# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:36:44 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  54  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   0.404   -4.2690   3.5634  -0.0915
 JRG  N     N  NH1    0  -0.672   -4.3085   1.1085   0.4075
 JRG  O     O  O      0  -0.603   -5.0101   3.3108  -1.0578
 JRG  CA    C  CH1    0  -0.179   -3.6495   2.3669   0.6725
 JRG  CB    C  CH2    0  -0.454   -2.1647   2.2518   0.3294
 JRG  CAA   C  CH3    0  -0.763   -9.4798  -1.4972  -4.0604
 JRG  OAD   O  O      0  -0.557   -6.1614   1.6707   1.5954
 JRG  CAI   C  CR16   0  -0.212    6.3244  -1.3323  -0.7808
 JRG  CAJ   C  CR16   0  -0.210    6.3164   0.8185   0.3177
 JRG  CAK   C  CR16   0  -0.262    4.9541  -1.4230  -0.5953
 JRG  CAL   C  CR16   0  -0.284    4.9466   0.7064   0.5086
 JRG  CAM   C  CH2    0  -0.427    0.0685   1.1591   0.7924
 JRG  CAN   C  CH2    0  -0.414   -1.4244   1.1629   1.0968
 JRG  CAO   C  CH2    0  -0.281    0.8023   0.0533   1.5417
 JRG  CAR   C  CH2    0  -0.460   -8.0813  -1.6695  -0.1501
 JRG  NAS   N  NH1    0  -0.645    2.2275   0.0397   1.2844
 JRG  NAU   N  NH1    0  -0.674   -6.2497  -0.1059   0.1817
 JRG  SAV   S  S2     0  -0.051   -9.2323  -2.4028  -2.5179
 JRG  CAX   C  C      0   0.407   -7.2446  -1.2423   2.1832
 JRG  CAY   C  C      0   0.741   -5.6077   0.9394   0.7815
 JRG  CAZ   C  C      0   0.528    2.7734  -0.5704   0.2233
 JRG  CBA   C  CR6    0  -0.223    6.9961  -0.2078  -0.3209
 JRG  CBB   C  CR6    0  -0.027    4.2542  -0.4161   0.0635
 JRG  CBD   C  CH1    0  -0.180   -7.4595  -0.6243   0.7775
 JRG  OXT   O  OC    -1  -0.623   -3.9306   4.6917   0.3224
 JRG  HN    H  HNH1   0   0.369   -4.0292   0.6518  -0.4483
 JRG  HA    H  HCH1   0   0.222   -3.7282   2.5716   1.7441
 JRG  HB    H  HCH2   0   0.216   -2.0502   2.0807  -0.7480
 JRG  HBA   H  HCH2   0   0.231   -1.7013   3.2184   0.5372
 JRG  HAA   H  HCH3   0   0.259  -10.1214  -0.6303  -3.9091
 JRG  HAAA  H  HCH3   0   0.259   -8.5302  -1.1727  -4.4838
 JRG  HAAB  H  HCH3   0   0.271   -9.9640  -2.1693  -4.7666
 JRG  HAI   H  HCR6   0   0.284    6.8499  -2.1337  -1.2814
 JRG  HAJ   H  HCR6   0   0.286    6.8315   1.7032   0.6653
 JRG  HAK   H  HCR6   0   0.271    4.4304  -2.2950  -0.9633
 JRG  HAL   H  HCR6   0   0.270    4.4307   1.5275   0.9901
 JRG  HAM   H  HCH2   0   0.224    0.2251   1.0300  -0.2825
 JRG  HAMA  H  HCH2   0   0.220    0.5045   2.1261   1.0606
 JRG  HAN   H  HCH2   0   0.212   -1.5806   1.3083   2.1713
 JRG  HANA  H  HCH2   0   0.219   -1.8458   0.1828   0.8563
 JRG  HAO   H  HCH2   0   0.248    0.6685   0.1767   2.6169
 JRG  HAOA  H  HCH2   0   0.239    0.3845  -0.9198   1.2788
 JRG  HAP   H  HCH2   0   0.255   -9.1158  -0.2642  -1.4222
 JRG  HAPA  H  HCH2   0   0.259   -7.5407  -0.7638  -2.0434
 JRG  HAR   H  HCH2   0   0.247   -8.9816  -2.0522   0.3333
 JRG  HARA  H  HCH2   0   0.232   -7.3974  -2.5179  -0.2604
 JRG  HNAS  H  HNH1   0   0.409    2.8211   0.5220   1.9384
 JRG  HNAU  H  HNH1   0   0.368   -5.6535  -0.8041  -0.2373
 JRG  HBD   H  HCH1   0   0.229   -8.1733   0.1982   0.8746
 JRG  CAP   C  CH2    0  -0.536   -8.4332  -1.1117  -1.5210
 JRG  IAH   I  I      0   0.067    9.0725  -0.0542  -0.6047
 JRG  OAC   O  OC    -1  -0.620   -8.2875  -1.4511   2.8361
 JRG  OAE   O  O      0  -0.490    2.1255  -1.2354  -0.5749
 JRG  OAG   O  O      0  -0.599   -6.0781  -1.5024   2.5248

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    1.549  0.020  1.549
 JRG  C    O     deloc     1.244  0.020  1.244
 JRG  C    OXT   deloc     1.249  0.020  1.249
 JRG  CAY  N     single    1.363  0.020  1.363
 JRG  N    CA    single    1.445  0.020  1.445
 JRG  N    HN    single    0.890  0.020  1.040
 JRG  CB   CA    single    1.528  0.020  1.528
 JRG  CA   HA    single    0.970  0.020  1.090
 JRG  CB   CAN   single    1.524  0.020  1.524
 JRG  CB   HB    single    0.970  0.020  1.090
 JRG  CB   HBA   single    0.970  0.020  1.090
 JRG  CAA  SAV   single    1.806  0.020  1.806
 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   deloc     1.248  0.020  1.248
 JRG  OAD  CAY   double    1.226  0.020  1.226
 JRG  OAE  CAZ   double    1.224  0.020  1.224
 JRG  OAG  CAX   deloc     1.243  0.020  1.243
 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    1.524  0.020  1.524
 JRG  CAM  CAN   single    1.524  0.020  1.524
 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    1.816  0.020  1.816
 JRG  CAP  CAR   single    1.521  0.020  1.521
 JRG  CAP  HAP   single    0.970  0.020  1.090
 JRG  CAP  HAPA  single    0.970  0.020  1.090
 JRG  CAR  CBD   single    1.530  0.020  1.530
 JRG  CAR  HAR   single    0.970  0.020  1.090
 JRG  CAR  HARA  single    0.970  0.020  1.090
 JRG  NAS  CAZ   single    1.340  0.020  1.340
 JRG  NAS  HNAS  single    0.860  0.020  1.020
 JRG  CBD  NAU   single    1.445  0.020  1.445
 JRG  NAU  CAY   single    1.365  0.020  1.365
 JRG  NAU  HNAU  single    0.890  0.020  1.040
 JRG  CAX  CBD   single    1.551  0.020  1.551
 JRG  CAZ  CBB   single    1.497  0.020  1.497
 JRG  CBD  HBD   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
 JRG  OXT   C    CA    115.23  3.000
 JRG  OXT   C    O     127.05  3.000
 JRG  CA    C    O     117.69  3.000
 JRG  HN    N    CAY   116.13  3.000
 JRG  HN    N    CA    115.04  3.000
 JRG  CAY   N    CA    119.51  3.000
 JRG  HA    CA   CB    107.69  3.000
 JRG  HA    CA   N     108.05  3.000
 JRG  CB    CA   N     109.65  3.000
 JRG  HA    CA   C     108.05  3.000
 JRG  CB    CA   C     109.64  3.000
 JRG  N     CA   C     113.57  3.000
 JRG  HBA   CB   HB    106.30  3.000
 JRG  HBA   CB   CAN   109.30  3.000
 JRG  HB    CB   CAN   109.42  3.000
 JRG  HBA   CB   CA    107.63  3.000
 JRG  HB    CB   CA    109.49  3.000
 JRG  CAN   CB   CA    114.38  3.000
 JRG  HAAB  CAA  HAAA  108.63  3.000
 JRG  HAAB  CAA  HAA   108.64  3.000
 JRG  HAAA  CAA  HAA   109.30  3.000
 JRG  HAAB  CAA  SAV   107.79  3.000
 JRG  HAAA  CAA  SAV   111.22  3.000
 JRG  HAA   CAA  SAV   111.18  3.000
 JRG  HAI   CAI  CBA   121.25  3.000
 JRG  HAI   CAI  CAK   119.60  3.000
 JRG  CBA   CAI  CAK   119.15  3.000
 JRG  HAJ   CAJ  CBA   121.34  3.000
 JRG  HAJ   CAJ  CAL   119.49  3.000
 JRG  CBA   CAJ  CAL   119.17  3.000
 JRG  HAK   CAK  CBB   120.04  3.000
 JRG  HAK   CAK  CAI   119.08  3.000
 JRG  CBB   CAK  CAI   120.88  3.000
 JRG  HAL   CAL  CBB   121.11  3.000
 JRG  HAL   CAL  CAJ   118.05  3.000
 JRG  CBB   CAL  CAJ   120.82  3.000
 JRG  HAMA  CAM  HAM   106.74  3.000
 JRG  HAMA  CAM  CAO   109.20  3.000
 JRG  HAM   CAM  CAO   109.18  3.000
 JRG  HAMA  CAM  CAN   109.84  3.000
 JRG  HAM   CAM  CAN   109.69  3.000
 JRG  CAO   CAM  CAN   112.05  3.000
 JRG  HANA  CAN  HAN   106.24  3.000
 JRG  HANA  CAN  CAM   109.35  3.000
 JRG  HAN   CAN  CAM   109.63  3.000
 JRG  HANA  CAN  CB    110.02  3.000
 JRG  HAN   CAN  CB    109.26  3.000
 JRG  CAM   CAN  CB    112.16  3.000
 JRG  HAOA  CAO  HAO   106.95  3.000
 JRG  HAOA  CAO  NAS   109.00  3.000
 JRG  HAO   CAO  NAS   107.28  3.000
 JRG  HAOA  CAO  CAM   110.13  3.000
 JRG  HAO   CAO  CAM   110.10  3.000
 JRG  NAS   CAO  CAM   113.16  3.000
 JRG  HARA  CAR  HAR   106.74  3.000
 JRG  HARA  CAR  CBD   109.66  3.000
 JRG  HAR   CAR  CBD   107.85  3.000
 JRG  HARA  CAR  CAP   109.74  3.000
 JRG  HAR   CAR  CAP   109.69  3.000
 JRG  CBD   CAR  CAP   112.95  3.000
 JRG  HNAS  NAS  CAZ   119.50  3.000
 JRG  HNAS  NAS  CAO   117.42  3.000
 JRG  CAZ   NAS  CAO   123.08  3.000
 JRG  HNAU  NAU  CBD   114.68  3.000
 JRG  HNAU  NAU  CAY   115.74  3.000
 JRG  CBD   NAU  CAY   119.16  3.000
 JRG  CAP   SAV  CAA    99.94  3.000
 JRG  CBD   CAX  OAG   117.55  3.000
 JRG  CBD   CAX  OAC   115.16  3.000
 JRG  OAG   CAX  OAC   127.26  3.000
 JRG  NAU   CAY  OAD   122.40  3.000
 JRG  NAU   CAY  N     115.01  3.000
 JRG  OAD   CAY  N     122.59  3.000
 JRG  CBB   CAZ  NAS   116.13  3.000
 JRG  CBB   CAZ  OAE   120.65  3.000
 JRG  NAS   CAZ  OAE   123.22  3.000
 JRG  CAJ   CBA  CAI   120.99  3.000
 JRG  CAJ   CBA  IAH   119.50  3.000
 JRG  CAI   CBA  IAH   119.51  3.000
 JRG  CAZ   CBB  CAL   122.75  3.000
 JRG  CAZ   CBB  CAK   118.24  3.000
 JRG  CAL   CBB  CAK   118.98  3.000
 JRG  HBD   CBD  CAX   108.05  3.000
 JRG  HBD   CBD  NAU   108.26  3.000
 JRG  CAX   CBD  NAU   113.63  3.000
 JRG  HBD   CBD  CAR   107.61  3.000
 JRG  CAX   CBD  CAR   109.50  3.000
 JRG  NAU   CBD  CAR   109.61  3.000
 JRG  HAPA  CAP  HAP   107.88  3.000
 JRG  HAPA  CAP  SAV   108.89  3.000
 JRG  HAP   CAP  SAV   109.04  3.000
 JRG  HAPA  CAP  CAR   111.04  3.000
 JRG  HAP   CAP  CAR   110.33  3.000
 JRG  SAV   CAP  CAR   109.61  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_19  CAO   NAS  CAZ  OAE     0.00   0.0  0
 JRG  Var_01    CAK   CBB  CAZ  OAE   -26.79  30.0  2
 JRG  Var_02    CAM   CAN  CB   CA   -175.83  30.0  3
 JRG  Var_03    CAO   CAM  CAN  CB   -178.97  30.0  1
 JRG  Var_04    CAR   CAP  SAV  CAA  -178.29  30.0  3
 JRG  Var_05    CAZ   NAS  CAO  CAM   -84.23  30.0  3
 JRG  Var_06    NAS   CAO  CAM  CAN  -179.17  30.0  3
 JRG  Var_07    CBD   CAR  CAP  SAV  -177.39  30.0  3
 JRG  Var_08    HAA   CAA  SAV  CAP   -61.00  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  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-3  OAE   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-5  CAX   0.020
 JRG  plan-5  CBD   0.020
 JRG  plan-5  OAC   0.020
 JRG  plan-5  OAG   0.020

