# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:55:41 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 3-methyl-2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC1=NC(=CC(=O)N1C)C(F)(F)F
#
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
 PWS  PWS  3-methyl-2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one  ligand  21  14  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PWS
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
 PWS  N1  N  N     0  -0.458   0.0064  -0.6651   0.0068
 PWS  C4  C  CT    0   1.062  -2.3462  -0.2982   0.0027
 PWS  C5  C  CR16  0  -0.466  -0.7230   1.6074   0.0062
 PWS  C6  C  CR6   0   0.601   0.6376   2.0769   0.0075
 PWS  N   N  NR6   0  -0.537   1.6000   1.0546   0.0040
 PWS  C   C  CH3   0  -0.756   1.6066  -2.9658   0.0151
 PWS  O   O  O     0  -0.466   0.9657   3.2489   0.0102
 PWS  C1  C  CR6   0   0.359   1.2342  -0.2540   0.0064
 PWS  C2  C  CH3   0  -0.561   3.0115   1.4196   0.0006
 PWS  C3  C  CR6   0   0.040  -0.9555   0.2784   0.0052
 PWS  F   F  F     0  -0.307  -2.5435  -1.0622   1.0796
 PWS  F1  F  F     0  -0.296  -3.2878   0.6446  -0.0015
 PWS  F2  F  F     0  -0.307  -2.5379  -1.0662  -1.0722
 PWS  S   S  S2    0   0.082   2.5330  -1.4210   0.0102
 PWS  H1  H  HCR6  0   0.297  -1.5087   2.3477   0.0059
 PWS  H2  H  HCH3  0   0.291   2.3598  -3.7506   0.0183
 PWS  H3  H  HCH3  0   0.287   0.9912  -3.0474   0.9062
 PWS  H4  H  HCH3  0   0.287   0.9922  -3.0538  -0.8761
 PWS  H5  H  HCH3  0   0.295   3.0943   2.4992  -0.0175
 PWS  H6  H  HCH3  0   0.277   3.5021   1.0453   0.8981
 PWS  H7  H  HCH3  0   0.277   3.5046   1.0161  -0.8827

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
 PWS  F   C4  single  1.335  0.020  1.335
 PWS  C   S   single  1.801  0.020  1.801
 PWS  C4  F1  single  1.332  0.020  1.332
 PWS  C4  F2  single  1.335  0.020  1.335
 PWS  C4  C3  single  1.506  0.020  1.506
 PWS  N1  C3  single  1.347  0.020  1.347
 PWS  N1  C1  double  1.295  0.020  1.295
 PWS  C3  C5  double  1.349  0.020  1.349
 PWS  S   C1  single  1.746  0.020  1.746
 PWS  C1  N   single  1.359  0.020  1.359
 PWS  C5  C6  single  1.439  0.020  1.439
 PWS  N   C6  single  1.404  0.020  1.404
 PWS  N   C2  single  1.458  0.020  1.458
 PWS  C6  O   double  1.217  0.020  1.217
 PWS  C5  H1  single  0.930  0.020  1.080
 PWS  C   H2  single  0.970  0.020  1.090
 PWS  C   H3  single  0.970  0.020  1.090
 PWS  C   H4  single  0.970  0.020  1.090
 PWS  C2  H5  single  0.970  0.020  1.090
 PWS  C2  H6  single  0.970  0.020  1.090
 PWS  C2  H7  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
 PWS  C3  N1  C1  117.04  3.000
 PWS  F2  C4  F1  107.65  3.000
 PWS  F2  C4  F   107.40  3.000
 PWS  F1  C4  F   107.65  3.000
 PWS  F2  C4  C3  110.75  3.000
 PWS  F1  C4  C3  112.45  3.000
 PWS  F   C4  C3  110.75  3.000
 PWS  H1  C5  C3  123.37  3.000
 PWS  H1  C5  C6  117.67  3.000
 PWS  C3  C5  C6  118.96  3.000
 PWS  O   C6  N   121.10  3.000
 PWS  O   C6  C5  124.67  3.000
 PWS  N   C6  C5  114.23  3.000
 PWS  C2  N   C1  120.11  3.000
 PWS  C2  N   C6  118.77  3.000
 PWS  C1  N   C6  121.12  3.000
 PWS  H4  C   H3  110.29  3.000
 PWS  H4  C   H2  109.61  3.000
 PWS  H3  C   H2  109.62  3.000
 PWS  H4  C   S   110.99  3.000
 PWS  H3  C   S   110.98  3.000
 PWS  H2  C   S   105.23  3.000
 PWS  S   C1  N   116.32  3.000
 PWS  N   C1  N1  124.13  3.000
 PWS  S   C1  N1  119.55  3.000
 PWS  H7  C2  H6  109.70  3.000
 PWS  H7  C2  H5  108.73  3.000
 PWS  H6  C2  H5  108.78  3.000
 PWS  H7  C2  N   110.33  3.000
 PWS  H6  C2  N   110.37  3.000
 PWS  H5  C2  N   108.88  3.000
 PWS  C5  C3  C4  122.44  3.000
 PWS  C5  C3  N1  124.52  3.000
 PWS  C4  C3  N1  113.04  3.000
 PWS  C1  S   C   100.99  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
 PWS  CONST_01  C6  N   C1  N1     0.00   0.0  0
 PWS  CONST_02  C1  N   C6  C5     0.00   0.0  0
 PWS  CONST_03  C3  N1  C1  N      0.00   0.0  0
 PWS  CONST_04  C2  N   C1  N1   180.00   0.0  0
 PWS  CONST_05  C2  N   C6  C5   180.00   0.0  0
 PWS  CONST_06  S   C1  N   C6   180.00   0.0  0
 PWS  CONST_07  C1  N   C6  O    180.00   0.0  0
 PWS  CONST_08  S   C1  N1  C3   180.00   0.0  0
 PWS  CONST_09  C2  N   C6  O      0.00   0.0  0
 PWS  CONST_10  S   C1  N   C2     0.00   0.0  0
 PWS  Var_01    F   C4  C3  N1    59.64  30.0  3
 PWS  Var_02    H5  C2  N   C6    -1.06  30.0  3
 PWS  Var_03    H2  C   S   C1  -179.96  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
 PWS  plan-1  N1  0.020
 PWS  plan-1  C4  0.020
 PWS  plan-1  C5  0.020
 PWS  plan-1  C6  0.020
 PWS  plan-1  N   0.020
 PWS  plan-1  O   0.020
 PWS  plan-1  C1  0.020
 PWS  plan-1  C2  0.020
 PWS  plan-1  C3  0.020
 PWS  plan-1  S   0.020
 PWS  plan-1  H1  0.020

