# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:04:20 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2S,3aS,7aS)-1-[(2S)-2-{[(1S)-1-carboxybutyl]amino}propanoyl]octahydro-1H-indole-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](N[C@@H](C)C(=O)N1[C@H]2CCCC[C@H]2C[C@H]1C(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
 X94  X94  '(2S,3aS,7aS)-1-[(2S)-2-{[(1S)-1-carboxybutyl]amino}propanoyl]octahydro-1H-indole-2-carboxylic acid (non-preferred name)'  ligand  50  24  .  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_X94
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
 X94  CAA   C  CH3    0  -0.662  -3.0812   3.0307   1.8059
 X94  CAH   C  CH2    0  -0.431  -2.7333   1.6610   1.2387
 X94  CAK   C  CH2    0  -0.377  -3.6858   1.2267   0.1344
 X94  CAU   C  CH1    0  -0.208  -3.3136  -0.1193  -0.4944
 X94  CAP   C  C      0   0.411  -4.4124  -0.5837  -1.4855
 X94  OAF   O  OC    -1  -0.614  -5.5722  -0.6454  -1.0325
 X94  OAC   O  O      0  -0.600  -4.0577  -0.8631  -2.6496
 X94  N     N  NH1    0  -0.616  -2.0075  -0.0528  -1.1322
 X94  CA    C  CH1    0  -0.215  -0.9660  -0.8587  -0.5238
 X94  CB    C  CH3    0  -0.669  -1.1965  -2.3717  -0.6454
 X94  C     C  C      0   0.551   0.3502  -0.5173  -1.2204
 X94  O     O  O      0  -0.525   0.3577  -0.3993  -2.4443
 X94  NAX   N  NT     0  -0.455   1.4640  -0.3969  -0.4804
 X94  CAW   C  CH1    0  -0.025   2.7729  -0.1986  -1.1202
 X94  CAL   C  CH2    0  -0.430   4.1521   0.9506   0.7643
 X94  CAI   C  CH2    0  -0.432   4.3432   2.1489  -0.1534
 X94  CAJ   C  CH2    0  -0.442   3.1084   2.3252  -1.0247
 X94  CAM   C  CH2    0  -0.446   2.9314   1.1008  -1.9070
 X94  CAT   C  CH1    0  -0.290   3.7765  -0.3498   0.0380
 X94  CAN   C  CH2    0  -0.452   3.0459  -1.3060   0.9778
 X94  CAV   C  CH1    0  -0.215   1.5805  -0.8570   0.8998
 X94  CAQ   C  C      0   0.427   1.1743   0.1756   1.9800
 X94  OAD   O  OC    -1  -0.616   1.2738  -0.2477   3.1505
 X94  OAG   O  O      0  -0.576   0.7737   1.2932   1.6161
 X94  HAA1  H  HCH3   0   0.211  -3.0271   3.8014   1.0340
 X94  HAA2  H  HCH3   0   0.209  -4.0943   3.0484   2.2136
 X94  HAA3  H  HCH3   0   0.221  -2.3986   3.3205   2.6062
 X94  HAH1  H  HCH2   0   0.237  -1.7067   1.6668   0.8693
 X94  HAH2  H  HCH2   0   0.193  -2.7543   0.9177   2.0438
 X94  HAK1  H  HCH2   0   0.198  -4.7015   1.1681   0.5333
 X94  HAK2  H  HCH2   0   0.190  -3.7042   1.9907  -0.6527
 X94  HAU   H  HCH1   0   0.201  -3.3110  -0.8620   0.3187
 X94  H     H  HNH1   0   0.331  -2.1385  -0.3509  -2.0931
 X94  HA    H  HCH1   0   0.258  -0.9176  -0.5868   0.5304
 X94  HB1C  H  HCH3   0   0.226  -0.4092  -2.9550  -0.1635
 X94  HB2C  H  HCH3   0   0.235  -2.1410  -2.6565  -0.1803
 X94  HB3C  H  HCH3   0   0.223  -1.2366  -2.6665  -1.6953
 X94  HAW   H  HCH1   0   0.231   2.9308  -1.0295  -1.8189
 X94  HAV   H  HCH1   0   0.250   0.9435  -1.7310   1.0564
 X94  HAM1  H  HCH2   0   0.211   3.8259   0.9874  -2.5299
 X94  HAM2  H  HCH2   0   0.243   2.0996   1.2240  -2.5979
 X94  HAT   H  HCH1   0   0.238   4.6905  -0.8003  -0.3580
 X94  HAJ1  H  HCH2   0   0.223   2.2273   2.4520  -0.3886
 X94  HAJ2  H  HCH2   0   0.220   3.1930   3.2200  -1.6464
 X94  HAI1  H  HCH2   0   0.222   4.5325   3.0429   0.4464
 X94  HAI2  H  HCH2   0   0.202   5.2224   2.0094  -0.7930
 X94  HAL1  H  HCH2   0   0.225   5.0569   0.7631   1.3490
 X94  HAL2  H  HCH2   0   0.229   3.3753   1.2092   1.4848
 X94  HAN1  H  HCH2   0   0.237   3.1370  -2.3343   0.6182
 X94  HAN2  H  HCH2   0   0.241   3.4253  -1.2826   1.9991

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
 X94  CAA  CAH   single  1.523  0.020  1.523
 X94  CAH  CAK   single  1.522  0.020  1.522
 X94  CAK  CAU   single  1.532  0.020  1.532
 X94  CAU  CAP   single  1.551  0.020  1.551
 X94  CAU  N     single  1.455  0.020  1.455
 X94  CAP  OAF   deloc   1.247  0.020  1.247
 X94  CAP  OAC   deloc   1.249  0.020  1.249
 X94  N    CA    single  1.451  0.020  1.451
 X94  CA   CB    single  1.535  0.020  1.535
 X94  CA   C     single  1.528  0.020  1.528
 X94  C    O     double  1.230  0.020  1.230
 X94  C    NAX   single  1.343  0.020  1.343
 X94  NAX  CAW   single  1.470  0.020  1.470
 X94  NAX  CAV   single  1.460  0.020  1.460
 X94  CAW  CAM   single  1.527  0.020  1.527
 X94  CAW  CAT   single  1.540  0.020  1.540
 X94  CAM  CAJ   single  1.519  0.020  1.519
 X94  CAJ  CAI   single  1.522  0.020  1.522
 X94  CAI  CAL   single  1.521  0.020  1.521
 X94  CAL  CAT   single  1.536  0.020  1.536
 X94  CAT  CAN   single  1.527  0.020  1.527
 X94  CAN  CAV   single  1.535  0.020  1.535
 X94  CAV  CAQ   single  1.549  0.020  1.549
 X94  CAQ  OAG   deloc   1.242  0.020  1.242
 X94  CAQ  OAD   deloc   1.249  0.020  1.249
 X94  CAA  HAA1  single  0.970  0.020  1.090
 X94  CAA  HAA2  single  0.970  0.020  1.090
 X94  CAA  HAA3  single  0.970  0.020  1.090
 X94  CAH  HAH1  single  0.970  0.020  1.090
 X94  CAH  HAH2  single  0.970  0.020  1.090
 X94  CAK  HAK1  single  0.970  0.020  1.090
 X94  CAK  HAK2  single  0.970  0.020  1.090
 X94  CAU  HAU   single  0.970  0.020  1.090
 X94  N    H     single  0.860  0.020  1.020
 X94  CA   HA    single  0.970  0.020  1.090
 X94  CB   HB1C  single  0.970  0.020  1.090
 X94  CB   HB2C  single  0.970  0.020  1.090
 X94  CB   HB3C  single  0.970  0.020  1.090
 X94  CAW  HAW   single  0.970  0.020  1.090
 X94  CAV  HAV   single  0.970  0.020  1.090
 X94  CAM  HAM1  single  0.970  0.020  1.090
 X94  CAM  HAM2  single  0.970  0.020  1.090
 X94  CAT  HAT   single  0.970  0.020  1.090
 X94  CAJ  HAJ1  single  0.970  0.020  1.090
 X94  CAJ  HAJ2  single  0.970  0.020  1.090
 X94  CAI  HAI1  single  0.970  0.020  1.090
 X94  CAI  HAI2  single  0.970  0.020  1.090
 X94  CAL  HAL1  single  0.970  0.020  1.090
 X94  CAL  HAL2  single  0.970  0.020  1.090
 X94  CAN  HAN1  single  0.970  0.020  1.090
 X94  CAN  HAN2  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
 X94  HAA3  CAA  HAA2  107.59  3.000
 X94  HAA3  CAA  HAA1  107.45  3.000
 X94  HAA2  CAA  HAA1  107.36  3.000
 X94  HAA3  CAA  CAH   111.67  3.000
 X94  HAA2  CAA  CAH   111.44  3.000
 X94  HAA1  CAA  CAH   111.11  3.000
 X94  HAH2  CAH  HAH1  105.69  3.000
 X94  HAH2  CAH  CAK   109.13  3.000
 X94  HAH1  CAH  CAK   110.17  3.000
 X94  HAH2  CAH  CAA   109.40  3.000
 X94  HAH1  CAH  CAA   109.65  3.000
 X94  CAK   CAH  CAA   112.58  3.000
 X94  HAK2  CAK  HAK1  106.48  3.000
 X94  HAK2  CAK  CAU   108.75  3.000
 X94  HAK1  CAK  CAU   109.18  3.000
 X94  HAK2  CAK  CAH   109.42  3.000
 X94  HAK1  CAK  CAH   109.40  3.000
 X94  CAU   CAK  CAH   113.37  3.000
 X94  HAU   CAU  N     110.63  3.000
 X94  HAU   CAU  CAP   105.76  3.000
 X94  N     CAU  CAP   111.69  3.000
 X94  HAU   CAU  CAK   106.86  3.000
 X94  N     CAU  CAK   110.97  3.000
 X94  CAP   CAU  CAK   110.69  3.000
 X94  OAC   CAP  OAF   126.30  3.000
 X94  OAC   CAP  CAU   117.49  3.000
 X94  OAF   CAP  CAU   116.22  3.000
 X94  H     N    CA    109.07  3.000
 X94  H     N    CAU   106.61  3.000
 X94  CA    N    CAU   115.80  3.000
 X94  HA    CA   C     110.31  3.000
 X94  HA    CA   CB    109.22  3.000
 X94  C     CA   CB    108.27  3.000
 X94  HA    CA   N     107.40  3.000
 X94  C     CA   N     107.65  3.000
 X94  CB    CA   N     113.98  3.000
 X94  HB3C  CB   HB2C  107.93  3.000
 X94  HB3C  CB   HB1C  107.86  3.000
 X94  HB2C  CB   HB1C  107.26  3.000
 X94  HB3C  CB   CA    110.36  3.000
 X94  HB2C  CB   CA    110.71  3.000
 X94  HB1C  CB   CA    112.53  3.000
 X94  NAX   C    O     122.34  3.000
 X94  NAX   C    CA    118.91  3.000
 X94  O     C    CA    118.72  3.000
 X94  CAV   NAX  CAW   112.52  3.000
 X94  CAV   NAX  C     123.99  3.000
 X94  CAW   NAX  C     120.72  3.000
 X94  HAW   CAW  CAT   108.11  3.000
 X94  HAW   CAW  CAM   107.54  3.000
 X94  CAT   CAW  CAM   113.78  3.000
 X94  HAW   CAW  NAX   107.64  3.000
 X94  CAT   CAW  NAX   103.86  3.000
 X94  CAM   CAW  NAX   115.55  3.000
 X94  HAL2  CAL  HAL1  106.07  3.000
 X94  HAL2  CAL  CAT   109.81  3.000
 X94  HAL1  CAL  CAT   108.06  3.000
 X94  HAL2  CAL  CAI   107.53  3.000
 X94  HAL1  CAL  CAI   110.71  3.000
 X94  CAT   CAL  CAI   114.35  3.000
 X94  HAI2  CAI  HAI1  106.59  3.000
 X94  HAI2  CAI  CAJ   109.36  3.000
 X94  HAI1  CAI  CAJ   111.10  3.000
 X94  HAI2  CAI  CAL   110.64  3.000
 X94  HAI1  CAI  CAL   109.57  3.000
 X94  CAJ   CAI  CAL   109.55  3.000
 X94  HAJ2  CAJ  HAJ1  107.35  3.000
 X94  HAJ2  CAJ  CAM   109.79  3.000
 X94  HAJ1  CAJ  CAM   109.71  3.000
 X94  HAJ2  CAJ  CAI   110.96  3.000
 X94  HAJ1  CAJ  CAI   109.52  3.000
 X94  CAM   CAJ  CAI   109.49  3.000
 X94  HAM2  CAM  HAM1  105.94  3.000
 X94  HAM2  CAM  CAJ   111.50  3.000
 X94  HAM1  CAM  CAJ   108.56  3.000
 X94  HAM2  CAM  CAW   110.12  3.000
 X94  HAM1  CAM  CAW   106.83  3.000
 X94  CAJ   CAM  CAW   113.49  3.000
 X94  HAT   CAT  CAN   111.40  3.000
 X94  HAT   CAT  CAL   108.40  3.000
 X94  CAN   CAT  CAL   110.87  3.000
 X94  HAT   CAT  CAW   108.23  3.000
 X94  CAN   CAT  CAW   102.27  3.000
 X94  CAL   CAT  CAW   115.59  3.000
 X94  HAN2  CAN  HAN1  107.43  3.000
 X94  HAN2  CAN  CAV   111.95  3.000
 X94  HAN1  CAN  CAV   109.76  3.000
 X94  HAN2  CAN  CAT   113.38  3.000
 X94  HAN1  CAN  CAT   110.29  3.000
 X94  CAV   CAN  CAT   104.03  3.000
 X94  HAV   CAV  CAQ   106.29  3.000
 X94  HAV   CAV  CAN   108.38  3.000
 X94  CAQ   CAV  CAN   114.21  3.000
 X94  HAV   CAV  NAX   109.95  3.000
 X94  CAQ   CAV  NAX   115.37  3.000
 X94  CAN   CAV  NAX   102.50  3.000
 X94  OAG   CAQ  OAD   127.27  3.000
 X94  OAD   CAQ  CAV   114.01  3.000
 X94  OAG   CAQ  CAV   118.71  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
 X94  CONST_01  CAW   NAX  C    CA   180.00   0.0  0
 X94  CONST_02  CAV   NAX  C    CA     0.00   0.0  0
 X94  CONST_03  CAW   NAX  C    O      0.00   0.0  0
 X94  Var_01    CAI   CAJ  CAM  CAW   59.23  30.0  1
 X94  Var_02    CAM   CAJ  CAI  CAL  -62.46  30.0  1
 X94  Var_03    CAT   CAL  CAI  CAJ   53.62  30.0  1
 X94  Var_04    CAU   CAK  CAH  CAA  177.28  30.0  3
 X94  Var_05    HAA1  CAA  CAH  CAK  -60.91  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
 X94  chir_01  CAU  CAK  CAP  N    negativ
 X94  chir_02  CA   N    CB   C    negativ
 X94  chir_03  CAW  NAX  CAT  CAM  positiv
 X94  chir_04  CAT  CAN  CAL  CAW  positiv
 X94  chir_05  CAV  NAX  CAQ  CAN  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
 X94  plan-1  CA   0.020
 X94  plan-1  C    0.020
 X94  plan-1  O    0.020
 X94  plan-1  NAX  0.020
 X94  plan-1  CAW  0.020
 X94  plan-1  CAV  0.020
 X94  plan-2  CAU  0.020
 X94  plan-2  CAP  0.020
 X94  plan-2  OAF  0.020
 X94  plan-2  OAC  0.020
 X94  plan-3  CAV  0.020
 X94  plan-3  CAQ  0.020
 X94  plan-3  OAD  0.020
 X94  plan-3  OAG  0.020

