# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 08:24:19 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=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
 PZA  PZA  'pyrazine-2-carboxamide   '  ligand  14  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PZA
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
 PZA  C   C  C     0   0.494  -0.1042   0.0043   1.7062
 PZA  N1  N  NH2   0  -0.802   1.0819   0.0263   2.3146
 PZA  O   O  O     0  -0.471  -1.1835  -0.0152   2.2797
 PZA  C1  C  CR16  0  -0.108   1.1856   0.0263  -1.6975
 PZA  C2  C  CR16  0  -0.086   0.0137   0.0070  -2.4460
 PZA  N2  N  N     0  -0.353  -1.1787  -0.0129  -1.8704
 PZA  C3  C  CR16  0  -0.057  -1.2082  -0.0135  -0.5445
 PZA  C4  C  CR6   0   0.077  -0.0386   0.0057   0.2057
 PZA  N3  N  N     0  -0.377   1.1535   0.0253  -0.3767
 PZA  H1  H  HNH2  0   0.410   1.1410   0.0247   3.3194
 PZA  H2  H  HNH2  0   0.414   1.9361   0.0393   1.7821
 PZA  H5  H  HCR6  0   0.288   0.0515   0.0080  -3.5283
 PZA  H4  H  HCR6  0   0.285  -2.1798  -0.0299  -0.0677
 PZA  H3  H  HCR6  0   0.286   2.1549   0.0421  -2.1795

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
 PZA  C   N1  single    1.333  0.020  1.333
 PZA  C   O   double    1.222  0.020  1.222
 PZA  C   C4  single    1.502  0.020  1.502
 PZA  N1  H1  single    0.860  0.020  1.020
 PZA  N1  H2  single    0.860  0.020  1.020
 PZA  C1  C2  aromatic  1.391  0.020  1.391
 PZA  C1  N3  aromatic  1.321  0.020  1.321
 PZA  C1  H3  single    0.930  0.020  1.080
 PZA  C2  N2  aromatic  1.324  0.020  1.324
 PZA  C2  H5  single    0.930  0.020  1.080
 PZA  N2  C3  aromatic  1.326  0.020  1.326
 PZA  C3  C4  aromatic  1.390  0.020  1.390
 PZA  C3  H4  single    0.930  0.020  1.080
 PZA  C4  N3  aromatic  1.327  0.020  1.327

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
 PZA  C4  C   O   120.48  3.000
 PZA  C4  C   N1  114.65  3.000
 PZA  O   C   N1  124.87  3.000
 PZA  H2  N1  H1  118.57  3.000
 PZA  H2  N1  C   120.91  3.000
 PZA  H1  N1  C   120.52  3.000
 PZA  H3  C1  N3  117.83  3.000
 PZA  H3  C1  C2  121.00  3.000
 PZA  N3  C1  C2  121.17  3.000
 PZA  H5  C2  N2  117.76  3.000
 PZA  H5  C2  C1  120.57  3.000
 PZA  N2  C2  C1  121.67  3.000
 PZA  C3  N2  C2  117.04  3.000
 PZA  H4  C3  C4  121.20  3.000
 PZA  H4  C3  N2  117.41  3.000
 PZA  C4  C3  N2  121.40  3.000
 PZA  N3  C4  C3  121.29  3.000
 PZA  N3  C4  C   118.54  3.000
 PZA  C3  C4  C   120.17  3.000
 PZA  C4  N3  C1  117.43  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
 PZA  CONST_01  C3  N2  C2  C1     0.00   0.0  0
 PZA  CONST_02  C3  C4  N3  C1     0.00   0.0  0
 PZA  CONST_03  C4  N3  C1  C2     0.00   0.0  0
 PZA  CONST_04  C4  C3  N2  C2     0.00   0.0  0
 PZA  CONST_05  N3  C1  C2  N2     0.00   0.0  0
 PZA  CONST_06  N3  C4  C3  N2     0.00   0.0  0
 PZA  CONST_07  N2  C3  C4  C    180.00   0.0  0
 PZA  CONST_08  C1  N3  C4  C    180.00   0.0  0
 PZA  CONST_09  H4  C3  N2  C2   180.00   0.0  0
 PZA  CONST_10  H3  C1  C2  N2   180.00   0.0  0
 PZA  CONST_11  H5  C2  N2  C3   180.00   0.0  0
 PZA  CONST_12  H1  N1  C   C4   180.00   0.0  0
 PZA  CONST_13  H2  N1  C   C4     0.00   0.0  0
 PZA  Var_01    C3  C4  C   N1  -179.88  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
 PZA  plan-1  C   0.020
 PZA  plan-1  C1  0.020
 PZA  plan-1  C2  0.020
 PZA  plan-1  N2  0.020
 PZA  plan-1  C3  0.020
 PZA  plan-1  C4  0.020
 PZA  plan-1  N3  0.020
 PZA  plan-1  H5  0.020
 PZA  plan-1  H4  0.020
 PZA  plan-1  H3  0.020
 PZA  plan-2  C   0.020
 PZA  plan-2  N1  0.020
 PZA  plan-2  O   0.020
 PZA  plan-2  C4  0.020
 PZA  plan-2  H1  0.020
 PZA  plan-2  H2  0.020

