# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:35:50 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-[(R)-methylsulfinyl]-2-oxo-6-[3-(trifluoromethoxy)phenyl]-1,2-dihydropyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S@@](=O)C1=C(C#N)C(=O)NC(=C1)c2cccc(OC(F)(F)F)c2
#
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
 H6D  H6D  4-[(R)-methylsulfinyl]-2-oxo-6-[3-(trifluoromethoxy)phenyl]-1,2-dihydropyridine-3-carbonitrile  ligand  32  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H6D
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
 H6D  C1   C  CH3   0  -0.805   4.8772   1.7668  -0.6320
 H6D  S2   S  S3    0   0.790   4.1890   1.2255   0.9500
 H6D  O3   O  O     0  -0.732   3.5469   2.4261   1.5783
 H6D  C4   C  CR6   0  -0.048   2.8537   0.2391   0.2311
 H6D  C5   C  CR16  0  -0.408   1.5838   0.8072   0.1632
 H6D  C6   C  CR6   0   0.448   0.5632   0.0463  -0.3517
 H6D  N7   N  NR16  0  -0.727   0.8108  -1.2157  -0.7586
 H6D  C8   C  CR6   0   0.563   2.0300  -1.8706  -0.7038
 H6D  O9   O  O     0  -0.446   2.1523  -3.0187  -1.0892
 H6D  C10  C  CR6   0  -0.189   3.0938  -1.0542  -0.1627
 H6D  C11  C  CSP   0   0.031   4.3758  -1.6499  -0.0640
 H6D  N12  N  NS    0  -0.229   5.4220  -2.1277   0.0177
 H6D  C13  C  CR6   0   0.059  -0.8131   0.5444  -0.4674
 H6D  C14  C  CR16  0  -0.280  -1.0415   1.8721  -0.8248
 H6D  C15  C  CR16  0  -0.236  -2.3374   2.3447  -0.9464
 H6D  C16  C  CR16  0  -0.292  -3.4180   1.5102  -0.7001
 H6D  C17  C  CR6   0   0.340  -3.1759   0.1974  -0.3332
 H6D  C18  C  CR16  0  -0.343  -1.8923  -0.3023  -0.2196
 H6D  O19  O  O2    0  -0.522  -4.2455  -0.6608  -0.1262
 H6D  C20  C  CT    0   1.077  -4.7663  -0.7235   1.1088
 H6D  F21  F  F     0  -0.297  -5.2625   0.4454   1.5158
 H6D  F22  F  F     0  -0.273  -5.7460  -1.6101   1.0849
 H6D  F23  F  F     0  -0.297  -3.8726  -1.1034   2.0222
 H6D  H1   H  HCH3  0   0.311   5.6976   2.4431  -0.3980
 H6D  H1A  H  HCH3  0   0.290   5.2631   0.9119  -1.1837
 H6D  H1B  H  HCH3  0   0.303   4.1122   2.2838  -1.2079
 H6D  H5   H  HCR6  0   0.313   1.3982   1.8048   0.5320
 H6D  HN7  H  HNR6  0   0.443   0.0566  -1.7475  -1.1784
 H6D  H14  H  HCR6  0   0.282  -0.2105   2.5302  -1.0407
 H6D  H15  H  HCR6  0   0.285  -2.5109   3.3697  -1.2426
 H6D  H16  H  HCR6  0   0.294  -4.4303   1.8749  -0.8106
 H6D  H18  H  HCR6  0   0.295  -1.7439  -1.3350   0.0709

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
 H6D  C1   S2   single    1.808  0.020  1.808
 H6D  S2   O3   double    1.500  0.020  1.500
 H6D  S2   C4   single    1.809  0.020  1.809
 H6D  C4   C5   single    1.393  0.020  1.393
 H6D  C4   C10  double    1.373  0.020  1.373
 H6D  C5   C6   double    1.373  0.020  1.373
 H6D  C6   N7   single    1.349  0.020  1.349
 H6D  C6   C13  single    1.468  0.020  1.468
 H6D  N7   C8   single    1.385  0.020  1.385
 H6D  C8   O9   double    1.217  0.020  1.217
 H6D  C8   C10  single    1.446  0.020  1.446
 H6D  C10  C11  single    1.417  0.020  1.417
 H6D  C11  N12  triple    1.153  0.020  1.153
 H6D  C13  C14  aromatic  1.394  0.020  1.394
 H6D  C13  C18  aromatic  1.394  0.020  1.394
 H6D  C14  C15  aromatic  1.385  0.020  1.385
 H6D  C15  C16  aromatic  1.387  0.020  1.387
 H6D  C16  C17  aromatic  1.384  0.020  1.384
 H6D  C17  C18  aromatic  1.382  0.020  1.382
 H6D  C17  O19  single    1.387  0.020  1.387
 H6D  O19  C20  single    1.342  0.020  1.342
 H6D  C20  F21  single    1.334  0.020  1.334
 H6D  C20  F22  single    1.322  0.020  1.322
 H6D  C20  F23  single    1.333  0.020  1.333
 H6D  C1   H1   single    0.970  0.020  1.090
 H6D  C1   H1A  single    0.970  0.020  1.090
 H6D  C1   H1B  single    0.970  0.020  1.090
 H6D  C5   H5   single    0.930  0.020  1.080
 H6D  N7   HN7  single    0.860  0.020  1.020
 H6D  C14  H14  single    0.930  0.020  1.080
 H6D  C15  H15  single    0.930  0.020  1.080
 H6D  C16  H16  single    0.930  0.020  1.080
 H6D  C18  H18  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
 H6D  H1B  C1   H1A  110.74  3.000
 H6D  H1B  C1   H1   110.39  3.000
 H6D  H1A  C1   H1   109.26  3.000
 H6D  H1B  C1   S2   109.74  3.000
 H6D  H1A  C1   S2   110.08  3.000
 H6D  H1   C1   S2   106.55  3.000
 H6D  C4   S2   O3   106.68  3.000
 H6D  C4   S2   C1    95.54  3.000
 H6D  O3   S2   C1   106.85  3.000
 H6D  C10  C4   C5   121.98  3.000
 H6D  C10  C4   S2   119.90  3.000
 H6D  C5   C4   S2   118.03  3.000
 H6D  H5   C5   C6   120.82  3.000
 H6D  H5   C5   C4   121.13  3.000
 H6D  C6   C5   C4   118.03  3.000
 H6D  C13  C6   N7   117.75  3.000
 H6D  C13  C6   C5   122.57  3.000
 H6D  N7   C6   C5   119.67  3.000
 H6D  HN7  N7   C8   115.03  3.000
 H6D  HN7  N7   C6   118.63  3.000
 H6D  C8   N7   C6   126.31  3.000
 H6D  C10  C8   O9   125.24  3.000
 H6D  C10  C8   N7   113.29  3.000
 H6D  O9   C8   N7   121.47  3.000
 H6D  C11  C10  C8   117.02  3.000
 H6D  C11  C10  C4   122.29  3.000
 H6D  C8   C10  C4   120.69  3.000
 H6D  N12  C11  C10  180.00  3.000
 H6D  C18  C13  C14  119.82  3.000
 H6D  C18  C13  C6   120.38  3.000
 H6D  C14  C13  C6   119.80  3.000
 H6D  H14  C14  C15  119.59  3.000
 H6D  H14  C14  C13  120.31  3.000
 H6D  C15  C14  C13  120.07  3.000
 H6D  H15  C15  C16  119.61  3.000
 H6D  H15  C15  C14  119.86  3.000
 H6D  C16  C15  C14  120.53  3.000
 H6D  H16  C16  C17  120.69  3.000
 H6D  H16  C16  C15  120.53  3.000
 H6D  C17  C16  C15  118.77  3.000
 H6D  O19  C17  C18  118.70  3.000
 H6D  O19  C17  C16  119.44  3.000
 H6D  C18  C17  C16  121.80  3.000
 H6D  H18  C18  C17  119.61  3.000
 H6D  H18  C18  C13  121.38  3.000
 H6D  C17  C18  C13  119.00  3.000
 H6D  C20  O19  C17  117.75  3.000
 H6D  F23  C20  F22  108.55  3.000
 H6D  F23  C20  F21  106.86  3.000
 H6D  F22  C20  F21  108.53  3.000
 H6D  F23  C20  O19  112.56  3.000
 H6D  F22  C20  O19  107.61  3.000
 H6D  F21  C20  O19  112.61  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
 H6D  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 H6D  CONST_02  C16  C17  C18  C13    0.00   0.0  0
 H6D  CONST_03  C17  C18  C13  C14    0.00   0.0  0
 H6D  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 H6D  CONST_05  C18  C13  C14  C15    0.00   0.0  0
 H6D  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 H6D  CONST_07  C15  C14  C13  C6   180.00   0.0  0
 H6D  CONST_08  C17  C18  C13  C6   180.00   0.0  0
 H6D  CONST_09  C10  C8   N7   C6     0.00   0.0  0
 H6D  CONST_10  O19  C17  C18  C13  180.00   0.0  0
 H6D  CONST_11  O19  C17  C16  C15  180.00   0.0  0
 H6D  CONST_12  O9   C8   N7   C6   180.00   0.0  0
 H6D  CONST_13  H14  C14  C13  C6     0.00   0.0  0
 H6D  CONST_14  H18  C18  C13  C6     0.00   0.0  0
 H6D  CONST_15  H15  C15  C14  C13  180.00   0.0  0
 H6D  CONST_16  H16  C16  C15  C14  180.00   0.0  0
 H6D  CONST_17  HN7  N7   C8   C10  180.00   0.0  0
 H6D  Var_01    C14  C13  C6   C5    37.85  30.0  2
 H6D  Var_02    C5   C4   S2   C1   -98.96  30.0  2
 H6D  Var_03    F21  C20  O19  C17   61.57  30.0  3
 H6D  Var_04    H1   C1   S2   C4   177.07  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
 H6D  plan-1  S2   0.020
 H6D  plan-1  C4   0.020
 H6D  plan-1  C5   0.020
 H6D  plan-1  C6   0.020
 H6D  plan-1  N7   0.020
 H6D  plan-1  C8   0.020
 H6D  plan-1  O9   0.020
 H6D  plan-1  C10  0.020
 H6D  plan-1  C11  0.020
 H6D  plan-1  N12  0.020
 H6D  plan-1  C13  0.020
 H6D  plan-1  H5   0.020
 H6D  plan-1  HN7  0.020
 H6D  plan-2  C6   0.020
 H6D  plan-2  C13  0.020
 H6D  plan-2  C14  0.020
 H6D  plan-2  C15  0.020
 H6D  plan-2  C16  0.020
 H6D  plan-2  C17  0.020
 H6D  plan-2  C18  0.020
 H6D  plan-2  O19  0.020
 H6D  plan-2  H14  0.020
 H6D  plan-2  H15  0.020
 H6D  plan-2  H16  0.020
 H6D  plan-2  H18  0.020
 H6D  plan-3  C1   0.020
 H6D  plan-3  S2   0.020
 H6D  plan-3  O3   0.020
 H6D  plan-3  C4   0.020

