# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:56:32 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-[(2-{5-[(3,5-dimethyl-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: Cc1[nH]nc(C)c1Cc2oc(nn2)c3sc4ccccc4c3OC5CCNCC5
#
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
 370  370  4-[(2-{5-[(3,5-dimethyl-1H-pyrazol-4-yl)methyl]-1,3,4-oxadiazol-2-yl}-1-benzothiophen-3-yl)oxy]piperidine  ligand  52  29  .  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_370
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
 370  C     C  CH3   0  -0.746  -4.2158   2.7028  -1.4162
 370  N     N  N     0  -0.308  -2.2600  -1.9495  -0.1159
 370  O     O  O     0  -0.419  -1.7858   0.1147  -0.5860
 370  S     S  S2    0   0.256   0.4196   2.0042  -0.2507
 370  C1    C  CR5   0   0.240  -4.8089   1.8720  -0.3311
 370  N1    N  N     0  -0.309  -0.9555  -1.7217   0.2405
 370  O1    O  O2    0  -0.481   2.0020  -1.3609   0.9038
 370  C2    C  CR5   0  -0.182  -4.7584   0.4689  -0.1945
 370  N2    N  NH1   0  -0.572   3.7817  -4.6518  -1.0905
 370  C3    C  CH2   0  -0.668  -4.0843  -0.5289  -1.0830
 370  N3    N  NR15  0  -0.489  -5.8400   1.3896   1.4426
 370  C4    C  CR5   0   0.487  -2.7212  -0.8511  -0.5967
 370  N4    N  N     0  -0.300  -5.4756   2.4140   0.6722
 370  C5    C  CR5   0   0.528  -0.7091  -0.4909  -0.0541
 370  C6    C  CR5   0  -0.451   0.4811   0.2974   0.0998
 370  C7    C  CR5   0   0.403   1.7104  -0.1096   0.5302
 370  C8    C  CH1   0   0.034   2.8641  -2.1159   0.0233
 370  C9    C  CH2   0  -0.474   3.6490  -3.0989   0.8683
 370  C10   C  CH2   0  -0.328   4.5185  -3.9771  -0.0366
 370  C11   C  CH2   0  -0.326   2.9982  -3.7171  -1.8795
 370  C12   C  CH2   0  -0.448   2.0618  -2.8376  -1.0454
 370  C13   C  CR56  0   0.164   2.6573   0.9706   0.5906
 370  C14   C  CR16  0  -0.305   3.9890   0.9481   1.0228
 370  C15   C  CR16  0  -0.252   4.7156   2.1191   1.0156
 370  C16   C  CR16  0  -0.258   4.1339   3.3215   0.5899
 370  C17   C  CR16  0  -0.280   2.8179   3.3683   0.1742
 370  C18   C  CR56  0  -0.221   2.0860   2.1839   0.1835
 370  C19   C  CR5   0   0.400  -5.4367   0.1971   0.9766
 370  C20   C  CH3   0  -0.741  -5.7212  -1.0957   1.6533
 370  H     H  HCH3  0   0.246  -4.5622   2.3820  -2.3998
 370  HA    H  HCH3  0   0.251  -4.4820   3.7511  -1.2918
 370  HB    H  HCH3  0   0.241  -3.1269   2.6323  -1.4228
 370  H3    H  HCH2  0   0.300  -4.6463  -1.4624  -1.1262
 370  H3A   H  HCH2  0   0.298  -4.0205  -0.1534  -2.1076
 370  H8    H  HCH1  0   0.228   3.5643  -1.4278  -0.4686
 370  H9    H  HCH2  0   0.243   4.2777  -2.5712   1.5911
 370  H9A   H  HCH2  0   0.232   2.9560  -3.7297   1.4344
 370  H10   H  HCH2  0   0.246   5.0404  -4.7223   0.5654
 370  H10A  H  HCH2  0   0.223   5.2913  -3.3575  -0.5041
 370  H11   H  HCH2  0   0.222   3.6914  -3.0787  -2.4376
 370  H11A  H  HCH2  0   0.245   2.4215  -4.2723  -2.6208
 370  H12   H  HCH2  0   0.232   1.2939  -3.4542  -0.5706
 370  H12A  H  HCH2  0   0.234   1.5490  -2.1220  -1.6934
 370  H14   H  HCR6  0   0.266   4.4406   0.0263   1.3664
 370  H15   H  HCR6  0   0.266   5.7449   2.1144   1.3483
 370  H16   H  HCR6  0   0.269   4.7220   4.2295   0.5968
 370  H17   H  HCR6  0   0.276   2.3679   4.2998  -0.1425
 370  H20   H  HCH3  0   0.261  -6.4449  -1.6843   1.0874
 370  H20A  H  HCH3  0   0.256  -4.8137  -1.6931   1.7416
 370  H20B  H  HCH3  0   0.261  -6.1231  -0.9470   2.6545
 370  HN3   H  HNR5  0   0.412  -6.3726   1.5610   2.2807
 370  HN2   H  HNH1  0   0.341   3.1602  -5.3348  -0.6725

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
 370  C1   C     single    1.490  0.020  1.490
 370  C    H     single    0.970  0.020  1.090
 370  C    HA    single    0.970  0.020  1.090
 370  C    HB    single    0.970  0.020  1.090
 370  C4   N     aromatic  1.285  0.020  1.285
 370  N    N1    aromatic  1.371  0.020  1.371
 370  C4   O     aromatic  1.344  0.020  1.344
 370  O    C5    aromatic  1.345  0.020  1.345
 370  C6   S     aromatic  1.743  0.020  1.743
 370  S    C18   aromatic  1.731  0.020  1.731
 370  N4   C1    aromatic  1.321  0.020  1.321
 370  C2   C1    aromatic  1.411  0.020  1.411
 370  N1   C5    aromatic  1.289  0.020  1.289
 370  C8   O1    single    1.445  0.020  1.445
 370  O1   C7    single    1.338  0.020  1.338
 370  C19  C2    aromatic  1.380  0.020  1.380
 370  C2   C3    single    1.497  0.020  1.497
 370  C11  N2    single    1.453  0.020  1.453
 370  N2   C10   single    1.452  0.020  1.452
 370  N2   HN2   single    0.890  0.020  1.040
 370  C3   C4    single    1.483  0.020  1.483
 370  C3   H3    single    0.970  0.020  1.090
 370  C3   H3A   single    0.970  0.020  1.090
 370  N3   C19   aromatic  1.342  0.020  1.342
 370  N3   N4    aromatic  1.333  0.020  1.333
 370  C5   C6    single    1.436  0.020  1.436
 370  C6   C7    aromatic  1.365  0.020  1.365
 370  C7   C13   aromatic  1.438  0.020  1.438
 370  C12  C8    single    1.519  0.020  1.519
 370  C8   C9    single    1.515  0.020  1.515
 370  C8   H8    single    0.970  0.020  1.090
 370  C10  C9    single    1.532  0.020  1.532
 370  C9   H9    single    0.970  0.020  1.090
 370  C9   H9A   single    0.970  0.020  1.090
 370  C10  H10   single    0.970  0.020  1.090
 370  C10  H10A  single    0.970  0.020  1.090
 370  C11  C12   single    1.532  0.020  1.532
 370  C11  H11   single    0.970  0.020  1.090
 370  C11  H11A  single    0.970  0.020  1.090
 370  C12  H12   single    0.970  0.020  1.090
 370  C12  H12A  single    0.970  0.020  1.090
 370  C18  C13   aromatic  1.402  0.020  1.402
 370  C13  C14   aromatic  1.400  0.020  1.400
 370  C14  C15   aromatic  1.378  0.020  1.378
 370  C14  H14   single    0.930  0.020  1.080
 370  C16  C15   aromatic  1.402  0.020  1.402
 370  C15  H15   single    0.930  0.020  1.080
 370  C17  C16   aromatic  1.381  0.020  1.381
 370  C16  H16   single    0.930  0.020  1.080
 370  C18  C17   aromatic  1.392  0.020  1.392
 370  C17  H17   single    0.930  0.020  1.080
 370  C20  C19   single    1.487  0.020  1.487
 370  C20  H20   single    0.970  0.020  1.090
 370  C20  H20A  single    0.970  0.020  1.090
 370  C20  H20B  single    0.970  0.020  1.090
 370  N3   HN3   single    0.860  0.020  1.020

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
 370  HB    C    HA    107.87  3.000
 370  HB    C    H     107.00  3.000
 370  HA    C    H     107.98  3.000
 370  HB    C    C1    111.44  3.000
 370  HA    C    C1    110.88  3.000
 370  H     C    C1    111.49  3.000
 370  C4    N    N1    107.26  3.000
 370  C5    O    C4    103.69  3.000
 370  C18   S    C6     90.99  3.000
 370  N4    C1   C2    110.65  3.000
 370  C2    C1   C     127.66  3.000
 370  N4    C1   C     121.69  3.000
 370  C5    N1   N     106.31  3.000
 370  C8    O1   C7    116.65  3.000
 370  C19   C2   C3    126.42  3.000
 370  C3    C2   C1    128.45  3.000
 370  C19   C2   C1    105.10  3.000
 370  HN2   N2   C11   109.08  3.000
 370  HN2   N2   C10   108.96  3.000
 370  C11   N2   C10   111.65  3.000
 370  H3A   C3   H3    106.68  3.000
 370  H3A   C3   C4    109.17  3.000
 370  H3    C3   C4    107.51  3.000
 370  H3A   C3   C2    110.71  3.000
 370  H3    C3   C2    111.23  3.000
 370  C4    C3   C2    111.36  3.000
 370  HN3   N3   C19   126.77  3.000
 370  HN3   N3   N4    119.64  3.000
 370  C19   N3   N4    113.58  3.000
 370  C3    C4   O     119.09  3.000
 370  C3    C4   N     129.69  3.000
 370  O     C4   N     111.19  3.000
 370  N3    N4   C1    105.17  3.000
 370  C6    C5   N1    131.15  3.000
 370  C6    C5   O     117.31  3.000
 370  N1    C5   O     111.55  3.000
 370  C7    C6   C5    128.08  3.000
 370  C7    C6   S     112.78  3.000
 370  C5    C6   S     119.12  3.000
 370  C13   C7   C6    112.49  3.000
 370  C13   C7   O1    123.19  3.000
 370  C6    C7   O1    124.28  3.000
 370  H8    C8   C12   108.63  3.000
 370  H8    C8   C9    109.03  3.000
 370  C12   C8   C9    110.96  3.000
 370  H8    C8   O1    109.02  3.000
 370  C9    C8   O1    107.95  3.000
 370  C12   C8   O1    111.21  3.000
 370  H9A   C9   H9    107.47  3.000
 370  H9A   C9   C10   109.54  3.000
 370  H9    C9   C10   109.92  3.000
 370  H9A   C9   C8    109.53  3.000
 370  H9    C9   C8    110.69  3.000
 370  C10   C9   C8    109.66  3.000
 370  H10A  C10  H10   106.53  3.000
 370  H10A  C10  C9    109.17  3.000
 370  H10   C10  C9    109.70  3.000
 370  H10A  C10  N2    108.13  3.000
 370  H10   C10  N2    109.02  3.000
 370  C9    C10  N2    114.02  3.000
 370  H11A  C11  H11   106.56  3.000
 370  H11A  C11  C12   109.82  3.000
 370  H11   C11  C12   109.25  3.000
 370  H11A  C11  N2    109.07  3.000
 370  H11   C11  N2    108.08  3.000
 370  C12   C11  N2    113.79  3.000
 370  H12A  C12  H12   107.28  3.000
 370  H12A  C12  C11   109.87  3.000
 370  H12   C12  C11   110.00  3.000
 370  H12A  C12  C8    110.72  3.000
 370  H12   C12  C8    109.48  3.000
 370  C11   C12  C8    109.46  3.000
 370  C18   C13  C14   119.42  3.000
 370  C14   C13  C7    128.85  3.000
 370  C18   C13  C7    111.70  3.000
 370  H14   C14  C15   120.35  3.000
 370  H14   C14  C13   120.56  3.000
 370  C15   C14  C13   119.09  3.000
 370  H15   C15  C16   119.47  3.000
 370  H15   C15  C14   119.76  3.000
 370  C16   C15  C14   120.77  3.000
 370  H16   C16  C17   119.45  3.000
 370  H16   C16  C15   119.49  3.000
 370  C17   C16  C15   121.06  3.000
 370  H17   C17  C18   121.04  3.000
 370  H17   C17  C16   120.91  3.000
 370  C18   C17  C16   118.05  3.000
 370  C17   C18  C13   121.61  3.000
 370  C17   C18  S     126.34  3.000
 370  C13   C18  S     112.04  3.000
 370  C20   C19  N3    123.85  3.000
 370  C20   C19  C2    130.65  3.000
 370  N3    C19  C2    105.50  3.000
 370  H20B  C20  H20A  107.91  3.000
 370  H20B  C20  H20   107.80  3.000
 370  H20A  C20  H20   107.38  3.000
 370  H20B  C20  C19   111.73  3.000
 370  H20A  C20  C19   110.74  3.000
 370  H20   C20  C19   111.10  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
 370  CONST_01  C5   O    C4   N      0.00   0.0  0
 370  CONST_02  O    C5   N1   N      0.00   0.0  0
 370  CONST_03  C6   C5   N1   N    180.00   0.0  0
 370  CONST_04  N1   N    C4   O      0.00   0.0  0
 370  CONST_05  S    C6   C5   O      0.00   0.0  0
 370  CONST_06  C7   C6   C5   O    180.00   0.0  0
 370  CONST_07  N1   C5   C6   S    180.00   0.0  0
 370  CONST_08  C13  C7   C6   S      0.00   0.0  0
 370  CONST_09  C7   C13  C18  S      0.00   0.0  0
 370  CONST_10  C14  C13  C18  S    180.00   0.0  0
 370  CONST_11  C16  C17  C18  S    180.00   0.0  0
 370  CONST_12  C19  N3   N4   C1     0.00   0.0  0
 370  CONST_13  N3   C19  C2   C1     0.00   0.0  0
 370  CONST_14  C4   O    C5   N1     0.00   0.0  0
 370  CONST_15  C7   C6   C5   N1     0.00   0.0  0
 370  CONST_16  N3   N4   C1   C2     0.00   0.0  0
 370  CONST_17  N4   N3   C19  C2     0.00   0.0  0
 370  CONST_18  C5   N1   N    C4     0.00   0.0  0
 370  CONST_19  C6   C5   O    C4   180.00   0.0  0
 370  CONST_20  C19  C2   C1   N4     0.00   0.0  0
 370  CONST_21  C18  S    C6   C5   180.00   0.0  0
 370  CONST_22  C13  C7   C6   C5   180.00   0.0  0
 370  CONST_23  C13  C18  S    C6     0.00   0.0  0
 370  CONST_24  C17  C18  S    C6   180.00   0.0  0
 370  CONST_25  C18  C13  C7   C6     0.00   0.0  0
 370  CONST_26  C14  C13  C7   C6   180.00   0.0  0
 370  CONST_27  C18  S    C6   C7     0.00   0.0  0
 370  CONST_28  C17  C18  C13  C7   180.00   0.0  0
 370  CONST_29  C15  C14  C13  C7   180.00   0.0  0
 370  CONST_30  C16  C17  C18  C13    0.00   0.0  0
 370  CONST_31  C16  C15  C14  C13    0.00   0.0  0
 370  CONST_32  C17  C18  C13  C14    0.00   0.0  0
 370  CONST_33  C17  C16  C15  C14    0.00   0.0  0
 370  CONST_34  C18  C13  C14  C15    0.00   0.0  0
 370  CONST_35  C18  C17  C16  C15    0.00   0.0  0
 370  CONST_36  N3   N4   C1   C    180.00   0.0  0
 370  CONST_37  C19  C2   C1   C    180.00   0.0  0
 370  CONST_38  O1   C7   C6   S    180.00   0.0  0
 370  CONST_39  C20  C19  C2   C1   180.00   0.0  0
 370  CONST_40  C3   C4   N    N1   180.00   0.0  0
 370  CONST_41  C5   C6   C7   O1     0.00   0.0  0
 370  CONST_42  C18  C13  C7   O1   180.00   0.0  0
 370  CONST_43  C14  C13  C7   O1     0.00   0.0  0
 370  CONST_44  N4   C1   C2   C3   180.00   0.0  0
 370  CONST_45  N3   C19  C2   C3   180.00   0.0  0
 370  CONST_46  C5   O    C4   C3   180.00   0.0  0
 370  CONST_47  C20  C19  N3   N4   180.00   0.0  0
 370  CONST_48  H17  C17  C18  S      0.00   0.0  0
 370  CONST_49  HN3  N3   N4   C1   180.00   0.0  0
 370  CONST_50  H14  C14  C13  C7     0.00   0.0  0
 370  CONST_51  H15  C15  C14  C13  180.00   0.0  0
 370  CONST_52  H16  C16  C15  C14  180.00   0.0  0
 370  Var_01    C8   C12  C11  N2    54.93  30.0  1
 370  Var_02    C8   C9   C10  N2   -54.21  30.0  1
 370  Var_03    C11  N2   C10  C9    53.55  30.0  1
 370  Var_04    C12  C11  N2   C10  -53.94  30.0  1
 370  Var_05    C2   C3   C4   N    112.73  30.0  2
 370  Var_06    C4   C3   C2   C1    94.26  30.0  2
 370  Var_07    C13  C7   O1   C8   -72.87  30.0  2
 370  Var_08    H    C    C1   C2    55.46  30.0  2
 370  Var_09    H20  C20  C19  C2   -69.98  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
 370  chir_01  C8  O1  C12  C9  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
 370  plan-1  N    0.020
 370  plan-1  O    0.020
 370  plan-1  N1   0.020
 370  plan-1  C3   0.020
 370  plan-1  C4   0.020
 370  plan-1  C5   0.020
 370  plan-1  C6   0.020
 370  plan-2  C    0.020
 370  plan-2  C1   0.020
 370  plan-2  C2   0.020
 370  plan-2  C3   0.020
 370  plan-2  N3   0.020
 370  plan-2  N4   0.020
 370  plan-2  C19  0.020
 370  plan-2  C20  0.020
 370  plan-2  HN3  0.020
 370  plan-3  S    0.020
 370  plan-3  O1   0.020
 370  plan-3  C5   0.020
 370  plan-3  C6   0.020
 370  plan-3  C7   0.020
 370  plan-3  C13  0.020
 370  plan-3  C14  0.020
 370  plan-3  C15  0.020
 370  plan-3  C16  0.020
 370  plan-3  C17  0.020
 370  plan-3  C18  0.020
 370  plan-3  H14  0.020
 370  plan-3  H15  0.020
 370  plan-3  H16  0.020
 370  plan-3  H17  0.020

