# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:24:40 2020
#   Inital geometry file: a 35 line input string
#   Ligand name: pyrimidin-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cncnc1
#
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
 T5V  T5V  'pyrimidin-5-amine        '  ligand  12  7  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T5V
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
 T5V  N1  N  N     0  -0.377  -1.1268   1.1857   0.0228
 T5V  N   N  NH2   0  -0.854   2.2994  -0.0338   0.1518
 T5V  C   C  CR6   0   0.223   0.9342  -0.0167   0.0715
 T5V  C1  C  CR16  0  -0.103   0.1956   1.1707   0.0479
 T5V  C2  C  CR16  0   0.010  -1.7499   0.0171   0.0181
 T5V  C3  C  CR16  0  -0.103   0.1657  -1.1851   0.0577
 T5V  N2  N  N     0  -0.377  -1.1567  -1.1666   0.0326
 T5V  H1  H  HNH2  0   0.389   2.7771   0.7959  -0.1616
 T5V  H   H  HNH2  0   0.389   2.7562  -0.8775  -0.1557
 T5V  H2  H  HCR6  0   0.275   0.7039   2.1309   0.0491
 T5V  H3  H  HCR6  0   0.253  -2.8335   0.0310  -0.0020
 T5V  H4  H  HCR6  0   0.275   0.6491  -2.1578   0.0671

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
 T5V  C   N   single    1.368  0.020  1.368
 T5V  C   C1  aromatic  1.399  0.020  1.399
 T5V  C1  N1  aromatic  1.323  0.020  1.323
 T5V  N1  C2  aromatic  1.324  0.020  1.324
 T5V  C2  N2  aromatic  1.324  0.020  1.324
 T5V  N2  C3  aromatic  1.323  0.020  1.323
 T5V  C3  C   aromatic  1.399  0.020  1.399
 T5V  N   H1  single    0.890  0.020  1.040
 T5V  N   H   single    0.860  0.020  1.020
 T5V  C1  H2  single    0.930  0.020  1.080
 T5V  C2  H3  single    0.930  0.020  1.080
 T5V  C3  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
 T5V  C2  N1  C1  117.42  3.000
 T5V  H   N   H1  112.32  3.000
 T5V  H   N   C   116.43  3.000
 T5V  H1  N   C   116.41  3.000
 T5V  C3  C   C1  114.77  3.000
 T5V  C3  C   N   122.59  3.000
 T5V  C1  C   N   122.60  3.000
 T5V  H2  C1  C   120.22  3.000
 T5V  H2  C1  N1  117.24  3.000
 T5V  C   C1  N1  122.54  3.000
 T5V  H3  C2  N2  117.35  3.000
 T5V  H3  C2  N1  117.34  3.000
 T5V  N2  C2  N1  125.31  3.000
 T5V  H4  C3  N2  117.23  3.000
 T5V  H4  C3  C   120.23  3.000
 T5V  N2  C3  C   122.54  3.000
 T5V  C3  N2  C2  117.42  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
 T5V  CONST_01  C3  C   C1  N1    0.00  0.0  0
 T5V  CONST_02  C3  N2  C2  N1    0.00  0.0  0
 T5V  CONST_03  C2  N1  C1  C     0.00  0.0  0
 T5V  CONST_04  C2  N2  C3  C     0.00  0.0  0
 T5V  CONST_05  N2  C3  C   C1    0.00  0.0  0
 T5V  CONST_06  N2  C2  N1  C1    0.00  0.0  0
 T5V  CONST_07  N   C   C1  N1  180.00  0.0  0
 T5V  CONST_08  N2  C3  C   N   180.00  0.0  0
 T5V  CONST_09  H4  C3  C   C1  180.00  0.0  0
 T5V  CONST_10  H3  C2  N1  C1  180.00  0.0  0
 T5V  CONST_11  H2  C1  N1  C2  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
 T5V  plan-1  N1  0.020
 T5V  plan-1  N   0.020
 T5V  plan-1  C   0.020
 T5V  plan-1  C1  0.020
 T5V  plan-1  C2  0.020
 T5V  plan-1  C3  0.020
 T5V  plan-1  N2  0.020
 T5V  plan-1  H2  0.020
 T5V  plan-1  H3  0.020
 T5V  plan-1  H4  0.020
 T5V  plan-2  N   0.020
 T5V  plan-2  C   0.020
 T5V  plan-2  H1  0.020
 T5V  plan-2  H   0.020

