# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:07:14 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 4-({2-[5-(3-methoxybenzyl)-1,3,4-oxadiazol-2-yl]-1-benzothiophen-3-yl}oxy)piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cc2oc(nn2)c3sc4ccccc4c3OC5CCNCC5)c1
#
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
 3F3  3F3  4-({2-[5-(3-methoxybenzyl)-1,3,4-oxadiazol-2-yl]-1-benzothiophen-3-yl}oxy)piperidine  ligand  53  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3F3
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
 3F3  C     C  CH3   0  -0.437   7.1247   1.0448  -2.8071
 3F3  O     O  O2    0  -0.472   6.3434   0.1798  -2.0065
 3F3  C1    C  CR6   0   0.398   5.7870   0.6705  -0.8835
 3F3  C22   C  CR16  0  -0.391   5.9201   1.9888  -0.4510
 3F3  C21   C  CR16  0  -0.227   5.3011   2.3838   0.7285
 3F3  C20   C  CR16  0  -0.332   4.5562   1.4911   1.4820
 3F3  C3    C  CR6   0   0.126   4.4262   0.1740   1.0508
 3F3  C2    C  CR16  0  -0.372   5.0369  -0.2301  -0.1263
 3F3  C4    C  CH2   0  -0.646   3.6043  -0.8184   1.8396
 3F3  C5    C  CR5   0   0.488   2.2993  -1.0732   1.1884
 3F3  O1    O  O     0  -0.417   1.4295  -0.0598   1.0346
 3F3  C6    C  CR5   0   0.531   0.3907  -0.6288   0.3972
 3F3  N1    N  N     0  -0.309   0.5992  -1.8823   0.1754
 3F3  N     N  N     0  -0.304   1.8376  -2.1633   0.6904
 3F3  C7    C  CR5   0  -0.448  -0.7280   0.2106   0.0725
 3F3  S     S  S2    0   0.257  -0.6709   1.9049   0.4730
 3F3  C19   C  CR56  0  -0.223  -2.2390   2.1502  -0.2190
 3F3  C18   C  CR16  0  -0.279  -2.9246   3.3596  -0.2955
 3F3  C17   C  CR16  0  -0.259  -4.1545   3.3705  -0.9229
 3F3  C16   C  CR16  0  -0.251  -4.6933   2.2009  -1.4771
 3F3  C15   C  CR16  0  -0.307  -4.0137   1.0047  -1.3984
 3F3  C14   C  CR56  0   0.163  -2.7739   0.9666  -0.7475
 3F3  C8    C  CR5   0   0.409  -1.8836  -0.1459  -0.5602
 3F3  O2    O  O2    0  -0.480  -2.1366  -1.3849  -0.9984
 3F3  C9    C  CH1   0   0.034  -3.1670  -2.1216  -0.3079
 3F3  C13   C  CH2   0  -0.457  -3.4488  -3.3650  -1.1283
 3F3  C12   C  CH2   0  -0.305  -4.4832  -4.2255  -0.4137
 3F3  N2    N  NH1   0  -0.594  -4.0085  -4.5654   0.9145
 3F3  C11   C  CH2   0  -0.299  -3.8211  -3.3816   1.7326
 3F3  C10   C  CH2   0  -0.452  -2.7560  -2.4854   1.1098
 3F3  HC1   H  HCH3  0   0.229   7.9903   1.4323  -2.2637
 3F3  HC2   H  HCH3  0   0.260   7.4750   0.4536  -3.6494
 3F3  HC3   H  HCH3  0   0.229   6.5409   1.8869  -3.1873
 3F3  H22   H  HCR6  0   0.281   6.4978   2.7122  -1.0097
 3F3  H2    H  HCR6  0   0.259   4.9377  -1.2541  -0.4693
 3F3  H21   H  HCR6  0   0.261   5.4085   3.4088   1.0589
 3F3  H20   H  HCR6  0   0.253   4.0815   1.8127   2.4002
 3F3  H41C  H  HCH2  0   0.306   4.1202  -1.7752   1.9213
 3F3  H42C  H  HCH2  0   0.304   3.4377  -0.4529   2.8554
 3F3  H18   H  HCR6  0   0.276  -2.5029   4.2669   0.1164
 3F3  H17   H  HCR6  0   0.269  -4.7048   4.2989  -0.9979
 3F3  H16   H  HCR6  0   0.266  -5.6508   2.2418  -1.9787
 3F3  H15   H  HCR6  0   0.265  -4.4292   0.1105  -1.8443
 3F3  H9    H  HCH1  0   0.222  -4.0775  -1.5094  -0.2659
 3F3  H131  H  HCH2  0   0.244  -3.8150  -3.0920  -2.1206
 3F3  H132  H  HCH2  0   0.231  -2.5241  -3.9350  -1.2550
 3F3  H101  H  HCH2  0   0.239  -1.7983  -3.0101   1.0855
 3F3  H102  H  HCH2  0   0.238  -2.6344  -1.5887   1.7225
 3F3  H121  H  HCH2  0   0.193  -5.4437  -3.6841  -0.3927
 3F3  H122  H  HCH2  0   0.241  -4.6509  -5.1431  -0.9795
 3F3  HA    H  HNH1  0   0.355  -4.6694  -5.1865   1.3619
 3F3  H111  H  HCH2  0   0.192  -4.7514  -2.8023   1.8567
 3F3  H112  H  HCH2  0   0.240  -3.5030  -3.6838   2.7317

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
 3F3  C    O     single    1.414  0.020  1.414
 3F3  O    C1    single    1.346  0.020  1.346
 3F3  C1   C22   aromatic  1.394  0.020  1.394
 3F3  C1   C2    aromatic  1.395  0.020  1.395
 3F3  C22  C21   aromatic  1.389  0.020  1.389
 3F3  C21  C20   aromatic  1.385  0.020  1.385
 3F3  C20  C3    aromatic  1.392  0.020  1.392
 3F3  C3   C2    aromatic  1.386  0.020  1.386
 3F3  C3   C4    single    1.511  0.020  1.511
 3F3  C4   C5    single    1.481  0.020  1.481
 3F3  C5   O1    aromatic  1.344  0.020  1.344
 3F3  C5   N     aromatic  1.284  0.020  1.284
 3F3  O1   C6    aromatic  1.345  0.020  1.345
 3F3  C6   N1    aromatic  1.290  0.020  1.290
 3F3  C6   C7    single    1.436  0.020  1.436
 3F3  N1   N     aromatic  1.370  0.020  1.370
 3F3  C7   S     aromatic  1.742  0.020  1.742
 3F3  C7   C8    aromatic  1.365  0.020  1.365
 3F3  S    C19   aromatic  1.731  0.020  1.731
 3F3  C19  C18   aromatic  1.392  0.020  1.392
 3F3  C19  C14   aromatic  1.402  0.020  1.402
 3F3  C18  C17   aromatic  1.381  0.020  1.381
 3F3  C17  C16   aromatic  1.402  0.020  1.402
 3F3  C16  C15   aromatic  1.378  0.020  1.378
 3F3  C15  C14   aromatic  1.401  0.020  1.401
 3F3  C14  C8    aromatic  1.437  0.020  1.437
 3F3  C8   O2    single    1.338  0.020  1.338
 3F3  O2   C9    single    1.443  0.020  1.443
 3F3  C9   C13   single    1.516  0.020  1.516
 3F3  C9   C10   single    1.520  0.020  1.520
 3F3  C13  C12   single    1.523  0.020  1.523
 3F3  C12  N2    single    1.451  0.020  1.451
 3F3  N2   C11   single    1.451  0.020  1.451
 3F3  C11  C10   single    1.525  0.020  1.525
 3F3  C    HC1   single    0.970  0.020  1.090
 3F3  C    HC2   single    0.970  0.020  1.090
 3F3  C    HC3   single    0.970  0.020  1.090
 3F3  C22  H22   single    0.930  0.020  1.080
 3F3  C2   H2    single    0.930  0.020  1.080
 3F3  C21  H21   single    0.930  0.020  1.080
 3F3  C20  H20   single    0.930  0.020  1.080
 3F3  C4   H41C  single    0.970  0.020  1.090
 3F3  C4   H42C  single    0.970  0.020  1.090
 3F3  C18  H18   single    0.930  0.020  1.080
 3F3  C17  H17   single    0.930  0.020  1.080
 3F3  C16  H16   single    0.930  0.020  1.080
 3F3  C15  H15   single    0.930  0.020  1.080
 3F3  C9   H9    single    0.970  0.020  1.090
 3F3  C13  H131  single    0.970  0.020  1.090
 3F3  C13  H132  single    0.970  0.020  1.090
 3F3  C10  H101  single    0.970  0.020  1.090
 3F3  C10  H102  single    0.970  0.020  1.090
 3F3  C12  H121  single    0.970  0.020  1.090
 3F3  C12  H122  single    0.970  0.020  1.090
 3F3  N2   HA    single    0.890  0.020  1.040
 3F3  C11  H111  single    0.970  0.020  1.090
 3F3  C11  H112  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
 3F3  HC3   C    HC2   108.76  3.000
 3F3  HC3   C    HC1   108.83  3.000
 3F3  HC2   C    HC1   108.83  3.000
 3F3  HC3   C    O     111.91  3.000
 3F3  HC2   C    O     106.51  3.000
 3F3  HC1   C    O     111.90  3.000
 3F3  C1    O    C     118.54  3.000
 3F3  C2    C1   C22   119.56  3.000
 3F3  C2    C1   O     116.09  3.000
 3F3  C22   C1   O     124.35  3.000
 3F3  H22   C22  C21   119.11  3.000
 3F3  H22   C22  C1    121.57  3.000
 3F3  C21   C22  C1    119.32  3.000
 3F3  H21   C21  C20   119.83  3.000
 3F3  H21   C21  C22   118.96  3.000
 3F3  C20   C21  C22   121.20  3.000
 3F3  H20   C20  C3    120.19  3.000
 3F3  H20   C20  C21   120.37  3.000
 3F3  C3    C20  C21   119.43  3.000
 3F3  C4    C3   C2    119.44  3.000
 3F3  C4    C3   C20   120.70  3.000
 3F3  C2    C3   C20   119.85  3.000
 3F3  H2    C2   C3    120.23  3.000
 3F3  H2    C2   C1    119.14  3.000
 3F3  C3    C2   C1    120.63  3.000
 3F3  H42C  C4   H41C  107.23  3.000
 3F3  H42C  C4   C5    109.39  3.000
 3F3  H41C  C4   C5    107.41  3.000
 3F3  H42C  C4   C3    110.41  3.000
 3F3  H41C  C4   C3    110.99  3.000
 3F3  C5    C4   C3    111.28  3.000
 3F3  N     C5   O1    111.28  3.000
 3F3  N     C5   C4    129.31  3.000
 3F3  O1    C5   C4    119.40  3.000
 3F3  C6    O1   C5    103.60  3.000
 3F3  C7    C6   N1    130.93  3.000
 3F3  C7    C6   O1    117.49  3.000
 3F3  N1    C6   O1    111.57  3.000
 3F3  N     N1   C6    106.30  3.000
 3F3  N1    N    C5    107.25  3.000
 3F3  C8    C7   S     112.85  3.000
 3F3  C8    C7   C6    127.73  3.000
 3F3  S     C7   C6    119.41  3.000
 3F3  C19   S    C7     90.93  3.000
 3F3  C14   C19  C18   121.64  3.000
 3F3  C14   C19  S     112.12  3.000
 3F3  C18   C19  S     126.22  3.000
 3F3  H18   C18  C17   120.90  3.000
 3F3  H18   C18  C19   121.03  3.000
 3F3  C17   C18  C19   118.06  3.000
 3F3  H17   C17  C16   119.54  3.000
 3F3  H17   C17  C18   119.43  3.000
 3F3  C16   C17  C18   121.02  3.000
 3F3  H16   C16  C15   119.73  3.000
 3F3  H16   C16  C17   119.47  3.000
 3F3  C15   C16  C17   120.80  3.000
 3F3  H15   C15  C14   120.59  3.000
 3F3  H15   C15  C16   120.29  3.000
 3F3  C14   C15  C16   119.12  3.000
 3F3  C8    C14  C15   129.05  3.000
 3F3  C8    C14  C19   111.59  3.000
 3F3  C15   C14  C19   119.33  3.000
 3F3  O2    C8   C14   123.84  3.000
 3F3  O2    C8   C7    123.62  3.000
 3F3  C14   C8   C7    112.51  3.000
 3F3  C9    O2   C8    116.81  3.000
 3F3  H9    C9   C10   108.78  3.000
 3F3  H9    C9   C13   108.90  3.000
 3F3  C10   C9   C13   111.02  3.000
 3F3  H9    C9   O2    109.02  3.000
 3F3  C10   C9   O2    112.05  3.000
 3F3  C13   C9   O2    107.01  3.000
 3F3  H132  C13  H131  107.97  3.000
 3F3  H132  C13  C12   109.51  3.000
 3F3  H131  C13  C12   109.86  3.000
 3F3  H132  C13  C9    109.45  3.000
 3F3  H131  C13  C9    110.42  3.000
 3F3  C12   C13  C9    109.60  3.000
 3F3  H122  C12  H121  106.79  3.000
 3F3  H122  C12  N2    109.15  3.000
 3F3  H121  C12  N2    112.50  3.000
 3F3  H122  C12  C13   109.64  3.000
 3F3  H121  C12  C13   108.84  3.000
 3F3  N2    C12  C13   109.85  3.000
 3F3  HA    N2   C11   109.63  3.000
 3F3  HA    N2   C12   109.58  3.000
 3F3  C11   N2   C12   111.54  3.000
 3F3  H112  C11  H111  106.76  3.000
 3F3  H112  C11  C10   109.45  3.000
 3F3  H111  C11  C10   109.05  3.000
 3F3  H112  C11  N2    109.14  3.000
 3F3  H111  C11  N2    112.52  3.000
 3F3  C10   C11  N2    109.84  3.000
 3F3  H102  C10  H101  108.00  3.000
 3F3  H102  C10  C11   109.33  3.000
 3F3  H101  C10  C11   109.83  3.000
 3F3  H102  C10  C9    110.89  3.000
 3F3  H101  C10  C9    109.34  3.000
 3F3  C11   C10  C9    109.43  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
 3F3  CONST_01  C20  C21  C22  C1     0.00   0.0  0
 3F3  CONST_02  C20  C3   C2   C1     0.00   0.0  0
 3F3  CONST_03  C3   C2   C1   C22    0.00   0.0  0
 3F3  CONST_04  C3   C20  C21  C22    0.00   0.0  0
 3F3  CONST_05  C2   C1   C22  C21    0.00   0.0  0
 3F3  CONST_06  C2   C3   C20  C21    0.00   0.0  0
 3F3  CONST_07  N1   C6   O1   C5     0.00   0.0  0
 3F3  CONST_08  C7   C6   O1   C5   180.00   0.0  0
 3F3  CONST_09  C6   N1   N    C5     0.00   0.0  0
 3F3  CONST_10  N1   N    C5   O1     0.00   0.0  0
 3F3  CONST_11  N    N1   C6   O1     0.00   0.0  0
 3F3  CONST_12  S    C7   C6   O1     0.00   0.0  0
 3F3  CONST_13  C8   C7   C6   O1   180.00   0.0  0
 3F3  CONST_14  N    C5   O1   C6     0.00   0.0  0
 3F3  CONST_15  C19  S    C7   C6   180.00   0.0  0
 3F3  CONST_16  C14  C8   C7   C6   180.00   0.0  0
 3F3  CONST_17  S    C7   C6   N1   180.00   0.0  0
 3F3  CONST_18  C8   C7   C6   N1     0.00   0.0  0
 3F3  CONST_19  C7   C6   N1   N    180.00   0.0  0
 3F3  CONST_20  C18  C19  S    C7   180.00   0.0  0
 3F3  CONST_21  C14  C19  S    C7     0.00   0.0  0
 3F3  CONST_22  C19  C14  C8   C7     0.00   0.0  0
 3F3  CONST_23  C15  C14  C8   C7   180.00   0.0  0
 3F3  CONST_24  C14  C8   C7   S      0.00   0.0  0
 3F3  CONST_25  C17  C18  C19  S    180.00   0.0  0
 3F3  CONST_26  C15  C14  C19  S    180.00   0.0  0
 3F3  CONST_27  C8   C14  C19  S      0.00   0.0  0
 3F3  CONST_28  C8   C7   S    C19    0.00   0.0  0
 3F3  CONST_29  C16  C17  C18  C19    0.00   0.0  0
 3F3  CONST_30  C16  C15  C14  C19    0.00   0.0  0
 3F3  CONST_31  C15  C14  C19  C18    0.00   0.0  0
 3F3  CONST_32  C8   C14  C19  C18  180.00   0.0  0
 3F3  CONST_33  C15  C16  C17  C18    0.00   0.0  0
 3F3  CONST_34  C14  C19  C18  C17    0.00   0.0  0
 3F3  CONST_35  C14  C15  C16  C17    0.00   0.0  0
 3F3  CONST_36  C8   C14  C15  C16  180.00   0.0  0
 3F3  CONST_37  C21  C22  C1   O    180.00   0.0  0
 3F3  CONST_38  C3   C2   C1   O    180.00   0.0  0
 3F3  CONST_39  C4   C3   C2   C1   180.00   0.0  0
 3F3  CONST_40  C4   C3   C20  C21  180.00   0.0  0
 3F3  CONST_41  C6   O1   C5   C4   180.00   0.0  0
 3F3  CONST_42  N1   N    C5   C4   180.00   0.0  0
 3F3  CONST_43  O2   C8   C7   C6     0.00   0.0  0
 3F3  CONST_44  O2   C8   C7   S    180.00   0.0  0
 3F3  CONST_45  O2   C8   C14  C19  180.00   0.0  0
 3F3  CONST_46  O2   C8   C14  C15    0.00   0.0  0
 3F3  CONST_47  H21  C21  C22  C1   180.00   0.0  0
 3F3  CONST_48  H2   C2   C1   C22  180.00   0.0  0
 3F3  CONST_49  H20  C20  C21  C22  180.00   0.0  0
 3F3  CONST_50  H22  C22  C21  C20  180.00   0.0  0
 3F3  CONST_51  H18  C18  C19  S      0.00   0.0  0
 3F3  CONST_52  H17  C17  C18  C19  180.00   0.0  0
 3F3  CONST_53  H15  C15  C14  C19  180.00   0.0  0
 3F3  CONST_54  H16  C16  C17  C18  180.00   0.0  0
 3F3  Var_01    N2   C12  C13  C9   -57.35  30.0  1
 3F3  Var_02    N2   C11  C10  C9    57.37  30.0  1
 3F3  Var_03    C11  N2   C12  C13   62.15  30.0  1
 3F3  Var_04    C10  C11  N2   C12  -62.23  30.0  1
 3F3  Var_05    C5   C4   C3   C20  104.16  30.0  2
 3F3  Var_06    O1   C5   C4   C3   -62.00  30.0  2
 3F3  Var_07    C22  C1   O    C      0.40  30.0  2
 3F3  Var_08    HC1  C    O    C1    61.03  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
 3F3  chir_01  C9  O2  C13  C10  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
 3F3  plan-1  C4   0.020
 3F3  plan-1  C5   0.020
 3F3  plan-1  O1   0.020
 3F3  plan-1  C6   0.020
 3F3  plan-1  N1   0.020
 3F3  plan-1  N    0.020
 3F3  plan-1  C7   0.020
 3F3  plan-2  O    0.020
 3F3  plan-2  C1   0.020
 3F3  plan-2  C22  0.020
 3F3  plan-2  C21  0.020
 3F3  plan-2  C20  0.020
 3F3  plan-2  C3   0.020
 3F3  plan-2  C2   0.020
 3F3  plan-2  C4   0.020
 3F3  plan-2  H22  0.020
 3F3  plan-2  H2   0.020
 3F3  plan-2  H21  0.020
 3F3  plan-2  H20  0.020
 3F3  plan-3  C6   0.020
 3F3  plan-3  C7   0.020
 3F3  plan-3  S    0.020
 3F3  plan-3  C19  0.020
 3F3  plan-3  C18  0.020
 3F3  plan-3  C17  0.020
 3F3  plan-3  C16  0.020
 3F3  plan-3  C15  0.020
 3F3  plan-3  C14  0.020
 3F3  plan-3  C8   0.020
 3F3  plan-3  O2   0.020
 3F3  plan-3  H18  0.020
 3F3  plan-3  H17  0.020
 3F3  plan-3  H16  0.020
 3F3  plan-3  H15  0.020

