# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:21:36 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 4,5,6,7-tetrahydro-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCc2cc[nH]c2C1
#
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
 JZ9  JZ9  4,5,6,7-tetrahydro-1H-indole  ligand  20  9  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JZ9
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
 JZ9  CAA   C  CR15  0  -0.071  -2.4545  -0.0572   0.0210
 JZ9  CAB   C  CR15  0  -0.416  -1.6719  -1.1835   0.0850
 JZ9  CAC   C  CH2   0  -0.445   2.1317  -0.6695  -0.3457
 JZ9  CAD   C  CH2   0  -0.442   2.1035   0.7021   0.3270
 JZ9  CAE   C  CH2   0  -0.495   0.9561  -1.5434   0.0979
 JZ9  CAF   C  CH2   0  -0.504   0.8660   1.5072  -0.0776
 JZ9  NAG   N  NR15  0  -0.639  -1.6276   1.0242  -0.0418
 JZ9  CAH   C  CR5   0  -0.006  -0.3156  -0.7548   0.0578
 JZ9  CAI   C  CR5   0   0.303  -0.3278   0.6170  -0.0181
 JZ9  HAA   H  HCR5  0   0.260  -3.5261   0.0575   0.0159
 JZ9  HAB   H  HCR5  0   0.229  -2.0307  -2.2004   0.1440
 JZ9  HAC   H  HCH2  0   0.217   2.0968  -0.5362  -1.4318
 JZ9  HACA  H  HCH2  0   0.229   3.0744  -1.1737  -0.1227
 JZ9  HAD   H  HCH2  0   0.220   2.1107   0.5695   1.4134
 JZ9  HADA  H  HCH2  0   0.232   3.0044   1.2647   0.0744
 JZ9  HAE   H  HCH2  0   0.230   0.8875  -2.4275  -0.5421
 JZ9  HAEA  H  HCH2  0   0.221   1.1440  -1.9192   1.1101
 JZ9  HAF   H  HCH2  0   0.242   0.7487   2.3735   0.5799
 JZ9  HAFA  H  HCH2  0   0.234   0.9994   1.9066  -1.0894
 JZ9  HNAG  H  HNR5  0   0.400  -1.9351   1.9809  -0.0984

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
 JZ9  CAA  CAB   aromatic  1.373  0.020  1.373
 JZ9  CAA  NAG   aromatic  1.363  0.020  1.363
 JZ9  CAB  CAH   aromatic  1.423  0.020  1.423
 JZ9  CAC  CAD   single    1.528  0.020  1.528
 JZ9  CAC  CAE   single    1.530  0.020  1.530
 JZ9  CAD  CAF   single    1.531  0.020  1.531
 JZ9  CAE  CAH   single    1.497  0.020  1.497
 JZ9  CAF  CAI   single    1.490  0.020  1.490
 JZ9  NAG  CAI   aromatic  1.362  0.020  1.362
 JZ9  CAH  CAI   aromatic  1.374  0.020  1.374
 JZ9  CAA  HAA   single    0.930  0.020  1.080
 JZ9  CAB  HAB   single    0.930  0.020  1.080
 JZ9  CAC  HAC   single    0.970  0.020  1.090
 JZ9  CAC  HACA  single    0.970  0.020  1.090
 JZ9  CAD  HAD   single    0.970  0.020  1.090
 JZ9  CAD  HADA  single    0.970  0.020  1.090
 JZ9  CAE  HAE   single    0.970  0.020  1.090
 JZ9  CAE  HAEA  single    0.970  0.020  1.090
 JZ9  CAF  HAF   single    0.970  0.020  1.090
 JZ9  CAF  HAFA  single    0.970  0.020  1.090
 JZ9  NAG  HNAG  single    0.860  0.020  1.020

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
 JZ9  HAA   CAA  NAG  121.24  3.000
 JZ9  HAA   CAA  CAB  130.87  3.000
 JZ9  NAG   CAA  CAB  107.89  3.000
 JZ9  HAB   CAB  CAH  126.98  3.000
 JZ9  HAB   CAB  CAA  125.85  3.000
 JZ9  CAH   CAB  CAA  107.17  3.000
 JZ9  HACA  CAC  HAC  106.64  3.000
 JZ9  HACA  CAC  CAE  109.89  3.000
 JZ9  HAC   CAC  CAE  109.42  3.000
 JZ9  HACA  CAC  CAD  109.91  3.000
 JZ9  HAC   CAC  CAD  109.07  3.000
 JZ9  CAE   CAC  CAD  111.76  3.000
 JZ9  HADA  CAD  HAD  106.66  3.000
 JZ9  HADA  CAD  CAF  109.57  3.000
 JZ9  HAD   CAD  CAF  109.36  3.000
 JZ9  HADA  CAD  CAC  110.21  3.000
 JZ9  HAD   CAD  CAC  109.15  3.000
 JZ9  CAF   CAD  CAC  111.75  3.000
 JZ9  HAEA  CAE  HAE  105.91  3.000
 JZ9  HAEA  CAE  CAH  110.55  3.000
 JZ9  HAE   CAE  CAH  110.91  3.000
 JZ9  HAEA  CAE  CAC  109.38  3.000
 JZ9  HAE   CAE  CAC  109.89  3.000
 JZ9  CAH   CAE  CAC  110.12  3.000
 JZ9  HAFA  CAF  HAF  106.22  3.000
 JZ9  HAFA  CAF  CAI  110.62  3.000
 JZ9  HAF   CAF  CAI  111.30  3.000
 JZ9  HAFA  CAF  CAD  109.71  3.000
 JZ9  HAF   CAF  CAD  110.14  3.000
 JZ9  CAI   CAF  CAD  108.84  3.000
 JZ9  HNAG  NAG  CAI  125.21  3.000
 JZ9  HNAG  NAG  CAA  124.85  3.000
 JZ9  CAI   NAG  CAA  109.93  3.000
 JZ9  CAI   CAH  CAE  122.34  3.000
 JZ9  CAI   CAH  CAB  107.07  3.000
 JZ9  CAE   CAH  CAB  130.59  3.000
 JZ9  CAH   CAI  NAG  107.93  3.000
 JZ9  CAH   CAI  CAF  126.26  3.000
 JZ9  NAG   CAI  CAF  125.80  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
 JZ9  CONST_01  CAI   CAH  CAB  CAA    0.00   0.0  0
 JZ9  CONST_02  CAH   CAI  NAG  CAA    0.00   0.0  0
 JZ9  CONST_03  CAI   NAG  CAA  CAB    0.00   0.0  0
 JZ9  CONST_04  NAG   CAI  CAH  CAB    0.00   0.0  0
 JZ9  CONST_05  CAH   CAB  CAA  NAG    0.00   0.0  0
 JZ9  CONST_06  HNAG  NAG  CAA  CAB  180.00   0.0  0
 JZ9  CONST_07  HAB   CAB  CAH  CAE    0.00   0.0  0
 JZ9  CONST_08  HAA   CAA  CAB  CAH  180.00   0.0  0
 JZ9  Var_01    CAC   CAE  CAH  CAB  164.18  30.0  1
 JZ9  Var_02    CAI   CAF  CAD  CAC   44.82  30.0  1
 JZ9  Var_03    CAH   CAE  CAC  CAD   46.13  30.0  1
 JZ9  Var_04    NAG   CAI  CAF  CAD  165.83  30.0  1
 JZ9  Var_05    CAF   CAD  CAC  CAE  -63.75  30.0  1

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
 JZ9  plan-1  CAA   0.020
 JZ9  plan-1  CAB   0.020
 JZ9  plan-1  CAE   0.020
 JZ9  plan-1  CAF   0.020
 JZ9  plan-1  NAG   0.020
 JZ9  plan-1  CAH   0.020
 JZ9  plan-1  CAI   0.020
 JZ9  plan-1  HAA   0.020
 JZ9  plan-1  HAB   0.020
 JZ9  plan-1  HNAG  0.020

