# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 17:56:41 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: ~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(6-oxidanylidene-1~{H}-pyridin-3-yl)methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1oc(CN(CC2=CNC(=O)C=C2)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
 VFZ  VFZ  "~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(6-oxidanylidene-1~{H}-pyridin-3-yl)methyl]ethanamide"
  ligand  43  27  .  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_VFZ
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
 VFZ  CL   CL  CL    0  -0.116  -37.2208  49.9829  29.5644
 VFZ  C16  C   CR6   0  -0.064  -35.5073  50.2151  29.6847
 VFZ  C15  C   CR16  0  -0.196  -34.7562  49.3062  30.4094
 VFZ  C14  C   CR16  0  -0.279  -33.3849  49.4817  30.5164
 VFZ  C13  C   CR16  0  -0.229  -32.7845  50.5656  29.8941
 VFZ  C12  C   CR16  0  -0.278  -33.5431  51.4697  29.1661
 VFZ  C11  C   CR6   0  -0.029  -34.9230  51.3144  29.0518
 VFZ  S    S   S2    0   0.121  -35.9918  52.4079  28.1814
 VFZ  C10  C   CH2   0  -0.789  -34.9031  53.7249  27.6326
 VFZ  C9   C   C     0   0.588  -34.0832  53.3649  26.3986
 VFZ  O1   O   O     0  -0.446  -34.1462  52.2607  25.8967
 VFZ  N3   N   NT    0  -0.469  -33.2840  54.3401  25.8925
 VFZ  C2   C   CH2   0  -0.455  -33.1400  55.6696  26.4548
 VFZ  C1   C   CR5   0   0.489  -33.8991  56.6921  25.6902
 VFZ  N2   N   N     0  -0.293  -33.4622  57.7152  25.0638
 VFZ  N1   N   N     0  -0.372  -34.5459  58.3522  24.5051
 VFZ  O2   O   O     0  -0.422  -35.2469  56.5866  25.5920
 VFZ  C    C   CR5   0   0.643  -35.5798  57.6483  24.8439
 VFZ  N    N   NH2   0  -0.843  -36.8788  57.8809  24.6000
 VFZ  C3   C   CH2   0  -0.357  -32.5225  54.0858  24.6859
 VFZ  C4   C   CR6   0  -0.055  -31.1018  53.6600  24.9444
 VFZ  C8   C   CR16  0  -0.129  -30.1566  53.6826  23.8834
 VFZ  C7   C   CR16  0  -0.456  -28.8692  53.2904  24.0591
 VFZ  C6   C   CR6   0   0.530  -28.3921  52.8311  25.3394
 VFZ  O    O   O     0  -0.502  -27.2491  52.4628  25.5918
 VFZ  N4   N   NR16  0  -0.663  -29.3660  52.8388  26.3180
 VFZ  C5   C   CR16  0   0.024  -30.6534  53.2258  26.1482
 VFZ  H1   H   HCR6  0   0.282  -35.2433  48.4670  30.8876
 VFZ  H2   H   HCR6  0   0.268  -32.7952  48.7739  31.0826
 VFZ  H3   H   HCR6  0   0.265  -31.7155  50.7138  29.9683
 VFZ  H4   H   HCR6  0   0.274  -33.0386  52.3028  28.6984
 VFZ  H5   H   HCH2  0   0.326  -34.2808  54.0669  28.4619
 VFZ  H6   H   HCH2  0   0.345  -35.5801  54.5529  27.4070
 VFZ  H7   H   HCH2  0   0.311  -33.4354  55.6860  27.5030
 VFZ  H8   H   HCH2  0   0.317  -32.0882  55.9600  26.4332
 VFZ  H9   H   HNH2  0   0.412  -37.0768  58.5609  23.8835
 VFZ  H10  H   HNH2  0   0.414  -37.5118  57.0965  24.6181
 VFZ  H11  H   HCH2  0   0.274  -32.5186  54.9997  24.0860
 VFZ  H12  H   HCH2  0   0.285  -33.0384  53.3345  24.0883
 VFZ  H13  H   HCR6  0   0.273  -30.4772  54.0274  22.9063
 VFZ  H14  H   HCR6  0   0.272  -28.1631  53.3173  23.2404
 VFZ  H16  H   HCR6  0   0.310  -31.2705  53.1683  27.0339
 VFZ  H15  H   HNR6  0   0.419  -29.0825  52.5286  27.2380

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
 VFZ  C8   C7   double    1.357  0.020  1.357
 VFZ  C8   C4   single    1.421  0.020  1.421
 VFZ  C7   C6   single    1.441  0.020  1.441
 VFZ  N1   C    aromatic  1.296  0.020  1.296
 VFZ  N1   N2   aromatic  1.376  0.020  1.376
 VFZ  N    C    single    1.342  0.020  1.342
 VFZ  C3   C4   single    1.506  0.020  1.506
 VFZ  C3   N3   single    1.449  0.020  1.449
 VFZ  C4   C5   double    1.356  0.020  1.356
 VFZ  C6   O    double    1.227  0.020  1.227
 VFZ  C6   N4   single    1.381  0.020  1.381
 VFZ  C    O2   aromatic  1.341  0.020  1.341
 VFZ  N2   C1   aromatic  1.277  0.020  1.277
 VFZ  C5   N4   single    1.355  0.020  1.355
 VFZ  O1   C9   double    1.215  0.020  1.215
 VFZ  N3   C9   single    1.359  0.020  1.359
 VFZ  N3   C2   single    1.451  0.020  1.451
 VFZ  O2   C1   aromatic  1.356  0.020  1.356
 VFZ  C1   C2   single    1.485  0.020  1.485
 VFZ  C9   C10  single    1.525  0.020  1.525
 VFZ  C10  S    single    1.795  0.020  1.795
 VFZ  S    C11  single    1.759  0.020  1.759
 VFZ  C11  C12  aromatic  1.393  0.020  1.393
 VFZ  C11  C16  aromatic  1.397  0.020  1.397
 VFZ  C12  C13  aromatic  1.387  0.020  1.387
 VFZ  C16  CL   single    1.733  0.020  1.733
 VFZ  C16  C15  aromatic  1.384  0.020  1.384
 VFZ  C13  C14  aromatic  1.387  0.020  1.387
 VFZ  C15  C14  aromatic  1.387  0.020  1.387
 VFZ  C15  H1   single    0.930  0.020  1.080
 VFZ  C14  H2   single    0.930  0.020  1.080
 VFZ  C13  H3   single    0.930  0.020  1.080
 VFZ  C12  H4   single    0.930  0.020  1.080
 VFZ  C10  H5   single    0.970  0.020  1.090
 VFZ  C10  H6   single    0.970  0.020  1.090
 VFZ  C2   H7   single    0.970  0.020  1.090
 VFZ  C2   H8   single    0.970  0.020  1.090
 VFZ  N    H9   single    0.890  0.020  1.040
 VFZ  N    H10  single    0.890  0.020  1.040
 VFZ  C3   H11  single    0.970  0.020  1.090
 VFZ  C3   H12  single    0.970  0.020  1.090
 VFZ  C8   H13  single    0.930  0.020  1.080
 VFZ  C7   H14  single    0.930  0.020  1.080
 VFZ  C5   H16  single    0.930  0.020  1.080
 VFZ  N4   H15  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
 VFZ  C11  C16  C15  121.81  3.000
 VFZ  C15  C16  CL   119.01  3.000
 VFZ  C11  C16  CL   119.18  3.000
 VFZ  H1   C15  C14  120.63  3.000
 VFZ  H1   C15  C16  119.77  3.000
 VFZ  C14  C15  C16  119.60  3.000
 VFZ  H2   C14  C13  120.70  3.000
 VFZ  H2   C14  C15  119.79  3.000
 VFZ  C13  C14  C15  119.51  3.000
 VFZ  H3   C13  C12  119.16  3.000
 VFZ  H3   C13  C14  120.28  3.000
 VFZ  C12  C13  C14  120.56  3.000
 VFZ  H4   C12  C11  120.85  3.000
 VFZ  H4   C12  C13  118.33  3.000
 VFZ  C11  C12  C13  120.81  3.000
 VFZ  S    C11  C12  124.96  3.000
 VFZ  C12  C11  C16  117.70  3.000
 VFZ  S    C11  C16  117.34  3.000
 VFZ  C10  S    C11  103.82  3.000
 VFZ  H6   C10  H5   105.82  3.000
 VFZ  H6   C10  C9   110.17  3.000
 VFZ  H5   C10  C9   112.47  3.000
 VFZ  H6   C10  S    104.08  3.000
 VFZ  H5   C10  S    110.08  3.000
 VFZ  C9   C10  S    113.60  3.000
 VFZ  N3   C9   O1   121.95  3.000
 VFZ  N3   C9   C10  116.64  3.000
 VFZ  O1   C9   C10  121.42  3.000
 VFZ  C3   N3   C2   115.55  3.000
 VFZ  C2   N3   C9   124.88  3.000
 VFZ  C3   N3   C9   119.55  3.000
 VFZ  H8   C2   H7   106.04  3.000
 VFZ  H8   C2   C1   107.41  3.000
 VFZ  H7   C2   C1   110.27  3.000
 VFZ  H8   C2   N3   109.38  3.000
 VFZ  H7   C2   N3   111.09  3.000
 VFZ  C1   C2   N3   112.37  3.000
 VFZ  O2   C1   N2   111.53  3.000
 VFZ  O2   C1   C2   119.47  3.000
 VFZ  N2   C1   C2   129.00  3.000
 VFZ  N1   N2   C1   107.51  3.000
 VFZ  C    N1   N2   105.71  3.000
 VFZ  C    O2   C1   103.05  3.000
 VFZ  N    C    O2   118.62  3.000
 VFZ  O2   C    N1   112.21  3.000
 VFZ  N    C    N1   129.10  3.000
 VFZ  H10  N    H9   114.50  3.000
 VFZ  H10  N    C    118.01  3.000
 VFZ  H9   N    C    115.87  3.000
 VFZ  H12  C3   H11  106.08  3.000
 VFZ  H12  C3   C4   110.24  3.000
 VFZ  H11  C3   C4   109.10  3.000
 VFZ  H12  C3   N3   109.20  3.000
 VFZ  H11  C3   N3   108.19  3.000
 VFZ  C4   C3   N3   113.74  3.000
 VFZ  C5   C4   C8   116.61  3.000
 VFZ  C5   C4   C3   123.71  3.000
 VFZ  C8   C4   C3   119.67  3.000
 VFZ  H13  C8   C7   119.26  3.000
 VFZ  H13  C8   C4   118.75  3.000
 VFZ  C7   C8   C4   121.98  3.000
 VFZ  H14  C7   C6   117.66  3.000
 VFZ  H14  C7   C8   120.95  3.000
 VFZ  C6   C7   C8   121.40  3.000
 VFZ  N4   C6   O    120.86  3.000
 VFZ  N4   C6   C7   113.22  3.000
 VFZ  O    C6   C7   125.92  3.000
 VFZ  H15  N4   C5   117.90  3.000
 VFZ  H15  N4   C6   116.44  3.000
 VFZ  C5   N4   C6   125.66  3.000
 VFZ  H16  C5   N4   115.12  3.000
 VFZ  H16  C5   C4   123.75  3.000
 VFZ  N4   C5   C4   121.12  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
 VFZ  CONST_01  C13  C12  C11  C16     0.00   0.0  0
 VFZ  CONST_02  C13  C14  C15  C16     0.00   0.0  0
 VFZ  CONST_03  C12  C11  C16  C15     0.00   0.0  0
 VFZ  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 VFZ  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 VFZ  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 VFZ  CONST_07  C    N1   N2   C1      0.00   0.0  0
 VFZ  CONST_08  N1   C    O2   C1      0.00   0.0  0
 VFZ  CONST_09  O2   C    N1   N2      0.00   0.0  0
 VFZ  CONST_10  C    O2   C1   N2      0.00   0.0  0
 VFZ  CONST_11  O2   C1   N2   N1      0.00   0.0  0
 VFZ  CONST_12  C5   N4   C6   C7      0.00   0.0  0
 VFZ  CONST_13  C12  C11  C16  CL    180.00   0.0  0
 VFZ  CONST_14  C14  C15  C16  CL    180.00   0.0  0
 VFZ  CONST_15  S    C11  C16  C15   180.00   0.0  0
 VFZ  CONST_16  S    C11  C12  C13   180.00   0.0  0
 VFZ  CONST_17  N1   N2   C1   C2    180.00   0.0  0
 VFZ  CONST_18  C    O2   C1   C2    180.00   0.0  0
 VFZ  CONST_19  N    C    O2   C1    180.00   0.0  0
 VFZ  CONST_20  N    C    N1   N2    180.00   0.0  0
 VFZ  CONST_21  C5   N4   C6   O     180.00   0.0  0
 VFZ  CONST_22  H4   C12  C11  C16   180.00   0.0  0
 VFZ  CONST_23  H2   C14  C15  C16   180.00   0.0  0
 VFZ  CONST_24  H3   C13  C14  C15   180.00   0.0  0
 VFZ  CONST_25  H4   C12  C13  C14   180.00   0.0  0
 VFZ  CONST_26  H1   C15  C14  C13   180.00   0.0  0
 VFZ  CONST_27  H2   C14  C13  C12   180.00   0.0  0
 VFZ  CONST_28  H3   C13  C12  C11   180.00   0.0  0
 VFZ  CONST_29  H1   C15  C16  C11   180.00   0.0  0
 VFZ  CONST_30  H15  N4   C6   C7    180.00   0.0  0
 VFZ  CONST_33  H9   N    C    O2    180.00   0.0  0
 VFZ  CONST_35  H15  N4   C6   O       0.00   0.0  0
 VFZ  CONST_36  C3   N3   C9   C10   180.00   0.0  0
 VFZ  CONST_37  C2   N3   C9   C10     0.00   0.0  0
 VFZ  CONST_38  C3   N3   C9   O1      0.00   0.0  0
 VFZ  CONST_39  C2   N3   C9   O1    180.00   0.0  0
 VFZ  Var_01    C6   C7   C8   C4     -0.13  30.0  1
 VFZ  Var_02    C6   N4   C5   C4     -0.21  30.0  1
 VFZ  Var_03    N4   C6   C7   C8      0.07  30.0  1
 VFZ  Var_04    N4   C5   C4   C8      0.14  30.0  1
 VFZ  Var_05    C5   C4   C8   C7      0.02  30.0  1
 VFZ  Var_06    C7   C8   C4   C3   -179.02  30.0  1
 VFZ  Var_07    N4   C5   C4   C3    179.14  30.0  1
 VFZ  Var_08    O    C6   C7   C8   -179.74  30.0  1
 VFZ  Var_09    H14  C7   C8   C4   -179.81  30.0  1
 VFZ  Var_10    H15  N4   C5   C4    179.65  30.0  1
 VFZ  Var_11    H16  C5   C4   C8    179.56  30.0  1
 VFZ  Var_12    H13  C8   C7   C6    179.66  30.0  1
 VFZ  Var_13    H16  C5   N4   C6   -179.67  30.0  1
 VFZ  Var_14    H14  C7   C6   N4    179.76  30.0  1
 VFZ  Var_15    H13  C8   C4   C5   -179.77  30.0  1
 VFZ  Var_16    C10  S    C11  C16   175.82  30.0  2
 VFZ  Var_17    C10  S    C11  C12    -3.58  30.0  2
 VFZ  Var_18    C8   C4   C3   N3   -165.20  30.0  3
 VFZ  Var_19    C5   C4   C3   N3     15.83  30.0  3
 VFZ  Var_20    N2   C1   C2   N3   -118.12  30.0  2
 VFZ  Var_21    O2   C1   C2   N3     61.41  30.0  2
 VFZ  Var_22    H7   C2   C1   N2    117.35  30.0  2
 VFZ  Var_23    H8   C2   C1   N2      2.22  30.0  2
 VFZ  Var_24    H7   C2   C1   O2    -63.13  30.0  2
 VFZ  Var_25    H8   C2   C1   O2   -178.25  30.0  2
 VFZ  Var_26    H13  C8   C4   C3      1.18  30.0  1
 VFZ  Var_27    H16  C5   C4   C3     -1.44  30.0  1
 VFZ  Var_28    H11  C3   C4   C8    -44.33  30.0  2
 VFZ  Var_29    H12  C3   C4   C8     71.79  30.0  2
 VFZ  Var_30    H14  C7   C6   O      -0.05  30.0  1
 VFZ  Var_31    H11  C3   C4   C5    136.70  30.0  2
 VFZ  Var_32    H12  C3   C4   C5   -107.19  30.0  2
 VFZ  Var_33    C9   C10  S    C11    79.07  30.0  1
 VFZ  Var_34    C4   C3   N3   C9    -96.46  30.0  2
 VFZ  Var_35    C1   C2   N3   C9   -102.76  30.0  3
 VFZ  Var_36    C4   C3   N3   C2     84.82  30.0  2
 VFZ  Var_37    C3   N3   C2   C1     75.88  30.0  2
 VFZ  Var_38    H5   C10  S    C11   -48.07  30.0  1
 VFZ  Var_39    H6   C10  S    C11  -161.09  30.0  1
 VFZ  Var_40    O1   C9   C10  S      -2.93  30.0  2
 VFZ  Var_41    N3   C9   C10  S     177.00  30.0  2
 VFZ  Var_42    H11  C3   N3   C9    142.16  30.0  2
 VFZ  Var_43    H12  C3   N3   C9     27.12  30.0  2
 VFZ  Var_44    H7   C2   N3   C9     21.32  30.0  3
 VFZ  Var_45    H8   C2   N3   C9    138.04  30.0  3
 VFZ  Var_46    H5   C10  C9   O1    122.96  30.0  3
 VFZ  Var_47    H6   C10  C9   O1   -119.25  30.0  3
 VFZ  Var_48    H5   C10  C9   N3    -57.11  30.0  3
 VFZ  Var_49    H6   C10  C9   N3     60.68  30.0  3
 VFZ  Var_50    H11  C3   N3   C2    -36.56  30.0  2
 VFZ  Var_51    H12  C3   N3   C2   -151.60  30.0  2
 VFZ  Var_52    H7   C2   N3   C3   -160.04  30.0  3
 VFZ  Var_53    H8   C2   N3   C3    -43.31  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
 VFZ  plan-1  C2   0.020
 VFZ  plan-1  C1   0.020
 VFZ  plan-1  N2   0.020
 VFZ  plan-1  N1   0.020
 VFZ  plan-1  O2   0.020
 VFZ  plan-1  C    0.020
 VFZ  plan-1  N    0.020
 VFZ  plan-2  CL   0.020
 VFZ  plan-2  C16  0.020
 VFZ  plan-2  C15  0.020
 VFZ  plan-2  C14  0.020
 VFZ  plan-2  C13  0.020
 VFZ  plan-2  C12  0.020
 VFZ  plan-2  C11  0.020
 VFZ  plan-2  S    0.020
 VFZ  plan-2  H1   0.020
 VFZ  plan-2  H2   0.020
 VFZ  plan-2  H3   0.020
 VFZ  plan-2  H4   0.020
 VFZ  plan-3  C10  0.020
 VFZ  plan-3  C9   0.020
 VFZ  plan-3  O1   0.020
 VFZ  plan-3  N3   0.020
 VFZ  plan-3  C2   0.020
 VFZ  plan-3  C3   0.020
 VFZ  plan-4  C    0.020
 VFZ  plan-4  N    0.020
 VFZ  plan-4  H9   0.020
 VFZ  plan-4  H10  0.020
 VFZ  plan-5  C7   0.020
 VFZ  plan-5  C6   0.020
 VFZ  plan-5  O    0.020
 VFZ  plan-5  N4   0.020
 VFZ  plan-5  C5   0.020
 VFZ  plan-5  H15  0.020

