# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 01:36:48 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: pyrazine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cnccn1
#
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
 VGL  VGL  'pyrazine-2-carboxylic acid'  ligand  12  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VGL
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
 VGL  C1  C  CR6    0   0.005  -0.1628  -0.0584  -0.0027
 VGL  C3  C  CR16   0  -0.128   1.7468  -1.2822  -0.0316
 VGL  C4  C  CR16   0  -0.102   2.5061  -0.1216  -0.0483
 VGL  C2  C  C      0   0.391  -1.6900   0.0176   0.0268
 VGL  C6  C  CR16   0  -0.088   0.6105   1.1030  -0.0214
 VGL  O1  O  O      0  -0.587  -2.1658   1.1683   0.0195
 VGL  O2  O  OC    -1  -0.584  -2.2968  -1.0620   0.0561
 VGL  N2  N  N      0  -0.356   0.4225  -1.2514  -0.0085
 VGL  N5  N  N      0  -0.357   1.9361   1.0761  -0.0432
 VGL  H6  H  HCR6   0   0.265   0.1360   2.0758  -0.0179
 VGL  H3  H  HCR6   0   0.268   2.2263  -2.2547  -0.0375
 VGL  H4  H  HCR6   0   0.272   3.5887  -0.1666  -0.0660

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
 VGL  C1  C2  single    1.529  0.020  1.529
 VGL  C1  C6  aromatic  1.395  0.020  1.395
 VGL  C1  N2  aromatic  1.329  0.020  1.329
 VGL  C3  C4  aromatic  1.387  0.020  1.387
 VGL  C3  N2  aromatic  1.325  0.020  1.325
 VGL  C4  N5  aromatic  1.326  0.020  1.326
 VGL  C2  O1  deloc     1.245  0.020  1.245
 VGL  C2  O2  deloc     1.239  0.020  1.239
 VGL  C6  N5  aromatic  1.326  0.020  1.326
 VGL  C6  H6  single    0.930  0.020  1.080
 VGL  C3  H3  single    0.930  0.020  1.080
 VGL  C4  H4  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
 VGL  N2  C1  C6  120.20  3.000
 VGL  N2  C1  C2  118.98  3.000
 VGL  C6  C1  C2  120.82  3.000
 VGL  H3  C3  N2  117.58  3.000
 VGL  H3  C3  C4  120.55  3.000
 VGL  N2  C3  C4  121.87  3.000
 VGL  H4  C4  N5  117.84  3.000
 VGL  H4  C4  C3  120.82  3.000
 VGL  N5  C4  C3  121.35  3.000
 VGL  O2  C2  O1  128.19  3.000
 VGL  O2  C2  C1  116.51  3.000
 VGL  O1  C2  C1  115.30  3.000
 VGL  H6  C6  N5  117.16  3.000
 VGL  H6  C6  C1  120.33  3.000
 VGL  N5  C6  C1  122.50  3.000
 VGL  C3  N2  C1  117.46  3.000
 VGL  C6  N5  C4  116.61  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
 VGL  CONST_01  C4  N5  C6  C1    0.00   0.0  0
 VGL  CONST_02  C4  C3  N2  C1    0.00   0.0  0
 VGL  CONST_03  C6  N5  C4  C3    0.00   0.0  0
 VGL  CONST_04  C6  C1  N2  C3    0.00   0.0  0
 VGL  CONST_05  N5  C6  C1  N2    0.00   0.0  0
 VGL  CONST_06  N5  C4  C3  N2    0.00   0.0  0
 VGL  CONST_07  C2  C1  N2  C3  180.00   0.0  0
 VGL  CONST_08  N5  C6  C1  C2  180.00   0.0  0
 VGL  CONST_09  H3  C3  N2  C1  180.00   0.0  0
 VGL  CONST_10  H6  C6  N5  C4  180.00   0.0  0
 VGL  CONST_11  H4  C4  N5  C6  180.00   0.0  0
 VGL  Var_01    O1  C2  C1  C6    0.67  30.0  2

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
 VGL  plan-1  C1  0.020
 VGL  plan-1  C3  0.020
 VGL  plan-1  C4  0.020
 VGL  plan-1  C2  0.020
 VGL  plan-1  C6  0.020
 VGL  plan-1  N2  0.020
 VGL  plan-1  N5  0.020
 VGL  plan-1  H6  0.020
 VGL  plan-1  H3  0.020
 VGL  plan-1  H4  0.020
 VGL  plan-2  C1  0.020
 VGL  plan-2  C2  0.020
 VGL  plan-2  O1  0.020
 VGL  plan-2  O2  0.020

