# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:31:03 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 4,6-dimethylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(N)n1
#
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
 5ZE  5ZE  4,6-dimethylpyrimidin-2-amine  ligand  18  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5ZE
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
 5ZE  C1  C  CH3   0  -0.695   2.5269   1.3354   0.0459
 5ZE  C2  C  CR6   0   0.293   1.1928   0.6615   0.0446
 5ZE  C3  C  CR16  0  -0.404   0.0086   1.3883   0.0781
 5ZE  C4  C  CR6   0   0.296  -1.1807   0.6711   0.0590
 5ZE  C5  C  CH3   0  -0.695  -2.5085   1.3561   0.0589
 5ZE  N6  N  N     0  -0.475  -1.1891  -0.6551   0.0224
 5ZE  C7  C  CR6   0   0.529  -0.0005  -1.2600  -0.0089
 5ZE  N8  N  NH2   0  -0.809  -0.0033  -2.6134  -0.0268
 5ZE  N9  N  N     0  -0.453   1.1907  -0.6631  -0.0005
 5ZE  H1  H  HCH3  0   0.248   3.0550   1.1334  -0.8865
 5ZE  H2  H  HCH3  0   0.230   2.4369   2.4136   0.1589
 5ZE  H3  H  HCH3  0   0.247   3.1478   0.9528   0.8558
 5ZE  H4  H  HCR6  0   0.229   0.0123   2.4683   0.1106
 5ZE  H5  H  HCH3  0   0.248  -3.0026   1.2186  -0.9038
 5ZE  H6  H  HCH3  0   0.246  -3.1631   0.9310   0.8191
 5ZE  H7  H  HCH3  0   0.231  -2.4137   2.4246   0.2391
 5ZE  H8  H  HNH2  0   0.365  -0.8598  -3.0849  -0.2507
 5ZE  H9  H  HNH2  0   0.369   0.8563  -3.0823  -0.2456

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
 5ZE  C5  C4  single    1.494  0.020  1.494
 5ZE  C4  C3  aromatic  1.389  0.020  1.389
 5ZE  C4  N6  aromatic  1.327  0.020  1.327
 5ZE  C3  C2  aromatic  1.390  0.020  1.390
 5ZE  N6  C7  aromatic  1.334  0.020  1.334
 5ZE  C2  C1  single    1.495  0.020  1.495
 5ZE  C2  N9  aromatic  1.325  0.020  1.325
 5ZE  C7  N9  aromatic  1.332  0.020  1.332
 5ZE  C7  N8  single    1.353  0.020  1.353
 5ZE  C1  H1  single    0.970  0.020  1.090
 5ZE  C1  H2  single    0.970  0.020  1.090
 5ZE  C1  H3  single    0.970  0.020  1.090
 5ZE  C3  H4  single    0.930  0.020  1.080
 5ZE  C5  H5  single    0.970  0.020  1.090
 5ZE  C5  H6  single    0.970  0.020  1.090
 5ZE  C5  H7  single    0.970  0.020  1.090
 5ZE  N8  H8  single    0.890  0.020  1.040
 5ZE  N8  H9  single    0.890  0.020  1.040

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
 5ZE  H3  C1  H2  108.54  3.000
 5ZE  H3  C1  H1  107.12  3.000
 5ZE  H2  C1  H1  108.21  3.000
 5ZE  H3  C1  C2  110.54  3.000
 5ZE  H2  C1  C2  111.91  3.000
 5ZE  H1  C1  C2  110.37  3.000
 5ZE  N9  C2  C3  121.48  3.000
 5ZE  N9  C2  C1  116.88  3.000
 5ZE  C3  C2  C1  121.65  3.000
 5ZE  H4  C3  C4  121.30  3.000
 5ZE  H4  C3  C2  121.36  3.000
 5ZE  C4  C3  C2  117.33  3.000
 5ZE  N6  C4  C5  116.91  3.000
 5ZE  N6  C4  C3  121.47  3.000
 5ZE  C5  C4  C3  121.62  3.000
 5ZE  H7  C5  H6  108.66  3.000
 5ZE  H7  C5  H5  108.03  3.000
 5ZE  H6  C5  H5  107.12  3.000
 5ZE  H7  C5  C4  111.90  3.000
 5ZE  H6  C5  C4  110.80  3.000
 5ZE  H5  C5  C4  110.17  3.000
 5ZE  C7  N6  C4  116.63  3.000
 5ZE  N9  C7  N8  116.74  3.000
 5ZE  N8  C7  N6  116.87  3.000
 5ZE  N9  C7  N6  126.39  3.000
 5ZE  H9  N8  H8  117.60  3.000
 5ZE  H9  N8  C7  117.93  3.000
 5ZE  H8  N8  C7  118.35  3.000
 5ZE  C7  N9  C2  116.70  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
 5ZE  CONST_01  N6  C4  C3  C2     0.00   0.0  0
 5ZE  CONST_02  N6  C7  N9  C2     0.00   0.0  0
 5ZE  CONST_03  C7  N6  C4  C3     0.00   0.0  0
 5ZE  CONST_04  C7  N9  C2  C3     0.00   0.0  0
 5ZE  CONST_05  N9  C2  C3  C4     0.00   0.0  0
 5ZE  CONST_06  N9  C7  N6  C4     0.00   0.0  0
 5ZE  CONST_07  C4  C3  C2  C1   180.00   0.0  0
 5ZE  CONST_08  C7  N9  C2  C1   180.00   0.0  0
 5ZE  CONST_09  C5  C4  C3  C2   180.00   0.0  0
 5ZE  CONST_10  N8  C7  N9  C2   180.00   0.0  0
 5ZE  CONST_11  N8  C7  N6  C4   180.00   0.0  0
 5ZE  CONST_12  C7  N6  C4  C5   180.00   0.0  0
 5ZE  CONST_13  H4  C3  C4  N6   180.00   0.0  0
 5ZE  CONST_15  H9  N8  C7  N6   180.00   0.0  0
 5ZE  Var_01    H5  C5  C4  C3   110.83  30.0  2
 5ZE  Var_02    H1  C1  C2  C3  -115.82  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
 5ZE  plan-1  C1  0.020
 5ZE  plan-1  C2  0.020
 5ZE  plan-1  C3  0.020
 5ZE  plan-1  C4  0.020
 5ZE  plan-1  C5  0.020
 5ZE  plan-1  N6  0.020
 5ZE  plan-1  C7  0.020
 5ZE  plan-1  N8  0.020
 5ZE  plan-1  N9  0.020
 5ZE  plan-1  H4  0.020
 5ZE  plan-2  C7  0.020
 5ZE  plan-2  N8  0.020
 5ZE  plan-2  H8  0.020
 5ZE  plan-2  H9  0.020

