# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:02:37 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: 4-chloro-6-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Cl)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
 DU7  DU7  4-chloro-6-methylpyrimidin-2-amine  ligand  15  9  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DU7
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
 DU7  C4  C   CR6   0   0.557  -1.0377  -1.1511   0.0079
 DU7  C3  C   CR6   0   0.214   0.8729   0.0174  -0.0667
 DU7  C2  C   CR16  0  -0.361   0.1962   1.2228  -0.0635
 DU7  C1  C   CR6   0   0.293  -1.1915   1.1182  -0.0172
 DU7  CL  CL  CL    0  -0.102   2.6053   0.0297  -0.1197
 DU7  N   N   N     0  -0.451   0.3053  -1.1575  -0.0323
 DU7  N1  N   NH2   0  -0.821  -1.6489  -2.3405   0.0353
 DU7  N2  N   N     0  -0.475  -1.8037  -0.0579   0.0187
 DU7  C   C   CH3   0  -0.719  -2.0587   2.3348  -0.0066
 DU7  H3  H   HCR6  0   0.284   0.7037   2.1743  -0.0949
 DU7  H5  H   HNH2  0   0.405  -1.1162  -3.1919   0.0511
 DU7  H4  H   HNH2  0   0.404  -2.6505  -2.3945   0.0839
 DU7  H2  H   HCH3  0   0.262  -2.6894   2.3399   0.8830
 DU7  H1  H   HCH3  0   0.250  -1.4729   3.2511  -0.0220
 DU7  H   H   HCH3  0   0.262  -2.7210   2.3316  -0.8730

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
 DU7  C   C1  single    1.494  0.020  1.494
 DU7  C1  N2  aromatic  1.326  0.020  1.326
 DU7  C1  C2  aromatic  1.392  0.020  1.392
 DU7  N2  C4  aromatic  1.335  0.020  1.335
 DU7  C2  C3  aromatic  1.382  0.020  1.382
 DU7  C4  N1  single    1.338  0.020  1.338
 DU7  C4  N   aromatic  1.344  0.020  1.344
 DU7  C3  N   aromatic  1.305  0.020  1.305
 DU7  C3  CL  single    1.733  0.020  1.733
 DU7  C2  H3  single    0.930  0.020  1.080
 DU7  N1  H5  single    0.860  0.020  1.020
 DU7  N1  H4  single    0.860  0.020  1.020
 DU7  C   H2  single    0.970  0.020  1.090
 DU7  C   H1  single    0.970  0.020  1.090
 DU7  C   H   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
 DU7  N2  C4  N1  117.77  3.000
 DU7  N1  C4  N   116.95  3.000
 DU7  N2  C4  N   125.29  3.000
 DU7  N   C3  CL  116.22  3.000
 DU7  CL  C3  C2  118.89  3.000
 DU7  N   C3  C2  124.89  3.000
 DU7  H3  C2  C1  122.41  3.000
 DU7  H3  C2  C3  122.59  3.000
 DU7  C1  C2  C3  114.99  3.000
 DU7  C   C1  N2  116.99  3.000
 DU7  N2  C1  C2  121.84  3.000
 DU7  C   C1  C2  121.17  3.000
 DU7  C3  N   C4  115.54  3.000
 DU7  H4  N1  H5  118.86  3.000
 DU7  H4  N1  C4  120.30  3.000
 DU7  H5  N1  C4  120.78  3.000
 DU7  C1  N2  C4  117.46  3.000
 DU7  H   C   H1  108.56  3.000
 DU7  H   C   H2  107.27  3.000
 DU7  H1  C   H2  108.61  3.000
 DU7  H   C   C1  110.15  3.000
 DU7  H1  C   C1  111.91  3.000
 DU7  H2  C   C1  110.20  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
 DU7  CONST_01  C2  C1  N2  C4     0.00   0.0  0
 DU7  CONST_02  C2  C3  N   C4     0.00   0.0  0
 DU7  CONST_03  N2  C1  C2  C3     0.00   0.0  0
 DU7  CONST_04  N2  C4  N   C3     0.00   0.0  0
 DU7  CONST_05  N   C4  N2  C1     0.00   0.0  0
 DU7  CONST_06  N   C3  C2  C1     0.00   0.0  0
 DU7  CONST_07  C   C1  N2  C4   180.00   0.0  0
 DU7  CONST_08  CL  C3  N   C4   180.00   0.0  0
 DU7  CONST_09  C   C1  C2  C3   180.00   0.0  0
 DU7  CONST_10  N1  C4  N   C3   180.00   0.0  0
 DU7  CONST_11  N1  C4  N2  C1   180.00   0.0  0
 DU7  CONST_12  CL  C3  C2  C1   180.00   0.0  0
 DU7  CONST_13  H3  C2  C3  N    180.00   0.0  0
 DU7  CONST_14  H5  N1  C4  N      0.00   0.0  0
 DU7  CONST_15  H4  N1  C4  N    180.00   0.0  0
 DU7  Var_01    H2  C   C1  C2  -121.91  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
 DU7  plan-1  C4  0.020
 DU7  plan-1  C3  0.020
 DU7  plan-1  C2  0.020
 DU7  plan-1  C1  0.020
 DU7  plan-1  CL  0.020
 DU7  plan-1  N   0.020
 DU7  plan-1  N1  0.020
 DU7  plan-1  N2  0.020
 DU7  plan-1  C   0.020
 DU7  plan-1  H3  0.020
 DU7  plan-2  C4  0.020
 DU7  plan-2  N1  0.020
 DU7  plan-2  H5  0.020
 DU7  plan-2  H4  0.020

