# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 11:38:44 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: 4,6-dichloro-2-(methylsulfanyl)pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc(Cl)cc(Cl)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
 HX5  HX5  4,6-dichloro-2-(methylsulfanyl)pyrimidine  ligand  14  10  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HX5
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
 HX5  C1   C   CR16  0  -0.267   1.4317   0.7991   0.0091
 HX5  C2   C   CR6   0   0.212   1.4504  -0.5869  -0.0242
 HX5  N3   N   N     0  -0.395   0.3743  -1.3335  -0.0369
 HX5  C4   C   CR6   0   0.237  -0.7882  -0.6864  -0.0170
 HX5  N5   N   N     0  -0.386  -0.9434   0.6279   0.0141
 HX5  C6   C   CR6   0   0.221   0.1604   1.3412   0.0270
 HX5  S7   S   S2    0   0.086  -2.1825  -1.7285  -0.0359
 HX5  C8   C   CH3   0  -0.770  -3.5454  -0.5494  -0.0099
 HX5  CL9  CL  CL    0  -0.059  -0.0247   3.0489   0.0694
 HX5  CL1  CL  CL    0  -0.059   2.9630  -1.4018  -0.0507
 HX5  H1   H   HCR6  0   0.325   2.3274   1.3999   0.0211
 HX5  H2   H   HCH3  0   0.283  -3.5280   0.0515   0.8953
 HX5  H3   H   HCH3  0   0.283  -3.5263   0.0917  -0.8870
 HX5  H4   H   HCH3  0   0.289  -4.4532  -1.1490  -0.0241

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
 HX5  CL9  C6   single    1.718  0.020  1.718
 HX5  N5   C6   aromatic  1.314  0.020  1.314
 HX5  N5   C4   aromatic  1.324  0.020  1.324
 HX5  C6   C1   aromatic  1.382  0.020  1.382
 HX5  S7   C4   single    1.741  0.020  1.741
 HX5  S7   C8   single    1.802  0.020  1.802
 HX5  C4   N3   aromatic  1.331  0.020  1.331
 HX5  C1   C2   aromatic  1.387  0.020  1.387
 HX5  N3   C2   aromatic  1.310  0.020  1.310
 HX5  C2   CL1  single    1.718  0.020  1.718
 HX5  C1   H1   single    0.930  0.020  1.080
 HX5  C8   H2   single    0.970  0.020  1.090
 HX5  C8   H3   single    0.970  0.020  1.090
 HX5  C8   H4   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
 HX5  H1   C1  C6  123.04  3.000
 HX5  H1   C1  C2  123.09  3.000
 HX5  C6   C1  C2  113.87  3.000
 HX5  CL1  C2  N3  116.92  3.000
 HX5  CL1  C2  C1  119.10  3.000
 HX5  N3   C2  C1  123.98  3.000
 HX5  C4   N3  C2  116.13  3.000
 HX5  S7   C4  N5  120.04  3.000
 HX5  S7   C4  N3  114.11  3.000
 HX5  N5   C4  N3  125.85  3.000
 HX5  C6   N5  C4  116.14  3.000
 HX5  CL9  C6  N5  116.69  3.000
 HX5  N5   C6  C1  124.02  3.000
 HX5  CL9  C6  C1  119.29  3.000
 HX5  C8   S7  C4  102.35  3.000
 HX5  H4   C8  H3  109.22  3.000
 HX5  H4   C8  H2  109.21  3.000
 HX5  H3   C8  H2  110.23  3.000
 HX5  H4   C8  S7  105.68  3.000
 HX5  H3   C8  S7  111.17  3.000
 HX5  H2   C8  S7  111.20  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
 HX5  CONST_01  C4   N5  C6  C1    0.00   0.0  0
 HX5  CONST_02  C4   N3  C2  C1    0.00   0.0  0
 HX5  CONST_03  N5   C6  C1  C2    0.00   0.0  0
 HX5  CONST_04  N5   C4  N3  C2    0.00   0.0  0
 HX5  CONST_05  C6   N5  C4  N3    0.00   0.0  0
 HX5  CONST_06  C6   C1  C2  N3    0.00   0.0  0
 HX5  CONST_07  CL9  C6  C1  C2  180.00   0.0  0
 HX5  CONST_08  S7   C4  N3  C2  180.00   0.0  0
 HX5  CONST_09  CL9  C6  N5  C4  180.00   0.0  0
 HX5  CONST_10  CL1  C2  N3  C4  180.00   0.0  0
 HX5  CONST_11  S7   C4  N5  C6  180.00   0.0  0
 HX5  CONST_12  CL1  C2  C1  C6  180.00   0.0  0
 HX5  CONST_13  H1   C1  C2  N3  180.00   0.0  0
 HX5  Var_01    H2   C8  S7  C4  -61.81  30.0  3

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
 HX5  plan-1  C1   0.020
 HX5  plan-1  C2   0.020
 HX5  plan-1  N3   0.020
 HX5  plan-1  C4   0.020
 HX5  plan-1  N5   0.020
 HX5  plan-1  C6   0.020
 HX5  plan-1  S7   0.020
 HX5  plan-1  CL9  0.020
 HX5  plan-1  CL1  0.020
 HX5  plan-1  H1   0.020

