# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 16:38:24 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (5R)-5-benzyl-2-sulfanylidene-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=S)S[C@@H]1Cc2ccccc2
#
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
 7R4  7R4  (5R)-5-benzyl-2-sulfanylidene-1,3-thiazolidin-4-one  ligand  23  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7R4
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
 7R4  C9   C  CR16  0  -0.266   4.3924   1.0413   0.3429
 7R4  C8   C  CR16  0  -0.240   3.5029   1.6409  -0.5375
 7R4  C10  C  CR16  0  -0.239   4.1313  -0.2382   0.8186
 7R4  C7   C  CR16  0  -0.299   2.3557   0.9662  -0.9370
 7R4  C11  C  CR16  0  -0.296   2.9858  -0.9094   0.4174
 7R4  C6   C  CR6   0   0.108   2.0852  -0.3148  -0.4646
 7R4  C2   C  CR5   0   0.630  -1.5109  -1.6697  -0.1413
 7R4  C13  C  CR5   0   0.036  -2.3906   0.4605   0.3374
 7R4  C3   C  CR15  0  -0.561  -0.2294  -0.9582   0.2465
 7R4  C5   C  CH2   0  -0.501   0.8247  -1.0323  -0.8600
 7R4  N12  N  NR15  0  -0.604  -2.5918  -0.8261  -0.0435
 7R4  S14  S  S1    0  -0.220  -3.5552   1.5954   0.4927
 7R4  S4   S  S2    0   0.195  -0.7069   0.7538   0.6381
 7R4  H1   H  HCR6  0   0.258   5.2861   1.5655   0.6559
 7R4  H2   H  HCR6  0   0.258   3.7006   2.6353  -0.9160
 7R4  H3   H  HCR6  0   0.258   4.8224  -0.7151   1.5015
 7R4  H4   H  HCR6  0   0.254   1.6686   1.4405  -1.6274
 7R4  H5   H  HCR6  0   0.254   2.7913  -1.9083   0.7913
 7R4  H6   H  HCR5  0   0.361   0.1504  -1.4251   1.1595
 7R4  H7   H  HCH2  0   0.283   0.4161  -0.6138  -1.7815
 7R4  H8   H  HCH2  0   0.288   1.0337  -2.0878  -1.0464
 7R4  H9   H  HNR5  0   0.441  -3.5251  -1.1487  -0.2702
 7R4  O1   O  O     0  -0.399  -1.5757  -2.8169  -0.4962

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
 7R4  C11  C10  aromatic  1.387  0.020  1.387
 7R4  C11  C6   aromatic  1.394  0.020  1.394
 7R4  C5   C6   single    1.503  0.020  1.503
 7R4  C5   C3   single    1.530  0.020  1.530
 7R4  C10  C9   aromatic  1.390  0.020  1.390
 7R4  C6   C7   aromatic  1.392  0.020  1.392
 7R4  O1   C2   double    1.203  0.020  1.203
 7R4  C9   C8   aromatic  1.388  0.020  1.388
 7R4  C7   C8   aromatic  1.390  0.020  1.390
 7R4  C2   C3   single    1.516  0.020  1.516
 7R4  C2   N12  single    1.375  0.020  1.375
 7R4  C3   S4   single    1.820  0.020  1.820
 7R4  N12  C13  single    1.357  0.020  1.357
 7R4  S4   C13  single    1.735  0.020  1.735
 7R4  C13  S14  double    1.634  0.020  1.634
 7R4  C9   H1   single    0.930  0.020  1.080
 7R4  C8   H2   single    0.930  0.020  1.080
 7R4  C10  H3   single    0.930  0.020  1.080
 7R4  C7   H4   single    0.930  0.020  1.080
 7R4  C11  H5   single    0.930  0.020  1.080
 7R4  C3   H6   single    0.970  0.020  1.090
 7R4  C5   H7   single    0.970  0.020  1.090
 7R4  C5   H8   single    0.970  0.020  1.090
 7R4  N12  H9   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
 7R4  H1   C9   C10  120.13  3.000
 7R4  H1   C9   C8   120.23  3.000
 7R4  C10  C9   C8   119.64  3.000
 7R4  H2   C8   C7   119.76  3.000
 7R4  H2   C8   C9   120.12  3.000
 7R4  C7   C8   C9   120.12  3.000
 7R4  H3   C10  C11  119.77  3.000
 7R4  H3   C10  C9   120.12  3.000
 7R4  C11  C10  C9   120.11  3.000
 7R4  H4   C7   C6   119.73  3.000
 7R4  H4   C7   C8   119.62  3.000
 7R4  C6   C7   C8   120.65  3.000
 7R4  H5   C11  C6   119.70  3.000
 7R4  H5   C11  C10  119.62  3.000
 7R4  C6   C11  C10  120.68  3.000
 7R4  C5   C6   C11  120.30  3.000
 7R4  C5   C6   C7   120.86  3.000
 7R4  C11  C6   C7   118.81  3.000
 7R4  O1   C2   N12  124.34  3.000
 7R4  N12  C2   C3   111.00  3.000
 7R4  O1   C2   C3   124.66  3.000
 7R4  S4   C13  S14  123.91  3.000
 7R4  S14  C13  N12  125.44  3.000
 7R4  S4   C13  N12  110.66  3.000
 7R4  H6   C3   S4   108.24  3.000
 7R4  H6   C3   C5   110.11  3.000
 7R4  S4   C3   C5   112.45  3.000
 7R4  H6   C3   C2   107.86  3.000
 7R4  S4   C3   C2   105.95  3.000
 7R4  C5   C3   C2   112.00  3.000
 7R4  H8   C5   H7   107.34  3.000
 7R4  H8   C5   C3   107.58  3.000
 7R4  H7   C5   C3   109.52  3.000
 7R4  H8   C5   C6   110.23  3.000
 7R4  H7   C5   C6   110.67  3.000
 7R4  C3   C5   C6   111.37  3.000
 7R4  H9   N12  C13  120.08  3.000
 7R4  H9   N12  C2   120.87  3.000
 7R4  C13  N12  C2   119.04  3.000
 7R4  C3   S4   C13   93.34  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
 7R4  CONST_01  C6   C11  C10  C9      0.00   0.0  0
 7R4  CONST_02  C6   C7   C8   C9      0.00   0.0  0
 7R4  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 7R4  CONST_04  C11  C6   C7   C8      0.00   0.0  0
 7R4  CONST_05  C7   C6   C11  C10     0.00   0.0  0
 7R4  CONST_06  C7   C8   C9   C10     0.00   0.0  0
 7R4  CONST_07  C3   C2   N12  C13     0.00   0.0  0
 7R4  CONST_08  C5   C6   C7   C8    180.00   0.0  0
 7R4  CONST_09  C5   C6   C11  C10   180.00   0.0  0
 7R4  CONST_10  O1   C2   N12  C13   180.00   0.0  0
 7R4  CONST_11  H5   C11  C10  C9    180.00   0.0  0
 7R4  CONST_12  H4   C7   C8   C9    180.00   0.0  0
 7R4  CONST_13  H3   C10  C9   C8    180.00   0.0  0
 7R4  CONST_14  H2   C8   C9   C10   180.00   0.0  0
 7R4  CONST_15  H1   C9   C8   C7    180.00   0.0  0
 7R4  CONST_16  H9   N12  C2   C3    180.00   0.0  0
 7R4  Var_01    S4   C13  N12  C2     -0.29  30.0  1
 7R4  Var_02    N12  C13  S4   C3     -0.54  30.0  1
 7R4  Var_03    C3   C5   C6   C7   -100.66  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 7R4  chir_01  C3  C5  C2  S4  positiv

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
 7R4  plan-1  C9   0.020
 7R4  plan-1  C8   0.020
 7R4  plan-1  C10  0.020
 7R4  plan-1  C7   0.020
 7R4  plan-1  C11  0.020
 7R4  plan-1  C6   0.020
 7R4  plan-1  C5   0.020
 7R4  plan-1  H1   0.020
 7R4  plan-1  H2   0.020
 7R4  plan-1  H3   0.020
 7R4  plan-1  H4   0.020
 7R4  plan-1  H5   0.020
 7R4  plan-2  C2   0.020
 7R4  plan-2  C13  0.020
 7R4  plan-2  C3   0.020
 7R4  plan-2  N12  0.020
 7R4  plan-2  H9   0.020
 7R4  plan-2  O1   0.020

