# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:56:42 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: (5Z)-5-[(3,4-dimethoxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)\C=C\2SC(=S)NC\2=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
 UL1  UL1  (5Z)-5-[(3,4-dimethoxyphenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one  ligand  29  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UL1
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
 UL1  CAA  C  CH3   0  -0.442   4.4330  453.7498   96.2649
 UL1  CAB  C  CH3   0  -0.446   2.0304  457.9385   98.6597
 UL1  CAF  C  CR16  0  -0.309   1.6162  452.9873   99.2803
 UL1  CAG  C  CR16  0  -0.373   2.5479  453.1987   98.2747
 UL1  CAH  C  CR16  0  -0.466   1.3350  455.3631   99.5278
 UL1  CAM  C  CR6   0   0.172   1.0075  454.0553   99.9344
 UL1  CAN  C  CR6   0   0.325   2.8825  454.4880   97.8896
 UL1  CAO  C  CR6   0   0.359   2.2529  455.5871   98.5245
 UL1  CAP  C  CR5   0   0.643  -1.3882  453.9649  102.9514
 UL1  CAQ  C  CR5   0   0.056  -1.2800  456.2150  103.6383
 UL1  CAR  C  CR5   0  -0.334  -0.4748  454.5264  101.9399
 UL1  NAI  N  NR15  0  -0.633  -1.7632  454.9683  103.8286
 UL1  OAJ  O  O2    0  -0.448   3.7637  454.8017   96.9385
 UL1  OAK  O  O2    0  -0.460   2.6183  456.7952   98.0708
 UL1  SAD  S  S1    0  -0.212  -1.5936  457.5329  104.5511
 UL1  SAL  S  S2    0   0.188  -0.2397  456.2388  102.2417
 UL1  H1   H  HCH3  0   0.266   5.1034  454.2213   95.5518
 UL1  H2   H  HCH3  0   0.236   5.0199  453.1385   96.9537
 UL1  H3   H  HCH3  0   0.237   3.7345  453.1069   95.7250
 UL1  H4   H  HCH3  0   0.268   2.4611  458.8000   98.1563
 UL1  H5   H  HCH3  0   0.233   0.9462  457.9561   98.5218
 UL1  H6   H  HCH3  0   0.231   2.2542  458.0071   99.7277
 UL1  H7   H  H     0   0.287  -0.1932  452.6964  101.0674
 UL1  H8   H  HCR6  0   0.270   1.3723  451.9719   99.5644
 UL1  H9   H  HCR6  0   0.294   3.0055  452.3426   97.7989
 UL1  H10  H  HCR6  0   0.271   0.8373  456.2131   99.9706
 UL1  H11  H  HNR5  0   0.440  -2.3830  454.7757  104.6060
 UL1  CAE  C  C1    0  -0.243   0.0837  453.7440  100.9977
 UL1  OAC  O  O     0  -0.410  -1.7678  452.8218  103.0380

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
 UL1  CAA  OAJ  single    1.417  0.020  1.417
 UL1  OAJ  CAN  single    1.334  0.020  1.334
 UL1  CAN  CAG  aromatic  1.387  0.020  1.387
 UL1  CAN  CAO  aromatic  1.417  0.020  1.417
 UL1  OAK  CAO  single    1.341  0.020  1.341
 UL1  OAK  CAB  single    1.414  0.020  1.414
 UL1  CAG  CAF  aromatic  1.387  0.020  1.387
 UL1  CAO  CAH  aromatic  1.378  0.020  1.378
 UL1  CAF  CAM  aromatic  1.392  0.020  1.392
 UL1  CAH  CAM  aromatic  1.408  0.020  1.408
 UL1  CAM  CAE  single    1.442  0.020  1.442
 UL1  CAE  CAR  double    1.346  0.020  1.346
 UL1  CAR  SAL  single    1.755  0.020  1.755
 UL1  CAR  CAP  single    1.474  0.020  1.474
 UL1  SAL  CAQ  single    1.742  0.020  1.742
 UL1  CAP  OAC  double    1.208  0.020  1.208
 UL1  CAP  NAI  single    1.385  0.020  1.385
 UL1  CAQ  NAI  single    1.351  0.020  1.351
 UL1  CAQ  SAD  double    1.633  0.020  1.633
 UL1  CAA  H1   single    0.970  0.020  1.090
 UL1  CAA  H2   single    0.970  0.020  1.090
 UL1  CAA  H3   single    0.970  0.020  1.090
 UL1  CAB  H4   single    0.970  0.020  1.090
 UL1  CAB  H5   single    0.970  0.020  1.090
 UL1  CAB  H6   single    0.970  0.020  1.090
 UL1  CAE  H7   single    0.930  0.020  1.080
 UL1  CAF  H8   single    0.930  0.020  1.080
 UL1  CAG  H9   single    0.930  0.020  1.080
 UL1  CAH  H10  single    0.930  0.020  1.080
 UL1  NAI  H11  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
 UL1  H3   CAA  H2   109.03  3.000
 UL1  H3   CAA  H1   109.00  3.000
 UL1  H2   CAA  H1   108.98  3.000
 UL1  H3   CAA  OAJ  111.71  3.000
 UL1  H2   CAA  OAJ  111.69  3.000
 UL1  H1   CAA  OAJ  106.34  3.000
 UL1  H6   CAB  H5   108.98  3.000
 UL1  H6   CAB  H4   108.77  3.000
 UL1  H5   CAB  H4   108.78  3.000
 UL1  H6   CAB  OAK  111.87  3.000
 UL1  H5   CAB  OAK  111.89  3.000
 UL1  H4   CAB  OAK  106.45  3.000
 UL1  H8   CAF  CAM  119.85  3.000
 UL1  H8   CAF  CAG  118.99  3.000
 UL1  CAM  CAF  CAG  121.15  3.000
 UL1  H9   CAG  CAN  120.80  3.000
 UL1  H9   CAG  CAF  118.87  3.000
 UL1  CAN  CAG  CAF  120.34  3.000
 UL1  H10  CAH  CAO  118.52  3.000
 UL1  H10  CAH  CAM  120.36  3.000
 UL1  CAO  CAH  CAM  121.07  3.000
 UL1  CAH  CAM  CAF  118.36  3.000
 UL1  CAH  CAM  CAE  124.21  3.000
 UL1  CAF  CAM  CAE  117.43  3.000
 UL1  OAJ  CAN  CAO  115.51  3.000
 UL1  CAO  CAN  CAG  119.32  3.000
 UL1  OAJ  CAN  CAG  125.18  3.000
 UL1  OAK  CAO  CAN  115.22  3.000
 UL1  OAK  CAO  CAH  125.04  3.000
 UL1  CAN  CAO  CAH  119.74  3.000
 UL1  OAC  CAP  NAI  123.74  3.000
 UL1  NAI  CAP  CAR  109.06  3.000
 UL1  OAC  CAP  CAR  127.20  3.000
 UL1  SAL  CAQ  SAD  123.49  3.000
 UL1  SAD  CAQ  NAI  126.68  3.000
 UL1  SAL  CAQ  NAI  109.84  3.000
 UL1  SAL  CAR  CAP  109.68  3.000
 UL1  CAP  CAR  CAE  121.07  3.000
 UL1  SAL  CAR  CAE  129.20  3.000
 UL1  H11  NAI  CAQ  120.17  3.000
 UL1  H11  NAI  CAP  120.95  3.000
 UL1  CAQ  NAI  CAP  118.87  3.000
 UL1  CAN  OAJ  CAA  118.44  3.000
 UL1  CAO  OAK  CAB  118.30  3.000
 UL1  CAR  SAL  CAQ   92.55  3.000
 UL1  H7   CAE  CAR  114.21  3.000
 UL1  H7   CAE  CAM  114.76  3.000
 UL1  CAR  CAE  CAM  131.02  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
 UL1  CONST_01  CAO  CAN  CAG  CAF     0.00   0.0  0
 UL1  CONST_02  CAO  CAH  CAM  CAF     0.00   0.0  0
 UL1  CONST_03  CAH  CAO  CAN  CAG     0.00   0.0  0
 UL1  CONST_04  CAH  CAM  CAF  CAG     0.00   0.0  0
 UL1  CONST_05  CAN  CAG  CAF  CAM     0.00   0.0  0
 UL1  CONST_06  CAN  CAO  CAH  CAM     0.00   0.0  0
 UL1  CONST_07  CAR  CAP  NAI  CAQ     0.00   0.0  0
 UL1  CONST_08  CAG  CAF  CAM  CAE   180.00   0.0  0
 UL1  CONST_09  CAO  CAH  CAM  CAE   180.00   0.0  0
 UL1  CONST_10  OAJ  CAN  CAG  CAF   180.00   0.0  0
 UL1  CONST_11  OAK  CAO  CAN  CAG   180.00   0.0  0
 UL1  CONST_12  OAJ  CAN  CAO  CAH   180.00   0.0  0
 UL1  CONST_13  OAK  CAO  CAH  CAM   180.00   0.0  0
 UL1  CONST_14  SAL  CAR  CAE  CAM     0.00   0.0  0
 UL1  CONST_15  CAP  CAR  CAE  CAM   180.00   0.0  0
 UL1  CONST_16  OAC  CAP  NAI  CAQ   180.00   0.0  0
 UL1  CONST_17  H10  CAH  CAM  CAF   180.00   0.0  0
 UL1  CONST_18  H8   CAF  CAM  CAH   180.00   0.0  0
 UL1  CONST_19  H9   CAG  CAF  CAM   180.00   0.0  0
 UL1  CONST_20  H11  NAI  CAP  CAR   180.00   0.0  0
 UL1  CONST_21  H7   CAE  CAR  CAP     0.00   0.0  0
 UL1  Var_01    CAR  CAE  CAM  CAF   167.44  30.0  2
 UL1  Var_02    CAG  CAN  OAJ  CAA    -0.70  30.0  2
 UL1  Var_03    CAN  CAO  OAK  CAB  -179.95  30.0  2
 UL1  Var_04    H1   CAA  OAJ  CAN  -179.27  30.0  3
 UL1  Var_05    H4   CAB  OAK  CAO   179.79  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
 UL1  plan-1  CAM  0.020
 UL1  plan-1  CAP  0.020
 UL1  plan-1  CAQ  0.020
 UL1  plan-1  CAR  0.020
 UL1  plan-1  NAI  0.020
 UL1  plan-1  SAD  0.020
 UL1  plan-1  SAL  0.020
 UL1  plan-1  H7   0.020
 UL1  plan-1  H11  0.020
 UL1  plan-1  CAE  0.020
 UL1  plan-1  OAC  0.020
 UL1  plan-2  CAF  0.020
 UL1  plan-2  CAG  0.020
 UL1  plan-2  CAH  0.020
 UL1  plan-2  CAM  0.020
 UL1  plan-2  CAN  0.020
 UL1  plan-2  CAO  0.020
 UL1  plan-2  OAJ  0.020
 UL1  plan-2  OAK  0.020
 UL1  plan-2  H8   0.020
 UL1  plan-2  H9   0.020
 UL1  plan-2  H10  0.020
 UL1  plan-2  CAE  0.020

