# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 08:07:24 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-(1,1-difluoroethyl)-5-methyl-N-[6-(trifluoromethyl)pyridin-3-yl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Nc2ccc(nc2)C(F)(F)F)n3nc(nc3n1)C(C)(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
 78Z  78Z  2-(1,1-difluoroethyl)-5-methyl-N-[6-(trifluoromethyl)pyridin-3-yl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine  ligand  36  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_78Z
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
 78Z  C10   C  CH3   0  -0.736  -4.5139   3.9453   0.6766
 78Z  C9    C  CR6   0   0.270  -3.6017   2.7764   0.4949
 78Z  N5    N  N     0  -0.475  -4.0015   1.6041   0.9498
 78Z  C11   C  CR56  0   0.594  -3.1748   0.5832   0.7629
 78Z  N4    N  N     0  -0.498  -3.3494  -0.6916   1.0690
 78Z  C12   C  CR5   0   0.219  -2.2347  -1.2701   0.6084
 78Z  N3    N  N     0  -0.277  -1.3565  -0.4843   0.0290
 78Z  N2    N  N     0  -0.423  -1.9509   0.7116   0.1426
 78Z  C8    C  CR16  0  -0.462  -2.3577   2.9702  -0.1343
 78Z  C7    C  CR6   0   0.692  -1.4973   1.9117  -0.3095
 78Z  C13   C  CT    0   0.736  -2.0238  -2.7509   0.7245
 78Z  C14   C  CH3   0  -0.763  -3.0086  -3.5665  -0.0667
 78Z  F4    F  F     0  -0.337  -0.7510  -3.0412   0.3424
 78Z  F5    F  F     0  -0.347  -2.1049  -3.0780   2.0507
 78Z  N1    N  NH1   0  -0.771  -0.3030   2.0004  -0.9435
 78Z  C2    C  CR6   0   0.270   0.8783   1.3301  -0.6313
 78Z  C3    C  CR16  0  -0.153   1.1707   0.8288   0.6293
 78Z  C4    C  CR16  0  -0.309   2.3867   0.1963   0.8309
 78Z  C5    C  CR6   0  -0.027   3.2670   0.1144  -0.2323
 78Z  N6    N  N     0  -0.409   3.0091   0.6180  -1.4315
 78Z  C1    C  CR16  0  -0.126   1.8466   1.2045  -1.6310
 78Z  C16   C  CT    0   1.049   4.6114  -0.5421  -0.1188
 78Z  F1    F  F     0  -0.311   4.7712  -1.4924  -1.0479
 78Z  F2    F  F     0  -0.313   5.6039   0.3397  -0.2983
 78Z  F3    F  F     0  -0.300   4.8005  -1.1145   1.0722
 78Z  H102  H  HCH3  0   0.266  -4.8353   4.3301  -0.2926
 78Z  H103  H  HCH3  0   0.261  -5.3935   3.6642   1.2504
 78Z  H101  H  HCH3  0   0.264  -4.0014   4.7591   1.1903
 78Z  H81   H  HCR6  0   0.302  -2.0553   3.9555  -0.4591
 78Z  H142  H  HCH3  0   0.264  -2.9126  -3.3423  -1.1284
 78Z  H143  H  HCH3  0   0.273  -2.8317  -4.6314   0.0852
 78Z  H141  H  HCH3  0   0.263  -4.0261  -3.3308   0.2396
 78Z  H11   H  HNH1  0   0.433  -0.2033   2.8117  -1.5379
 78Z  H31   H  HCR6  0   0.298   0.4860   0.9390   1.4585
 78Z  H41   H  HCR6  0   0.291   2.6284  -0.1982   1.8071
 78Z  H12   H  HCR6  0   0.291   1.6557   1.6046  -2.6212

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
 78Z  C10  C9    single    1.494  0.020  1.494
 78Z  N5   C9    aromatic  1.319  0.020  1.319
 78Z  N5   C11   aromatic  1.327  0.020  1.327
 78Z  C9   C8    aromatic  1.407  0.020  1.407
 78Z  C11  N4    aromatic  1.323  0.020  1.323
 78Z  C11  N2    aromatic  1.378  0.020  1.378
 78Z  N4   C12   aromatic  1.338  0.020  1.338
 78Z  C8   C7    aromatic  1.375  0.020  1.375
 78Z  F5   C13   single    1.368  0.020  1.368
 78Z  N2   C7    aromatic  1.360  0.020  1.360
 78Z  N2   N3    aromatic  1.340  0.020  1.340
 78Z  C7   N1    single    1.355  0.020  1.355
 78Z  C12  C13   single    1.500  0.020  1.500
 78Z  C12  N3    aromatic  1.313  0.020  1.313
 78Z  C13  C14   single    1.504  0.020  1.504
 78Z  C13  F4    single    1.360  0.020  1.360
 78Z  N1   C2    single    1.394  0.020  1.394
 78Z  C2   C3    aromatic  1.388  0.020  1.388
 78Z  C2   C1    aromatic  1.397  0.020  1.397
 78Z  C3   C4    aromatic  1.385  0.020  1.385
 78Z  C1   N6    aromatic  1.317  0.020  1.317
 78Z  C4   C5    aromatic  1.383  0.020  1.383
 78Z  N6   C5    aromatic  1.326  0.020  1.326
 78Z  C5   C16   single    1.500  0.020  1.500
 78Z  F2   C16   single    1.340  0.020  1.340
 78Z  C16  F1    single    1.339  0.020  1.339
 78Z  C16  F3    single    1.335  0.020  1.335
 78Z  C10  H102  single    0.970  0.020  1.090
 78Z  C10  H103  single    0.970  0.020  1.090
 78Z  C10  H101  single    0.970  0.020  1.090
 78Z  C8   H81   single    0.930  0.020  1.080
 78Z  C14  H142  single    0.970  0.020  1.090
 78Z  C14  H143  single    0.970  0.020  1.090
 78Z  C14  H141  single    0.970  0.020  1.090
 78Z  N1   H11   single    0.860  0.020  1.020
 78Z  C3   H31   single    0.930  0.020  1.080
 78Z  C4   H41   single    0.930  0.020  1.080
 78Z  C1   H12   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
 78Z  H101  C10  H103  108.94  3.000
 78Z  H101  C10  H102  107.08  3.000
 78Z  H103  C10  H102  108.76  3.000
 78Z  H101  C10  C9    110.76  3.000
 78Z  H103  C10  C9    110.85  3.000
 78Z  H102  C10  C9    110.35  3.000
 78Z  C8    C9   N5    122.97  3.000
 78Z  C8    C9   C10   119.10  3.000
 78Z  N5    C9   C10   117.92  3.000
 78Z  C11   N5   C9    116.50  3.000
 78Z  N2    C11  N4    108.13  3.000
 78Z  N2    C11  N5    123.03  3.000
 78Z  N4    C11  N5    128.81  3.000
 78Z  C12   N4   C11   103.13  3.000
 78Z  C13   C12  N3    122.06  3.000
 78Z  N3    C12  N4    116.77  3.000
 78Z  C13   C12  N4    121.16  3.000
 78Z  N2    N3   C12   101.54  3.000
 78Z  C7    N2   N3    127.67  3.000
 78Z  N3    N2   C11   110.42  3.000
 78Z  C7    N2   C11   121.87  3.000
 78Z  H81   C8   C7    119.24  3.000
 78Z  H81   C8   C9    120.48  3.000
 78Z  C7    C8   C9    120.26  3.000
 78Z  N1    C7   C8    124.09  3.000
 78Z  N1    C7   N2    120.48  3.000
 78Z  C8    C7   N2    115.35  3.000
 78Z  F5    C13  F4    106.07  3.000
 78Z  F4    C13  C14   110.44  3.000
 78Z  F5    C13  C14   109.97  3.000
 78Z  F4    C13  C12   108.69  3.000
 78Z  C14   C13  C12   113.74  3.000
 78Z  F5    C13  C12   107.61  3.000
 78Z  H141  C14  H143  108.91  3.000
 78Z  H141  C14  H142  108.18  3.000
 78Z  H143  C14  H142  108.82  3.000
 78Z  H141  C14  C13   110.29  3.000
 78Z  H143  C14  C13   110.50  3.000
 78Z  H142  C14  C13   110.09  3.000
 78Z  H11   N1   C2    115.74  3.000
 78Z  H11   N1   C7    114.50  3.000
 78Z  C2    N1   C7    127.64  3.000
 78Z  C1    C2   C3    118.12  3.000
 78Z  C1    C2   N1    118.06  3.000
 78Z  C3    C2   N1    123.77  3.000
 78Z  H31   C3   C4    119.40  3.000
 78Z  H31   C3   C2    121.77  3.000
 78Z  C4    C3   C2    118.81  3.000
 78Z  H41   C4   C5    122.06  3.000
 78Z  H41   C4   C3    119.64  3.000
 78Z  C5    C4   C3    118.29  3.000
 78Z  C16   C5   N6    114.14  3.000
 78Z  C16   C5   C4    122.56  3.000
 78Z  N6    C5   C4    123.30  3.000
 78Z  C1    N6   C5    118.54  3.000
 78Z  H12   C1   N6    117.24  3.000
 78Z  H12   C1   C2    119.86  3.000
 78Z  N6    C1   C2    122.90  3.000
 78Z  F3    C16  F2    107.27  3.000
 78Z  F3    C16  F1    107.33  3.000
 78Z  F2    C16  F1    106.61  3.000
 78Z  F3    C16  C5    112.46  3.000
 78Z  F1    C16  C5    111.41  3.000
 78Z  F2    C16  C5    111.45  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
 78Z  CONST_01  N4    C11  N5   C9    180.00   0.0  0
 78Z  CONST_02  N2    C11  N5   C9      0.00   0.0  0
 78Z  CONST_03  N2    C7   C8   C9      0.00   0.0  0
 78Z  CONST_04  C7    C8   C9   N5      0.00   0.0  0
 78Z  CONST_05  C12   N4   C11  N5    180.00   0.0  0
 78Z  CONST_06  C7    N2   C11  N5      0.00   0.0  0
 78Z  CONST_07  N3    N2   C11  N5    180.00   0.0  0
 78Z  CONST_08  C8    C9   N5   C11     0.00   0.0  0
 78Z  CONST_09  N3    C12  N4   C11     0.00   0.0  0
 78Z  CONST_10  C8    C7   N2   C11     0.00   0.0  0
 78Z  CONST_11  C12   N3   N2   C11     0.00   0.0  0
 78Z  CONST_12  C7    N2   C11  N4    180.00   0.0  0
 78Z  CONST_13  N3    N2   C11  N4      0.00   0.0  0
 78Z  CONST_14  N2    N3   C12  N4      0.00   0.0  0
 78Z  CONST_15  N2    C11  N4   C12     0.00   0.0  0
 78Z  CONST_16  C7    N2   N3   C12   180.00   0.0  0
 78Z  CONST_17  C8    C7   N2   N3    180.00   0.0  0
 78Z  CONST_18  C5    C4   C3   C2      0.00   0.0  0
 78Z  CONST_19  C5    N6   C1   C2      0.00   0.0  0
 78Z  CONST_20  N6    C1   C2   C3      0.00   0.0  0
 78Z  CONST_21  N6    C5   C4   C3      0.00   0.0  0
 78Z  CONST_22  C1    C2   C3   C4      0.00   0.0  0
 78Z  CONST_23  C1    N6   C5   C4      0.00   0.0  0
 78Z  CONST_24  C11   N5   C9   C10   180.00   0.0  0
 78Z  CONST_25  C7    C8   C9   C10   180.00   0.0  0
 78Z  CONST_26  N1    C7   C8   C9    180.00   0.0  0
 78Z  CONST_27  C13   C12  N4   C11   180.00   0.0  0
 78Z  CONST_28  N1    C7   N2   C11   180.00   0.0  0
 78Z  CONST_29  N1    C7   N2   N3      0.00   0.0  0
 78Z  CONST_30  C13   C12  N3   N2    180.00   0.0  0
 78Z  CONST_31  C4    C3   C2   N1    180.00   0.0  0
 78Z  CONST_32  N6    C1   C2   N1    180.00   0.0  0
 78Z  CONST_33  C16   C5   C4   C3    180.00   0.0  0
 78Z  CONST_34  C16   C5   N6   C1    180.00   0.0  0
 78Z  CONST_35  H81   C8   C9   N5    180.00   0.0  0
 78Z  CONST_36  H41   C4   C3   C2    180.00   0.0  0
 78Z  CONST_37  H12   C1   C2   C3    180.00   0.0  0
 78Z  CONST_38  H31   C3   C4   C5    180.00   0.0  0
 78Z  Var_01    C2    N1   C7   N2    -39.59  30.0  2
 78Z  Var_02    C3    C2   N1   C7    -23.76  30.0  2
 78Z  Var_03    F5    C13  C12  N4    -57.66  30.0  2
 78Z  Var_04    F2    C16  C5   C4   -115.59  30.0  2
 78Z  Var_05    H102  C10  C9   N5   -116.33  30.0  2
 78Z  Var_06    H142  C14  C13  C12    61.94  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
 78Z  plan-1  N1   0.020
 78Z  plan-1  C2   0.020
 78Z  plan-1  C3   0.020
 78Z  plan-1  C4   0.020
 78Z  plan-1  C5   0.020
 78Z  plan-1  N6   0.020
 78Z  plan-1  C1   0.020
 78Z  plan-1  C16  0.020
 78Z  plan-1  H31  0.020
 78Z  plan-1  H41  0.020
 78Z  plan-1  H12  0.020
 78Z  plan-2  C10  0.020
 78Z  plan-2  C9   0.020
 78Z  plan-2  N5   0.020
 78Z  plan-2  C11  0.020
 78Z  plan-2  N4   0.020
 78Z  plan-2  C12  0.020
 78Z  plan-2  N3   0.020
 78Z  plan-2  N2   0.020
 78Z  plan-2  C8   0.020
 78Z  plan-2  C7   0.020
 78Z  plan-2  C13  0.020
 78Z  plan-2  N1   0.020
 78Z  plan-2  H81  0.020

