# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:41:34 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4,4,4-trifluoro-1-{4-[3-(1,3-thiazol-2-yl)-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)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
 3SE  3SE  4,4,4-trifluoro-1-{4-[3-(1,3-thiazol-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}butan-1-one  ligand  39  24  .  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_3SE
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
 3SE  O    O  O     0  -0.499  -3.6631  -1.8355  -1.3016
 3SE  C3   C  C     0   0.593  -3.3078  -1.2047  -0.3153
 3SE  C2   C  CH2   0  -0.639  -4.1333  -0.0386   0.2006
 3SE  C1   C  CH2   0  -0.634  -5.3880   0.1622  -0.6367
 3SE  C    C  CT    0   1.002  -6.2114   1.3284  -0.1663
 3SE  F2   F  F     0  -0.312  -7.3137   1.4896  -0.9145
 3SE  F1   F  F     0  -0.316  -6.6276   1.1913   1.1038
 3SE  F    F  F     0  -0.316  -5.5386   2.4902  -0.2202
 3SE  N    N  NT    0  -0.457  -2.1843  -1.5100   0.3690
 3SE  C8   C  CH2   0  -0.326  -1.2853  -2.5492  -0.1018
 3SE  C7   C  CH2   0  -0.422   0.0348  -1.9499  -0.5694
 3SE  C6   C  CH1   0  -0.410   0.6632  -1.1230   0.5601
 3SE  C5   C  CH2   0  -0.419  -0.3325  -0.0714   1.0696
 3SE  C4   C  CH2   0  -0.334  -1.6373  -0.7457   1.4743
 3SE  C9   C  CR5   0   0.566   1.9470  -0.5033   0.1503
 3SE  N2   N  N     0  -0.438   3.1247  -0.6820   0.6494
 3SE  C10  C  CR5   0   0.323   3.8929   0.1469  -0.1103
 3SE  N1   N  N     0  -0.142   3.2339   0.7952  -1.0217
 3SE  O1   O  O     0  -0.321   1.9524   0.3693  -0.8531
 3SE  C11  C  CR5   0  -0.043   5.3234   0.3099   0.0755
 3SE  S    S  S2    0   0.287   6.2437   1.3914  -0.9002
 3SE  C13  C  CR15  0  -0.490   7.6394   0.9462  -0.0241
 3SE  C12  C  CR15  0  -0.019   7.3168   0.0269   0.9263
 3SE  N3   N  N     0  -0.363   6.0053  -0.3265   0.9755
 3SE  H2   H  HCH2  0   0.290  -4.3969  -0.2162   1.2459
 3SE  H2A  H  HCH2  0   0.287  -3.5182   0.8649   0.1864
 3SE  H1   H  HCH2  0   0.283  -5.1297   0.3367  -1.6819
 3SE  H1A  H  HCH2  0   0.284  -6.0188  -0.7273  -0.6054
 3SE  H8   H  HCH2  0   0.251  -1.1062  -3.2519   0.7184
 3SE  H8A  H  HCH2  0   0.274  -1.7568  -3.1035  -0.9079
 3SE  H7   H  HCH2  0   0.265   0.7070  -2.7553  -0.8713
 3SE  H7A  H  HCH2  0   0.248  -0.1442  -1.3234  -1.4469
 3SE  H6   H  HCH1  0   0.291   0.9096  -1.7952   1.3871
 3SE  H5   H  HCH2  0   0.266   0.0803   0.4551   1.9319
 3SE  H5A  H  HCH2  0   0.249  -0.5329   0.6714   0.2932
 3SE  H4   H  HCH2  0   0.285  -2.3424  -0.0011   1.8316
 3SE  H4A  H  HCH2  0   0.257  -1.4537  -1.4292   2.3092
 3SE  H13  H  HCR5  0   0.320   8.6049   1.3734  -0.2432
 3SE  H12  H  HCR5  0   0.281   8.0190  -0.4168   1.6166

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
 3SE  O    C3   double    1.223  0.020  1.223
 3SE  C3   N    single    1.350  0.020  1.350
 3SE  C3   C2   single    1.519  0.020  1.519
 3SE  C1   C2   single    1.522  0.020  1.522
 3SE  C2   H2   single    0.970  0.020  1.090
 3SE  C2   H2A  single    0.970  0.020  1.090
 3SE  C    C1   single    1.503  0.020  1.503
 3SE  C1   H1   single    0.970  0.020  1.090
 3SE  C1   H1A  single    0.970  0.020  1.090
 3SE  F2   C    single    1.342  0.020  1.342
 3SE  F1   C    single    1.344  0.020  1.344
 3SE  C    F    single    1.344  0.020  1.344
 3SE  C4   N    single    1.451  0.020  1.451
 3SE  N    C8   single    1.453  0.020  1.453
 3SE  C8   C7   single    1.523  0.020  1.523
 3SE  C8   H8   single    0.970  0.020  1.090
 3SE  C8   H8A  single    0.970  0.020  1.090
 3SE  C6   C7   single    1.534  0.020  1.534
 3SE  C7   H7   single    0.970  0.020  1.090
 3SE  C7   H7A  single    0.970  0.020  1.090
 3SE  C5   C6   single    1.535  0.020  1.535
 3SE  C6   C9   single    1.483  0.020  1.483
 3SE  C6   H6   single    0.970  0.020  1.090
 3SE  C4   C5   single    1.523  0.020  1.523
 3SE  C5   H5   single    0.970  0.020  1.090
 3SE  C5   H5A  single    0.970  0.020  1.090
 3SE  C4   H4   single    0.970  0.020  1.090
 3SE  C4   H4A  single    0.970  0.020  1.090
 3SE  N2   C9   aromatic  1.291  0.020  1.291
 3SE  C9   O1   aromatic  1.330  0.020  1.330
 3SE  N2   C10  aromatic  1.362  0.020  1.362
 3SE  C11  C10  single    1.452  0.020  1.452
 3SE  C10  N1   aromatic  1.298  0.020  1.298
 3SE  O1   N1   aromatic  1.361  0.020  1.361
 3SE  N3   C11  aromatic  1.296  0.020  1.296
 3SE  C11  S    aromatic  1.723  0.020  1.723
 3SE  C13  S    aromatic  1.707  0.020  1.707
 3SE  C12  C13  aromatic  1.361  0.020  1.361
 3SE  C13  H13  single    0.930  0.020  1.080
 3SE  C12  N3   aromatic  1.359  0.020  1.359
 3SE  C12  H12  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
 3SE  N    C3   C2   116.97  3.000
 3SE  C2   C3   O    120.78  3.000
 3SE  N    C3   O    122.24  3.000
 3SE  H2A  C2   H2   106.42  3.000
 3SE  H2A  C2   C1   110.35  3.000
 3SE  H2   C2   C1   110.42  3.000
 3SE  H2A  C2   C3   108.92  3.000
 3SE  H2   C2   C3   109.35  3.000
 3SE  C1   C2   C3   111.25  3.000
 3SE  H1A  C1   H1   107.15  3.000
 3SE  H1A  C1   C    107.87  3.000
 3SE  H1   C1   C    107.78  3.000
 3SE  H1A  C1   C2   110.70  3.000
 3SE  H1   C1   C2   110.68  3.000
 3SE  C    C1   C2   112.45  3.000
 3SE  F    C    F1   106.34  3.000
 3SE  F    C    F2   106.57  3.000
 3SE  F1   C    F2   106.55  3.000
 3SE  F    C    C1   112.58  3.000
 3SE  F1   C    C1   112.72  3.000
 3SE  F2   C    C1   111.64  3.000
 3SE  C4   N    C8   112.98  3.000
 3SE  C8   N    C3   120.83  3.000
 3SE  C4   N    C3   125.49  3.000
 3SE  H8A  C8   H8   107.43  3.000
 3SE  H8A  C8   C7   110.44  3.000
 3SE  H8   C8   C7   109.92  3.000
 3SE  H8A  C8   N    109.70  3.000
 3SE  H8   C8   N    108.52  3.000
 3SE  C7   C8   N    110.76  3.000
 3SE  H7A  C7   H7   107.57  3.000
 3SE  H7A  C7   C6   110.44  3.000
 3SE  H7   C7   C6   110.43  3.000
 3SE  H7A  C7   C8   109.27  3.000
 3SE  H7   C7   C8   109.16  3.000
 3SE  C6   C7   C8   109.93  3.000
 3SE  H6   C6   C9   105.70  3.000
 3SE  H6   C6   C5   108.43  3.000
 3SE  C9   C6   C5   111.53  3.000
 3SE  H6   C6   C7   108.52  3.000
 3SE  C9   C6   C7   112.10  3.000
 3SE  C5   C6   C7   110.35  3.000
 3SE  H5A  C5   H5   107.62  3.000
 3SE  H5A  C5   C4   109.42  3.000
 3SE  H5   C5   C4   109.12  3.000
 3SE  H5A  C5   C6   110.41  3.000
 3SE  H5   C5   C6   110.32  3.000
 3SE  C4   C5   C6   109.90  3.000
 3SE  H4A  C4   H4   106.62  3.000
 3SE  H4A  C4   C5   109.60  3.000
 3SE  H4   C4   C5   109.88  3.000
 3SE  H4A  C4   N    108.39  3.000
 3SE  H4   C4   N    111.53  3.000
 3SE  C5   C4   N    110.71  3.000
 3SE  O1   C9   N2   112.25  3.000
 3SE  O1   C9   C6   119.09  3.000
 3SE  N2   C9   C6   128.66  3.000
 3SE  C10  N2   C9   102.39  3.000
 3SE  C11  C10  N1   122.27  3.000
 3SE  N1   C10  N2   114.16  3.000
 3SE  C11  C10  N2   123.57  3.000
 3SE  O1   N1   C10  103.57  3.000
 3SE  N1   O1   C9   107.62  3.000
 3SE  N3   C11  S    114.86  3.000
 3SE  S    C11  C10  121.63  3.000
 3SE  N3   C11  C10  123.51  3.000
 3SE  C13  S    C11   88.99  3.000
 3SE  H13  C13  C12  128.44  3.000
 3SE  H13  C13  S    121.64  3.000
 3SE  C12  C13  S    109.92  3.000
 3SE  H12  C12  N3   119.83  3.000
 3SE  H12  C12  C13  124.73  3.000
 3SE  N3   C12  C13  115.44  3.000
 3SE  C12  N3   C11  110.78  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
 3SE  CONST_01  C11  C10  N2   C9    180.00   0.0  0
 3SE  CONST_02  N1   C10  N2   C9      0.00   0.0  0
 3SE  CONST_03  C10  N1   O1   C9      0.00   0.0  0
 3SE  CONST_04  N1   O1   C9   N2      0.00   0.0  0
 3SE  CONST_05  N3   C11  C10  N2      0.00   0.0  0
 3SE  CONST_06  S    C11  C10  N2    180.00   0.0  0
 3SE  CONST_07  O1   N1   C10  N2      0.00   0.0  0
 3SE  CONST_08  O1   C9   N2   C10     0.00   0.0  0
 3SE  CONST_09  C12  N3   C11  C10   180.00   0.0  0
 3SE  CONST_10  C13  S    C11  C10   180.00   0.0  0
 3SE  CONST_11  N3   C11  C10  N1    180.00   0.0  0
 3SE  CONST_12  S    C11  C10  N1      0.00   0.0  0
 3SE  CONST_13  C11  C10  N1   O1    180.00   0.0  0
 3SE  CONST_14  C13  C12  N3   C11     0.00   0.0  0
 3SE  CONST_15  C12  C13  S    C11     0.00   0.0  0
 3SE  CONST_16  C12  N3   C11  S       0.00   0.0  0
 3SE  CONST_17  N3   C12  C13  S       0.00   0.0  0
 3SE  CONST_18  N3   C11  S    C13     0.00   0.0  0
 3SE  CONST_19  C10  N2   C9   C6    180.00   0.0  0
 3SE  CONST_20  N1   O1   C9   C6    180.00   0.0  0
 3SE  CONST_21  H12  C12  N3   C11   180.00   0.0  0
 3SE  CONST_22  H13  C13  S    C11   180.00   0.0  0
 3SE  CONST_23  C4   N    C3   O     180.00   0.0  0
 3SE  CONST_24  C8   N    C3   O       0.00   0.0  0
 3SE  CONST_25  C4   N    C3   C2      0.00   0.0  0
 3SE  CONST_26  C8   N    C3   C2    180.00   0.0  0
 3SE  Var_01    C6   C5   C4   N     -56.18  30.0  1
 3SE  Var_02    C6   C7   C8   N      56.01  30.0  1
 3SE  Var_03    C5   C4   N    C8     59.46  30.0  1
 3SE  Var_04    C4   N    C8   C7    -59.38  30.0  1
 3SE  Var_05    N    C3   C2   C1   -178.16  30.0  2
 3SE  Var_06    C    C1   C2   C3   -178.82  30.0  2
 3SE  Var_07    F2   C    C1   C2   -179.93  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
 3SE  chir_01  C6  C7  C5  C9  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
 3SE  plan-1  C6   0.020
 3SE  plan-1  C9   0.020
 3SE  plan-1  N2   0.020
 3SE  plan-1  C10  0.020
 3SE  plan-1  N1   0.020
 3SE  plan-1  O1   0.020
 3SE  plan-1  C11  0.020
 3SE  plan-2  C10  0.020
 3SE  plan-2  C11  0.020
 3SE  plan-2  S    0.020
 3SE  plan-2  C13  0.020
 3SE  plan-2  C12  0.020
 3SE  plan-2  N3   0.020
 3SE  plan-2  H13  0.020
 3SE  plan-2  H12  0.020
 3SE  plan-3  O    0.020
 3SE  plan-3  C3   0.020
 3SE  plan-3  C2   0.020
 3SE  plan-3  N    0.020
 3SE  plan-3  C8   0.020
 3SE  plan-3  C4   0.020

