# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 10:31:26 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[6-(trifluoromethyl)pyridin-2-yl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(nc(NCCNc2cccc(n2)C(F)(F)F)c1Cl)c3ccccn3
#
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
 TFD  TFD  N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[6-(trifluoromethyl)pyridin-2-yl]ethane-1,2-diamine  ligand  44  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TFD
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
 TFD  F1   F   F     0  -0.302  -6.0813  -2.3035   0.5320
 TFD  C18  C   CT    0   1.036  -6.6166  -1.0841   0.5559
 TFD  F2   F   F     0  -0.306  -7.7381  -1.1248  -0.1721
 TFD  F3   F   F     0  -0.317  -6.9842  -0.8403   1.8234
 TFD  C14  C   CR6   0  -0.007  -5.6622  -0.0289   0.0614
 TFD  N6   N   N     0  -0.482  -4.3873  -0.2762   0.3088
 TFD  C15  C   CR16  0  -0.349  -6.1386   1.1150  -0.5465
 TFD  C16  C   CR16  0  -0.142  -5.1865   2.0651  -0.9110
 TFD  C17  C   CR16  0  -0.388  -3.8513   1.8392  -0.6672
 TFD  C13  C   CR6   0   0.500  -3.4777   0.6290  -0.0500
 TFD  N5   N   NH1   0  -0.667  -2.1829   0.3049   0.1972
 TFD  C11  C   CH2   0  -0.304  -1.1031   1.2549   0.1104
 TFD  C10  C   CH2   0  -0.273   0.2215   0.5354   0.3073
 TFD  N4   N   NH1   0  -0.679   1.2900   1.5063   0.2742
 TFD  C7   C   CR6   0   0.639   2.5838   1.1658   0.2074
 TFD  C8   C   CR6   0  -0.246   3.6149   2.1284   0.2484
 TFD  CL   CL  CL    0  -0.108   3.2297   3.8049   0.3982
 TFD  N3   N   N     0  -0.462   2.8960  -0.1224   0.0873
 TFD  C6   C   CR6   0   0.358   4.1762  -0.4420   0.0040
 TFD  N2   N   N     0  -0.480   5.1961   0.3998   0.0390
 TFD  C9   C   CR6   0   0.333   4.9226   1.7020   0.1625
 TFD  C12  C   CH3   0  -0.737   6.0723   2.6547   0.2009
 TFD  C5   C   CR6   0   0.143   4.5141  -1.8849  -0.1382
 TFD  N1   N   N     0  -0.406   3.5017  -2.7442  -0.2027
 TFD  C1   C   CR16  0  -0.085   3.7761  -4.0336  -0.3284
 TFD  C2   C   CR16  0  -0.312   5.0672  -4.5399  -0.3962
 TFD  C3   C   CR16  0  -0.152   6.1221  -3.6438  -0.3297
 TFD  C4   C   CR16  0  -0.295   5.8448  -2.2929  -0.1987
 TFD  H1   H   HCR6  0   0.276  -7.1903   1.2837  -0.7235
 TFD  H2   H   HCR6  0   0.279  -5.4961   2.9856  -1.3875
 TFD  H3   H   HCR6  0   0.283  -3.1153   2.5811  -0.9412
 TFD  H4   H   HNH1  0   0.387  -2.0596  -0.4686   0.8333
 TFD  H5   H   HCH2  0   0.254  -1.1023   1.7282  -0.8740
 TFD  H6   H   HCH2  0   0.238  -1.2082   2.0545   0.8560
 TFD  H7   H   HCH2  0   0.243   0.2166  -0.0106   1.2577
 TFD  H8   H   HCH2  0   0.259   0.3653  -0.1983  -0.4857
 TFD  H9   H   HNH1  0   0.400   1.0639   2.4574   0.5173
 TFD  H10  H   HCH3  0   0.262   6.0944   3.2047   1.1428
 TFD  H11  H   HCH3  0   0.262   7.0085   2.1130   0.0929
 TFD  H12  H   HCH3  0   0.261   5.9989   3.3920  -0.5992
 TFD  H13  H   HCR6  0   0.263   2.9258  -4.7047  -0.3802
 TFD  H14  H   HCR6  0   0.274   5.2328  -5.6036  -0.4965
 TFD  H15  H   HCR6  0   0.275   7.1464  -3.9887  -0.3789
 TFD  H16  H   HCR6  0   0.273   6.6393  -1.5636  -0.1443

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
 TFD  F1   C18  single    1.332  0.020  1.332
 TFD  F2   C18  single    1.338  0.020  1.338
 TFD  C15  C16  aromatic  1.394  0.020  1.394
 TFD  C15  C14  aromatic  1.380  0.020  1.380
 TFD  C18  C14  single    1.506  0.020  1.506
 TFD  C18  F3   single    1.342  0.020  1.342
 TFD  C16  C17  aromatic  1.376  0.020  1.376
 TFD  C14  N6   aromatic  1.322  0.020  1.322
 TFD  C17  C13  aromatic  1.409  0.020  1.409
 TFD  N6   C13  aromatic  1.332  0.020  1.332
 TFD  C13  N5   single    1.357  0.020  1.357
 TFD  C12  C9   single    1.494  0.020  1.494
 TFD  CL   C8   single    1.727  0.020  1.727
 TFD  C9   C8   aromatic  1.378  0.020  1.378
 TFD  C9   N2   aromatic  1.336  0.020  1.336
 TFD  C8   C7   aromatic  1.411  0.020  1.411
 TFD  N5   C11  single    1.441  0.020  1.441
 TFD  N2   C6   aromatic  1.323  0.020  1.323
 TFD  C7   N4   single    1.339  0.020  1.339
 TFD  C7   N3   aromatic  1.331  0.020  1.331
 TFD  N4   C10  single    1.444  0.020  1.444
 TFD  C6   N3   aromatic  1.322  0.020  1.322
 TFD  C6   C5   single    1.489  0.020  1.489
 TFD  C11  C10  single    1.520  0.020  1.520
 TFD  C5   N1   aromatic  1.330  0.020  1.330
 TFD  C5   C4   aromatic  1.393  0.020  1.393
 TFD  N1   C1   aromatic  1.324  0.020  1.324
 TFD  C4   C3   aromatic  1.385  0.020  1.385
 TFD  C1   C2   aromatic  1.388  0.020  1.388
 TFD  C3   C2   aromatic  1.386  0.020  1.386
 TFD  C15  H1   single    0.930  0.020  1.080
 TFD  C16  H2   single    0.930  0.020  1.080
 TFD  C17  H3   single    0.930  0.020  1.080
 TFD  N5   H4   single    0.890  0.020  1.040
 TFD  C11  H5   single    0.970  0.020  1.090
 TFD  C11  H6   single    0.970  0.020  1.090
 TFD  C10  H7   single    0.970  0.020  1.090
 TFD  C10  H8   single    0.970  0.020  1.090
 TFD  N4   H9   single    0.860  0.020  1.020
 TFD  C12  H10  single    0.970  0.020  1.090
 TFD  C12  H11  single    0.970  0.020  1.090
 TFD  C12  H12  single    0.970  0.020  1.090
 TFD  C1   H13  single    0.930  0.020  1.080
 TFD  C2   H14  single    0.930  0.020  1.080
 TFD  C3   H15  single    0.930  0.020  1.080
 TFD  C4   H16  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
 TFD  C14  C18  F3   110.87  3.000
 TFD  F3   C18  F2   106.85  3.000
 TFD  C14  C18  F2   111.96  3.000
 TFD  F3   C18  F1   107.06  3.000
 TFD  C14  C18  F1   112.38  3.000
 TFD  F2   C18  F1   107.42  3.000
 TFD  C15  C14  N6   124.77  3.000
 TFD  N6   C14  C18  114.75  3.000
 TFD  C15  C14  C18  120.43  3.000
 TFD  C13  N6   C14  118.74  3.000
 TFD  H1   C15  C16  121.07  3.000
 TFD  H1   C15  C14  122.53  3.000
 TFD  C16  C15  C14  116.39  3.000
 TFD  H2   C16  C17  119.71  3.000
 TFD  H2   C16  C15  119.98  3.000
 TFD  C17  C16  C15  120.31  3.000
 TFD  H3   C17  C13  121.35  3.000
 TFD  H3   C17  C16  120.22  3.000
 TFD  C13  C17  C16  118.43  3.000
 TFD  N5   C13  C17  122.53  3.000
 TFD  N5   C13  N6   116.10  3.000
 TFD  C17  C13  N6   121.36  3.000
 TFD  H4   N5   C11  116.86  3.000
 TFD  H4   N5   C13  114.48  3.000
 TFD  C11  N5   C13  123.12  3.000
 TFD  H6   C11  H5   107.25  3.000
 TFD  H6   C11  C10  109.87  3.000
 TFD  H5   C11  C10  108.73  3.000
 TFD  H6   C11  N5   111.56  3.000
 TFD  H5   C11  N5   109.91  3.000
 TFD  C10  C11  N5   109.46  3.000
 TFD  H8   C10  H7   107.23  3.000
 TFD  H8   C10  N4   109.77  3.000
 TFD  H7   C10  N4   110.98  3.000
 TFD  H8   C10  C11  109.84  3.000
 TFD  H7   C10  C11  110.13  3.000
 TFD  N4   C10  C11  108.88  3.000
 TFD  H9   N4   C7   117.96  3.000
 TFD  H9   N4   C10  117.59  3.000
 TFD  C7   N4   C10  123.02  3.000
 TFD  N3   C7   C8   119.44  3.000
 TFD  N3   C7   N4   118.49  3.000
 TFD  C8   C7   N4   122.06  3.000
 TFD  C9   C8   CL   121.16  3.000
 TFD  C9   C8   C7   118.71  3.000
 TFD  CL   C8   C7   120.12  3.000
 TFD  C6   N3   C7   117.82  3.000
 TFD  C5   C6   N2   116.38  3.000
 TFD  C5   C6   N3   117.39  3.000
 TFD  N2   C6   N3   126.23  3.000
 TFD  C9   N2   C6   117.70  3.000
 TFD  C12  C9   N2   117.81  3.000
 TFD  N2   C9   C8   120.09  3.000
 TFD  C12  C9   C8   122.10  3.000
 TFD  H12  C12  H11  108.79  3.000
 TFD  H12  C12  H10  107.10  3.000
 TFD  H11  C12  H10  108.64  3.000
 TFD  H12  C12  C9   111.13  3.000
 TFD  H11  C12  C9   110.03  3.000
 TFD  H10  C12  C9   111.06  3.000
 TFD  C4   C5   N1   122.41  3.000
 TFD  C4   C5   C6   120.32  3.000
 TFD  N1   C5   C6   117.27  3.000
 TFD  C1   N1   C5   118.43  3.000
 TFD  H13  C1   C2   120.07  3.000
 TFD  H13  C1   N1   116.40  3.000
 TFD  C2   C1   N1   123.53  3.000
 TFD  H14  C2   C3   121.61  3.000
 TFD  H14  C2   C1   120.38  3.000
 TFD  C3   C2   C1   118.01  3.000
 TFD  H15  C3   C4   120.31  3.000
 TFD  H15  C3   C2   120.82  3.000
 TFD  C4   C3   C2   118.87  3.000
 TFD  H16  C4   C3   121.07  3.000
 TFD  H16  C4   C5   120.19  3.000
 TFD  C3   C4   C5   118.74  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
 TFD  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 TFD  CONST_02  C17  C13  N6   C14     0.00   0.0  0
 TFD  CONST_03  C16  C15  C14  N6      0.00   0.0  0
 TFD  CONST_04  C16  C17  C13  N6      0.00   0.0  0
 TFD  CONST_05  C13  C17  C16  C15     0.00   0.0  0
 TFD  CONST_06  C13  N6   C14  C15     0.00   0.0  0
 TFD  CONST_07  N2   C9   C8   C7      0.00   0.0  0
 TFD  CONST_08  N2   C6   N3   C7      0.00   0.0  0
 TFD  CONST_09  C5   C6   N3   C7    180.00   0.0  0
 TFD  CONST_10  C6   N2   C9   C8      0.00   0.0  0
 TFD  CONST_11  C6   N3   C7   C8      0.00   0.0  0
 TFD  CONST_12  C9   C8   C7   N3      0.00   0.0  0
 TFD  CONST_13  C9   N2   C6   N3      0.00   0.0  0
 TFD  CONST_14  N1   C5   C6   N3      0.00   0.0  0
 TFD  CONST_15  C4   C5   C6   N3    180.00   0.0  0
 TFD  CONST_16  C1   N1   C5   C6    180.00   0.0  0
 TFD  CONST_17  C3   C4   C5   C6    180.00   0.0  0
 TFD  CONST_18  N1   C5   C6   N2    180.00   0.0  0
 TFD  CONST_19  C4   C5   C6   N2      0.00   0.0  0
 TFD  CONST_20  C5   C6   N2   C9    180.00   0.0  0
 TFD  CONST_21  C2   C1   N1   C5      0.00   0.0  0
 TFD  CONST_22  C2   C3   C4   C5      0.00   0.0  0
 TFD  CONST_23  C3   C4   C5   N1      0.00   0.0  0
 TFD  CONST_24  C3   C2   C1   N1      0.00   0.0  0
 TFD  CONST_25  C4   C5   N1   C1      0.00   0.0  0
 TFD  CONST_26  C4   C3   C2   C1      0.00   0.0  0
 TFD  CONST_27  C16  C15  C14  C18   180.00   0.0  0
 TFD  CONST_28  C13  N6   C14  C18   180.00   0.0  0
 TFD  CONST_29  N5   C13  N6   C14   180.00   0.0  0
 TFD  CONST_30  N5   C13  C17  C16   180.00   0.0  0
 TFD  CONST_31  C9   C8   C7   N4    180.00   0.0  0
 TFD  CONST_32  C6   N3   C7   N4    180.00   0.0  0
 TFD  CONST_33  C12  C9   C8   C7    180.00   0.0  0
 TFD  CONST_34  N2   C9   C8   CL    180.00   0.0  0
 TFD  CONST_35  N3   C7   C8   CL    180.00   0.0  0
 TFD  CONST_36  C12  C9   N2   C6    180.00   0.0  0
 TFD  CONST_37  H2   C16  C15  C14   180.00   0.0  0
 TFD  CONST_38  H1   C15  C14  N6    180.00   0.0  0
 TFD  CONST_39  H3   C17  C13  N6    180.00   0.0  0
 TFD  CONST_40  H16  C4   C5   C6      0.00   0.0  0
 TFD  CONST_41  H13  C1   N1   C5    180.00   0.0  0
 TFD  CONST_42  H15  C3   C4   C5    180.00   0.0  0
 TFD  CONST_43  H14  C2   C1   N1    180.00   0.0  0
 TFD  CONST_44  C11  N5   C13  N6    180.00   0.0  0
 TFD  CONST_45  C11  N5   C13  C17     0.00   0.0  0
 TFD  CONST_46  C8   C7   N4   C10   180.00   0.0  0
 TFD  CONST_47  N3   C7   N4   C10     0.00   0.0  0
 TFD  CONST_49  H9   N4   C7   C8      0.00   0.0  0
 TFD  Var_01    C15  C14  C18  F1    150.91  30.0  2
 TFD  Var_02    H10  C12  C9   C8     61.14  30.0  2
 TFD  Var_03    C10  C11  N5   C13  -174.24  30.0  3
 TFD  Var_04    C7   N4   C10  C11  -169.12  30.0  2
 TFD  Var_05    N4   C10  C11  N5   -177.61  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
 TFD  plan-1  C18  0.020
 TFD  plan-1  C14  0.020
 TFD  plan-1  N6   0.020
 TFD  plan-1  C15  0.020
 TFD  plan-1  C16  0.020
 TFD  plan-1  C17  0.020
 TFD  plan-1  C13  0.020
 TFD  plan-1  N5   0.020
 TFD  plan-1  H1   0.020
 TFD  plan-1  H2   0.020
 TFD  plan-1  H3   0.020
 TFD  plan-2  N4   0.020
 TFD  plan-2  C7   0.020
 TFD  plan-2  C8   0.020
 TFD  plan-2  CL   0.020
 TFD  plan-2  N3   0.020
 TFD  plan-2  C6   0.020
 TFD  plan-2  N2   0.020
 TFD  plan-2  C9   0.020
 TFD  plan-2  C12  0.020
 TFD  plan-2  C5   0.020
 TFD  plan-3  C6   0.020
 TFD  plan-3  C5   0.020
 TFD  plan-3  N1   0.020
 TFD  plan-3  C1   0.020
 TFD  plan-3  C2   0.020
 TFD  plan-3  C3   0.020
 TFD  plan-3  C4   0.020
 TFD  plan-3  H13  0.020
 TFD  plan-3  H14  0.020
 TFD  plan-3  H15  0.020
 TFD  plan-3  H16  0.020
 TFD  plan-4  C13  0.020
 TFD  plan-4  N5   0.020
 TFD  plan-4  C11  0.020
 TFD  plan-4  H4   0.020
 TFD  plan-5  C10  0.020
 TFD  plan-5  N4   0.020
 TFD  plan-5  C7   0.020
 TFD  plan-5  H9   0.020

