# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 19:16:36 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 5-methoxy-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2[nH]ccc2c1
#
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
 BZ3  BZ3  '5-methoxy-1H-indole      '  ligand  20  11  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BZ3
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
 BZ3  CAA   C  CH3   0  -0.432   3.7726   0.1285   0.0255
 BZ3  CAB   C  CR15  0  -0.024  -3.1536  -0.3389   0.0030
 BZ3  CAC   C  CR16  0  -0.405   1.1542   1.1454   0.0316
 BZ3  CAD   C  CR15  0  -0.427  -2.2155  -1.3327  -0.0074
 BZ3  CAE   C  CR16  0  -0.290  -0.1454   1.6214   0.0339
 BZ3  CAF   C  CR16  0  -0.452   0.3802  -1.1551   0.0008
 BZ3  NAG   N  NR15  0  -0.680  -2.5420   0.8785   0.0190
 BZ3  OAH   O  O2    0  -0.483   2.6736  -0.7549   0.0130
 BZ3  CAI   C  CR6   0   0.376   1.4192  -0.2375   0.0153
 BZ3  CAJ   C  CR56  0   0.076  -0.9381  -0.6905   0.0036
 BZ3  CAK   C  CR56  0   0.328  -1.1849   0.7007   0.0202
 BZ3  HAA   H  HCH3  0   0.222   3.7895   0.7569   0.9206
 BZ3  HAAA  H  HCH3  0   0.255   4.6674  -0.4901   0.0224
 BZ3  HAAB  H  HCH3  0   0.222   3.7958   0.7750  -0.8564
 BZ3  HAC   H  HCR6  0   0.272   1.9610   1.8647   0.0427
 BZ3  HAD   H  HCR5  0   0.245  -2.4133  -2.3927  -0.0196
 BZ3  HAE   H  HCR6  0   0.263  -0.3334   2.6875   0.0465
 BZ3  HAF   H  HCR6  0   0.247   0.5950  -2.2173  -0.0119
 BZ3  HNAG  H  HNR5  0   0.408  -3.0182   1.7645   0.0293
 BZ3  HAB   H  HCR5  0   0.280  -4.2296  -0.4096   0.0007

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
 BZ3  OAH  CAA   single    1.410  0.020  1.410
 BZ3  CAA  HAA   single    0.970  0.020  1.090
 BZ3  CAA  HAAA  single    0.970  0.020  1.090
 BZ3  CAA  HAAB  single    0.970  0.020  1.090
 BZ3  NAG  CAB   aromatic  1.363  0.020  1.363
 BZ3  CAD  CAB   aromatic  1.367  0.020  1.367
 BZ3  CAB  HAB   single    0.930  0.020  1.080
 BZ3  CAC  CAI   aromatic  1.408  0.020  1.408
 BZ3  CAC  CAE   aromatic  1.384  0.020  1.384
 BZ3  CAC  HAC   single    0.930  0.020  1.080
 BZ3  CAJ  CAD   aromatic  1.430  0.020  1.430
 BZ3  CAD  HAD   single    0.930  0.020  1.080
 BZ3  CAE  CAK   aromatic  1.389  0.020  1.389
 BZ3  CAE  HAE   single    0.930  0.020  1.080
 BZ3  CAI  CAF   aromatic  1.386  0.020  1.386
 BZ3  CAF  CAJ   aromatic  1.398  0.020  1.398
 BZ3  CAF  HAF   single    0.930  0.020  1.080
 BZ3  CAK  NAG   aromatic  1.369  0.020  1.369
 BZ3  OAH  CAI   single    1.357  0.020  1.357
 BZ3  CAK  CAJ   aromatic  1.413  0.020  1.413
 BZ3  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
 BZ3  HAAB  CAA  HAAA  108.44  3.000
 BZ3  HAAB  CAA  HAA   108.66  3.000
 BZ3  HAAA  CAA  HAA   108.44  3.000
 BZ3  HAAB  CAA  OAH   112.31  3.000
 BZ3  HAAA  CAA  OAH   106.55  3.000
 BZ3  HAA   CAA  OAH   112.29  3.000
 BZ3  HAB   CAB  NAG   120.43  3.000
 BZ3  HAB   CAB  CAD   129.59  3.000
 BZ3  NAG   CAB  CAD   109.98  3.000
 BZ3  HAC   CAC  CAI   120.88  3.000
 BZ3  HAC   CAC  CAE   118.17  3.000
 BZ3  CAI   CAC  CAE   120.96  3.000
 BZ3  HAD   CAD  CAJ   127.26  3.000
 BZ3  HAD   CAD  CAB   126.08  3.000
 BZ3  CAJ   CAD  CAB   106.66  3.000
 BZ3  HAE   CAE  CAK   121.53  3.000
 BZ3  HAE   CAE  CAC   120.11  3.000
 BZ3  CAK   CAE  CAC   118.35  3.000
 BZ3  HAF   CAF  CAJ   120.84  3.000
 BZ3  HAF   CAF  CAI   120.02  3.000
 BZ3  CAJ   CAF  CAI   119.14  3.000
 BZ3  HNAG  NAG  CAK   125.72  3.000
 BZ3  HNAG  NAG  CAB   125.07  3.000
 BZ3  CAK   NAG  CAB   109.21  3.000
 BZ3  CAI   OAH  CAA   118.79  3.000
 BZ3  OAH   CAI  CAF   116.14  3.000
 BZ3  OAH   CAI  CAC   123.25  3.000
 BZ3  CAF   CAI  CAC   120.61  3.000
 BZ3  CAK   CAJ  CAF   119.47  3.000
 BZ3  CAK   CAJ  CAD   106.63  3.000
 BZ3  CAF   CAJ  CAD   133.89  3.000
 BZ3  CAJ   CAK  NAG   107.53  3.000
 BZ3  CAJ   CAK  CAE   121.47  3.000
 BZ3  NAG   CAK  CAE   131.00  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
 BZ3  CONST_01  CAE   CAK  NAG  CAB  180.00   0.0  0
 BZ3  CONST_02  CAJ   CAK  NAG  CAB    0.00   0.0  0
 BZ3  CONST_03  CAF   CAJ  CAD  CAB  180.00   0.0  0
 BZ3  CONST_04  CAK   CAJ  CAD  CAB    0.00   0.0  0
 BZ3  CONST_05  CAJ   CAF  CAI  CAC    0.00   0.0  0
 BZ3  CONST_06  NAG   CAK  CAE  CAC  180.00   0.0  0
 BZ3  CONST_07  CAJ   CAK  CAE  CAC    0.00   0.0  0
 BZ3  CONST_08  CAK   NAG  CAB  CAD    0.00   0.0  0
 BZ3  CONST_09  CAI   CAF  CAJ  CAD  180.00   0.0  0
 BZ3  CONST_10  CAE   CAK  CAJ  CAD  180.00   0.0  0
 BZ3  CONST_11  NAG   CAK  CAJ  CAD    0.00   0.0  0
 BZ3  CONST_12  CAF   CAI  CAC  CAE    0.00   0.0  0
 BZ3  CONST_13  CAF   CAJ  CAK  CAE    0.00   0.0  0
 BZ3  CONST_14  NAG   CAK  CAJ  CAF  180.00   0.0  0
 BZ3  CONST_15  CAJ   CAD  CAB  NAG    0.00   0.0  0
 BZ3  CONST_16  CAK   CAE  CAC  CAI    0.00   0.0  0
 BZ3  CONST_17  CAK   CAJ  CAF  CAI    0.00   0.0  0
 BZ3  CONST_18  OAH   CAI  CAC  CAE  180.00   0.0  0
 BZ3  CONST_19  CAJ   CAF  CAI  OAH  180.00   0.0  0
 BZ3  CONST_20  HAF   CAF  CAI  CAC  180.00   0.0  0
 BZ3  CONST_21  HNAG  NAG  CAB  CAD  180.00   0.0  0
 BZ3  CONST_22  HAC   CAC  CAI  CAF  180.00   0.0  0
 BZ3  CONST_23  HAD   CAD  CAJ  CAF    0.00   0.0  0
 BZ3  CONST_24  HAE   CAE  CAK  NAG    0.00   0.0  0
 BZ3  CONST_25  HAB   CAB  CAD  CAJ  180.00   0.0  0
 BZ3  Var_01    CAC   CAI  OAH  CAA   -0.09  30.0  2
 BZ3  Var_02    HAA   CAA  OAH  CAI   61.35  30.0  3

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
 BZ3  plan-1  CAB   0.020
 BZ3  plan-1  CAC   0.020
 BZ3  plan-1  CAD   0.020
 BZ3  plan-1  CAE   0.020
 BZ3  plan-1  CAF   0.020
 BZ3  plan-1  NAG   0.020
 BZ3  plan-1  OAH   0.020
 BZ3  plan-1  CAI   0.020
 BZ3  plan-1  CAJ   0.020
 BZ3  plan-1  CAK   0.020
 BZ3  plan-1  HAC   0.020
 BZ3  plan-1  HAD   0.020
 BZ3  plan-1  HAE   0.020
 BZ3  plan-1  HAF   0.020
 BZ3  plan-1  HNAG  0.020
 BZ3  plan-1  HAB   0.020

