# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 10:19:38 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  27  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  -0.615   0.4735  -1.1516  -0.7722
 Q42  CBB   C  CH1   0  -0.045  -0.8670  -0.5822  -0.6556
 Q42  CAP   C  CH2   0  -0.448  -1.9178  -1.4565  -0.0040
 Q42  CAM   C  CH2   0  -0.437  -3.2326  -0.6715   0.0574
 Q42  CAL   C  CH2   0  -0.435  -3.0806   0.6994   0.7220
 Q42  CAO   C  CH2   0  -0.426  -1.9621   1.5393   0.0962
 Q42  CAZ   C  CH1   0  -0.221  -0.6842   0.7222   0.1066
 Q42  CAR   C  CH2   0  -0.489   0.5716   1.2664  -0.5505
 Q42  CBA   C  CH1   0  -0.185   1.4124  -0.0294  -0.7717
 Q42  CAU   C  C     0   0.526   2.4512  -0.1682   0.3176
 Q42  OAF   O  O     0  -0.440   2.3812  -0.9353   1.2464
 Q42  OAC   O  OH1   0  -0.590   3.4590   0.6754   0.1423
 Q42  HBB   H  HCH1  0   0.207  -1.2217  -0.3308  -1.6670
 Q42  HBA   H  HCH1  0   0.274   1.9453   0.0389  -1.7251
 Q42  HAP1  H  HCH2  0   0.234  -2.0597  -2.3897  -0.5549
 Q42  HAP2  H  HCH2  0   0.212  -1.5916  -1.7257   1.0074
 Q42  HAZ   H  HCH1  0   0.219  -0.4505   0.4679   1.1508
 Q42  HAM1  H  HCH2  0   0.214  -3.6095  -0.5356  -0.9621
 Q42  HAM2  H  HCH2  0   0.233  -3.9882  -1.2550   0.5882
 Q42  HAL1  H  HCH2  0   0.230  -4.0301   1.2377   0.6717
 Q42  HAL2  H  HCH2  0   0.213  -2.8628   0.5612   1.7865
 Q42  HAO1  H  HCH2  0   0.210  -2.2237   1.8048  -0.9344
 Q42  HAO2  H  HCH2  0   0.230  -1.8425   2.4776   0.6437
 Q42  HAR1  H  HCH2  0   0.246   0.3337   1.7142  -1.5182
 Q42  HAR2  H  HCH2  0   0.256   1.0908   2.0218   0.0397
 Q42  HAC   H  HOH1  0   0.483   4.0943   0.5936   0.8693
 Q42  H2    H  HNH1  0   0.344   0.6554  -1.7428   0.0316

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  1.461  0.020  1.461
 Q42  NBC  CBA   single  1.463  0.020  1.463
 Q42  CBB  CAP   single  1.514  0.020  1.514
 Q42  CBB  CAZ   single  1.522  0.020  1.522
 Q42  CAP  CAM   single  1.533  0.020  1.533
 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  1.518  0.020  1.518
 Q42  CAR  CBA   single  1.560  0.020  1.560
 Q42  CBA  CAU   single  1.512  0.020  1.512
 Q42  CAU  OAF   double  1.207  0.020  1.207
 Q42  CAU  OAC   single  1.326  0.020  1.326
 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  OAC  HAC   single  0.850  0.020  0.980
 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   109.37  3.000
 Q42  H2    NBC  CBB   109.18  3.000
 Q42  CBA   NBC  CBB   106.85  3.000
 Q42  HBB   CBB  CAZ   107.64  3.000
 Q42  HBB   CBB  CAP   107.67  3.000
 Q42  CAZ   CBB  CAP   111.26  3.000
 Q42  HBB   CBB  NBC   108.14  3.000
 Q42  CAZ   CBB  NBC   105.30  3.000
 Q42  CAP   CBB  NBC   116.49  3.000
 Q42  HAP2  CAP  HAP1  107.10  3.000
 Q42  HAP2  CAP  CAM   110.13  3.000
 Q42  HAP1  CAP  CAM   110.25  3.000
 Q42  HAP2  CAP  CBB   109.41  3.000
 Q42  HAP1  CAP  CBB   111.48  3.000
 Q42  CAM   CAP  CBB   108.47  3.000
 Q42  HAM2  CAM  HAM1  106.29  3.000
 Q42  HAM2  CAM  CAL   109.64  3.000
 Q42  HAM1  CAM  CAL   109.10  3.000
 Q42  HAM2  CAM  CAP   109.83  3.000
 Q42  HAM1  CAM  CAP   108.75  3.000
 Q42  CAL   CAM  CAP   113.00  3.000
 Q42  HAL2  CAL  HAL1  106.24  3.000
 Q42  HAL2  CAL  CAO   108.72  3.000
 Q42  HAL1  CAL  CAO   110.21  3.000
 Q42  HAL2  CAL  CAM   109.18  3.000
 Q42  HAL1  CAL  CAM   109.56  3.000
 Q42  CAO   CAL  CAM   112.70  3.000
 Q42  HAO2  CAO  HAO1  106.81  3.000
 Q42  HAO2  CAO  CAZ   111.52  3.000
 Q42  HAO1  CAO  CAZ   109.76  3.000
 Q42  HAO2  CAO  CAL   110.24  3.000
 Q42  HAO1  CAO  CAL   110.04  3.000
 Q42  CAZ   CAO  CAL   108.48  3.000
 Q42  HAZ   CAZ  CAR   108.54  3.000
 Q42  HAZ   CAZ  CAO   108.07  3.000
 Q42  CAR   CAZ  CAO   120.05  3.000
 Q42  HAZ   CAZ  CBB   107.63  3.000
 Q42  CAR   CAZ  CBB   100.94  3.000
 Q42  CAO   CAZ  CBB   110.92  3.000
 Q42  HAR2  CAR  HAR1  107.42  3.000
 Q42  HAR2  CAR  CBA   113.30  3.000
 Q42  HAR1  CAR  CBA   109.40  3.000
 Q42  HAR2  CAR  CAZ   114.08  3.000
 Q42  HAR1  CAR  CAZ   110.50  3.000
 Q42  CBA   CAR  CAZ   102.09  3.000
 Q42  HBA   CBA  CAU   107.39  3.000
 Q42  HBA   CBA  CAR   109.52  3.000
 Q42  CAU   CBA  CAR   110.14  3.000
 Q42  HBA   CBA  NBC   111.11  3.000
 Q42  CAU   CBA  NBC   111.76  3.000
 Q42  CAR   CBA  NBC   106.93  3.000
 Q42  OAC   CAU  OAF   123.39  3.000
 Q42  OAC   CAU  CBA   111.63  3.000
 Q42  OAF   CAU  CBA   124.97  3.000
 Q42  HAC   OAC  CAU   110.21  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  CONST_01  HAC  OAC  CAU  CBA  180.00   0.0  0
 Q42  Var_01    CAL  CAM  CAP  CBB  -53.21  30.0  1
 Q42  Var_02    CAO  CAL  CAM  CAP   52.86  30.0  1
 Q42  Var_03    CAZ  CAO  CAL  CAM  -53.70  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
 Q42  plan-1  HAC  0.020

