# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:31:33 2021
#   Inital geometry file: a 44 line input string
#   Ligand name: 5-oxidanyl-1~{H}-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=CNC(=O)C=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
 G6C  G6C  5-oxidanyl-1~{H}-pyridin-2-one  ligand  13  8  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G6C
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
 G6C  OB   O  OH1   0  -0.633  44.6390  54.7888  110.5214
 G6C  CG   C  CR6   0   0.227  43.3258  54.6090  110.7905
 G6C  CD1  C  CR16  0  -0.096  42.5775  55.4227  111.5775
 G6C  CD2  C  CR16  0  -0.185  42.6844  53.4868  110.2049
 G6C  NE1  N  NR16  0  -0.647  41.2583  55.1524  111.7852
 G6C  CE2  C  CR16  0  -0.439  41.3683  53.2388  110.4257
 G6C  CZ   C  CR6   0   0.523  40.5607  54.0940  111.2595
 G6C  OH   O  O     0  -0.528  39.3640  53.9314  111.5041
 G6C  H1   H  HOH1  0   0.474  44.9763  55.5684  110.9757
 G6C  H2   H  HCR6  0   0.314  42.9643  56.3039  112.0700
 G6C  H3   H  HCR6  0   0.290  43.2627  52.8231  109.5730
 G6C  H5   H  HCR6  0   0.278  40.8888  52.3809  109.9749
 G6C  H4   H  HNR6  0   0.422  40.7424  55.7866  112.3796

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
 G6C  CD2  CE2  double  1.357  0.020  1.357
 G6C  CD2  CG   single  1.419  0.020  1.419
 G6C  CE2  CZ   single  1.442  0.020  1.442
 G6C  OB   CG   single  1.353  0.020  1.353
 G6C  CG   CD1  double  1.357  0.020  1.357
 G6C  CZ   OH   double  1.232  0.020  1.232
 G6C  CZ   NE1  single  1.372  0.020  1.372
 G6C  CD1  NE1  single  1.363  0.020  1.363
 G6C  OB   H1   single  0.850  0.020  0.980
 G6C  CD1  H2   single  0.930  0.020  1.080
 G6C  CD2  H3   single  0.930  0.020  1.080
 G6C  CE2  H5   single  0.930  0.020  1.080
 G6C  NE1  H4   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
 G6C  H1   OB   CG   110.72  3.000
 G6C  CD2  CG   CD1  117.66  3.000
 G6C  CD1  CG   OB   124.82  3.000
 G6C  CD2  CG   OB   117.51  3.000
 G6C  H2   CD1  NE1  116.02  3.000
 G6C  H2   CD1  CG   123.76  3.000
 G6C  NE1  CD1  CG   120.22  3.000
 G6C  H3   CD2  CE2  120.03  3.000
 G6C  H3   CD2  CG   118.93  3.000
 G6C  CE2  CD2  CG   121.04  3.000
 G6C  H4   NE1  CZ   116.73  3.000
 G6C  H4   NE1  CD1  117.34  3.000
 G6C  CZ   NE1  CD1  125.93  3.000
 G6C  H5   CE2  CZ   117.61  3.000
 G6C  H5   CE2  CD2  120.47  3.000
 G6C  CZ   CE2  CD2  121.92  3.000
 G6C  OH   CZ   CE2  125.48  3.000
 G6C  OH   CZ   NE1  121.29  3.000
 G6C  CE2  CZ   NE1  113.22  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
 G6C  CONST_01  CE2  CZ   NE1  CD1    0.00  0.0  0
 G6C  CONST_02  OH   CZ   NE1  CD1  180.00  0.0  0
 G6C  CONST_03  H4   NE1  CZ   CE2  180.00  0.0  0

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
 G6C  plan-1  OB   0.020
 G6C  plan-1  CG   0.020
 G6C  plan-1  CD1  0.020
 G6C  plan-1  CD2  0.020
 G6C  plan-1  NE1  0.020
 G6C  plan-1  CE2  0.020
 G6C  plan-1  CZ   0.020
 G6C  plan-1  OH   0.020
 G6C  plan-1  H2   0.020
 G6C  plan-1  H3   0.020
 G6C  plan-1  H5   0.020
 G6C  plan-1  H4   0.020

