# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:20:06 2021
#   Inital geometry file: a 59 line input string
#   Ligand name: (3S)-N-methyl-6-oxo-3,6-dihydropyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H]1C=CC(=O)N=C1
#
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
 WQM  WQM  (3S)-N-methyl-6-oxo-3,6-dihydropyridine-3-carboxamide  ligand  19  11  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WQM
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
 WQM  N1  N  NH1   0  -0.611  -0.6833  15.6488   0.1912
 WQM  C4  C  CR16  0  -0.090  -3.6662  15.5396  -1.4926
 WQM  C5  C  CR16  0  -0.386  -4.8115  14.8640  -1.5438
 WQM  C6  C  CR16  0   0.045  -4.0266  15.7326   0.9443
 WQM  C7  C  CR6   0   0.472  -5.5053  14.4831  -0.3084
 WQM  C1  C  CH3   0  -0.516   0.5520  14.9410   0.4452
 WQM  C2  C  C     0   0.575  -1.8521  15.0215   0.0939
 WQM  C3  C  CR16  0  -0.595  -3.0719  15.9257  -0.1866
 WQM  N2  N  N     0  -0.405  -5.1162  15.0816   0.9046
 WQM  O2  O  O     0  -0.464  -2.0025  13.8177   0.2114
 WQM  H1  H  HNH1  0   0.417  -0.6487  16.6490   0.0859
 WQM  H2  H  HCR6  0   0.302  -3.1230  15.7986  -2.3928
 WQM  H3  H  HCR6  0   0.285  -5.2475  14.5497  -2.4832
 WQM  H4  H  HCR6  0   0.298  -3.7459  16.1873   1.8920
 WQM  H5  H  HCH3  0   0.258   1.3649  15.6602   0.4388
 WQM  H6  H  HCH3  0   0.246   0.5351  14.4450   1.4157
 WQM  H7  H  HCH3  0   0.247   0.7453  14.1925  -0.3227
 WQM  H8  H  HCR6  0   0.335  -2.7618  16.9749  -0.2000
 WQM  O1  O  O     0  -0.412  -6.4176  13.6857  -0.2990

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
 WQM  C5  C4  double  1.331  0.020  1.331
 WQM  C5  C7  single  1.467  0.020  1.467
 WQM  C4  C3  single  1.486  0.020  1.486
 WQM  O1  C7  double  1.212  0.020  1.212
 WQM  C7  N2  single  1.407  0.020  1.407
 WQM  N1  C1  single  1.446  0.020  1.446
 WQM  N1  C2  single  1.330  0.020  1.330
 WQM  C3  C2  single  1.544  0.020  1.544
 WQM  C3  C6  single  1.493  0.020  1.493
 WQM  N2  C6  double  1.270  0.020  1.270
 WQM  C2  O2  double  1.219  0.020  1.219
 WQM  N1  H1  single  0.860  0.020  1.020
 WQM  C4  H2  single  0.930  0.020  1.080
 WQM  C5  H3  single  0.930  0.020  1.080
 WQM  C6  H4  single  0.930  0.020  1.080
 WQM  C1  H5  single  0.970  0.020  1.090
 WQM  C1  H6  single  0.970  0.020  1.090
 WQM  C1  H7  single  0.970  0.020  1.090
 WQM  C3  H8  single  0.970  0.020  1.090

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
 WQM  H1  N1  C2  119.42  3.000
 WQM  H1  N1  C1  118.39  3.000
 WQM  C2  N1  C1  122.18  3.000
 WQM  H2  C4  C3  117.90  3.000
 WQM  H2  C4  C5  121.41  3.000
 WQM  C3  C4  C5  120.66  3.000
 WQM  H3  C5  C7  117.71  3.000
 WQM  H3  C5  C4  121.84  3.000
 WQM  C7  C5  C4  120.42  3.000
 WQM  H4  C6  N2  117.57  3.000
 WQM  H4  C6  C3  116.16  3.000
 WQM  N2  C6  C3  126.26  3.000
 WQM  O1  C7  N2  118.77  3.000
 WQM  N2  C7  C5  118.99  3.000
 WQM  O1  C7  C5  122.23  3.000
 WQM  H7  C1  H6  108.52  3.000
 WQM  H7  C1  H5  108.55  3.000
 WQM  H6  C1  H5  108.57  3.000
 WQM  H7  C1  N1  111.34  3.000
 WQM  H6  C1  N1  111.46  3.000
 WQM  H5  C1  N1  108.32  3.000
 WQM  O2  C2  C3  119.90  3.000
 WQM  O2  C2  N1  124.55  3.000
 WQM  C3  C2  N1  115.55  3.000
 WQM  H8  C3  C2  109.87  3.000
 WQM  H8  C3  C6  108.34  3.000
 WQM  C2  C3  C6  106.97  3.000
 WQM  H8  C3  C4  110.60  3.000
 WQM  C6  C3  C4  112.12  3.000
 WQM  C2  C3  C4  108.87  3.000
 WQM  C7  N2  C6  118.83  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
 WQM  CONST_01  C3  C2  N1  C1  180.00   0.0  0
 WQM  CONST_02  H1  N1  C2  C3    0.00   0.0  0
 WQM  CONST_03  O2  C2  N1  C1    0.00   0.0  0
 WQM  Var_01    N2  C7  C5  C4   13.86  30.0  1
 WQM  Var_02    C3  C4  C5  C7   -0.27  30.0  1
 WQM  Var_03    C3  C6  N2  C7   -0.85  30.0  1
 WQM  Var_04    H5  C1  N1  C2  177.65  30.0  3

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
 WQM  chir_01  C3  C4  C2  C6  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
 WQM  plan-1  N1  0.020
 WQM  plan-1  C1  0.020
 WQM  plan-1  C2  0.020
 WQM  plan-1  C3  0.020
 WQM  plan-1  O2  0.020
 WQM  plan-1  H1  0.020
 WQM  plan-2  C5  0.020
 WQM  plan-2  C7  0.020
 WQM  plan-2  N2  0.020
 WQM  plan-2  O1  0.020

