# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 07:43:32 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  56  28  .  2021-08-25  2021-08-25  
;
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  CR16  0  -0.313  -5.1304  -1.8972  -0.7689
 X92  CAI   C  CR16  0  -0.239  -6.3581  -2.2238  -1.3304
 X92  CAG   C  CR16  0  -0.272  -7.5053  -1.5452  -0.9411
 X92  CAH   C  CR16  0  -0.240  -7.4152  -0.5410   0.0150
 X92  CAJ   C  CR16  0  -0.308  -6.1861  -0.2195   0.5743
 X92  CAV   C  CR6   0   0.137  -5.0276  -0.8920   0.1896
 X92  CAM   C  CH2   0  -0.525  -3.6912  -0.5053   0.7603
 X92  CAP   C  CH2   0  -0.446  -3.0896   0.6806   0.0001
 X92  CAX   C  CH1   0  -0.178  -1.7273   1.1235   0.5564
 X92  CAS   C  C     0   0.537  -1.3635   2.4529  -0.0856
 X92  OAE   O  OH1   0  -0.595  -2.0031   3.4592   0.5030
 X92  OAB   O  O     0  -0.424  -0.6197   2.5957  -1.0203
 X92  HAJ   H  HCR6  0   0.247  -6.1257   0.5630   1.3219
 X92  HAH   H  HCR6  0   0.253  -8.3042  -0.0076   0.3270
 X92  HAG   H  HCR6  0   0.254  -8.4631  -1.7967  -1.3779
 X92  HAI   H  HCR6  0   0.254  -6.4172  -3.0105  -2.0715
 X92  HAK   H  HCR6  0   0.247  -4.2407  -2.4344  -1.0777
 X92  HAM1  H  HCH2  0   0.253  -3.7977  -0.2335   1.8139
 X92  HAM2  H  HCH2  0   0.247  -3.0243  -1.3700   0.7234
 X92  HAP1  H  HCH2  0   0.249  -2.9736   0.4288  -1.0576
 X92  HAP2  H  HCH2  0   0.260  -3.7905   1.5156   0.0546
 X92  HAX   H  HCH1  0   0.245  -1.8578   1.3078   1.6339
 X92  HAE   H  HOH1  0   0.481  -1.8053   4.2905   0.0463
 X92  N     N  NH1   0  -0.608  -0.7213   0.1376   0.2530
 X92  CA    C  CH1   0  -0.220   0.5356   0.2785   0.9600
 X92  CB    C  CH3   0  -0.672   0.4595   0.0669   2.4788
 X92  C     C  C     0   0.563   1.5045  -0.7634   0.4098
 X92  O     O  O     0  -0.495   1.0989  -1.8877   0.1484
 X92  H     H  HNH1  0   0.356  -1.0840  -0.7948   0.3972
 X92  HA    H  HCH1  0   0.262   0.8963   1.2912   0.7807
 X92  HB1C  H  HCH3  0   0.235   0.1355  -0.9482   2.7112
 X92  HB2C  H  HCH3  0   0.242   1.4276   0.2326   2.9540
 X92  HB3C  H  HCH3  0   0.248  -0.2460   0.7611   2.9349
 X92  NBB   N  NR5   0  -0.478   2.8096  -0.4459   0.3296
 X92  CBA   C  CR15  0  -0.052   3.8223  -1.4617   0.1096
 X92  CAO   C  CH2   0  -0.440   4.1511  -1.8217  -1.3387
 X92  CAL   C  CH2   0  -0.459   5.5708  -2.3692  -1.2137
 X92  CAN   C  CH2   0  -0.436   6.2568  -1.4560  -0.1777
 X92  CAY   C  CR15  0  -0.275   5.1136  -0.8354   0.6473
 X92  CAQ   C  CH2   0  -0.476   4.8998   0.6653   0.4224
 X92  CAZ   C  CR15  0  -0.194   3.3705   0.8778   0.5008
 X92  CAT   C  C     0   0.534   2.9441   1.8198  -0.6089
 X92  OAF   O  OH1   0  -0.590   3.1722   3.0806  -0.2689
 X92  OAC   O  O     0  -0.419   2.5064   1.4717  -1.6727
 X92  HBA   H  HCR5  0   0.261   3.5502  -2.3663   0.6571
 X92  HAZ   H  HCR5  0   0.300   3.0987   1.3048   1.4704
 X92  HAO1  H  HCH2  0   0.242   3.4468  -2.5360  -1.7654
 X92  HAO2  H  HCH2  0   0.228   4.1308  -0.9254  -1.9641
 X92  HAY   H  HCR5  0   0.263   5.2252  -1.0339   1.7147
 X92  HAL1  H  HCH2  0   0.228   5.5334  -3.3951  -0.8387
 X92  HAL2  H  HCH2  0   0.238   6.1018  -2.3989  -2.1655
 X92  HAN1  H  HCH2  0   0.240   6.9543  -2.0129   0.4477
 X92  HAN2  H  HCH2  0   0.233   6.8372  -0.6764  -0.6753
 X92  HAQ1  H  HCH2  0   0.276   5.4159   1.2835   1.1544
 X92  HAQ2  H  HCH2  0   0.259   5.2784   0.9499  -0.5621
 X92  HAF   H  HOH1  0   0.485   2.9552   3.6726  -1.0051

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  1.388  0.020  1.388
 X92  CAJ  CAV   aromatic  1.394  0.020  1.394
 X92  CAH  CAG   aromatic  1.389  0.020  1.389
 X92  CAG  CAI   aromatic  1.389  0.020  1.389
 X92  CAI  CAK   aromatic  1.389  0.020  1.389
 X92  CAK  CAV   aromatic  1.393  0.020  1.393
 X92  CAV  CAM   single    1.504  0.020  1.504
 X92  CAM  CAP   single    1.532  0.020  1.532
 X92  CAP  CAX   single    1.537  0.020  1.537
 X92  CAX  CAS   single    1.520  0.020  1.520
 X92  CAX  N     single    1.441  0.020  1.441
 X92  CAS  OAE   single    1.330  0.020  1.330
 X92  CAS  OAB   double    1.203  0.020  1.203
 X92  N    CA    single    1.449  0.020  1.449
 X92  CA   CB    single    1.535  0.020  1.535
 X92  CA   C     single    1.525  0.020  1.525
 X92  C    O     double    1.223  0.020  1.223
 X92  C    NBB   single    1.345  0.020  1.345
 X92  NBB  CBA   single    1.451  0.020  1.451
 X92  NBB  CAZ   single    1.448  0.020  1.448
 X92  CBA  CAO   single    1.528  0.020  1.528
 X92  CBA  CAY   single    1.533  0.020  1.533
 X92  CAO  CAL   single    1.527  0.020  1.527
 X92  CAL  CAN   single    1.542  0.020  1.542
 X92  CAN  CAY   single    1.540  0.020  1.540
 X92  CAY  CAQ   single    1.532  0.020  1.532
 X92  CAQ  CAZ   single    1.546  0.020  1.546
 X92  CAZ  CAT   single    1.517  0.020  1.517
 X92  CAT  OAF   single    1.326  0.020  1.326
 X92  CAT  OAC   double    1.202  0.020  1.202
 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  OAE  HAE   single    0.850  0.020  0.980
 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
 X92  OAF  HAF   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
 X92  HAK   CAK  CAV   119.54  3.000
 X92  HAK   CAK  CAI   119.58  3.000
 X92  CAV   CAK  CAI   120.88  3.000
 X92  HAI   CAI  CAG   120.14  3.000
 X92  HAI   CAI  CAK   119.73  3.000
 X92  CAG   CAI  CAK   120.13  3.000
 X92  HAG   CAG  CAH   120.20  3.000
 X92  HAG   CAG  CAI   120.29  3.000
 X92  CAH   CAG  CAI   119.51  3.000
 X92  HAH   CAH  CAJ   119.79  3.000
 X92  HAH   CAH  CAG   120.08  3.000
 X92  CAJ   CAH  CAG   120.13  3.000
 X92  HAJ   CAJ  CAV   119.50  3.000
 X92  HAJ   CAJ  CAH   119.63  3.000
 X92  CAV   CAJ  CAH   120.87  3.000
 X92  CAM   CAV  CAJ   120.66  3.000
 X92  CAM   CAV  CAK   120.82  3.000
 X92  CAJ   CAV  CAK   118.48  3.000
 X92  HAM2  CAM  HAM1  106.78  3.000
 X92  HAM2  CAM  CAP   110.86  3.000
 X92  HAM1  CAM  CAP   108.91  3.000
 X92  HAM2  CAM  CAV   109.03  3.000
 X92  HAM1  CAM  CAV   110.07  3.000
 X92  CAP   CAM  CAV   111.09  3.000
 X92  HAP2  CAP  HAP1  107.01  3.000
 X92  HAP2  CAP  CAX   109.31  3.000
 X92  HAP1  CAP  CAX   108.81  3.000
 X92  HAP2  CAP  CAM   108.38  3.000
 X92  HAP1  CAP  CAM   110.09  3.000
 X92  CAX   CAP  CAM   113.06  3.000
 X92  N     CAX  HAX   113.79  3.000
 X92  HAX   CAX  CAS   107.18  3.000
 X92  N     CAX  CAS   110.02  3.000
 X92  HAX   CAX  CAP   107.31  3.000
 X92  N     CAX  CAP   110.21  3.000
 X92  CAS   CAX  CAP   108.13  3.000
 X92  OAB   CAS  OAE   123.47  3.000
 X92  OAB   CAS  CAX   125.44  3.000
 X92  OAE   CAS  CAX   111.08  3.000
 X92  HAE   OAE  CAS   110.03  3.000
 X92  H     N    CA    109.35  3.000
 X92  H     N    CAX   110.53  3.000
 X92  CA    N    CAX   115.87  3.000
 X92  HA    CA   C     111.41  3.000
 X92  HA    CA   CB    107.90  3.000
 X92  C     CA   CB    107.11  3.000
 X92  HA    CA   N     107.28  3.000
 X92  C     CA   N     107.97  3.000
 X92  CB    CA   N     115.23  3.000
 X92  HB3C  CB   HB2C  107.18  3.000
 X92  HB3C  CB   HB1C  108.14  3.000
 X92  HB2C  CB   HB1C  108.19  3.000
 X92  HB3C  CB   CA    111.00  3.000
 X92  HB2C  CB   CA    111.47  3.000
 X92  HB1C  CB   CA    110.72  3.000
 X92  NBB   C    O     121.71  3.000
 X92  NBB   C    CA    118.45  3.000
 X92  O     C    CA    119.61  3.000
 X92  CAZ   NBB  CBA   112.80  3.000
 X92  CAZ   NBB  C     125.77  3.000
 X92  CBA   NBB  C     121.39  3.000
 X92  HBA   CBA  CAY   111.88  3.000
 X92  HBA   CBA  CAO   109.49  3.000
 X92  CAY   CBA  CAO   104.33  3.000
 X92  HBA   CBA  NBB   109.27  3.000
 X92  CAY   CBA  NBB   104.40  3.000
 X92  CAO   CBA  NBB   117.31  3.000
 X92  HAO2  CAO  HAO1  107.54  3.000
 X92  HAO2  CAO  CAL   111.00  3.000
 X92  HAO1  CAO  CAL   113.45  3.000
 X92  HAO2  CAO  CBA   110.18  3.000
 X92  HAO1  CAO  CBA   112.72  3.000
 X92  CAL   CAO  CBA   101.94  3.000
 X92  HAL2  CAL  HAL1  106.90  3.000
 X92  HAL2  CAL  CAN   112.70  3.000
 X92  HAL1  CAL  CAN   109.92  3.000
 X92  HAL2  CAL  CAO   113.02  3.000
 X92  HAL1  CAL  CAO   109.45  3.000
 X92  CAN   CAL  CAO   104.85  3.000
 X92  HAN2  CAN  HAN1  106.62  3.000
 X92  HAN2  CAN  CAY   110.55  3.000
 X92  HAN1  CAN  CAY   111.94  3.000
 X92  HAN2  CAN  CAL   110.68  3.000
 X92  HAN1  CAN  CAL   111.56  3.000
 X92  CAY   CAN  CAL   105.56  3.000
 X92  HAY   CAY  CAQ   109.62  3.000
 X92  HAY   CAY  CAN   112.00  3.000
 X92  CAQ   CAY  CAN   114.80  3.000
 X92  HAY   CAY  CBA   110.80  3.000
 X92  CAQ   CAY  CBA   103.37  3.000
 X92  CAN   CAY  CBA   105.83  3.000
 X92  HAQ2  CAQ  HAQ1  107.09  3.000
 X92  HAQ2  CAQ  CAZ   110.65  3.000
 X92  HAQ1  CAQ  CAZ   110.91  3.000
 X92  HAQ2  CAQ  CAY   109.82  3.000
 X92  HAQ1  CAQ  CAY   113.05  3.000
 X92  CAZ   CAQ  CAY   105.38  3.000
 X92  HAZ   CAZ  CAT   109.65  3.000
 X92  HAZ   CAZ  CAQ   110.15  3.000
 X92  CAT   CAZ  CAQ   109.05  3.000
 X92  HAZ   CAZ  NBB   111.44  3.000
 X92  CAT   CAZ  NBB   111.86  3.000
 X92  CAQ   CAZ  NBB   104.57  3.000
 X92  OAC   CAT  OAF   124.42  3.000
 X92  OAC   CAT  CAZ   124.75  3.000
 X92  OAF   CAT  CAZ   110.77  3.000
 X92  HAF   OAF  CAT   110.34  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  CONST_18  HAF  OAF  CAT  CAZ  180.00   0.0  0
 X92  CONST_19  HAE  OAE  CAS  CAX  180.00   0.0  0
 X92  Var_01    CAN  CAL  CAO  CBA  -39.13  30.0  1
 X92  Var_02    CAY  CAN  CAL  CAO   22.63  30.0  1
 X92  Var_03    CAP  CAM  CAV  CAK   94.43  30.0  2
 X92  Var_04    CAX  CAP  CAM  CAV  179.40  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-3  HAE  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
 X92  plan-4  HAF  0.020

