# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 04:07:00 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: 6-methyl-3~{H}-pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=NC(=O)CC=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
 7RE  7RE  "6-methyl-3H-pyridin-2-one"
  ligand  15  8  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7RE
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
 7RE  C01  C  CH3   0  -0.732  11.1674  22.4339  -6.0977
 7RE  C02  C  CR6   0   0.265  11.0055  23.8863  -5.8084
 7RE  C04  C  CR6   0   0.456  11.9103  26.0165  -5.6749
 7RE  C06  C  C     0  -0.651  10.5751  26.5984  -5.2677
 7RE  C07  C  CR16  0  -0.141   9.4720  25.6195  -5.1378
 7RE  C08  C  CR16  0  -0.292   9.6801  24.3284  -5.3949
 7RE  N03  N  N     0  -0.455  12.0325  24.6578  -5.9369
 7RE  O05  O  O     0  -0.422  12.8841  26.7303  -5.7805
 7RE  H1   H  HCH3  0   0.261  12.1864  22.1957  -6.3904
 7RE  H2   H  HCH3  0   0.266  10.8954  21.8450  -5.2192
 7RE  H3   H  HCH3  0   0.267  10.4831  22.1337  -6.8943
 7RE  H4   H  H     0   0.309  10.7010  27.1428  -4.3254
 7RE  H5   H  H     0   0.311  10.2973  27.3720  -5.9929
 7RE  H6   H  HCR6  0   0.286   8.4992  25.9832  -4.8312
 7RE  H7   H  HCR6  0   0.272   8.8927  23.5916  -5.3093

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
 7RE  C01  C02  single  1.490  0.020  1.490
 7RE  N03  C02  double  1.291  0.020  1.291
 7RE  N03  C04  single  1.389  0.020  1.389
 7RE  O05  C04  double  1.212  0.020  1.212
 7RE  C02  C08  single  1.457  0.020  1.457
 7RE  C04  C06  single  1.512  0.020  1.512
 7RE  C08  C07  double  1.333  0.020  1.333
 7RE  C06  C07  single  1.481  0.020  1.481
 7RE  C01  H1   single  0.970  0.020  1.090
 7RE  C01  H2   single  0.970  0.020  1.090
 7RE  C01  H3   single  0.970  0.020  1.090
 7RE  C06  H4   single  0.970  0.020  1.090
 7RE  C06  H5   single  0.970  0.020  1.090
 7RE  C07  H6   single  0.930  0.020  1.080
 7RE  C08  H7   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
 7RE  H3   C01  H2   106.41  3.000
 7RE  H3   C01  H1   109.32  3.000
 7RE  H2   C01  H1   109.39  3.000
 7RE  H3   C01  C02  109.97  3.000
 7RE  H2   C01  C02  110.03  3.000
 7RE  H1   C01  C02  111.59  3.000
 7RE  N03  C02  C08  124.79  3.000
 7RE  C08  C02  C01  116.73  3.000
 7RE  N03  C02  C01  118.48  3.000
 7RE  O05  C04  N03  119.27  3.000
 7RE  O05  C04  C06  120.41  3.000
 7RE  N03  C04  C06  120.32  3.000
 7RE  H5   C06  H4   104.33  3.000
 7RE  H5   C06  C07  109.62  3.000
 7RE  H4   C06  C07  109.80  3.000
 7RE  H5   C06  C04  108.50  3.000
 7RE  H4   C06  C04  108.74  3.000
 7RE  C07  C06  C04  115.28  3.000
 7RE  H6   C07  C08  121.35  3.000
 7RE  H6   C07  C06  118.17  3.000
 7RE  C08  C07  C06  120.48  3.000
 7RE  H7   C08  C07  122.07  3.000
 7RE  H7   C08  C02  118.54  3.000
 7RE  C07  C08  C02  119.39  3.000
 7RE  C04  N03  C02  119.72  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
 7RE  Var_01  C06  C04  N03  C02    -1.24  30.0  1
 7RE  Var_02  C06  C07  C08  C02    -0.10  30.0  1
 7RE  Var_03  C08  C02  N03  C04    -0.14  30.0  1
 7RE  Var_04  C08  C07  C06  C04    -1.14  30.0  1
 7RE  Var_05  N03  C02  C08  C07     0.86  30.0  1
 7RE  Var_06  N03  C04  C06  C07     1.84  30.0  1
 7RE  Var_07  C04  N03  C02  C01   179.94  30.0  1
 7RE  Var_08  C07  C08  C02  C01  -179.22  30.0  1
 7RE  Var_09  O05  C04  N03  C02   179.00  30.0  1
 7RE  Var_10  O05  C04  C06  C07  -178.40  30.0  1
 7RE  Var_11  H6   C07  C08  C02   179.82  30.0  1
 7RE  Var_12  H6   C07  C06  C04   178.93  30.0  1
 7RE  Var_13  H7   C08  C07  C06  -179.93  30.0  1
 7RE  Var_14  H4   C06  C07  C08  -124.35  30.0  1
 7RE  Var_15  H5   C06  C07  C08   121.60  30.0  1
 7RE  Var_16  H7   C08  C02  N03  -179.31  30.0  1
 7RE  Var_17  H4   C06  C04  N03   125.61  30.0  1
 7RE  Var_18  H5   C06  C04  N03  -121.49  30.0  1
 7RE  Var_19  H7   C08  C02  C01     0.61  30.0  1
 7RE  Var_20  H1   C01  C02  C08  -179.58  30.0  3
 7RE  Var_21  H2   C01  C02  C08   -57.96  30.0  3
 7RE  Var_22  H3   C01  C02  C08    58.94  30.0  3
 7RE  Var_23  H1   C01  C02  N03     0.35  30.0  3
 7RE  Var_24  H2   C01  C02  N03   121.97  30.0  3
 7RE  Var_25  H3   C01  C02  N03  -121.14  30.0  3
 7RE  Var_26  H4   C06  C04  O05   -54.64  30.0  1
 7RE  Var_27  H5   C06  C04  O05    58.26  30.0  1

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
 7RE  plan-1  C04  0.020
 7RE  plan-1  C06  0.020
 7RE  plan-1  N03  0.020
 7RE  plan-1  O05  0.020

