# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:34:04 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[(1S,2R)-2-phenylcyclopropyl]-4-[3-(propan-2-yl)-1,2,4-oxadiazol-5-yl]piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1noc(n1)[C@H]2CCN(CC2)C(=O)N[C@H]3C[C@@H]3c4ccccc4
#
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
 S82  S82  N-[(1S,2R)-2-phenylcyclopropyl]-4-[3-(propan-2-yl)-1,2,4-oxadiazol-5-yl]piperidine-1-carboxamide  ligand  52  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S82
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
 S82  N1    N  NT    0  -0.486  -0.1059   2.2808  -0.3314
 S82  C2    C  C     0   0.737  -1.1062   1.5475  -0.9208
 S82  N3    N  NH1   0  -0.692  -2.0504   1.0261  -0.0849
 S82  C4    C  CH1   0  -0.037  -3.1622   0.3249  -0.6274
 S82  C5    C  CH1   0  -0.413  -3.6991  -0.8285   0.1773
 S82  C6    C  CH2   0  -0.468  -2.9673  -1.0665  -1.1149
 S82  C7    C  CR6   0   0.232  -5.1586  -1.0475   0.3170
 S82  C8    C  CR16  0  -0.325  -5.6728  -1.4491   1.5496
 S82  C9    C  CR16  0  -0.240  -7.0350  -1.6496   1.7273
 S82  C10   C  CR16  0  -0.276  -7.9130  -1.4499   0.6710
 S82  C11   C  CR16  0  -0.236  -7.4131  -1.0531  -0.5631
 S82  C12   C  CR16  0  -0.356  -6.0510  -0.8566  -0.7390
 S82  O13   O  O     0  -0.529  -1.1658   1.3769  -2.1318
 S82  C14   C  CH2   0  -0.329   1.0017   2.7033  -1.1724
 S82  C15   C  CH2   0  -0.430   2.1072   1.6545  -1.1974
 S82  C16   C  CH1   0  -0.390   2.5703   1.3444   0.2340
 S82  C17   C  CH2   0  -0.421   1.3775   0.9828   1.1300
 S82  C18   C  CH2   0  -0.350   0.3153   2.0728   1.0460
 S82  C19   C  CR5   0   0.549   3.6145   0.2885   0.2535
 S82  N20   N  N     0  -0.455   4.8475   0.3813   0.6224
 S82  C21   C  CR5   0   0.342   5.3242  -0.8872   0.4255
 S82  N22   N  N     0  -0.160   4.4316  -1.7054  -0.0365
 S82  O23   O  O     0  -0.335   3.3016  -0.9350  -0.1527
 S82  C24   C  CH1   0  -0.342   6.7381  -1.2705   0.7096
 S82  C25   C  CH3   0  -0.658   6.9868  -2.7613   0.5214
 S82  C26   C  CH3   0  -0.656   7.6840  -0.4297  -0.1504
 S82  HN3   H  HNH1  0   0.399  -2.1818   1.4256   0.8296
 S82  H4    H  HCH1  0   0.263  -3.9032   0.9256  -1.1511
 S82  H5    H  HCH1  0   0.269  -3.1331  -1.0608   1.0735
 S82  H6    H  HCH2  0   0.259  -3.5345  -1.3865  -1.9803
 S82  H6A   H  HCH2  0   0.266  -1.9730  -1.4881  -1.0469
 S82  H8    H  HCR6  0   0.250  -4.9963  -1.6063   2.3817
 S82  H9    H  HCR6  0   0.254  -7.4093  -1.9618   2.6937
 S82  H10   H  HCR6  0   0.254  -8.9759  -1.6021   0.8065
 S82  H11   H  HCR6  0   0.255  -8.0874  -0.8959  -1.3952
 S82  H12   H  HCR6  0   0.248  -5.6895  -0.5505  -1.7134
 S82  H14   H  HCH2  0   0.268   0.6471   2.9113  -2.1781
 S82  H14A  H  HCH2  0   0.248   1.3887   3.6426  -0.7670
 S82  H15   H  HCH2  0   0.244   1.7348   0.7489  -1.6836
 S82  H15A  H  HCH2  0   0.259   2.9479   2.0202  -1.7908
 S82  H16   H  HCH1  0   0.283   3.0471   2.2408   0.6418
 S82  H17   H  HCH2  0   0.242   0.9398   0.0295   0.8212
 S82  H17A  H  HCH2  0   0.263   1.7071   0.8697   2.1646
 S82  H18   H  HCH2  0   0.257   0.7197   3.0178   1.4181
 S82  H18A  H  HCH2  0   0.264  -0.5220   1.8305   1.6955
 S82  H24   H  HCH1  0   0.265   6.9206  -1.0139   1.7586
 S82  H25   H  HCH3  0   0.239   8.0191  -2.9963   0.7790
 S82  H25A  H  HCH3  0   0.238   6.3397  -3.3662   1.1561
 S82  H25B  H  HCH3  0   0.227   6.8250  -3.0655  -0.5137
 S82  H26   H  HCH3  0   0.241   7.5363   0.6373   0.0124
 S82  H26A  H  HCH3  0   0.241   8.7195  -0.6651   0.0950
 S82  H26B  H  HCH3  0   0.230   7.5342  -0.6363  -1.2114

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
 S82  N1   C2    single    1.373  0.020  1.373
 S82  N1   C14   single    1.454  0.020  1.454
 S82  N1   C18   single    1.455  0.020  1.455
 S82  C2   N3    single    1.365  0.020  1.365
 S82  C2   O13   double    1.224  0.020  1.224
 S82  N3   C4    single    1.422  0.020  1.422
 S82  C4   C5    single    1.505  0.020  1.505
 S82  C4   C6    single    1.487  0.020  1.487
 S82  C5   C6    single    1.504  0.020  1.504
 S82  C5   C7    single    1.482  0.020  1.482
 S82  C7   C8    aromatic  1.395  0.020  1.395
 S82  C7   C12   aromatic  1.396  0.020  1.396
 S82  C8   C9    aromatic  1.388  0.020  1.388
 S82  C9   C10   aromatic  1.388  0.020  1.388
 S82  C10  C11   aromatic  1.389  0.020  1.389
 S82  C11  C12   aromatic  1.387  0.020  1.387
 S82  C14  C15   single    1.524  0.020  1.524
 S82  C15  C16   single    1.536  0.020  1.536
 S82  C16  C17   single    1.535  0.020  1.535
 S82  C16  C19   single    1.485  0.020  1.485
 S82  C17  C18   single    1.524  0.020  1.524
 S82  C19  N20   aromatic  1.290  0.020  1.290
 S82  C19  O23   aromatic  1.327  0.020  1.327
 S82  N20  C21   aromatic  1.369  0.020  1.369
 S82  C21  N22   aromatic  1.296  0.020  1.296
 S82  C21  C24   single    1.492  0.020  1.492
 S82  N22  O23   aromatic  1.373  0.020  1.373
 S82  C24  C25   single    1.523  0.020  1.523
 S82  C24  C26   single    1.530  0.020  1.530
 S82  N3   HN3   single    0.890  0.020  1.040
 S82  C4   H4    single    0.970  0.020  1.090
 S82  C5   H5    single    0.970  0.020  1.090
 S82  C6   H6    single    0.970  0.020  1.090
 S82  C6   H6A   single    0.970  0.020  1.090
 S82  C8   H8    single    0.930  0.020  1.080
 S82  C9   H9    single    0.930  0.020  1.080
 S82  C10  H10   single    0.930  0.020  1.080
 S82  C11  H11   single    0.930  0.020  1.080
 S82  C12  H12   single    0.930  0.020  1.080
 S82  C14  H14   single    0.970  0.020  1.090
 S82  C14  H14A  single    0.970  0.020  1.090
 S82  C15  H15   single    0.970  0.020  1.090
 S82  C15  H15A  single    0.970  0.020  1.090
 S82  C16  H16   single    0.970  0.020  1.090
 S82  C17  H17   single    0.970  0.020  1.090
 S82  C17  H17A  single    0.970  0.020  1.090
 S82  C18  H18   single    0.970  0.020  1.090
 S82  C18  H18A  single    0.970  0.020  1.090
 S82  C24  H24   single    0.970  0.020  1.090
 S82  C25  H25   single    0.970  0.020  1.090
 S82  C25  H25A  single    0.970  0.020  1.090
 S82  C25  H25B  single    0.970  0.020  1.090
 S82  C26  H26   single    0.970  0.020  1.090
 S82  C26  H26A  single    0.970  0.020  1.090
 S82  C26  H26B  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
 S82  C18   N1   C14   111.63  3.000
 S82  C18   N1   C2    122.74  3.000
 S82  C14   N1   C2    117.51  3.000
 S82  O13   C2   N3    121.26  3.000
 S82  O13   C2   N1    122.30  3.000
 S82  N3    C2   N1    116.43  3.000
 S82  HN3   N3   C4    116.12  3.000
 S82  HN3   N3   C2    119.68  3.000
 S82  C4    N3   C2    119.71  3.000
 S82  H4    C4   C6    116.61  3.000
 S82  H4    C4   C5    115.94  3.000
 S82  C6    C4   C5     60.34  3.000
 S82  H4    C4   N3    116.34  3.000
 S82  C6    C4   N3    118.95  3.000
 S82  C5    C4   N3    116.92  3.000
 S82  H5    C5   C7    113.84  3.000
 S82  H5    C5   C6    114.96  3.000
 S82  C7    C5   C6    122.46  3.000
 S82  H5    C5   C4    114.80  3.000
 S82  C7    C5   C4    120.98  3.000
 S82  C6    C5   C4     59.23  3.000
 S82  H6A   C6   H6    114.60  3.000
 S82  H6A   C6   C5    117.04  3.000
 S82  H6    C6   C5    118.59  3.000
 S82  H6A   C6   C4    117.67  3.000
 S82  H6    C6   C4    118.02  3.000
 S82  C5    C6   C4     60.43  3.000
 S82  C12   C7   C8    118.19  3.000
 S82  C12   C7   C5    122.55  3.000
 S82  C8    C7   C5    119.26  3.000
 S82  H8    C8   C9    119.56  3.000
 S82  H8    C8   C7    119.35  3.000
 S82  C9    C8   C7    121.09  3.000
 S82  H9    C9   C10   120.15  3.000
 S82  H9    C9   C8    119.68  3.000
 S82  C10   C9   C8    120.17  3.000
 S82  H10   C10  C11   120.32  3.000
 S82  H10   C10  C9    120.38  3.000
 S82  C11   C10  C9    119.30  3.000
 S82  H11   C11  C12   119.58  3.000
 S82  H11   C11  C10   120.00  3.000
 S82  C12   C11  C10   120.42  3.000
 S82  H12   C12  C11   118.79  3.000
 S82  H12   C12  C7    120.39  3.000
 S82  C11   C12  C7    120.82  3.000
 S82  H14A  C14  H14   107.10  3.000
 S82  H14A  C14  C15   109.90  3.000
 S82  H14   C14  C15   110.69  3.000
 S82  H14A  C14  N1    107.75  3.000
 S82  H14   C14  N1    110.03  3.000
 S82  C15   C14  N1    111.24  3.000
 S82  H15A  C15  H15   107.34  3.000
 S82  H15A  C15  C16   109.99  3.000
 S82  H15   C15  C16   110.48  3.000
 S82  H15A  C15  C14   109.68  3.000
 S82  H15   C15  C14   109.29  3.000
 S82  C16   C15  C14   110.02  3.000
 S82  H16   C16  C19   105.73  3.000
 S82  H16   C16  C17   108.30  3.000
 S82  C19   C16  C17   111.79  3.000
 S82  H16   C16  C15   108.26  3.000
 S82  C19   C16  C15   111.58  3.000
 S82  C17   C16  C15   110.93  3.000
 S82  H17A  C17  H17   107.35  3.000
 S82  H17A  C17  C18   109.68  3.000
 S82  H17   C17  C18   109.21  3.000
 S82  H17A  C17  C16   110.05  3.000
 S82  H17   C17  C16   110.58  3.000
 S82  C18   C17  C16   109.93  3.000
 S82  H18A  C18  H18   105.92  3.000
 S82  H18A  C18  C17   110.14  3.000
 S82  H18   C18  C17   109.97  3.000
 S82  H18A  C18  N1    111.99  3.000
 S82  H18   C18  N1    107.81  3.000
 S82  C17   C18  N1    110.86  3.000
 S82  O23   C19  N20   112.29  3.000
 S82  O23   C19  C16   119.07  3.000
 S82  N20   C19  C16   128.65  3.000
 S82  C21   N20  C19   103.00  3.000
 S82  C24   C21  N22   123.94  3.000
 S82  C24   C21  N20   122.71  3.000
 S82  N22   C21  N20   113.35  3.000
 S82  O23   N22  C21   104.06  3.000
 S82  N22   O23  C19   107.31  3.000
 S82  H24   C24  C26   107.85  3.000
 S82  H24   C24  C25   108.70  3.000
 S82  C26   C24  C25   111.56  3.000
 S82  H24   C24  C21   106.26  3.000
 S82  C26   C24  C21   109.73  3.000
 S82  C25   C24  C21   112.49  3.000
 S82  H25B  C25  H25A  108.05  3.000
 S82  H25B  C25  H25   107.74  3.000
 S82  H25A  C25  H25   107.77  3.000
 S82  H25B  C25  C24   111.47  3.000
 S82  H25A  C25  C24   111.99  3.000
 S82  H25   C25  C24   109.66  3.000
 S82  H26B  C26  H26A  107.96  3.000
 S82  H26B  C26  H26   108.18  3.000
 S82  H26A  C26  H26   107.86  3.000
 S82  H26B  C26  C24   110.95  3.000
 S82  H26A  C26  C24   110.00  3.000
 S82  H26   C26  C24   111.75  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
 S82  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 S82  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 S82  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 S82  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 S82  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 S82  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 S82  CONST_07  N22  C21  N20  C19     0.00   0.0  0
 S82  CONST_08  C21  N22  O23  C19     0.00   0.0  0
 S82  CONST_09  N22  O23  C19  N20     0.00   0.0  0
 S82  CONST_10  O23  N22  C21  N20     0.00   0.0  0
 S82  CONST_11  O23  C19  N20  C21     0.00   0.0  0
 S82  CONST_12  C9   C8   C7   C5    180.00   0.0  0
 S82  CONST_13  C11  C12  C7   C5    180.00   0.0  0
 S82  CONST_14  C21  N20  C19  C16   180.00   0.0  0
 S82  CONST_15  N22  O23  C19  C16   180.00   0.0  0
 S82  CONST_16  C24  C21  N20  C19   180.00   0.0  0
 S82  CONST_17  C24  C21  N22  O23   180.00   0.0  0
 S82  CONST_18  H8   C8   C7   C5      0.00   0.0  0
 S82  CONST_19  H12  C12  C7   C5      0.00   0.0  0
 S82  CONST_20  H9   C9   C8   C7    180.00   0.0  0
 S82  CONST_21  H11  C11  C12  C7    180.00   0.0  0
 S82  CONST_22  H10  C10  C9   C8    180.00   0.0  0
 S82  CONST_23  C14  N1   C2   O13     0.00   0.0  0
 S82  CONST_25  C4   N3   C2   N1    180.00   0.0  0
 S82  CONST_26  C14  N1   C2   N3    180.00   0.0  0
 S82  CONST_28  O13  C2   N3   C4      0.00   0.0  0
 S82  Var_01    C16  C15  C14  N1    -55.81  30.0  1
 S82  Var_02    C16  C17  C18  N1     56.68  30.0  1
 S82  Var_03    C8   C7   C5   C4   -140.01  30.0  2
 S82  Var_04    C7   C5   C6   C4    109.34  30.0  1
 S82  Var_05    C17  C18  N1   C14   -60.90  30.0  1
 S82  Var_06    C18  N1   C14  C15    60.53  30.0  1
 S82  Var_07    C5   C4   N3   C2    146.07  30.0  3
 S82  Var_08    C25  C24  C21  N20   175.13  30.0  2
 S82  Var_09    H25  C25  C24  C21  -177.71  30.0  3
 S82  Var_10    H26  C26  C24  C21    56.96  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
 S82  chir_03  C16  C15  C17  C19  negativ
 S82  chir_04  C4   N3   C5   C6   both
 S82  chir_05  C5   C4   C6   C7   both

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
 S82  plan-1  C16  0.020
 S82  plan-1  C19  0.020
 S82  plan-1  N20  0.020
 S82  plan-1  C21  0.020
 S82  plan-1  N22  0.020
 S82  plan-1  O23  0.020
 S82  plan-1  C24  0.020
 S82  plan-2  N1   0.020
 S82  plan-2  C2   0.020
 S82  plan-2  N3   0.020
 S82  plan-2  C4   0.020
 S82  plan-2  O13  0.020
 S82  plan-2  C14  0.020
 S82  plan-2  C18  0.020
 S82  plan-2  HN3  0.020
 S82  plan-3  C5   0.020
 S82  plan-3  C7   0.020
 S82  plan-3  C8   0.020
 S82  plan-3  C9   0.020
 S82  plan-3  C10  0.020
 S82  plan-3  C11  0.020
 S82  plan-3  C12  0.020
 S82  plan-3  H8   0.020
 S82  plan-3  H9   0.020
 S82  plan-3  H10  0.020
 S82  plan-3  H11  0.020
 S82  plan-3  H12  0.020

