# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:03:17 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N~2~-{[(1S)-1-carboxy-3-(methylsulfanyl)propyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NC(=O)N[C@@H](CCCCNC(=O)c1ccc(I)cc1)C(O)=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
 JRG  JRG  N~2~-{[(1S)-1-carboxy-3-(methylsulfanyl)propyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine  ligand  56  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JRG
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
 JRG  C     C  C     0   0.541  -4.4373   3.6250   0.6757
 JRG  N     N  NH1   0  -0.682  -4.4021   1.1945   0.4804
 JRG  O     O  O     0  -0.435  -5.1701   3.7524  -0.2701
 JRG  CA    C  CH1   0  -0.179  -3.7423   2.3277   1.0630
 JRG  CB    C  CH2   0  -0.464  -2.2723   2.3726   0.6326
 JRG  CAA   C  CH3   0  -0.763  -9.2354  -1.4254  -4.2824
 JRG  OAC   O  OH1   0  -0.591  -8.4373  -1.5286   2.6550
 JRG  OAD   O  O     0  -0.535  -6.2206   1.4206   1.8143
 JRG  OAE   O  O     0  -0.488   2.5382  -2.0927   0.4434
 JRG  OAG   O  O     0  -0.433  -6.2245  -1.7621   2.4532
 JRG  CAI   C  CR16  0  -0.213   6.6651  -1.3296   0.1101
 JRG  CAJ   C  CR16  0  -0.210   6.0685   0.8504  -0.7433
 JRG  CAK   C  CR16  0  -0.260   5.3320  -1.5721   0.4004
 JRG  CAL   C  CR16  0  -0.279   4.7396   0.5987  -0.4334
 JRG  CAM   C  CH2   0  -0.459  -0.0163   1.2431   0.7006
 JRG  CAN   C  CH2   0  -0.420  -1.4920   1.1372   1.0634
 JRG  CAO   C  CH2   0  -0.248   0.7460  -0.0123   1.0939
 JRG  CAR   C  CH2   0  -0.469  -8.0068  -1.7508  -0.3340
 JRG  NAS   N  NH1   0  -0.650   2.1515   0.1102   0.7690
 JRG  NAU   N  NH1   0  -0.683  -6.2392  -0.1567   0.1860
 JRG  SAV   S  S2    0  -0.039  -9.0315  -2.3938  -2.7726
 JRG  CAX   C  C     0   0.541  -7.2817  -1.3829   2.0224
 JRG  CAY   C  C     0   0.768  -5.6548   0.8572   0.8858
 JRG  CAZ   C  C     0   0.527   2.9354  -0.9351   0.4671
 JRG  CBA   C  CR6   0  -0.223   7.0224  -0.1162  -0.4621
 JRG  CBB   C  CR6   0  -0.034   4.3604  -0.6085   0.1465
 JRG  CBD   C  CH1   0  -0.175  -7.4700  -0.7190   0.6643
 JRG  OXT   O  OH1   0  -0.593  -4.1059   4.6145   1.4942
 JRG  HN    H  HNH1  0   0.399  -4.0850   0.8857  -0.4258
 JRG  HA    H  HCH1  0   0.283  -3.7750   2.2403   2.1523
 JRG  HB    H  HCH2  0   0.245  -2.2103   2.4939  -0.4540
 JRG  HBA   H  HCH2  0   0.259  -1.8112   3.2607   1.0696
 JRG  HAA   H  HCH3  0   0.262  -9.9017  -0.5795  -4.1210
 JRG  HAAA  H  HCH3  0   0.262  -8.2768  -1.0660  -4.6536
 JRG  HAAB  H  HCH3  0   0.275  -9.6774  -2.0774  -5.0337
 JRG  HOAC  H  HOH1  0   0.485  -8.3058  -2.0007   3.4909
 JRG  HAI   H  HCR6  0   0.284   7.4065  -2.0854   0.3296
 JRG  HAJ   H  HCR6  0   0.286   6.3403   1.7901  -1.2035
 JRG  HAK   H  HCR6  0   0.272   5.0511  -2.5204   0.8385
 JRG  HAL   H  HCR6  0   0.270   4.0037   1.3538  -0.6786
 JRG  HAM   H  HCH2  0   0.234   0.0918   1.4086  -0.3752
 JRG  HAMA  H  HCH2  0   0.231   0.4212   2.1144   1.1988
 JRG  HAN   H  HCH2  0   0.229  -1.5959   1.0009   2.1444
 JRG  HANA  H  HCH2  0   0.230  -1.9142   0.2429   0.5980
 JRG  HAO   H  HCH2  0   0.235   0.6181  -0.2083   2.1637
 JRG  HAOA  H  HCH2  0   0.244   0.3424  -0.8737   0.5622
 JRG  HAP   H  HCH2  0   0.266  -9.0249  -0.3056  -1.5735
 JRG  HAPA  H  HCH2  0   0.267  -7.4121  -0.7305  -2.1542
 JRG  HAR   H  HCH2  0   0.273  -8.9160  -2.1937   0.0762
 JRG  HARA  H  HCH2  0   0.259  -7.2822  -2.5619  -0.4491
 JRG  HNAS  H  HNH1  0   0.405   2.5839   1.0024   0.9499
 JRG  HNAU  H  HNH1  0   0.397  -5.6426  -0.7597  -0.3599
 JRG  HBD   H  HCH1  0   0.288  -8.2145   0.0741   0.7717
 JRG  HOXT  H  HOH1  0   0.483  -4.5220   5.4407   1.2059
 JRG  IAH   I  I     0   0.068   9.0395   0.2580  -0.9169
 JRG  CAP   C  CH2   0  -0.542  -8.3148  -1.1277  -1.6879

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
 JRG  CA   C     single    1.522  0.020  1.522
 JRG  C    O     double    1.203  0.020  1.203
 JRG  C    OXT   single    1.326  0.020  1.326
 JRG  CAY  N     single    1.359  0.020  1.359
 JRG  N    CA    single    1.435  0.020  1.435
 JRG  N    HN    single    0.890  0.020  1.040
 JRG  CB   CA    single    1.532  0.020  1.532
 JRG  CA   HA    single    0.970  0.020  1.090
 JRG  CB   CAN   single    1.523  0.020  1.523
 JRG  CB   HB    single    0.970  0.020  1.090
 JRG  CB   HBA   single    0.970  0.020  1.090
 JRG  CAA  SAV   single    1.805  0.020  1.805
 JRG  CAA  HAA   single    0.970  0.020  1.090
 JRG  CAA  HAAA  single    0.970  0.020  1.090
 JRG  CAA  HAAB  single    0.970  0.020  1.090
 JRG  CAX  OAC   single    1.325  0.020  1.325
 JRG  OAC  HOAC  single    0.850  0.020  0.980
 JRG  OAD  CAY   double    1.225  0.020  1.225
 JRG  OAE  CAZ   double    1.224  0.020  1.224
 JRG  OAG  CAX   double    1.203  0.020  1.203
 JRG  CBA  IAH   single    2.101  0.020  2.101
 JRG  CAK  CAI   aromatic  1.386  0.020  1.386
 JRG  CAI  CBA   aromatic  1.388  0.020  1.388
 JRG  CAI  HAI   single    0.930  0.020  1.080
 JRG  CAL  CAJ   aromatic  1.388  0.020  1.388
 JRG  CAJ  CBA   aromatic  1.387  0.020  1.387
 JRG  CAJ  HAJ   single    0.930  0.020  1.080
 JRG  CBB  CAK   aromatic  1.392  0.020  1.392
 JRG  CAK  HAK   single    0.930  0.020  1.080
 JRG  CBB  CAL   aromatic  1.392  0.020  1.392
 JRG  CAL  HAL   single    0.930  0.020  1.080
 JRG  CAM  CAO   single    1.521  0.020  1.521
 JRG  CAM  CAN   single    1.523  0.020  1.523
 JRG  CAM  HAM   single    0.970  0.020  1.090
 JRG  CAM  HAMA  single    0.970  0.020  1.090
 JRG  CAN  HAN   single    0.970  0.020  1.090
 JRG  CAN  HANA  single    0.970  0.020  1.090
 JRG  CAO  NAS   single    1.448  0.020  1.448
 JRG  CAO  HAO   single    0.970  0.020  1.090
 JRG  CAO  HAOA  single    0.970  0.020  1.090
 JRG  SAV  CAP   single    1.815  0.020  1.815
 JRG  CAP  CAR   single    1.522  0.020  1.522
 JRG  CAP  HAP   single    0.970  0.020  1.090
 JRG  CAP  HAPA  single    0.970  0.020  1.090
 JRG  CAR  CBD   single    1.533  0.020  1.533
 JRG  CAR  HAR   single    0.970  0.020  1.090
 JRG  CAR  HARA  single    0.970  0.020  1.090
 JRG  NAS  CAZ   single    1.341  0.020  1.341
 JRG  NAS  HNAS  single    0.860  0.020  1.020
 JRG  CBD  NAU   single    1.435  0.020  1.435
 JRG  NAU  CAY   single    1.364  0.020  1.364
 JRG  NAU  HNAU  single    0.890  0.020  1.040
 JRG  CAX  CBD   single    1.523  0.020  1.523
 JRG  CAZ  CBB   single    1.497  0.020  1.497
 JRG  CBD  HBD   single    0.970  0.020  1.090
 JRG  OXT  HOXT  single    0.850  0.020  0.980

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
 JRG  OXT   C    CA    111.40  3.000
 JRG  OXT   C    O     123.94  3.000
 JRG  CA    C    O     124.64  3.000
 JRG  HN    N    CAY   118.80  3.000
 JRG  HN    N    CA    117.53  3.000
 JRG  CAY   N    CA    119.91  3.000
 JRG  HA    CA   CB    108.11  3.000
 JRG  HA    CA   N     109.13  3.000
 JRG  CB    CA   N     110.50  3.000
 JRG  HA    CA   C     107.94  3.000
 JRG  CB    CA   C     109.98  3.000
 JRG  N     CA   C     111.09  3.000
 JRG  HBA   CB   HB    106.45  3.000
 JRG  HBA   CB   CAN   109.27  3.000
 JRG  HB    CB   CAN   109.96  3.000
 JRG  HBA   CB   CA    108.46  3.000
 JRG  HB    CB   CA    109.65  3.000
 JRG  CAN   CB   CA    112.84  3.000
 JRG  HAAB  CAA  HAAA  108.66  3.000
 JRG  HAAB  CAA  HAA   108.61  3.000
 JRG  HAAA  CAA  HAA   109.44  3.000
 JRG  HAAB  CAA  SAV   107.57  3.000
 JRG  HAAA  CAA  SAV   111.27  3.000
 JRG  HAA   CAA  SAV   111.22  3.000
 JRG  HOAC  OAC  CAX   110.30  3.000
 JRG  HAI   CAI  CBA   121.21  3.000
 JRG  HAI   CAI  CAK   119.66  3.000
 JRG  CBA   CAI  CAK   119.13  3.000
 JRG  HAJ   CAJ  CBA   121.28  3.000
 JRG  HAJ   CAJ  CAL   119.58  3.000
 JRG  CBA   CAJ  CAL   119.14  3.000
 JRG  HAK   CAK  CBB   119.97  3.000
 JRG  HAK   CAK  CAI   119.21  3.000
 JRG  CBB   CAK  CAI   120.81  3.000
 JRG  HAL   CAL  CBB   120.94  3.000
 JRG  HAL   CAL  CAJ   118.29  3.000
 JRG  CBB   CAL  CAJ   120.75  3.000
 JRG  HAMA  CAM  HAM   106.72  3.000
 JRG  HAMA  CAM  CAO   109.82  3.000
 JRG  HAM   CAM  CAO   109.25  3.000
 JRG  HAMA  CAM  CAN   109.51  3.000
 JRG  HAM   CAM  CAN   109.91  3.000
 JRG  CAO   CAM  CAN   111.51  3.000
 JRG  HANA  CAN  HAN   106.37  3.000
 JRG  HANA  CAN  CAM   109.25  3.000
 JRG  HAN   CAN  CAM   109.63  3.000
 JRG  HANA  CAN  CB    110.20  3.000
 JRG  HAN   CAN  CB    109.37  3.000
 JRG  CAM   CAN  CB    111.87  3.000
 JRG  HAOA  CAO  HAO   106.97  3.000
 JRG  HAOA  CAO  NAS   108.48  3.000
 JRG  HAO   CAO  NAS   110.35  3.000
 JRG  HAOA  CAO  CAM   109.92  3.000
 JRG  HAO   CAO  CAM   109.99  3.000
 JRG  NAS   CAO  CAM   111.03  3.000
 JRG  HARA  CAR  HAR   106.89  3.000
 JRG  HARA  CAR  CBD   109.62  3.000
 JRG  HAR   CAR  CBD   108.67  3.000
 JRG  HARA  CAR  CAP   110.13  3.000
 JRG  HAR   CAR  CAP   109.39  3.000
 JRG  CBD   CAR  CAP   112.00  3.000
 JRG  HNAS  NAS  CAZ   118.67  3.000
 JRG  HNAS  NAS  CAO   116.82  3.000
 JRG  CAZ   NAS  CAO   123.51  3.000
 JRG  HNAU  NAU  CBD   116.96  3.000
 JRG  HNAU  NAU  CAY   117.95  3.000
 JRG  CBD   NAU  CAY   119.20  3.000
 JRG  CAP   SAV  CAA    99.80  3.000
 JRG  CBD   CAX  OAG   124.42  3.000
 JRG  CBD   CAX  OAC   111.44  3.000
 JRG  OAG   CAX  OAC   124.10  3.000
 JRG  NAU   CAY  OAD   122.22  3.000
 JRG  NAU   CAY  N     115.25  3.000
 JRG  OAD   CAY  N     122.53  3.000
 JRG  CBB   CAZ  NAS   115.76  3.000
 JRG  CBB   CAZ  OAE   120.74  3.000
 JRG  NAS   CAZ  OAE   123.50  3.000
 JRG  CAJ   CBA  CAI   121.05  3.000
 JRG  CAJ   CBA  IAH   119.49  3.000
 JRG  CAI   CBA  IAH   119.46  3.000
 JRG  CAZ   CBB  CAL   122.54  3.000
 JRG  CAZ   CBB  CAK   118.33  3.000
 JRG  CAL   CBB  CAK   119.10  3.000
 JRG  HBD   CBD  CAX   108.23  3.000
 JRG  HBD   CBD  NAU   109.42  3.000
 JRG  CAX   CBD  NAU   111.21  3.000
 JRG  HBD   CBD  CAR   108.29  3.000
 JRG  CAX   CBD  CAR   109.30  3.000
 JRG  NAU   CBD  CAR   110.31  3.000
 JRG  HOXT  OXT  C     110.20  3.000
 JRG  HAPA  CAP  HAP   107.98  3.000
 JRG  HAPA  CAP  SAV   108.98  3.000
 JRG  HAP   CAP  SAV   109.33  3.000
 JRG  HAPA  CAP  CAR   111.21  3.000
 JRG  HAP   CAP  CAR   110.28  3.000
 JRG  SAV   CAP  CAR   109.02  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
 JRG  CONST_01  CAL   CBB  CAK  CAI     0.00   0.0  0
 JRG  CONST_02  CAL   CAJ  CBA  CAI     0.00   0.0  0
 JRG  CONST_03  CAK   CBB  CAL  CAJ     0.00   0.0  0
 JRG  CONST_04  CAK   CAI  CBA  CAJ     0.00   0.0  0
 JRG  CONST_05  CBB   CAK  CAI  CBA     0.00   0.0  0
 JRG  CONST_06  CBB   CAL  CAJ  CBA     0.00   0.0  0
 JRG  CONST_07  CAK   CAI  CBA  IAH   180.00   0.0  0
 JRG  CONST_08  CAL   CAJ  CBA  IAH   180.00   0.0  0
 JRG  CONST_09  CAZ   CBB  CAK  CAI   180.00   0.0  0
 JRG  CONST_10  CAZ   CBB  CAL  CAJ   180.00   0.0  0
 JRG  CONST_11  HAJ   CAJ  CBA  CAI   180.00   0.0  0
 JRG  CONST_12  HAI   CAI  CBA  CAJ   180.00   0.0  0
 JRG  CONST_13  HAL   CAL  CBB  CAK   180.00   0.0  0
 JRG  CONST_14  HAK   CAK  CBB  CAL   180.00   0.0  0
 JRG  CONST_15  CBB   CAZ  NAS  CAO   180.00   0.0  0
 JRG  CONST_16  HNAS  NAS  CAZ  CBB     0.00   0.0  0
 JRG  CONST_17  OAD   CAY  N    CA      0.00   0.0  0
 JRG  CONST_18  CBD   NAU  CAY  OAD     0.00   0.0  0
 JRG  CONST_19  CAO   NAS  CAZ  OAE     0.00   0.0  0
 JRG  CONST_20  CBD   NAU  CAY  N     180.00   0.0  0
 JRG  CONST_21  NAU   CAY  N    CA    180.00   0.0  0
 JRG  CONST_24  HOXT  OXT  C    O       0.00   0.0  0
 JRG  CONST_25  HOAC  OAC  CAX  OAG     0.00   0.0  0
 JRG  Var_01    CAK   CBB  CAZ  OAE   -28.12  30.0  2
 JRG  Var_02    CAM   CAN  CB   CA   -176.47  30.0  3
 JRG  Var_03    CAO   CAM  CAN  CB   -178.17  30.0  1
 JRG  Var_04    CAR   CAP  SAV  CAA  -178.03  30.0  3
 JRG  Var_05    CAZ   NAS  CAO  CAM  -150.95  30.0  3
 JRG  Var_06    NAS   CAO  CAM  CAN  -178.84  30.0  3
 JRG  Var_07    CBD   CAR  CAP  SAV  -176.78  30.0  3
 JRG  Var_08    HAA   CAA  SAV  CAP   -60.62  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
 JRG  chir_01  CA   C    N    CB   negativ
 JRG  chir_02  CBD  NAU  CAR  CAX  negativ

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
 JRG  plan-1  CAI   0.020
 JRG  plan-1  CAJ   0.020
 JRG  plan-1  CAK   0.020
 JRG  plan-1  CAL   0.020
 JRG  plan-1  CAZ   0.020
 JRG  plan-1  CBA   0.020
 JRG  plan-1  CBB   0.020
 JRG  plan-1  HAI   0.020
 JRG  plan-1  HAJ   0.020
 JRG  plan-1  HAK   0.020
 JRG  plan-1  HAL   0.020
 JRG  plan-1  IAH   0.020
 JRG  plan-2  N     0.020
 JRG  plan-2  CA    0.020
 JRG  plan-2  OAD   0.020
 JRG  plan-2  NAU   0.020
 JRG  plan-2  CAY   0.020
 JRG  plan-2  CBD   0.020
 JRG  plan-2  HN    0.020
 JRG  plan-2  HNAU  0.020
 JRG  plan-3  OAE   0.020
 JRG  plan-3  CAO   0.020
 JRG  plan-3  NAS   0.020
 JRG  plan-3  CAZ   0.020
 JRG  plan-3  CBB   0.020
 JRG  plan-3  HNAS  0.020
 JRG  plan-4  C     0.020
 JRG  plan-4  O     0.020
 JRG  plan-4  CA    0.020
 JRG  plan-4  OXT   0.020
 JRG  plan-4  HOXT  0.020
 JRG  plan-5  OAC   0.020
 JRG  plan-5  OAG   0.020
 JRG  plan-5  CAX   0.020
 JRG  plan-5  CBD   0.020
 JRG  plan-5  HOAC  0.020

