  0.020  1.090
 PVC  CP3  CP4   single  1.524  0.020  1.524
 PVC  CP3  HP31  single  0.970  0.020  1.090
 PVC  CP3  HP32  single  0.970  0.020  1.090
 PVC  CP4  CP5   single  1.523  0.020  1.523
 PVC  CP4  HP41  single  0.970  0.020  1.090
 PVC  CP4  HP42  single  0.970  0.020  1.090
 PVC  CP5  CP6   single  1.524  0.020  1.524
 PVC  CP5  HP51  single  0.970  0.020  1.090
 PVC  CP5  HP52  single  0.970  0.020  1.090
 PVC  CP6  CP7   single  1.524  0.020  1.524
 PVC  CP6  HP61  single  0.970  0.020  1.090
 PVC  CP6  HP62  single  0.970  0.020  1.090
 PVC  CP7  CP8   single  1.524  0.020  1.524
 PVC  CP7  HP71  single  0.970  0.020  1.090
 PVC  CP7  HP72  single  0.970  0.020  1.090
 PVC  CP8  CP9   single  1.524  0.020  1.524
 PVC  CP8  HP81  single  0.970  0.020  1.090
 PVC  CP8  HP82  single  0.970  0.020  1.090
 PVC  CP9  CPA   single  1.524  0.020  1.524
 PVC  CP9  HP91  single  0.970  0.020  1.090
 PVC  CP9  HP92  single  0.970  0.020  1.090
 PVC  CPA  CPB   single  1.524  0.020  1.524
 PVC  CPA  HPA1  single  0.970  0.020  1.090
 PVC  CPA  HPA2  single  0.970  0.020  1.090
 PVC  CPB  CPC   single  1.524  0.020  1.524
 PVC  CPB  HPB1  single  0.970  0.020  1.090
 PVC  CPB  HPB2  single  0.970  0.020  1.090
 PVC  CPC  CPD   single  1.524  0.020  1.524
 PVC  CPC  HPC1  single  0.970  0.020  1.090
 PVC  CPC  HPC2  single  0.970  0.020  1.090
 PVC  CPD  CPE   single  1.524  0.020  1.524
 PVC  CPD  HPD1  single  0.970  0.020  1.090
 PVC  CPD  HPD2  single  0.970  0.020  1.090
 PVC  CC6  CC5   single  1.519  0.020  1.519
 PVC  CC6  O6    single  1.427  0.020  1.427
 PVC  CC6  HC61  single  0.970  0.020  1.090
 PVC  CC6  HC62  single  0.970  0.020  1.090
 PVC  CC5  CC4   single  1.541  0.020  1.541
 PVC  CC5  O5    single  1.405  0.020  1.405
 PVC  CC5  HC5   single  0.970  0.020  1.090
 PVC  CC4  CC3   single  1.514  0.020  1.514
 PVC  CC4  O4    single  1.404  0.020  1.404
 PVC  CC4  HC4   single  0.970  0.020  1.090
 PVC  CC3  CC2   double  1.352  0.020  1.352
 PVC  CC3  O3    single  1.332  0.020  1.332
 PVC  CC2  CC1   single  1.462  0.020  1.462
 PVC  CC2  O2    single  1.374  0.020  1.374
 PVC  CC1  OC1   double  1.211  0.020  1.211
 PVC  CC1  OC2   single  1.329  0.020  1.329
 PVC  O2   H2    single  0.850  0.020  0.980
 PVC  O3   H3    single  0.850  0.020  0.980
 PVC  O4   H4    single  0.850  0.020  0.980
 PVC  O5   H5    single  0.850  0.020  0.980
 PVC  OC2  HC2   single  0.850  0.020  0.980
 PVC  CPE  CPF   single  1.524  0.020  1.524
 PVC  CPE  HPE1  single  0.970  0.020  1.090
 PVC  CPE  HPE2  single  0.970  0.020  1.090
 PVC  CPF  CPG   single  1.523  0.020  1.523
 PVC  CPF  HPF1  single  0.970  0.020  1.090
 PVC  CPF  HPF2  single  0.970  0.020  1.090
 PVC  CPG  HPG1  single  0.970  0.020  1.090
 PVC  CPG  HPG2  single  0.970  0.020  1.090
 PVC  CPG  HPG3  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PVC  O6    CP1  CP2   111.44  3.000
 PVC  O6    CP1  OP    123.14  3.000
 PVC  CP2   CP1  OP    125.42  3.000
 PVC  HP22  CP2  HP21  105.44  3.000
 PVC  HP22  CP2  CP3   110.66  3.000
 PVC  HP21  CP2  CP3   110.38  3.000
 PVC  HP22  CP2  CP1   108.57  3.000
 PVC  HP21  CP2  CP1   107.68  3.000
 PVC  CP3   CP2  CP1   113.74  3.000
 PVC  HP32  CP3  HP31  106.44  3.000
 PVC  HP32  CP3  CP4   109.38  3.000
 PVC  HP31  CP3  CP4   109.26  3.000
 PVC  HP32  CP3  CP2   109.98  3.000
 PVC  HP31  CP3  CP2   109.75  3.000
 PVC  CP4   CP3  CP2   111.88  3.000
 PVC  HP42  CP4  HP41  106.07  3.000
 PVC  HP42  CP4  CP5   109.30  3.000
 PVC  HP41  CP4  CP5   109.54  3.000
 PVC  HP42  CP4  CP3   109.49  3.000
 PVC  HP41  CP4  CP3   109.46  3.000
 PVC  CP5   CP4  CP3   112.77  3.000
 PVC  HP52  CP5  HP51  106.02  3.000
 PVC  HP52  CP5  CP6   109.38  3.000
 PVC  HP51  CP5  CP6   109.23  3.000
 PVC  HP52  CP5  CP4   109.46  3.000
 PVC  HP51  CP5  CP4   109.25  3.000
 PVC  CP6   CP5  CP4   113.24  3.000
 PVC  HP62  CP6  HP61  106.01  3.000
 PVC  HP62  CP6  CP7   109.27  3.000
 PVC  HP61  CP6  CP7   109.48  3.000
 PVC  HP62  CP6  CP5   109.28  3.000
 PVC  HP61  CP6  CP5   109.38  3.000
 PVC  CP7   CP6  CP5   113.16  3.000
 PVC  HP72  CP7  HP71  105.99  3.000
 PVC  HP72  CP7  CP8   109.35  3.000
 PVC  HP71  CP7  CP8   109.24  3.000
 PVC  HP72  CP7  CP6   109.44  3.000
 PVC  HP71  CP7  CP6   109.25  3.000
 PVC  CP8   CP7  CP6   113.31  3.000
 PVC  HP82  CP8  HP81  105.98  3.000
 PVC  HP82  CP8  CP9   109.29  3.000
 PVC  HP81  CP8  CP9   109.44  3.000
 PVC  HP82  CP8  CP7   109.27  3.000
 PVC  HP81  CP8  CP7   109.36  3.000
 PVC  CP9   CP8  CP7   113.24  3.000
 PVC  HP92  CP9  HP91  105.98  3.000
 PVC  HP92  CP9  CPA   109.33  3.000
 PVC  HP91  CP9  CPA   109.27  3.000
 PVC  HP92  CP9  CP8   109.42  3.000
 PVC  HP91  CP9  CP8   109.29  3.000
 PVC  CPA   CP9  CP8   113.30  3.000
 PVC  HPA2  CPA  HPA1  105.97  3.000
 PVC  HPA2  CPA  CPB   109.31  3.000
 PVC  HPA1  CPA  CPB   109.41  3.000
 PVC  HPA2  CPA  CP9   109.26  3.000
 PVC  HPA1  CPA  CP9   109.35  3.000
 PVC  CPB   CPA  CP9   113.28  3.000
 PVC  HPB2  CPB  HPB1  105.99  3.000
 PVC  HPB2  CPB  CPC   109.31  3.000
 PVC  HPB1  CPB  CPC   109.30  3.000
 PVC  HPB2  CPB  CPA   109.40  3.000
 PVC  HPB1  CPB  CPA   109.33  3.000
 PVC  CPC   CPB  CPA   113.26  3.000
 PVC  HPC2  CPC  HPC1  105.97  3.000
 PVC  HPC2  CPC  CPD   109.35  3.000
 PVC  HPC1  CPC  CPD   109.37  3.000
 PVC  HPC2  CPC  CPB   109.26  3.000
 PVC  HPC1  CPC  CPB   109.32  3.000
 PVC  CPD   CPC  CPB   113.32  3.000
 PVC  HPD2  CPD  HPD1  105.99  3.000
 PVC  HPD2  CPD  CPE   109.30  3.000
 PVC  HPD1  CPD  CPE   109.33  3.000
 PVC  HPD2  CPD  CPC   109.37  3.000
 PVC  HPD1  CPD  CPC   109.36  3.000
 PVC  CPE   CPD  CPC   113.23  3.000
 PVC  HC62  CC6  HC61  107.92  3.000
 PVC  HC62  CC6  O6    110.29  3.000
 PVC  HC61  CC6  O6    110.31  3.000
 PVC  HC62  CC6  CC5   110.04  3.000
 PVC  HC61  CC6  CC5   111.04  3.000
 PVC  O6    CC6  CC5   107.26  3.000
 PVC  HC5   CC5  O5    106.08  3.000
 PVC  HC5   CC5  CC4   107.26  3.000
 PVC  O5    CC5  CC4   112.39  3.000
 PVC  HC5   CC5  CC6   108.56  3.000
 PVC  O5    CC5  CC6   112.53  3.000
 PVC  CC4   CC5  CC6   109.76  3.000
 PVC  HC4   CC4  O4    105.61  3.000
 PVC  HC4   CC4  CC3   109.40  3.000
 PVC  O4    CC4  CC3   111.25  3.000
 PVC  HC4   CC4  CC5   107.92  3.000
 PVC  O4    CC4  CC5   112.66  3.000
 PVC  CC3   CC4  CC5   109.83  3.000
 PVC  O3    CC3  CC2   119.69  3.000
 PVC  O3    CC3  CC4   111.90  3.000
 PVC  CC2   CC3  CC4   128.36  3.000
 PVC  O2    CC2  CC1   115.14  3.000
 PVC  O2    CC2  CC3   116.01  3.000
 PVC  CC1   CC2  CC3   128.84  3.000
 PVC  OC2   CC1  OC1   122.93  3.000
 PVC  OC2   CC1  CC2   115.05  3.000
 PVC  OC1   CC1  CC2   122.02  3.000
 PVC  H2    O2   CC2   110.04  3.000
 PVC  H3    O3   CC3   109.48  3.000
 PVC  H4    O4   CC4   110.12  3.000
 PVC  H5    O5   CC5   109.86  3.000
 PVC  CC6   O6   CP1   117.90  3.000
 PVC  HC2   OC2  CC1   109.68  3.000
 PVC  HPE2  CPE  HPE1  105.94  3.000
 PVC  HPE2  CPE  CPF   109.30  3.000
 PVC  HPE1  CPE  CPF   109.27  3.000
 PVC  HPE2  CPE  CPD   109.32  3.000
 PVC  HPE1  CPE  CPD   109.34  3.000
 PVC  CPF   CPE  CPD   113.41  3.000
 PVC  HPF2  CPF  HPF1  106.01  3.000
 PVC  HPF2  CPF  CPG   109.62  3.000
 PVC  HPF1  CPF  CPG   109.64  3.000
 PVC  HPF2  CPF  CPE   109.28  3.000
 PVC  HPF1  CPF  CPE   109.33  3.000
 PVC  CPG   CPF  CPE   112.75  3.000
 PVC  HPG3  CPG  HPG2  107.54  3.000
 PVC  HPG3  CPG  HPG1  107.64  3.000
 PVC  HPG2  CPG  HPG1  107.60  3.000
 PVC  HPG3  CPG  CPF   111.07  3.000
 PVC  HPG2  CPG  CPF   111.05  3.000
 PVC  HPG1  CPG  CPF   111.74  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PVC  CONST_01  HC2   OC2  CC1  CC2   180.00   0.0  0
 PVC  Var_01    CC1   CC2  CC3  CC4     4.94   0.0  2
 PVC  Var_02    CP4   CP3  CP2  CP1   179.88  30.0  3
 PVC  Var_03    CC5   CC6  O6   CP1   175.10  30.0  1
 PVC  Var_04    CP3   CP2  CP1  OP     -8.24  30.0  3
 PVC  Var_05    CP5   CP4  CP3  CP2   178.55  30.0  3
 PVC  Var_06    CP6   CP5  CP4  CP3   179.90  30.0  3
 PVC  Var_07    CP7   CP6  CP5  CP4   178.25  30.0  3
 PVC  Var_08    CP8   CP7  CP6  CP5  -179.93  30.0  3
 PVC  Var_09    CP9   CP8  CP7  CP6   178.56  30.0  3
 PVC  Var_10    CPA   CP9  CP8  CP7  -179.97  30.0  3
 PVC  Var_11    CPB   CPA  CP9  CP8   179.07  30.0  3
 PVC  Var_12    CPC   CPB  CPA  CP9  -179.97  30.0  3
 PVC  Var_13    CPD   CPC  CPB  CPA   179.66  30.0  3
 PVC  Var_14    CPE   CPD  CPC  CPB  -179.98  30.0  3
 PVC  Var_15    CPF   CPE  CPD  CPC  -179.85  30.0  3
 PVC  Var_16    CPG   CPF  CPE  CPD  -179.97  30.0  3
 PVC  Var_17    OC1   CC1  CC2  CC3   174.67  30.0  2
 PVC  Var_18    HPG1  CPG  CPF  CPE  -179.72  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PVC  chir_01  CC5  CC6  CC4  O5   negativ
 PVC  chir_02  CC4  O4   CC5  CC3  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PVC  plan-1  CC2  0.020
 PVC  plan-1  CC1  0.020
 PVC  plan-1  OC1  0.020
 PVC  plan-1  OC2  0.020
 PVC  plan-1  HC2  0.020
 PVC  plan-2  CP1  0.020
 PVC  plan-2  OP   0.020
 PVC  plan-2  CP2  0.020
 PVC  plan-2  O6   0.020
 PVC  plan-3  CC4  0.020
 PVC  plan-3  CC3  0.020
 PVC  plan-3  CC2  0.020
 PVC  plan-3  CC1  0.020
 PVC  plan-3  O2   0.020
 PVC  plan-3  O3   0.020

