# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:02:48 2020
#   Inital geometry file: a 31 line input string
#   Ligand name: pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1cncnc1
#
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
 P1R  P1R  'pyrimidine               '  ligand  10  6  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P1R
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
 P1R  C5  C  CR16  0  -0.333   0.0189  -1.3419   0.0037
 P1R  C6  C  CR16  0  -0.025   1.1805  -0.5890   0.0247
 P1R  N1  N  N     0  -0.392   1.1595   0.7389   0.0548
 P1R  C4  C  CR16  0  -0.025  -1.1731  -0.6377   0.0155
 P1R  N3  N  N     0  -0.392  -1.2072   0.6900   0.0454
 P1R  C2  C  CR16  0   0.054  -0.0362   1.3093   0.0636
 P1R  H5  H  HCR6  0   0.285   0.0411  -2.4214  -0.0203
 P1R  H6  H  HCR6  0   0.282   2.1546  -1.0648   0.0172
 P1R  H4  H  HCR6  0   0.282  -2.1260  -1.1542   0.0001
 P1R  H2  H  HCR6  0   0.265  -0.0587   2.3934   0.0881

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
 P1R  C5  C6  aromatic  1.384  0.020  1.384
 P1R  C5  C4  aromatic  1.384  0.020  1.384
 P1R  C5  H5  single    0.930  0.020  1.080
 P1R  C6  N1  aromatic  1.328  0.020  1.328
 P1R  C6  H6  single    0.930  0.020  1.080
 P1R  N1  C2  aromatic  1.325  0.020  1.325
 P1R  C4  N3  aromatic  1.328  0.020  1.328
 P1R  C4  H4  single    0.930  0.020  1.080
 P1R  N3  C2  aromatic  1.325  0.020  1.325
 P1R  C2  H2  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
 P1R  H5  C5  C4  121.76  3.000
 P1R  H5  C5  C6  121.78  3.000
 P1R  C4  C5  C6  116.46  3.000
 P1R  H6  C6  N1  116.94  3.000
 P1R  H6  C6  C5  121.01  3.000
 P1R  N1  C6  C5  122.06  3.000
 P1R  C2  N1  C6  116.40  3.000
 P1R  H4  C4  N3  117.00  3.000
 P1R  H4  C4  C5  120.95  3.000
 P1R  N3  C4  C5  122.05  3.000
 P1R  C2  N3  C4  116.40  3.000
 P1R  H2  C2  N3  116.69  3.000
 P1R  H2  C2  N1  116.69  3.000
 P1R  N3  C2  N1  126.62  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
 P1R  CONST_01  C2  N1  C6  C5    0.00  0.0  0
 P1R  CONST_02  C2  N3  C4  C5    0.00  0.0  0
 P1R  CONST_03  N3  C4  C5  C6    0.00  0.0  0
 P1R  CONST_04  N3  C2  N1  C6    0.00  0.0  0
 P1R  CONST_05  C4  C5  C6  N1    0.00  0.0  0
 P1R  CONST_06  C4  N3  C2  N1    0.00  0.0  0
 P1R  CONST_07  H4  C4  C5  C6  180.00  0.0  0
 P1R  CONST_08  H2  C2  N1  C6  180.00  0.0  0
 P1R  CONST_09  H5  C5  C6  N1  180.00  0.0  0
 P1R  CONST_10  H6  C6  C5  C4  180.00  0.0  0

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
 P1R  plan-1  C5  0.020
 P1R  plan-1  C6  0.020
 P1R  plan-1  N1  0.020
 P1R  plan-1  C4  0.020
 P1R  plan-1  N3  0.020
 P1R  plan-1  C2  0.020
 P1R  plan-1  H5  0.020
 P1R  plan-1  H6  0.020
 P1R  plan-1  H4  0.020
 P1R  plan-1  H2  0.020

