# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:06:16 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (5R)-5-[(2,4-dimethoxyphenyl)methyl]-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@H]2SC(=O)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
 7QY  7QY  (5R)-5-[(2,4-dimethoxyphenyl)methyl]-1,3-thiazolidine-2,4-dione  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_7QY
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
 7QY  C7   C  CR16  0  -0.271  -1.1700   1.0675   1.1042
 7QY  C8   C  CR16  0  -0.403  -2.4339   1.5221   0.7394
 7QY  C12  C  CR16  0  -0.480  -2.8420  -0.6235  -0.2913
 7QY  C6   C  CR6   0  -0.006  -0.7140  -0.2021   0.7983
 7QY  C9   C  CR6   0   0.396  -3.2712   0.6669   0.0350
 7QY  C13  C  CR6   0   0.378  -1.5794  -1.0527   0.0869
 7QY  C2   C  CR5   0   0.624   3.0363  -1.0392   0.4131
 7QY  C17  C  CR5   0   0.402   3.4813   1.0131  -0.6648
 7QY  C3   C  CR15  0  -0.554   1.6251  -0.6773  -0.0051
 7QY  C11  C  CH3   0  -0.436  -5.0085   2.2756  -0.0858
 7QY  C15  C  CH3   0  -0.438  -1.9079  -3.1910  -0.9008
 7QY  C5   C  CH2   0  -0.486   0.6664  -0.6438   1.1889
 7QY  N16  N  NR15  0  -0.659   3.9382  -0.0969   0.0042
 7QY  O18  O  O     0  -0.403   4.1658   1.9130  -1.0687
 7QY  O10  O  O2    0  -0.471  -4.5119   0.9847  -0.3779
 7QY  O14  O  O2    0  -0.468  -1.0975  -2.2776  -0.1897
 7QY  S4   S  S2    0   0.084   1.7283   0.9338  -0.8414
 7QY  H1   H  HCR6  0   0.256  -0.5182   1.7348   1.6551
 7QY  H2   H  HCR6  0   0.275  -2.7325   2.5240   1.0128
 7QY  H3   H  HCR6  0   0.284  -3.5172  -1.2648  -0.8428
 7QY  H4   H  HCR5  0   0.353   1.2946  -1.4206  -0.7336
 7QY  H5   H  HCH3  0   0.229  -5.0710   2.4547   0.9906
 7QY  H6   H  HCH3  0   0.229  -4.3965   3.0600  -0.5384
 7QY  H7   H  HCH3  0   0.260  -6.0094   2.3247  -0.5077
 7QY  H8   H  HCH3  0   0.231  -2.8278  -3.4262  -0.3599
 7QY  H9   H  HCH3  0   0.231  -2.1669  -2.8174  -1.8943
 7QY  H10  H  HCH3  0   0.263  -1.3238  -4.1012  -1.0100
 7QY  H11  H  HCH2  0   0.277   1.0629   0.0361   1.9454
 7QY  H12  H  HCH2  0   0.278   0.6521  -1.6408   1.6339
 7QY  H13  H  HNR5  0   0.439   4.9260  -0.1914   0.2102
 7QY  O1   O  O     0  -0.412   3.3199  -2.0322   1.0345

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
 7QY  C15  O14  single    1.413  0.020  1.413
 7QY  O14  C13  single    1.345  0.020  1.345
 7QY  C13  C12  aromatic  1.386  0.020  1.386
 7QY  C13  C6   aromatic  1.407  0.020  1.407
 7QY  O1   C2   double    1.205  0.020  1.205
 7QY  C5   C6   single    1.501  0.020  1.501
 7QY  C5   C3   single    1.532  0.020  1.532
 7QY  C12  C9   aromatic  1.399  0.020  1.399
 7QY  C6   C7   aromatic  1.383  0.020  1.383
 7QY  C11  O10  single    1.414  0.020  1.414
 7QY  C2   C3   single    1.516  0.020  1.516
 7QY  C2   N16  single    1.367  0.020  1.367
 7QY  C9   O10  single    1.346  0.020  1.346
 7QY  C9   C8   aromatic  1.389  0.020  1.389
 7QY  C7   C8   aromatic  1.392  0.020  1.392
 7QY  C3   S4   single    1.818  0.020  1.818
 7QY  N16  C17  single    1.374  0.020  1.374
 7QY  C17  S4   single    1.764  0.020  1.764
 7QY  C17  O18  double    1.201  0.020  1.201
 7QY  C7   H1   single    0.930  0.020  1.080
 7QY  C8   H2   single    0.930  0.020  1.080
 7QY  C12  H3   single    0.930  0.020  1.080
 7QY  C3   H4   single    0.970  0.020  1.090
 7QY  C11  H5   single    0.970  0.020  1.090
 7QY  C11  H6   single    0.970  0.020  1.090
 7QY  C11  H7   single    0.970  0.020  1.090
 7QY  C15  H8   single    0.970  0.020  1.090
 7QY  C15  H9   single    0.970  0.020  1.090
 7QY  C15  H10  single    0.970  0.020  1.090
 7QY  C5   H11  single    0.970  0.020  1.090
 7QY  C5   H12  single    0.970  0.020  1.090
 7QY  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
 7QY  H1   C7   C6   118.65  3.000
 7QY  H1   C7   C8   118.58  3.000
 7QY  C6   C7   C8   122.76  3.000
 7QY  H2   C8   C9   122.18  3.000
 7QY  H2   C8   C7   119.17  3.000
 7QY  C9   C8   C7   118.64  3.000
 7QY  H3   C12  C13  121.59  3.000
 7QY  H3   C12  C9   118.31  3.000
 7QY  C13  C12  C9   120.10  3.000
 7QY  C5   C6   C13  121.30  3.000
 7QY  C5   C6   C7   121.04  3.000
 7QY  C13  C6   C7   117.65  3.000
 7QY  O10  C9   C12  115.42  3.000
 7QY  O10  C9   C8   124.48  3.000
 7QY  C12  C9   C8   120.10  3.000
 7QY  O14  C13  C6   115.74  3.000
 7QY  C6   C13  C12  120.74  3.000
 7QY  O14  C13  C12  123.51  3.000
 7QY  O1   C2   N16  124.54  3.000
 7QY  N16  C2   C3   111.54  3.000
 7QY  O1   C2   C3   123.92  3.000
 7QY  S4   C17  O18  124.52  3.000
 7QY  O18  C17  N16  125.43  3.000
 7QY  S4   C17  N16  110.05  3.000
 7QY  H4   C3   S4   108.27  3.000
 7QY  H4   C3   C5   110.21  3.000
 7QY  S4   C3   C5   112.01  3.000
 7QY  H4   C3   C2   107.66  3.000
 7QY  S4   C3   C2   106.60  3.000
 7QY  C5   C3   C2   111.89  3.000
 7QY  H7   C11  H6   108.81  3.000
 7QY  H7   C11  H5   108.79  3.000
 7QY  H6   C11  H5   108.80  3.000
 7QY  H7   C11  O10  106.53  3.000
 7QY  H6   C11  O10  111.91  3.000
 7QY  H5   C11  O10  111.91  3.000
 7QY  H10  C15  H9   108.81  3.000
 7QY  H10  C15  H8   108.78  3.000
 7QY  H9   C15  H8   108.91  3.000
 7QY  H10  C15  O14  106.48  3.000
 7QY  H9   C15  O14  111.87  3.000
 7QY  H8   C15  O14  111.89  3.000
 7QY  H12  C5   H11  106.92  3.000
 7QY  H12  C5   C3   107.82  3.000
 7QY  H11  C5   C3   109.06  3.000
 7QY  H12  C5   C6   111.26  3.000
 7QY  H11  C5   C6   109.33  3.000
 7QY  C3   C5   C6   112.29  3.000
 7QY  H13  N16  C17  119.89  3.000
 7QY  H13  N16  C2   121.20  3.000
 7QY  C17  N16  C2   118.89  3.000
 7QY  C11  O10  C9   118.44  3.000
 7QY  C15  O14  C13  119.12  3.000
 7QY  C3   S4   C17   92.88  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
 7QY  CONST_01  C12  C13  C6   C7      0.00   0.0  0
 7QY  CONST_02  C12  C9   C8   C7      0.00   0.0  0
 7QY  CONST_03  C13  C12  C9   C8      0.00   0.0  0
 7QY  CONST_04  C13  C6   C7   C8      0.00   0.0  0
 7QY  CONST_05  C9   C12  C13  C6      0.00   0.0  0
 7QY  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 7QY  CONST_07  C3   C2   N16  C17     0.00   0.0  0
 7QY  CONST_08  O14  C13  C6   C7    180.00   0.0  0
 7QY  CONST_09  O10  C9   C8   C7    180.00   0.0  0
 7QY  CONST_10  C5   C6   C7   C8    180.00   0.0  0
 7QY  CONST_11  C5   C6   C13  C12   180.00   0.0  0
 7QY  CONST_12  O14  C13  C12  C9    180.00   0.0  0
 7QY  CONST_13  O10  C9   C12  C13   180.00   0.0  0
 7QY  CONST_14  O1   C2   N16  C17   180.00   0.0  0
 7QY  CONST_15  H3   C12  C9   C8    180.00   0.0  0
 7QY  CONST_16  H2   C8   C9   C12   180.00   0.0  0
 7QY  CONST_17  H1   C7   C8   C9    180.00   0.0  0
 7QY  CONST_18  H13  N16  C2   C3    180.00   0.0  0
 7QY  Var_01    S4   C17  N16  C2     -0.12  30.0  1
 7QY  Var_02    N16  C17  S4   C3     -1.06  30.0  1
 7QY  Var_03    C3   C5   C6   C7   -104.86  30.0  2
 7QY  Var_04    H5   C11  O10  C9    -61.57  30.0  3
 7QY  Var_05    H8   C15  O14  C13   -61.33  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
 7QY  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
 7QY  plan-1  C7   0.020
 7QY  plan-1  C8   0.020
 7QY  plan-1  C12  0.020
 7QY  plan-1  C6   0.020
 7QY  plan-1  C9   0.020
 7QY  plan-1  C13  0.020
 7QY  plan-1  C5   0.020
 7QY  plan-1  O10  0.020
 7QY  plan-1  O14  0.020
 7QY  plan-1  H1   0.020
 7QY  plan-1  H2   0.020
 7QY  plan-1  H3   0.020
 7QY  plan-2  C17  0.020
 7QY  plan-2  N16  0.020
 7QY  plan-2  O18  0.020
 7QY  plan-2  S4   0.020
 7QY  plan-3  C2   0.020
 7QY  plan-3  C17  0.020
 7QY  plan-3  C3   0.020
 7QY  plan-3  N16  0.020
 7QY  plan-3  H13  0.020
 7QY  plan-3  O1   0.020

