# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:31:20 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 3-oxo-3-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC#N)N1CCC(CC1)c2onc(n2)c3sccc3
#
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
 FO5  FO5  3-oxo-3-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}propanenitrile  ligand  35  21  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FO5
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
 FO5  C    C  C     0   0.589   4.5930   0.1898   0.2373
 FO5  N    N  NS    0  -0.262   7.5595  -1.5068  -0.2886
 FO5  O    O  O     0  -0.480   5.1273   0.1437   1.3329
 FO5  S    S  S2    0   0.264  -4.9472   0.9807  -0.3794
 FO5  C1   C  CH2   0  -0.715   5.2845  -0.4469  -0.9677
 FO5  N1   N  NT    0  -0.455   3.4123   0.7838   0.0023
 FO5  O1   O  O     0  -0.328  -0.8061  -1.2878   0.4192
 FO5  C2   C  CSP   0   0.149   6.5516  -1.0302  -0.5674
 FO5  N2   N  N     0  -0.156  -2.1185  -1.6745   0.4602
 FO5  C3   C  CH2   0  -0.323   2.6535   1.3839   1.0887
 FO5  N3   N  N     0  -0.460  -1.9551   0.4813  -0.1024
 FO5  C4   C  CH2   0  -0.424   1.3223   0.6693   1.2712
 FO5  C5   C  CH1   0  -0.413   0.5362   0.6792  -0.0462
 FO5  C6   C  CH2   0  -0.418   1.3840   0.0763  -1.1736
 FO5  C7   C  CH2   0  -0.333   2.7168   0.8070  -1.2728
 FO5  C8   C  CR5   0   0.571  -0.7738  -0.0058   0.0810
 FO5  C9   C  CR5   0   0.341  -2.7645  -0.5911   0.1434
 FO5  C10  C  CR5   0  -0.279  -4.2034  -0.5095   0.0536
 FO5  C11  C  CR15  0  -0.210  -5.1329  -1.4893   0.2714
 FO5  C12  C  CR15  0  -0.168  -6.4574  -1.0266   0.0865
 FO5  C13  C  CR15  0  -0.460  -6.5047   0.2901  -0.2679
 FO5  H1   H  HCH2  0   0.346   4.6709  -1.2344  -1.4119
 FO5  H1A  H  HCH2  0   0.349   5.4763   0.2883  -1.7526
 FO5  H3   H  HCH2  0   0.280   3.2358   1.3453   2.0046
 FO5  H3A  H  HCH2  0   0.256   2.4842   2.4389   0.8511
 FO5  H4   H  HCH2  0   0.250   1.5045  -0.3567   1.6006
 FO5  H4A  H  HCH2  0   0.268   0.7533   1.1707   2.0558
 FO5  H5   H  HCH1  0   0.292   0.3047   1.7165  -0.3043
 FO5  H6   H  HCH2  0   0.251   1.5662  -0.9853  -0.9883
 FO5  H6A  H  HCH2  0   0.270   0.8628   0.1591  -2.1287
 FO5  H7   H  HCH2  0   0.263   2.5508   1.8501  -1.5593
 FO5  H7A  H  HCH2  0   0.290   3.3206   0.3601  -2.0571
 FO5  H11  H  HCR5  0   0.274  -4.8772  -2.5009   0.5528
 FO5  H12  H  HCR5  0   0.276  -7.3355  -1.6426   0.2124
 FO5  H13  H  HCR5  0   0.305  -7.3785   0.8900  -0.4713

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
 FO5  C    O    double    1.220  0.020  1.220
 FO5  C    C1   single    1.528  0.020  1.528
 FO5  C    N1   single    1.342  0.020  1.342
 FO5  N    C2   triple    1.149  0.020  1.149
 FO5  S    C10  aromatic  1.721  0.020  1.721
 FO5  S    C13  aromatic  1.707  0.020  1.707
 FO5  C1   C2   single    1.451  0.020  1.451
 FO5  N1   C3   single    1.455  0.020  1.455
 FO5  N1   C7   single    1.453  0.020  1.453
 FO5  O1   N2   aromatic  1.369  0.020  1.369
 FO5  O1   C8   aromatic  1.326  0.020  1.326
 FO5  N2   C9   aromatic  1.301  0.020  1.301
 FO5  C3   C4   single    1.522  0.020  1.522
 FO5  N3   C8   aromatic  1.291  0.020  1.291
 FO5  N3   C9   aromatic  1.366  0.020  1.366
 FO5  C4   C5   single    1.534  0.020  1.534
 FO5  C5   C6   single    1.534  0.020  1.534
 FO5  C5   C8   single    1.484  0.020  1.484
 FO5  C6   C7   single    1.523  0.020  1.523
 FO5  C9   C10  single    1.444  0.020  1.444
 FO5  C10  C11  aromatic  1.368  0.020  1.368
 FO5  C11  C12  aromatic  1.415  0.020  1.415
 FO5  C12  C13  aromatic  1.364  0.020  1.364
 FO5  C1   H1   single    0.970  0.020  1.090
 FO5  C1   H1A  single    0.970  0.020  1.090
 FO5  C3   H3   single    0.970  0.020  1.090
 FO5  C3   H3A  single    0.970  0.020  1.090
 FO5  C4   H4   single    0.970  0.020  1.090
 FO5  C4   H4A  single    0.970  0.020  1.090
 FO5  C5   H5   single    0.970  0.020  1.090
 FO5  C6   H6   single    0.970  0.020  1.090
 FO5  C6   H6A  single    0.970  0.020  1.090
 FO5  C7   H7   single    0.970  0.020  1.090
 FO5  C7   H7A  single    0.970  0.020  1.090
 FO5  C11  H11  single    0.930  0.020  1.080
 FO5  C12  H12  single    0.930  0.020  1.080
 FO5  C13  H13  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
 FO5  N1   C    C1   116.38  3.000
 FO5  N1   C    O    124.00  3.000
 FO5  C1   C    O    119.62  3.000
 FO5  C13  S    C10   91.58  3.000
 FO5  H1A  C1   H1   106.95  3.000
 FO5  H1A  C1   C2   108.38  3.000
 FO5  H1   C1   C2   108.23  3.000
 FO5  H1A  C1   C    111.44  3.000
 FO5  H1   C1   C    111.52  3.000
 FO5  C2   C1   C    110.19  3.000
 FO5  C7   N1   C3   113.53  3.000
 FO5  C7   N1   C    125.58  3.000
 FO5  C3   N1   C    120.70  3.000
 FO5  C8   O1   N2   107.70  3.000
 FO5  C1   C2   N    180.00  3.000
 FO5  C9   N2   O1   103.51  3.000
 FO5  H3A  C3   H3   107.47  3.000
 FO5  H3A  C3   C4   110.08  3.000
 FO5  H3   C3   C4   110.56  3.000
 FO5  H3A  C3   N1   108.43  3.000
 FO5  H3   C3   N1   109.60  3.000
 FO5  C4   C3   N1   110.62  3.000
 FO5  C9   N3   C8   102.73  3.000
 FO5  H4A  C4   H4   107.56  3.000
 FO5  H4A  C4   C5   110.32  3.000
 FO5  H4   C4   C5   110.50  3.000
 FO5  H4A  C4   C3   109.06  3.000
 FO5  H4   C4   C3   109.34  3.000
 FO5  C5   C4   C3   110.01  3.000
 FO5  H5   C5   C8   105.74  3.000
 FO5  H5   C5   C6   108.44  3.000
 FO5  C8   C5   C6   111.68  3.000
 FO5  H5   C5   C4   108.49  3.000
 FO5  C8   C5   C4   112.08  3.000
 FO5  C6   C5   C4   110.21  3.000
 FO5  H6A  C6   H6   107.56  3.000
 FO5  H6A  C6   C7   108.94  3.000
 FO5  H6   C6   C7   109.34  3.000
 FO5  H6A  C6   C5   110.46  3.000
 FO5  H6   C6   C5   110.44  3.000
 FO5  C7   C6   C5   110.05  3.000
 FO5  H7A  C7   H7   106.71  3.000
 FO5  H7A  C7   C6   109.64  3.000
 FO5  H7   C7   C6   109.97  3.000
 FO5  H7A  C7   N1   111.17  3.000
 FO5  H7   C7   N1   108.52  3.000
 FO5  C6   C7   N1   110.74  3.000
 FO5  C5   C8   N3   128.43  3.000
 FO5  C5   C8   O1   119.31  3.000
 FO5  N3   C8   O1   112.25  3.000
 FO5  C10  C9   N3   122.34  3.000
 FO5  C10  C9   N2   123.86  3.000
 FO5  N3   C9   N2   113.80  3.000
 FO5  C11  C10  C9   128.80  3.000
 FO5  C11  C10  S    111.51  3.000
 FO5  C9   C10  S    119.69  3.000
 FO5  H11  C11  C12  124.16  3.000
 FO5  H11  C11  C10  123.44  3.000
 FO5  C12  C11  C10  112.39  3.000
 FO5  H12  C12  C13  123.54  3.000
 FO5  H12  C12  C11  124.01  3.000
 FO5  C13  C12  C11  112.45  3.000
 FO5  H13  C13  C12  127.84  3.000
 FO5  H13  C13  S    120.09  3.000
 FO5  C12  C13  S    112.07  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
 FO5  CONST_01  N2   C9   C10  S    180.00   0.0  0
 FO5  CONST_02  N3   C9   C10  S      0.00   0.0  0
 FO5  CONST_03  C12  C11  C10  S      0.00   0.0  0
 FO5  CONST_04  C11  C12  C13  S      0.00   0.0  0
 FO5  CONST_05  N3   C9   N2   O1     0.00   0.0  0
 FO5  CONST_06  C10  C9   N2   O1   180.00   0.0  0
 FO5  CONST_07  C9   N3   C8   O1     0.00   0.0  0
 FO5  CONST_08  N3   C8   O1   N2     0.00   0.0  0
 FO5  CONST_09  C8   N3   C9   N2     0.00   0.0  0
 FO5  CONST_10  C11  C10  C9   N2     0.00   0.0  0
 FO5  CONST_11  C11  C10  C9   N3   180.00   0.0  0
 FO5  CONST_12  C9   N2   O1   C8     0.00   0.0  0
 FO5  CONST_13  C10  C9   N3   C8   180.00   0.0  0
 FO5  CONST_14  C13  S    C10  C9   180.00   0.0  0
 FO5  CONST_15  C12  C11  C10  C9   180.00   0.0  0
 FO5  CONST_16  C12  C13  S    C10    0.00   0.0  0
 FO5  CONST_17  C13  C12  C11  C10    0.00   0.0  0
 FO5  CONST_18  C13  S    C10  C11    0.00   0.0  0
 FO5  CONST_19  C5   C8   O1   N2   180.00   0.0  0
 FO5  CONST_20  C9   N3   C8   C5   180.00   0.0  0
 FO5  CONST_21  H11  C11  C10  S    180.00   0.0  0
 FO5  CONST_22  H12  C12  C13  S    180.00   0.0  0
 FO5  CONST_23  H13  C13  S    C10  180.00   0.0  0
 FO5  CONST_24  C3   N1   C    O      0.00   0.0  0
 FO5  CONST_25  C7   N1   C    O    180.00   0.0  0
 FO5  CONST_26  C3   N1   C    C1   180.00   0.0  0
 FO5  CONST_27  C7   N1   C    C1     0.00   0.0  0
 FO5  Var_01    C5   C4   C3   N1   -55.99  30.0  1
 FO5  Var_02    C5   C6   C7   N1    55.65  30.0  1
 FO5  Var_03    C6   C7   N1   C3   -58.46  30.0  1
 FO5  Var_04    C7   N1   C3   C4    58.64  30.0  1
 FO5  Var_05    C2   C1   C    N1   179.19  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
 FO5  chir_01  C5  C4  C6  C8  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
 FO5  plan-1  S    0.020
 FO5  plan-1  C9   0.020
 FO5  plan-1  C10  0.020
 FO5  plan-1  C11  0.020
 FO5  plan-1  C12  0.020
 FO5  plan-1  C13  0.020
 FO5  plan-1  H11  0.020
 FO5  plan-1  H12  0.020
 FO5  plan-1  H13  0.020
 FO5  plan-2  O1   0.020
 FO5  plan-2  N2   0.020
 FO5  plan-2  N3   0.020
 FO5  plan-2  C5   0.020
 FO5  plan-2  C8   0.020
 FO5  plan-2  C9   0.020
 FO5  plan-2  C10  0.020
 FO5  plan-3  C    0.020
 FO5  plan-3  O    0.020
 FO5  plan-3  C1   0.020
 FO5  plan-3  N1   0.020
 FO5  plan-3  C3   0.020
 FO5  plan-3  C7   0.020

