# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 09:47:37 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 4-methyl-6-(trifluoromethyl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nc(N)n1)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
 A13  A13  4-methyl-6-(trifluoromethyl)pyrimidin-2-amine  ligand  18  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A13
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
 A13  C1    C  CR6   0   0.303   1.7431  -1.1469  -0.0294
 A13  C2    C  CR16  0  -0.401   0.3468  -1.2510  -0.0318
 A13  C3    C  CR6   0   0.045  -0.3359  -0.0563  -0.0065
 A13  N4    N  N     0  -0.482   0.2447   1.1288   0.0220
 A13  C5    C  CR6   0   0.550   1.5801   1.1244   0.0240
 A13  N6    N  N     0  -0.464   2.3487   0.0253   0.0006
 A13  N7    N  NH2   0  -0.823   2.2046   2.3080   0.0428
 A13  C8    C  CH3   0  -0.725   2.6015  -2.3677  -0.0875
 A13  C9    C  CT    0   1.048  -1.8428   0.0042  -0.0082
 A13  F10   F  F     0  -0.308  -2.2988   0.6425   1.0728
 A13  F11   F  F     0  -0.309  -2.2933   0.6655  -1.0781
 A13  F12   F  F     0  -0.298  -2.3991  -1.2077  -0.0227
 A13  H2    H  HCR6  0   0.278  -0.1417  -2.2131  -0.0513
 A13  HN71  H  HNH2  0   0.404   1.6802   3.1608   0.1253
 A13  HN72  H  HNH2  0   0.403   3.2063   2.3501   0.1018
 A13  H81   H  HCH3  0   0.267   2.8375  -2.6023  -1.1276
 A13  H82   H  HCH3  0   0.258   3.5420  -2.2079   0.4363
 A13  H83   H  HCH3  0   0.254   2.0965  -3.2333   0.3368

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
 A13  C1  C2    aromatic  1.400  0.020  1.400
 A13  C1  N6    aromatic  1.320  0.020  1.320
 A13  C1  C8    single    1.494  0.020  1.494
 A13  C2  C3    aromatic  1.376  0.020  1.376
 A13  C2  H2    single    0.930  0.020  1.080
 A13  C3  N4    aromatic  1.320  0.020  1.320
 A13  C3  C9    single    1.508  0.020  1.508
 A13  N4  C5    aromatic  1.335  0.020  1.335
 A13  C5  N6    aromatic  1.341  0.020  1.341
 A13  C5  N7    single    1.338  0.020  1.338
 A13  N7  HN71  single    0.860  0.020  1.020
 A13  N7  HN72  single    0.860  0.020  1.020
 A13  C8  H81   single    0.970  0.020  1.090
 A13  C8  H82   single    0.970  0.020  1.090
 A13  C8  H83   single    0.970  0.020  1.090
 A13  C9  F10   single    1.336  0.020  1.336
 A13  C9  F11   single    1.336  0.020  1.336
 A13  C9  F12   single    1.334  0.020  1.334

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
 A13  C8    C1  N6    117.59  3.000
 A13  C8    C1  C2    120.82  3.000
 A13  N6    C1  C2    121.58  3.000
 A13  H2    C2  C3    123.35  3.000
 A13  H2    C2  C1    121.18  3.000
 A13  C3    C2  C1    115.48  3.000
 A13  C9    C3  N4    113.80  3.000
 A13  C9    C3  C2    122.04  3.000
 A13  N4    C3  C2    124.16  3.000
 A13  C5    N4  C3    115.91  3.000
 A13  N7    C5  N6    117.23  3.000
 A13  N7    C5  N4    117.62  3.000
 A13  N6    C5  N4    125.15  3.000
 A13  C5    N6  C1    117.73  3.000
 A13  HN72  N7  HN71  118.70  3.000
 A13  HN72  N7  C5    120.22  3.000
 A13  HN71  N7  C5    120.56  3.000
 A13  H83   C8  H82   109.28  3.000
 A13  H83   C8  H81   107.51  3.000
 A13  H82   C8  H81   107.65  3.000
 A13  H83   C8  C1    111.61  3.000
 A13  H82   C8  C1    110.97  3.000
 A13  H81   C8  C1    109.68  3.000
 A13  F12   C9  F11   107.48  3.000
 A13  F12   C9  F10   107.50  3.000
 A13  F11   C9  F10   107.25  3.000
 A13  F12   C9  C3    112.36  3.000
 A13  F11   C9  C3    110.96  3.000
 A13  F10   C9  C3    111.07  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
 A13  CONST_01  N4    C3  C2  C1    0.00   0.0  0
 A13  CONST_02  N4    C5  N6  C1    0.00   0.0  0
 A13  CONST_03  C5    N6  C1  C2    0.00   0.0  0
 A13  CONST_04  C5    N4  C3  C2    0.00   0.0  0
 A13  CONST_05  N6    C1  C2  C3    0.00   0.0  0
 A13  CONST_06  N6    C5  N4  C3    0.00   0.0  0
 A13  CONST_07  C9    C3  C2  C1  180.00   0.0  0
 A13  CONST_08  N7    C5  N6  C1  180.00   0.0  0
 A13  CONST_09  C8    C1  C2  C3  180.00   0.0  0
 A13  CONST_10  N7    C5  N4  C3  180.00   0.0  0
 A13  CONST_11  C9    C3  N4  C5  180.00   0.0  0
 A13  CONST_12  C8    C1  N6  C5  180.00   0.0  0
 A13  CONST_13  H2    C2  C3  N4  180.00   0.0  0
 A13  CONST_14  HN71  N7  C5  N4    0.00   0.0  0
 A13  CONST_15  HN72  N7  C5  N4  180.00   0.0  0
 A13  Var_01    F10   C9  C3  C2  121.09  30.0  2
 A13  Var_02    H81   C8  C1  C2   91.80  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
 A13  plan-1  C1    0.020
 A13  plan-1  C2    0.020
 A13  plan-1  C3    0.020
 A13  plan-1  N4    0.020
 A13  plan-1  C5    0.020
 A13  plan-1  N6    0.020
 A13  plan-1  N7    0.020
 A13  plan-1  C8    0.020
 A13  plan-1  C9    0.020
 A13  plan-1  H2    0.020
 A13  plan-2  C5    0.020
 A13  plan-2  N7    0.020
 A13  plan-2  HN71  0.020
 A13  plan-2  HN72  0.020

