# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 23:36:31 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-({3-[({4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@@H](NC(=O)c1cccc(CNc2ccc(cc2)\C=C3/SC(=O)NC3=O)c1)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
 VSV  VSV  'N-({3-[({4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-D-glutamic acid'  ligand  53  34  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VSV
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
 VSV  OE1   O  OC    -1  -0.634    9.5761   2.4513   0.4367
 VSV  CD    C  C      0   0.412    9.2798   1.2374   0.4332
 VSV  OE2   O  O      0  -0.609   10.0628   0.2886   0.2291
 VSV  CG    C  CH2    0  -0.577    7.8008   0.9058   0.6989
 VSV  CB    C  CH2    0  -0.439    7.4664  -0.5729   0.8153
 VSV  C     C  C      0   0.414    5.7289  -2.3432   1.3806
 VSV  O     O  O     -1  -0.598    4.9839  -2.9396   0.5847
 VSV  OXT   O  OC     0  -0.618    6.3123  -2.8242   2.3728
 VSV  N     N  NH1    0  -0.629    5.1615  -0.2913   0.0861
 VSV  CAU   C  C      0   0.538    3.8740   0.0201   0.2751
 VSV  OBC   O  O      0  -0.502    3.3238  -0.0221   1.3699
 VSV  CAT   C  CR6    0  -0.021    3.1195   0.4708  -0.9387
 VSV  CAQ   C  CR16   0  -0.316    1.7346   0.3468  -0.9302
 VSV  CAS   C  CR16   0  -0.306    3.7453   1.0390  -2.0478
 VSV  CAR   C  CR16   0  -0.226    2.9902   1.4621  -3.1297
 VSV  CAP   C  CR16   0  -0.307    1.6087   1.3246  -3.1141
 VSV  CAO   C  CR6    0   0.094    0.9701   0.7622  -2.0150
 VSV  CAN   C  CH2    0  -0.329   -0.5260   0.5991  -1.9978
 VSV  NAY   N  NH1    0  -0.688   -1.0902   1.2140  -0.8193
 VSV  CAA   C  C      0   0.410   -2.3726   1.0631  -0.4203
 VSV  CAC   C  C1     0  -0.339   -2.8484   1.7856   0.6932
 VSV  CAE   C  C1     0  -0.281   -4.1377   1.6247   1.1320
 VSV  CAB   C  C1     0  -0.336   -3.2681   0.1898  -1.0675
 VSV  CAG   C  C1     0  -0.302   -4.5599   0.0414  -0.6126
 VSV  CAF   C  C      0   0.132   -5.0411   0.7494   0.4989
 VSV  CAH   C  C1     0  -0.248   -6.3709   0.6617   1.0365
 VSV  CAI   C  CR5    0  -0.332   -7.4536  -0.0392   0.6447
 VSV  SBG   S  S2     0   0.067   -7.6183  -1.1293  -0.7233
 VSV  CAL   C  CR5    0   0.427   -9.3208  -1.4455  -0.3423
 VSV  NAX   N  NR15   0  -0.684   -9.6742  -0.7382   0.7704
 VSV  CA    C  CH1    0  -0.200    5.9943  -0.8349   1.1351
 VSV  CAK   C  CR5    0   0.625   -8.7251   0.0557   1.3797
 VSV  OBE   O  O      0  -0.424   -8.9429   0.7187   2.3690
 VSV  OBH   O  O      0  -0.403  -10.0270  -2.1739  -0.9853
 VSV  HG1C  H  HCH2   0   0.216    7.4889   1.4233   1.6136
 VSV  HG2C  H  HCH2   0   0.222    7.2042   1.3642  -0.0978
 VSV  HB1C  H  HCH2   0   0.209    7.7383  -1.0944  -0.1084
 VSV  HB2C  H  HCH2   0   0.226    8.0636  -1.0281   1.6056
 VSV  HA    H  HCH1   0   0.232    5.7455  -0.3056   2.0580
 VSV  HB    H  HNH1   0   0.391    5.4770  -0.4406  -0.8593
 VSV  HAQ   H  HCR6   0   0.257    1.2478  -0.0847  -0.0644
 VSV  HAS   H  HCR6   0   0.257    4.8179   1.1855  -2.0684
 VSV  HAR   H  HCR6   0   0.265    3.4775   1.9148  -3.9827
 VSV  HAP   H  HCR6   0   0.261    1.0246   1.6666  -3.9597
 VSV  HAN1  H  HCH2   0   0.254   -0.9547   1.0166  -2.9160
 VSV  HAN2  H  HCH2   0   0.261   -0.7680  -0.4678  -1.9959
 VSV  HAY   H  HNH1   0   0.397   -0.5727   1.9789  -0.4164
 VSV  HAC   H  H      0   0.268   -2.1843   2.4694   1.2076
 VSV  HAB   H  H      0   0.278   -2.9569  -0.3726  -1.9370
 VSV  HAE   H  H      0   0.263   -4.4699   2.1897   1.9947
 VSV  HAG   H  H      0   0.256   -5.1910  -0.6495  -1.1541
 VSV  HAH   H  H      0   0.279   -6.5399   1.2734   1.9182
 VSV  HAX   H  HNR5   0   0.438  -10.6196  -0.7944   1.1289

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
 VSV  OE1  CD    deloc     1.250  0.020  1.250
 VSV  CD   OE2   deloc     1.247  0.020  1.247
 VSV  CD   CG    single    1.539  0.020  1.539
 VSV  CG   CB    single    1.520  0.020  1.520
 VSV  CB   CA    single    1.529  0.020  1.529
 VSV  C    O     deloc     1.243  0.020  1.243
 VSV  C    OXT   deloc     1.247  0.020  1.247
 VSV  C    CA    single    1.551  0.020  1.551
 VSV  N    CAU   single    1.338  0.020  1.338
 VSV  N    CA    single    1.446  0.020  1.446
 VSV  CAU  OBC   double    1.226  0.020  1.226
 VSV  CAU  CAT   single    1.499  0.020  1.499
 VSV  CAT  CAQ   aromatic  1.390  0.020  1.390
 VSV  CAT  CAS   aromatic  1.394  0.020  1.394
 VSV  CAQ  CAO   aromatic  1.391  0.020  1.391
 VSV  CAS  CAR   aromatic  1.386  0.020  1.386
 VSV  CAR  CAP   aromatic  1.388  0.020  1.388
 VSV  CAP  CAO   aromatic  1.390  0.020  1.390
 VSV  CAO  CAN   single    1.505  0.020  1.505
 VSV  CAN  NAY   single    1.444  0.020  1.444
 VSV  NAY  CAA   single    1.352  0.020  1.352
 VSV  CAA  CAC   aromatic  1.410  0.020  1.410
 VSV  CAA  CAB   aromatic  1.408  0.020  1.408
 VSV  CAC  CAE   aromatic  1.371  0.020  1.371
 VSV  CAE  CAF   aromatic  1.408  0.020  1.408
 VSV  CAB  CAG   aromatic  1.378  0.020  1.378
 VSV  CAG  CAF   aromatic  1.403  0.020  1.403
 VSV  CAF  CAH   single    1.437  0.020  1.437
 VSV  CAH  CAI   double    1.348  0.020  1.348
 VSV  CAI  SBG   single    1.757  0.020  1.757
 VSV  CAI  CAK   single    1.472  0.020  1.472
 VSV  SBG  CAL   single    1.773  0.020  1.773
 VSV  CAL  NAX   single    1.365  0.020  1.365
 VSV  CAL  OBH   double    1.201  0.020  1.201
 VSV  NAX  CAK   single    1.379  0.020  1.379
 VSV  CAK  OBE   double    1.211  0.020  1.211
 VSV  CG   HG1C  single    0.970  0.020  1.090
 VSV  CG   HG2C  single    0.970  0.020  1.090
 VSV  CB   HB1C  single    0.970  0.020  1.090
 VSV  CB   HB2C  single    0.970  0.020  1.090
 VSV  CA   HA    single    0.970  0.020  1.090
 VSV  N    HB    single    0.890  0.020  1.040
 VSV  CAQ  HAQ   single    0.930  0.020  1.080
 VSV  CAS  HAS   single    0.930  0.020  1.080
 VSV  CAR  HAR   single    0.930  0.020  1.080
 VSV  CAP  HAP   single    0.930  0.020  1.080
 VSV  CAN  HAN1  single    0.970  0.020  1.090
 VSV  CAN  HAN2  single    0.970  0.020  1.090
 VSV  NAY  HAY   single    0.860  0.020  1.020
 VSV  CAC  HAC   single    0.930  0.020  1.080
 VSV  CAB  HAB   single    0.930  0.020  1.080
 VSV  CAE  HAE   single    0.930  0.020  1.080
 VSV  CAG  HAG   single    0.930  0.020  1.080
 VSV  CAH  HAH   single    0.930  0.020  1.080
 VSV  NAX  HAX   single    0.860  0.020  1.020

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
 VSV  CG    CD   OE2   117.89  3.000
 VSV  CG    CD   OE1   115.90  3.000
 VSV  OE2   CD   OE1   126.21  3.000
 VSV  HG2C  CG   HG1C  104.73  3.000
 VSV  HG2C  CG   CB    110.04  3.000
 VSV  HG1C  CG   CB    109.43  3.000
 VSV  HG2C  CG   CD    107.92  3.000
 VSV  HG1C  CG   CD    108.41  3.000
 VSV  CB    CG   CD    115.73  3.000
 VSV  HB2C  CB   HB1C  106.06  3.000
 VSV  HB2C  CB   CA    107.71  3.000
 VSV  HB1C  CB   CA    109.51  3.000
 VSV  HB2C  CB   CG    109.94  3.000
 VSV  HB1C  CB   CG    110.12  3.000
 VSV  CA    CB   CG    113.23  3.000
 VSV  CA    C    OXT   114.89  3.000
 VSV  CA    C    O     117.90  3.000
 VSV  OXT   C    O     127.21  3.000
 VSV  HB    N    CA    116.40  3.000
 VSV  HB    N    CAU   117.92  3.000
 VSV  CA    N    CAU   122.64  3.000
 VSV  CAT   CAU  OBC   120.51  3.000
 VSV  CAT   CAU  N     116.10  3.000
 VSV  OBC   CAU  N     123.36  3.000
 VSV  CAS   CAT  CAQ   119.22  3.000
 VSV  CAS   CAT  CAU   122.74  3.000
 VSV  CAQ   CAT  CAU   118.01  3.000
 VSV  HAQ   CAQ  CAO   119.70  3.000
 VSV  HAQ   CAQ  CAT   119.22  3.000
 VSV  CAO   CAQ  CAT   121.07  3.000
 VSV  HAS   CAS  CAR   118.93  3.000
 VSV  HAS   CAS  CAT   120.99  3.000
 VSV  CAR   CAS  CAT   120.06  3.000
 VSV  HAR   CAR  CAP   119.91  3.000
 VSV  HAR   CAR  CAS   119.87  3.000
 VSV  CAP   CAR  CAS   120.22  3.000
 VSV  HAP   CAP  CAO   119.82  3.000
 VSV  HAP   CAP  CAR   119.78  3.000
 VSV  CAO   CAP  CAR   120.40  3.000
 VSV  CAN   CAO  CAP   120.64  3.000
 VSV  CAN   CAO  CAQ   120.35  3.000
 VSV  CAP   CAO  CAQ   119.02  3.000
 VSV  HAN2  CAN  HAN1  106.65  3.000
 VSV  HAN2  CAN  NAY   109.11  3.000
 VSV  HAN1  CAN  NAY   111.63  3.000
 VSV  HAN2  CAN  CAO   109.00  3.000
 VSV  HAN1  CAN  CAO   109.75  3.000
 VSV  NAY   CAN  CAO   110.58  3.000
 VSV  HAY   NAY  CAA   117.00  3.000
 VSV  HAY   NAY  CAN   116.67  3.000
 VSV  CAA   NAY  CAN   124.34  3.000
 VSV  CAB   CAA  CAC   117.78  3.000
 VSV  CAB   CAA  NAY   122.47  3.000
 VSV  CAC   CAA  NAY   119.74  3.000
 VSV  HAC   CAC  CAE   119.90  3.000
 VSV  HAC   CAC  CAA   119.45  3.000
 VSV  CAE   CAC  CAA   120.65  3.000
 VSV  HAE   CAE  CAF   119.04  3.000
 VSV  HAE   CAE  CAC   118.81  3.000
 VSV  CAF   CAE  CAC   122.15  3.000
 VSV  HAB   CAB  CAG   118.64  3.000
 VSV  HAB   CAB  CAA   120.61  3.000
 VSV  CAG   CAB  CAA   120.75  3.000
 VSV  HAG   CAG  CAF   121.28  3.000
 VSV  HAG   CAG  CAB   116.79  3.000
 VSV  CAF   CAG  CAB   121.93  3.000
 VSV  CAH   CAF  CAG   125.66  3.000
 VSV  CAH   CAF  CAE   117.61  3.000
 VSV  CAG   CAF  CAE   116.74  3.000
 VSV  HAH   CAH  CAI   113.81  3.000
 VSV  HAH   CAH  CAF   114.40  3.000
 VSV  CAI   CAH  CAF   131.78  3.000
 VSV  CAK   CAI  SBG   110.35  3.000
 VSV  CAK   CAI  CAH   121.02  3.000
 VSV  SBG   CAI  CAH   128.62  3.000
 VSV  CAL   SBG  CAI    91.91  3.000
 VSV  OBH   CAL  NAX   126.76  3.000
 VSV  OBH   CAL  SBG   123.89  3.000
 VSV  NAX   CAL  SBG   109.35  3.000
 VSV  HAX   NAX  CAK   121.19  3.000
 VSV  HAX   NAX  CAL   120.10  3.000
 VSV  CAK   NAX  CAL   118.70  3.000
 VSV  HA    CA   N     107.43  3.000
 VSV  HA    CA   C     107.36  3.000
 VSV  N     CA   C     112.45  3.000
 VSV  HA    CA   CB    108.24  3.000
 VSV  N     CA   CB    109.78  3.000
 VSV  C     CA   CB    111.38  3.000
 VSV  OBE   CAK  NAX   123.54  3.000
 VSV  OBE   CAK  CAI   126.78  3.000
 VSV  NAX   CAK  CAI   109.68  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
 VSV  CONST_01  CAP  CAO  CAQ  CAT     0.00   0.0  0
 VSV  CONST_02  CAP  CAR  CAS  CAT     0.00   0.0  0
 VSV  CONST_03  CAR  CAS  CAT  CAQ     0.00   0.0  0
 VSV  CONST_04  CAR  CAP  CAO  CAQ     0.00   0.0  0
 VSV  CONST_05  CAO  CAQ  CAT  CAS     0.00   0.0  0
 VSV  CONST_06  CAO  CAP  CAR  CAS     0.00   0.0  0
 VSV  CONST_07  CAF  CAE  CAC  CAA     0.00   0.0  0
 VSV  CONST_08  CAF  CAG  CAB  CAA     0.00   0.0  0
 VSV  CONST_09  CAG  CAB  CAA  CAC     0.00   0.0  0
 VSV  CONST_10  CAG  CAF  CAE  CAC     0.00   0.0  0
 VSV  CONST_11  CAB  CAA  CAC  CAE     0.00   0.0  0
 VSV  CONST_12  CAB  CAG  CAF  CAE     0.00   0.0  0
 VSV  CONST_13  CAL  NAX  CAK  CAI     0.00   0.0  0
 VSV  CONST_14  CAO  CAQ  CAT  CAU   180.00   0.0  0
 VSV  CONST_15  CAR  CAS  CAT  CAU   180.00   0.0  0
 VSV  CONST_16  CAN  CAO  CAQ  CAT   180.00   0.0  0
 VSV  CONST_17  CAN  CAO  CAP  CAR   180.00   0.0  0
 VSV  CONST_18  CAE  CAC  CAA  NAY   180.00   0.0  0
 VSV  CONST_19  CAG  CAB  CAA  NAY   180.00   0.0  0
 VSV  CONST_20  CAH  CAF  CAE  CAC   180.00   0.0  0
 VSV  CONST_21  CAH  CAF  CAG  CAB   180.00   0.0  0
 VSV  CONST_22  OBE  CAK  NAX  CAL   180.00   0.0  0
 VSV  CONST_23  HAR  CAR  CAS  CAT   180.00   0.0  0
 VSV  CONST_24  HAS  CAS  CAT  CAQ   180.00   0.0  0
 VSV  CONST_25  HAP  CAP  CAO  CAQ   180.00   0.0  0
 VSV  CONST_26  HAQ  CAQ  CAT  CAS   180.00   0.0  0
 VSV  CONST_27  HAE  CAE  CAC  CAA   180.00   0.0  0
 VSV  CONST_28  HAG  CAG  CAB  CAA   180.00   0.0  0
 VSV  CONST_29  HAB  CAB  CAA  CAC   180.00   0.0  0
 VSV  CONST_30  HAC  CAC  CAA  CAB   180.00   0.0  0
 VSV  CONST_31  HAX  NAX  CAK  CAI   180.00   0.0  0
 VSV  CONST_32  CAC  CAA  NAY  CAN   180.00   0.0  0
 VSV  CONST_33  CAB  CAA  NAY  CAN     0.00   0.0  0
 VSV  CONST_34  HAY  NAY  CAA  CAC     0.00   0.0  0
 VSV  CONST_35  CA   N    CAU  CAT   180.00   0.0  0
 VSV  CONST_37  CA   N    CAU  OBC     0.00   0.0  0
 VSV  Var_01    CAI  CAH  CAF  CAE   177.96  30.0  2
 VSV  Var_02    SBG  CAI  CAH  CAF    -0.30  30.0  2
 VSV  Var_03    CAQ  CAT  CAU  N     157.39  30.0  2
 VSV  Var_04    NAY  CAN  CAO  CAQ    54.23  30.0  2
 VSV  Var_05    CAA  NAY  CAN  CAO  -169.64  30.0  3
 VSV  Var_06    CB   CG   CD   OE1  -174.84  30.0  3
 VSV  Var_07    CA   CB   CG   CD    177.66  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
 VSV  chir_01  CA  CB  C  N  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
 VSV  plan-1  CAH  0.020
 VSV  plan-1  CAI  0.020
 VSV  plan-1  SBG  0.020
 VSV  plan-1  CAL  0.020
 VSV  plan-1  NAX  0.020
 VSV  plan-1  CAK  0.020
 VSV  plan-1  OBE  0.020
 VSV  plan-1  OBH  0.020
 VSV  plan-1  HAX  0.020
 VSV  plan-2  CAU  0.020
 VSV  plan-2  CAT  0.020
 VSV  plan-2  CAQ  0.020
 VSV  plan-2  CAS  0.020
 VSV  plan-2  CAR  0.020
 VSV  plan-2  CAP  0.020
 VSV  plan-2  CAO  0.020
 VSV  plan-2  CAN  0.020
 VSV  plan-2  HAQ  0.020
 VSV  plan-2  HAS  0.020
 VSV  plan-2  HAR  0.020
 VSV  plan-2  HAP  0.020
 VSV  plan-3  NAY  0.020
 VSV  plan-3  CAA  0.020
 VSV  plan-3  CAC  0.020
 VSV  plan-3  CAE  0.020
 VSV  plan-3  CAB  0.020
 VSV  plan-3  CAG  0.020
 VSV  plan-3  CAF  0.020
 VSV  plan-3  CAH  0.020
 VSV  plan-3  HAC  0.020
 VSV  plan-3  HAB  0.020
 VSV  plan-3  HAE  0.020
 VSV  plan-3  HAG  0.020
 VSV  plan-4  N    0.020
 VSV  plan-4  CAU  0.020
 VSV  plan-4  OBC  0.020
 VSV  plan-4  CAT  0.020
 VSV  plan-4  CA   0.020
 VSV  plan-4  HB   0.020
 VSV  plan-5  CAN  0.020
 VSV  plan-5  NAY  0.020
 VSV  plan-5  CAA  0.020
 VSV  plan-5  HAY  0.020
 VSV  plan-6  OE1  0.020
 VSV  plan-6  CD   0.020
 VSV  plan-6  OE2  0.020
 VSV  plan-6  CG   0.020
 VSV  plan-7  C    0.020
 VSV  plan-7  O    0.020
 VSV  plan-7  OXT  0.020
 VSV  plan-7  CA   0.020

