# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:25:45 2021
#   Inital geometry file: a 48 line input string
#   Ligand name: 2-(trifluoromethyl)pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cnc(nc1)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
 S7J  S7J  2-(trifluoromethyl)pyrimidine-5-carboxamide  ligand  17  13  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S7J
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
 S7J  N1  N  N     0  -0.393  40.0961  4.3089  73.4328
 S7J  C4  C  CR16  0   0.010  37.8412  4.6170  74.8944
 S7J  C5  C  CT    0   1.042  39.1287  5.6002  71.6551
 S7J  N   N  NH2   0  -0.810  39.5733  2.3104  77.1200
 S7J  C   C  C     0   0.508  38.7604  3.3264  76.8157
 S7J  O   O  O     0  -0.466  37.9488  3.8066  77.5909
 S7J  C1  C  CR6   0  -0.163  38.8913  3.8836  75.4331
 S7J  C2  C  CR16  0  -0.006  40.0256  3.7686  74.6412
 S7J  C3  C  CR6   0   0.149  39.0276  4.9604  73.0231
 S7J  F   F  F     0  -0.296  37.9328  5.7730  71.1017
 S7J  F1  F  F     0  -0.299  39.8639  4.8613  70.8281
 S7J  F2  F  F     0  -0.311  39.7108  6.8013  71.7484
 S7J  N2  N  N     0  -0.395  37.9037  5.1516  73.6840
 S7J  H1  H  HCR6  0   0.299  36.9249  4.7692  75.4522
 S7J  H2  H  HNH2  0   0.416  39.5286  1.8946  78.0367
 S7J  H3  H  HNH2  0   0.421  40.1538  1.8474  76.4425
 S7J  H4  H  HCR6  0   0.294  40.9128  3.2462  74.9804

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
 S7J  F1  C5  single    1.331  0.020  1.331
 S7J  F   C5  single    1.329  0.020  1.329
 S7J  C5  F2  single    1.338  0.020  1.338
 S7J  C5  C3  single    1.514  0.020  1.514
 S7J  C3  N1  aromatic  1.317  0.020  1.317
 S7J  C3  N2  aromatic  1.318  0.020  1.318
 S7J  N1  C2  aromatic  1.326  0.020  1.326
 S7J  N2  C4  aromatic  1.325  0.020  1.325
 S7J  C2  C1  aromatic  1.388  0.020  1.388
 S7J  C4  C1  aromatic  1.390  0.020  1.390
 S7J  C1  C   single    1.496  0.020  1.496
 S7J  C   N   single    1.336  0.020  1.336
 S7J  C   O   double    1.221  0.020  1.221
 S7J  C4  H1  single    0.930  0.020  1.080
 S7J  N   H2  single    0.860  0.020  1.020
 S7J  N   H3  single    0.860  0.020  1.020
 S7J  C2  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
 S7J  C3  N1  C2  116.24  3.000
 S7J  H1  C4  N2  116.98  3.000
 S7J  H1  C4  C1  120.91  3.000
 S7J  N2  C4  C1  122.11  3.000
 S7J  F2  C5  F1  107.54  3.000
 S7J  F2  C5  F   107.69  3.000
 S7J  F1  C5  F   108.10  3.000
 S7J  F2  C5  C3  110.21  3.000
 S7J  F   C5  C3  111.79  3.000
 S7J  F1  C5  C3  111.34  3.000
 S7J  H3  N   H2  116.67  3.000
 S7J  H3  N   C   123.23  3.000
 S7J  H2  N   C   119.60  3.000
 S7J  C1  C   O   119.89  3.000
 S7J  O   C   N   123.98  3.000
 S7J  C1  C   N   116.13  3.000
 S7J  C2  C1  C   124.59  3.000
 S7J  C   C1  C4  119.25  3.000
 S7J  C2  C1  C4  116.11  3.000
 S7J  H4  C2  C1  122.01  3.000
 S7J  H4  C2  N1  115.99  3.000
 S7J  C1  C2  N1  121.99  3.000
 S7J  N2  C3  C5  116.67  3.000
 S7J  N2  C3  N1  127.43  3.000
 S7J  C5  C3  N1  115.86  3.000
 S7J  C3  N2  C4  116.10  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
 S7J  CONST_01  C4  N2  C3  N1    0.00   0.0  0
 S7J  CONST_02  C4  C1  C2  N1    0.00   0.0  0
 S7J  CONST_03  C3  N1  C2  C1    0.00   0.0  0
 S7J  CONST_04  C3  N2  C4  C1    0.00   0.0  0
 S7J  CONST_05  N2  C3  N1  C2    0.00   0.0  0
 S7J  CONST_06  N2  C4  C1  C2    0.00   0.0  0
 S7J  CONST_07  C   C1  C2  N1  180.00   0.0  0
 S7J  CONST_08  C5  C3  N2  C4  180.00   0.0  0
 S7J  CONST_09  C2  N1  C3  C5  180.00   0.0  0
 S7J  CONST_10  N2  C4  C1  C   180.00   0.0  0
 S7J  CONST_11  H4  C2  C1  C4  180.00   0.0  0
 S7J  CONST_12  H1  C4  C1  C2  180.00   0.0  0
 S7J  CONST_13  H2  N   C   C1  180.00   0.0  0
 S7J  CONST_14  H3  N   C   C1    0.00   0.0  0
 S7J  Var_01    F1  C5  C3  N1   34.78  30.0  3
 S7J  Var_02    N   C   C1  C4  159.58  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
 S7J  plan-1  N1  0.020
 S7J  plan-1  C4  0.020
 S7J  plan-1  C5  0.020
 S7J  plan-1  C   0.020
 S7J  plan-1  C1  0.020
 S7J  plan-1  C2  0.020
 S7J  plan-1  C3  0.020
 S7J  plan-1  N2  0.020
 S7J  plan-1  H1  0.020
 S7J  plan-1  H4  0.020
 S7J  plan-2  N   0.020
 S7J  plan-2  C   0.020
 S7J  plan-2  O   0.020
 S7J  plan-2  C1  0.020
 S7J  plan-2  H2  0.020
 S7J  plan-2  H3  0.020

