# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 01:14:21 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-[(5-oxidanyl-1,3,4-oxadiazol-2-yl)methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1oc(CN(Cc2ccc(cc2)C#N)C(=O)CSc3ccccc3Cl)nn1
#
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
 VGQ  VGQ  "2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-[(5-oxidanyl-1,3,4-oxadiazol-2-yl)methyl]ethanamide"
  ligand  43  28  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VGQ
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
 VGQ  C23  C   CR16  0  -0.229   5.2746  50.1964  -31.4844
 VGQ  C24  C   CR16  0  -0.278   4.9177  49.4896  -30.3461
 VGQ  C11  C   CR16  0  -0.226   8.4144  50.3512  -37.0748
 VGQ  C13  C   CR16  0  -0.226   7.5549  49.2173  -35.1190
 VGQ  C10  C   CR16  0  -0.285   7.1176  50.5237  -37.5301
 VGQ  C14  C   CR16  0  -0.275   6.2675  49.3991  -35.5859
 VGQ  C22  C   CR16  0  -0.269   4.3019  50.7006  -32.3341
 VGQ  C25  C   CR16  0  -0.196   3.5755  49.2913  -30.0593
 VGQ  C12  C   CR6   0  -0.007   8.6324  49.7039  -35.8614
 VGQ  C9   C   CR6   0   0.114   6.0332  50.0692  -36.7874
 VGQ  C21  C   CR6   0  -0.032   2.9479  50.5100  -32.0659
 VGQ  C26  C   CR6   0  -0.064   2.6108  49.7990  -30.9126
 VGQ  C5   C   CR5   0   0.490   5.6184  53.0606  -36.2361
 VGQ  C2   C   CR5   0   0.633   7.3681  53.1320  -35.0845
 VGQ  C17  C   C     0   0.606   3.1256  50.8225  -35.3883
 VGQ  C8   C   CH2   0  -0.408   4.6226  50.3479  -37.2481
 VGQ  C6   C   CH2   0  -0.438   4.2221  52.6922  -36.5999
 VGQ  C19  C   CH2   0  -0.788   2.4902  51.8546  -34.4590
 VGQ  N16  N   NS    0  -0.248  11.0383  49.4207  -34.9750
 VGQ  N4   N   N     0  -0.290   6.4771  53.7207  -36.9146
 VGQ  N3   N   N     0  -0.358   7.6315  53.7793  -36.1646
 VGQ  N7   N   NT    0  -0.455   3.9376  51.2923  -36.3714
 VGQ  O18  O   O     0  -0.454   2.9012  49.6364  -35.2504
 VGQ  O28  O   O     0  -0.404   6.1227  52.6639  -35.0447
 VGQ  O1   O   OH1   0  -0.569   8.1062  52.8642  -34.0439
 VGQ  S20  S   S2    0   0.122   1.6316  51.1162  -33.0663
 VGQ  CL1  CL  CL    0  -0.116   0.9384  49.5451  -30.5354
 VGQ  H1   H   HCR6  0   0.265   6.3171  50.3624  -31.7219
 VGQ  H2   H   HCR6  0   0.268   5.6740  49.0937  -29.6822
 VGQ  H3   H   HCR6  0   0.282   9.2488  50.7243  -37.6530
 VGQ  H4   H   HCR6  0   0.280   7.7273  48.7047  -34.1821
 VGQ  H5   H   HCR6  0   0.276   6.9500  51.0388  -38.4674
 VGQ  H6   H   HCR6  0   0.272   5.4384  49.0232  -35.0016
 VGQ  H7   H   HCR6  0   0.265   4.6225  51.2522  -33.2051
 VGQ  H8   H   HCR6  0   0.281   3.2760  48.7440  -29.1755
 VGQ  H9   H   HCH2  0   0.288   4.6362  50.7692  -38.2546
 VGQ  H10  H   HCH2  0   0.296   4.0456  49.4266  -37.2901
 VGQ  H11  H   HCH2  0   0.317   4.0910  52.9302  -37.6571
 VGQ  H12  H   HCH2  0   0.323   3.5182  53.3235  -36.0596
 VGQ  H13  H   HCH2  0   0.319   3.1959  52.6065  -34.1051
 VGQ  H14  H   HCH2  0   0.355   1.7108  52.4015  -34.9986
 VGQ  H15  H   HOH1  0   0.508   8.9965  53.2288  -34.1543
 VGQ  C15  C   CSP   0   0.053   9.9635  49.5448  -35.3717

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
 VGQ  C10  C11  aromatic  1.385  0.020  1.385
 VGQ  C10  C9   aromatic  1.391  0.020  1.391
 VGQ  C11  C12  aromatic  1.392  0.020  1.392
 VGQ  C8   C9   single    1.510  0.020  1.510
 VGQ  C8   N7   single    1.459  0.020  1.459
 VGQ  C9   C14  aromatic  1.395  0.020  1.395
 VGQ  N4   C5   aromatic  1.278  0.020  1.278
 VGQ  N4   N3   aromatic  1.378  0.020  1.378
 VGQ  C6   N7   single    1.447  0.020  1.447
 VGQ  C6   C5   single    1.489  0.020  1.489
 VGQ  C12  C15  single    1.427  0.020  1.427
 VGQ  C12  C13  aromatic  1.396  0.020  1.396
 VGQ  N7   C17  single    1.359  0.020  1.359
 VGQ  C15  N16  triple    1.152  0.020  1.152
 VGQ  C5   O28  aromatic  1.353  0.020  1.353
 VGQ  C14  C13  aromatic  1.381  0.020  1.381
 VGQ  N3   C2   aromatic  1.286  0.020  1.286
 VGQ  C17  O18  double    1.215  0.020  1.215
 VGQ  C17  C19  single    1.527  0.020  1.527
 VGQ  O28  C2   aromatic  1.331  0.020  1.331
 VGQ  C19  S20  single    1.795  0.020  1.795
 VGQ  C2   O1   single    1.304  0.020  1.304
 VGQ  S20  C21  single    1.761  0.020  1.761
 VGQ  C22  C21  aromatic  1.393  0.020  1.393
 VGQ  C22  C23  aromatic  1.386  0.020  1.386
 VGQ  C21  C26  aromatic  1.396  0.020  1.396
 VGQ  C23  C24  aromatic  1.387  0.020  1.387
 VGQ  C26  CL1  single    1.733  0.020  1.733
 VGQ  C26  C25  aromatic  1.384  0.020  1.384
 VGQ  C24  C25  aromatic  1.387  0.020  1.387
 VGQ  C23  H1   single    0.930  0.020  1.080
 VGQ  C24  H2   single    0.930  0.020  1.080
 VGQ  C11  H3   single    0.930  0.020  1.080
 VGQ  C13  H4   single    0.930  0.020  1.080
 VGQ  C10  H5   single    0.930  0.020  1.080
 VGQ  C14  H6   single    0.930  0.020  1.080
 VGQ  C22  H7   single    0.930  0.020  1.080
 VGQ  C25  H8   single    0.930  0.020  1.080
 VGQ  C8   H9   single    0.970  0.020  1.090
 VGQ  C8   H10  single    0.970  0.020  1.090
 VGQ  C6   H11  single    0.970  0.020  1.090
 VGQ  C6   H12  single    0.970  0.020  1.090
 VGQ  C19  H13  single    0.970  0.020  1.090
 VGQ  C19  H14  single    0.970  0.020  1.090
 VGQ  O1   H15  single    0.850  0.020  0.980

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
 VGQ  H1   C23  C22  119.05  3.000
 VGQ  H1   C23  C24  120.42  3.000
 VGQ  C22  C23  C24  120.53  3.000
 VGQ  H2   C24  C25  119.84  3.000
 VGQ  H2   C24  C23  120.70  3.000
 VGQ  C25  C24  C23  119.46  3.000
 VGQ  H3   C11  C12  120.36  3.000
 VGQ  H3   C11  C10  120.24  3.000
 VGQ  C12  C11  C10  119.40  3.000
 VGQ  H4   C13  C12  120.18  3.000
 VGQ  H4   C13  C14  120.23  3.000
 VGQ  C12  C13  C14  119.58  3.000
 VGQ  H5   C10  C9   119.82  3.000
 VGQ  H5   C10  C11  119.26  3.000
 VGQ  C9   C10  C11  120.91  3.000
 VGQ  H6   C14  C9   120.21  3.000
 VGQ  H6   C14  C13  119.08  3.000
 VGQ  C9   C14  C13  120.71  3.000
 VGQ  H7   C22  C21  120.91  3.000
 VGQ  H7   C22  C23  118.16  3.000
 VGQ  C21  C22  C23  120.93  3.000
 VGQ  H8   C25  C26  119.74  3.000
 VGQ  H8   C25  C24  120.62  3.000
 VGQ  C26  C25  C24  119.64  3.000
 VGQ  C13  C12  C11  120.30  3.000
 VGQ  C13  C12  C15  119.90  3.000
 VGQ  C11  C12  C15  119.79  3.000
 VGQ  C8   C9   C14  120.55  3.000
 VGQ  C14  C9   C10  119.07  3.000
 VGQ  C8   C9   C10  120.34  3.000
 VGQ  S20  C21  C26  117.65  3.000
 VGQ  C26  C21  C22  117.60  3.000
 VGQ  S20  C21  C22  124.75  3.000
 VGQ  CL1  C26  C21  119.17  3.000
 VGQ  CL1  C26  C25  118.99  3.000
 VGQ  C21  C26  C25  121.85  3.000
 VGQ  O28  C5   N4   111.62  3.000
 VGQ  O28  C5   C6   119.47  3.000
 VGQ  N4   C5   C6   128.91  3.000
 VGQ  O1   C2   O28  115.70  3.000
 VGQ  O1   C2   N3   131.12  3.000
 VGQ  O28  C2   N3   113.18  3.000
 VGQ  O18  C17  N7   122.00  3.000
 VGQ  O18  C17  C19  120.92  3.000
 VGQ  N7   C17  C19  117.08  3.000
 VGQ  H10  C8   H9   107.33  3.000
 VGQ  H10  C8   N7   108.80  3.000
 VGQ  H9   C8   N7   108.07  3.000
 VGQ  H10  C8   C9   110.55  3.000
 VGQ  H9   C8   C9   109.94  3.000
 VGQ  N7   C8   C9   112.00  3.000
 VGQ  H12  C6   H11  106.06  3.000
 VGQ  H12  C6   N7   110.82  3.000
 VGQ  H11  C6   N7   109.90  3.000
 VGQ  H12  C6   C5   109.97  3.000
 VGQ  H11  C6   C5   107.17  3.000
 VGQ  N7   C6   C5   112.65  3.000
 VGQ  H14  C19  H13  106.04  3.000
 VGQ  H14  C19  S20  104.33  3.000
 VGQ  H13  C19  S20  109.97  3.000
 VGQ  H14  C19  C17  109.51  3.000
 VGQ  H13  C19  C17  113.22  3.000
 VGQ  S20  C19  C17  113.15  3.000
 VGQ  N3   N4   C5   107.21  3.000
 VGQ  N4   N3   C2   105.31  3.000
 VGQ  C6   N7   C8   116.04  3.000
 VGQ  C6   N7   C17  124.50  3.000
 VGQ  C8   N7   C17  119.43  3.000
 VGQ  C2   O28  C5   102.66  3.000
 VGQ  H15  O1   C2   110.62  3.000
 VGQ  C19  S20  C21  102.99  3.000
 VGQ  N16  C15  C12  180.00  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
 VGQ  CONST_01  C26  C21  C22  C23     0.00   0.0  0
 VGQ  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 VGQ  CONST_03  C21  C22  C23  C24     0.00   0.0  0
 VGQ  CONST_04  C21  C26  C25  C24     0.00   0.0  0
 VGQ  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 VGQ  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 VGQ  CONST_07  C10  C11  C12  C13     0.00   0.0  0
 VGQ  CONST_08  C10  C9   C14  C13     0.00   0.0  0
 VGQ  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 VGQ  CONST_10  C25  C24  C23  C22     0.00   0.0  0
 VGQ  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 VGQ  CONST_12  C9   C14  C13  C12     0.00   0.0  0
 VGQ  CONST_13  C2   N3   N4   C5      0.00   0.0  0
 VGQ  CONST_14  N3   C2   O28  C5      0.00   0.0  0
 VGQ  CONST_15  N4   C5   O28  C2      0.00   0.0  0
 VGQ  CONST_16  O28  C2   N3   N4      0.00   0.0  0
 VGQ  CONST_17  O28  C5   N4   N3      0.00   0.0  0
 VGQ  CONST_18  C10  C11  C12  C15   180.00   0.0  0
 VGQ  CONST_19  C14  C13  C12  C15   180.00   0.0  0
 VGQ  CONST_20  S20  C21  C22  C23   180.00   0.0  0
 VGQ  CONST_21  CL1  C26  C25  C24   180.00   0.0  0
 VGQ  CONST_22  C8   C9   C10  C11   180.00   0.0  0
 VGQ  CONST_23  C8   C9   C14  C13   180.00   0.0  0
 VGQ  CONST_24  CL1  C26  C21  C22   180.00   0.0  0
 VGQ  CONST_25  S20  C21  C26  C25   180.00   0.0  0
 VGQ  CONST_26  O1   C2   O28  C5    180.00   0.0  0
 VGQ  CONST_27  C6   C5   O28  C2    180.00   0.0  0
 VGQ  CONST_28  N3   N4   C5   C6    180.00   0.0  0
 VGQ  CONST_29  O1   C2   N3   N4    180.00   0.0  0
 VGQ  CONST_30  H8   C25  C24  C23   180.00   0.0  0
 VGQ  CONST_31  H7   C22  C23  C24   180.00   0.0  0
 VGQ  CONST_32  H4   C13  C12  C11   180.00   0.0  0
 VGQ  CONST_33  H3   C11  C12  C13   180.00   0.0  0
 VGQ  CONST_34  H6   C14  C9   C10   180.00   0.0  0
 VGQ  CONST_35  H5   C10  C9   C14   180.00   0.0  0
 VGQ  CONST_36  H2   C24  C23  C22   180.00   0.0  0
 VGQ  CONST_37  H1   C23  C24  C25   180.00   0.0  0
 VGQ  CONST_38  H5   C10  C11  C12   180.00   0.0  0
 VGQ  CONST_39  H6   C14  C13  C12   180.00   0.0  0
 VGQ  CONST_40  H3   C11  C10  C9    180.00   0.0  0
 VGQ  CONST_41  H4   C13  C14  C9    180.00   0.0  0
 VGQ  CONST_42  H1   C23  C22  C21   180.00   0.0  0
 VGQ  CONST_43  H8   C25  C26  C21   180.00   0.0  0
 VGQ  CONST_44  H7   C22  C21  C26   180.00   0.0  0
 VGQ  CONST_45  H2   C24  C25  C26   180.00   0.0  0
 VGQ  CONST_46  O18  C17  N7   C8      0.00   0.0  0
 VGQ  CONST_47  C19  C17  N7   C8    180.00   0.0  0
 VGQ  CONST_48  O18  C17  N7   C6    180.00   0.0  0
 VGQ  CONST_49  C19  C17  N7   C6      0.00   0.0  0
 VGQ  Var_01    N7   C8   C9   C10  -110.95  30.0  2
 VGQ  Var_02    N7   C8   C9   C14    66.53  30.0  2
 VGQ  Var_03    C19  S20  C21  C22     4.16  30.0  3
 VGQ  Var_04    C19  S20  C21  C26  -176.56  30.0  3
 VGQ  Var_05    N7   C6   C5   N4    131.28  30.0  2
 VGQ  Var_06    O28  C5   C6   N7    -47.87  30.0  2
 VGQ  Var_07    H9   C8   C9   C10     9.21  30.0  2
 VGQ  Var_08    H10  C8   C9   C10   127.54  30.0  2
 VGQ  Var_09    H9   C8   C9   C14  -173.31  30.0  2
 VGQ  Var_10    H10  C8   C9   C14   -54.99  30.0  2
 VGQ  Var_11    H11  C6   C5   N4     10.29  30.0  2
 VGQ  Var_12    H12  C6   C5   N4   -104.56  30.0  2
 VGQ  Var_13    H11  C6   C5   O28  -168.86  30.0  2
 VGQ  Var_14    H12  C6   C5   O28    76.29  30.0  2
 VGQ  Var_15    C6   N7   C8   C9     81.63  30.0  3
 VGQ  Var_16    C17  N7   C8   C9    -96.37  30.0  3
 VGQ  Var_17    C17  C19  S20  C21    71.36  30.0  2
 VGQ  Var_18    C8   N7   C6   C5    -68.62  30.0  3
 VGQ  Var_19    C17  N7   C6   C5    109.27  30.0  3
 VGQ  Var_20    H13  C19  S20  C21   -56.34  30.0  2
 VGQ  Var_21    H14  C19  S20  C21  -169.68  30.0  2
 VGQ  Var_22    S20  C19  C17  N7   -171.84  30.0  3
 VGQ  Var_23    S20  C19  C17  O18     8.60  30.0  3
 VGQ  Var_24    H9   C8   N7   C17   142.38  30.0  1
 VGQ  Var_25    H10  C8   N7   C17    26.14  30.0  1
 VGQ  Var_26    H11  C6   N7   C17  -131.31  30.0  2
 VGQ  Var_27    H12  C6   N7   C17   -14.41  30.0  2
 VGQ  Var_28    H11  C6   N7   C8     50.81  30.0  2
 VGQ  Var_29    H12  C6   N7   C8    167.70  30.0  2
 VGQ  Var_30    H9   C8   N7   C6    -39.63  30.0  1
 VGQ  Var_31    H10  C8   N7   C6   -155.86  30.0  1
 VGQ  Var_32    H13  C19  C17  N7    -45.86  30.0  3
 VGQ  Var_33    H14  C19  C17  N7     72.24  30.0  3
 VGQ  Var_34    H13  C19  C17  O18   134.58  30.0  3
 VGQ  Var_35    H14  C19  C17  O18  -107.32  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
 VGQ  plan-1  C5   0.020
 VGQ  plan-1  C2   0.020
 VGQ  plan-1  C6   0.020
 VGQ  plan-1  N4   0.020
 VGQ  plan-1  N3   0.020
 VGQ  plan-1  O28  0.020
 VGQ  plan-1  O1   0.020
 VGQ  plan-2  C11  0.020
 VGQ  plan-2  C13  0.020
 VGQ  plan-2  C10  0.020
 VGQ  plan-2  C14  0.020
 VGQ  plan-2  C12  0.020
 VGQ  plan-2  C9   0.020
 VGQ  plan-2  C8   0.020
 VGQ  plan-2  N16  0.020
 VGQ  plan-2  H3   0.020
 VGQ  plan-2  H4   0.020
 VGQ  plan-2  H5   0.020
 VGQ  plan-2  H6   0.020
 VGQ  plan-2  C15  0.020
 VGQ  plan-3  C23  0.020
 VGQ  plan-3  C24  0.020
 VGQ  plan-3  C22  0.020
 VGQ  plan-3  C25  0.020
 VGQ  plan-3  C21  0.020
 VGQ  plan-3  C26  0.020
 VGQ  plan-3  S20  0.020
 VGQ  plan-3  CL1  0.020
 VGQ  plan-3  H1   0.020
 VGQ  plan-3  H2   0.020
 VGQ  plan-3  H7   0.020
 VGQ  plan-3  H8   0.020
 VGQ  plan-4  C17  0.020
 VGQ  plan-4  C8   0.020
 VGQ  plan-4  C6   0.020
 VGQ  plan-4  C19  0.020
 VGQ  plan-4  N7   0.020
 VGQ  plan-4  O18  0.020

