# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:39:03 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (5~{Z})-5-[(3-ethoxy-4-oxidanyl-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cc(ccc1O)\C=C2/SC(=S)NC2=O
#
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
 4VZ  4VZ  "(5~{Z})-5-[(3-ethoxy-4-oxidanyl-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one"  ligand  29  18  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4VZ
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
 4VZ  C01  C  CH3   0  -0.680  21.2671  24.5158  -31.0072
 4VZ  C02  C  CH2   0  -0.190  20.2986  23.3592  -31.0372
 4VZ  O03  O  O2    0  -0.488  19.1376  23.7709  -31.7505
 4VZ  C04  C  CR6   0   0.349  18.1176  22.9087  -31.9039
 4VZ  C05  C  CR6   0   0.293  17.0137  23.4348  -32.6093
 4VZ  O06  O  OH1   0  -0.608  17.0273  24.6856  -33.0803
 4VZ  C07  C  CR16  0  -0.332  15.8923  22.6460  -32.8081
 4VZ  C08  C  CR16  0  -0.311  15.8593  21.3498  -32.3252
 4VZ  C09  C  CR6   0   0.170  16.9515  20.8038  -31.6474
 4VZ  C10  C  C1    0  -0.245  16.8408  19.4336  -31.2119
 4VZ  C11  C  C     0  -0.334  17.7613  18.5771  -30.7305
 4VZ  S12  S  S2    0   0.189  19.4839  18.8130  -30.4948
 4VZ  C13  C  C     0   0.056  19.7123  17.1747  -29.9491
 4VZ  S14  S  S1    0  -0.215  21.1640  16.5687  -29.5068
 4VZ  N15  N  NH1   0  -0.634  18.5308  16.5210  -29.9527
 4VZ  C16  C  C     0   0.639  17.3929  17.1989  -30.3603
 4VZ  O17  O  O     0  -0.403  16.2933  16.7023  -30.3939
 4VZ  C18  C  CR16  0  -0.466  18.0829  21.6123  -31.4362
 4VZ  H1   H  HCH3  0   0.241  22.1643  24.2170  -30.4664
 4VZ  H2   H  HCH3  0   0.237  21.5647  24.8130  -32.0127
 4VZ  H3   H  HCH3  0   0.238  20.8412  25.3803  -30.4985
 4VZ  H4   H  HCH2  0   0.232  20.0235  23.0606  -30.0203
 4VZ  H5   H  HCH2  0   0.231  20.7493  22.4914  -31.5302
 4VZ  H6   H  HOH1  0   0.477  17.8660  25.1174  -32.8698
 4VZ  H7   H  HCR6  0   0.276  15.0437  23.0558  -33.3406
 4VZ  H8   H  HCR6  0   0.268  14.9744  20.7471  -32.4857
 4VZ  H9   H  H     0   0.287  15.8453  19.0106  -31.3064
 4VZ  H11  H  HNH1  0   0.439  18.4846  15.5521  -29.6597
 4VZ  H12  H  HCR6  0   0.284  18.9273  21.2427  -30.8728

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
 4VZ  O06  C05  single    1.337  0.020  1.337
 4VZ  C07  C05  aromatic  1.385  0.020  1.385
 4VZ  C07  C08  aromatic  1.384  0.020  1.384
 4VZ  C05  C04  aromatic  1.412  0.020  1.412
 4VZ  C08  C09  aromatic  1.397  0.020  1.397
 4VZ  C04  O03  single    1.344  0.020  1.344
 4VZ  C04  C18  aromatic  1.379  0.020  1.379
 4VZ  C09  C18  aromatic  1.407  0.020  1.407
 4VZ  C09  C10  single    1.442  0.020  1.442
 4VZ  O03  C02  single    1.423  0.020  1.423
 4VZ  C10  C11  double    1.346  0.020  1.346
 4VZ  C02  C01  single    1.509  0.020  1.509
 4VZ  C11  S12  single    1.755  0.020  1.755
 4VZ  C11  C16  single    1.474  0.020  1.474
 4VZ  S12  C13  single    1.742  0.020  1.742
 4VZ  O17  C16  double    1.207  0.020  1.207
 4VZ  C16  N15  single    1.386  0.020  1.386
 4VZ  C13  N15  single    1.350  0.020  1.350
 4VZ  C13  S14  double    1.634  0.020  1.634
 4VZ  C01  H1   single    0.970  0.020  1.090
 4VZ  C01  H2   single    0.970  0.020  1.090
 4VZ  C01  H3   single    0.970  0.020  1.090
 4VZ  C02  H4   single    0.970  0.020  1.090
 4VZ  C02  H5   single    0.970  0.020  1.090
 4VZ  O06  H6   single    0.850  0.020  0.980
 4VZ  C07  H7   single    0.930  0.020  1.080
 4VZ  C08  H8   single    0.930  0.020  1.080
 4VZ  C10  H9   single    0.930  0.020  1.080
 4VZ  N15  H11  single    0.860  0.020  1.020
 4VZ  C18  H12  single    0.930  0.020  1.080

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
 4VZ  H3   C01  H2   108.73  3.000
 4VZ  H3   C01  H1   107.92  3.000
 4VZ  H2   C01  H1   107.93  3.000
 4VZ  H3   C01  C02  111.50  3.000
 4VZ  H2   C01  C02  111.47  3.000
 4VZ  H1   C01  C02  109.16  3.000
 4VZ  H5   C02  H4   107.78  3.000
 4VZ  H5   C02  O03  109.83  3.000
 4VZ  H4   C02  O03  109.83  3.000
 4VZ  H5   C02  C01  110.62  3.000
 4VZ  H4   C02  C01  110.60  3.000
 4VZ  O03  C02  C01  108.17  3.000
 4VZ  C04  O03  C02  119.37  3.000
 4VZ  C18  C04  C05  120.01  3.000
 4VZ  C18  C04  O03  125.70  3.000
 4VZ  C05  C04  O03  114.29  3.000
 4VZ  C07  C05  O06  119.37  3.000
 4VZ  C07  C05  C04  119.51  3.000
 4VZ  O06  C05  C04  121.12  3.000
 4VZ  H6   O06  C05  110.50  3.000
 4VZ  H7   C07  C08  120.51  3.000
 4VZ  H7   C07  C05  119.32  3.000
 4VZ  C08  C07  C05  120.17  3.000
 4VZ  H8   C08  C09  119.58  3.000
 4VZ  H8   C08  C07  119.29  3.000
 4VZ  C09  C08  C07  121.13  3.000
 4VZ  C18  C09  C10  124.24  3.000
 4VZ  C10  C09  C08  117.26  3.000
 4VZ  C18  C09  C08  118.50  3.000
 4VZ  H9   C10  C11  114.21  3.000
 4VZ  H9   C10  C09  114.47  3.000
 4VZ  C11  C10  C09  131.30  3.000
 4VZ  C16  C11  S12  109.72  3.000
 4VZ  C16  C11  C10  120.92  3.000
 4VZ  S12  C11  C10  129.32  3.000
 4VZ  C13  S12  C11   92.54  3.000
 4VZ  N15  C13  S14  126.77  3.000
 4VZ  S14  C13  S12  123.37  3.000
 4VZ  N15  C13  S12  109.86  3.000
 4VZ  H11  N15  C16  121.03  3.000
 4VZ  H11  N15  C13  120.13  3.000
 4VZ  C16  N15  C13  118.85  3.000
 4VZ  O17  C16  N15  123.71  3.000
 4VZ  N15  C16  C11  109.03  3.000
 4VZ  O17  C16  C11  127.26  3.000
 4VZ  H12  C18  C09  120.69  3.000
 4VZ  H12  C18  C04  118.62  3.000
 4VZ  C09  C18  C04  120.66  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
 4VZ  CONST_01  C08  C07  C05  C04     0.00   0.0  0
 4VZ  CONST_02  C08  C09  C18  C04     0.00   0.0  0
 4VZ  CONST_03  C09  C08  C07  C05     0.00   0.0  0
 4VZ  CONST_04  C09  C18  C04  C05     0.00   0.0  0
 4VZ  CONST_05  C18  C04  C05  C07     0.00   0.0  0
 4VZ  CONST_06  C18  C09  C08  C07     0.00   0.0  0
 4VZ  CONST_07  C13  N15  C16  C11     0.00   0.0  0
 4VZ  CONST_08  C07  C05  C04  O03   180.00   0.0  0
 4VZ  CONST_09  C09  C18  C04  O03   180.00   0.0  0
 4VZ  CONST_10  C10  C09  C18  C04   180.00   0.0  0
 4VZ  CONST_11  C08  C07  C05  O06   180.00   0.0  0
 4VZ  CONST_12  C18  C04  C05  O06   180.00   0.0  0
 4VZ  CONST_13  C10  C09  C08  C07   180.00   0.0  0
 4VZ  CONST_14  S12  C11  C10  C09     0.00   0.0  0
 4VZ  CONST_15  C16  C11  C10  C09   180.00   0.0  0
 4VZ  CONST_16  O17  C16  N15  C13   180.00   0.0  0
 4VZ  CONST_17  H7   C07  C05  C04   180.00   0.0  0
 4VZ  CONST_18  H8   C08  C07  C05   180.00   0.0  0
 4VZ  CONST_19  H12  C18  C04  C05   180.00   0.0  0
 4VZ  CONST_20  H12  C18  C09  C08   180.00   0.0  0
 4VZ  CONST_21  H7   C07  C08  C09   180.00   0.0  0
 4VZ  CONST_22  H8   C08  C09  C18   180.00   0.0  0
 4VZ  CONST_23  H11  N15  C16  C11   180.00   0.0  0
 4VZ  CONST_24  H9   C10  C11  S12   180.00   0.0  0
 4VZ  CONST_25  H9   C10  C11  C16     0.00   0.0  0
 4VZ  CONST_26  H11  N15  C16  O17     0.00   0.0  0
 4VZ  Var_01    N15  C13  S12  C11    -0.28  30.0  1
 4VZ  Var_02    N15  C16  C11  S12    -0.50  30.0  1
 4VZ  Var_03    C16  N15  C13  S12     0.02  30.0  1
 4VZ  Var_04    C16  C11  S12  C13     0.45  30.0  1
 4VZ  Var_05    C11  C10  C09  C08   168.59  30.0  2
 4VZ  Var_06    C13  S12  C11  C10  -177.27  30.0  1
 4VZ  Var_07    N15  C16  C11  C10   177.44  30.0  1
 4VZ  Var_08    C18  C09  C10  C11   -11.20  30.0  1
 4VZ  Var_09    S14  C13  S12  C11   179.83  30.0  1
 4VZ  Var_10    O17  C16  C11  S12   179.59  30.0  1
 4VZ  Var_11    C16  N15  C13  S14   179.90  30.0  1
 4VZ  Var_12    H11  N15  C13  S12  -179.89  30.0  1
 4VZ  Var_13    C05  C04  O03  C02   179.06  30.0  2
 4VZ  Var_14    C18  C04  O03  C02    -0.74  30.0  2
 4VZ  Var_15    O17  C16  C11  C10    -2.46  30.0  1
 4VZ  Var_16    H9   C10  C09  C08   -10.02  30.0  2
 4VZ  Var_17    H11  N15  C13  S14    -0.00  30.0  1
 4VZ  Var_18    H9   C10  C09  C18   170.20  30.0  2
 4VZ  Var_19    C04  O03  C02  C01  -179.49  30.0  1
 4VZ  Var_20    H4   C02  O03  C04   -58.69  30.0  3
 4VZ  Var_21    H5   C02  O03  C04    59.68  30.0  3
 4VZ  Var_22    H1   C01  C02  O03  -179.85  30.0  3
 4VZ  Var_23    H2   C01  C02  O03   -60.72  30.0  3
 4VZ  Var_24    H3   C01  C02  O03    61.00  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
 4VZ  plan-1  O03  0.020
 4VZ  plan-1  C04  0.020
 4VZ  plan-1  C05  0.020
 4VZ  plan-1  O06  0.020
 4VZ  plan-1  C07  0.020
 4VZ  plan-1  C08  0.020
 4VZ  plan-1  C09  0.020
 4VZ  plan-1  C10  0.020
 4VZ  plan-1  C18  0.020
 4VZ  plan-1  H7   0.020
 4VZ  plan-1  H8   0.020
 4VZ  plan-1  H12  0.020
 4VZ  plan-2  C11  0.020
 4VZ  plan-2  C13  0.020
 4VZ  plan-2  N15  0.020
 4VZ  plan-2  C16  0.020
 4VZ  plan-2  O17  0.020
 4VZ  plan-2  H11  0.020
 4VZ  plan-3  C09  0.020
 4VZ  plan-3  C10  0.020
 4VZ  plan-3  C11  0.020
 4VZ  plan-3  S12  0.020
 4VZ  plan-3  C16  0.020
 4VZ  plan-3  H9   0.020
 4VZ  plan-4  S12  0.020
 4VZ  plan-4  C13  0.020
 4VZ  plan-4  S14  0.020
 4VZ  plan-4  N15  0.020

