# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:48:56 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2S,3aS,6aS)-1-[(2S)-2-{[(1R)-1-carboxy-3-phenylpropyl]amino}propanoyl]octahydrocyclopenta[b]pyrrole-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]3CCC[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
 X92  X92  '(2S,3aS,6aS)-1-[(2S)-2-{[(1R)-1-carboxy-3-phenylpropyl]amino}propanoyl]octahydrocyclopenta[b]pyrrole-2-carboxylic acid (non-preferred name)'  ligand  54  28  .  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_X92
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
 X92  CAK   C  C1     0  -0.312  -4.9955  -1.4824  -1.3104
 X92  CAI   C  C1     0  -0.240  -6.2336  -1.7066  -1.8977
 X92  CAG   C  C1     0  -0.276  -7.3988  -1.4727  -1.1782
 X92  CAH   C  C1     0  -0.240  -7.3142  -1.0156   0.1307
 X92  CAJ   C  C1     0  -0.314  -6.0730  -0.7935   0.7131
 X92  CAV   C  C      0   0.144  -4.8969  -1.0239   0.0022
 X92  CAM   C  CH2    0  -0.523  -3.5553  -0.7323   0.6139
 X92  CAP   C  CH2    0  -0.420  -3.1127   0.7053   0.3261
 X92  CAX   C  CH1    0  -0.161  -1.7902   1.1071   0.9847
 X92  CAS   C  C      0   0.392  -1.5499   2.6036   0.6781
 X92  OAE   O  OC    -1  -0.619  -1.9462   3.4097   1.5467
 X92  OAB   O  O      0  -0.596  -1.0311   2.8883  -0.4166
 X92  HAJ   H  H      0   0.244  -6.0162  -0.4403   1.7366
 X92  HAH   H  H      0   0.251  -8.2166  -0.8337   0.7006
 X92  HAG   H  H      0   0.251  -8.3650  -1.6485  -1.6331
 X92  HAI   H  H      0   0.251  -6.2887  -2.0664  -2.9175
 X92  HAK   H  H      0   0.244  -4.0898  -1.6676  -1.8771
 X92  HAM1  H  HCH2   0   0.236  -3.5971  -0.8896   1.6955
 X92  HAM2  H  HCH2   0   0.236  -2.8235  -1.4394   0.2155
 X92  HAP1  H  HCH2   0   0.218  -3.0271   0.8477  -0.7553
 X92  HAP2  H  HCH2   0   0.224  -3.8947   1.3854   0.6769
 X92  HAX   H  HCH1   0   0.179  -1.9244   1.0104   2.0740
 X92  N     N  NH1    0  -0.618  -0.7277   0.2509   0.4875
 X92  CA    C  CH1    0  -0.206   0.6142   0.5727   0.9325
 X92  CB    C  CH3    0  -0.691   0.7645   0.8016   2.4468
 X92  C     C  C      0   0.545   1.5240  -0.5980   0.5707
 X92  O     O  O      0  -0.523   1.0766  -1.7445   0.5706
 X92  H     H  HNH1   0   0.335  -0.9153  -0.7035   0.7681
 X92  HA    H  HCH1   0   0.273   0.9260   1.4796   0.4172
 X92  HB1C  H  HCH3   0   0.223   0.4412  -0.0778   3.0075
 X92  HB2C  H  HCH3   0   0.236   1.7996   1.0146   2.7186
 X92  HB3C  H  HCH3   0   0.240   0.1638   1.6499   2.7749
 X92  NBB   N  NT     0  -0.464   2.8258  -0.3534   0.3783
 X92  CBA   C  CH1    0  -0.052   3.7799  -1.4379   0.2719
 X92  CAO   C  CH2    0  -0.440   3.9409  -2.0713  -1.1107
 X92  CAL   C  CH2    0  -0.458   5.3569  -2.6395  -1.0527
 X92  CAN   C  CH2    0  -0.436   6.1724  -1.6110  -0.2407
 X92  CAY   C  CH1    0  -0.270   5.1374  -0.7805   0.5410
 X92  CAQ   C  CH2    0  -0.477   4.9327   0.6463   0.0238
 X92  CAZ   C  CH1    0  -0.174   3.4336   0.9568   0.2000
 X92  CAT   C  C      0   0.408   2.9394   1.7386  -1.0368
 X92  OAF   O  OC    -1  -0.617   3.2242   2.9527  -1.0237
 X92  OAC   O  O      0  -0.588   2.3755   1.1004  -1.9406
 X92  HBA   H  HCH1   0   0.243   3.5497  -2.2113   1.0086
 X92  HAZ   H  HCH1   0   0.237   3.2845   1.5683   1.0956
 X92  HAO1  H  HCH2   0   0.232   3.1810  -2.8264  -1.3150
 X92  HAO2  H  HCH2   0   0.227   3.8481  -1.2967  -1.8762
 X92  HAY   H  HCH1   0   0.246   5.3532  -0.7607   1.6115
 X92  HAL1  H  HCH2   0   0.222   5.3415  -3.5980  -0.5278
 X92  HAL2  H  HCH2   0   0.231   5.7806  -2.8275  -2.0400
 X92  HAN1  H  HCH2   0   0.233   6.8837  -2.1047   0.4223
 X92  HAN2  H  HCH2   0   0.228   6.7587  -0.9672  -0.8994
 X92  HAQ1  H  HCH2   0   0.250   5.5554   1.3763   0.5397
 X92  HAQ2  H  HCH2   0   0.235   5.2061   0.6918  -1.0341

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
 X92  CAJ  CAH   aromatic  1.389  0.020  1.389
 X92  CAJ  CAV   aromatic  1.393  0.020  1.393
 X92  CAH  CAG   aromatic  1.389  0.020  1.389
 X92  CAG  CAI   aromatic  1.389  0.020  1.389
 X92  CAI  CAK   aromatic  1.388  0.020  1.388
 X92  CAK  CAV   aromatic  1.394  0.020  1.394
 X92  CAV  CAM   single    1.503  0.020  1.503
 X92  CAM  CAP   single    1.532  0.020  1.532
 X92  CAP  CAX   single    1.531  0.020  1.531
 X92  CAX  CAS   single    1.546  0.020  1.546
 X92  CAX  N     single    1.452  0.020  1.452
 X92  CAS  OAE   deloc     1.250  0.020  1.250
 X92  CAS  OAB   deloc     1.244  0.020  1.244
 X92  N    CA    single    1.450  0.020  1.450
 X92  CA   CB    single    1.539  0.020  1.539
 X92  CA   C     single    1.526  0.020  1.526
 X92  C    O     double    1.231  0.020  1.231
 X92  C    NBB   single    1.338  0.020  1.338
 X92  NBB  CBA   single    1.448  0.020  1.448
 X92  NBB  CAZ   single    1.455  0.020  1.455
 X92  CBA  CAO   single    1.529  0.020  1.529
 X92  CBA  CAY   single    1.532  0.020  1.532
 X92  CAO  CAL   single    1.527  0.020  1.527
 X92  CAL  CAN   single    1.543  0.020  1.543
 X92  CAN  CAY   single    1.540  0.020  1.540
 X92  CAY  CAQ   single    1.531  0.020  1.531
 X92  CAQ  CAZ   single    1.541  0.020  1.541
 X92  CAZ  CAT   single    1.544  0.020  1.544
 X92  CAT  OAF   deloc     1.247  0.020  1.247
 X92  CAT  OAC   deloc     1.242  0.020  1.242
 X92  CAJ  HAJ   single    0.930  0.020  1.080
 X92  CAH  HAH   single    0.930  0.020  1.080
 X92  CAG  HAG   single    0.930  0.020  1.080
 X92  CAI  HAI   single    0.930  0.020  1.080
 X92  CAK  HAK   single    0.930  0.020  1.080
 X92  CAM  HAM1  single    0.970  0.020  1.090
 X92  CAM  HAM2  single    0.970  0.020  1.090
 X92  CAP  HAP1  single    0.970  0.020  1.090
 X92  CAP  HAP2  single    0.970  0.020  1.090
 X92  CAX  HAX   single    0.970  0.020  1.090
 X92  N    H     single    0.860  0.020  1.020
 X92  CA   HA    single    0.970  0.020  1.090
 X92  CB   HB1C  single    0.970  0.020  1.090
 X92  CB   HB2C  single    0.970  0.020  1.090
 X92  CB   HB3C  single    0.970  0.020  1.090
 X92  CBA  HBA   single    0.970  0.020  1.090
 X92  CAZ  HAZ   single    0.970  0.020  1.090
 X92  CAO  HAO1  single    0.970  0.020  1.090
 X92  CAO  HAO2  single    0.970  0.020  1.090
 X92  CAY  HAY   single    0.970  0.020  1.090
 X92  CAL  HAL1  single    0.970  0.020  1.090
 X92  CAL  HAL2  single    0.970  0.020  1.090
 X92  CAN  HAN1  single    0.970  0.020  1.090
 X92  CAN  HAN2  single    0.970  0.020  1.090
 X92  CAQ  HAQ1  single    0.970  0.020  1.090
 X92  CAQ  HAQ2  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
 X92  HAK   CAK  CAV   119.29  3.000
 X92  HAK   CAK  CAI   119.75  3.000
 X92  CAV   CAK  CAI   120.96  3.000
 X92  HAI   CAI  CAG   120.06  3.000
 X92  HAI   CAI  CAK   119.83  3.000
 X92  CAG   CAI  CAK   120.11  3.000
 X92  HAG   CAG  CAH   120.26  3.000
 X92  HAG   CAG  CAI   120.25  3.000
 X92  CAH   CAG  CAI   119.50  3.000
 X92  HAH   CAH  CAJ   119.83  3.000
 X92  HAH   CAH  CAG   120.03  3.000
 X92  CAJ   CAH  CAG   120.14  3.000
 X92  HAJ   CAJ  CAV   119.42  3.000
 X92  HAJ   CAJ  CAH   119.66  3.000
 X92  CAV   CAJ  CAH   120.93  3.000
 X92  CAM   CAV  CAJ   120.91  3.000
 X92  CAM   CAV  CAK   120.68  3.000
 X92  CAJ   CAV  CAK   118.36  3.000
 X92  HAM2  CAM  HAM1  107.04  3.000
 X92  HAM2  CAM  CAP   110.21  3.000
 X92  HAM1  CAM  CAP   109.38  3.000
 X92  HAM2  CAM  CAV   108.90  3.000
 X92  HAM1  CAM  CAV   109.90  3.000
 X92  CAP   CAM  CAV   111.32  3.000
 X92  HAP2  CAP  HAP1  106.97  3.000
 X92  HAP2  CAP  CAX   108.44  3.000
 X92  HAP1  CAP  CAX   108.88  3.000
 X92  HAP2  CAP  CAM   108.46  3.000
 X92  HAP1  CAP  CAM   109.30  3.000
 X92  CAX   CAP  CAM   114.52  3.000
 X92  N     CAX  HAX   112.08  3.000
 X92  HAX   CAX  CAS   107.45  3.000
 X92  N     CAX  CAS   112.89  3.000
 X92  HAX   CAX  CAP   107.28  3.000
 X92  N     CAX  CAP   109.27  3.000
 X92  CAS   CAX  CAP   107.63  3.000
 X92  OAB   CAS  OAE   126.60  3.000
 X92  OAB   CAS  CAX   117.43  3.000
 X92  OAE   CAS  CAX   115.92  3.000
 X92  H     N    CA    107.20  3.000
 X92  H     N    CAX   108.99  3.000
 X92  CA    N    CAX   116.18  3.000
 X92  HA    CA   C     110.86  3.000
 X92  HA    CA   CB    108.29  3.000
 X92  C     CA   CB    106.81  3.000
 X92  HA    CA   N     107.74  3.000
 X92  C     CA   N     107.98  3.000
 X92  CB    CA   N     115.18  3.000
 X92  HB3C  CB   HB2C  107.21  3.000
 X92  HB3C  CB   HB1C  108.00  3.000
 X92  HB2C  CB   HB1C  108.07  3.000
 X92  HB3C  CB   CA    110.99  3.000
 X92  HB2C  CB   CA    111.52  3.000
 X92  HB1C  CB   CA    110.89  3.000
 X92  NBB   C    O     121.59  3.000
 X92  NBB   C    CA    118.28  3.000
 X92  O     C    CA    119.86  3.000
 X92  CAZ   NBB  CBA   112.95  3.000
 X92  CAZ   NBB  C     126.04  3.000
 X92  CBA   NBB  C     120.96  3.000
 X92  HBA   CBA  CAY   111.83  3.000
 X92  HBA   CBA  CAO   109.79  3.000
 X92  CAY   CBA  CAO   104.08  3.000
 X92  HBA   CBA  NBB   109.98  3.000
 X92  CAY   CBA  NBB   104.45  3.000
 X92  CAO   CBA  NBB   116.48  3.000
 X92  HAO2  CAO  HAO1  107.47  3.000
 X92  HAO2  CAO  CAL   111.66  3.000
 X92  HAO1  CAO  CAL   113.30  3.000
 X92  HAO2  CAO  CBA   109.31  3.000
 X92  HAO1  CAO  CBA   112.51  3.000
 X92  CAL   CAO  CBA   102.56  3.000
 X92  HAL2  CAL  HAL1  106.80  3.000
 X92  HAL2  CAL  CAN   112.70  3.000
 X92  HAL1  CAL  CAN   109.83  3.000
 X92  HAL2  CAL  CAO   112.95  3.000
 X92  HAL1  CAL  CAO   109.36  3.000
 X92  CAN   CAL  CAO   105.18  3.000
 X92  HAN2  CAN  HAN1  106.47  3.000
 X92  HAN2  CAN  CAY   110.44  3.000
 X92  HAN1  CAN  CAY   111.96  3.000
 X92  HAN2  CAN  CAL   111.06  3.000
 X92  HAN1  CAN  CAL   111.27  3.000
 X92  CAY   CAN  CAL   105.74  3.000
 X92  HAY   CAY  CAQ   109.91  3.000
 X92  HAY   CAY  CAN   111.99  3.000
 X92  CAQ   CAY  CAN   114.88  3.000
 X92  HAY   CAY  CBA   110.80  3.000
 X92  CAQ   CAY  CBA   102.83  3.000
 X92  CAN   CAY  CBA   105.96  3.000
 X92  HAQ2  CAQ  HAQ1  106.70  3.000
 X92  HAQ2  CAQ  CAZ   110.20  3.000
 X92  HAQ1  CAQ  CAZ   111.52  3.000
 X92  HAQ2  CAQ  CAY   109.39  3.000
 X92  HAQ1  CAQ  CAY   112.84  3.000
 X92  CAZ   CAQ  CAY   106.21  3.000
 X92  HAZ   CAZ  CAT   109.20  3.000
 X92  HAZ   CAZ  CAQ   109.79  3.000
 X92  CAT   CAZ  CAQ   108.77  3.000
 X92  HAZ   CAZ  NBB   110.23  3.000
 X92  CAT   CAZ  NBB   114.85  3.000
 X92  CAQ   CAZ  NBB   103.82  3.000
 X92  OAC   CAT  OAF   127.71  3.000
 X92  OAC   CAT  CAZ   117.90  3.000
 X92  OAF   CAT  CAZ   114.29  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
 X92  CONST_01  CAH  CAG  CAI  CAK    0.00   0.0  0
 X92  CONST_02  CAH  CAJ  CAV  CAK    0.00   0.0  0
 X92  CONST_03  CAJ  CAH  CAG  CAI    0.00   0.0  0
 X92  CONST_04  CAJ  CAV  CAK  CAI    0.00   0.0  0
 X92  CONST_05  CAV  CAJ  CAH  CAG    0.00   0.0  0
 X92  CONST_06  CAV  CAK  CAI  CAG    0.00   0.0  0
 X92  CONST_07  CAM  CAV  CAK  CAI  180.00   0.0  0
 X92  CONST_08  CAM  CAV  CAJ  CAH  180.00   0.0  0
 X92  CONST_09  HAG  CAG  CAI  CAK  180.00   0.0  0
 X92  CONST_10  HAJ  CAJ  CAV  CAK  180.00   0.0  0
 X92  CONST_11  HAH  CAH  CAG  CAI  180.00   0.0  0
 X92  CONST_12  HAK  CAK  CAI  CAG  180.00   0.0  0
 X92  CONST_13  HAI  CAI  CAG  CAH  180.00   0.0  0
 X92  CONST_14  CBA  NBB  C    CA   180.00   0.0  0
 X92  CONST_15  CAZ  NBB  C    CA     0.00   0.0  0
 X92  CONST_16  CBA  NBB  C    O      0.00   0.0  0
 X92  CONST_17  CAZ  NBB  C    O    180.00   0.0  0
 X92  Var_01    CAN  CAL  CAO  CBA  -36.93  30.0  1
 X92  Var_02    CAY  CAN  CAL  CAO   19.48  30.0  1
 X92  Var_03    CAP  CAM  CAV  CAK   87.62  30.0  2
 X92  Var_04    CAX  CAP  CAM  CAV  176.63  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
 X92  chir_01  CAX  CAP  CAS  N    positiv
 X92  chir_02  CA   N    CB   C    negativ
 X92  chir_03  CBA  NBB  CAY  CAO  positiv
 X92  chir_04  CAY  CBA  CAN  CAQ  negativ
 X92  chir_05  CAZ  NBB  CAT  CAQ  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
 X92  plan-1  CAK  0.020
 X92  plan-1  CAI  0.020
 X92  plan-1  CAG  0.020
 X92  plan-1  CAH  0.020
 X92  plan-1  CAJ  0.020
 X92  plan-1  CAV  0.020
 X92  plan-1  CAM  0.020
 X92  plan-1  HAJ  0.020
 X92  plan-1  HAH  0.020
 X92  plan-1  HAG  0.020
 X92  plan-1  HAI  0.020
 X92  plan-1  HAK  0.020
 X92  plan-2  CA   0.020
 X92  plan-2  C    0.020
 X92  plan-2  O    0.020
 X92  plan-2  NBB  0.020
 X92  plan-2  CBA  0.020
 X92  plan-2  CAZ  0.020
 X92  plan-3  CAX  0.020
 X92  plan-3  CAS  0.020
 X92  plan-3  OAE  0.020
 X92  plan-3  OAB  0.020
 X92  plan-4  CAZ  0.020
 X92  plan-4  CAT  0.020
 X92  plan-4  OAF  0.020
 X92  plan-4  OAC  0.020

