# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 19:39:42 2022
#   Inital geometry file: a 41 line input string
#   Ligand name: 6-(trifluoromethyl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(ncn1)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
 8XF  8XF  "6-(trifluoromethyl)pyrimidin-4-amine"
  ligand  15  11  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8XF
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
 8XF  N1  N  N     0  -0.446  23.9184  33.4654   8.1783
 8XF  N2  N  N     0  -0.453  23.8167  35.8066   7.8351
 8XF  C4  C  CR16  0   0.058  24.2543  34.5883   7.5710
 8XF  C3  C  CR6   0   0.530  23.0299  33.5496   9.1746
 8XF  C2  C  CR16  0  -0.395  22.4797  34.8005   9.5355
 8XF  C1  C  CR6   0   0.018  22.9251  35.8792   8.8244
 8XF  N   N  NH2   0  -0.818  22.6838  32.4282   9.8060
 8XF  C   C  CT    0   1.044  22.4623  37.2704   9.1776
 8XF  F   F  F     0  -0.299  22.4382  38.0737   8.1177
 8XF  F1  F  F     0  -0.312  23.2884  37.8186  10.0782
 8XF  F2  F  F     0  -0.302  21.2383  37.2715   9.7110
 8XF  H3  H  HCR6  0   0.262  24.9727  34.4977   6.7629
 8XF  H   H  HCR6  0   0.294  21.7570  34.8807  10.3355
 8XF  H2  H  HNH2  0   0.405  23.1024  31.5513   9.5464
 8XF  H1  H  HNH2  0   0.414  22.0378  32.4365  10.5761

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
 8XF  C4  N2  aromatic  1.321  0.020  1.321
 8XF  C4  N1  aromatic  1.320  0.020  1.320
 8XF  N2  C1  aromatic  1.334  0.020  1.334
 8XF  F   C   single    1.330  0.020  1.330
 8XF  N1  C3  aromatic  1.338  0.020  1.338
 8XF  C1  C   single    1.508  0.020  1.508
 8XF  C1  C2  aromatic  1.367  0.020  1.367
 8XF  C   F2  single    1.335  0.020  1.335
 8XF  C   F1  single    1.339  0.020  1.339
 8XF  C3  C2  aromatic  1.413  0.020  1.413
 8XF  C3  N   single    1.333  0.020  1.333
 8XF  C4  H3  single    0.930  0.020  1.080
 8XF  C2  H   single    0.930  0.020  1.080
 8XF  N   H2  single    0.860  0.020  1.020
 8XF  N   H1  single    0.860  0.020  1.020

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
 8XF  C3  N1  C4  117.26  3.000
 8XF  C1  N2  C4  114.83  3.000
 8XF  H3  C4  N2  116.43  3.000
 8XF  H3  C4  N1  116.11  3.000
 8XF  N2  C4  N1  127.46  3.000
 8XF  N   C3  C2  121.51  3.000
 8XF  N   C3  N1  118.19  3.000
 8XF  C2  C3  N1  120.30  3.000
 8XF  H   C2  C1  122.98  3.000
 8XF  H   C2  C3  120.98  3.000
 8XF  C1  C2  C3  116.03  3.000
 8XF  C   C1  C2  120.42  3.000
 8XF  C2  C1  N2  124.12  3.000
 8XF  C   C1  N2  115.41  3.000
 8XF  H1  N   H2  118.20  3.000
 8XF  H1  N   C3  121.53  3.000
 8XF  H2  N   C3  120.21  3.000
 8XF  F2  C   F1  107.25  3.000
 8XF  F1  C   F   107.44  3.000
 8XF  F2  C   F   107.53  3.000
 8XF  F1  C   C1  110.23  3.000
 8XF  F2  C   C1  112.06  3.000
 8XF  F   C   C1  112.09  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
 8XF  CONST_01  C1  N2  C4  N1     0.00   0.0  0
 8XF  CONST_02  C1  C2  C3  N1     0.00   0.0  0
 8XF  CONST_03  C3  N1  C4  N2     0.00   0.0  0
 8XF  CONST_04  C3  C2  C1  N2     0.00   0.0  0
 8XF  CONST_05  C2  C1  N2  C4     0.00   0.0  0
 8XF  CONST_06  C2  C3  N1  C4     0.00   0.0  0
 8XF  CONST_07  C   C1  N2  C4   180.00   0.0  0
 8XF  CONST_08  N   C3  N1  C4   180.00   0.0  0
 8XF  CONST_09  C   C1  C2  C3   180.00   0.0  0
 8XF  CONST_10  N   C3  C2  C1   180.00   0.0  0
 8XF  CONST_11  H   C2  C3  N1   180.00   0.0  0
 8XF  CONST_12  H   C2  C1  N2   180.00   0.0  0
 8XF  CONST_13  H3  C4  N1  C3   180.00   0.0  0
 8XF  CONST_14  H3  C4  N2  C1   180.00   0.0  0
 8XF  CONST_15  H2  N   C3  N1     0.00   0.0  0
 8XF  CONST_16  H1  N   C3  N1   180.00   0.0  0
 8XF  CONST_17  H2  N   C3  C2   180.00   0.0  0
 8XF  CONST_18  H1  N   C3  C2     0.00   0.0  0
 8XF  Var_01    F   C   C1  N2    32.30  30.0  2
 8XF  Var_02    F2  C   C1  N2   153.32  30.0  2
 8XF  Var_03    F1  C   C1  N2   -87.32  30.0  2
 8XF  Var_04    F   C   C1  C2  -150.44  30.0  2
 8XF  Var_05    F2  C   C1  C2   -29.42  30.0  2
 8XF  Var_06    F1  C   C1  C2    89.94  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
 8XF  plan-1  N1  0.020
 8XF  plan-1  N2  0.020
 8XF  plan-1  C4  0.020
 8XF  plan-1  C3  0.020
 8XF  plan-1  C2  0.020
 8XF  plan-1  C1  0.020
 8XF  plan-1  N   0.020
 8XF  plan-1  C   0.020
 8XF  plan-1  H3  0.020
 8XF  plan-1  H   0.020
 8XF  plan-2  C3  0.020
 8XF  plan-2  N   0.020
 8XF  plan-2  H2  0.020
 8XF  plan-2  H1  0.020

