# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 03:52:48 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: (5~{Z})-5-[(3-ethynyl-4-methoxy-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(\C=C2/SC(=S)NC2=O)cc1C#C
#
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
 4WD  4WD  "(5~{Z})-5-[(3-ethynyl-4-methoxy-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one"  ligand  27  18  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4WD
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
 4WD  C15  C  CR16  0  -0.275  -35.9066  27.8778  10.1210
 4WD  C16  C  CR16  0  -0.376  -36.1876  28.9225   9.2629
 4WD  C01  C  CH3   0  -0.444  -36.8584  31.1059   7.6170
 4WD  O02  O  O2    0  -0.439  -37.7125  30.6953   8.6737
 4WD  C03  C  CR6   0   0.386  -37.3486  29.6728   9.4396
 4WD  C04  C  CR6   0  -0.141  -38.2182  29.3552  10.5040
 4WD  C05  C  CR16  0  -0.332  -37.9192  28.2954  11.3470
 4WD  C06  C  CR6   0   0.152  -36.7630  27.5286  11.1728
 4WD  C07  C  C1    0  -0.250  -36.3801  26.4082  12.0016
 4WD  C08  C  CR5   0  -0.329  -37.0503  25.7476  12.9618
 4WD  S09  S  S2    0   0.193  -38.6864  25.9927  13.5411
 4WD  C10  C  CR5   0   0.057  -38.5763  24.6585  14.6565
 4WD  S11  S  S1    0  -0.206  -39.8023  24.2056  15.6353
 4WD  N12  N  NR15  0  -0.634  -37.3531  24.0909  14.5728
 4WD  C13  C  CR5   0   0.642  -36.4349  24.6098  13.6749
 4WD  O14  O  O     0  -0.399  -35.3202  24.1736  13.5276
 4WD  C17  C  CSP   0   0.345  -39.3928  30.1321  10.7147
 4WD  C18  C  CSP1  0  -0.554  -40.3862  30.7812  10.9128
 4WD  H1   H  HCR6  0   0.279  -34.9962  27.3109   9.9691
 4WD  H2   H  HCR6  0   0.297  -35.4932  29.1429   8.4643
 4WD  H3   H  HCH3  0   0.268  -37.3394  31.9630   7.1544
 4WD  H4   H  HCH3  0   0.241  -35.8763  31.4049   7.9890
 4WD  H5   H  HCH3  0   0.241  -36.7360  30.3191   6.8700
 4WD  H6   H  HCR6  0   0.266  -38.6089  28.1117  12.1588
 4WD  H7   H  H     0   0.290  -35.3833  26.0234  11.8077
 4WD  H9   H  HNR5  0   0.440  -37.1183  23.2958  15.1560
 4WD  H10  H  H     0   0.282  -41.2663  31.3569  11.0893

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
 4WD  C01  O02  single    1.419  0.020  1.419
 4WD  O02  C03  single    1.328  0.020  1.328
 4WD  C03  C16  aromatic  1.394  0.020  1.394
 4WD  C03  C04  aromatic  1.411  0.020  1.411
 4WD  C16  C15  aromatic  1.381  0.020  1.381
 4WD  C18  C17  triple    1.203  0.020  1.203
 4WD  C17  C04  single    1.424  0.020  1.424
 4WD  C04  C05  aromatic  1.387  0.020  1.387
 4WD  C15  C06  aromatic  1.401  0.020  1.401
 4WD  C05  C06  aromatic  1.398  0.020  1.398
 4WD  C06  C07  single    1.445  0.020  1.445
 4WD  C07  C08  double    1.344  0.020  1.344
 4WD  C08  S09  single    1.753  0.020  1.753
 4WD  C08  C13  single    1.477  0.020  1.477
 4WD  S09  C10  single    1.742  0.020  1.742
 4WD  O14  C13  double    1.206  0.020  1.206
 4WD  C13  N12  single    1.385  0.020  1.385
 4WD  N12  C10  single    1.351  0.020  1.351
 4WD  C10  S11  double    1.633  0.020  1.633
 4WD  C15  H1   single    0.929  0.020  1.085
 4WD  C16  H2   single    0.929  0.020  1.085
 4WD  C01  H3   single    0.939  0.020  1.096
 4WD  C01  H4   single    0.939  0.020  1.096
 4WD  C01  H5   single    0.939  0.020  1.096
 4WD  C05  H6   single    0.929  0.020  1.085
 4WD  C07  H7   single    0.930  0.020  1.086
 4WD  N12  H9   single    0.868  0.020  1.013
 4WD  C18  H10  single    0.913  0.020  1.066

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
 4WD  H1   C15  C06  119.26  3.000
 4WD  H1   C15  C16  118.67  3.000
 4WD  C06  C15  C16  122.07  3.000
 4WD  H2   C16  C03  121.27  3.000
 4WD  H2   C16  C15  118.86  3.000
 4WD  C03  C16  C15  119.87  3.000
 4WD  H5   C01  H4   109.25  3.000
 4WD  H5   C01  H3   109.07  3.000
 4WD  H4   C01  H3   109.11  3.000
 4WD  H5   C01  O02  111.61  3.000
 4WD  H4   C01  O02  111.52  3.000
 4WD  H3   C01  O02  106.19  3.000
 4WD  C03  O02  C01  119.15  3.000
 4WD  C04  C03  O02  116.07  3.000
 4WD  C04  C03  C16  119.21  3.000
 4WD  O02  C03  C16  124.72  3.000
 4WD  C17  C04  C05  120.32  3.000
 4WD  C05  C04  C03  119.85  3.000
 4WD  C17  C04  C03  119.82  3.000
 4WD  H6   C05  C06  121.87  3.000
 4WD  H6   C05  C04  116.67  3.000
 4WD  C06  C05  C04  121.44  3.000
 4WD  C07  C06  C05  124.94  3.000
 4WD  C07  C06  C15  117.51  3.000
 4WD  C05  C06  C15  117.55  3.000
 4WD  H7   C07  C08  114.26  3.000
 4WD  H7   C07  C06  114.55  3.000
 4WD  C08  C07  C06  131.18  3.000
 4WD  C13  C08  S09  109.69  3.000
 4WD  C13  C08  C07  121.04  3.000
 4WD  S09  C08  C07  129.24  3.000
 4WD  C10  S09  C08   92.61  3.000
 4WD  N12  C10  S11  126.90  3.000
 4WD  S11  C10  S09  123.27  3.000
 4WD  N12  C10  S09  109.83  3.000
 4WD  H9   N12  C13  120.88  3.000
 4WD  H9   N12  C10  120.24  3.000
 4WD  C13  N12  C10  118.88  3.000
 4WD  O14  C13  N12  123.81  3.000
 4WD  N12  C13  C08  108.99  3.000
 4WD  O14  C13  C08  127.21  3.000
 4WD  C18  C17  C04  180.00  3.000
 4WD  H10  C18  C17  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
 4WD  CONST_01  C04  C03  C16  C15     0.00   0.0  0
 4WD  CONST_02  C04  C05  C06  C15     0.00   0.0  0
 4WD  CONST_03  C05  C04  C03  C16     0.00   0.0  0
 4WD  CONST_04  C05  C06  C15  C16     0.00   0.0  0
 4WD  CONST_05  C06  C15  C16  C03     0.00   0.0  0
 4WD  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 4WD  CONST_07  C10  N12  C13  C08     0.00   0.0  0
 4WD  CONST_08  O02  C03  C16  C15   180.00   0.0  0
 4WD  CONST_09  C17  C04  C03  C16   180.00   0.0  0
 4WD  CONST_10  C07  C06  C15  C16   180.00   0.0  0
 4WD  CONST_11  C05  C04  C03  O02   180.00   0.0  0
 4WD  CONST_12  C07  C06  C05  C04   180.00   0.0  0
 4WD  CONST_13  C17  C04  C05  C06   180.00   0.0  0
 4WD  CONST_14  S09  C08  C07  C06     0.00   0.0  0
 4WD  CONST_15  C13  C08  C07  C06   180.00   0.0  0
 4WD  CONST_16  O14  C13  N12  C10   180.00   0.0  0
 4WD  CONST_17  H6   C05  C06  C15   180.00   0.0  0
 4WD  CONST_18  H1   C15  C16  C03   180.00   0.0  0
 4WD  CONST_19  H6   C05  C04  C03   180.00   0.0  0
 4WD  CONST_20  H2   C16  C03  C04   180.00   0.0  0
 4WD  CONST_21  H1   C15  C06  C05   180.00   0.0  0
 4WD  CONST_22  H2   C16  C15  C06   180.00   0.0  0
 4WD  CONST_23  H9   N12  C13  C08   180.00   0.0  0
 4WD  CONST_24  H7   C07  C08  S09   180.00   0.0  0
 4WD  CONST_25  H7   C07  C08  C13     0.00   0.0  0
 4WD  CONST_26  H9   N12  C13  O14     0.00   0.0  0
 4WD  Var_01    N12  C10  S09  C08     0.40  30.0  1
 4WD  Var_02    N12  C13  C08  S09     0.36  30.0  1
 4WD  Var_03    C13  N12  C10  S09    -0.27  30.0  1
 4WD  Var_04    C13  C08  S09  C10    -0.44  30.0  1
 4WD  Var_05    C08  C07  C06  C15  -171.10  30.0  2
 4WD  Var_06    C08  C07  C06  C05     9.34  30.0  2
 4WD  Var_07    C10  S09  C08  C07   177.82  30.0  1
 4WD  Var_08    N12  C13  C08  C07  -178.06  30.0  1
 4WD  Var_09    S11  C10  S09  C08  -179.61  30.0  1
 4WD  Var_10    O14  C13  C08  S09  -179.68  30.0  1
 4WD  Var_11    C13  N12  C10  S11   179.75  30.0  1
 4WD  Var_12    H9   N12  C10  S09  -179.94  30.0  1
 4WD  Var_13    C01  O02  C03  C16    -2.15  30.0  2
 4WD  Var_14    C04  C03  O02  C01   177.45  30.0  2
 4WD  Var_15    O14  C13  C08  C07     1.89  30.0  1
 4WD  Var_16    H7   C07  C06  C15     7.97  30.0  2
 4WD  Var_17    H7   C07  C06  C05  -171.59  30.0  2
 4WD  Var_18    H9   N12  C10  S11     0.08  30.0  1
 4WD  Var_19    H3   C01  O02  C03  -178.38  30.0  3
 4WD  Var_20    H4   C01  O02  C03   -59.63  30.0  3
 4WD  Var_21    H5   C01  O02  C03    62.87  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
 4WD  plan-1  C15  0.020
 4WD  plan-1  C16  0.020
 4WD  plan-1  O02  0.020
 4WD  plan-1  C03  0.020
 4WD  plan-1  C04  0.020
 4WD  plan-1  C05  0.020
 4WD  plan-1  C06  0.020
 4WD  plan-1  C07  0.020
 4WD  plan-1  C17  0.020
 4WD  plan-1  C18  0.020
 4WD  plan-1  H1   0.020
 4WD  plan-1  H2   0.020
 4WD  plan-1  H6   0.020
 4WD  plan-2  C08  0.020
 4WD  plan-2  C10  0.020
 4WD  plan-2  N12  0.020
 4WD  plan-2  C13  0.020
 4WD  plan-2  O14  0.020
 4WD  plan-2  H9   0.020
 4WD  plan-3  C06  0.020
 4WD  plan-3  C07  0.020
 4WD  plan-3  C08  0.020
 4WD  plan-3  S09  0.020
 4WD  plan-3  C13  0.020
 4WD  plan-3  H7   0.020
 4WD  plan-4  S09  0.020
 4WD  plan-4  C10  0.020
 4WD  plan-4  S11  0.020
 4WD  plan-4  N12  0.020

