# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 07:40:25 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1H-indole-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1ccc2cc[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
 F9Y  F9Y  '1H-indole-6-carbonitrile '  ligand  17  11  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F9Y
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
 F9Y  CAB  C  CSP   0   0.013  -2.8860  -0.2937  -0.0507
 F9Y  CAC  C  CR6   0  -0.007  -1.4986   0.0375  -0.0331
 F9Y  CAD  C  CR16  0  -0.245  -1.1157   1.3948  -0.0215
 F9Y  CAE  C  CR16  0  -0.304   0.2136   1.7472  -0.0048
 F9Y  CAF  C  CR56  0   0.084   1.1865   0.7408   0.0002
 F9Y  CAG  C  CR56  0   0.389   0.7761  -0.6127  -0.0113
 F9Y  CAH  C  CR16  0  -0.271  -0.5598  -0.9844  -0.0278
 F9Y  CAJ  C  CR15  0   0.010   3.0023  -0.5665   0.0128
 F9Y  CAK  C  CR15  0  -0.377   2.6111   0.7397   0.0155
 F9Y  NAA  N  NS    0  -0.200  -4.0085  -0.5551  -0.0642
 F9Y  NAI  N  NR15  0  -0.689   1.9056  -1.3789  -0.0031
 F9Y  HAD  H  HCR6  0   0.254  -1.8807   2.1582  -0.0263
 F9Y  HAE  H  HCR6  0   0.237   0.4974   2.7910   0.0031
 F9Y  HAH  H  HCR6  0   0.246  -0.8699  -2.0207  -0.0343
 F9Y  HAJ  H  HCR5  0   0.255   3.9955  -0.9847   0.0227
 F9Y  HAK  H  HCR5  0   0.230   3.2635   1.5966   0.0267
 F9Y  HAI  H  HNR5  0   0.375   1.9294  -2.3823  -0.0095

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
 F9Y  NAA  CAB  triple    1.153  0.020  1.153
 F9Y  CAB  CAC  single    1.427  0.020  1.427
 F9Y  CAC  CAD  aromatic  1.410  0.020  1.410
 F9Y  CAC  CAH  aromatic  1.388  0.020  1.388
 F9Y  CAD  CAE  aromatic  1.375  0.020  1.375
 F9Y  CAH  CAG  aromatic  1.387  0.020  1.387
 F9Y  CAE  CAF  aromatic  1.400  0.020  1.400
 F9Y  CAG  CAF  aromatic  1.414  0.020  1.414
 F9Y  CAG  NAI  aromatic  1.365  0.020  1.365
 F9Y  CAF  CAK  aromatic  1.425  0.020  1.425
 F9Y  NAI  CAJ  aromatic  1.365  0.020  1.365
 F9Y  CAK  CAJ  aromatic  1.364  0.020  1.364
 F9Y  CAD  HAD  single    0.930  0.020  1.080
 F9Y  CAE  HAE  single    0.930  0.020  1.080
 F9Y  CAH  HAH  single    0.930  0.020  1.080
 F9Y  CAJ  HAJ  single    0.930  0.020  1.080
 F9Y  CAK  HAK  single    0.930  0.020  1.080
 F9Y  NAI  HAI  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
 F9Y  NAA  CAB  CAC  180.00  3.000
 F9Y  CAH  CAC  CAD  121.67  3.000
 F9Y  CAH  CAC  CAB  119.14  3.000
 F9Y  CAD  CAC  CAB  119.19  3.000
 F9Y  HAD  CAD  CAE  120.22  3.000
 F9Y  HAD  CAD  CAC  119.17  3.000
 F9Y  CAE  CAD  CAC  120.61  3.000
 F9Y  HAE  CAE  CAF  120.76  3.000
 F9Y  HAE  CAE  CAD  120.06  3.000
 F9Y  CAF  CAE  CAD  119.18  3.000
 F9Y  CAK  CAF  CAG  106.83  3.000
 F9Y  CAK  CAF  CAE  134.07  3.000
 F9Y  CAG  CAF  CAE  119.10  3.000
 F9Y  NAI  CAG  CAH  130.30  3.000
 F9Y  NAI  CAG  CAF  107.28  3.000
 F9Y  CAH  CAG  CAF  122.42  3.000
 F9Y  HAH  CAH  CAG  122.21  3.000
 F9Y  HAH  CAH  CAC  120.77  3.000
 F9Y  CAG  CAH  CAC  117.02  3.000
 F9Y  HAJ  CAJ  NAI  120.64  3.000
 F9Y  HAJ  CAJ  CAK  129.50  3.000
 F9Y  NAI  CAJ  CAK  109.85  3.000
 F9Y  HAK  CAK  CAJ  126.04  3.000
 F9Y  HAK  CAK  CAF  127.24  3.000
 F9Y  CAJ  CAK  CAF  106.72  3.000
 F9Y  HAI  NAI  CAJ  125.17  3.000
 F9Y  HAI  NAI  CAG  125.51  3.000
 F9Y  CAJ  NAI  CAG  109.32  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
 F9Y  CONST_01  CAF  CAE  CAD  CAC    0.00  0.0  0
 F9Y  CONST_02  CAF  CAG  CAH  CAC    0.00  0.0  0
 F9Y  CONST_03  NAI  CAG  CAH  CAC  180.00  0.0  0
 F9Y  CONST_04  CAG  CAH  CAC  CAD    0.00  0.0  0
 F9Y  CONST_05  CAG  CAF  CAE  CAD    0.00  0.0  0
 F9Y  CONST_06  CAK  CAF  CAE  CAD  180.00  0.0  0
 F9Y  CONST_07  CAH  CAC  CAD  CAE    0.00  0.0  0
 F9Y  CONST_08  CAH  CAG  CAF  CAE    0.00  0.0  0
 F9Y  CONST_09  NAI  CAG  CAF  CAE  180.00  0.0  0
 F9Y  CONST_10  CAJ  CAK  CAF  CAE  180.00  0.0  0
 F9Y  CONST_11  CAJ  NAI  CAG  CAF    0.00  0.0  0
 F9Y  CONST_12  NAI  CAJ  CAK  CAF    0.00  0.0  0
 F9Y  CONST_13  CAJ  CAK  CAF  CAG    0.00  0.0  0
 F9Y  CONST_14  CAK  CAJ  NAI  CAG    0.00  0.0  0
 F9Y  CONST_15  CAK  CAF  CAG  CAH  180.00  0.0  0
 F9Y  CONST_16  CAJ  NAI  CAG  CAH  180.00  0.0  0
 F9Y  CONST_17  NAI  CAG  CAF  CAK    0.00  0.0  0
 F9Y  CONST_18  CAE  CAD  CAC  CAB  180.00  0.0  0
 F9Y  CONST_19  CAG  CAH  CAC  CAB  180.00  0.0  0
 F9Y  CONST_20  HAE  CAE  CAD  CAC  180.00  0.0  0
 F9Y  CONST_21  HAH  CAH  CAC  CAD  180.00  0.0  0
 F9Y  CONST_22  HAK  CAK  CAF  CAE    0.00  0.0  0
 F9Y  CONST_23  HAD  CAD  CAE  CAF  180.00  0.0  0
 F9Y  CONST_24  HAI  NAI  CAG  CAF  180.00  0.0  0
 F9Y  CONST_25  HAJ  CAJ  CAK  CAF  180.00  0.0  0

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
 F9Y  plan-1  CAB  0.020
 F9Y  plan-1  CAC  0.020
 F9Y  plan-1  CAD  0.020
 F9Y  plan-1  CAE  0.020
 F9Y  plan-1  CAF  0.020
 F9Y  plan-1  CAG  0.020
 F9Y  plan-1  CAH  0.020
 F9Y  plan-1  CAJ  0.020
 F9Y  plan-1  CAK  0.020
 F9Y  plan-1  NAA  0.020
 F9Y  plan-1  NAI  0.020
 F9Y  plan-1  HAD  0.020
 F9Y  plan-1  HAE  0.020
 F9Y  plan-1  HAH  0.020
 F9Y  plan-1  HAJ  0.020
 F9Y  plan-1  HAK  0.020
 F9Y  plan-1  HAI  0.020

