# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:06:10 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (3-chloro-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]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(Cl)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
 7OY  7OY  (3-chloro-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]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_7OY
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
 7OY  N3    N   N     0  -0.453  -5.9261   1.0668  -0.1516
 7OY  C4    C   CR56  0   0.577  -5.4316  -0.1411  -0.4166
 7OY  C6    C   CR6   0   0.541  -3.1944   0.4663   0.1749
 7OY  C8    C   CR15  0   0.048  -5.0902  -2.1307  -0.9363
 7OY  C13   C   CR6   0   0.775  -0.0831  -1.3281   1.5220
 7OY  C20   C   CR16  0  -0.221   3.4494   0.9498   0.0604
 7OY  C21   C   CR6   0  -0.220   4.8055   0.7133   0.1955
 7OY  C22   C   CR16  0  -0.404   4.6263  -1.2157  -1.2382
 7OY  C23   C   CR16  0  -0.236   3.2644  -0.9887  -1.3559
 7OY  C18   C   CR6   0  -0.093   2.6718   0.0883  -0.7046
 7OY  C27   C   CR6   0   0.619   5.3820  -0.3659  -0.4571
 7OY  C1    C   CR16  0  -0.449  -3.6989   1.7041   0.4431
 7OY  C2    C   CR6   0   0.275  -5.0804   1.9775   0.2688
 7OY  C12   C   C     0  -0.562  -1.5476  -0.9693   1.4225
 7OY  C16   C   C     0  -0.307  -1.0809  -0.3154  -0.9723
 7OY  C14   C   C     0  -0.452   0.5343  -1.6923   0.1810
 7OY  C11   C   CR16  0  -0.405  -1.7524   0.1089   0.3457
 7OY  N7    N   N     0  -0.493  -6.0664  -1.2172  -0.8479
 7OY  N9    N   N     0  -0.281  -3.8838  -1.7267  -0.5960
 7OY  N5    N   N     0  -0.410  -4.0994  -0.4464  -0.2615
 7OY  N15   N   NR6   0  -0.465   0.3261  -0.5875  -0.7344
 7OY  O19   O   O     0  -0.457   0.9041   1.5447  -1.2342
 7OY  F28   F   F     0  -0.288   6.6899  -0.5764  -0.3237
 7OY  F26   F   F     0  -0.337   0.0895  -2.3611   2.3932
 7OY  H1    H   HCR5  0   0.283  -5.2607  -3.1446  -1.2661
 7OY  H5    H   HCR6  0   0.295   3.0037   1.7997   0.5596
 7OY  H6    H   HCR6  0   0.300   5.1001  -2.0445  -1.7469
 7OY  H7    H   HCR6  0   0.290   2.6701  -1.6518  -1.9709
 7OY  H8    H   HCR6  0   0.294  -3.0359   2.4811   0.7958
 7OY  H9    H   H     0   0.283  -2.0970  -1.8742   1.1583
 7OY  H10   H   H     0   0.297  -1.9143  -0.6222   2.3905
 7OY  H11   H   H     0   0.282  -1.5363  -1.2274  -1.3593
 7OY  H12   H   H     0   0.293  -1.1863   0.4592  -1.7271
 7OY  H13   H   H     0   0.313   1.5897  -1.9224   0.3105
 7OY  H14   H   H     0   0.293   0.0466  -2.5855  -0.2141
 7OY  H15   H   HCR6  0   0.307  -1.2668   1.0304   0.6773
 7OY  C10   C   CH3   0  -0.731  -5.5982   3.3490   0.5496
 7OY  F25   F   F     0  -0.347   0.6192  -0.2726   2.0441
 7OY  C17   C   C     0   0.535   1.2271   0.4197  -0.8952
 7OY  CL24  CL  CL    0  -0.083   5.7925   1.7442   1.1571
 7OY  H2    H   HCH3  0   0.271  -5.3838   4.0059  -0.2962
 7OY  H3    H   HCH3  0   0.262  -6.6746   3.3363   0.7032
 7OY  H4    H   HCH3  0   0.259  -5.1143   3.7826   1.4236

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
 7OY  F26  C13   single    1.362  0.020  1.362
 7OY  C14  C13   single    1.521  0.020  1.521
 7OY  C14  N15   single    1.450  0.020  1.450
 7OY  O19  C17   double    1.218  0.020  1.218
 7OY  C13  F25   single    1.371  0.020  1.371
 7OY  C13  C12   single    1.511  0.020  1.511
 7OY  C17  N15   single    1.361  0.020  1.361
 7OY  C17  C18   single    1.494  0.020  1.494
 7OY  N15  C16   single    1.453  0.020  1.453
 7OY  C12  C11   single    1.538  0.020  1.538
 7OY  C23  C18   aromatic  1.391  0.020  1.391
 7OY  C23  C22   aromatic  1.386  0.020  1.386
 7OY  C16  C11   single    1.539  0.020  1.539
 7OY  C18  C20   aromatic  1.390  0.020  1.390
 7OY  C11  C6    single    1.495  0.020  1.495
 7OY  C22  C27   aromatic  1.380  0.020  1.380
 7OY  C20  C21   aromatic  1.383  0.020  1.383
 7OY  C1   C6    aromatic  1.363  0.020  1.363
 7OY  C1   C2    aromatic  1.419  0.020  1.419
 7OY  C6   N5    aromatic  1.357  0.020  1.357
 7OY  C27  C21   aromatic  1.387  0.020  1.387
 7OY  C27  F28   single    1.331  0.020  1.331
 7OY  C21  CL24  single    1.721  0.020  1.721
 7OY  C10  C2    single    1.493  0.020  1.493
 7OY  C2   N3    aromatic  1.312  0.020  1.312
 7OY  N5   N9    aromatic  1.341  0.020  1.341
 7OY  N5   C4    aromatic  1.376  0.020  1.376
 7OY  N9   C8    aromatic  1.317  0.020  1.317
 7OY  N3   C4    aromatic  1.332  0.020  1.332
 7OY  C4   N7    aromatic  1.322  0.020  1.322
 7OY  C8   N7    aromatic  1.340  0.020  1.340
 7OY  C8   H1    single    0.930  0.020  1.080
 7OY  C10  H2    single    0.970  0.020  1.090
 7OY  C10  H3    single    0.970  0.020  1.090
 7OY  C10  H4    single    0.970  0.020  1.090
 7OY  C20  H5    single    0.930  0.020  1.080
 7OY  C22  H6    single    0.930  0.020  1.080
 7OY  C23  H7    single    0.930  0.020  1.080
 7OY  C1   H8    single    0.930  0.020  1.080
 7OY  C12  H9    single    0.970  0.020  1.090
 7OY  C12  H10   single    0.970  0.020  1.090
 7OY  C16  H11   single    0.970  0.020  1.090
 7OY  C16  H12   single    0.970  0.020  1.090
 7OY  C14  H13   single    0.970  0.020  1.090
 7OY  C14  H14   single    0.970  0.020  1.090
 7OY  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
 7OY  C2    N3   C4   117.00  3.000
 7OY  N5    C4   N7   108.74  3.000
 7OY  N7    C4   N3   128.68  3.000
 7OY  N5    C4   N3   122.58  3.000
 7OY  N5    C6   C11  121.26  3.000
 7OY  N5    C6   C1   115.28  3.000
 7OY  C11   C6   C1   123.46  3.000
 7OY  H1    C8   N9   120.77  3.000
 7OY  H1    C8   N7   123.05  3.000
 7OY  N9    C8   N7   116.18  3.000
 7OY  F26   C13  F25  105.98  3.000
 7OY  F25   C13  C14  108.19  3.000
 7OY  F26   C13  C14  109.32  3.000
 7OY  F25   C13  C12  109.81  3.000
 7OY  C14   C13  C12  113.10  3.000
 7OY  F26   C13  C12  110.18  3.000
 7OY  H5    C20  C18  120.70  3.000
 7OY  H5    C20  C21  119.55  3.000
 7OY  C18   C20  C21  119.75  3.000
 7OY  CL24  C21  C27  119.39  3.000
 7OY  CL24  C21  C20  120.96  3.000
 7OY  C27   C21  C20  119.65  3.000
 7OY  H6    C22  C27  119.89  3.000
 7OY  H6    C22  C23  121.06  3.000
 7OY  C27   C22  C23  119.05  3.000
 7OY  H7    C23  C18  120.43  3.000
 7OY  H7    C23  C22  119.19  3.000
 7OY  C18   C23  C22  120.38  3.000
 7OY  C23   C18  C20  119.95  3.000
 7OY  C20   C18  C17  118.26  3.000
 7OY  C23   C18  C17  121.59  3.000
 7OY  F28   C27  C22  119.83  3.000
 7OY  F28   C27  C21  118.96  3.000
 7OY  C22   C27  C21  121.20  3.000
 7OY  H8    C1   C2   119.93  3.000
 7OY  H8    C1   C6   119.34  3.000
 7OY  C2    C1   C6   120.73  3.000
 7OY  C1    C2   C10  119.45  3.000
 7OY  C10   C2   N3   118.32  3.000
 7OY  C1    C2   N3   122.22  3.000
 7OY  H10   C12  H9   108.02  3.000
 7OY  H10   C12  C11  110.68  3.000
 7OY  H9    C12  C11  110.18  3.000
 7OY  H10   C12  C13  110.03  3.000
 7OY  H9    C12  C13  107.88  3.000
 7OY  C11   C12  C13  109.98  3.000
 7OY  H12   C16  H11  108.01  3.000
 7OY  H12   C16  N15  109.95  3.000
 7OY  H11   C16  N15  107.82  3.000
 7OY  H12   C16  C11  110.86  3.000
 7OY  H11   C16  C11  110.63  3.000
 7OY  N15   C16  C11  109.51  3.000
 7OY  H14   C14  H13  107.67  3.000
 7OY  H14   C14  N15  109.32  3.000
 7OY  H13   C14  N15  112.06  3.000
 7OY  H14   C14  C13  109.50  3.000
 7OY  H13   C14  C13  109.85  3.000
 7OY  N15   C14  C13  108.42  3.000
 7OY  H15   C11  C16  107.36  3.000
 7OY  H15   C11  C12  108.64  3.000
 7OY  C16   C11  C12  110.38  3.000
 7OY  H15   C11  C6   105.16  3.000
 7OY  C16   C11  C6   112.88  3.000
 7OY  C12   C11  C6   112.09  3.000
 7OY  C8    N7   C4   103.10  3.000
 7OY  N5    N9   C8   102.13  3.000
 7OY  N9    N5   C6   127.96  3.000
 7OY  N9    N5   C4   109.85  3.000
 7OY  C6    N5   C4   122.19  3.000
 7OY  C14   N15  C16  112.66  3.000
 7OY  C16   N15  C17  118.89  3.000
 7OY  C14   N15  C17  122.92  3.000
 7OY  H4    C10  H3   109.34  3.000
 7OY  H4    C10  H2   107.14  3.000
 7OY  H3    C10  H2   108.11  3.000
 7OY  H4    C10  C2   111.26  3.000
 7OY  H3    C10  C2   111.05  3.000
 7OY  H2    C10  C2   109.81  3.000
 7OY  O19   C17  N15  122.73  3.000
 7OY  N15   C17  C18  117.44  3.000
 7OY  O19   C17  C18  119.77  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
 7OY  CONST_01  C6    C1   C2   N3      0.00   0.0  0
 7OY  CONST_02  C6    N5   C4   N3      0.00   0.0  0
 7OY  CONST_03  N9    N5   C4   N3    180.00   0.0  0
 7OY  CONST_04  C8    N7   C4   N3    180.00   0.0  0
 7OY  CONST_05  C1    C6   N5   C4      0.00   0.0  0
 7OY  CONST_06  C8    N9   N5   C4      0.00   0.0  0
 7OY  CONST_07  C1    C2   N3   C4      0.00   0.0  0
 7OY  CONST_08  N9    C8   N7   C4      0.00   0.0  0
 7OY  CONST_09  C8    N9   N5   C6    180.00   0.0  0
 7OY  CONST_10  N7    C4   N5   C6    180.00   0.0  0
 7OY  CONST_11  N5    C4   N7   C8      0.00   0.0  0
 7OY  CONST_12  C22   C23  C18  C20     0.00   0.0  0
 7OY  CONST_13  C22   C27  C21  C20     0.00   0.0  0
 7OY  CONST_14  C23   C18  C20  C21     0.00   0.0  0
 7OY  CONST_15  C23   C22  C27  C21     0.00   0.0  0
 7OY  CONST_16  C27   C22  C23  C18     0.00   0.0  0
 7OY  CONST_17  C27   C21  C20  C18     0.00   0.0  0
 7OY  CONST_18  N9    N5   C6   C1    180.00   0.0  0
 7OY  CONST_19  N5    C6   C1   C2      0.00   0.0  0
 7OY  CONST_20  N5    C4   N3   C2      0.00   0.0  0
 7OY  CONST_21  N7    C4   N3   C2    180.00   0.0  0
 7OY  CONST_22  N9    N5   C4   N7      0.00   0.0  0
 7OY  CONST_23  N5    N9   C8   N7      0.00   0.0  0
 7OY  CONST_24  C11   C6   N5   C4    180.00   0.0  0
 7OY  CONST_25  C11   C6   C1   C2    180.00   0.0  0
 7OY  CONST_26  N9    N5   C6   C11     0.00   0.0  0
 7OY  CONST_27  C10   C2   N3   C4    180.00   0.0  0
 7OY  CONST_28  C10   C2   C1   C6    180.00   0.0  0
 7OY  CONST_29  C22   C23  C18  C17   180.00   0.0  0
 7OY  CONST_30  C21   C20  C18  C17   180.00   0.0  0
 7OY  CONST_31  F28   C27  C21  C20   180.00   0.0  0
 7OY  CONST_32  CL24  C21  C27  C22   180.00   0.0  0
 7OY  CONST_33  F28   C27  C22  C23   180.00   0.0  0
 7OY  CONST_34  CL24  C21  C20  C18   180.00   0.0  0
 7OY  CONST_36  C16   N15  C17  C18   180.00   0.0  0
 7OY  CONST_37  H8    C1   C2   N3    180.00   0.0  0
 7OY  CONST_38  H1    C8   N7   C4    180.00   0.0  0
 7OY  CONST_39  H7    C23  C18  C20   180.00   0.0  0
 7OY  CONST_40  H6    C22  C27  C21   180.00   0.0  0
 7OY  CONST_41  H5    C20  C18  C23   180.00   0.0  0
 7OY  CONST_42  O19   C17  N15  C16     0.00   0.0  0
 7OY  Var_01    C16   N15  C14  C13   -61.67  30.0  1
 7OY  Var_02    N15   C14  C13  C12    56.19  30.0  1
 7OY  Var_03    C11   C12  C13  C14   -52.22  30.0  1
 7OY  Var_04    C11   C16  N15  C14    62.86  30.0  1
 7OY  Var_05    N15   C17  C18  C20  -134.29  30.0  2
 7OY  Var_06    H2    C10  C2   N3    -99.40  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
 7OY  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
 7OY  plan-1  C20   0.020
 7OY  plan-1  C21   0.020
 7OY  plan-1  C22   0.020
 7OY  plan-1  C23   0.020
 7OY  plan-1  C18   0.020
 7OY  plan-1  C27   0.020
 7OY  plan-1  F28   0.020
 7OY  plan-1  H5    0.020
 7OY  plan-1  H6    0.020
 7OY  plan-1  H7    0.020
 7OY  plan-1  C17   0.020
 7OY  plan-1  CL24  0.020
 7OY  plan-2  N3    0.020
 7OY  plan-2  C4    0.020
 7OY  plan-2  C6    0.020
 7OY  plan-2  C8    0.020
 7OY  plan-2  C1    0.020
 7OY  plan-2  C2    0.020
 7OY  plan-2  C11   0.020
 7OY  plan-2  N7    0.020
 7OY  plan-2  N9    0.020
 7OY  plan-2  N5    0.020
 7OY  plan-2  H1    0.020
 7OY  plan-2  H8    0.020
 7OY  plan-2  C10   0.020
 7OY  plan-3  C18   0.020
 7OY  plan-3  C16   0.020
 7OY  plan-3  C14   0.020
 7OY  plan-3  N15   0.020
 7OY  plan-3  O19   0.020
 7OY  plan-3  C17   0.020

