# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:43:53 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 1~{H}-indole-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1c[nH]c2ccccc12
#
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
 98Z  98Z  1~{H}-indole-3-carbonitrile  ligand  17  11  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_98Z
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
 98Z  C10  C  CR16  0  -0.354  185.1178  285.3760  109.1202
 98Z  N01  N  NS    0  -0.265  183.8909  284.5737  105.3264
 98Z  C02  C  CSP   0  -0.029  184.4368  284.0753  106.2136
 98Z  C03  C  CR5   0  -0.120  185.0984  283.4944  107.3113
 98Z  C04  C  CR15  0   0.026  185.6074  282.2163  107.3689
 98Z  N05  N  NR15  0  -0.672  186.1708  282.0200  108.5751
 98Z  C06  C  CR56  0   0.355  186.0523  283.1515  109.3429
 98Z  C07  C  CR16  0  -0.292  186.4832  283.4059  110.6422
 98Z  C08  C  CR16  0  -0.274  186.2186  284.6586  111.1604
 98Z  C09  C  CR16  0  -0.259  185.5426  285.6331  110.4085
 98Z  C11  C  CR56  0   0.109  185.3749  284.1161  108.5758
 98Z  H1   H  HCR6  0   0.251  184.5974  286.1327  108.5466
 98Z  H2   H  HCR5  0   0.314  185.5966  281.4414  106.6194
 98Z  H3   H  HNR5  0   0.427  186.6165  281.1625  108.8631
 98Z  H4   H  HCR6  0   0.269  187.0043  282.6541  111.2204
 98Z  H5   H  HCR6  0   0.257  186.5388  284.8942  112.1667
 98Z  H6   H  HCR6  0   0.255  185.3534  286.6029  110.8497

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
 98Z  N01  C02  triple    1.155  0.020  1.155
 98Z  C02  C03  single    1.407  0.020  1.407
 98Z  C03  C04  aromatic  1.377  0.020  1.377
 98Z  C03  C11  aromatic  1.436  0.020  1.436
 98Z  C04  N05  aromatic  1.346  0.020  1.346
 98Z  N05  C06  aromatic  1.372  0.020  1.372
 98Z  C11  C10  aromatic  1.396  0.020  1.396
 98Z  C11  C06  aromatic  1.406  0.020  1.406
 98Z  C10  C09  aromatic  1.381  0.020  1.381
 98Z  C06  C07  aromatic  1.392  0.020  1.392
 98Z  C09  C08  aromatic  1.404  0.020  1.404
 98Z  C07  C08  aromatic  1.381  0.020  1.381
 98Z  C10  H1   single    0.930  0.020  1.080
 98Z  C04  H2   single    0.930  0.020  1.080
 98Z  N05  H3   single    0.860  0.020  1.020
 98Z  C07  H4   single    0.930  0.020  1.080
 98Z  C08  H5   single    0.930  0.020  1.080
 98Z  C09  H6   single    0.930  0.020  1.080

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
 98Z  H1   C10  C11  120.84  3.000
 98Z  H1   C10  C09  120.80  3.000
 98Z  C11  C10  C09  118.37  3.000
 98Z  C03  C02  N01  180.00  3.000
 98Z  C11  C03  C04  107.09  3.000
 98Z  C11  C03  C02  126.78  3.000
 98Z  C04  C03  C02  126.14  3.000
 98Z  H2   C04  N05  121.50  3.000
 98Z  H2   C04  C03  129.37  3.000
 98Z  N05  C04  C03  109.13  3.000
 98Z  H3   N05  C06  125.41  3.000
 98Z  H3   N05  C04  124.41  3.000
 98Z  C06  N05  C04  110.18  3.000
 98Z  C11  C06  C07  122.19  3.000
 98Z  C07  C06  N05  130.24  3.000
 98Z  C11  C06  N05  107.58  3.000
 98Z  H4   C07  C08  121.46  3.000
 98Z  H4   C07  C06  121.37  3.000
 98Z  C08  C07  C06  117.17  3.000
 98Z  H5   C08  C09  119.29  3.000
 98Z  H5   C08  C07  119.33  3.000
 98Z  C09  C08  C07  121.38  3.000
 98Z  H6   C09  C08  119.19  3.000
 98Z  H6   C09  C10  119.58  3.000
 98Z  C08  C09  C10  121.23  3.000
 98Z  C06  C11  C03  106.03  3.000
 98Z  C06  C11  C10  119.67  3.000
 98Z  C03  C11  C10  134.31  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
 98Z  CONST_01  C04  C03  C11  C10  180.00  0.0  0
 98Z  CONST_02  N05  C06  C11  C10  180.00  0.0  0
 98Z  CONST_03  C07  C06  C11  C10    0.00  0.0  0
 98Z  CONST_04  C07  C08  C09  C10    0.00  0.0  0
 98Z  CONST_05  C06  N05  C04  C03    0.00  0.0  0
 98Z  CONST_06  C09  C10  C11  C03  180.00  0.0  0
 98Z  CONST_07  N05  C06  C11  C03    0.00  0.0  0
 98Z  CONST_08  C07  C06  C11  C03  180.00  0.0  0
 98Z  CONST_09  C06  C11  C03  C04    0.00  0.0  0
 98Z  CONST_10  C11  C06  N05  C04    0.00  0.0  0
 98Z  CONST_11  C07  C06  N05  C04  180.00  0.0  0
 98Z  CONST_12  C11  C03  C04  N05    0.00  0.0  0
 98Z  CONST_13  C08  C07  C06  N05  180.00  0.0  0
 98Z  CONST_14  C09  C10  C11  C06    0.00  0.0  0
 98Z  CONST_15  C09  C08  C07  C06    0.00  0.0  0
 98Z  CONST_16  C11  C10  C09  C08    0.00  0.0  0
 98Z  CONST_17  C11  C06  C07  C08    0.00  0.0  0
 98Z  CONST_18  C02  C03  C11  C10    0.00  0.0  0
 98Z  CONST_19  N05  C04  C03  C02  180.00  0.0  0
 98Z  CONST_20  C06  C11  C03  C02  180.00  0.0  0
 98Z  CONST_21  H5   C08  C09  C10  180.00  0.0  0
 98Z  CONST_22  H3   N05  C04  C03  180.00  0.0  0
 98Z  CONST_23  H1   C10  C11  C03    0.00  0.0  0
 98Z  CONST_24  H4   C07  C06  N05    0.00  0.0  0
 98Z  CONST_25  H2   C04  N05  C06  180.00  0.0  0
 98Z  CONST_26  H6   C09  C08  C07  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
 98Z  plan-1  C10  0.020
 98Z  plan-1  N01  0.020
 98Z  plan-1  C02  0.020
 98Z  plan-1  C03  0.020
 98Z  plan-1  C04  0.020
 98Z  plan-1  N05  0.020
 98Z  plan-1  C06  0.020
 98Z  plan-1  C07  0.020
 98Z  plan-1  C08  0.020
 98Z  plan-1  C09  0.020
 98Z  plan-1  C11  0.020
 98Z  plan-1  H1   0.020
 98Z  plan-1  H2   0.020
 98Z  plan-1  H3   0.020
 98Z  plan-1  H4   0.020
 98Z  plan-1  H5   0.020
 98Z  plan-1  H6   0.020

