# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:19:42 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[5-(trifluoromethyl)pyridin-2-yl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(nc(NCCNc2ccc(cn2)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
 TFV  TFV  N-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-N'-[5-(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_TFV
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
 TFV  F3   F   F     0  -0.307   6.9174   2.3328  -0.8422
 TFV  C18  C   CT    0   1.060   6.2757   1.2952  -1.3912
 TFV  F1   F   F     0  -0.318   6.0877   1.5919  -2.6881
 TFV  F2   F   F     0  -0.319   7.1319   0.2579  -1.3736
 TFV  C15  C   CR6   0  -0.343   4.9995   0.9815  -0.7011
 TFV  C14  C   CR16  0  -0.068   4.6204   1.5971   0.4814
 TFV  N6   N   N     0  -0.464   3.4993   1.3239   1.1254
 TFV  C16  C   CR16  0  -0.152   4.1292   0.0263  -1.2337
 TFV  C17  C   CR16  0  -0.399   2.9581  -0.2697  -0.5838
 TFV  C13  C   CR6   0   0.522   2.6705   0.4019   0.6238
 TFV  N5   N   NH1   0  -0.661   1.5580   0.1480   1.3395
 TFV  C11  C   CH2   0  -0.268   0.5014  -0.7394   0.9223
 TFV  C10  C   CH2   0  -0.321  -0.4586  -0.9775   2.0836
 TFV  N4   N   NH1   0  -0.670  -1.5006  -1.9111   1.7381
 TFV  C7   C   CR6   0   0.637  -2.5911  -1.5775   1.0332
 TFV  N3   N   N     0  -0.455  -2.7702  -0.2995   0.7082
 TFV  C8   C   CR6   0  -0.246  -3.5538  -2.5322   0.6432
 TFV  CL   CL  CL    0  -0.109  -3.3432  -4.1953   1.0585
 TFV  C9   C   CR6   0   0.333  -4.6539  -2.1087  -0.0722
 TFV  C12  C   CH3   0  -0.738  -5.7158  -3.0548  -0.5278
 TFV  N2   N   N     0  -0.480  -4.7983  -0.8163  -0.3787
 TFV  C6   C   CR6   0   0.357  -3.8563   0.0199   0.0276
 TFV  C5   C   CR6   0   0.140  -4.0445   1.4535  -0.3269
 TFV  N1   N   N     0  -0.400  -3.1237   2.3117   0.1012
 TFV  C4   C   CR16  0  -0.294  -5.1481   1.8552  -1.0762
 TFV  C3   C   CR16  0  -0.153  -5.2885   3.1978  -1.3877
 TFV  C2   C   CR16  0  -0.312  -4.3280   4.0922  -0.9434
 TFV  C1   C   CR16  0  -0.086  -3.2662   3.5930  -0.2008
 TFV  H1   H   HCR6  0   0.272   5.2474   2.3529   0.9405
 TFV  H2   H   HCR6  0   0.282   4.3586  -0.4821  -2.1619
 TFV  H3   H   HCR6  0   0.283   2.2771  -0.9959  -1.0033
 TFV  H4   H   HNH1  0   0.390   1.3822   0.7772   2.1078
 TFV  H5   H   HCH2  0   0.243  -0.0507  -0.3354   0.0667
 TFV  H6   H   HCH2  0   0.242   0.9234  -1.7000   0.6170
 TFV  H7   H   HCH2  0   0.271   0.0858  -1.3915   2.9320
 TFV  H8   H   HCH2  0   0.260  -0.9039  -0.0344   2.4023
 TFV  H9   H   HNH1  0   0.402  -1.3239  -2.8861   1.9138
 TFV  H10  H   HCH3  0   0.262  -6.1886  -3.5525   0.3198
 TFV  H11  H   HCH3  0   0.262  -6.4779  -2.5170  -1.0855
 TFV  H12  H   HCH3  0   0.261  -5.3006  -3.8360  -1.1657
 TFV  H13  H   HCR6  0   0.272  -5.8766   1.1285  -1.4041
 TFV  H14  H   HCR6  0   0.275  -6.1362   3.5380  -1.9675
 TFV  H15  H   HCR6  0   0.274  -4.3942   5.1490  -1.1620
 TFV  H16  H   HCR6  0   0.262  -2.4965   4.2632   0.1662

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
 TFV  C1   C2   aromatic  1.389  0.020  1.389
 TFV  C1   N1   aromatic  1.324  0.020  1.324
 TFV  C2   C3   aromatic  1.386  0.020  1.386
 TFV  N1   C5   aromatic  1.330  0.020  1.330
 TFV  C3   C4   aromatic  1.385  0.020  1.385
 TFV  C5   C4   aromatic  1.393  0.020  1.393
 TFV  C5   C6   single    1.489  0.020  1.489
 TFV  N2   C6   aromatic  1.323  0.020  1.323
 TFV  N2   C9   aromatic  1.336  0.020  1.336
 TFV  C6   N3   aromatic  1.321  0.020  1.321
 TFV  C12  C9   single    1.493  0.020  1.493
 TFV  C9   C8   aromatic  1.379  0.020  1.379
 TFV  N3   C7   aromatic  1.331  0.020  1.331
 TFV  C8   C7   aromatic  1.411  0.020  1.411
 TFV  C8   CL   single    1.727  0.020  1.727
 TFV  C7   N4   single    1.341  0.020  1.341
 TFV  N4   C10  single    1.441  0.020  1.441
 TFV  C10  C11  single    1.525  0.020  1.525
 TFV  C11  N5   single    1.441  0.020  1.441
 TFV  N6   C14  aromatic  1.321  0.020  1.321
 TFV  N6   C13  aromatic  1.337  0.020  1.337
 TFV  N5   C13  single    1.347  0.020  1.347
 TFV  C14  C15  aromatic  1.386  0.020  1.386
 TFV  F2   C18  single    1.345  0.020  1.345
 TFV  C13  C17  aromatic  1.411  0.020  1.411
 TFV  C15  C18  single    1.484  0.020  1.484
 TFV  C15  C16  aromatic  1.398  0.020  1.398
 TFV  C17  C16  aromatic  1.372  0.020  1.372
 TFV  C18  F1   single    1.344  0.020  1.344
 TFV  C18  F3   single    1.338  0.020  1.338
 TFV  C14  H1   single    0.930  0.020  1.080
 TFV  C16  H2   single    0.930  0.020  1.080
 TFV  C17  H3   single    0.930  0.020  1.080
 TFV  N5   H4   single    0.860  0.020  1.020
 TFV  C11  H5   single    0.970  0.020  1.090
 TFV  C11  H6   single    0.970  0.020  1.090
 TFV  C10  H7   single    0.970  0.020  1.090
 TFV  C10  H8   single    0.970  0.020  1.090
 TFV  N4   H9   single    0.860  0.020  1.020
 TFV  C12  H10  single    0.970  0.020  1.090
 TFV  C12  H11  single    0.970  0.020  1.090
 TFV  C12  H12  single    0.970  0.020  1.090
 TFV  C4   H13  single    0.930  0.020  1.080
 TFV  C3   H14  single    0.930  0.020  1.080
 TFV  C2   H15  single    0.930  0.020  1.080
 TFV  C1   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
 TFV  C15  C18  F2   112.22  3.000
 TFV  C15  C18  F1   112.03  3.000
 TFV  F2   C18  F1   105.78  3.000
 TFV  F1   C18  F3   106.98  3.000
 TFV  C15  C18  F3   112.68  3.000
 TFV  F2   C18  F3   106.71  3.000
 TFV  C16  C15  C14  117.28  3.000
 TFV  C16  C15  C18  120.17  3.000
 TFV  C14  C15  C18  122.54  3.000
 TFV  H1   C14  N6   115.37  3.000
 TFV  H1   C14  C15  120.85  3.000
 TFV  N6   C14  C15  123.78  3.000
 TFV  C13  N6   C14  119.04  3.000
 TFV  H2   C16  C17  119.05  3.000
 TFV  H2   C16  C15  121.04  3.000
 TFV  C17  C16  C15  119.90  3.000
 TFV  H3   C17  C13  121.58  3.000
 TFV  H3   C17  C16  119.95  3.000
 TFV  C13  C17  C16  118.46  3.000
 TFV  N5   C13  C17  122.22  3.000
 TFV  C17  C13  N6   121.52  3.000
 TFV  N5   C13  N6   116.26  3.000
 TFV  H4   N5   C11  118.48  3.000
 TFV  H4   N5   C13  115.54  3.000
 TFV  C11  N5   C13  124.58  3.000
 TFV  H6   C11  H5   107.49  3.000
 TFV  H6   C11  C10  108.57  3.000
 TFV  H5   C11  C10  109.57  3.000
 TFV  H6   C11  N5   109.82  3.000
 TFV  H5   C11  N5   111.62  3.000
 TFV  C10  C11  N5   109.70  3.000
 TFV  H8   C10  H7   107.76  3.000
 TFV  H8   C10  N4   109.57  3.000
 TFV  H7   C10  N4   107.56  3.000
 TFV  H8   C10  C11  110.16  3.000
 TFV  H7   C10  C11  109.73  3.000
 TFV  N4   C10  C11  111.94  3.000
 TFV  H9   N4   C7   118.41  3.000
 TFV  H9   N4   C10  117.31  3.000
 TFV  C7   N4   C10  123.57  3.000
 TFV  C8   C7   N3   119.37  3.000
 TFV  C8   C7   N4   122.14  3.000
 TFV  N3   C7   N4   118.48  3.000
 TFV  C6   N3   C7   117.95  3.000
 TFV  C9   C8   CL   121.18  3.000
 TFV  CL   C8   C7   120.13  3.000
 TFV  C9   C8   C7   118.69  3.000
 TFV  N2   C9   C12  117.78  3.000
 TFV  C12  C9   C8   122.07  3.000
 TFV  N2   C9   C8   120.15  3.000
 TFV  H12  C12  H11  108.74  3.000
 TFV  H12  C12  H10  107.02  3.000
 TFV  H11  C12  H10  108.70  3.000
 TFV  H12  C12  C9   111.19  3.000
 TFV  H11  C12  C9   109.98  3.000
 TFV  H10  C12  C9   111.11  3.000
 TFV  C6   N2   C9   117.64  3.000
 TFV  C5   C6   N2   116.45  3.000
 TFV  N2   C6   N3   126.20  3.000
 TFV  C5   C6   N3   117.35  3.000
 TFV  C4   C5   N1   122.39  3.000
 TFV  C4   C5   C6   120.39  3.000
 TFV  N1   C5   C6   117.22  3.000
 TFV  C1   N1   C5   118.46  3.000
 TFV  H13  C4   C3   121.03  3.000
 TFV  H13  C4   C5   120.24  3.000
 TFV  C3   C4   C5   118.73  3.000
 TFV  H14  C3   C2   120.79  3.000
 TFV  H14  C3   C4   120.31  3.000
 TFV  C2   C3   C4   118.90  3.000
 TFV  H15  C2   C1   120.43  3.000
 TFV  H15  C2   C3   121.58  3.000
 TFV  C1   C2   C3   118.00  3.000
 TFV  H16  C1   C2   120.10  3.000
 TFV  H16  C1   N1   116.38  3.000
 TFV  C2   C1   N1   123.52  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
 TFV  CONST_01  C13  N6   C14  C15     0.00   0.0  0
 TFV  CONST_02  C13  C17  C16  C15     0.00   0.0  0
 TFV  CONST_03  C17  C13  N6   C14     0.00   0.0  0
 TFV  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 TFV  CONST_05  C16  C15  C14  N6      0.00   0.0  0
 TFV  CONST_06  C16  C17  C13  N6      0.00   0.0  0
 TFV  CONST_07  C5   C6   N3   C7    180.00   0.0  0
 TFV  CONST_08  N2   C6   N3   C7      0.00   0.0  0
 TFV  CONST_09  N2   C9   C8   C7      0.00   0.0  0
 TFV  CONST_10  N1   C5   C6   N3      0.00   0.0  0
 TFV  CONST_11  C4   C5   C6   N3    180.00   0.0  0
 TFV  CONST_12  C9   N2   C6   N3      0.00   0.0  0
 TFV  CONST_13  C9   C8   C7   N3      0.00   0.0  0
 TFV  CONST_14  C6   N2   C9   C8      0.00   0.0  0
 TFV  CONST_15  C6   N3   C7   C8      0.00   0.0  0
 TFV  CONST_16  C5   C6   N2   C9    180.00   0.0  0
 TFV  CONST_17  N1   C5   C6   N2    180.00   0.0  0
 TFV  CONST_18  C4   C5   C6   N2      0.00   0.0  0
 TFV  CONST_19  C1   N1   C5   C6    180.00   0.0  0
 TFV  CONST_20  C3   C4   C5   C6    180.00   0.0  0
 TFV  CONST_21  C2   C1   N1   C5      0.00   0.0  0
 TFV  CONST_22  C2   C3   C4   C5      0.00   0.0  0
 TFV  CONST_23  C3   C2   C1   N1      0.00   0.0  0
 TFV  CONST_24  C3   C4   C5   N1      0.00   0.0  0
 TFV  CONST_25  C1   C2   C3   C4      0.00   0.0  0
 TFV  CONST_26  C1   N1   C5   C4      0.00   0.0  0
 TFV  CONST_27  N6   C14  C15  C18   180.00   0.0  0
 TFV  CONST_28  C17  C16  C15  C18   180.00   0.0  0
 TFV  CONST_29  N5   C13  N6   C14   180.00   0.0  0
 TFV  CONST_30  N5   C13  C17  C16   180.00   0.0  0
 TFV  CONST_31  C6   N3   C7   N4    180.00   0.0  0
 TFV  CONST_32  C9   C8   C7   N4    180.00   0.0  0
 TFV  CONST_33  C12  C9   C8   C7    180.00   0.0  0
 TFV  CONST_34  CL   C8   C7   N3    180.00   0.0  0
 TFV  CONST_35  N2   C9   C8   CL    180.00   0.0  0
 TFV  CONST_36  C6   N2   C9   C12   180.00   0.0  0
 TFV  CONST_37  H3   C17  C16  C15   180.00   0.0  0
 TFV  CONST_38  H2   C16  C15  C14   180.00   0.0  0
 TFV  CONST_39  H1   C14  C15  C16   180.00   0.0  0
 TFV  CONST_40  H13  C4   C5   C6      0.00   0.0  0
 TFV  CONST_41  H16  C1   N1   C5    180.00   0.0  0
 TFV  CONST_42  H14  C3   C4   C5    180.00   0.0  0
 TFV  CONST_43  H15  C2   C1   N1    180.00   0.0  0
 TFV  CONST_44  C11  N5   C13  N6    180.00   0.0  0
 TFV  CONST_45  C11  N5   C13  C17     0.00   0.0  0
 TFV  CONST_46  N3   C7   N4   C10     0.00   0.0  0
 TFV  CONST_47  C8   C7   N4   C10   180.00   0.0  0
 TFV  CONST_48  H4   N5   C13  N6      0.00   0.0  0
 TFV  CONST_49  H9   N4   C7   N3    180.00   0.0  0
 TFV  Var_01    C14  C15  C18  F3     -7.71  30.0  2
 TFV  Var_02    H10  C12  C9   C8     60.54  30.0  2
 TFV  Var_03    C10  C11  N5   C13   169.61  30.0  1
 TFV  Var_04    C7   N4   C10  C11   -80.03  30.0  1
 TFV  Var_05    N4   C10  C11  N5   -177.21  30.0  1

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
 TFV  plan-1  C18  0.020
 TFV  plan-1  C15  0.020
 TFV  plan-1  C14  0.020
 TFV  plan-1  N6   0.020
 TFV  plan-1  C16  0.020
 TFV  plan-1  C17  0.020
 TFV  plan-1  C13  0.020
 TFV  plan-1  N5   0.020
 TFV  plan-1  H1   0.020
 TFV  plan-1  H2   0.020
 TFV  plan-1  H3   0.020
 TFV  plan-2  N4   0.020
 TFV  plan-2  C7   0.020
 TFV  plan-2  N3   0.020
 TFV  plan-2  C8   0.020
 TFV  plan-2  CL   0.020
 TFV  plan-2  C9   0.020
 TFV  plan-2  C12  0.020
 TFV  plan-2  N2   0.020
 TFV  plan-2  C6   0.020
 TFV  plan-2  C5   0.020
 TFV  plan-3  C6   0.020
 TFV  plan-3  C5   0.020
 TFV  plan-3  N1   0.020
 TFV  plan-3  C4   0.020
 TFV  plan-3  C3   0.020
 TFV  plan-3  C2   0.020
 TFV  plan-3  C1   0.020
 TFV  plan-3  H13  0.020
 TFV  plan-3  H14  0.020
 TFV  plan-3  H15  0.020
 TFV  plan-3  H16  0.020
 TFV  plan-4  C13  0.020
 TFV  plan-4  N5   0.020
 TFV  plan-4  C11  0.020
 TFV  plan-4  H4   0.020
 TFV  plan-5  C10  0.020
 TFV  plan-5  N4   0.020
 TFV  plan-5  C7   0.020
 TFV  plan-5  H9   0.020

