# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:18:30 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 2-[(3S)-2-oxidanylidene-1,3-dihydroindol-3-yl]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2ccccc2[C@@H]1CC#N
#
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
 NYK  NYK  2-[(3S)-2-oxidanylidene-1,3-dihydroindol-3-yl]ethanenitrile  ligand  21  13  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NYK
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
 NYK  C01   C  CH2   0  -0.535  -1.5631  -1.1666  -0.5032
 NYK  C02   C  CSP   0   0.130  -2.9969  -1.0441  -0.2839
 NYK  N03   N  NS    0  -0.270  -4.1328  -0.9919  -0.1117
 NYK  C04   C  CR15  0  -0.462  -0.7344  -0.2704   0.4228
 NYK  C05   C  CR5   0   0.554  -0.9675   1.2134   0.1344
 NYK  N06   N  NR15  0  -0.737   0.2456   1.7680  -0.1222
 NYK  C07   C  CR56  0   0.387   1.2726   0.8317  -0.0848
 NYK  C08   C  CR16  0  -0.304   2.6230   1.0204  -0.3075
 NYK  C09   C  CR16  0  -0.263   3.4507  -0.0963  -0.2111
 NYK  C10   C  CR16  0  -0.263   2.9393  -1.3502   0.0978
 NYK  C11   C  CR16  0  -0.324   1.5728  -1.5177   0.3230
 NYK  C12   C  CR56  0   0.066   0.7447  -0.4195   0.2286
 NYK  O13   O  O     0  -0.440  -2.0374   1.7817   0.1238
 NYK  H01   H  HCH2  0   0.332  -1.2986  -2.2118  -0.3325
 NYK  H01A  H  HCH2  0   0.325  -1.3495  -0.9488  -1.5513
 NYK  H04   H  HCR5  0   0.337  -1.0173  -0.4689   1.4620
 NYK  HN06  H  HNR5  0   0.416   0.3712   2.7438  -0.3467
 NYK  H08   H  HCR6  0   0.271   3.0262   1.9951  -0.5485
 NYK  H09   H  HCR6  0   0.263   4.5131   0.0206  -0.3802
 NYK  H10   H  HCR6  0   0.258   3.6046  -2.2000   0.1674
 NYK  H11   H  HCR6  0   0.259   1.1758  -2.4942   0.5712

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
 NYK  C01  C02   single    1.456  0.020  1.456
 NYK  C01  C04   single    1.532  0.020  1.532
 NYK  C02  N03   triple    1.150  0.020  1.150
 NYK  C04  C05   single    1.529  0.020  1.529
 NYK  C04  C12   single    1.499  0.020  1.499
 NYK  C05  N06   single    1.358  0.020  1.358
 NYK  C05  O13   double    1.212  0.020  1.212
 NYK  N06  C07   single    1.390  0.020  1.390
 NYK  C07  C08   aromatic  1.382  0.020  1.382
 NYK  C07  C12   aromatic  1.394  0.020  1.394
 NYK  C08  C09   aromatic  1.393  0.020  1.393
 NYK  C09  C10   aromatic  1.389  0.020  1.389
 NYK  C10  C11   aromatic  1.395  0.020  1.395
 NYK  C11  C12   aromatic  1.379  0.020  1.379
 NYK  C01  H01   single    0.970  0.020  1.090
 NYK  C01  H01A  single    0.970  0.020  1.090
 NYK  C04  H04   single    0.970  0.020  1.090
 NYK  N06  HN06  single    0.860  0.020  1.020
 NYK  C08  H08   single    0.930  0.020  1.080
 NYK  C09  H09   single    0.930  0.020  1.080
 NYK  C10  H10   single    0.930  0.020  1.080
 NYK  C11  H11   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
 NYK  H01A  C01  H01  107.09  3.000
 NYK  H01A  C01  C04  110.96  3.000
 NYK  H01   C01  C04  109.55  3.000
 NYK  H01A  C01  C02  108.70  3.000
 NYK  H01   C01  C02  107.20  3.000
 NYK  C04   C01  C02  113.11  3.000
 NYK  N03   C02  C01  180.00  3.000
 NYK  H04   C04  C12  111.09  3.000
 NYK  H04   C04  C05  108.39  3.000
 NYK  C12   C04  C05  102.85  3.000
 NYK  H04   C04  C01  109.13  3.000
 NYK  C12   C04  C01  113.40  3.000
 NYK  C05   C04  C01  111.78  3.000
 NYK  O13   C05  N06  126.55  3.000
 NYK  O13   C05  C04  126.25  3.000
 NYK  N06   C05  C04  107.20  3.000
 NYK  HN06  N06  C07  124.42  3.000
 NYK  HN06  N06  C05  123.23  3.000
 NYK  C07   N06  C05  112.31  3.000
 NYK  C12   C07  C08  121.95  3.000
 NYK  C12   C07  N06  109.32  3.000
 NYK  C08   C07  N06  128.73  3.000
 NYK  H08   C08  C09  121.07  3.000
 NYK  H08   C08  C07  121.55  3.000
 NYK  C09   C08  C07  117.38  3.000
 NYK  H09   C09  C10  119.59  3.000
 NYK  H09   C09  C08  119.07  3.000
 NYK  C10   C09  C08  121.35  3.000
 NYK  H10   C10  C11  119.86  3.000
 NYK  H10   C10  C09  119.81  3.000
 NYK  C11   C10  C09  120.33  3.000
 NYK  H11   C11  C12  120.91  3.000
 NYK  H11   C11  C10  120.29  3.000
 NYK  C12   C11  C10  118.80  3.000
 NYK  C11   C12  C07  120.20  3.000
 NYK  C11   C12  C04  131.53  3.000
 NYK  C07   C12  C04  108.28  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
 NYK  CONST_01  C10   C09  C08  C07     0.00   0.0  0
 NYK  CONST_02  C10   C11  C12  C07     0.00   0.0  0
 NYK  CONST_03  C11   C12  C07  C08     0.00   0.0  0
 NYK  CONST_04  C11   C10  C09  C08     0.00   0.0  0
 NYK  CONST_05  C12   C07  C08  C09     0.00   0.0  0
 NYK  CONST_06  C12   C11  C10  C09     0.00   0.0  0
 NYK  CONST_07  C07   N06  C05  C04     0.00   0.0  0
 NYK  CONST_08  O13   C05  N06  C07   180.00   0.0  0
 NYK  CONST_09  H11   C11  C12  C04     0.00   0.0  0
 NYK  CONST_10  H08   C08  C07  N06     0.00   0.0  0
 NYK  CONST_11  H09   C09  C08  C07   180.00   0.0  0
 NYK  CONST_12  H10   C10  C09  C08   180.00   0.0  0
 NYK  CONST_13  HN06  N06  C05  C04   180.00   0.0  0
 NYK  Var_01    C04   C01  C02  N03  -134.40  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
 NYK  chir_01  C04  C01  C05  C12  positiv

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
 NYK  plan-1  C04   0.020
 NYK  plan-1  C05   0.020
 NYK  plan-1  N06   0.020
 NYK  plan-1  C07   0.020
 NYK  plan-1  C08   0.020
 NYK  plan-1  C09   0.020
 NYK  plan-1  C10   0.020
 NYK  plan-1  C11   0.020
 NYK  plan-1  C12   0.020
 NYK  plan-1  O13   0.020
 NYK  plan-1  HN06  0.020
 NYK  plan-1  H08   0.020
 NYK  plan-1  H09   0.020
 NYK  plan-1  H10   0.020
 NYK  plan-1  H11   0.020

