# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:15:40 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 3-(5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=CC(=CNC1=O)c2cccc(c2)C#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
 28B  28B  3-(5-hydroxy-6-oxo-1,6-dihydropyridin-3-yl)benzonitrile  ligand  24  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_28B
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
 28B  O01  O  O     0  -0.510   4.5283   0.9413  -0.1789
 28B  C02  C  CR6   0   0.457   3.3407   0.6178  -0.1738
 28B  C03  C  CR6   0   0.205   2.8738  -0.6253   0.4112
 28B  O04  O  OH1   0  -0.621   3.8058  -1.4149   0.9605
 28B  C05  C  CR16  0  -0.281   1.5579  -0.9546   0.4074
 28B  C06  C  CR6   0  -0.044   0.5905  -0.0838  -0.1753
 28B  C07  C  CR6   0   0.105  -0.8382  -0.4381  -0.1908
 28B  C08  C  CR16  0  -0.292  -1.2439  -1.7614  -0.3773
 28B  C09  C  CR16  0  -0.228  -2.5873  -2.1048  -0.4010
 28B  C10  C  CR16  0  -0.253  -3.5615  -1.1340  -0.2432
 28B  C11  C  CR6   0   0.030  -3.1647   0.1889  -0.0544
 28B  C12  C  CSP   0   0.053  -4.1536   1.2035   0.1246
 28B  N13  N  NS    0  -0.249  -4.9545   2.0192   0.2687
 28B  C14  C  CR16  0  -0.314  -1.8166   0.5371  -0.0200
 28B  C15  C  CR16  0  -0.006   1.0321   1.0768  -0.7265
 28B  N16  N  NR16  0  -0.655   2.3538   1.3892  -0.7106
 28B  H1   H  HOH1  0   0.469   4.6668  -0.9815   0.8640
 28B  H2   H  HCR6  0   0.279   1.2422  -1.8807   0.8726
 28B  H3   H  HCR6  0   0.272  -0.5021  -2.5359  -0.5240
 28B  H4   H  HCR6  0   0.277  -2.8750  -3.1361  -0.5524
 28B  H5   H  HCR6  0   0.284  -4.6111  -1.3929  -0.2636
 28B  H6   H  HCR6  0   0.281  -1.5374   1.5670   0.1604
 28B  H7   H  HCR6  0   0.309   0.3913   1.7937  -1.2176
 28B  H8   H  HNR6  0   0.431   2.6423   2.2601  -1.1366

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
 28B  N13  C12  triple    1.152  0.020  1.152
 28B  C12  C11  single    1.428  0.020  1.428
 28B  C11  C10  aromatic  1.394  0.020  1.394
 28B  C11  C14  aromatic  1.393  0.020  1.393
 28B  C10  C09  aromatic  1.384  0.020  1.384
 28B  C14  C07  aromatic  1.392  0.020  1.392
 28B  C09  C08  aromatic  1.387  0.020  1.387
 28B  C07  C08  aromatic  1.397  0.020  1.397
 28B  C07  C06  single    1.472  0.020  1.472
 28B  C15  C06  double    1.359  0.020  1.359
 28B  C15  N16  single    1.358  0.020  1.358
 28B  C06  C05  single    1.426  0.020  1.426
 28B  N16  C02  single    1.363  0.020  1.363
 28B  C05  C03  double    1.356  0.020  1.356
 28B  C02  C03  single    1.451  0.020  1.451
 28B  C02  O01  double    1.231  0.020  1.231
 28B  C03  O04  single    1.339  0.020  1.339
 28B  O04  H1   single    0.850  0.020  0.980
 28B  C05  H2   single    0.930  0.020  1.080
 28B  C08  H3   single    0.930  0.020  1.080
 28B  C09  H4   single    0.930  0.020  1.080
 28B  C10  H5   single    0.930  0.020  1.080
 28B  C14  H6   single    0.930  0.020  1.080
 28B  C15  H7   single    0.930  0.020  1.080
 28B  N16  H8   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
 28B  N16  C02  C03  114.25  3.000
 28B  C03  C02  O01  122.50  3.000
 28B  N16  C02  O01  123.25  3.000
 28B  C05  C03  O04  122.22  3.000
 28B  O04  C03  C02  116.52  3.000
 28B  C05  C03  C02  121.26  3.000
 28B  H1   O04  C03  108.29  3.000
 28B  H2   C05  C06  119.98  3.000
 28B  H2   C05  C03  119.27  3.000
 28B  C06  C05  C03  120.73  3.000
 28B  C15  C06  C07  121.12  3.000
 28B  C15  C06  C05  117.83  3.000
 28B  C07  C06  C05  121.05  3.000
 28B  C14  C07  C08  118.43  3.000
 28B  C08  C07  C06  120.76  3.000
 28B  C14  C07  C06  120.82  3.000
 28B  H3   C08  C09  118.97  3.000
 28B  H3   C08  C07  119.80  3.000
 28B  C09  C08  C07  121.22  3.000
 28B  H4   C09  C10  119.83  3.000
 28B  H4   C09  C08  119.76  3.000
 28B  C10  C09  C08  120.41  3.000
 28B  H5   C10  C11  120.40  3.000
 28B  H5   C10  C09  120.87  3.000
 28B  C11  C10  C09  118.73  3.000
 28B  C14  C11  C12  119.31  3.000
 28B  C14  C11  C10  121.07  3.000
 28B  C12  C11  C10  119.62  3.000
 28B  N13  C12  C11  180.00  3.000
 28B  H6   C14  C11  119.46  3.000
 28B  H6   C14  C07  120.39  3.000
 28B  C11  C14  C07  120.14  3.000
 28B  H7   C15  N16  115.48  3.000
 28B  H7   C15  C06  123.98  3.000
 28B  N16  C15  C06  120.53  3.000
 28B  H8   N16  C15  118.08  3.000
 28B  H8   N16  C02  116.53  3.000
 28B  C15  N16  C02  125.39  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
 28B  CONST_01  C10  C11  C14  C07    0.00   0.0  0
 28B  CONST_02  C10  C09  C08  C07    0.00   0.0  0
 28B  CONST_03  C11  C10  C09  C08    0.00   0.0  0
 28B  CONST_04  C11  C14  C07  C08    0.00   0.0  0
 28B  CONST_05  C14  C11  C10  C09    0.00   0.0  0
 28B  CONST_06  C14  C07  C08  C09    0.00   0.0  0
 28B  CONST_07  C11  C14  C07  C06  180.00   0.0  0
 28B  CONST_08  C09  C08  C07  C06  180.00   0.0  0
 28B  CONST_09  C15  N16  C02  C03    0.00   0.0  0
 28B  CONST_10  C12  C11  C14  C07  180.00   0.0  0
 28B  CONST_11  C12  C11  C10  C09  180.00   0.0  0
 28B  CONST_12  C15  N16  C02  O01  180.00   0.0  0
 28B  CONST_13  H6   C14  C07  C06    0.00   0.0  0
 28B  CONST_14  H3   C08  C07  C06    0.00   0.0  0
 28B  CONST_15  H4   C09  C08  C07  180.00   0.0  0
 28B  CONST_16  H5   C10  C09  C08  180.00   0.0  0
 28B  CONST_17  H8   N16  C02  C03  180.00   0.0  0
 28B  Var_01    C14  C07  C06  C05  143.35  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
 28B  plan-1  C06  0.020
 28B  plan-1  C07  0.020
 28B  plan-1  C08  0.020
 28B  plan-1  C09  0.020
 28B  plan-1  C10  0.020
 28B  plan-1  C11  0.020
 28B  plan-1  C12  0.020
 28B  plan-1  N13  0.020
 28B  plan-1  C14  0.020
 28B  plan-1  H3   0.020
 28B  plan-1  H4   0.020
 28B  plan-1  H5   0.020
 28B  plan-1  H6   0.020
 28B  plan-2  O01  0.020
 28B  plan-2  C02  0.020
 28B  plan-2  C03  0.020
 28B  plan-2  O04  0.020
 28B  plan-2  C05  0.020
 28B  plan-2  C06  0.020
 28B  plan-2  C07  0.020
 28B  plan-2  C15  0.020
 28B  plan-2  N16  0.020
 28B  plan-2  H2   0.020
 28B  plan-2  H7   0.020
 28B  plan-2  H8   0.020

