# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 18:02:35 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](3,4-difluorophenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc([C@@H]2CN(CC(F)(F)C2)C(=O)c3ccc(F)c(F)c3)n4ncnc4n1
#
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
 7P4  7P4  '[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](3,4-difluorophenyl)methanone'  ligand  43  28  .  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_7P4
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
 7P4  N3   N  N     0  -0.454  -5.7288  -0.8933   0.1960
 7P4  C4   C  CR56  0   0.579  -5.1516   0.2508   0.5626
 7P4  C6   C  CR6   0   0.539  -2.9760  -0.4236  -0.1702
 7P4  C8   C  CR15  0   0.048  -4.6713   2.1529   1.2671
 7P4  C13  C  CR6   0   0.775   0.1880   1.3165  -1.4604
 7P4  C20  C  CR16  0  -0.421   3.6839  -1.2247  -0.2477
 7P4  C21  C  CR6   0   0.414   5.0388  -1.0174  -0.3732
 7P4  C22  C  CR16  0  -0.394   4.9500   0.7981   1.1941
 7P4  C26  C  CR6   0   0.403   5.6705  -0.0150   0.3457
 7P4  C23  C  CR16  0  -0.252   3.5802   0.6102   1.3104
 7P4  C18  C  CR6   0  -0.077   2.9443  -0.3932   0.5882
 7P4  C1   C  CR16  0  -0.448  -3.5649  -1.5942  -0.5439
 7P4  C2   C  CR6   0   0.276  -4.9558  -1.8019  -0.3482
 7P4  C12  C  C     0  -0.562  -1.2890   1.0202  -1.3459
 7P4  C16  C  C     0  -0.304  -0.7856   0.1284   0.9660
 7P4  C14  C  C     0  -0.450   0.8619   1.5282  -0.1142
 7P4  C11  C  CR16  0  -0.404  -1.5207  -0.1353  -0.3584
 7P4  N7   N  N     0  -0.492  -5.7045   1.3116   1.1241
 7P4  N9   N  N     0  -0.280  -3.5037   1.7157   0.8428
 7P4  N5   N  N     0  -0.410  -3.8089   0.4917   0.3894
 7P4  N15  N  NR6   0  -0.468   0.6249   0.3572   0.7060
 7P4  O19  O  O     0  -0.458   1.1345  -1.8249   1.0350
 7P4  F28  F  F     0  -0.302   5.7671  -1.7886  -1.1841
 7P4  F25  F  F     0  -0.338   0.3884   2.4151  -2.2410
 7P4  H1   H  HCR5  0   0.283  -4.7681   3.1359   1.7030
 7P4  H5   H  HCR6  0   0.297   3.2131  -2.0236  -0.8062
 7P4  H6   H  HCR6  0   0.301   5.4564   1.5697   1.7583
 7P4  H7   H  HCR6  0   0.288   3.0159   1.2464   1.9796
 7P4  H8   H  HCR6  0   0.294  -2.9643  -2.3685  -0.9994
 7P4  H9   H  H     0   0.283  -1.7870   1.9256  -0.9942
 7P4  H10  H  H     0   0.297  -1.6972   0.7709  -2.3275
 7P4  H11  H  H     0   0.282  -1.1817   1.0189   1.4553
 7P4  H12  H  H     0   0.292  -0.9035  -0.7109   1.6463
 7P4  H13  H  H     0   0.312   1.9236   1.7152  -0.2592
 7P4  H14  H  H     0   0.292   0.4331   2.4061   0.3739
 7P4  H15  H  HCR6  0   0.307  -1.1031  -1.0492  -0.7891
 7P4  C10  C  CH3   0  -0.737  -5.5655  -3.0938  -0.7791
 7P4  F24  F  F     0  -0.347   0.8204   0.2797  -2.0966
 7P4  C17  C  C     0   0.539   1.4913  -0.6892   0.7749
 7P4  F27  F  F     0  -0.299   6.9869   0.1491   0.2064
 7P4  H2   H  HCH3  0   0.266  -5.0803  -3.9324  -0.2779
 7P4  H3   H  HCH3  0   0.262  -6.6294  -3.1179  -0.5577
 7P4  H4   H  HCH3  0   0.266  -5.4256  -3.2401  -1.8514

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
 7P4  F25  C13  single    1.363  0.020  1.363
 7P4  C14  C13  single    1.520  0.020  1.520
 7P4  C14  N15  single    1.449  0.020  1.449
 7P4  O19  C17  double    1.219  0.020  1.219
 7P4  C13  F24  single    1.371  0.020  1.371
 7P4  C13  C12  single    1.511  0.020  1.511
 7P4  N15  C17  single    1.360  0.020  1.360
 7P4  N15  C16  single    1.452  0.020  1.452
 7P4  C17  C18  single    1.494  0.020  1.494
 7P4  C12  C11  single    1.538  0.020  1.538
 7P4  C16  C11  single    1.538  0.020  1.538
 7P4  C23  C18  aromatic  1.390  0.020  1.390
 7P4  C23  C22  aromatic  1.388  0.020  1.388
 7P4  C18  C20  aromatic  1.392  0.020  1.392
 7P4  C11  C6   single    1.496  0.020  1.496
 7P4  C22  C26  aromatic  1.378  0.020  1.378
 7P4  C20  C21  aromatic  1.376  0.020  1.376
 7P4  C1   C6   aromatic  1.363  0.020  1.363
 7P4  C1   C2   aromatic  1.420  0.020  1.420
 7P4  C6   N5   aromatic  1.358  0.020  1.358
 7P4  C26  C21  aromatic  1.386  0.020  1.386
 7P4  C26  F27  single    1.334  0.020  1.334
 7P4  C21  F28  single    1.335  0.020  1.335
 7P4  C10  C2   single    1.492  0.020  1.492
 7P4  C2   N3   aromatic  1.311  0.020  1.311
 7P4  N5   N9   aromatic  1.340  0.020  1.340
 7P4  N5   C4   aromatic  1.375  0.020  1.375
 7P4  N9   C8   aromatic  1.317  0.020  1.317
 7P4  N3   C4   aromatic  1.333  0.020  1.333
 7P4  C4   N7   aromatic  1.322  0.020  1.322
 7P4  C8   N7   aromatic  1.340  0.020  1.340
 7P4  C8   H1   single    0.930  0.020  1.080
 7P4  C10  H2   single    0.970  0.020  1.090
 7P4  C10  H3   single    0.970  0.020  1.090
 7P4  C10  H4   single    0.970  0.020  1.090
 7P4  C20  H5   single    0.930  0.020  1.080
 7P4  C22  H6   single    0.930  0.020  1.080
 7P4  C23  H7   single    0.930  0.020  1.080
 7P4  C1   H8   single    0.930  0.020  1.080
 7P4  C12  H9   single    0.970  0.020  1.090
 7P4  C12  H10  single    0.970  0.020  1.090
 7P4  C16  H11  single    0.970  0.020  1.090
 7P4  C16  H12  single    0.970  0.020  1.090
 7P4  C14  H13  single    0.970  0.020  1.090
 7P4  C14  H14  single    0.970  0.020  1.090
 7P4  C11  H15  single    0.970  0.020  1.090

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
 7P4  C2   N3   C4   116.97  3.000
 7P4  N5   C4   N7   108.75  3.000
 7P4  N7   C4   N3   128.66  3.000
 7P4  N5   C4   N3   122.59  3.000
 7P4  N5   C6   C11  121.24  3.000
 7P4  N5   C6   C1   115.27  3.000
 7P4  C11  C6   C1   123.49  3.000
 7P4  H1   C8   N9   120.79  3.000
 7P4  H1   C8   N7   123.06  3.000
 7P4  N9   C8   N7   116.15  3.000
 7P4  F25  C13  F24  106.02  3.000
 7P4  F24  C13  C14  108.16  3.000
 7P4  F25  C13  C14  109.26  3.000
 7P4  F24  C13  C12  109.74  3.000
 7P4  C14  C13  C12  113.18  3.000
 7P4  F25  C13  C12  110.20  3.000
 7P4  H5   C20  C18  121.31  3.000
 7P4  H5   C20  C21  119.49  3.000
 7P4  C18  C20  C21  119.20  3.000
 7P4  F28  C21  C26  118.96  3.000
 7P4  F28  C21  C20  120.36  3.000
 7P4  C26  C21  C20  120.68  3.000
 7P4  H6   C22  C23  121.00  3.000
 7P4  H6   C22  C26  119.80  3.000
 7P4  C23  C22  C26  119.19  3.000
 7P4  F27  C26  C22  120.50  3.000
 7P4  F27  C26  C21  118.99  3.000
 7P4  C22  C26  C21  120.51  3.000
 7P4  H7   C23  C18  120.47  3.000
 7P4  H7   C23  C22  119.14  3.000
 7P4  C18  C23  C22  120.38  3.000
 7P4  C23  C18  C20  120.01  3.000
 7P4  C20  C18  C17  118.25  3.000
 7P4  C23  C18  C17  121.51  3.000
 7P4  H8   C1   C2   119.85  3.000
 7P4  H8   C1   C6   119.40  3.000
 7P4  C2   C1   C6   120.75  3.000
 7P4  C1   C2   C10  119.15  3.000
 7P4  C10  C2   N3   118.61  3.000
 7P4  C1   C2   N3   122.23  3.000
 7P4  H10  C12  H9   107.97  3.000
 7P4  H10  C12  C11  110.45  3.000
 7P4  H9   C12  C11  110.35  3.000
 7P4  H10  C12  C13  110.01  3.000
 7P4  H9   C12  C13  107.93  3.000
 7P4  C11  C12  C13  110.08  3.000
 7P4  H12  C16  H11  108.08  3.000
 7P4  H12  C16  N15  109.83  3.000
 7P4  H11  C16  N15  107.72  3.000
 7P4  H12  C16  C11  110.79  3.000
 7P4  H11  C16  C11  110.66  3.000
 7P4  N15  C16  C11  109.70  3.000
 7P4  H14  C14  H13  107.73  3.000
 7P4  H14  C14  N15  109.41  3.000
 7P4  H13  C14  N15  111.96  3.000
 7P4  H14  C14  C13  109.49  3.000
 7P4  H13  C14  C13  109.79  3.000
 7P4  N15  C14  C13  108.43  3.000
 7P4  H15  C11  C16  107.46  3.000
 7P4  H15  C11  C12  108.52  3.000
 7P4  C16  C11  C12  110.63  3.000
 7P4  H15  C11  C6   105.07  3.000
 7P4  C16  C11  C6   112.95  3.000
 7P4  C12  C11  C6   111.86  3.000
 7P4  C8   N7   C4   103.10  3.000
 7P4  N5   N9   C8   102.13  3.000
 7P4  N9   N5   C6   127.96  3.000
 7P4  N9   N5   C4   109.86  3.000
 7P4  C6   N5   C4   122.18  3.000
 7P4  C14  N15  C16  112.80  3.000
 7P4  C16  N15  C17  119.23  3.000
 7P4  C14  N15  C17  123.10  3.000
 7P4  H4   C10  H3   108.83  3.000
 7P4  H4   C10  H2   106.94  3.000
 7P4  H3   C10  H2   108.95  3.000
 7P4  H4   C10  C2   110.33  3.000
 7P4  H3   C10  C2   111.12  3.000
 7P4  H2   C10  C2   110.56  3.000
 7P4  O19  C17  N15  122.77  3.000
 7P4  N15  C17  C18  117.42  3.000
 7P4  O19  C17  C18  119.73  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
 7P4  CONST_01  C6   C1   C2   N3      0.00   0.0  0
 7P4  CONST_02  C6   N5   C4   N3      0.00   0.0  0
 7P4  CONST_03  N9   N5   C4   N3    180.00   0.0  0
 7P4  CONST_04  C8   N7   C4   N3    180.00   0.0  0
 7P4  CONST_05  C1   C6   N5   C4      0.00   0.0  0
 7P4  CONST_06  C8   N9   N5   C4      0.00   0.0  0
 7P4  CONST_07  C1   C2   N3   C4      0.00   0.0  0
 7P4  CONST_08  N9   C8   N7   C4      0.00   0.0  0
 7P4  CONST_09  C8   N9   N5   C6    180.00   0.0  0
 7P4  CONST_10  N7   C4   N5   C6    180.00   0.0  0
 7P4  CONST_11  N5   C4   N7   C8      0.00   0.0  0
 7P4  CONST_12  C22  C23  C18  C20     0.00   0.0  0
 7P4  CONST_13  C22  C26  C21  C20     0.00   0.0  0
 7P4  CONST_14  C23  C18  C20  C21     0.00   0.0  0
 7P4  CONST_15  C23  C22  C26  C21     0.00   0.0  0
 7P4  CONST_16  C18  C23  C22  C26     0.00   0.0  0
 7P4  CONST_17  C18  C20  C21  C26     0.00   0.0  0
 7P4  CONST_18  N9   N5   C6   C1    180.00   0.0  0
 7P4  CONST_19  N5   C6   C1   C2      0.00   0.0  0
 7P4  CONST_20  N5   C4   N3   C2      0.00   0.0  0
 7P4  CONST_21  N7   C4   N3   C2    180.00   0.0  0
 7P4  CONST_22  N9   N5   C4   N7      0.00   0.0  0
 7P4  CONST_23  N5   N9   C8   N7      0.00   0.0  0
 7P4  CONST_24  C11  C6   N5   C4    180.00   0.0  0
 7P4  CONST_25  C11  C6   C1   C2    180.00   0.0  0
 7P4  CONST_26  N9   N5   C6   C11     0.00   0.0  0
 7P4  CONST_27  C10  C2   N3   C4    180.00   0.0  0
 7P4  CONST_28  C10  C2   C1   C6    180.00   0.0  0
 7P4  CONST_29  C22  C23  C18  C17   180.00   0.0  0
 7P4  CONST_30  C21  C20  C18  C17   180.00   0.0  0
 7P4  CONST_31  F27  C26  C21  C20   180.00   0.0  0
 7P4  CONST_32  F28  C21  C26  C22   180.00   0.0  0
 7P4  CONST_33  F27  C26  C22  C23   180.00   0.0  0
 7P4  CONST_34  F28  C21  C20  C18   180.00   0.0  0
 7P4  CONST_36  C16  N15  C17  C18   180.00   0.0  0
 7P4  CONST_37  H8   C1   C2   N3    180.00   0.0  0
 7P4  CONST_38  H1   C8   N7   C4    180.00   0.0  0
 7P4  CONST_39  H7   C23  C18  C20   180.00   0.0  0
 7P4  CONST_40  H6   C22  C26  C21   180.00   0.0  0
 7P4  CONST_41  H5   C20  C21  C26   180.00   0.0  0
 7P4  CONST_42  O19  C17  N15  C16     0.00   0.0  0
 7P4  Var_01    C16  N15  C14  C13   -61.57  30.0  1
 7P4  Var_02    N15  C14  C13  C12    56.16  30.0  1
 7P4  Var_03    C11  C12  C13  C14   -51.93  30.0  1
 7P4  Var_04    C11  C16  N15  C14    62.45  30.0  1
 7P4  Var_05    N15  C17  C18  C20  -134.66  30.0  2
 7P4  Var_06    H2   C10  C2   N3   -122.05  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7P4  chir_01  C11  C12  C16  C6  negativ

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
 7P4  plan-1  C20  0.020
 7P4  plan-1  C21  0.020
 7P4  plan-1  C22  0.020
 7P4  plan-1  C26  0.020
 7P4  plan-1  C23  0.020
 7P4  plan-1  C18  0.020
 7P4  plan-1  F28  0.020
 7P4  plan-1  H5   0.020
 7P4  plan-1  H6   0.020
 7P4  plan-1  H7   0.020
 7P4  plan-1  C17  0.020
 7P4  plan-1  F27  0.020
 7P4  plan-2  N3   0.020
 7P4  plan-2  C4   0.020
 7P4  plan-2  C6   0.020
 7P4  plan-2  C8   0.020
 7P4  plan-2  C1   0.020
 7P4  plan-2  C2   0.020
 7P4  plan-2  C11  0.020
 7P4  plan-2  N7   0.020
 7P4  plan-2  N9   0.020
 7P4  plan-2  N5   0.020
 7P4  plan-2  H1   0.020
 7P4  plan-2  H8   0.020
 7P4  plan-2  C10  0.020
 7P4  plan-3  C18  0.020
 7P4  plan-3  C16  0.020
 7P4  plan-3  C14  0.020
 7P4  plan-3  N15  0.020
 7P4  plan-3  O19  0.020
 7P4  plan-3  C17  0.020

