# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:39:25 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S,3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@H]2CCCC[C@@H]2N1
#
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
 Q42  Q42  '(2S,3aR,7aS)-2,3,3a,4,5,6,7,7a-octahydro-1H-indole-2-carboxylic acid'  ligand  26  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q42
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
 Q42  NBC   N  NH1    0  -0.621   0.4756  -1.1208  -0.7281
 Q42  CBB   C  CH1    0  -0.042  -0.8683  -0.5640  -0.6378
 Q42  CAP   C  CH2    0  -0.444  -1.9324  -1.4518  -0.0253
 Q42  CAM   C  CH2    0  -0.435  -3.2550  -0.6792   0.0119
 Q42  CAL   C  CH2    0  -0.432  -3.1313   0.6837   0.6989
 Q42  CAO   C  CH2    0  -0.425  -2.0028   1.5398   0.1145
 Q42  CAZ   C  CH1    0  -0.220  -0.7168   0.7356   0.1433
 Q42  CAR   C  CH2    0  -0.471   0.5521   1.2909  -0.4800
 Q42  CBA   C  CH1    0  -0.199   1.4113   0.0116  -0.6800
 Q42  CAU   C  C      0   0.398   2.4610  -0.1334   0.4443
 Q42  OAF   O  O      0  -0.601   2.3242  -1.0783   1.2485
 Q42  OAC   O  OC    -1  -0.617   3.3642   0.7255   0.4538
 Q42  HBB   H  HCH1   0   0.189  -1.2044  -0.2986  -1.6536
 Q42  HBA   H  HCH1   0   0.212   1.9627   0.0928  -1.6239
 Q42  HAP1  H  HCH2   0   0.226  -2.0526  -2.3801  -0.5905
 Q42  HAP2  H  HCH2   0   0.206  -1.6314  -1.7322   0.9912
 Q42  HAZ   H  HCH1   0   0.206  -0.5036   0.4692   1.1892
 Q42  HAM1  H  HCH2   0   0.210  -3.6052  -0.5312  -1.0156
 Q42  HAM2  H  HCH2   0   0.228  -4.0215  -1.2749   0.5134
 Q42  HAL1  H  HCH2   0   0.225  -4.0842   1.2149   0.6321
 Q42  HAL2  H  HCH2   0   0.209  -2.9403   0.5313   1.7668
 Q42  HAO1  H  HCH2   0   0.204  -2.2420   1.8184  -0.9185
 Q42  HAO2  H  HCH2   0   0.223  -1.9078   2.4722   0.6777
 Q42  HAR1  H  HCH2   0   0.214   0.3189   1.7544  -1.4439
 Q42  HAR2  H  HCH2   0   0.229   1.0582   2.0421   0.1268
 Q42  H2    H  HNH1   0   0.327   0.6625  -1.6659   0.1098

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
 Q42  NBC  CBB   single  1.457  0.020  1.457
 Q42  NBC  CBA   single  1.470  0.020  1.470
 Q42  CBB  CAP   single  1.515  0.020  1.515
 Q42  CBB  CAZ   single  1.524  0.020  1.524
 Q42  CAP  CAM   single  1.532  0.020  1.532
 Q42  CAM  CAL   single  1.531  0.020  1.531
 Q42  CAL  CAO   single  1.532  0.020  1.532
 Q42  CAO  CAZ   single  1.517  0.020  1.517
 Q42  CAZ  CAR   single  1.519  0.020  1.519
 Q42  CAR  CBA   single  1.554  0.020  1.554
 Q42  CBA  CAU   single  1.545  0.020  1.545
 Q42  CAU  OAF   deloc   1.248  0.020  1.248
 Q42  CAU  OAC   deloc   1.246  0.020  1.246
 Q42  CBB  HBB   single  0.970  0.020  1.090
 Q42  CBA  HBA   single  0.970  0.020  1.090
 Q42  CAP  HAP1  single  0.970  0.020  1.090
 Q42  CAP  HAP2  single  0.970  0.020  1.090
 Q42  CAZ  HAZ   single  0.970  0.020  1.090
 Q42  CAM  HAM1  single  0.970  0.020  1.090
 Q42  CAM  HAM2  single  0.970  0.020  1.090
 Q42  CAL  HAL1  single  0.970  0.020  1.090
 Q42  CAL  HAL2  single  0.970  0.020  1.090
 Q42  CAO  HAO1  single  0.970  0.020  1.090
 Q42  CAO  HAO2  single  0.970  0.020  1.090
 Q42  CAR  HAR1  single  0.970  0.020  1.090
 Q42  CAR  HAR2  single  0.970  0.020  1.090
 Q42  NBC  H2    single  0.890  0.020  1.040

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
 Q42  H2    NBC  CBA   105.60  3.000
 Q42  H2    NBC  CBB   108.86  3.000
 Q42  CBA   NBC  CBB   106.90  3.000
 Q42  HBB   CBB  CAZ   107.29  3.000
 Q42  HBB   CBB  CAP   107.42  3.000
 Q42  CAZ   CBB  CAP   111.24  3.000
 Q42  HBB   CBB  NBC   108.42  3.000
 Q42  CAZ   CBB  NBC   105.42  3.000
 Q42  CAP   CBB  NBC   116.67  3.000
 Q42  HAP2  CAP  HAP1  106.99  3.000
 Q42  HAP2  CAP  CAM   110.09  3.000
 Q42  HAP1  CAP  CAM   110.23  3.000
 Q42  HAP2  CAP  CBB   109.37  3.000
 Q42  HAP1  CAP  CBB   111.45  3.000
 Q42  CAM   CAP  CBB   108.70  3.000
 Q42  HAM2  CAM  HAM1  106.25  3.000
 Q42  HAM2  CAM  CAL   109.63  3.000
 Q42  HAM1  CAM  CAL   109.05  3.000
 Q42  HAM2  CAM  CAP   109.98  3.000
 Q42  HAM1  CAM  CAP   108.74  3.000
 Q42  CAL   CAM  CAP   112.95  3.000
 Q42  HAL2  CAL  HAL1  106.22  3.000
 Q42  HAL2  CAL  CAO   108.73  3.000
 Q42  HAL1  CAL  CAO   110.31  3.000
 Q42  HAL2  CAL  CAM   109.12  3.000
 Q42  HAL1  CAL  CAM   109.56  3.000
 Q42  CAO   CAL  CAM   112.68  3.000
 Q42  HAO2  CAO  HAO1  106.71  3.000
 Q42  HAO2  CAO  CAZ   111.63  3.000
 Q42  HAO1  CAO  CAZ   109.73  3.000
 Q42  HAO2  CAO  CAL   110.12  3.000
 Q42  HAO1  CAO  CAL   109.91  3.000
 Q42  CAZ   CAO  CAL   108.72  3.000
 Q42  HAZ   CAZ  CAR   108.46  3.000
 Q42  HAZ   CAZ  CAO   108.10  3.000
 Q42  CAR   CAZ  CAO   120.44  3.000
 Q42  HAZ   CAZ  CBB   107.46  3.000
 Q42  CAR   CAZ  CBB   100.63  3.000
 Q42  CAO   CAZ  CBB   110.99  3.000
 Q42  HAR2  CAR  HAR1  107.29  3.000
 Q42  HAR2  CAR  CBA   112.47  3.000
 Q42  HAR1  CAR  CBA   110.68  3.000
 Q42  HAR2  CAR  CAZ   114.29  3.000
 Q42  HAR1  CAR  CAZ   109.76  3.000
 Q42  CBA   CAR  CAZ   102.34  3.000
 Q42  HBA   CBA  CAU   106.96  3.000
 Q42  HBA   CBA  CAR   109.15  3.000
 Q42  CAU   CBA  CAR   111.06  3.000
 Q42  HBA   CBA  NBC   110.43  3.000
 Q42  CAU   CBA  NBC   112.59  3.000
 Q42  CAR   CBA  NBC   106.65  3.000
 Q42  OAC   CAU  OAF   126.59  3.000
 Q42  OAC   CAU  CBA   115.68  3.000
 Q42  OAF   CAU  CBA   117.73  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
 Q42  Var_01  CAL  CAM  CAP  CBB  -53.25  30.0  1
 Q42  Var_02  CAO  CAL  CAM  CAP   52.80  30.0  1
 Q42  Var_03  CAZ  CAO  CAL  CAM  -53.59  30.0  1

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
 Q42  chir_01  CBB  NBC  CAP  CAZ  negativ
 Q42  chir_02  CAZ  CAR  CAO  CBB  negativ
 Q42  chir_03  CBA  NBC  CAR  CAU  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
 Q42  plan-1  CBA  0.020
 Q42  plan-1  CAU  0.020
 Q42  plan-1  OAF  0.020
 Q42  plan-1  OAC  0.020

