# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:07:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-(3-fluoropyridin-4-yl)-2-[6-(trifluoromethyl)pyridin-2-yl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cnccc1Nc2nc(nc3[nH]ccc23)c4cccc(n4)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
 D0A  D0A  N-(3-fluoropyridin-4-yl)-2-[6-(trifluoromethyl)pyridin-2-yl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  37  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D0A
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
 D0A  C13  C  CR16  0  -0.384  -0.5053  -2.2575   0.0825
 D0A  C17  C  CR6   0   0.354  -2.6583  -3.2226   0.1501
 D0A  C16  C  CR16  0  -0.207  -2.0847  -4.4708   0.1591
 D0A  C19  C  CR16  0  -0.293   1.8890   3.1596  -0.0633
 D0A  C20  C  CR16  0  -0.137   3.2708   3.1876  -0.0774
 D0A  C21  C  CR16  0  -0.315   3.9783   1.9943  -0.0164
 D0A  C22  C  CR6   0  -0.024   3.2397   0.8255   0.0589
 D0A  C24  C  CT    0   1.056   3.8954  -0.5254   0.1709
 D0A  C11  C  CR6   0   0.154   1.2453   1.9247   0.0141
 D0A  C12  C  CR6   0   0.311  -1.8889  -2.0560   0.1104
 D0A  C1   C  CR56  0  -0.114  -2.8987   1.5281   0.0271
 D0A  C2   C  CR56  0   0.518  -2.2394   2.7689  -0.0103
 D0A  N3   N  N     0  -0.467  -0.9220   2.9508  -0.0143
 D0A  C4   C  CR6   0   0.378  -0.2359   1.8262   0.0228
 D0A  N5   N  N     0  -0.489  -0.7362   0.5914   0.0630
 D0A  C6   C  CR6   0   0.533  -2.0414   0.4160   0.0637
 D0A  C7   C  CR15  0  -0.433  -4.2979   1.7892   0.0111
 D0A  C8   C  CR15  0  -0.003  -4.4262   3.1480  -0.0333
 D0A  N9   N  NR15  0  -0.669  -3.1875   3.7324  -0.0455
 D0A  N10  N  NH1   0  -0.776  -2.5533  -0.8494   0.0991
 D0A  C14  C  CR16  0  -0.080  -0.0177  -3.5553   0.0942
 D0A  N15  N  N     0  -0.407  -0.7677  -4.6481   0.1310
 D0A  F18  F  F     0  -0.308  -3.9971  -3.1079   0.1812
 D0A  N23  N  N     0  -0.420   1.9208   0.7860   0.0764
 D0A  F25  F  F     0  -0.313   3.8372  -0.9849   1.4277
 D0A  F26  F  F     0  -0.305   3.2960  -1.4312  -0.6042
 D0A  F27  F  F     0  -0.303   5.1847  -0.4894  -0.1768
 D0A  H32  H  HCR6  0   0.336   0.1783  -1.4242   0.0548
 D0A  H34  H  HCR6  0   0.285  -2.7184  -5.3510   0.1907
 D0A  H35  H  HCR6  0   0.280   1.3127   4.0721  -0.1136
 D0A  H36  H  HCR6  0   0.287   3.7985   4.1294  -0.1389
 D0A  H37  H  HCR6  0   0.289   5.0586   1.9935  -0.0276
 D0A  H28  H  HCR5  0   0.263  -5.1095   1.0802   0.0282
 D0A  H29  H  HCR5  0   0.296  -5.3159   3.7550  -0.0595
 D0A  H30  H  HNR5  0   0.420  -3.0097   4.7239  -0.0767
 D0A  H31  H  HNH1  0   0.424  -3.5602  -0.9059   0.1086
 D0A  H33  H  HCR6  0   0.263   1.0558  -3.7060   0.0712

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
 D0A  N15  C14  aromatic  1.326  0.020  1.326
 D0A  N15  C16  aromatic  1.329  0.020  1.329
 D0A  C14  C13  aromatic  1.386  0.020  1.386
 D0A  C16  C17  aromatic  1.374  0.020  1.374
 D0A  C13  C12  aromatic  1.398  0.020  1.398
 D0A  C17  C12  aromatic  1.398  0.020  1.398
 D0A  C17  F18  single    1.344  0.020  1.344
 D0A  C20  C21  aromatic  1.389  0.020  1.389
 D0A  C20  C19  aromatic  1.382  0.020  1.382
 D0A  C21  C22  aromatic  1.385  0.020  1.385
 D0A  C12  N10  single    1.377  0.020  1.377
 D0A  C19  C11  aromatic  1.395  0.020  1.395
 D0A  F27  C24  single    1.336  0.020  1.336
 D0A  C22  C24  single    1.506  0.020  1.506
 D0A  C22  N23  aromatic  1.320  0.020  1.320
 D0A  F26  C24  single    1.334  0.020  1.334
 D0A  N10  C6   single    1.365  0.020  1.365
 D0A  C24  F25  single    1.339  0.020  1.339
 D0A  C11  N23  aromatic  1.325  0.020  1.325
 D0A  C11  C4   single    1.485  0.020  1.485
 D0A  N5   C6   aromatic  1.317  0.020  1.317
 D0A  N5   C4   aromatic  1.333  0.020  1.333
 D0A  C6   C1   aromatic  1.405  0.020  1.405
 D0A  C4   N3   aromatic  1.318  0.020  1.318
 D0A  C1   C2   aromatic  1.406  0.020  1.406
 D0A  C1   C7   aromatic  1.423  0.020  1.423
 D0A  N3   C2   aromatic  1.330  0.020  1.330
 D0A  C2   N9   aromatic  1.352  0.020  1.352
 D0A  C7   C8   aromatic  1.366  0.020  1.366
 D0A  N9   C8   aromatic  1.370  0.020  1.370
 D0A  C13  H32  single    0.930  0.020  1.080
 D0A  C16  H34  single    0.930  0.020  1.080
 D0A  C19  H35  single    0.930  0.020  1.080
 D0A  C20  H36  single    0.930  0.020  1.080
 D0A  C21  H37  single    0.930  0.020  1.080
 D0A  C7   H28  single    0.930  0.020  1.080
 D0A  C8   H29  single    0.930  0.020  1.080
 D0A  N9   H30  single    0.860  0.020  1.020
 D0A  N10  H31  single    0.860  0.020  1.020
 D0A  C14  H33  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
 D0A  H32  C13  C14  120.05  3.000
 D0A  H32  C13  C12  121.09  3.000
 D0A  C14  C13  C12  118.86  3.000
 D0A  F18  C17  C12  118.53  3.000
 D0A  F18  C17  C16  119.56  3.000
 D0A  C12  C17  C16  121.91  3.000
 D0A  H34  C16  N15  118.11  3.000
 D0A  H34  C16  C17  119.56  3.000
 D0A  N15  C16  C17  122.33  3.000
 D0A  H35  C19  C11  120.28  3.000
 D0A  H35  C19  C20  121.05  3.000
 D0A  C11  C19  C20  118.67  3.000
 D0A  H36  C20  C21  120.15  3.000
 D0A  H36  C20  C19  120.40  3.000
 D0A  C21  C20  C19  119.45  3.000
 D0A  H37  C21  C22  122.23  3.000
 D0A  H37  C21  C20  120.64  3.000
 D0A  C22  C21  C20  117.13  3.000
 D0A  N23  C22  C24  114.03  3.000
 D0A  N23  C22  C21  124.00  3.000
 D0A  C24  C22  C21  121.94  3.000
 D0A  F27  C24  F26  107.50  3.000
 D0A  F26  C24  F25  107.01  3.000
 D0A  F27  C24  F25  107.18  3.000
 D0A  F25  C24  C22  111.02  3.000
 D0A  F26  C24  C22  111.73  3.000
 D0A  F27  C24  C22  112.13  3.000
 D0A  N23  C11  C4   116.82  3.000
 D0A  C4   C11  C19  121.30  3.000
 D0A  N23  C11  C19  121.88  3.000
 D0A  N10  C12  C17  117.76  3.000
 D0A  N10  C12  C13  127.11  3.000
 D0A  C17  C12  C13  115.14  3.000
 D0A  C7   C1   C6   138.20  3.000
 D0A  C7   C1   C2   107.38  3.000
 D0A  C6   C1   C2   114.42  3.000
 D0A  N9   C2   N3   126.66  3.000
 D0A  N9   C2   C1   107.51  3.000
 D0A  N3   C2   C1   125.83  3.000
 D0A  C4   N3   C2   113.51  3.000
 D0A  N5   C4   N3   126.59  3.000
 D0A  N3   C4   C11  117.55  3.000
 D0A  N5   C4   C11  115.86  3.000
 D0A  C6   N5   C4   119.70  3.000
 D0A  N10  C6   N5   119.67  3.000
 D0A  N5   C6   C1   119.96  3.000
 D0A  N10  C6   C1   120.37  3.000
 D0A  H28  C7   C8   125.76  3.000
 D0A  H28  C7   C1   128.26  3.000
 D0A  C8   C7   C1   105.98  3.000
 D0A  H29  C8   N9   120.41  3.000
 D0A  H29  C8   C7   129.72  3.000
 D0A  N9   C8   C7   109.87  3.000
 D0A  H30  N9   C8   125.42  3.000
 D0A  H30  N9   C2   125.32  3.000
 D0A  C8   N9   C2   109.26  3.000
 D0A  H31  N10  C6   115.25  3.000
 D0A  H31  N10  C12  115.62  3.000
 D0A  C6   N10  C12  129.13  3.000
 D0A  H33  C14  N15  116.49  3.000
 D0A  H33  C14  C13  118.57  3.000
 D0A  N15  C14  C13  124.94  3.000
 D0A  C14  N15  C16  116.82  3.000
 D0A  C11  N23  C22  118.88  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
 D0A  CONST_01  C16  N15  C14  C13    0.00   0.0  0
 D0A  CONST_02  C16  C17  C12  C13    0.00   0.0  0
 D0A  CONST_03  C14  N15  C16  C17    0.00   0.0  0
 D0A  CONST_04  C14  C13  C12  C17    0.00   0.0  0
 D0A  CONST_05  C22  C21  C20  C19    0.00   0.0  0
 D0A  CONST_06  C22  N23  C11  C19    0.00   0.0  0
 D0A  CONST_07  N5   C4   C11  C19  180.00   0.0  0
 D0A  CONST_08  N3   C4   C11  C19    0.00   0.0  0
 D0A  CONST_09  N23  C22  C21  C20    0.00   0.0  0
 D0A  CONST_10  N23  C11  C19  C20    0.00   0.0  0
 D0A  CONST_11  C4   C11  C19  C20  180.00   0.0  0
 D0A  CONST_12  C11  C19  C20  C21    0.00   0.0  0
 D0A  CONST_13  C11  N23  C22  C21    0.00   0.0  0
 D0A  CONST_14  C4   C11  N23  C22  180.00   0.0  0
 D0A  CONST_15  C6   N5   C4   C11  180.00   0.0  0
 D0A  CONST_16  C2   N3   C4   C11  180.00   0.0  0
 D0A  CONST_17  N15  C14  C13  C12    0.00   0.0  0
 D0A  CONST_18  N15  C16  C17  C12    0.00   0.0  0
 D0A  CONST_19  C4   N5   C6   C1     0.00   0.0  0
 D0A  CONST_20  C4   N3   C2   C1     0.00   0.0  0
 D0A  CONST_21  C8   N9   C2   C1     0.00   0.0  0
 D0A  CONST_22  N9   C8   C7   C1     0.00   0.0  0
 D0A  CONST_23  N5   C6   C1   C2     0.00   0.0  0
 D0A  CONST_24  C8   C7   C1   C2     0.00   0.0  0
 D0A  CONST_25  N5   C4   N3   C2     0.00   0.0  0
 D0A  CONST_26  C7   C8   N9   C2     0.00   0.0  0
 D0A  CONST_27  N23  C11  C4   N3   180.00   0.0  0
 D0A  CONST_28  C6   N5   C4   N3     0.00   0.0  0
 D0A  CONST_29  C6   C1   C2   N3     0.00   0.0  0
 D0A  CONST_30  C7   C1   C2   N3   180.00   0.0  0
 D0A  CONST_31  C8   N9   C2   N3   180.00   0.0  0
 D0A  CONST_32  N9   C2   N3   C4   180.00   0.0  0
 D0A  CONST_33  C7   C1   C6   N5   180.00   0.0  0
 D0A  CONST_34  N23  C11  C4   N5     0.00   0.0  0
 D0A  CONST_35  N9   C2   C1   C6   180.00   0.0  0
 D0A  CONST_36  C8   C7   C1   C6   180.00   0.0  0
 D0A  CONST_37  N9   C2   C1   C7     0.00   0.0  0
 D0A  CONST_38  F18  C17  C12  C13  180.00   0.0  0
 D0A  CONST_39  N10  C12  C17  C16  180.00   0.0  0
 D0A  CONST_40  C24  C22  C21  C20  180.00   0.0  0
 D0A  CONST_41  C11  N23  C22  C24  180.00   0.0  0
 D0A  CONST_42  N10  C6   C1   C2   180.00   0.0  0
 D0A  CONST_43  N10  C6   N5   C4   180.00   0.0  0
 D0A  CONST_44  N10  C6   C1   C7     0.00   0.0  0
 D0A  CONST_45  C14  C13  C12  N10  180.00   0.0  0
 D0A  CONST_46  F18  C17  C16  N15  180.00   0.0  0
 D0A  CONST_47  H32  C13  C12  C17  180.00   0.0  0
 D0A  CONST_48  H33  C14  N15  C16  180.00   0.0  0
 D0A  CONST_49  H37  C21  C20  C19  180.00   0.0  0
 D0A  CONST_50  H35  C19  C20  C21  180.00   0.0  0
 D0A  CONST_51  H36  C20  C21  C22  180.00   0.0  0
 D0A  CONST_52  H34  C16  C17  C12  180.00   0.0  0
 D0A  CONST_53  H30  N9   C2   C1   180.00   0.0  0
 D0A  CONST_54  H29  C8   C7   C1   180.00   0.0  0
 D0A  CONST_55  H28  C7   C1   C2   180.00   0.0  0
 D0A  Var_01    C6   N10  C12  C13   -0.26  30.0  2
 D0A  Var_02    N5   C6   N10  C12   -1.41  30.0  2
 D0A  Var_03    F27  C24  C22  C21  -17.17  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
 D0A  plan-1  C19  0.020
 D0A  plan-1  C20  0.020
 D0A  plan-1  C21  0.020
 D0A  plan-1  C22  0.020
 D0A  plan-1  C24  0.020
 D0A  plan-1  C11  0.020
 D0A  plan-1  C4   0.020
 D0A  plan-1  N23  0.020
 D0A  plan-1  H35  0.020
 D0A  plan-1  H36  0.020
 D0A  plan-1  H37  0.020
 D0A  plan-2  C13  0.020
 D0A  plan-2  C17  0.020
 D0A  plan-2  C16  0.020
 D0A  plan-2  C12  0.020
 D0A  plan-2  N10  0.020
 D0A  plan-2  C14  0.020
 D0A  plan-2  N15  0.020
 D0A  plan-2  F18  0.020
 D0A  plan-2  H32  0.020
 D0A  plan-2  H34  0.020
 D0A  plan-2  H33  0.020
 D0A  plan-3  C11  0.020
 D0A  plan-3  C1   0.020
 D0A  plan-3  C2   0.020
 D0A  plan-3  N3   0.020
 D0A  plan-3  C4   0.020
 D0A  plan-3  N5   0.020
 D0A  plan-3  C6   0.020
 D0A  plan-3  C7   0.020
 D0A  plan-3  C8   0.020
 D0A  plan-3  N9   0.020
 D0A  plan-3  N10  0.020
 D0A  plan-3  H28  0.020
 D0A  plan-3  H29  0.020
 D0A  plan-3  H30  0.020

