# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 17:59:17 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3R)-3-azanyl-4-methyl-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2NC(=O)[C@H](N)c12
#
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
 BY4  BY4  (3R)-3-azanyl-4-methyl-1,3-dihydroindol-2-one  ligand  22  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BY4
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
 BY4  C01   C  CH3   0  -0.755   1.6799   2.3470   0.3183
 BY4  C02   C  CR6   0   0.057   1.5141   0.8657   0.1499
 BY4  C03   C  CR16  0  -0.323   2.6257   0.0232   0.0302
 BY4  C04   C  CR16  0  -0.251   2.4781  -1.3488  -0.1184
 BY4  C05   C  CR16  0  -0.327   1.2196  -1.9440  -0.1467
 BY4  C06   C  CR56  0   0.408   0.1292  -1.1043  -0.0301
 BY4  C07   C  CR56  0   0.023   0.2625   0.2754   0.1070
 BY4  C08   C  CR15  0  -0.325  -1.1087   0.8783   0.2226
 BY4  C09   C  CR5   0   0.547  -2.0182  -0.3510   0.1171
 BY4  N10   N  NR15  0  -0.741  -1.2200  -1.4406  -0.0147
 BY4  O11   O  O     0  -0.454  -3.2309  -0.3460   0.1303
 BY4  N12   N  NH2   0  -0.789  -1.4402   1.7822  -0.8682
 BY4  H011  H  HCH3  0   0.251   1.4539   2.8820  -0.6062
 BY4  H012  H  HCH3  0   0.248   1.0186   2.7422   1.0911
 BY4  H013  H  HCH3  0   0.259   2.7021   2.5995   0.5953
 BY4  H03   H  HCR6  0   0.247   3.6204   0.4507   0.0634
 BY4  H04   H  HCR6  0   0.258   3.3584  -1.9724  -0.2064
 BY4  H05   H  HCR6  0   0.266   1.1060  -3.0149  -0.2497
 BY4  H10   H  HNR5  0   0.412  -1.5734  -2.3811  -0.1100
 BY4  H08   H  HCR5  0   0.272  -1.2499   1.3153   1.2239
 BY4  H121  H  HNH2  0   0.357  -2.3897   2.1129  -0.7418
 BY4  H122  H  HNH2  0   0.363  -0.8582   2.6082  -0.8098

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
 BY4  C01  C02   single    1.500  0.020  1.500
 BY4  C02  C03   aromatic  1.400  0.020  1.400
 BY4  C02  C07   aromatic  1.384  0.020  1.384
 BY4  C03  C04   aromatic  1.388  0.020  1.388
 BY4  C04  C05   aromatic  1.392  0.020  1.392
 BY4  C05  C06   aromatic  1.381  0.020  1.381
 BY4  C06  C07   aromatic  1.393  0.020  1.393
 BY4  C06  N10   single    1.391  0.020  1.391
 BY4  C07  C08   single    1.502  0.020  1.502
 BY4  C08  C09   single    1.533  0.020  1.533
 BY4  C08  N12   single    1.455  0.020  1.455
 BY4  C09  N10   single    1.357  0.020  1.357
 BY4  C09  O11   double    1.213  0.020  1.213
 BY4  C01  H011  single    0.970  0.020  1.090
 BY4  C01  H012  single    0.970  0.020  1.090
 BY4  C01  H013  single    0.970  0.020  1.090
 BY4  C03  H03   single    0.930  0.020  1.080
 BY4  C04  H04   single    0.930  0.020  1.080
 BY4  C05  H05   single    0.930  0.020  1.080
 BY4  N10  H10   single    0.860  0.020  1.020
 BY4  C08  H08   single    0.970  0.020  1.090
 BY4  N12  H121  single    0.890  0.020  1.040
 BY4  N12  H122  single    0.890  0.020  1.040

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
 BY4  H013  C01  H012  107.74  3.000
 BY4  H013  C01  H011  107.23  3.000
 BY4  H012  C01  H011  107.26  3.000
 BY4  H013  C01  C02   111.19  3.000
 BY4  H012  C01  C02   111.73  3.000
 BY4  H011  C01  C02   111.47  3.000
 BY4  C07   C02  C03   117.30  3.000
 BY4  C07   C02  C01   121.63  3.000
 BY4  C03   C02  C01   121.07  3.000
 BY4  H03   C03  C04   119.41  3.000
 BY4  H03   C03  C02   119.28  3.000
 BY4  C04   C03  C02   121.31  3.000
 BY4  H04   C04  C05   119.15  3.000
 BY4  H04   C04  C03   119.46  3.000
 BY4  C05   C04  C03   121.39  3.000
 BY4  H05   C05  C06   121.80  3.000
 BY4  H05   C05  C04   121.33  3.000
 BY4  C06   C05  C04   116.87  3.000
 BY4  N10   C06  C07   109.35  3.000
 BY4  N10   C06  C05   128.31  3.000
 BY4  C07   C06  C05   122.34  3.000
 BY4  C08   C07  C06   108.53  3.000
 BY4  C08   C07  C02   130.66  3.000
 BY4  C06   C07  C02   120.79  3.000
 BY4  H08   C08  N12   113.95  3.000
 BY4  H08   C08  C09   107.74  3.000
 BY4  N12   C08  C09   108.15  3.000
 BY4  H08   C08  C07   110.25  3.000
 BY4  N12   C08  C07   113.55  3.000
 BY4  C09   C08  C07   102.38  3.000
 BY4  O11   C09  N10   126.33  3.000
 BY4  O11   C09  C08   126.10  3.000
 BY4  N10   C09  C08   107.56  3.000
 BY4  H10   N10  C09   123.46  3.000
 BY4  H10   N10  C06   124.34  3.000
 BY4  C09   N10  C06   112.19  3.000
 BY4  H122  N12  H121  105.38  3.000
 BY4  H122  N12  C08   109.43  3.000
 BY4  H121  N12  C08   108.82  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
 BY4  CONST_01  C05   C04  C03  C02    0.00   0.0  0
 BY4  CONST_02  C05   C06  C07  C02    0.00   0.0  0
 BY4  CONST_03  C06   C07  C02  C03    0.00   0.0  0
 BY4  CONST_04  C06   C05  C04  C03    0.00   0.0  0
 BY4  CONST_05  C07   C02  C03  C04    0.00   0.0  0
 BY4  CONST_06  C07   C06  C05  C04    0.00   0.0  0
 BY4  CONST_07  C08   C09  N10  C06    0.00   0.0  0
 BY4  CONST_08  C04   C03  C02  C01  180.00   0.0  0
 BY4  CONST_09  C06   C07  C02  C01  180.00   0.0  0
 BY4  CONST_10  C08   C07  C02  C01    0.00   0.0  0
 BY4  CONST_11  O11   C09  N10  C06  180.00   0.0  0
 BY4  CONST_12  H04   C04  C03  C02  180.00   0.0  0
 BY4  CONST_13  H05   C05  C04  C03  180.00   0.0  0
 BY4  CONST_14  H03   C03  C04  C05  180.00   0.0  0
 BY4  CONST_15  H10   N10  C09  C08  180.00   0.0  0
 BY4  Var_01    H011  C01  C02  C03  104.39  30.0  2

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
 BY4  chir_01  C08  C07  C09  N12  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
 BY4  plan-1  C01  0.020
 BY4  plan-1  C02  0.020
 BY4  plan-1  C03  0.020
 BY4  plan-1  C04  0.020
 BY4  plan-1  C05  0.020
 BY4  plan-1  C06  0.020
 BY4  plan-1  C07  0.020
 BY4  plan-1  C08  0.020
 BY4  plan-1  C09  0.020
 BY4  plan-1  N10  0.020
 BY4  plan-1  O11  0.020
 BY4  plan-1  H03  0.020
 BY4  plan-1  H04  0.020
 BY4  plan-1  H05  0.020
 BY4  plan-1  H10  0.020

