# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:05:18 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5,5,5-trifluoro-1-{4-[3-(1,3-thiazol-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}pentan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)CCCC(=O)N1CCC(CC1)c2onc(n2)c3sccn3
#
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
 3SF  3SF  5,5,5-trifluoro-1-{4-[3-(1,3-thiazol-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}pentan-1-one  ligand  42  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3SF
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
 3SF  C    C  CT    0   1.002  -7.0736   1.2526  -0.0395
 3SF  F    F  F     0  -0.314  -7.8358   2.0359   0.7404
 3SF  N    N  NT    0  -0.455  -1.5194  -1.6174   0.2885
 3SF  O    O  O     0  -0.498  -2.9974  -1.6092  -1.4130
 3SF  S    S  S2    0   0.291   6.7499  -0.4355   0.4248
 3SF  C1   C  CH2   0  -0.647  -5.7680   0.9044   0.6186
 3SF  F1   F  F     0  -0.316  -7.8103   0.1665  -0.3263
 3SF  N1   N  N     0  -0.132   3.5282   1.5748  -0.7486
 3SF  O1   O  O     0  -0.323   2.2937   1.0391  -0.5191
 3SF  C2   C  CH2   0  -0.441  -4.8809   0.0046  -0.2351
 3SF  F2   F  F     0  -0.316  -6.9063   1.9133  -1.1972
 3SF  N2   N  N     0  -0.456   3.7082  -0.3812   0.3174
 3SF  C3   C  CH2   0  -0.608  -3.5830  -0.3028   0.4973
 3SF  N3   N  N     0  -0.365   6.4375   1.8144  -0.7481
 3SF  C4   C  C     0   0.580  -2.6762  -1.2258  -0.2966
 3SF  C5   C  CH2   0  -0.326  -0.5501  -2.4042  -0.4523
 3SF  C6   C  CH2   0  -0.424   0.6621  -1.5595  -0.8190
 3SF  C7   C  CH1   0  -0.415   1.2749  -0.9422   0.4479
 3SF  C8   C  CH2   0  -0.419   0.2134  -0.1655   1.2362
 3SF  C9   C  CH2   0  -0.335  -0.9814  -1.0694   1.5196
 3SF  C10  C  CR5   0   0.577   2.4608  -0.1172   0.1120
 3SF  C11  C  CR5   0   0.317   4.3332   0.6945  -0.2359
 3SF  C12  C  CR5   0  -0.034   5.7784   0.8163  -0.2481
 3SF  C13  C  CR15  0  -0.017   7.7762   1.6187  -0.6143
 3SF  C14  C  CR15  0  -0.495   8.1388   0.4569  -0.0027
 3SF  H1   H  HCH2  0   0.275  -5.2519   1.8390   0.8519
 3SF  H1A  H  HCH2  0   0.275  -5.9933   0.4216   1.5728
 3SF  H2   H  HCH2  0   0.247  -5.4011  -0.9257  -0.4662
 3SF  H2A  H  HCH2  0   0.247  -4.6572   0.4913  -1.1852
 3SF  H3   H  HCH2  0   0.272  -3.0535   0.6300   0.7165
 3SF  H3A  H  HCH2  0   0.274  -3.8032  -0.7537   1.4696
 3SF  H5   H  HCH2  0   0.250  -0.2393  -3.2505   0.1682
 3SF  H5A  H  HCH2  0   0.273  -1.0142  -2.8104  -1.3457
 3SF  H6   H  HCH2  0   0.264   1.3990  -2.1832  -1.3285
 3SF  H6A  H  HCH2  0   0.248   0.3613  -0.7744  -1.5172
 3SF  H7   H  HCH1  0   0.292   1.6489  -1.7567   1.0752
 3SF  H8   H  HCH2  0   0.266   0.6276   0.1902   2.1810
 3SF  H8A  H  HCH2  0   0.247  -0.1201   0.7100   0.6730
 3SF  H9   H  HCH2  0   0.284  -1.7406  -0.5233   2.0709
 3SF  H9A  H  HCH2  0   0.256  -0.6695  -1.9000   2.1605
 3SF  H13  H  HCR5  0   0.281   8.4684   2.3622  -0.9809
 3SF  H14  H  HCR5  0   0.320   9.1318   0.0959   0.2102

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
 3SF  F    C    single    1.343  0.020  1.343
 3SF  F2   C    single    1.343  0.020  1.343
 3SF  C    F1   single    1.343  0.020  1.343
 3SF  C    C1   single    1.503  0.020  1.503
 3SF  C4   N    single    1.354  0.020  1.354
 3SF  C9   N    single    1.451  0.020  1.451
 3SF  N    C5   single    1.452  0.020  1.452
 3SF  O    C4   double    1.223  0.020  1.223
 3SF  C14  S    aromatic  1.705  0.020  1.705
 3SF  C12  S    aromatic  1.722  0.020  1.722
 3SF  C2   C1   single    1.525  0.020  1.525
 3SF  C1   H1   single    0.970  0.020  1.090
 3SF  C1   H1A  single    0.970  0.020  1.090
 3SF  C11  N1   aromatic  1.298  0.020  1.298
 3SF  O1   N1   aromatic  1.365  0.020  1.365
 3SF  C10  O1   aromatic  1.328  0.020  1.328
 3SF  C2   C3   single    1.522  0.020  1.522
 3SF  C2   H2   single    0.970  0.020  1.090
 3SF  C2   H2A  single    0.970  0.020  1.090
 3SF  N2   C10  aromatic  1.291  0.020  1.291
 3SF  N2   C11  aromatic  1.361  0.020  1.361
 3SF  C4   C3   single    1.518  0.020  1.518
 3SF  C3   H3   single    0.970  0.020  1.090
 3SF  C3   H3A  single    0.970  0.020  1.090
 3SF  C13  N3   aromatic  1.360  0.020  1.360
 3SF  N3   C12  aromatic  1.296  0.020  1.296
 3SF  C5   C6   single    1.522  0.020  1.522
 3SF  C5   H5   single    0.970  0.020  1.090
 3SF  C5   H5A  single    0.970  0.020  1.090
 3SF  C7   C6   single    1.537  0.020  1.537
 3SF  C6   H6   single    0.970  0.020  1.090
 3SF  C6   H6A  single    0.970  0.020  1.090
 3SF  C8   C7   single    1.533  0.020  1.533
 3SF  C7   C10  single    1.483  0.020  1.483
 3SF  C7   H7   single    0.970  0.020  1.090
 3SF  C9   C8   single    1.525  0.020  1.525
 3SF  C8   H8   single    0.970  0.020  1.090
 3SF  C8   H8A  single    0.970  0.020  1.090
 3SF  C9   H9   single    0.970  0.020  1.090
 3SF  C9   H9A  single    0.970  0.020  1.090
 3SF  C12  C11  single    1.450  0.020  1.450
 3SF  C13  C14  aromatic  1.362  0.020  1.362
 3SF  C13  H13  single    0.930  0.020  1.080
 3SF  C14  H14  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
 3SF  F2   C    F1   106.37  3.000
 3SF  F1   C    C1   112.49  3.000
 3SF  F2   C    C1   112.52  3.000
 3SF  C1   C    F    111.96  3.000
 3SF  F1   C    F    106.52  3.000
 3SF  F2   C    F    106.53  3.000
 3SF  C9   N    C5   112.97  3.000
 3SF  C5   N    C4   120.43  3.000
 3SF  C9   N    C4   125.04  3.000
 3SF  C14  S    C12   88.92  3.000
 3SF  H1A  C1   H1   106.78  3.000
 3SF  H1A  C1   C2   110.37  3.000
 3SF  H1   C1   C2   110.45  3.000
 3SF  H1A  C1   C    107.79  3.000
 3SF  H1   C1   C    107.79  3.000
 3SF  C2   C1   C    113.39  3.000
 3SF  C11  N1   O1   103.19  3.000
 3SF  C10  O1   N1   107.93  3.000
 3SF  H2A  C2   H2   107.09  3.000
 3SF  H2A  C2   C3   109.54  3.000
 3SF  H2   C2   C3   109.66  3.000
 3SF  H2A  C2   C1   110.10  3.000
 3SF  H2   C2   C1   110.15  3.000
 3SF  C3   C2   C1   110.24  3.000
 3SF  C11  N2   C10  102.55  3.000
 3SF  H3A  C3   H3   105.70  3.000
 3SF  H3A  C3   C4   109.53  3.000
 3SF  H3   C3   C4   109.50  3.000
 3SF  H3A  C3   C2   109.84  3.000
 3SF  H3   C3   C2   109.68  3.000
 3SF  C4   C3   C2   112.37  3.000
 3SF  C13  N3   C12  110.60  3.000
 3SF  C3   C4   O    120.73  3.000
 3SF  C3   C4   N    117.39  3.000
 3SF  O    C4   N    121.87  3.000
 3SF  H5A  C5   H5   107.38  3.000
 3SF  H5A  C5   C6   110.47  3.000
 3SF  H5   C5   C6   109.84  3.000
 3SF  H5A  C5   N    109.72  3.000
 3SF  H5   C5   N    108.62  3.000
 3SF  C6   C5   N    110.73  3.000
 3SF  H6A  C6   H6   107.33  3.000
 3SF  H6A  C6   C7   110.35  3.000
 3SF  H6   C6   C7   110.19  3.000
 3SF  H6A  C6   C5   109.47  3.000
 3SF  H6   C6   C5   109.45  3.000
 3SF  C7   C6   C5   109.99  3.000
 3SF  H7   C7   C10  105.71  3.000
 3SF  H7   C7   C8   108.60  3.000
 3SF  C10  C7   C8   112.84  3.000
 3SF  H7   C7   C6   108.05  3.000
 3SF  C10  C7   C6   110.83  3.000
 3SF  C8   C7   C6   110.56  3.000
 3SF  H8A  C8   H8   107.50  3.000
 3SF  H8A  C8   C9   109.36  3.000
 3SF  H8   C8   C9   109.25  3.000
 3SF  H8A  C8   C7   110.61  3.000
 3SF  H8   C8   C7   110.33  3.000
 3SF  C9   C8   C7   109.74  3.000
 3SF  H9A  C9   H9   106.49  3.000
 3SF  H9A  C9   C8   109.60  3.000
 3SF  H9   C9   C8   110.13  3.000
 3SF  H9A  C9   N    108.41  3.000
 3SF  H9   C9   N    111.19  3.000
 3SF  C8   C9   N    110.90  3.000
 3SF  C7   C10  N2   128.50  3.000
 3SF  C7   C10  O1   119.43  3.000
 3SF  N2   C10  O1   112.03  3.000
 3SF  C12  C11  N2   121.82  3.000
 3SF  C12  C11  N1   123.88  3.000
 3SF  N2   C11  N1   114.30  3.000
 3SF  C11  C12  N3   125.07  3.000
 3SF  C11  C12  S    119.86  3.000
 3SF  N3   C12  S    115.07  3.000
 3SF  H13  C13  C14  124.68  3.000
 3SF  H13  C13  N3   119.91  3.000
 3SF  C14  C13  N3   115.41  3.000
 3SF  H14  C14  C13  128.29  3.000
 3SF  H14  C14  S    121.70  3.000
 3SF  C13  C14  S    110.01  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
 3SF  CONST_01  N3   C13  C14  S       0.00   0.0  0
 3SF  CONST_02  C13  N3   C12  S       0.00   0.0  0
 3SF  CONST_03  N1   C11  C12  S     180.00   0.0  0
 3SF  CONST_04  N2   C11  C12  S       0.00   0.0  0
 3SF  CONST_05  C10  N2   C11  N1      0.00   0.0  0
 3SF  CONST_06  N3   C12  C11  N1      0.00   0.0  0
 3SF  CONST_07  N2   C10  O1   N1      0.00   0.0  0
 3SF  CONST_08  N2   C11  N1   O1      0.00   0.0  0
 3SF  CONST_09  C12  C11  N1   O1    180.00   0.0  0
 3SF  CONST_10  C11  N2   C10  O1      0.00   0.0  0
 3SF  CONST_11  N3   C12  C11  N2    180.00   0.0  0
 3SF  CONST_12  C14  S    C12  N3      0.00   0.0  0
 3SF  CONST_13  C11  N1   O1   C10     0.00   0.0  0
 3SF  CONST_14  C12  C11  N2   C10   180.00   0.0  0
 3SF  CONST_15  C14  S    C12  C11   180.00   0.0  0
 3SF  CONST_16  C13  N3   C12  C11   180.00   0.0  0
 3SF  CONST_17  C13  C14  S    C12     0.00   0.0  0
 3SF  CONST_18  C14  C13  N3   C12     0.00   0.0  0
 3SF  CONST_19  C7   C10  O1   N1    180.00   0.0  0
 3SF  CONST_20  C11  N2   C10  C7    180.00   0.0  0
 3SF  CONST_21  H13  C13  C14  S     180.00   0.0  0
 3SF  CONST_22  H14  C14  C13  N3    180.00   0.0  0
 3SF  CONST_23  C9   N    C4   O     180.00   0.0  0
 3SF  CONST_24  C5   N    C4   O       0.00   0.0  0
 3SF  CONST_25  C9   N    C4   C3      0.00   0.0  0
 3SF  CONST_26  C5   N    C4   C3    180.00   0.0  0
 3SF  Var_01    C7   C8   C9   N     -56.03  30.0  1
 3SF  Var_02    C7   C6   C5   N      55.87  30.0  1
 3SF  Var_03    C8   C9   N    C5     59.55  30.0  1
 3SF  Var_04    C9   N    C5   C6    -59.39  30.0  1
 3SF  Var_05    C2   C3   C4   N    -176.94  30.0  3
 3SF  Var_06    C3   C2   C1   C    -179.96  30.0  2
 3SF  Var_07    C2   C1   C    F     179.50  30.0  3
 3SF  Var_08    C4   C3   C2   C1    178.57  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
 3SF  chir_01  C7  C6  C8  C10  positiv

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
 3SF  plan-1  N1   0.020
 3SF  plan-1  O1   0.020
 3SF  plan-1  N2   0.020
 3SF  plan-1  C7   0.020
 3SF  plan-1  C10  0.020
 3SF  plan-1  C11  0.020
 3SF  plan-1  C12  0.020
 3SF  plan-2  S    0.020
 3SF  plan-2  N3   0.020
 3SF  plan-2  C11  0.020
 3SF  plan-2  C12  0.020
 3SF  plan-2  C13  0.020
 3SF  plan-2  C14  0.020
 3SF  plan-2  H13  0.020
 3SF  plan-2  H14  0.020
 3SF  plan-3  N    0.020
 3SF  plan-3  O    0.020
 3SF  plan-3  C3   0.020
 3SF  plan-3  C4   0.020
 3SF  plan-3  C5   0.020
 3SF  plan-3  C9   0.020

