# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 08:13:56 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-[(5-methyl-1,3,4-oxadiazol-2-yl)methyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(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
 VJE  VJE  "2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-[(5-methyl-1,3,4-oxadiazol-2-yl)methyl]ethanamide"
  ligand  45  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_VJE
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
 VJE  C15  C   CSP   0   0.052  -50.4277   7.5024  11.8291
 VJE  C26  C   CR16  0  -0.231  -46.1726   8.4186  16.0171
 VJE  C25  C   CR16  0  -0.277  -45.4604   7.3921  16.6190
 VJE  C11  C   CR16  0  -0.220  -51.7375   9.1679  13.0411
 VJE  C13  C   CR16  0  -0.225  -49.8634   8.0982  14.1293
 VJE  C10  C   CR16  0  -0.281  -51.9602   9.9158  14.1853
 VJE  C14  C   CR16  0  -0.277  -50.1035   8.8470  15.2649
 VJE  C27  C   CR16  0  -0.272  -46.6231   9.4943  16.7664
 VJE  C24  C   CR16  0  -0.196  -45.1966   7.4506  17.9790
 VJE  C12  C   CR6   0  -0.011  -50.6813   8.2611  13.0104
 VJE  C9   C   CR6   0   0.102  -51.1474   9.7716  15.3045
 VJE  C21  C   CR6   0  -0.036  -46.3848   9.5639  18.1376
 VJE  C22  C   CR6   0  -0.066  -45.6559   8.5260  18.7210
 VJE  C2   C   CR5   0   0.459  -48.7156  11.5407  13.0912
 VJE  C5   C   CR5   0   0.480  -49.7108  12.3911  14.7479
 VJE  C17  C   C     0   0.606  -49.3653  10.9255  17.8564
 VJE  C8   C   CH2   0  -0.397  -51.3869  10.6127  16.5370
 VJE  C6   C   CH2   0  -0.448  -50.0356  12.6375  16.1793
 VJE  C19  C   CH2   0  -0.786  -48.1079  11.7460  18.1369
 VJE  N16  N   NS    0  -0.248  -50.2198   6.8922  10.8741
 VJE  N3   N   N     0  -0.310  -49.6951  12.2315  12.6252
 VJE  N4   N   N     0  -0.289  -50.3427  12.7813  13.7030
 VJE  N7   N   NT    0  -0.456  -50.2193  11.4008  16.9118
 VJE  O18  O   O     0  -0.455  -49.5870   9.8962  18.4625
 VJE  O28  O   O     0  -0.398  -48.6642  11.6150  14.4333
 VJE  S20  S   S2    0   0.122  -46.9246  10.8814  19.1760
 VJE  CL1  CL  CL    0  -0.116  -45.3127   8.5808  20.4186
 VJE  H1   H   HCR6  0   0.268  -46.3823   8.3928  14.9556
 VJE  H2   H   HCR6  0   0.268  -45.1071   6.5504  16.0390
 VJE  H3   H   HCR6  0   0.281  -52.3711   9.2976  12.1742
 VJE  H4   H   HCR6  0   0.282  -49.0425   7.3938  14.1077
 VJE  H5   H   HCR6  0   0.274  -52.7714  10.6327  14.1960
 VJE  H6   H   HCR6  0   0.273  -49.4631   8.7044  16.1247
 VJE  H7   H   HCR6  0   0.271  -47.1606  10.2808  16.2575
 VJE  H8   H   HCR6  0   0.282  -44.6353   6.6635  18.4645
 VJE  H9   H   HCH3  0   0.277  -47.9353  10.7362  11.3106
 VJE  H10  H   HCH3  0   0.280  -46.7100  11.1287  12.5247
 VJE  H11  H   HCH3  0   0.278  -47.7239   9.7001  12.7307
 VJE  H12  H   HCH2  0   0.287  -52.2173  11.2991  16.3630
 VJE  H13  H   HCH2  0   0.297  -51.6693   9.9780  17.3753
 VJE  H14  H   HCH2  0   0.322  -49.2650  13.2514  16.6421
 VJE  H15  H   HCH2  0   0.317  -50.9547  13.2250  16.2111
 VJE  H16  H   HCH2  0   0.316  -47.6205  12.1081  17.2328
 VJE  H17  H   HCH2  0   0.355  -48.3778  12.6366  18.7125
 VJE  C1   C   CH3   0  -0.755  -47.7141  10.7309  12.3742

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
 VJE  N16  C15  triple    1.152  0.020  1.152
 VJE  C15  C12  single    1.427  0.020  1.427
 VJE  N3   C2   aromatic  1.286  0.020  1.286
 VJE  N3   N4   aromatic  1.372  0.020  1.372
 VJE  C12  C11  aromatic  1.392  0.020  1.392
 VJE  C12  C13  aromatic  1.396  0.020  1.396
 VJE  C1   C2   single    1.474  0.020  1.474
 VJE  C11  C10  aromatic  1.385  0.020  1.385
 VJE  C2   O28  aromatic  1.345  0.020  1.345
 VJE  N4   C5   aromatic  1.282  0.020  1.282
 VJE  C13  C14  aromatic  1.381  0.020  1.381
 VJE  C10  C9   aromatic  1.391  0.020  1.391
 VJE  O28  C5   aromatic  1.340  0.020  1.340
 VJE  C5   C6   single    1.488  0.020  1.488
 VJE  C14  C9   aromatic  1.395  0.020  1.395
 VJE  C9   C8   single    1.511  0.020  1.511
 VJE  C6   N7   single    1.449  0.020  1.449
 VJE  C26  C25  aromatic  1.387  0.020  1.387
 VJE  C26  C27  aromatic  1.386  0.020  1.386
 VJE  C8   N7   single    1.458  0.020  1.458
 VJE  N7   C17  single    1.359  0.020  1.359
 VJE  C25  C24  aromatic  1.387  0.020  1.387
 VJE  C27  C21  aromatic  1.394  0.020  1.394
 VJE  C17  C19  single    1.527  0.020  1.527
 VJE  C17  O18  double    1.215  0.020  1.215
 VJE  C19  S20  single    1.796  0.020  1.796
 VJE  C24  C22  aromatic  1.385  0.020  1.385
 VJE  C21  C22  aromatic  1.396  0.020  1.396
 VJE  C21  S20  single    1.762  0.020  1.762
 VJE  C22  CL1  single    1.733  0.020  1.733
 VJE  C26  H1   single    0.930  0.020  1.080
 VJE  C25  H2   single    0.930  0.020  1.080
 VJE  C11  H3   single    0.930  0.020  1.080
 VJE  C13  H4   single    0.930  0.020  1.080
 VJE  C10  H5   single    0.930  0.020  1.080
 VJE  C14  H6   single    0.930  0.020  1.080
 VJE  C27  H7   single    0.930  0.020  1.080
 VJE  C24  H8   single    0.930  0.020  1.080
 VJE  C1   H9   single    0.970  0.020  1.090
 VJE  C1   H10  single    0.970  0.020  1.090
 VJE  C1   H11  single    0.970  0.020  1.090
 VJE  C8   H12  single    0.970  0.020  1.090
 VJE  C8   H13  single    0.970  0.020  1.090
 VJE  C6   H14  single    0.970  0.020  1.090
 VJE  C6   H15  single    0.970  0.020  1.090
 VJE  C19  H16  single    0.970  0.020  1.090
 VJE  C19  H17  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
 VJE  N16  C15  C12  180.00  3.000
 VJE  H1   C26  C27  119.05  3.000
 VJE  H1   C26  C25  120.50  3.000
 VJE  C27  C26  C25  120.45  3.000
 VJE  H2   C25  C24  119.78  3.000
 VJE  H2   C25  C26  120.74  3.000
 VJE  C24  C25  C26  119.48  3.000
 VJE  H3   C11  C12  120.32  3.000
 VJE  H3   C11  C10  120.21  3.000
 VJE  C12  C11  C10  119.47  3.000
 VJE  H4   C13  C12  120.31  3.000
 VJE  H4   C13  C14  120.08  3.000
 VJE  C12  C13  C14  119.60  3.000
 VJE  H5   C10  C9   119.91  3.000
 VJE  H5   C10  C11  119.10  3.000
 VJE  C9   C10  C11  120.99  3.000
 VJE  H6   C14  C9   120.52  3.000
 VJE  H6   C14  C13  118.63  3.000
 VJE  C9   C14  C13  120.84  3.000
 VJE  H7   C27  C21  120.82  3.000
 VJE  H7   C27  C26  118.18  3.000
 VJE  C21  C27  C26  121.00  3.000
 VJE  H8   C24  C22  119.78  3.000
 VJE  H8   C24  C25  120.54  3.000
 VJE  C22  C24  C25  119.68  3.000
 VJE  C13  C12  C11  120.19  3.000
 VJE  C13  C12  C15  119.84  3.000
 VJE  C11  C12  C15  119.96  3.000
 VJE  C8   C9   C14  120.70  3.000
 VJE  C8   C9   C10  120.40  3.000
 VJE  C14  C9   C10  118.90  3.000
 VJE  S20  C21  C22  118.00  3.000
 VJE  S20  C21  C27  124.39  3.000
 VJE  C22  C21  C27  117.60  3.000
 VJE  CL1  C22  C21  119.30  3.000
 VJE  CL1  C22  C24  118.93  3.000
 VJE  C21  C22  C24  121.78  3.000
 VJE  O28  C2   N3   111.16  3.000
 VJE  O28  C2   C1   119.32  3.000
 VJE  N3   C2   C1   129.52  3.000
 VJE  O28  C5   N4   111.71  3.000
 VJE  O28  C5   C6   119.47  3.000
 VJE  N4   C5   C6   128.75  3.000
 VJE  O18  C17  N7   121.89  3.000
 VJE  O18  C17  C19  120.91  3.000
 VJE  N7   C17  C19  117.20  3.000
 VJE  H13  C8   H12  106.98  3.000
 VJE  H13  C8   N7   108.96  3.000
 VJE  H12  C8   N7   108.08  3.000
 VJE  H13  C8   C9   110.16  3.000
 VJE  H12  C8   C9   109.91  3.000
 VJE  N7   C8   C9   112.56  3.000
 VJE  H15  C6   H14  106.27  3.000
 VJE  H15  C6   N7   109.75  3.000
 VJE  H14  C6   N7   110.86  3.000
 VJE  H15  C6   C5   107.52  3.000
 VJE  H14  C6   C5   110.35  3.000
 VJE  N7   C6   C5   111.87  3.000
 VJE  H17  C19  H16  106.05  3.000
 VJE  H17  C19  S20  104.47  3.000
 VJE  H16  C19  S20  110.21  3.000
 VJE  H17  C19  C17  109.31  3.000
 VJE  H16  C19  C17  113.24  3.000
 VJE  S20  C19  C17  112.95  3.000
 VJE  N4   N3   C2   106.86  3.000
 VJE  N3   N4   C5   106.59  3.000
 VJE  C6   N7   C8   115.66  3.000
 VJE  C8   N7   C17  119.53  3.000
 VJE  C6   N7   C17  124.76  3.000
 VJE  C5   O28  C2   103.67  3.000
 VJE  C19  S20  C21  102.75  3.000
 VJE  H11  C1   H10  107.93  3.000
 VJE  H11  C1   H9   108.82  3.000
 VJE  H10  C1   H9   108.71  3.000
 VJE  H11  C1   C2   110.74  3.000
 VJE  H10  C1   C2   110.98  3.000
 VJE  H9   C1   C2   109.59  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
 VJE  CONST_01  C22  C24  C25  C26     0.00   0.0  0
 VJE  CONST_02  C22  C21  C27  C26     0.00   0.0  0
 VJE  CONST_03  C21  C27  C26  C25     0.00   0.0  0
 VJE  CONST_04  C21  C22  C24  C25     0.00   0.0  0
 VJE  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 VJE  CONST_06  C14  C9   C10  C11     0.00   0.0  0
 VJE  CONST_07  C10  C11  C12  C13     0.00   0.0  0
 VJE  CONST_08  C10  C9   C14  C13     0.00   0.0  0
 VJE  CONST_09  C24  C25  C26  C27     0.00   0.0  0
 VJE  CONST_10  C24  C22  C21  C27     0.00   0.0  0
 VJE  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 VJE  CONST_12  C9   C14  C13  C12     0.00   0.0  0
 VJE  CONST_13  C5   N4   N3   C2      0.00   0.0  0
 VJE  CONST_14  N4   C5   O28  C2      0.00   0.0  0
 VJE  CONST_15  N3   C2   O28  C5      0.00   0.0  0
 VJE  CONST_16  O28  C5   N4   N3      0.00   0.0  0
 VJE  CONST_17  O28  C2   N3   N4      0.00   0.0  0
 VJE  CONST_18  C10  C11  C12  C15   180.00   0.0  0
 VJE  CONST_19  C14  C13  C12  C15   180.00   0.0  0
 VJE  CONST_20  S20  C21  C27  C26   180.00   0.0  0
 VJE  CONST_21  CL1  C22  C24  C25   180.00   0.0  0
 VJE  CONST_22  C8   C9   C10  C11   180.00   0.0  0
 VJE  CONST_23  C8   C9   C14  C13   180.00   0.0  0
 VJE  CONST_24  CL1  C22  C21  C27   180.00   0.0  0
 VJE  CONST_25  S20  C21  C22  C24   180.00   0.0  0
 VJE  CONST_26  C6   C5   O28  C2    180.00   0.0  0
 VJE  CONST_27  C1   C2   O28  C5    180.00   0.0  0
 VJE  CONST_28  N4   N3   C2   C1    180.00   0.0  0
 VJE  CONST_29  N3   N4   C5   C6    180.00   0.0  0
 VJE  CONST_30  H8   C24  C25  C26   180.00   0.0  0
 VJE  CONST_31  H7   C27  C26  C25   180.00   0.0  0
 VJE  CONST_32  H4   C13  C12  C11   180.00   0.0  0
 VJE  CONST_33  H3   C11  C12  C13   180.00   0.0  0
 VJE  CONST_34  H6   C14  C9   C10   180.00   0.0  0
 VJE  CONST_35  H5   C10  C9   C14   180.00   0.0  0
 VJE  CONST_36  H2   C25  C26  C27   180.00   0.0  0
 VJE  CONST_37  H1   C26  C25  C24   180.00   0.0  0
 VJE  CONST_38  H5   C10  C11  C12   180.00   0.0  0
 VJE  CONST_39  H6   C14  C13  C12   180.00   0.0  0
 VJE  CONST_40  H3   C11  C10  C9    180.00   0.0  0
 VJE  CONST_41  H4   C13  C14  C9    180.00   0.0  0
 VJE  CONST_42  H1   C26  C27  C21   180.00   0.0  0
 VJE  CONST_43  H8   C24  C22  C21   180.00   0.0  0
 VJE  CONST_44  H2   C25  C24  C22   180.00   0.0  0
 VJE  CONST_45  H7   C27  C21  C22   180.00   0.0  0
 VJE  CONST_46  C19  C17  N7   C8    180.00   0.0  0
 VJE  CONST_47  O18  C17  N7   C8      0.00   0.0  0
 VJE  CONST_48  C19  C17  N7   C6      0.00   0.0  0
 VJE  CONST_49  O18  C17  N7   C6    180.00   0.0  0
 VJE  Var_01    N7   C8   C9   C10  -122.23  30.0  2
 VJE  Var_02    N7   C8   C9   C14    57.24  30.0  2
 VJE  Var_03    C19  S20  C21  C27    13.56  30.0  2
 VJE  Var_04    C19  S20  C21  C22  -167.21  30.0  2
 VJE  Var_05    N7   C6   C5   N4    121.31  30.0  2
 VJE  Var_06    O28  C5   C6   N7    -55.31  30.0  1
 VJE  Var_07    H12  C8   C9   C10    -1.70  30.0  2
 VJE  Var_08    H13  C8   C9   C10   115.94  30.0  2
 VJE  Var_09    H12  C8   C9   C14   177.77  30.0  2
 VJE  Var_10    H13  C8   C9   C14   -64.59  30.0  2
 VJE  Var_11    H9   C1   C2   N3     -3.03  30.0  2
 VJE  Var_12    H10  C1   C2   N3    117.05  30.0  2
 VJE  Var_13    H11  C1   C2   N3   -123.10  30.0  2
 VJE  Var_14    H14  C6   C5   N4   -114.76  30.0  2
 VJE  Var_15    H15  C6   C5   N4      0.74  30.0  2
 VJE  Var_16    H9   C1   C2   O28   176.83  30.0  2
 VJE  Var_17    H10  C1   C2   O28   -63.09  30.0  2
 VJE  Var_18    H11  C1   C2   O28    56.76  30.0  2
 VJE  Var_19    H14  C6   C5   O28    68.62  30.0  2
 VJE  Var_20    H15  C6   C5   O28  -175.88  30.0  2
 VJE  Var_21    C6   N7   C8   C9     81.47  30.0  3
 VJE  Var_22    C17  N7   C8   C9    -95.96  30.0  3
 VJE  Var_23    C17  C19  S20  C21    67.50  30.0  1
 VJE  Var_24    C8   N7   C6   C5    -67.26  30.0  3
 VJE  Var_25    C17  N7   C6   C5    110.02  30.0  3
 VJE  Var_26    H16  C19  S20  C21   -60.27  30.0  1
 VJE  Var_27    H17  C19  S20  C21  -173.80  30.0  1
 VJE  Var_28    S20  C19  C17  N7   -169.71  30.0  3
 VJE  Var_29    S20  C19  C17  O18    10.65  30.0  3
 VJE  Var_30    H14  C6   N7   C17   -13.63  30.0  2
 VJE  Var_31    H15  C6   N7   C17  -130.72  30.0  2
 VJE  Var_32    H12  C8   N7   C17   142.46  30.0  2
 VJE  Var_33    H13  C8   N7   C17    26.54  30.0  2
 VJE  Var_34    H14  C6   N7   C8    169.09  30.0  2
 VJE  Var_35    H15  C6   N7   C8     52.00  30.0  2
 VJE  Var_36    H12  C8   N7   C6    -40.11  30.0  2
 VJE  Var_37    H13  C8   N7   C6   -156.03  30.0  2
 VJE  Var_38    H16  C19  C17  N7    -43.55  30.0  3
 VJE  Var_39    H17  C19  C17  N7     74.44  30.0  3
 VJE  Var_40    H16  C19  C17  O18   136.81  30.0  3
 VJE  Var_41    H17  C19  C17  O18  -105.20  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
 VJE  plan-1  C2   0.020
 VJE  plan-1  C5   0.020
 VJE  plan-1  C6   0.020
 VJE  plan-1  N3   0.020
 VJE  plan-1  N4   0.020
 VJE  plan-1  O28  0.020
 VJE  plan-1  C1   0.020
 VJE  plan-2  C26  0.020
 VJE  plan-2  C25  0.020
 VJE  plan-2  C27  0.020
 VJE  plan-2  C24  0.020
 VJE  plan-2  C21  0.020
 VJE  plan-2  C22  0.020
 VJE  plan-2  S20  0.020
 VJE  plan-2  CL1  0.020
 VJE  plan-2  H1   0.020
 VJE  plan-2  H2   0.020
 VJE  plan-2  H7   0.020
 VJE  plan-2  H8   0.020
 VJE  plan-3  C15  0.020
 VJE  plan-3  C11  0.020
 VJE  plan-3  C13  0.020
 VJE  plan-3  C10  0.020
 VJE  plan-3  C14  0.020
 VJE  plan-3  C12  0.020
 VJE  plan-3  C9   0.020
 VJE  plan-3  C8   0.020
 VJE  plan-3  N16  0.020
 VJE  plan-3  H3   0.020
 VJE  plan-3  H4   0.020
 VJE  plan-3  H5   0.020
 VJE  plan-3  H6   0.020
 VJE  plan-4  C17  0.020
 VJE  plan-4  C8   0.020
 VJE  plan-4  C6   0.020
 VJE  plan-4  C19  0.020
 VJE  plan-4  N7   0.020
 VJE  plan-4  O18  0.020

