# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 22:07:23 2020
#   Inital geometry file: a 48 line input string
#   Ligand name: N-methylpyrimidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ncccn1
#
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
 8RY  8RY  N-methylpyrimidine-2-carboxamide  ligand  17  10  .  2021-08-06  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_8RY
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
 8RY  N1  N  NH1   0  -0.626  -1.9739   0.6454  -0.0020
 8RY  N3  N  N     0  -0.391   1.0689  -1.2304   0.0137
 8RY  C4  C  CR16  0  -0.006   1.9696   1.3267   0.0049
 8RY  C5  C  CR16  0  -0.339   2.8900   0.2926   0.0067
 8RY  C6  C  CR16  0  -0.020   2.3743  -0.9927   0.0106
 8RY  C1  C  CH3   0  -0.513  -3.4150   0.5835  -0.0022
 8RY  C2  C  C     0   0.490  -1.2109  -0.4476   0.0143
 8RY  C3  C  CR6   0   0.284   0.2771  -0.1721   0.0114
 8RY  N2  N  N     0  -0.420   0.6639   1.0948   0.0069
 8RY  O1  O  O     0  -0.477  -1.6408  -1.5897   0.0288
 8RY  H1  H  HNH1  0   0.412  -1.5161   1.5433  -0.0062
 8RY  H3  H  HCR6  0   0.294   3.9539   0.4774   0.0056
 8RY  H4  H  HCR6  0   0.287   3.0302  -1.8553   0.0111
 8RY  H5  H  HCH3  0   0.253  -3.8017   1.5953  -0.0804
 8RY  H6  H  HCH3  0   0.242  -3.7891   0.0053  -0.8473
 8RY  H7  H  HCH3  0   0.241  -3.8000   0.1369   0.9155
 8RY  H2  H  HCR6  0   0.288   2.2860   2.3627   0.0017

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
 8RY  C4  C5  aromatic  1.384  0.020  1.384
 8RY  C4  N2  aromatic  1.326  0.020  1.326
 8RY  C5  C6  aromatic  1.385  0.020  1.385
 8RY  N2  C3  aromatic  1.325  0.020  1.325
 8RY  C6  N3  aromatic  1.327  0.020  1.327
 8RY  C3  N3  aromatic  1.322  0.020  1.322
 8RY  C3  C2  single    1.513  0.020  1.513
 8RY  O1  C2  double    1.220  0.020  1.220
 8RY  C2  N1  single    1.333  0.020  1.333
 8RY  N1  C1  single    1.442  0.020  1.442
 8RY  N1  H1  single    0.860  0.020  1.020
 8RY  C4  H2  single    0.930  0.020  1.080
 8RY  C5  H3  single    0.930  0.020  1.080
 8RY  C6  H4  single    0.930  0.020  1.080
 8RY  C1  H5  single    0.970  0.020  1.090
 8RY  C1  H6  single    0.970  0.020  1.090
 8RY  C1  H7  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
 8RY  H1  N1  C2  118.07  3.000
 8RY  H1  N1  C1  119.47  3.000
 8RY  C2  N1  C1  122.46  3.000
 8RY  C3  N3  C6  116.48  3.000
 8RY  H2  C4  N2  117.06  3.000
 8RY  H2  C4  C5  121.34  3.000
 8RY  N2  C4  C5  121.60  3.000
 8RY  H3  C5  C6  121.72  3.000
 8RY  H3  C5  C4  121.82  3.000
 8RY  C6  C5  C4  116.46  3.000
 8RY  H4  C6  C5  120.89  3.000
 8RY  H4  C6  N3  116.92  3.000
 8RY  C5  C6  N3  122.19  3.000
 8RY  H7  C1  H6  108.30  3.000
 8RY  H7  C1  H5  108.44  3.000
 8RY  H6  C1  H5  108.43  3.000
 8RY  H7  C1  N1  111.72  3.000
 8RY  H6  C1  N1  111.45  3.000
 8RY  H5  C1  N1  108.40  3.000
 8RY  O1  C2  C3  121.12  3.000
 8RY  O1  C2  N1  124.46  3.000
 8RY  C3  C2  N1  114.43  3.000
 8RY  N2  C3  C2  117.47  3.000
 8RY  C2  C3  N3  116.31  3.000
 8RY  N2  C3  N3  126.22  3.000
 8RY  C3  N2  C4  117.05  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
 8RY  CONST_01  C4  C5  C6  N3     0.00   0.0  0
 8RY  CONST_02  C4  N2  C3  N3     0.00   0.0  0
 8RY  CONST_03  C3  N2  C4  C5     0.00   0.0  0
 8RY  CONST_04  C3  N3  C6  C5     0.00   0.0  0
 8RY  CONST_05  N2  C4  C5  C6     0.00   0.0  0
 8RY  CONST_06  N2  C3  N3  C6     0.00   0.0  0
 8RY  CONST_07  C2  C3  N2  C4   180.00   0.0  0
 8RY  CONST_08  C2  C3  N3  C6   180.00   0.0  0
 8RY  CONST_09  H3  C5  C6  N3   180.00   0.0  0
 8RY  CONST_10  H4  C6  C5  C4   180.00   0.0  0
 8RY  CONST_11  H2  C4  C5  C6   180.00   0.0  0
 8RY  CONST_12  C3  C2  N1  C1   180.00   0.0  0
 8RY  CONST_13  H1  N1  C2  C3     0.00   0.0  0
 8RY  CONST_14  O1  C2  N1  C1     0.00   0.0  0
 8RY  Var_01    N2  C3  C2  N1     0.66  30.0  2
 8RY  Var_02    H5  C1  N1  C2  -176.48  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
 8RY  plan-1  N3  0.020
 8RY  plan-1  C4  0.020
 8RY  plan-1  C5  0.020
 8RY  plan-1  C6  0.020
 8RY  plan-1  C2  0.020
 8RY  plan-1  C3  0.020
 8RY  plan-1  N2  0.020
 8RY  plan-1  H3  0.020
 8RY  plan-1  H4  0.020
 8RY  plan-1  H2  0.020
 8RY  plan-2  N1  0.020
 8RY  plan-2  C1  0.020
 8RY  plan-2  C2  0.020
 8RY  plan-2  C3  0.020
 8RY  plan-2  O1  0.020
 8RY  plan-2  H1  0.020

