# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:06:48 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (5R)-5-[(2,4-dimethoxyphenyl)methyl]-2-sulfanylidene-1,3-thiazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@H]2SC(=S)NC2=O)c(OC)c1
#
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
 7R1  7R1  (5R)-5-[(2,4-dimethoxyphenyl)methyl]-2-sulfanylidene-1,3-thiazolidin-4-one  ligand  31  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7R1
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
 7R1  C7   C  CR16  0  -0.273  -1.3982  -1.0449  -1.1227
 7R1  C8   C  CR16  0  -0.402  -2.6033  -1.6352  -0.7538
 7R1  C12  C  CR16  0  -0.479  -3.2065   0.4271   0.3489
 7R1  C6   C  CR6   0  -0.006  -1.0671   0.2554  -0.7850
 7R1  C9   C  CR6   0   0.396  -3.5106  -0.8892  -0.0129
 7R1  C13  C  CR6   0   0.380  -2.0006   0.9926  -0.0343
 7R1  C2   C  CR5   0   0.630   2.5637   1.5183  -0.4057
 7R1  C17  C  CR5   0   0.036   3.2686  -0.5008   0.5783
 7R1  C3   C  CR15  0  -0.566   1.2155   0.9625   0.0026
 7R1  C11  C  CH3   0  -0.437  -5.0846  -2.6603   0.0610
 7R1  C15  C  CH3   0  -0.438  -2.5123   3.0467   1.0517
 7R1  C5   C  CH2   0  -0.488   0.2531   0.8487  -1.1837
 7R1  N16  N  NR15  0  -0.605   3.5797   0.6690  -0.0349
 7R1  O10  O  O2    0  -0.471  -4.7073  -1.3415   0.4036
 7R1  O14  O  O2    0  -0.469  -1.6394   2.2509   0.2741
 7R1  S18  S  S1    0  -0.224   4.3454  -1.6276   1.0693
 7R1  S4   S  S2    0   0.194   1.5511  -0.6517   0.7707
 7R1  H1   H  HCR6  0   0.257  -0.6932  -1.6267  -1.7041
 7R1  H2   H  HCR6  0   0.275  -2.8050  -2.6537  -1.0531
 7R1  H3   H  HCR6  0   0.285  -3.9332   0.9806   0.9288
 7R1  H4   H  HCR5  0   0.360   0.7978   1.6248   0.7644
 7R1  H5   H  HCH3  0   0.229  -5.1375  -2.8012  -1.0217
 7R1  H6   H  HCH3  0   0.229  -4.4002  -3.4024   0.4799
 7R1  H7   H  HCH3  0   0.260  -6.0737  -2.8189   0.4835
 7R1  H8   H  HCH3  0   0.232  -3.4625   3.2255   0.5426
 7R1  H9   H  HCH3  0   0.231  -2.7120   2.5970   2.0271
 7R1  H10  H  HCH3  0   0.263  -2.0099   3.9989   1.2007
 7R1  H11  H  HCH2  0   0.280   0.7105   0.2289  -1.9568
 7R1  H12  H  HCH2  0   0.281   0.1284   1.8477  -1.6068
 7R1  H13  H  HNR5  0   0.440   4.5470   0.8968  -0.2324
 7R1  O1   O  O     0  -0.401   2.7292   2.5596  -0.9851

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
 7R1  C7   C8   aromatic  1.392  0.020  1.392
 7R1  C7   C6   aromatic  1.384  0.020  1.384
 7R1  C8   C9   aromatic  1.389  0.020  1.389
 7R1  C12  C9   aromatic  1.399  0.020  1.399
 7R1  C12  C13  aromatic  1.386  0.020  1.386
 7R1  C6   C13  aromatic  1.407  0.020  1.407
 7R1  C6   C5   single    1.501  0.020  1.501
 7R1  C9   O10  single    1.345  0.020  1.345
 7R1  C13  O14  single    1.345  0.020  1.345
 7R1  C2   C3   single    1.514  0.020  1.514
 7R1  C2   N16  single    1.375  0.020  1.375
 7R1  C2   O1   double    1.203  0.020  1.203
 7R1  C17  N16  single    1.357  0.020  1.357
 7R1  C17  S18  double    1.634  0.020  1.634
 7R1  C17  S4   single    1.735  0.020  1.735
 7R1  C3   C5   single    1.532  0.020  1.532
 7R1  C3   S4   single    1.819  0.020  1.819
 7R1  C11  O10  single    1.414  0.020  1.414
 7R1  C15  O14  single    1.414  0.020  1.414
 7R1  C7   H1   single    0.930  0.020  1.080
 7R1  C8   H2   single    0.930  0.020  1.080
 7R1  C12  H3   single    0.930  0.020  1.080
 7R1  C3   H4   single    0.970  0.020  1.090
 7R1  C11  H5   single    0.970  0.020  1.090
 7R1  C11  H6   single    0.970  0.020  1.090
 7R1  C11  H7   single    0.970  0.020  1.090
 7R1  C15  H8   single    0.970  0.020  1.090
 7R1  C15  H9   single    0.970  0.020  1.090
 7R1  C15  H10  single    0.970  0.020  1.090
 7R1  C5   H11  single    0.970  0.020  1.090
 7R1  C5   H12  single    0.970  0.020  1.090
 7R1  N16  H13  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
 7R1  H1   C7   C6   118.68  3.000
 7R1  H1   C7   C8   118.56  3.000
 7R1  C6   C7   C8   122.76  3.000
 7R1  H2   C8   C9   122.15  3.000
 7R1  H2   C8   C7   119.21  3.000
 7R1  C9   C8   C7   118.64  3.000
 7R1  H3   C12  C13  121.59  3.000
 7R1  H3   C12  C9   118.29  3.000
 7R1  C13  C12  C9   120.11  3.000
 7R1  C5   C6   C13  121.21  3.000
 7R1  C5   C6   C7   121.13  3.000
 7R1  C13  C6   C7   117.65  3.000
 7R1  O10  C9   C12  115.45  3.000
 7R1  O10  C9   C8   124.45  3.000
 7R1  C12  C9   C8   120.10  3.000
 7R1  O14  C13  C6   115.75  3.000
 7R1  O14  C13  C12  123.51  3.000
 7R1  C6   C13  C12  120.74  3.000
 7R1  O1   C2   N16  124.25  3.000
 7R1  O1   C2   C3   124.75  3.000
 7R1  N16  C2   C3   111.00  3.000
 7R1  S4   C17  S18  123.99  3.000
 7R1  S4   C17  N16  110.61  3.000
 7R1  S18  C17  N16  125.39  3.000
 7R1  H4   C3   S4   108.31  3.000
 7R1  H4   C3   C5   110.18  3.000
 7R1  S4   C3   C5   112.15  3.000
 7R1  H4   C3   C2   107.81  3.000
 7R1  S4   C3   C2   105.98  3.000
 7R1  C5   C3   C2   112.20  3.000
 7R1  H7   C11  H6   108.77  3.000
 7R1  H7   C11  H5   108.79  3.000
 7R1  H6   C11  H5   108.81  3.000
 7R1  H7   C11  O10  106.54  3.000
 7R1  H6   C11  O10  111.92  3.000
 7R1  H5   C11  O10  111.90  3.000
 7R1  H10  C15  H9   108.83  3.000
 7R1  H10  C15  H8   108.81  3.000
 7R1  H9   C15  H8   108.93  3.000
 7R1  H10  C15  O14  106.44  3.000
 7R1  H9   C15  O14  111.84  3.000
 7R1  H8   C15  O14  111.88  3.000
 7R1  H12  C5   H11  107.03  3.000
 7R1  H12  C5   C3   107.68  3.000
 7R1  H11  C5   C3   109.12  3.000
 7R1  H12  C5   C6   111.35  3.000
 7R1  H11  C5   C6   109.41  3.000
 7R1  C3   C5   C6   112.10  3.000
 7R1  H13  N16  C17  120.05  3.000
 7R1  H13  N16  C2   120.93  3.000
 7R1  C17  N16  C2   119.01  3.000
 7R1  C11  O10  C9   118.42  3.000
 7R1  C15  O14  C13  119.13  3.000
 7R1  C3   S4   C17   93.36  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
 7R1  CONST_01  C12  C9   C8   C7      0.00   0.0  0
 7R1  CONST_02  C12  C13  C6   C7      0.00   0.0  0
 7R1  CONST_03  C13  C6   C7   C8      0.00   0.0  0
 7R1  CONST_04  C13  C12  C9   C8      0.00   0.0  0
 7R1  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 7R1  CONST_06  C9   C12  C13  C6      0.00   0.0  0
 7R1  CONST_07  C3   C2   N16  C17     0.00   0.0  0
 7R1  CONST_08  O10  C9   C8   C7    180.00   0.0  0
 7R1  CONST_09  O14  C13  C6   C7    180.00   0.0  0
 7R1  CONST_10  C5   C6   C7   C8    180.00   0.0  0
 7R1  CONST_11  C5   C6   C13  C12   180.00   0.0  0
 7R1  CONST_12  O14  C13  C12  C9    180.00   0.0  0
 7R1  CONST_13  O10  C9   C12  C13   180.00   0.0  0
 7R1  CONST_14  O1   C2   N16  C17   180.00   0.0  0
 7R1  CONST_15  H3   C12  C9   C8    180.00   0.0  0
 7R1  CONST_16  H2   C8   C9   C12   180.00   0.0  0
 7R1  CONST_17  H1   C7   C8   C9    180.00   0.0  0
 7R1  CONST_18  H13  N16  C2   C3    180.00   0.0  0
 7R1  Var_01    S4   C17  N16  C2     -0.40  30.0  1
 7R1  Var_02    N16  C17  S4   C3     -0.74  30.0  1
 7R1  Var_03    C3   C5   C6   C7   -105.71  30.0  2
 7R1  Var_04    H5   C11  O10  C9    -60.82  30.0  3
 7R1  Var_05    H8   C15  O14  C13   -62.95  30.0  3

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
 7R1  chir_01  C3  C2  C5  S4  negativ

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
 7R1  plan-1  C7   0.020
 7R1  plan-1  C8   0.020
 7R1  plan-1  C12  0.020
 7R1  plan-1  C6   0.020
 7R1  plan-1  C9   0.020
 7R1  plan-1  C13  0.020
 7R1  plan-1  C5   0.020
 7R1  plan-1  O10  0.020
 7R1  plan-1  O14  0.020
 7R1  plan-1  H1   0.020
 7R1  plan-1  H2   0.020
 7R1  plan-1  H3   0.020
 7R1  plan-2  C2   0.020
 7R1  plan-2  C17  0.020
 7R1  plan-2  C3   0.020
 7R1  plan-2  N16  0.020
 7R1  plan-2  H13  0.020
 7R1  plan-2  O1   0.020

