# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 02:10:56 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-(thiophen-2-ylacetyl)-4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cc1sccc1)N2CCC(CC2)c3onc(n3)c4sccc4
#
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
 RF3  RF3  1-(thiophen-2-ylacetyl)-4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine  ligand  41  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RF3
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
 RF3  C40   C  CR15  0  -0.240   6.5577  -0.3692  -0.8538
 RF3  C38   C  CR15  0  -0.186   7.6573   0.4120  -0.4007
 RF3  C36   C  CR15  0  -0.472   7.2614   1.5214   0.2798
 RF3  S35   S  S2    0   0.206   5.5522   1.6166   0.3781
 RF3  C01   C  CR5   0  -0.101   5.3483   0.1547  -0.5079
 RF3  C02   C  CH2   0  -0.703   3.9982  -0.3834  -0.8326
 RF3  C05   C  C     0   0.573   3.2596  -0.9103   0.3943
 RF3  O07   O  O     0  -0.485   3.7596  -0.8270   1.5052
 RF3  N06   N  NT    0  -0.453   2.0488  -1.4702   0.1826
 RF3  C19   C  CH2   0  -0.324   1.2267  -1.9048   1.2987
 RF3  C16   C  CH2   0  -0.422  -0.0025  -1.0153   1.4390
 RF3  C08   C  CH2   0  -0.333   1.3459  -1.4996  -1.0869
 RF3  C11   C  CH2   0  -0.419   0.1182  -0.5974  -1.0431
 RF3  C14   C  CH1   0  -0.411  -0.7908  -1.0085   0.1232
 RF3  C22   C  CR5   0   0.570  -2.0050  -0.1583   0.1909
 RF3  N26   N  N     0  -0.461  -3.2309  -0.5010  -0.0251
 RF3  O23   O  O     0  -0.328  -1.8885   1.1291   0.4871
 RF3  N24   N  N     0  -0.157  -3.1434   1.6772   0.4625
 RF3  C25   C  CR5   0   0.340  -3.9078   0.6715   0.1527
 RF3  C27   C  CR5   0  -0.278  -5.3413   0.7613   0.0028
 RF3  C28   C  CR15  0  -0.211  -6.1547   1.8528   0.1369
 RF3  C30   C  CR15  0  -0.169  -7.5165   1.5414  -0.0900
 RF3  C32   C  CR15  0  -0.460  -7.7070   0.2244  -0.3910
 RF3  S34   S  S2    0   0.264  -6.2403  -0.6494  -0.4023
 RF3  H40   H  HCR5  0   0.260   6.6596  -1.2848  -1.4207
 RF3  H38   H  HCR5  0   0.264   8.6927   0.1579  -0.5764
 RF3  H36   H  HCR5  0   0.292   7.8784   2.2831   0.7309
 RF3  H02   H  HCH2  0   0.298   3.3882   0.3827  -1.3209
 RF3  H02A  H  HCH2  0   0.305   4.1183  -1.1835  -1.5668
 RF3  H19   H  HCH2  0   0.250   0.9175  -2.9400   1.1226
 RF3  H19A  H  HCH2  0   0.274   1.8138  -1.8911   2.2123
 RF3  H16   H  HCH2  0   0.264  -0.6258  -1.3904   2.2525
 RF3  H16A  H  HCH2  0   0.248   0.3127  -0.0028   1.7031
 RF3  H08   H  HCH2  0   0.286   1.9964  -1.2022  -1.9036
 RF3  H08A  H  HCH2  0   0.258   1.0409  -2.5310  -1.2890
 RF3  H11   H  HCH2  0   0.248   0.4385   0.4419  -0.9311
 RF3  H11A  H  HCH2  0   0.266  -0.4199  -0.6755  -1.9895
 RF3  H14   H  HCH1  0   0.289  -1.1578  -2.0215  -0.0676
 RF3  H28   H  HCR5  0   0.274  -5.7923   2.8394   0.3883
 RF3  H30   H  HCR5  0   0.276  -8.3183   2.2624  -0.0325
 RF3  H32   H  HCR5  0   0.305  -8.6372  -0.2775  -0.6085

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
 RF3  C38  C40   aromatic  1.423  0.020  1.423
 RF3  C01  C40   aromatic  1.363  0.020  1.363
 RF3  C40  H40   single    0.930  0.020  1.080
 RF3  C36  C38   aromatic  1.360  0.020  1.360
 RF3  C38  H38   single    0.930  0.020  1.080
 RF3  S35  C36   aromatic  1.715  0.020  1.715
 RF3  C36  H36   single    0.930  0.020  1.080
 RF3  S35  C01   aromatic  1.722  0.020  1.722
 RF3  C01  C02   single    1.489  0.020  1.489
 RF3  C05  C02   single    1.526  0.020  1.526
 RF3  C02  H02   single    0.970  0.020  1.090
 RF3  C02  H02A  single    0.970  0.020  1.090
 RF3  O07  C05   double    1.221  0.020  1.221
 RF3  C05  N06   single    1.351  0.020  1.351
 RF3  C08  N06   single    1.451  0.020  1.451
 RF3  N06  C19   single    1.453  0.020  1.453
 RF3  C19  C16   single    1.524  0.020  1.524
 RF3  C19  H19   single    0.970  0.020  1.090
 RF3  C19  H19A  single    0.970  0.020  1.090
 RF3  C14  C16   single    1.534  0.020  1.534
 RF3  C16  H16   single    0.970  0.020  1.090
 RF3  C16  H16A  single    0.970  0.020  1.090
 RF3  C08  C11   single    1.524  0.020  1.524
 RF3  C08  H08   single    0.970  0.020  1.090
 RF3  C08  H08A  single    0.970  0.020  1.090
 RF3  C11  C14   single    1.535  0.020  1.535
 RF3  C11  H11   single    0.970  0.020  1.090
 RF3  C11  H11A  single    0.970  0.020  1.090
 RF3  C14  C22   single    1.484  0.020  1.484
 RF3  C14  H14   single    0.970  0.020  1.090
 RF3  N26  C22   aromatic  1.291  0.020  1.291
 RF3  C22  O23   aromatic  1.326  0.020  1.326
 RF3  N26  C25   aromatic  1.366  0.020  1.366
 RF3  O23  N24   aromatic  1.370  0.020  1.370
 RF3  C25  N24   aromatic  1.301  0.020  1.301
 RF3  C27  C25   single    1.444  0.020  1.444
 RF3  S34  C27   aromatic  1.721  0.020  1.721
 RF3  C27  C28   aromatic  1.368  0.020  1.368
 RF3  C30  C28   aromatic  1.415  0.020  1.415
 RF3  C28  H28   single    0.930  0.020  1.080
 RF3  C32  C30   aromatic  1.364  0.020  1.364
 RF3  C30  H30   single    0.930  0.020  1.080
 RF3  S34  C32   aromatic  1.707  0.020  1.707
 RF3  C32  H32   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
 RF3  H40   C40  C01  122.82  3.000
 RF3  H40   C40  C38  123.97  3.000
 RF3  C01   C40  C38  113.20  3.000
 RF3  H38   C38  C36  123.50  3.000
 RF3  H38   C38  C40  124.03  3.000
 RF3  C36   C38  C40  112.46  3.000
 RF3  H36   C36  S35  120.45  3.000
 RF3  H36   C36  C38  128.20  3.000
 RF3  S35   C36  C38  111.35  3.000
 RF3  C01   S35  C36   92.37  3.000
 RF3  C02   C01  S35  121.76  3.000
 RF3  C02   C01  C40  127.62  3.000
 RF3  S35   C01  C40  110.61  3.000
 RF3  H02A  C02  H02  105.91  3.000
 RF3  H02A  C02  C05  109.92  3.000
 RF3  H02   C02  C05  109.32  3.000
 RF3  H02A  C02  C01  108.15  3.000
 RF3  H02   C02  C01  110.47  3.000
 RF3  C05   C02  C01  112.85  3.000
 RF3  N06   C05  O07  122.54  3.000
 RF3  N06   C05  C02  116.81  3.000
 RF3  O07   C05  C02  120.65  3.000
 RF3  C08   N06  C19  113.07  3.000
 RF3  C19   N06  C05  120.72  3.000
 RF3  C08   N06  C05  125.42  3.000
 RF3  H19A  C19  H19  107.46  3.000
 RF3  H19A  C19  C16  110.56  3.000
 RF3  H19   C19  C16  109.82  3.000
 RF3  H19A  C19  N06  109.67  3.000
 RF3  H19   C19  N06  108.61  3.000
 RF3  C16   C19  N06  110.65  3.000
 RF3  H16A  C16  H16  107.64  3.000
 RF3  H16A  C16  C14  110.57  3.000
 RF3  H16   C16  C14  110.33  3.000
 RF3  H16A  C16  C19  109.30  3.000
 RF3  H16   C16  C19  109.19  3.000
 RF3  C14   C16  C19  109.76  3.000
 RF3  H08A  C08  H08  106.63  3.000
 RF3  H08A  C08  C11  109.80  3.000
 RF3  H08   C08  C11  110.00  3.000
 RF3  H08A  C08  N06  108.40  3.000
 RF3  H08   C08  N06  111.24  3.000
 RF3  C11   C08  N06  110.67  3.000
 RF3  H11A  C11  H11  107.53  3.000
 RF3  H11A  C11  C14  110.35  3.000
 RF3  H11   C11  C14  110.50  3.000
 RF3  H11A  C11  C08  109.27  3.000
 RF3  H11   C11  C08  109.25  3.000
 RF3  C14   C11  C08  109.90  3.000
 RF3  H14   C14  C22  105.30  3.000
 RF3  H14   C14  C11  108.30  3.000
 RF3  C22   C14  C11  111.46  3.000
 RF3  H14   C14  C16  108.53  3.000
 RF3  C22   C14  C16  112.58  3.000
 RF3  C11   C14  C16  110.41  3.000
 RF3  O23   C22  N26  112.24  3.000
 RF3  O23   C22  C14  119.64  3.000
 RF3  N26   C22  C14  128.11  3.000
 RF3  C25   N26  C22  102.76  3.000
 RF3  N24   O23  C22  107.70  3.000
 RF3  C25   N24  O23  103.49  3.000
 RF3  C27   C25  N24  124.06  3.000
 RF3  C27   C25  N26  122.13  3.000
 RF3  N24   C25  N26  113.81  3.000
 RF3  S34   C27  C28  111.50  3.000
 RF3  C28   C27  C25  129.03  3.000
 RF3  S34   C27  C25  119.47  3.000
 RF3  H28   C28  C30  124.11  3.000
 RF3  H28   C28  C27  123.50  3.000
 RF3  C30   C28  C27  112.39  3.000
 RF3  H30   C30  C32  123.54  3.000
 RF3  H30   C30  C28  123.99  3.000
 RF3  C32   C30  C28  112.47  3.000
 RF3  H32   C32  S34  120.08  3.000
 RF3  H32   C32  C30  127.86  3.000
 RF3  S34   C32  C30  112.06  3.000
 RF3  C32   S34  C27   91.59  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
 RF3  CONST_01  S35  C36  C38  C40     0.00   0.0  0
 RF3  CONST_02  C36  S35  C01  C40     0.00   0.0  0
 RF3  CONST_03  S35  C01  C40  C38     0.00   0.0  0
 RF3  CONST_04  C01  S35  C36  C38     0.00   0.0  0
 RF3  CONST_05  C01  C40  C38  C36     0.00   0.0  0
 RF3  CONST_06  N24  C25  N26  C22     0.00   0.0  0
 RF3  CONST_07  C27  C25  N26  C22   180.00   0.0  0
 RF3  CONST_08  C25  N24  O23  C22     0.00   0.0  0
 RF3  CONST_09  N24  O23  C22  N26     0.00   0.0  0
 RF3  CONST_10  O23  N24  C25  N26     0.00   0.0  0
 RF3  CONST_11  S34  C27  C25  N26     0.00   0.0  0
 RF3  CONST_12  C28  C27  C25  N26   180.00   0.0  0
 RF3  CONST_13  C25  N26  C22  O23     0.00   0.0  0
 RF3  CONST_14  C27  C25  N24  O23   180.00   0.0  0
 RF3  CONST_15  S34  C27  C25  N24   180.00   0.0  0
 RF3  CONST_16  C28  C27  C25  N24     0.00   0.0  0
 RF3  CONST_17  C32  S34  C27  C25   180.00   0.0  0
 RF3  CONST_18  C30  C28  C27  C25   180.00   0.0  0
 RF3  CONST_19  C30  C32  S34  C27     0.00   0.0  0
 RF3  CONST_20  C32  C30  C28  C27     0.00   0.0  0
 RF3  CONST_21  C32  S34  C27  C28     0.00   0.0  0
 RF3  CONST_22  S34  C32  C30  C28     0.00   0.0  0
 RF3  CONST_23  S34  C27  C28  C30     0.00   0.0  0
 RF3  CONST_24  C25  N26  C22  C14   180.00   0.0  0
 RF3  CONST_25  N24  O23  C22  C14   180.00   0.0  0
 RF3  CONST_26  C02  C01  C40  C38   180.00   0.0  0
 RF3  CONST_27  C02  C01  S35  C36   180.00   0.0  0
 RF3  CONST_28  H36  C36  C38  C40   180.00   0.0  0
 RF3  CONST_29  H40  C40  C38  C36   180.00   0.0  0
 RF3  CONST_30  H38  C38  C36  S35   180.00   0.0  0
 RF3  CONST_31  H28  C28  C27  C25     0.00   0.0  0
 RF3  CONST_32  H32  C32  S34  C27   180.00   0.0  0
 RF3  CONST_33  H30  C30  C28  C27   180.00   0.0  0
 RF3  CONST_34  C08  N06  C05  C02     0.00   0.0  0
 RF3  CONST_35  C19  N06  C05  C02   180.00   0.0  0
 RF3  CONST_36  C08  N06  C05  O07   180.00   0.0  0
 RF3  CONST_37  C19  N06  C05  O07     0.00   0.0  0
 RF3  Var_01    C14  C11  C08  N06   -55.95  30.0  1
 RF3  Var_02    C14  C16  C19  N06    56.29  30.0  1
 RF3  Var_03    C11  C08  N06  C19    59.33  30.0  1
 RF3  Var_04    C08  N06  C19  C16   -59.54  30.0  1
 RF3  Var_05    C05  C02  C01  C40   111.19  30.0  2
 RF3  Var_06    N06  C05  C02  C01  -177.24  30.0  1

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
 RF3  chir_01  C14  C16  C11  C22  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
 RF3  plan-1  C40  0.020
 RF3  plan-1  C38  0.020
 RF3  plan-1  C36  0.020
 RF3  plan-1  S35  0.020
 RF3  plan-1  C01  0.020
 RF3  plan-1  C02  0.020
 RF3  plan-1  H40  0.020
 RF3  plan-1  H38  0.020
 RF3  plan-1  H36  0.020
 RF3  plan-2  C14  0.020
 RF3  plan-2  C22  0.020
 RF3  plan-2  N26  0.020
 RF3  plan-2  O23  0.020
 RF3  plan-2  N24  0.020
 RF3  plan-2  C25  0.020
 RF3  plan-2  C27  0.020
 RF3  plan-3  C25  0.020
 RF3  plan-3  C27  0.020
 RF3  plan-3  C28  0.020
 RF3  plan-3  C30  0.020
 RF3  plan-3  C32  0.020
 RF3  plan-3  S34  0.020
 RF3  plan-3  H28  0.020
 RF3  plan-3  H30  0.020
 RF3  plan-3  H32  0.020
 RF3  plan-4  C02  0.020
 RF3  plan-4  C05  0.020
 RF3  plan-4  O07  0.020
 RF3  plan-4  N06  0.020
 RF3  plan-4  C19  0.020
 RF3  plan-4  C08  0.020

