# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 12:48:29 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: ~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1oc(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
 VFN  VFN  "~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide"
  ligand  44  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_VFN
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
 VFN  C23  C   CR16  0  -0.233  -36.8702   8.3918  33.3917
 VFN  C24  C   CR16  0  -0.277  -37.6689   7.4146  32.8174
 VFN  C11  C   CR16  0  -0.224  -31.5592   9.3840  36.3828
 VFN  C13  C   CR16  0  -0.226  -33.1873   8.0766  35.1629
 VFN  C10  C   CR16  0  -0.284  -31.2848  10.0985  35.2282
 VFN  C14  C   CR16  0  -0.276  -32.9004   8.7969  34.0199
 VFN  C22  C   CR16  0  -0.271  -36.4161   9.4622  32.6372
 VFN  C25  C   CR16  0  -0.196  -38.0150   7.5169  31.4785
 VFN  C12  C   CR6   0  -0.009  -32.5196   8.3763  36.3518
 VFN  C9   C   CR6   0   0.116  -31.9594   9.8272  34.0429
 VFN  C21  C   CR6   0  -0.033  -36.7434   9.5787  31.2878
 VFN  C26  C   CR6   0  -0.066  -37.5549   8.5881  30.7314
 VFN  C5   C   CR5   0   0.487  -33.4114  12.4600  34.6148
 VFN  C2   C   CR5   0   0.646  -34.3707  11.5841  36.2772
 VFN  C17  C   C     0   0.605  -33.7514  10.9729  31.5157
 VFN  C8   C   CH2   0  -0.407  -31.7154  10.6703  32.8136
 VFN  C6   C   CH2   0  -0.444  -33.0823  12.6895  33.1822
 VFN  C19  C   CH2   0  -0.786  -35.0311  11.7703  31.2688
 VFN  N16  N   NS    0  -0.248  -33.0735   7.0608  38.5000
 VFN  N4   N   N     0  -0.292  -32.8859  12.9806  35.6550
 VFN  N3   N   N     0  -0.370  -33.5022  12.4213  36.7511
 VFN  N1   N   NH2   0  -0.846  -35.2536  10.8105  36.9285
 VFN  N7   N   NT    0  -0.453  -32.8909  11.4550  32.4498
 VFN  O18  O   O     0  -0.456  -33.5232   9.9537  30.8942
 VFN  O28  O   O     0  -0.421  -34.3802  11.5717  34.9373
 VFN  S20  S   S2    0   0.121  -36.2170  10.8949  30.2424
 VFN  CL1  CL  CL    0  -0.116  -38.0019   8.6986  29.0605
 VFN  H1   H   HCR6  0   0.270  -36.5933   8.3303  34.4362
 VFN  H2   H   HCR6  0   0.268  -38.0244   6.5769  33.4017
 VFN  H3   H   HCR6  0   0.281  -31.0381   9.6139  37.3024
 VFN  H4   H   HCR6  0   0.279  -33.9279   7.2884  35.1380
 VFN  H5   H   HCR6  0   0.275  -30.5484  10.8913  35.2591
 VFN  H6   H   HCR6  0   0.271  -33.4236   8.5558  33.1045
 VFN  H7   H   HCR6  0   0.267  -35.8069  10.2067  33.1275
 VFN  H8   H   HCR6  0   0.282  -38.6393   6.7668  31.0120
 VFN  H9   H   HCH2  0   0.295  -31.4345  10.0444  31.9689
 VFN  H10  H   HCH2  0   0.287  -30.8892  11.3603  32.9927
 VFN  H11  H   HCH2  0   0.314  -32.1658  13.2816  33.1505
 VFN  H12  H   HCH2  0   0.318  -33.8504  13.3002  32.7098
 VFN  H13  H   HCH2  0   0.355  -34.7940  12.6750  30.7010
 VFN  H14  H   HCH2  0   0.316  -35.5086  12.1075  32.1881
 VFN  H15  H   HNH2  0   0.417  -35.5851   9.9825  36.4577
 VFN  H16  H   HNH2  0   0.411  -35.0851  10.6880  37.9143
 VFN  C15  C   CSP   0   0.052  -32.8251   7.6487  37.5405

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
 VFN  CL1  C26  single    1.733  0.020  1.733
 VFN  S20  C21  single    1.761  0.020  1.761
 VFN  S20  C19  single    1.796  0.020  1.796
 VFN  C26  C21  aromatic  1.396  0.020  1.396
 VFN  C26  C25  aromatic  1.385  0.020  1.385
 VFN  C21  C22  aromatic  1.393  0.020  1.393
 VFN  O18  C17  double    1.215  0.020  1.215
 VFN  C19  C17  single    1.528  0.020  1.528
 VFN  C25  C24  aromatic  1.387  0.020  1.387
 VFN  C17  N7   single    1.358  0.020  1.358
 VFN  C22  C23  aromatic  1.386  0.020  1.386
 VFN  N7   C8   single    1.459  0.020  1.459
 VFN  N7   C6   single    1.448  0.020  1.448
 VFN  C24  C23  aromatic  1.387  0.020  1.387
 VFN  C8   C9   single    1.511  0.020  1.511
 VFN  C6   C5   single    1.488  0.020  1.488
 VFN  C9   C14  aromatic  1.395  0.020  1.395
 VFN  C9   C10  aromatic  1.390  0.020  1.390
 VFN  C14  C13  aromatic  1.381  0.020  1.381
 VFN  C5   O28  aromatic  1.353  0.020  1.353
 VFN  C5   N4   aromatic  1.276  0.020  1.276
 VFN  O28  C2   aromatic  1.340  0.020  1.340
 VFN  C10  C11  aromatic  1.385  0.020  1.385
 VFN  C13  C12  aromatic  1.396  0.020  1.396
 VFN  N4   N3   aromatic  1.376  0.020  1.376
 VFN  C2   N1   single    1.342  0.020  1.342
 VFN  C2   N3   aromatic  1.296  0.020  1.296
 VFN  C11  C12  aromatic  1.392  0.020  1.392
 VFN  C12  C15  single    1.427  0.020  1.427
 VFN  C15  N16  triple    1.152  0.020  1.152
 VFN  C23  H1   single    0.930  0.020  1.080
 VFN  C24  H2   single    0.930  0.020  1.080
 VFN  C11  H3   single    0.930  0.020  1.080
 VFN  C13  H4   single    0.930  0.020  1.080
 VFN  C10  H5   single    0.930  0.020  1.080
 VFN  C14  H6   single    0.930  0.020  1.080
 VFN  C22  H7   single    0.930  0.020  1.080
 VFN  C25  H8   single    0.930  0.020  1.080
 VFN  C8   H9   single    0.970  0.020  1.090
 VFN  C8   H10  single    0.970  0.020  1.090
 VFN  C6   H11  single    0.970  0.020  1.090
 VFN  C6   H12  single    0.970  0.020  1.090
 VFN  C19  H13  single    0.970  0.020  1.090
 VFN  C19  H14  single    0.970  0.020  1.090
 VFN  N1   H15  single    0.890  0.020  1.040
 VFN  N1   H16  single    0.890  0.020  1.040

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
 VFN  H1   C23  C22  119.04  3.000
 VFN  H1   C23  C24  120.47  3.000
 VFN  C22  C23  C24  120.50  3.000
 VFN  H2   C24  C25  119.79  3.000
 VFN  H2   C24  C23  120.76  3.000
 VFN  C25  C24  C23  119.45  3.000
 VFN  H3   C11  C12  120.33  3.000
 VFN  H3   C11  C10  120.24  3.000
 VFN  C12  C11  C10  119.43  3.000
 VFN  H4   C13  C12  120.23  3.000
 VFN  H4   C13  C14  120.21  3.000
 VFN  C12  C13  C14  119.57  3.000
 VFN  H5   C10  C9   119.82  3.000
 VFN  H5   C10  C11  119.25  3.000
 VFN  C9   C10  C11  120.91  3.000
 VFN  H6   C14  C9   120.32  3.000
 VFN  H6   C14  C13  118.92  3.000
 VFN  C9   C14  C13  120.76  3.000
 VFN  H7   C22  C21  120.97  3.000
 VFN  H7   C22  C23  118.05  3.000
 VFN  C21  C22  C23  120.98  3.000
 VFN  H8   C25  C26  119.70  3.000
 VFN  H8   C25  C24  120.62  3.000
 VFN  C26  C25  C24  119.68  3.000
 VFN  C13  C12  C11  120.28  3.000
 VFN  C11  C12  C15  119.88  3.000
 VFN  C13  C12  C15  119.84  3.000
 VFN  C8   C9   C14  120.50  3.000
 VFN  C14  C9   C10  119.03  3.000
 VFN  C8   C9   C10  120.43  3.000
 VFN  S20  C21  C26  117.87  3.000
 VFN  C26  C21  C22  117.59  3.000
 VFN  S20  C21  C22  124.54  3.000
 VFN  CL1  C26  C21  119.27  3.000
 VFN  C21  C26  C25  121.80  3.000
 VFN  CL1  C26  C25  118.93  3.000
 VFN  O28  C5   N4   111.60  3.000
 VFN  N4   C5   C6   129.10  3.000
 VFN  O28  C5   C6   119.28  3.000
 VFN  O28  C2   N1   118.37  3.000
 VFN  N1   C2   N3   129.46  3.000
 VFN  O28  C2   N3   112.11  3.000
 VFN  O18  C17  N7   122.03  3.000
 VFN  N7   C17  C19  117.15  3.000
 VFN  O18  C17  C19  120.82  3.000
 VFN  H10  C8   H9   107.20  3.000
 VFN  H10  C8   N7   108.11  3.000
 VFN  H9   C8   N7   108.89  3.000
 VFN  H10  C8   C9   109.97  3.000
 VFN  H9   C8   C9   110.63  3.000
 VFN  N7   C8   C9   111.89  3.000
 VFN  H12  C6   H11  105.99  3.000
 VFN  H12  C6   N7   110.60  3.000
 VFN  H11  C6   N7   109.68  3.000
 VFN  H12  C6   C5   110.37  3.000
 VFN  H11  C6   C5   107.31  3.000
 VFN  N7   C6   C5   112.63  3.000
 VFN  H14  C19  H13  106.08  3.000
 VFN  H14  C19  S20  110.11  3.000
 VFN  H13  C19  S20  104.45  3.000
 VFN  H14  C19  C17  113.10  3.000
 VFN  H13  C19  C17  109.50  3.000
 VFN  S20  C19  C17  113.01  3.000
 VFN  N3   N4   C5   107.39  3.000
 VFN  N4   N3   C2   105.74  3.000
 VFN  H16  N1   H15  114.32  3.000
 VFN  H16  N1   C2   115.78  3.000
 VFN  H15  N1   C2   117.57  3.000
 VFN  C6   N7   C8   116.02  3.000
 VFN  C6   N7   C17  124.52  3.000
 VFN  C8   N7   C17  119.39  3.000
 VFN  C2   O28  C5   103.13  3.000
 VFN  C19  S20  C21  102.85  3.000
 VFN  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
 VFN  CONST_01  C26  C21  C22  C23     0.00   0.0  0
 VFN  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 VFN  CONST_03  C21  C26  C25  C24     0.00   0.0  0
 VFN  CONST_04  C21  C22  C23  C24     0.00   0.0  0
 VFN  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 VFN  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 VFN  CONST_07  C10  C9   C14  C13     0.00   0.0  0
 VFN  CONST_08  C10  C11  C12  C13     0.00   0.0  0
 VFN  CONST_09  C25  C26  C21  C22     0.00   0.0  0
 VFN  CONST_10  C25  C24  C23  C22     0.00   0.0  0
 VFN  CONST_11  C9   C14  C13  C12     0.00   0.0  0
 VFN  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 VFN  CONST_13  N3   C2   O28  C5      0.00   0.0  0
 VFN  CONST_14  C2   N3   N4   C5      0.00   0.0  0
 VFN  CONST_15  N4   C5   O28  C2      0.00   0.0  0
 VFN  CONST_16  O28  C2   N3   N4      0.00   0.0  0
 VFN  CONST_17  O28  C5   N4   N3      0.00   0.0  0
 VFN  CONST_18  C14  C13  C12  C15   180.00   0.0  0
 VFN  CONST_19  C10  C11  C12  C15   180.00   0.0  0
 VFN  CONST_20  S20  C21  C22  C23   180.00   0.0  0
 VFN  CONST_21  CL1  C26  C25  C24   180.00   0.0  0
 VFN  CONST_22  C8   C9   C10  C11   180.00   0.0  0
 VFN  CONST_23  C8   C9   C14  C13   180.00   0.0  0
 VFN  CONST_24  CL1  C26  C21  C22   180.00   0.0  0
 VFN  CONST_25  S20  C21  C26  C25   180.00   0.0  0
 VFN  CONST_26  N1   C2   O28  C5    180.00   0.0  0
 VFN  CONST_27  C6   C5   O28  C2    180.00   0.0  0
 VFN  CONST_28  N3   N4   C5   C6    180.00   0.0  0
 VFN  CONST_29  N1   C2   N3   N4    180.00   0.0  0
 VFN  CONST_30  H8   C25  C24  C23   180.00   0.0  0
 VFN  CONST_31  H7   C22  C23  C24   180.00   0.0  0
 VFN  CONST_32  H4   C13  C12  C11   180.00   0.0  0
 VFN  CONST_33  H3   C11  C12  C13   180.00   0.0  0
 VFN  CONST_34  H6   C14  C9   C10   180.00   0.0  0
 VFN  CONST_35  H5   C10  C9   C14   180.00   0.0  0
 VFN  CONST_36  H2   C24  C23  C22   180.00   0.0  0
 VFN  CONST_37  H1   C23  C24  C25   180.00   0.0  0
 VFN  CONST_38  H6   C14  C13  C12   180.00   0.0  0
 VFN  CONST_39  H5   C10  C11  C12   180.00   0.0  0
 VFN  CONST_40  H4   C13  C14  C9    180.00   0.0  0
 VFN  CONST_41  H3   C11  C10  C9    180.00   0.0  0
 VFN  CONST_42  H8   C25  C26  C21   180.00   0.0  0
 VFN  CONST_43  H1   C23  C22  C21   180.00   0.0  0
 VFN  CONST_44  H7   C22  C21  C26   180.00   0.0  0
 VFN  CONST_45  H2   C24  C25  C26   180.00   0.0  0
 VFN  CONST_49  H16  N1   C2   O28   180.00   0.0  0
 VFN  CONST_50  O18  C17  N7   C8      0.00   0.0  0
 VFN  CONST_51  C19  C17  N7   C8    180.00   0.0  0
 VFN  CONST_52  O18  C17  N7   C6    180.00   0.0  0
 VFN  CONST_53  C19  C17  N7   C6      0.00   0.0  0
 VFN  Var_01    N7   C8   C9   C10  -112.75  30.0  2
 VFN  Var_02    N7   C8   C9   C14    64.87  30.0  2
 VFN  Var_03    C19  S20  C21  C22     8.70  30.0  2
 VFN  Var_04    C19  S20  C21  C26  -171.90  30.0  2
 VFN  Var_05    N7   C6   C5   N4    130.25  30.0  1
 VFN  Var_06    O28  C5   C6   N7    -48.58  30.0  2
 VFN  Var_07    H9   C8   C9   C10   125.64  30.0  2
 VFN  Var_08    H10  C8   C9   C10     7.41  30.0  2
 VFN  Var_09    H9   C8   C9   C14   -56.74  30.0  2
 VFN  Var_10    H10  C8   C9   C14  -174.97  30.0  2
 VFN  Var_11    H11  C6   C5   N4      9.45  30.0  1
 VFN  Var_12    H12  C6   C5   N4   -105.60  30.0  1
 VFN  Var_13    H11  C6   C5   O28  -169.38  30.0  1
 VFN  Var_14    H12  C6   C5   O28    75.57  30.0  1
 VFN  Var_15    C17  N7   C8   C9    -95.41  30.0  2
 VFN  Var_16    C6   N7   C8   C9     81.67  30.0  2
 VFN  Var_17    C17  C19  S20  C21    68.94  30.0  3
 VFN  Var_18    C17  N7   C6   C5    109.13  30.0  1
 VFN  Var_19    C8   N7   C6   C5    -67.79  30.0  1
 VFN  Var_20    H13  C19  S20  C21  -172.11  30.0  3
 VFN  Var_21    H14  C19  S20  C21   -58.61  30.0  3
 VFN  Var_22    S20  C19  C17  N7   -169.67  30.0  2
 VFN  Var_23    S20  C19  C17  O18    10.47  30.0  2
 VFN  Var_24    H9   C8   N7   C17    27.19  30.0  3
 VFN  Var_25    H10  C8   N7   C17   143.34  30.0  3
 VFN  Var_26    H11  C6   N7   C17  -131.44  30.0  3
 VFN  Var_27    H12  C6   N7   C17   -14.90  30.0  3
 VFN  Var_28    H11  C6   N7   C8     51.64  30.0  3
 VFN  Var_29    H12  C6   N7   C8    168.18  30.0  3
 VFN  Var_30    H9   C8   N7   C6   -155.72  30.0  3
 VFN  Var_31    H10  C8   N7   C6    -39.57  30.0  3
 VFN  Var_32    H13  C19  C17  N7     74.35  30.0  2
 VFN  Var_33    H14  C19  C17  N7    -43.71  30.0  2
 VFN  Var_34    H13  C19  C17  O18  -105.50  30.0  2
 VFN  Var_35    H14  C19  C17  O18   136.43  30.0  2

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
 VFN  plan-1  C5   0.020
 VFN  plan-1  C2   0.020
 VFN  plan-1  C6   0.020
 VFN  plan-1  N4   0.020
 VFN  plan-1  N3   0.020
 VFN  plan-1  N1   0.020
 VFN  plan-1  O28  0.020
 VFN  plan-2  C11  0.020
 VFN  plan-2  C13  0.020
 VFN  plan-2  C10  0.020
 VFN  plan-2  C14  0.020
 VFN  plan-2  C12  0.020
 VFN  plan-2  C9   0.020
 VFN  plan-2  C8   0.020
 VFN  plan-2  N16  0.020
 VFN  plan-2  H3   0.020
 VFN  plan-2  H4   0.020
 VFN  plan-2  H5   0.020
 VFN  plan-2  H6   0.020
 VFN  plan-2  C15  0.020
 VFN  plan-3  C23  0.020
 VFN  plan-3  C24  0.020
 VFN  plan-3  C22  0.020
 VFN  plan-3  C25  0.020
 VFN  plan-3  C21  0.020
 VFN  plan-3  C26  0.020
 VFN  plan-3  S20  0.020
 VFN  plan-3  CL1  0.020
 VFN  plan-3  H1   0.020
 VFN  plan-3  H2   0.020
 VFN  plan-3  H7   0.020
 VFN  plan-3  H8   0.020
 VFN  plan-4  C17  0.020
 VFN  plan-4  C8   0.020
 VFN  plan-4  C6   0.020
 VFN  plan-4  C19  0.020
 VFN  plan-4  N7   0.020
 VFN  plan-4  O18  0.020
 VFN  plan-5  C2   0.020
 VFN  plan-5  N1   0.020
 VFN  plan-5  H15  0.020
 VFN  plan-5  H16  0.020

