# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:40:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-methyl-5-(3-{4-[(S)-methylsulfinyl]phenyl}-1-benzofuran-5-yl)-1,3,4-oxadiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(nn1)c2ccc3occ(c4ccc(cc4)[S@](C)=O)c3c2
#
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
 G3B  G3B  2-methyl-5-(3-{4-[(S)-methylsulfinyl]phenyl}-1-benzofuran-5-yl)-1,3,4-oxadiazole  ligand  38  24  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G3B
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
 G3B  O21   O  O     0  -0.766   5.3900   2.2930  -1.3524
 G3B  S24   S  S3    0   0.764   5.5312   1.3492  -0.1853
 G3B  C18   C  CH3   0  -0.799   5.2619   2.3425   1.2998
 G3B  C14   C  CR6   0  -0.228   4.0205   0.3897  -0.0895
 G3B  C5    C  CR16  0  -0.210   2.9253   0.7549  -0.8540
 G3B  C6    C  CR16  0  -0.219   3.9862  -0.7418   0.7127
 G3B  C3    C  CR16  0  -0.302   2.8265  -1.4950   0.7758
 G3B  C10   C  CR6   0   0.060   1.7060  -1.1436   0.0194
 G3B  C2    C  CR16  0  -0.317   1.7721  -0.0118  -0.7945
 G3B  C12   C  CR5   0   0.005   0.4964  -1.9635   0.0621
 G3B  C9    C  CR56  0   0.077  -0.8822  -1.5327   0.0259
 G3B  C13   C  CR56  0   0.382  -1.6408  -2.7042   0.0905
 G3B  O22   O  O     0  -0.425  -0.8314  -3.7785   0.1587
 G3B  C8    C  CR15  0  -0.015   0.4407  -3.3130   0.1424
 G3B  C4    C  CR16  0  -0.321  -3.0234  -2.7200   0.0960
 G3B  C7    C  CR16  0  -0.408  -1.5333  -0.3063  -0.0169
 G3B  C11   C  CR6   0  -0.029  -2.9244  -0.2953  -0.0115
 G3B  C1    C  CR16  0  -0.294  -3.6581  -1.4935   0.0401
 G3B  C15   C  CR5   0   0.479  -3.6080   0.9871  -0.0562
 G3B  O23   O  O     0  -0.414  -4.9492   1.0358  -0.0505
 G3B  C16   C  CR5   0   0.458  -5.2234   2.3528  -0.0969
 G3B  C17   C  CH3   0  -0.758  -6.6280   2.8008  -0.1041
 G3B  N20   N  N     0  -0.310  -4.1445   3.0505  -0.1284
 G3B  N19   N  N     0  -0.321  -3.0972   2.1684  -0.1026
 G3B  H18   H  HCH3  0   0.289   4.3291   2.8957   1.2009
 G3B  H18A  H  HCH3  0   0.281   5.2304   1.6953   2.1742
 G3B  H18B  H  HCH3  0   0.294   6.1022   3.0297   1.3878
 G3B  H5    H  HCR6  0   0.279   2.9683   1.6226  -1.4988
 G3B  H6    H  HCR6  0   0.280   4.8504  -1.0366   1.2960
 G3B  H3    H  HCR6  0   0.265   2.7903  -2.3603   1.4250
 G3B  H2    H  HCR6  0   0.265   0.9275   0.2641  -1.4128
 G3B  H8    H  HCR5  0   0.304   1.2193  -4.0591   0.1740
 G3B  H4    H  HCR6  0   0.285  -3.5867  -3.6416   0.1461
 G3B  H7    H  HCR6  0   0.268  -0.9804   0.6233  -0.0464
 G3B  H1    H  HCR6  0   0.270  -4.7390  -1.4714   0.0423
 G3B  H17   H  HCH3  0   0.277  -7.1496   2.4607   0.7908
 G3B  H17A  H  HCH3  0   0.276  -6.6624   3.8863  -0.1368
 G3B  H17B  H  HCH3  0   0.277  -7.1583   2.4075  -0.9717

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
 G3B  O21  S24   double    1.508  0.020  1.508
 G3B  S24  C18   single    1.807  0.020  1.807
 G3B  S24  C14   single    1.792  0.020  1.792
 G3B  C14  C5    aromatic  1.385  0.020  1.385
 G3B  C14  C6    aromatic  1.387  0.020  1.387
 G3B  C5   C2    aromatic  1.386  0.020  1.386
 G3B  C6   C3    aromatic  1.384  0.020  1.384
 G3B  C3   C10   aromatic  1.397  0.020  1.397
 G3B  C10  C2    aromatic  1.396  0.020  1.396
 G3B  C10  C12   single    1.462  0.020  1.462
 G3B  C12  C9    aromatic  1.445  0.020  1.445
 G3B  C12  C8    aromatic  1.353  0.020  1.353
 G3B  C9   C13   aromatic  1.397  0.020  1.397
 G3B  C9   C7    aromatic  1.389  0.020  1.389
 G3B  C13  O22   aromatic  1.347  0.020  1.347
 G3B  C13  C4    aromatic  1.383  0.020  1.383
 G3B  O22  C8    aromatic  1.355  0.020  1.355
 G3B  C4   C1    aromatic  1.382  0.020  1.382
 G3B  C7   C11   aromatic  1.391  0.020  1.391
 G3B  C11  C1    aromatic  1.406  0.020  1.406
 G3B  C11  C15   single    1.454  0.020  1.454
 G3B  C15  O23   aromatic  1.342  0.020  1.342
 G3B  C15  N19   aromatic  1.288  0.020  1.288
 G3B  O23  C16   aromatic  1.346  0.020  1.346
 G3B  C16  C17   single    1.474  0.020  1.474
 G3B  C16  N20   aromatic  1.285  0.020  1.285
 G3B  N20  N19   aromatic  1.370  0.020  1.370
 G3B  C18  H18   single    0.970  0.020  1.090
 G3B  C18  H18A  single    0.970  0.020  1.090
 G3B  C18  H18B  single    0.970  0.020  1.090
 G3B  C5   H5    single    0.930  0.020  1.080
 G3B  C6   H6    single    0.930  0.020  1.080
 G3B  C3   H3    single    0.930  0.020  1.080
 G3B  C2   H2    single    0.930  0.020  1.080
 G3B  C8   H8    single    0.930  0.020  1.080
 G3B  C4   H4    single    0.930  0.020  1.080
 G3B  C7   H7    single    0.930  0.020  1.080
 G3B  C1   H1    single    0.930  0.020  1.080
 G3B  C17  H17   single    0.970  0.020  1.090
 G3B  C17  H17A  single    0.970  0.020  1.090
 G3B  C17  H17B  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
 G3B  C14   S24  C18    97.17  3.000
 G3B  C14   S24  O21   107.31  3.000
 G3B  C18   S24  O21   106.15  3.000
 G3B  H18B  C18  H18A  109.43  3.000
 G3B  H18B  C18  H18   110.35  3.000
 G3B  H18A  C18  H18   110.51  3.000
 G3B  H18B  C18  S24   107.35  3.000
 G3B  H18A  C18  S24   109.74  3.000
 G3B  H18   C18  S24   109.41  3.000
 G3B  C6    C14  C5    120.99  3.000
 G3B  C6    C14  S24   119.23  3.000
 G3B  C5    C14  S24   119.74  3.000
 G3B  H5    C5   C2    120.15  3.000
 G3B  H5    C5   C14   120.61  3.000
 G3B  C2    C5   C14   119.24  3.000
 G3B  H6    C6   C3    119.71  3.000
 G3B  H6    C6   C14   120.90  3.000
 G3B  C3    C6   C14   119.39  3.000
 G3B  H3    C3   C10   119.94  3.000
 G3B  H3    C3   C6    119.37  3.000
 G3B  C10   C3   C6    120.69  3.000
 G3B  C12   C10  C2    120.73  3.000
 G3B  C12   C10  C3    120.45  3.000
 G3B  C2    C10  C3    118.81  3.000
 G3B  H2    C2   C10   120.19  3.000
 G3B  H2    C2   C5    118.92  3.000
 G3B  C10   C2   C5    120.86  3.000
 G3B  C8    C12  C9    105.05  3.000
 G3B  C8    C12  C10   126.52  3.000
 G3B  C9    C12  C10   128.43  3.000
 G3B  C7    C9   C13   119.16  3.000
 G3B  C7    C9   C12   135.34  3.000
 G3B  C13   C9   C12   105.48  3.000
 G3B  C4    C13  O22   126.27  3.000
 G3B  C4    C13  C9    123.55  3.000
 G3B  O22   C13  C9    110.18  3.000
 G3B  C8    O22  C13   106.83  3.000
 G3B  H8    C8   O22   116.08  3.000
 G3B  H8    C8   C12   131.44  3.000
 G3B  O22   C8   C12   112.47  3.000
 G3B  H4    C4   C1    121.26  3.000
 G3B  H4    C4   C13   122.07  3.000
 G3B  C1    C4   C13   116.67  3.000
 G3B  H7    C7   C11   120.29  3.000
 G3B  H7    C7   C9    121.32  3.000
 G3B  C11   C7   C9    118.39  3.000
 G3B  C15   C11  C1    120.50  3.000
 G3B  C15   C11  C7    118.49  3.000
 G3B  C1    C11  C7    121.01  3.000
 G3B  H1    C1   C11   120.29  3.000
 G3B  H1    C1   C4    118.50  3.000
 G3B  C11   C1   C4    121.20  3.000
 G3B  N19   C15  O23   111.30  3.000
 G3B  N19   C15  C11   128.59  3.000
 G3B  O23   C15  C11   120.11  3.000
 G3B  C16   O23  C15   103.82  3.000
 G3B  N20   C16  C17   129.39  3.000
 G3B  N20   C16  O23   111.16  3.000
 G3B  C17   C16  O23   119.45  3.000
 G3B  H17B  C17  H17A  108.73  3.000
 G3B  H17B  C17  H17   107.94  3.000
 G3B  H17A  C17  H17   108.74  3.000
 G3B  H17B  C17  C16   110.96  3.000
 G3B  H17A  C17  C16   109.51  3.000
 G3B  H17   C17  C16   110.91  3.000
 G3B  N19   N20  C16   106.96  3.000
 G3B  N20   N19  C15   106.75  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
 G3B  CONST_01  C10  C2   C5   C14    0.00   0.0  0
 G3B  CONST_02  C10  C3   C6   C14    0.00   0.0  0
 G3B  CONST_03  C3   C6   C14  C5     0.00   0.0  0
 G3B  CONST_04  C3   C10  C2   C5     0.00   0.0  0
 G3B  CONST_05  C12  C10  C2   C5   180.00   0.0  0
 G3B  CONST_06  C2   C5   C14  C6     0.00   0.0  0
 G3B  CONST_07  C2   C10  C3   C6     0.00   0.0  0
 G3B  CONST_08  C12  C10  C3   C6   180.00   0.0  0
 G3B  CONST_11  C13  C9   C12  C10  180.00   0.0  0
 G3B  CONST_12  C7   C9   C12  C10    0.00   0.0  0
 G3B  CONST_13  O22  C8   C12  C10  180.00   0.0  0
 G3B  CONST_16  O22  C13  C9   C12    0.00   0.0  0
 G3B  CONST_17  C4   C13  C9   C12  180.00   0.0  0
 G3B  CONST_18  C11  C7   C9   C12  180.00   0.0  0
 G3B  CONST_19  C13  O22  C8   C12    0.00   0.0  0
 G3B  CONST_20  O22  C8   C12  C9     0.00   0.0  0
 G3B  CONST_21  C8   O22  C13  C9     0.00   0.0  0
 G3B  CONST_22  C1   C4   C13  C9     0.00   0.0  0
 G3B  CONST_23  C1   C11  C7   C9     0.00   0.0  0
 G3B  CONST_24  C15  C11  C7   C9   180.00   0.0  0
 G3B  CONST_25  C8   C12  C9   C13    0.00   0.0  0
 G3B  CONST_26  C11  C7   C9   C13    0.00   0.0  0
 G3B  CONST_27  C11  C1   C4   C13    0.00   0.0  0
 G3B  CONST_28  C7   C9   C13  O22  180.00   0.0  0
 G3B  CONST_29  C1   C4   C13  O22  180.00   0.0  0
 G3B  CONST_30  C7   C9   C12  C8   180.00   0.0  0
 G3B  CONST_31  C4   C13  O22  C8   180.00   0.0  0
 G3B  CONST_32  C7   C9   C13  C4     0.00   0.0  0
 G3B  CONST_33  C7   C11  C1   C4     0.00   0.0  0
 G3B  CONST_34  C15  C11  C1   C4   180.00   0.0  0
 G3B  CONST_35  O23  C15  C11  C7   180.00   0.0  0
 G3B  CONST_36  N19  C15  C11  C7     0.00   0.0  0
 G3B  CONST_37  C16  O23  C15  C11  180.00   0.0  0
 G3B  CONST_38  N20  N19  C15  C11  180.00   0.0  0
 G3B  CONST_39  O23  C15  C11  C1     0.00   0.0  0
 G3B  CONST_40  N19  C15  C11  C1   180.00   0.0  0
 G3B  CONST_41  N20  C16  O23  C15    0.00   0.0  0
 G3B  CONST_42  C16  N20  N19  C15    0.00   0.0  0
 G3B  CONST_43  N20  N19  C15  O23    0.00   0.0  0
 G3B  CONST_44  N19  N20  C16  O23    0.00   0.0  0
 G3B  CONST_45  N19  C15  O23  C16    0.00   0.0  0
 G3B  CONST_46  C2   C5   C14  S24  180.00   0.0  0
 G3B  CONST_47  C3   C6   C14  S24  180.00   0.0  0
 G3B  CONST_48  C17  C16  O23  C15  180.00   0.0  0
 G3B  CONST_49  N19  N20  C16  C17  180.00   0.0  0
 G3B  CONST_50  H2   C2   C5   C14  180.00   0.0  0
 G3B  CONST_51  H3   C3   C6   C14  180.00   0.0  0
 G3B  CONST_52  H6   C6   C14  C5   180.00   0.0  0
 G3B  CONST_53  H5   C5   C14  C6   180.00   0.0  0
 G3B  CONST_54  H8   C8   C12  C10    0.00   0.0  0
 G3B  CONST_55  H7   C7   C9   C12    0.00   0.0  0
 G3B  CONST_56  H4   C4   C13  C9   180.00   0.0  0
 G3B  CONST_57  H1   C1   C4   C13  180.00   0.0  0
 G3B  Var_01    C5   C14  S24  O21  -10.83  30.0  2
 G3B  Var_02    H17  C17  C16  O23   59.60  30.0  2
 G3B  Var_03    H18  C18  S24  C14  -58.66  30.0  3

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
 G3B  plan-1  C11  0.020
 G3B  plan-1  C15  0.020
 G3B  plan-1  O23  0.020
 G3B  plan-1  C16  0.020
 G3B  plan-1  C17  0.020
 G3B  plan-1  N20  0.020
 G3B  plan-1  N19  0.020
 G3B  plan-2  S24  0.020
 G3B  plan-2  C14  0.020
 G3B  plan-2  C5   0.020
 G3B  plan-2  C6   0.020
 G3B  plan-2  C3   0.020
 G3B  plan-2  C10  0.020
 G3B  plan-2  C2   0.020
 G3B  plan-2  C12  0.020
 G3B  plan-2  H5   0.020
 G3B  plan-2  H6   0.020
 G3B  plan-2  H3   0.020
 G3B  plan-2  H2   0.020
 G3B  plan-3  C10  0.020
 G3B  plan-3  C12  0.020
 G3B  plan-3  C9   0.020
 G3B  plan-3  C13  0.020
 G3B  plan-3  O22  0.020
 G3B  plan-3  C8   0.020
 G3B  plan-3  C4   0.020
 G3B  plan-3  C7   0.020
 G3B  plan-3  C11  0.020
 G3B  plan-3  C1   0.020
 G3B  plan-3  C15  0.020
 G3B  plan-3  H8   0.020
 G3B  plan-3  H4   0.020
 G3B  plan-3  H7   0.020
 G3B  plan-3  H1   0.020
 G3B  plan-4  O21  0.020
 G3B  plan-4  S24  0.020
 G3B  plan-4  C18  0.020
 G3B  plan-4  C14  0.020

