# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:29:05 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (2S,3aR,7aS)-1-[(2S)-2-{[(1S)-1-carboxy-3-phenylpropyl]amino}propanoyl]octahydro-1H-indole-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N[C@@H](CCc1ccccc1)C(O)=O)C(=O)N2[C@H]3CCCC[C@@H]3C[C@H]2C(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
 X93  X93  '(2S,3aR,7aS)-1-[(2S)-2-{[(1S)-1-carboxy-3-phenylpropyl]amino}propanoyl]octahydro-1H-indole-2-carboxylic acid (non-preferred name)'  ligand  57  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X93
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
 X93  CAY   C  CH1    0  -0.209  -2.0045  -2.0520  -1.1783
 X93  CAQ   C  CH2    0  -0.385  -3.0361  -1.0163  -0.7243
 X93  CAN   C  CH2    0  -0.540  -2.6275  -0.2904   0.5571
 X93  CAW   C  CR6    0   0.150  -3.6035   0.7753   0.9749
 X93  CAJ   C  CR16   0  -0.311  -4.9335   0.4623   1.2593
 X93  CAK   C  CR16   0  -0.336  -3.2027   2.1061   1.0793
 X93  CAH   C  CR16   0  -0.241  -5.8380   1.4492   1.6250
 X93  CAI   C  CR16   0  -0.241  -4.1055   3.0982   1.4442
 X93  CAG   C  CR16   0  -0.277  -5.4280   2.7743   1.7155
 X93  CAT   C  C      0   0.412  -2.5804  -2.9390  -2.3157
 X93  OAB   O  O      0  -0.599  -1.9002  -3.0543  -3.3560
 X93  OAE   O  OC    -1  -0.610  -3.6787  -3.4813  -2.0880
 X93  N     N  NH1    0  -0.620  -0.7618  -1.4170  -1.5854
 X93  CA    C  CH1    0  -0.212   0.3632  -1.5548  -0.6831
 X93  C     C  C      0   0.542   1.4907  -0.6698  -1.2098
 X93  O     O  O      0  -0.527   1.7367  -0.6693  -2.4150
 X93  CB    C  CH3    0  -0.667   0.9063  -2.9830  -0.5426
 X93  NBC   N  NT     0  -0.473   2.2103   0.0379  -0.3332
 X93  CBB   C  CH1    0   0.042   3.3730   0.8275  -0.7323
 X93  CAP   C  CH2    0  -0.443   3.2248   1.9222  -1.7773
 X93  CAM   C  CH2    0  -0.444   4.6011   2.5775  -1.9545
 X93  CAL   C  CH2    0  -0.434   5.2219   3.0727  -0.6458
 X93  CAO   C  CH2    0  -0.425   5.2397   1.9937   0.4408
 X93  CAZ   C  CH1    0  -0.272   3.8326   1.4490   0.5815
 X93  CAR   C  CH2    0  -0.450   3.4941   0.3719   1.5936
 X93  CBA   C  CH1    0  -0.236   2.0923  -0.0436   1.1219
 X93  CAU   C  C      0   0.446   1.0053   0.8969   1.7037
 X93  OAF   O  O      0  -0.580   0.4414   1.6814   0.9218
 X93  OAC   O  OC    -1  -0.614   0.8231   0.7768   2.9310
 X93  HAY   H  HCH1   0   0.203  -1.8429  -2.7392  -0.3317
 X93  HAQ1  H  HCH2   0   0.205  -3.1828  -0.2877  -1.5286
 X93  HAQ2  H  HCH2   0   0.211  -3.9943  -1.5131  -0.5652
 X93  HAN1  H  HCH2   0   0.222  -2.5293  -1.0316   1.3590
 X93  HAN2  H  HCH2   0   0.268  -1.6437   0.1635   0.4355
 X93  HAJ   H  HCR6   0   0.241  -5.2683  -0.5672   1.1951
 X93  HAK   H  HCR6   0   0.252  -2.1658   2.3592   0.8877
 X93  HAH   H  HCR6   0   0.249  -6.8653   1.1842   1.8418
 X93  HAI   H  HCR6   0   0.248  -3.7742   4.1267   1.5168
 X93  HAG   H  HCR6   0   0.249  -6.1329   3.5457   1.9988
 X93  H     H  HNH1   0   0.333  -0.5214  -1.7995  -2.4931
 X93  HA    H  HCH1   0   0.252   0.0375  -1.2149   0.2993
 X93  HB1C  H  HCH3   0   0.225   1.2703  -3.3527  -1.5024
 X93  HB2C  H  HCH3   0   0.227   1.7287  -3.0370   0.1742
 X93  HB3C  H  HCH3   0   0.236   0.1264  -3.6608  -0.1937
 X93  HBB   H  HCH1   0   0.211   4.1526   0.1363  -1.0880
 X93  HBA   H  HCH1   0   0.252   1.8809  -1.0682   1.4369
 X93  HAP1  H  HCH2   0   0.238   2.8818   1.5289  -2.7328
 X93  HAP2  H  HCH2   0   0.212   2.4845   2.6536  -1.4379
 X93  HAZ   H  HCH1   0   0.228   3.1763   2.3043   0.7897
 X93  HAM1  H  HCH2   0   0.212   5.2757   1.8467  -2.4140
 X93  HAM2  H  HCH2   0   0.231   4.5259   3.4064  -2.6620
 X93  HAL1  H  HCH2   0   0.227   6.2329   3.4413  -0.8356
 X93  HAL2  H  HCH2   0   0.213   4.6460   3.9283  -0.2777
 X93  HAO1  H  HCH2   0   0.210   5.9319   1.1882   0.1704
 X93  HAO2  H  HCH2   0   0.229   5.5942   2.4138   1.3853
 X93  HAR1  H  HCH2   0   0.227   4.1915  -0.4687   1.5188
 X93  HAR2  H  HCH2   0   0.242   3.4906   0.7161   2.6269

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
 X93  CAJ  CAH   aromatic  1.388  0.020  1.388
 X93  CAJ  CAW   aromatic  1.396  0.020  1.396
 X93  CAH  CAG   aromatic  1.390  0.020  1.390
 X93  CAG  CAI   aromatic  1.388  0.020  1.388
 X93  CAI  CAK   aromatic  1.390  0.020  1.390
 X93  CAK  CAW   aromatic  1.394  0.020  1.394
 X93  CAW  CAN   single    1.504  0.020  1.504
 X93  CAN  CAQ   single    1.528  0.020  1.528
 X93  CAQ  CAY   single    1.531  0.020  1.531
 X93  CAY  CAT   single    1.553  0.020  1.553
 X93  CAY  N     single    1.454  0.020  1.454
 X93  CAT  OAE   deloc     1.246  0.020  1.246
 X93  CAT  OAB   deloc     1.248  0.020  1.248
 X93  N    CA    single    1.449  0.020  1.449
 X93  CA   CB    single    1.534  0.020  1.534
 X93  CA   C     single    1.527  0.020  1.527
 X93  C    O     double    1.230  0.020  1.230
 X93  C    NBC   single    1.337  0.020  1.337
 X93  NBC  CBB   single    1.461  0.020  1.461
 X93  NBC  CBA   single    1.462  0.020  1.462
 X93  CBB  CAP   single    1.521  0.020  1.521
 X93  CBB  CAZ   single    1.524  0.020  1.524
 X93  CAP  CAM   single    1.535  0.020  1.535
 X93  CAM  CAL   single    1.531  0.020  1.531
 X93  CAL  CAO   single    1.531  0.020  1.531
 X93  CAO  CAZ   single    1.515  0.020  1.515
 X93  CAZ  CAR   single    1.516  0.020  1.516
 X93  CAR  CBA   single    1.536  0.020  1.536
 X93  CBA  CAU   single    1.551  0.020  1.551
 X93  CAU  OAF   deloc     1.243  0.020  1.243
 X93  CAU  OAC   deloc     1.247  0.020  1.247
 X93  CAJ  HAJ   single    0.930  0.020  1.080
 X93  CAH  HAH   single    0.930  0.020  1.080
 X93  CAG  HAG   single    0.930  0.020  1.080
 X93  CAI  HAI   single    0.930  0.020  1.080
 X93  CAK  HAK   single    0.930  0.020  1.080
 X93  CAN  HAN1  single    0.970  0.020  1.090
 X93  CAN  HAN2  single    0.970  0.020  1.090
 X93  CAQ  HAQ1  single    0.970  0.020  1.090
 X93  CAQ  HAQ2  single    0.970  0.020  1.090
 X93  CAY  HAY   single    0.970  0.020  1.090
 X93  N    H     single    0.860  0.020  1.020
 X93  CA   HA    single    0.970  0.020  1.090
 X93  CB   HB1C  single    0.970  0.020  1.090
 X93  CB   HB2C  single    0.970  0.020  1.090
 X93  CB   HB3C  single    0.970  0.020  1.090
 X93  CBB  HBB   single    0.970  0.020  1.090
 X93  CBA  HBA   single    0.970  0.020  1.090
 X93  CAP  HAP1  single    0.970  0.020  1.090
 X93  CAP  HAP2  single    0.970  0.020  1.090
 X93  CAZ  HAZ   single    0.970  0.020  1.090
 X93  CAM  HAM1  single    0.970  0.020  1.090
 X93  CAM  HAM2  single    0.970  0.020  1.090
 X93  CAL  HAL1  single    0.970  0.020  1.090
 X93  CAL  HAL2  single    0.970  0.020  1.090
 X93  CAO  HAO1  single    0.970  0.020  1.090
 X93  CAO  HAO2  single    0.970  0.020  1.090
 X93  CAR  HAR1  single    0.970  0.020  1.090
 X93  CAR  HAR2  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
 X93  HAY   CAY  N     111.23  3.000
 X93  HAY   CAY  CAT   105.12  3.000
 X93  N     CAY  CAT   111.18  3.000
 X93  HAY   CAY  CAQ   107.02  3.000
 X93  N     CAY  CAQ   111.32  3.000
 X93  CAT   CAY  CAQ   110.72  3.000
 X93  HAQ2  CAQ  HAQ1  107.00  3.000
 X93  HAQ2  CAQ  CAN   109.20  3.000
 X93  HAQ1  CAQ  CAN   109.61  3.000
 X93  HAQ2  CAQ  CAY   109.09  3.000
 X93  HAQ1  CAQ  CAY   108.82  3.000
 X93  CAN   CAQ  CAY   112.95  3.000
 X93  HAN2  CAN  HAN1  106.39  3.000
 X93  HAN2  CAN  CAW   108.75  3.000
 X93  HAN1  CAN  CAW   109.51  3.000
 X93  HAN2  CAN  CAQ   110.21  3.000
 X93  HAN1  CAN  CAQ   108.43  3.000
 X93  CAW   CAN  CAQ   113.32  3.000
 X93  CAK   CAW  CAJ   118.22  3.000
 X93  CAK   CAW  CAN   120.71  3.000
 X93  CAJ   CAW  CAN   121.07  3.000
 X93  HAJ   CAJ  CAH   119.31  3.000
 X93  HAJ   CAJ  CAW   119.67  3.000
 X93  CAH   CAJ  CAW   121.02  3.000
 X93  HAK   CAK  CAI   120.05  3.000
 X93  HAK   CAK  CAW   118.99  3.000
 X93  CAI   CAK  CAW   120.95  3.000
 X93  HAH   CAH  CAG   120.01  3.000
 X93  HAH   CAH  CAJ   119.81  3.000
 X93  CAG   CAH  CAJ   120.19  3.000
 X93  HAI   CAI  CAG   119.99  3.000
 X93  HAI   CAI  CAK   119.78  3.000
 X93  CAG   CAI  CAK   120.23  3.000
 X93  HAG   CAG  CAI   120.34  3.000
 X93  HAG   CAG  CAH   120.28  3.000
 X93  CAI   CAG  CAH   119.38  3.000
 X93  OAE   CAT  OAB   126.33  3.000
 X93  OAB   CAT  CAY   117.45  3.000
 X93  OAE   CAT  CAY   116.21  3.000
 X93  H     N    CA    109.73  3.000
 X93  H     N    CAY   106.77  3.000
 X93  CA    N    CAY   116.60  3.000
 X93  HA    CA   CB    108.29  3.000
 X93  HA    CA   C     110.55  3.000
 X93  CB    CA   C     108.04  3.000
 X93  HA    CA   N     107.44  3.000
 X93  C     CA   N     107.66  3.000
 X93  CB    CA   N     114.86  3.000
 X93  NBC   C    O     122.32  3.000
 X93  NBC   C    CA    118.56  3.000
 X93  O     C    CA    119.07  3.000
 X93  HB3C  CB   HB2C  107.33  3.000
 X93  HB3C  CB   HB1C  108.03  3.000
 X93  HB2C  CB   HB1C  108.02  3.000
 X93  HB3C  CB   CA    110.77  3.000
 X93  HB2C  CB   CA    111.87  3.000
 X93  HB1C  CB   CA    110.67  3.000
 X93  CBA   NBC  CBB   111.48  3.000
 X93  CBA   NBC  C     125.43  3.000
 X93  CBB   NBC  C     122.37  3.000
 X93  HBB   CBB  CAZ   108.72  3.000
 X93  HBB   CBB  CAP   107.40  3.000
 X93  CAZ   CBB  CAP   109.16  3.000
 X93  HBB   CBB  NBC   108.21  3.000
 X93  CAZ   CBB  NBC   102.99  3.000
 X93  CAP   CBB  NBC   119.94  3.000
 X93  HAP2  CAP  HAP1  107.49  3.000
 X93  HAP2  CAP  CAM   110.91  3.000
 X93  HAP1  CAP  CAM   109.60  3.000
 X93  HAP2  CAP  CBB   109.50  3.000
 X93  HAP1  CAP  CBB   111.95  3.000
 X93  CAM   CAP  CBB   107.42  3.000
 X93  HAM2  CAM  HAM1  106.08  3.000
 X93  HAM2  CAM  CAL   109.64  3.000
 X93  HAM1  CAM  CAL   108.94  3.000
 X93  HAM2  CAM  CAP   109.70  3.000
 X93  HAM1  CAM  CAP   108.41  3.000
 X93  CAL   CAM  CAP   113.77  3.000
 X93  HAL2  CAL  HAL1  106.34  3.000
 X93  HAL2  CAL  CAO   108.55  3.000
 X93  HAL1  CAL  CAO   110.49  3.000
 X93  HAL2  CAL  CAM   109.08  3.000
 X93  HAL1  CAL  CAM   109.63  3.000
 X93  CAO   CAL  CAM   112.55  3.000
 X93  HAO2  CAO  HAO1  106.91  3.000
 X93  HAO2  CAO  CAZ   111.05  3.000
 X93  HAO1  CAO  CAZ   110.20  3.000
 X93  HAO2  CAO  CAL   110.25  3.000
 X93  HAO1  CAO  CAL   110.49  3.000
 X93  CAZ   CAO  CAL   107.96  3.000
 X93  HAZ   CAZ  CAR   107.06  3.000
 X93  HAZ   CAZ  CAO   107.02  3.000
 X93  CAR   CAZ  CAO   121.64  3.000
 X93  HAZ   CAZ  CBB   107.51  3.000
 X93  CAR   CAZ  CBB   102.61  3.000
 X93  CAO   CAZ  CBB   110.27  3.000
 X93  HAR2  CAR  HAR1  108.03  3.000
 X93  HAR2  CAR  CBA   111.95  3.000
 X93  HAR1  CAR  CBA   110.65  3.000
 X93  HAR2  CAR  CAZ   114.17  3.000
 X93  HAR1  CAR  CAZ   110.96  3.000
 X93  CBA   CAR  CAZ   101.00  3.000
 X93  HBA   CBA  CAU   108.96  3.000
 X93  HBA   CBA  CAR   109.98  3.000
 X93  CAU   CBA  CAR   111.13  3.000
 X93  HBA   CBA  NBC   110.78  3.000
 X93  CAU   CBA  NBC   113.34  3.000
 X93  CAR   CBA  NBC   102.53  3.000
 X93  OAC   CAU  OAF   127.87  3.000
 X93  OAC   CAU  CBA   114.42  3.000
 X93  OAF   CAU  CBA   117.70  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
 X93  CONST_01  CAG  CAH  CAJ  CAW    0.00   0.0  0
 X93  CONST_02  CAG  CAI  CAK  CAW    0.00   0.0  0
 X93  CONST_03  CAI  CAG  CAH  CAJ    0.00   0.0  0
 X93  CONST_04  CAI  CAK  CAW  CAJ    0.00   0.0  0
 X93  CONST_05  CAH  CAG  CAI  CAK    0.00   0.0  0
 X93  CONST_06  CAH  CAJ  CAW  CAK    0.00   0.0  0
 X93  CONST_07  CAH  CAJ  CAW  CAN  180.00   0.0  0
 X93  CONST_08  CAI  CAK  CAW  CAN  180.00   0.0  0
 X93  CONST_09  HAH  CAH  CAJ  CAW  180.00   0.0  0
 X93  CONST_10  HAI  CAI  CAK  CAW  180.00   0.0  0
 X93  CONST_11  HAG  CAG  CAH  CAJ  180.00   0.0  0
 X93  CONST_12  HAK  CAK  CAW  CAJ  180.00   0.0  0
 X93  CONST_13  HAJ  CAJ  CAW  CAK  180.00   0.0  0
 X93  CONST_14  CBB  NBC  C    CA   180.00   0.0  0
 X93  CONST_15  CBA  NBC  C    CA     0.00   0.0  0
 X93  CONST_16  CBB  NBC  C    O      0.00   0.0  0
 X93  CONST_17  CBA  NBC  C    O    180.00   0.0  0
 X93  Var_01    CAL  CAM  CAP  CBB  -53.87  30.0  1
 X93  Var_02    CAO  CAL  CAM  CAP   51.43  30.0  1
 X93  Var_03    CAZ  CAO  CAL  CAM  -52.76  30.0  1
 X93  Var_04    CAJ  CAW  CAN  CAQ   59.88  30.0  2
 X93  Var_05    CAW  CAN  CAQ  CAY  177.24  30.0  2

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
 X93  chir_01  CAY  CAQ  CAT  N    negativ
 X93  chir_02  CA   N    CB   C    negativ
 X93  chir_03  CBB  NBC  CAZ  CAP  positiv
 X93  chir_04  CAZ  CAR  CAO  CBB  negativ
 X93  chir_05  CBA  NBC  CAU  CAR  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
 X93  plan-1  CAN  0.020
 X93  plan-1  CAW  0.020
 X93  plan-1  CAJ  0.020
 X93  plan-1  CAK  0.020
 X93  plan-1  CAH  0.020
 X93  plan-1  CAI  0.020
 X93  plan-1  CAG  0.020
 X93  plan-1  HAJ  0.020
 X93  plan-1  HAK  0.020
 X93  plan-1  HAH  0.020
 X93  plan-1  HAI  0.020
 X93  plan-1  HAG  0.020
 X93  plan-2  CA   0.020
 X93  plan-2  C    0.020
 X93  plan-2  O    0.020
 X93  plan-2  NBC  0.020
 X93  plan-2  CBB  0.020
 X93  plan-2  CBA  0.020
 X93  plan-3  CAY  0.020
 X93  plan-3  CAT  0.020
 X93  plan-3  OAB  0.020
 X93  plan-3  OAE  0.020
 X93  plan-4  CBA  0.020
 X93  plan-4  CAU  0.020
 X93  plan-4  OAF  0.020
 X93  plan-4  OAC  0.020

