# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:46:02 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-[(2-{5-[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]-1,3,4-oxadiazol-2-yl}-1-benzothiophen-3-yl)oxy]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(C)c(Cc2oc(nn2)c3sc4ccccc4c3OC5CCNCC5)c1C
#
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
 YNE  YNE  4-[(2-{5-[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]-1,3,4-oxadiazol-2-yl}-1-benzothiophen-3-yl)oxy]piperidine  ligand  55  30  .  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_YNE
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
 YNE  C4    C  CH3   0  -0.750  -4.0386   2.1268  -1.4621
 YNE  C3    C  CR5   0   0.417  -4.6621   1.2243  -0.4596
 YNE  N1    N  NR5   0  -0.323  -5.4557   1.6605   0.5385
 YNE  C2    C  CH3   0  -0.520  -5.8939   3.0122   0.7823
 YNE  N     N  N     0  -0.314  -5.8993   0.6682   1.3145
 YNE  C5    C  CR5   0  -0.209  -4.5832  -0.1461  -0.3099
 YNE  C1    C  CR5   0   0.262  -5.3739  -0.4359   0.8197
 YNE  C     C  CH3   0  -0.746  -5.6216  -1.7712   1.4321
 YNE  C6    C  CH2   0  -0.675  -3.7798  -1.1173  -1.1155
 YNE  C7    C  CR5   0   0.487  -2.4167  -1.2807  -0.5549
 YNE  O     O  O     0  -0.417  -1.5769  -0.2314  -0.5797
 YNE  C8    C  CR5   0   0.526  -0.4703  -0.6950   0.0270
 YNE  N3    N  N     0  -0.310  -0.6131  -1.9210   0.4000
 YNE  N2    N  N     0  -0.307  -1.8757  -2.2960   0.0161
 YNE  C9    C  CR5   0  -0.448   0.6353   0.2120   0.1604
 YNE  S     S  S2    0   0.257   0.4038   1.8929  -0.2392
 YNE  C21   C  CR56  0  -0.221   2.0419   2.2524   0.1922
 YNE  C20   C  CR16  0  -0.280   2.6520   3.5034   0.1528
 YNE  C19   C  CR16  0  -0.258   3.9647   3.5990   0.5703
 YNE  C18   C  CR16  0  -0.252   4.6630   2.4722   1.0265
 YNE  C17   C  CR16  0  -0.305   4.0573   1.2349   1.0632
 YNE  C16   C  CR56  0   0.164   2.7311   1.1138   0.6315
 YNE  C10   C  CR5   0   0.402   1.8983  -0.0570   0.6010
 YNE  O1    O  O2    0  -0.480   2.3185  -1.2632   1.0019
 YNE  C11   C  CH1   0   0.025   3.2153  -1.9603   0.1108
 YNE  C15   C  CH2   0  -0.458   4.0855  -2.8760   0.9487
 YNE  C14   C  CH2   0  -0.304   4.9982  -3.6853   0.0347
 YNE  N4    N  NH1   0  -0.595   4.2041  -4.4360  -0.9199
 YNE  C13   C  CH2   0  -0.301   3.4272  -3.5596  -1.7782
 YNE  C12   C  CH2   0  -0.435   2.4483  -2.7484  -0.9375
 YNE  H41C  H  HCH3  0   0.260  -3.3461   2.8297  -0.9956
 YNE  H42C  H  HCH3  0   0.261  -3.4753   1.5500  -2.1925
 YNE  H43C  H  HCH3  0   0.261  -4.7830   2.7093  -2.0060
 YNE  H21C  H  HCH3  0   0.254  -6.8519   3.2138   0.3030
 YNE  H22C  H  HCH3  0   0.264  -5.9945   3.1664   1.8534
 YNE  H23C  H  HCH3  0   0.259  -5.1571   3.7143   0.4001
 YNE  H61C  H  HCH2  0   0.298  -4.2532  -2.0995  -1.1265
 YNE  H62C  H  HCH2  0   0.301  -3.7018  -0.7982  -2.1581
 YNE  HC1   H  HCH3  0   0.246  -6.1104  -2.4479   0.7287
 YNE  HC2   H  HCH3  0   0.243  -4.6892  -2.2485   1.7388
 YNE  HC3   H  HCH3  0   0.251  -6.2599  -1.6839   2.3098
 YNE  H20   H  HCR6  0   0.275   2.1123   4.3776  -0.1867
 YNE  H19   H  HCR6  0   0.269   4.4584   4.5615   0.5530
 YNE  H18   H  HCR6  0   0.266   5.6867   2.5801   1.3588
 YNE  H17   H  HCR6  0   0.265   4.5967   0.3703   1.4288
 YNE  H11   H  HCH1  0   0.226   3.8571  -1.2287  -0.3984
 YNE  H151  H  HCH2  0   0.244   4.6872  -2.2963   1.6530
 YNE  H152  H  HCH2  0   0.232   3.4533  -3.5549   1.5281
 YNE  H121  H  HCH2  0   0.233   1.7398  -3.4165  -0.4433
 YNE  H122  H  HCH2  0   0.236   1.8775  -2.0774  -1.5834
 YNE  H141  H  HCH2  0   0.194   5.7096  -2.9986  -0.4539
 YNE  H142  H  HCH2  0   0.241   5.5908  -4.3799   0.6320
 YNE  H4    H  HNH1  0   0.355   4.8129  -5.0115  -1.4867
 YNE  H131  H  HCH2  0   0.194   4.0593  -2.8665  -2.3576
 YNE  H132  H  HCH2  0   0.240   2.8765  -4.1643  -2.5007

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
 YNE  C4   C3    single    1.486  0.020  1.486
 YNE  C3   N1    aromatic  1.348  0.020  1.348
 YNE  C3   C5    aromatic  1.381  0.020  1.381
 YNE  N1   C2    single    1.442  0.020  1.442
 YNE  N1   N     aromatic  1.335  0.020  1.335
 YNE  N    C1    aromatic  1.319  0.020  1.319
 YNE  C5   C1    aromatic  1.409  0.020  1.409
 YNE  C5   C6    single    1.496  0.020  1.496
 YNE  C1   C     single    1.490  0.020  1.490
 YNE  C6   C7    single    1.483  0.020  1.483
 YNE  C7   O     aromatic  1.344  0.020  1.344
 YNE  C7   N2    aromatic  1.284  0.020  1.284
 YNE  O    C8    aromatic  1.345  0.020  1.345
 YNE  C8   N3    aromatic  1.289  0.020  1.289
 YNE  C8   C9    single    1.436  0.020  1.436
 YNE  N3   N2    aromatic  1.372  0.020  1.372
 YNE  C9   S     aromatic  1.743  0.020  1.743
 YNE  C9   C10   aromatic  1.364  0.020  1.364
 YNE  S    C21   aromatic  1.732  0.020  1.732
 YNE  C21  C20   aromatic  1.392  0.020  1.392
 YNE  C21  C16   aromatic  1.402  0.020  1.402
 YNE  C20  C19   aromatic  1.381  0.020  1.381
 YNE  C19  C18   aromatic  1.402  0.020  1.402
 YNE  C18  C17   aromatic  1.378  0.020  1.378
 YNE  C17  C16   aromatic  1.400  0.020  1.400
 YNE  C16  C10   aromatic  1.437  0.020  1.437
 YNE  C10  O1    single    1.339  0.020  1.339
 YNE  O1   C11   single    1.444  0.020  1.444
 YNE  C11  C15   single    1.516  0.020  1.516
 YNE  C11  C12   single    1.519  0.020  1.519
 YNE  C15  C14   single    1.524  0.020  1.524
 YNE  C14  N4    single    1.451  0.020  1.451
 YNE  N4   C13   single    1.452  0.020  1.452
 YNE  C13  C12   single    1.524  0.020  1.524
 YNE  C4   H41C  single    0.970  0.020  1.090
 YNE  C4   H42C  single    0.970  0.020  1.090
 YNE  C4   H43C  single    0.970  0.020  1.090
 YNE  C2   H21C  single    0.970  0.020  1.090
 YNE  C2   H22C  single    0.970  0.020  1.090
 YNE  C2   H23C  single    0.970  0.020  1.090
 YNE  C6   H61C  single    0.970  0.020  1.090
 YNE  C6   H62C  single    0.970  0.020  1.090
 YNE  C    HC1   single    0.970  0.020  1.090
 YNE  C    HC2   single    0.970  0.020  1.090
 YNE  C    HC3   single    0.970  0.020  1.090
 YNE  C20  H20   single    0.930  0.020  1.080
 YNE  C19  H19   single    0.930  0.020  1.080
 YNE  C18  H18   single    0.930  0.020  1.080
 YNE  C17  H17   single    0.930  0.020  1.080
 YNE  C11  H11   single    0.970  0.020  1.090
 YNE  C15  H151  single    0.970  0.020  1.090
 YNE  C15  H152  single    0.970  0.020  1.090
 YNE  C12  H121  single    0.970  0.020  1.090
 YNE  C12  H122  single    0.970  0.020  1.090
 YNE  C14  H141  single    0.970  0.020  1.090
 YNE  C14  H142  single    0.970  0.020  1.090
 YNE  N4   H4    single    0.890  0.020  1.040
 YNE  C13  H131  single    0.970  0.020  1.090
 YNE  C13  H132  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
 YNE  H43C  C4   H42C  107.56  3.000
 YNE  H43C  C4   H41C  107.59  3.000
 YNE  H42C  C4   H41C  107.46  3.000
 YNE  H43C  C4   C3    111.99  3.000
 YNE  H42C  C4   C3    110.38  3.000
 YNE  H41C  C4   C3    111.65  3.000
 YNE  C5    C3   N1    105.93  3.000
 YNE  C5    C3   C4    130.69  3.000
 YNE  N1    C3   C4    123.38  3.000
 YNE  N     N1   C2    119.83  3.000
 YNE  N     N1   C3    112.67  3.000
 YNE  C2    N1   C3    127.42  3.000
 YNE  H23C  C2   H22C  108.52  3.000
 YNE  H23C  C2   H21C  108.76  3.000
 YNE  H22C  C2   H21C  109.01  3.000
 YNE  H23C  C2   N1    109.88  3.000
 YNE  H22C  C2   N1    109.14  3.000
 YNE  H21C  C2   N1    111.48  3.000
 YNE  C1    N    N1    105.76  3.000
 YNE  C6    C5   C1    126.84  3.000
 YNE  C6    C5   C3    128.07  3.000
 YNE  C1    C5   C3    105.01  3.000
 YNE  C     C1   C5    127.39  3.000
 YNE  C     C1   N     122.00  3.000
 YNE  C5    C1   N     110.61  3.000
 YNE  HC3   C    HC2   108.02  3.000
 YNE  HC3   C    HC1   107.86  3.000
 YNE  HC2   C    HC1   107.01  3.000
 YNE  HC3   C    C1    110.91  3.000
 YNE  HC2   C    C1    111.43  3.000
 YNE  HC1   C    C1    111.42  3.000
 YNE  H62C  C6   H61C  106.52  3.000
 YNE  H62C  C6   C7    109.10  3.000
 YNE  H61C  C6   C7    107.68  3.000
 YNE  H62C  C6   C5    111.25  3.000
 YNE  H61C  C6   C5    110.92  3.000
 YNE  C7    C6   C5    111.20  3.000
 YNE  N2    C7   O     111.23  3.000
 YNE  N2    C7   C6    129.96  3.000
 YNE  O     C7   C6    118.77  3.000
 YNE  C8    O    C7    103.69  3.000
 YNE  C9    C8   N3    131.21  3.000
 YNE  C9    C8   O     117.24  3.000
 YNE  N3    C8   O     111.55  3.000
 YNE  N2    N3   C8    106.31  3.000
 YNE  N3    N2   C7    107.21  3.000
 YNE  C10   C9   S     112.77  3.000
 YNE  C10   C9   C8    128.17  3.000
 YNE  S     C9   C8    119.04  3.000
 YNE  C21   S    C9     91.00  3.000
 YNE  C16   C21  C20   121.56  3.000
 YNE  C16   C21  S     112.00  3.000
 YNE  C20   C21  S     126.44  3.000
 YNE  H20   C20  C19   120.88  3.000
 YNE  H20   C20  C21   121.08  3.000
 YNE  C19   C20  C21   118.04  3.000
 YNE  H19   C19  C18   119.53  3.000
 YNE  H19   C19  C20   119.38  3.000
 YNE  C18   C19  C20   121.08  3.000
 YNE  H18   C18  C17   119.82  3.000
 YNE  H18   C18  C19   119.42  3.000
 YNE  C17   C18  C19   120.75  3.000
 YNE  H17   C17  C16   120.47  3.000
 YNE  H17   C17  C18   120.46  3.000
 YNE  C16   C17  C18   119.07  3.000
 YNE  C10   C16  C17   128.76  3.000
 YNE  C10   C16  C21   111.73  3.000
 YNE  C17   C16  C21   119.48  3.000
 YNE  O1    C10  C16   123.08  3.000
 YNE  O1    C10  C9    124.40  3.000
 YNE  C16   C10  C9    112.50  3.000
 YNE  C11   O1   C10   116.44  3.000
 YNE  H11   C11  C12   108.70  3.000
 YNE  H11   C11  C15   108.85  3.000
 YNE  C12   C11  C15   110.97  3.000
 YNE  H11   C11  O1    109.11  3.000
 YNE  C12   C11  O1    111.27  3.000
 YNE  C15   C11  O1    107.88  3.000
 YNE  H152  C15  H151  107.83  3.000
 YNE  H152  C15  C14   109.52  3.000
 YNE  H151  C15  C14   109.78  3.000
 YNE  H152  C15  C11   109.63  3.000
 YNE  H151  C15  C11   110.61  3.000
 YNE  C14   C15  C11   109.45  3.000
 YNE  H142  C14  H141  106.77  3.000
 YNE  H142  C14  N4    109.15  3.000
 YNE  H141  C14  N4    112.56  3.000
 YNE  H142  C14  C15   109.57  3.000
 YNE  H141  C14  C15   108.74  3.000
 YNE  N4    C14  C15   109.97  3.000
 YNE  H4    N4   C13   109.53  3.000
 YNE  H4    N4   C14   109.49  3.000
 YNE  C13   N4   C14   111.68  3.000
 YNE  H132  C13  H131  106.84  3.000
 YNE  H132  C13  C12   109.63  3.000
 YNE  H131  C13  C12   108.87  3.000
 YNE  H132  C13  N4    109.08  3.000
 YNE  H131  C13  N4    112.53  3.000
 YNE  C12   C13  N4    109.81  3.000
 YNE  H122  C12  H121  107.72  3.000
 YNE  H122  C12  C13   109.66  3.000
 YNE  H121  C12  C13   109.92  3.000
 YNE  H122  C12  C11   110.68  3.000
 YNE  H121  C12  C11   109.43  3.000
 YNE  C13   C12  C11   109.42  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
 YNE  CONST_01  C1    N    N1   C3     0.00   0.0  0
 YNE  CONST_02  N     C1   C5   C3     0.00   0.0  0
 YNE  CONST_03  C1    C5   C3   N1     0.00   0.0  0
 YNE  CONST_04  C5    C1   N    N1     0.00   0.0  0
 YNE  CONST_05  C5    C3   N1   N      0.00   0.0  0
 YNE  CONST_06  N3    C8   O    C7     0.00   0.0  0
 YNE  CONST_07  C9    C8   O    C7   180.00   0.0  0
 YNE  CONST_08  C8    N3   N2   C7     0.00   0.0  0
 YNE  CONST_09  N3    N2   C7   O      0.00   0.0  0
 YNE  CONST_10  N2    N3   C8   O      0.00   0.0  0
 YNE  CONST_11  S     C9   C8   O      0.00   0.0  0
 YNE  CONST_12  C10   C9   C8   O    180.00   0.0  0
 YNE  CONST_13  N2    C7   O    C8     0.00   0.0  0
 YNE  CONST_14  C21   S    C9   C8   180.00   0.0  0
 YNE  CONST_15  C16   C10  C9   C8   180.00   0.0  0
 YNE  CONST_16  S     C9   C8   N3   180.00   0.0  0
 YNE  CONST_17  C10   C9   C8   N3     0.00   0.0  0
 YNE  CONST_18  C9    C8   N3   N2   180.00   0.0  0
 YNE  CONST_19  C20   C21  S    C9   180.00   0.0  0
 YNE  CONST_20  C16   C21  S    C9     0.00   0.0  0
 YNE  CONST_21  C21   C16  C10  C9     0.00   0.0  0
 YNE  CONST_22  C17   C16  C10  C9   180.00   0.0  0
 YNE  CONST_23  C16   C10  C9   S      0.00   0.0  0
 YNE  CONST_24  C19   C20  C21  S    180.00   0.0  0
 YNE  CONST_25  C17   C16  C21  S    180.00   0.0  0
 YNE  CONST_26  C10   C16  C21  S      0.00   0.0  0
 YNE  CONST_27  C10   C9   S    C21    0.00   0.0  0
 YNE  CONST_28  C18   C19  C20  C21    0.00   0.0  0
 YNE  CONST_29  C18   C17  C16  C21    0.00   0.0  0
 YNE  CONST_30  C17   C16  C21  C20    0.00   0.0  0
 YNE  CONST_31  C10   C16  C21  C20  180.00   0.0  0
 YNE  CONST_32  C17   C18  C19  C20    0.00   0.0  0
 YNE  CONST_33  C16   C21  C20  C19    0.00   0.0  0
 YNE  CONST_34  C16   C17  C18  C19    0.00   0.0  0
 YNE  CONST_35  C10   C16  C17  C18  180.00   0.0  0
 YNE  CONST_36  N     N1   C3   C4   180.00   0.0  0
 YNE  CONST_37  C1    C5   C3   C4   180.00   0.0  0
 YNE  CONST_38  C     C1   C5   C3   180.00   0.0  0
 YNE  CONST_39  C6    C5   C3   N1   180.00   0.0  0
 YNE  CONST_40  C     C1   N    N1   180.00   0.0  0
 YNE  CONST_41  C5    C3   N1   C2   180.00   0.0  0
 YNE  CONST_42  C1    N    N1   C2   180.00   0.0  0
 YNE  CONST_43  C6    C5   C1   N    180.00   0.0  0
 YNE  CONST_44  C8    O    C7   C6   180.00   0.0  0
 YNE  CONST_45  N3    N2   C7   C6   180.00   0.0  0
 YNE  CONST_46  O1    C10  C9   C8     0.00   0.0  0
 YNE  CONST_47  O1    C10  C9   S    180.00   0.0  0
 YNE  CONST_48  O1    C10  C16  C21  180.00   0.0  0
 YNE  CONST_49  O1    C10  C16  C17    0.00   0.0  0
 YNE  CONST_50  H20   C20  C21  S      0.00   0.0  0
 YNE  CONST_51  H19   C19  C20  C21  180.00   0.0  0
 YNE  CONST_52  H17   C17  C16  C21  180.00   0.0  0
 YNE  CONST_53  H18   C18  C19  C20  180.00   0.0  0
 YNE  Var_01    N4    C14  C15  C11  -57.28  30.0  1
 YNE  Var_02    N4    C13  C12  C11   57.44  30.0  1
 YNE  Var_03    C13   N4   C14  C15   61.81  30.0  1
 YNE  Var_04    C12   C13  N4   C14  -61.89  30.0  1
 YNE  Var_05    C7    C6   C5   C3    88.43  30.0  2
 YNE  Var_06    O     C7   C6   C5   -65.77  30.0  2
 YNE  Var_07    H21C  C2   N1   C3    92.26  30.0  2
 YNE  Var_08    H41C  C4   C3   N1    62.83  30.0  2
 YNE  Var_09    HC1   C    C1   N    119.49  30.0  2

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
 YNE  chir_01  C11  O1  C15  C12  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
 YNE  plan-1  C4   0.020
 YNE  plan-1  C3   0.020
 YNE  plan-1  N1   0.020
 YNE  plan-1  C2   0.020
 YNE  plan-1  N    0.020
 YNE  plan-1  C5   0.020
 YNE  plan-1  C1   0.020
 YNE  plan-1  C    0.020
 YNE  plan-1  C6   0.020
 YNE  plan-2  C6   0.020
 YNE  plan-2  C7   0.020
 YNE  plan-2  O    0.020
 YNE  plan-2  C8   0.020
 YNE  plan-2  N3   0.020
 YNE  plan-2  N2   0.020
 YNE  plan-2  C9   0.020
 YNE  plan-3  C8   0.020
 YNE  plan-3  C9   0.020
 YNE  plan-3  S    0.020
 YNE  plan-3  C21  0.020
 YNE  plan-3  C20  0.020
 YNE  plan-3  C19  0.020
 YNE  plan-3  C18  0.020
 YNE  plan-3  C17  0.020
 YNE  plan-3  C16  0.020
 YNE  plan-3  C10  0.020
 YNE  plan-3  O1   0.020
 YNE  plan-3  H20  0.020
 YNE  plan-3  H19  0.020
 YNE  plan-3  H18  0.020
 YNE  plan-3  H17  0.020

