# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:11:49 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 4,4,4-tris(fluoranyl)-1-[4-(3-phenyl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)CCC(=O)N1CCC(CC1)c2onc(n2)c3ccccc3
#
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
 GH5  GH5  4,4,4-tris(fluoranyl)-1-[4-(3-phenyl-1,2,4-oxadiazol-5-yl)piperidin-1-yl]butan-1-one  ligand  43  25  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GH5
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
 GH5  C4   C  C     0   0.593  -3.1796   1.2146  -0.2931
 GH5  C14  C  CR16  0  -0.239   7.5137  -1.5435  -0.6810
 GH5  C5   C  CH2   0  -0.335  -1.4714   0.7018   1.4456
 GH5  C6   C  CH2   0  -0.419  -0.1852   0.0194   0.9988
 GH5  C11  C  CR5   0   0.321   4.0140  -0.2577  -0.2661
 GH5  C7   C  CH1   0  -0.409   0.8113   1.0669   0.4824
 GH5  C8   C  CH2   0  -0.422   0.1664   1.9229  -0.6143
 GH5  C9   C  CH2   0  -0.325  -1.1348   2.5298  -0.1052
 GH5  C10  C  CR5   0   0.574   2.0759   0.4341   0.0315
 GH5  C12  C  CR6   0   0.001   5.4510  -0.4537  -0.0811
 GH5  C13  C  CR16  0  -0.281   6.1540  -1.3636  -0.8720
 GH5  N1   N  NT    0  -0.456  -2.0349   1.4920   0.3671
 GH5  N2   N  N     0  -0.156   3.3248  -0.8563  -1.1915
 GH5  C3   C  CH2   0  -0.639  -4.0028   0.0448   0.2179
 GH5  N3   N  N     0  -0.463   3.2615   0.5663   0.5230
 GH5  C1   C  CT    0   1.002  -6.0892  -1.3117  -0.1396
 GH5  F2   F  F     0  -0.312  -7.1990  -1.4634  -0.8786
 GH5  F3   F  F     0  -0.316  -6.4927  -1.1846   1.1355
 GH5  C2   C  CH2   0  -0.634  -5.2670  -0.1437  -0.6077
 GH5  O1   O  O     0  -0.499  -3.5552   1.8722  -1.2541
 GH5  O2   O  O     0  -0.327   2.0503  -0.4036  -0.9977
 GH5  C15  C  CR16  0  -0.251   8.1842  -0.8190   0.2979
 GH5  C16  C  CR16  0  -0.240   7.4883   0.0880   1.0852
 GH5  C17  C  CR16  0  -0.288   6.1260   0.2712   0.8988
 GH5  H2   H  HCH2  0   0.285  -2.1779  -0.0391   1.8082
 GH5  H3   H  HCH2  0   0.256  -1.2598   1.3687   2.2874
 GH5  H4   H  HCH2  0   0.265   0.2428  -0.5249   1.8426
 GH5  H5   H  HCH2  0   0.248  -0.4115  -0.7099   0.2168
 GH5  H6   H  HCH1  0   0.288   1.0890   1.7185   1.3161
 GH5  H7   H  HCH2  0   0.264   0.8424   2.7243  -0.9185
 GH5  H8   H  HCH2  0   0.247  -0.0439   1.3160  -1.4987
 GH5  H9   H  HCH2  0   0.249  -0.9303   3.2161   0.7231
 GH5  H10  H  HCH2  0   0.274  -1.6184   3.1041  -0.8901
 GH5  H11  H  HCR6  0   0.261   5.6394  -1.9328  -1.6353
 GH5  H12  H  HCH2  0   0.286  -3.3918  -0.8608   0.1891
 GH5  H13  H  HCH2  0   0.290  -4.2550   0.2141   1.2676
 GH5  H14  H  HCH2  0   0.283  -5.8949   0.7472  -0.5617
 GH5  H15  H  HCH2  0   0.283  -5.0208  -0.3093  -1.6574
 GH5  H16  H  HCR6  0   0.265   9.2463  -0.9632   0.4462
 GH5  H17  H  HCR6  0   0.264   8.0064   0.6528   1.8488
 GH5  H18  H  HCR6  0   0.262   5.5865   0.9776   1.5157
 GH5  H1   H  HCR6  0   0.265   8.0528  -2.2528  -1.2949
 GH5  F1   F  F     0  -0.316  -5.4201  -2.4749  -0.2101

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
 GH5  O1   C4   double    1.224  0.020  1.224
 GH5  F2   C1   single    1.342  0.020  1.342
 GH5  C2   C1   single    1.503  0.020  1.503
 GH5  C2   C3   single    1.522  0.020  1.522
 GH5  C1   F3   single    1.343  0.020  1.343
 GH5  C1   F1   single    1.344  0.020  1.344
 GH5  C4   C3   single    1.519  0.020  1.519
 GH5  C4   N1   single    1.350  0.020  1.350
 GH5  C9   C8   single    1.523  0.020  1.523
 GH5  C9   N1   single    1.453  0.020  1.453
 GH5  C8   C7   single    1.533  0.020  1.533
 GH5  N1   C5   single    1.451  0.020  1.451
 GH5  C16  C17  aromatic  1.387  0.020  1.387
 GH5  C16  C15  aromatic  1.388  0.020  1.388
 GH5  C17  C12  aromatic  1.393  0.020  1.393
 GH5  N3   C10  aromatic  1.290  0.020  1.290
 GH5  N3   C11  aromatic  1.367  0.020  1.367
 GH5  C7   C6   single    1.535  0.020  1.535
 GH5  C7   C10  single    1.484  0.020  1.484
 GH5  C15  C14  aromatic  1.390  0.020  1.390
 GH5  C5   C6   single    1.523  0.020  1.523
 GH5  C12  C11  single    1.462  0.020  1.462
 GH5  C12  C13  aromatic  1.396  0.020  1.396
 GH5  C10  O2   aromatic  1.327  0.020  1.327
 GH5  C11  N2   aromatic  1.300  0.020  1.300
 GH5  C14  C13  aromatic  1.385  0.020  1.385
 GH5  O2   N2   aromatic  1.366  0.020  1.366
 GH5  C14  H1   single    0.930  0.020  1.080
 GH5  C5   H2   single    0.970  0.020  1.090
 GH5  C5   H3   single    0.970  0.020  1.090
 GH5  C6   H4   single    0.970  0.020  1.090
 GH5  C6   H5   single    0.970  0.020  1.090
 GH5  C7   H6   single    0.970  0.020  1.090
 GH5  C8   H7   single    0.970  0.020  1.090
 GH5  C8   H8   single    0.970  0.020  1.090
 GH5  C9   H9   single    0.970  0.020  1.090
 GH5  C9   H10  single    0.970  0.020  1.090
 GH5  C13  H11  single    0.930  0.020  1.080
 GH5  C3   H12  single    0.970  0.020  1.090
 GH5  C3   H13  single    0.970  0.020  1.090
 GH5  C2   H14  single    0.970  0.020  1.090
 GH5  C2   H15  single    0.970  0.020  1.090
 GH5  C15  H16  single    0.930  0.020  1.080
 GH5  C16  H17  single    0.930  0.020  1.080
 GH5  C17  H18  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
 GH5  O1   C4   C3   120.78  3.000
 GH5  C3   C4   N1   116.95  3.000
 GH5  O1   C4   N1   122.26  3.000
 GH5  H1   C14  C15  120.06  3.000
 GH5  H1   C14  C13  119.75  3.000
 GH5  C15  C14  C13  120.19  3.000
 GH5  H3   C5   H2   106.54  3.000
 GH5  H3   C5   N1   108.35  3.000
 GH5  H2   C5   N1   111.54  3.000
 GH5  H3   C5   C6   109.59  3.000
 GH5  H2   C5   C6   109.98  3.000
 GH5  N1   C5   C6   110.73  3.000
 GH5  H5   C6   H4   107.55  3.000
 GH5  H5   C6   C7   110.42  3.000
 GH5  H4   C6   C7   110.23  3.000
 GH5  H5   C6   C5   109.51  3.000
 GH5  H4   C6   C5   109.14  3.000
 GH5  C7   C6   C5   109.95  3.000
 GH5  N3   C11  N2   113.37  3.000
 GH5  N2   C11  C12  123.33  3.000
 GH5  N3   C11  C12  123.29  3.000
 GH5  H6   C7   C10  105.61  3.000
 GH5  H6   C7   C8   108.62  3.000
 GH5  C10  C7   C8   112.27  3.000
 GH5  H6   C7   C6   108.35  3.000
 GH5  C10  C7   C6   111.37  3.000
 GH5  C8   C7   C6   110.40  3.000
 GH5  H8   C8   H7   107.54  3.000
 GH5  H8   C8   C9   109.10  3.000
 GH5  H7   C8   C9   109.25  3.000
 GH5  H8   C8   C7   110.46  3.000
 GH5  H7   C8   C7   110.41  3.000
 GH5  C9   C8   C7   110.03  3.000
 GH5  H10  C9   H9   107.37  3.000
 GH5  H10  C9   N1   109.68  3.000
 GH5  H9   C9   N1   108.51  3.000
 GH5  H10  C9   C8   110.45  3.000
 GH5  H9   C9   C8   110.06  3.000
 GH5  N1   C9   C8   110.69  3.000
 GH5  O2   C10  N3   112.20  3.000
 GH5  O2   C10  C7   119.22  3.000
 GH5  N3   C10  C7   128.57  3.000
 GH5  C17  C12  C13  119.59  3.000
 GH5  C13  C12  C11  120.72  3.000
 GH5  C17  C12  C11  119.70  3.000
 GH5  H11  C13  C12  120.20  3.000
 GH5  H11  C13  C14  119.72  3.000
 GH5  C12  C13  C14  120.08  3.000
 GH5  C9   N1   C5   112.96  3.000
 GH5  C5   N1   C4   125.50  3.000
 GH5  C9   N1   C4   120.87  3.000
 GH5  O2   N2   C11  103.95  3.000
 GH5  H13  C3   H12  106.42  3.000
 GH5  H13  C3   C2   110.40  3.000
 GH5  H12  C3   C2   110.34  3.000
 GH5  H13  C3   C4   109.20  3.000
 GH5  H12  C3   C4   109.05  3.000
 GH5  C2   C3   C4   111.29  3.000
 GH5  C10  N3   C11  102.96  3.000
 GH5  C2   C1   F3   112.73  3.000
 GH5  F3   C1   F2   106.56  3.000
 GH5  C2   C1   F2   111.64  3.000
 GH5  F3   C1   F1   106.33  3.000
 GH5  C2   C1   F1   112.58  3.000
 GH5  F2   C1   F1   106.56  3.000
 GH5  H15  C2   H14  107.12  3.000
 GH5  H15  C2   C1   107.76  3.000
 GH5  H14  C2   C1   107.85  3.000
 GH5  H15  C2   C3   110.70  3.000
 GH5  H14  C2   C3   110.75  3.000
 GH5  C1   C2   C3   112.44  3.000
 GH5  N2   O2   C10  107.52  3.000
 GH5  H16  C15  C16  120.09  3.000
 GH5  H16  C15  C14  120.03  3.000
 GH5  C16  C15  C14  119.88  3.000
 GH5  H17  C16  C17  119.75  3.000
 GH5  H17  C16  C15  120.09  3.000
 GH5  C17  C16  C15  120.16  3.000
 GH5  H18  C17  C16  119.96  3.000
 GH5  H18  C17  C12  119.94  3.000
 GH5  C16  C17  C12  120.10  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
 GH5  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 GH5  CONST_02  C17  C12  C13  C14     0.00   0.0  0
 GH5  CONST_03  C11  C12  C13  C14   180.00   0.0  0
 GH5  CONST_04  O2   C10  N3   C11     0.00   0.0  0
 GH5  CONST_05  C16  C17  C12  C11   180.00   0.0  0
 GH5  CONST_06  C10  O2   N2   C11     0.00   0.0  0
 GH5  CONST_07  C12  C11  N3   C10   180.00   0.0  0
 GH5  CONST_08  N2   C11  N3   C10     0.00   0.0  0
 GH5  CONST_09  C15  C16  C17  C12     0.00   0.0  0
 GH5  CONST_10  O2   N2   C11  C12   180.00   0.0  0
 GH5  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 GH5  CONST_12  C16  C17  C12  C13     0.00   0.0  0
 GH5  CONST_13  N3   C11  C12  C13   180.00   0.0  0
 GH5  CONST_14  N2   C11  C12  C13     0.00   0.0  0
 GH5  CONST_15  C16  C15  C14  C13     0.00   0.0  0
 GH5  CONST_16  C17  C12  C11  N2    180.00   0.0  0
 GH5  CONST_17  N3   C10  O2   N2      0.00   0.0  0
 GH5  CONST_18  C17  C12  C11  N3      0.00   0.0  0
 GH5  CONST_19  O2   N2   C11  N3      0.00   0.0  0
 GH5  CONST_20  C7   C10  N3   C11   180.00   0.0  0
 GH5  CONST_21  N2   O2   C10  C7    180.00   0.0  0
 GH5  CONST_22  H17  C16  C15  C14   180.00   0.0  0
 GH5  CONST_23  H18  C17  C12  C11     0.00   0.0  0
 GH5  CONST_24  H11  C13  C12  C11     0.00   0.0  0
 GH5  CONST_25  H1   C14  C13  C12   180.00   0.0  0
 GH5  CONST_26  H16  C15  C14  C13   180.00   0.0  0
 GH5  CONST_27  O1   C4   N1   C5    180.00   0.0  0
 GH5  CONST_28  C3   C4   N1   C5      0.00   0.0  0
 GH5  CONST_29  O1   C4   N1   C9      0.00   0.0  0
 GH5  CONST_30  C3   C4   N1   C9    180.00   0.0  0
 GH5  Var_01    C8   C9   N1   C5     59.43  30.0  1
 GH5  Var_02    C9   N1   C5   C6    -59.53  30.0  1
 GH5  Var_03    N1   C9   C8   C7    -55.97  30.0  1
 GH5  Var_04    N1   C5   C6   C7     56.10  30.0  1
 GH5  Var_05    C2   C3   C4   N1    179.42  30.0  3
 GH5  Var_06    C1   C2   C3   C4    178.94  30.0  1
 GH5  Var_07    F2   C1   C2   C3   -179.97  30.0  3

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
 GH5  chir_01  C7  C8  C6  C10  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
 GH5  plan-1  C11  0.020
 GH5  plan-1  C7   0.020
 GH5  plan-1  C10  0.020
 GH5  plan-1  C12  0.020
 GH5  plan-1  N2   0.020
 GH5  plan-1  N3   0.020
 GH5  plan-1  O2   0.020
 GH5  plan-2  C14  0.020
 GH5  plan-2  C11  0.020
 GH5  plan-2  C12  0.020
 GH5  plan-2  C13  0.020
 GH5  plan-2  C15  0.020
 GH5  plan-2  C16  0.020
 GH5  plan-2  C17  0.020
 GH5  plan-2  H11  0.020
 GH5  plan-2  H16  0.020
 GH5  plan-2  H17  0.020
 GH5  plan-2  H18  0.020
 GH5  plan-2  H1   0.020
 GH5  plan-3  C4   0.020
 GH5  plan-3  C5   0.020
 GH5  plan-3  C9   0.020
 GH5  plan-3  N1   0.020
 GH5  plan-3  C3   0.020
 GH5  plan-3  O1   0.020

