# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:00:57 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 2,5-dimethylpyrazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnc(C)cn1
#
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
 25R  25R  '2,5-dimethylpyrazine     '  ligand  16  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_25R
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
 25R  N1   N  N     0  -0.371  -0.7146   1.1768  -0.0255
 25R  C2   C  CR6   0   0.200  -1.3542   0.0110  -0.0159
 25R  C3   C  CR16  0  -0.134  -0.6229  -1.1744   0.0127
 25R  N4   N  N     0  -0.371   0.7001  -1.1958   0.0256
 25R  C5   C  CR6   0   0.200   1.3399  -0.0301   0.0130
 25R  C6   C  CR16  0  -0.134   0.6085   1.1553  -0.0104
 25R  C7   C  CH3   0  -0.717  -2.8488   0.0183  -0.0432
 25R  C8   C  CH3   0  -0.716   2.8347  -0.0372   0.0172
 25R  H3   H  HCR6  0   0.263  -1.1322  -2.1324   0.0289
 25R  H6   H  HCR6  0   0.263   1.1176   2.1135  -0.0133
 25R  H7   H  HCH3  0   0.257  -3.2162   0.3460  -1.0171
 25R  H7A  H  HCH3  0   0.247  -3.2560  -0.9722   0.1520
 25R  H7B  H  HCH3  0   0.255  -3.2466   0.7065   0.7024
 25R  H8   H  HCH3  0   0.257   3.2222  -0.3945  -0.9383
 25R  H8A  H  HCH3  0   0.247   3.2375   0.9592   0.1899
 25R  H8B  H  HCH3  0   0.255   3.2172  -0.7016   0.7918

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
 25R  N1  C2   aromatic  1.330  0.020  1.330
 25R  N1  C6   aromatic  1.323  0.020  1.323
 25R  C2  C3   aromatic  1.393  0.020  1.393
 25R  C2  C7   single    1.495  0.020  1.495
 25R  C3  N4   aromatic  1.323  0.020  1.323
 25R  N4  C5   aromatic  1.330  0.020  1.330
 25R  C5  C6   aromatic  1.393  0.020  1.393
 25R  C5  C8   single    1.495  0.020  1.495
 25R  C3  H3   single    0.930  0.020  1.080
 25R  C6  H6   single    0.930  0.020  1.080
 25R  C7  H7   single    0.970  0.020  1.090
 25R  C7  H7A  single    0.970  0.020  1.090
 25R  C7  H7B  single    0.970  0.020  1.090
 25R  C8  H8   single    0.970  0.020  1.090
 25R  C8  H8A  single    0.970  0.020  1.090
 25R  C8  H8B  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
 25R  C6   N1  C2   117.81  3.000
 25R  C7   C2  C3   121.96  3.000
 25R  C7   C2  N1   118.46  3.000
 25R  C3   C2  N1   119.58  3.000
 25R  H3   C3  N4   117.06  3.000
 25R  H3   C3  C2   120.34  3.000
 25R  N4   C3  C2   122.60  3.000
 25R  C5   N4  C3   117.83  3.000
 25R  C8   C5  C6   121.94  3.000
 25R  C8   C5  N4   118.48  3.000
 25R  C6   C5  N4   119.57  3.000
 25R  H6   C6  C5   120.34  3.000
 25R  H6   C6  N1   117.05  3.000
 25R  C5   C6  N1   122.61  3.000
 25R  H7B  C7  H7A  108.39  3.000
 25R  H7B  C7  H7   107.34  3.000
 25R  H7A  C7  H7   107.90  3.000
 25R  H7B  C7  C2   110.83  3.000
 25R  H7A  C7  C2   111.48  3.000
 25R  H7   C7  C2   110.75  3.000
 25R  H8B  C8  H8A  108.38  3.000
 25R  H8B  C8  H8   107.34  3.000
 25R  H8A  C8  H8   107.89  3.000
 25R  H8B  C8  C5   110.85  3.000
 25R  H8A  C8  C5   111.48  3.000
 25R  H8   C8  C5   110.74  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
 25R  CONST_01  N4  C3  C2  N1    0.00   0.0  0
 25R  CONST_02  N4  C5  C6  N1    0.00   0.0  0
 25R  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 25R  CONST_04  C5  N4  C3  C2    0.00   0.0  0
 25R  CONST_05  C6  N1  C2  C3    0.00   0.0  0
 25R  CONST_06  C6  C5  N4  C3    0.00   0.0  0
 25R  CONST_07  C8  C5  C6  N1  180.00   0.0  0
 25R  CONST_08  C8  C5  N4  C3  180.00   0.0  0
 25R  CONST_09  C7  C2  C3  N4  180.00   0.0  0
 25R  CONST_10  C7  C2  N1  C6  180.00   0.0  0
 25R  CONST_11  H3  C3  C2  N1  180.00   0.0  0
 25R  CONST_12  H6  C6  N1  C2  180.00   0.0  0
 25R  Var_01    H7  C7  C2  N1   70.34  30.0  2
 25R  Var_02    H8  C8  C5  N4   70.32  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
 25R  plan-1  N1  0.020
 25R  plan-1  C2  0.020
 25R  plan-1  C3  0.020
 25R  plan-1  N4  0.020
 25R  plan-1  C5  0.020
 25R  plan-1  C6  0.020
 25R  plan-1  C7  0.020
 25R  plan-1  C8  0.020
 25R  plan-1  H3  0.020
 25R  plan-1  H6  0.020

