# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:02:31 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5S)-5-({4-[2-(3-methoxyphenyl)-2-oxoethoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)C(=O)COc2ccc(C[C@@H]3SC(=O)NC3=O)cc2
#
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
 GH1  GH1  (5S)-5-({4-[2-(3-methoxyphenyl)-2-oxoethoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione  ligand  43  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GH1
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
 GH1  C13  C  CR6   0   0.374    0.0999  -1.1492  -0.0350
 GH1  C15  C  CR16  0  -0.288    1.9463  -0.0301  -1.0911
 GH1  C17  C  CR16  0  -0.279    2.3117  -2.0941   0.0455
 GH1  C20  C  CR15  0  -0.554    5.1294  -0.6047   0.1966
 GH1  C21  C  CR5   0   0.623    6.6071  -0.5253  -0.1368
 GH1  C24  C  CR5   0   0.404    6.3081   1.6381   0.7587
 GH1  C01  C  CH3   0  -0.439   -9.3695   0.7942   0.3214
 GH1  C03  C  CR6   0   0.410   -7.0208   0.4991   0.1564
 GH1  C04  C  CR16  0  -0.374   -6.8577   1.6647  -0.5917
 GH1  C05  C  CR16  0  -0.222   -5.5889   2.0340  -1.0201
 GH1  C06  C  CR16  0  -0.319   -4.4797   1.2653  -0.7162
 GH1  C07  C  CR6   0  -0.003   -4.6405   0.0992   0.0354
 GH1  C08  C  CR16  0  -0.359   -5.9069  -0.2768   0.4668
 GH1  C09  C  C     0   0.341   -3.4897  -0.7713   0.3971
 GH1  C14  C  CR16  0  -0.360    0.5927  -0.0785  -0.7717
 GH1  C16  C  CR6   0   0.091    2.8241  -1.0289  -0.6973
 GH1  C18  C  CR16  0  -0.330    0.9723  -2.1599   0.3746
 GH1  C19  C  CH2   0  -0.496    4.2873  -0.9578  -1.0308
 GH1  N23  N  NR15  0  -0.658    7.1335   0.6878   0.2073
 GH1  O10  O  O     0  -0.371   -3.6302  -1.7745   1.0550
 GH1  O12  O  O2    0  -0.467   -1.1921  -1.3016   0.3281
 GH1  O25  O  O     0  -0.401    6.6425   2.7409   1.0948
 GH1  S26  S  S2    0   0.086    4.6670   1.0066   0.9007
 GH1  H1   H  HCR6  0   0.258    2.3140   0.8112  -1.6662
 GH1  H2   H  HCR6  0   0.257    2.9696  -2.8924   0.3702
 GH1  H3   H  HCH3  0   0.231   -9.3337   1.7970   0.7545
 GH1  H4   H  HCH3  0   0.231   -9.5383   0.8788  -0.7551
 GH1  H5   H  HCH3  0   0.262  -10.1998   0.2508   0.7648
 GH1  H6   H  HCR6  0   0.290   -7.6997   2.2932  -0.8489
 GH1  H7   H  HCR6  0   0.271   -5.4726   2.9388  -1.6015
 GH1  H8   H  HCR6  0   0.263   -3.5085   1.5857  -1.0673
 GH1  H9   H  HCR6  0   0.272   -6.0390  -1.1798   1.0495
 GH1  H11  H  HCH2  0   0.267   -2.1476  -0.2645  -1.1914
 GH1  H12  H  HCH2  0   0.268   -1.8933   0.6506   0.2981
 GH1  H13  H  HCR6  0   0.281   -0.0473   0.7254  -1.1087
 GH1  H14  H  HCR6  0   0.265    0.5893  -2.9972   0.9445
 GH1  H15  H  HCH2  0   0.279    4.4597  -0.2185  -1.8152
 GH1  H16  H  HCH2  0   0.283    4.6363  -1.9221  -1.4071
 GH1  H17  H  HNR5  0   0.440    8.1107   0.9011   0.0430
 GH1  H19  H  HCR5  0   0.353    5.0025  -1.3681   0.9685
 GH1  O22  O  O     0  -0.410    7.2292  -1.4207  -0.6496
 GH1  C11  C  CH2   0  -0.300   -2.1221  -0.3479  -0.0971
 GH1  O02  O  O2    0  -0.470   -8.2020   0.0509   0.6149

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
 GH1  C05  C04  aromatic  1.389  0.020  1.389
 GH1  C05  C06  aromatic  1.383  0.020  1.383
 GH1  C04  C03  aromatic  1.395  0.020  1.395
 GH1  C06  C07  aromatic  1.397  0.020  1.397
 GH1  C01  O02  single    1.415  0.020  1.415
 GH1  C03  O02  single    1.344  0.020  1.344
 GH1  C03  C08  aromatic  1.393  0.020  1.393
 GH1  C07  C08  aromatic  1.390  0.020  1.390
 GH1  C07  C09  single    1.488  0.020  1.488
 GH1  C09  O10  double    1.208  0.020  1.208
 GH1  C09  C11  single    1.515  0.020  1.515
 GH1  C11  O12  single    1.398  0.020  1.398
 GH1  O12  C13  single    1.351  0.020  1.351
 GH1  C13  C18  aromatic  1.397  0.020  1.397
 GH1  C13  C14  aromatic  1.390  0.020  1.390
 GH1  C18  C17  aromatic  1.381  0.020  1.381
 GH1  C14  C15  aromatic  1.392  0.020  1.392
 GH1  C17  C16  aromatic  1.396  0.020  1.396
 GH1  C15  C16  aromatic  1.387  0.020  1.387
 GH1  C16  C19  single    1.502  0.020  1.502
 GH1  C19  C20  single    1.530  0.020  1.530
 GH1  S26  C20  single    1.818  0.020  1.818
 GH1  S26  C24  single    1.764  0.020  1.764
 GH1  C20  C21  single    1.517  0.020  1.517
 GH1  C24  O25  double    1.200  0.020  1.200
 GH1  C24  N23  single    1.374  0.020  1.374
 GH1  C21  N23  single    1.366  0.020  1.366
 GH1  C21  O22  double    1.205  0.020  1.205
 GH1  C15  H1   single    0.930  0.020  1.080
 GH1  C17  H2   single    0.930  0.020  1.080
 GH1  C01  H3   single    0.970  0.020  1.090
 GH1  C01  H4   single    0.970  0.020  1.090
 GH1  C01  H5   single    0.970  0.020  1.090
 GH1  C04  H6   single    0.930  0.020  1.080
 GH1  C05  H7   single    0.930  0.020  1.080
 GH1  C06  H8   single    0.930  0.020  1.080
 GH1  C08  H9   single    0.930  0.020  1.080
 GH1  C11  H11  single    0.970  0.020  1.090
 GH1  C11  H12  single    0.970  0.020  1.090
 GH1  C14  H13  single    0.930  0.020  1.080
 GH1  C18  H14  single    0.930  0.020  1.080
 GH1  C19  H15  single    0.970  0.020  1.090
 GH1  C19  H16  single    0.970  0.020  1.090
 GH1  N23  H17  single    0.860  0.020  1.020
 GH1  C20  H19  single    0.970  0.020  1.090

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
 GH1  O12  C13  C18  115.92  3.000
 GH1  C18  C13  C14  119.44  3.000
 GH1  O12  C13  C14  124.65  3.000
 GH1  H1   C15  C16  119.69  3.000
 GH1  H1   C15  C14  118.62  3.000
 GH1  C16  C15  C14  121.70  3.000
 GH1  H2   C17  C18  118.82  3.000
 GH1  H2   C17  C16  119.90  3.000
 GH1  C18  C17  C16  121.28  3.000
 GH1  H19  C20  S26  108.42  3.000
 GH1  H19  C20  C19  109.97  3.000
 GH1  S26  C20  C19  112.04  3.000
 GH1  H19  C20  C21  107.75  3.000
 GH1  S26  C20  C21  106.65  3.000
 GH1  C19  C20  C21  111.84  3.000
 GH1  O22  C21  N23  124.61  3.000
 GH1  O22  C21  C20  123.89  3.000
 GH1  N23  C21  C20  111.49  3.000
 GH1  S26  C24  O25  124.44  3.000
 GH1  O25  C24  N23  125.47  3.000
 GH1  S26  C24  N23  110.09  3.000
 GH1  H5   C01  H4   108.82  3.000
 GH1  H5   C01  H3   108.79  3.000
 GH1  H4   C01  H3   108.92  3.000
 GH1  H5   C01  O02  106.45  3.000
 GH1  H4   C01  O02  111.87  3.000
 GH1  H3   C01  O02  111.89  3.000
 GH1  O02  C03  C08  116.18  3.000
 GH1  C08  C03  C04  119.45  3.000
 GH1  O02  C03  C04  124.37  3.000
 GH1  H6   C04  C05  118.89  3.000
 GH1  H6   C04  C03  121.47  3.000
 GH1  C05  C04  C03  119.63  3.000
 GH1  H7   C05  C06  119.78  3.000
 GH1  H7   C05  C04  119.10  3.000
 GH1  C06  C05  C04  121.12  3.000
 GH1  H8   C06  C07  121.70  3.000
 GH1  H8   C06  C05  118.96  3.000
 GH1  C07  C06  C05  119.33  3.000
 GH1  C09  C07  C08  118.11  3.000
 GH1  C09  C07  C06  122.03  3.000
 GH1  C08  C07  C06  119.86  3.000
 GH1  H9   C08  C07  120.26  3.000
 GH1  H9   C08  C03  119.15  3.000
 GH1  C07  C08  C03  120.60  3.000
 GH1  O10  C09  C11  121.00  3.000
 GH1  C11  C09  C07  117.10  3.000
 GH1  O10  C09  C07  121.90  3.000
 GH1  H13  C14  C15  118.57  3.000
 GH1  H13  C14  C13  121.87  3.000
 GH1  C15  C14  C13  119.56  3.000
 GH1  C19  C16  C17  120.78  3.000
 GH1  C19  C16  C15  121.29  3.000
 GH1  C17  C16  C15  117.92  3.000
 GH1  H14  C18  C17  120.35  3.000
 GH1  H14  C18  C13  119.54  3.000
 GH1  C17  C18  C13  120.10  3.000
 GH1  H16  C19  H15  107.45  3.000
 GH1  H16  C19  C16  110.23  3.000
 GH1  H15  C19  C16  110.21  3.000
 GH1  H16  C19  C20  107.71  3.000
 GH1  H15  C19  C20  109.46  3.000
 GH1  C16  C19  C20  111.65  3.000
 GH1  H17  N23  C24  119.91  3.000
 GH1  H17  N23  C21  121.16  3.000
 GH1  C24  N23  C21  118.92  3.000
 GH1  C11  O12  C13  118.52  3.000
 GH1  C24  S26  C20   92.84  3.000
 GH1  H12  C11  H11  107.13  3.000
 GH1  H12  C11  O12  111.85  3.000
 GH1  H11  C11  O12  111.74  3.000
 GH1  H12  C11  C09  108.97  3.000
 GH1  H11  C11  C09  109.00  3.000
 GH1  O12  C11  C09  108.10  3.000
 GH1  C03  O02  C01  118.64  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
 GH1  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 GH1  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 GH1  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 GH1  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 GH1  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 GH1  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 GH1  CONST_07  C06  C05  C04  C03     0.00   0.0  0
 GH1  CONST_08  C06  C07  C08  C03     0.00   0.0  0
 GH1  CONST_09  C07  C06  C05  C04     0.00   0.0  0
 GH1  CONST_10  C07  C08  C03  C04     0.00   0.0  0
 GH1  CONST_11  C08  C03  C04  C05     0.00   0.0  0
 GH1  CONST_12  C08  C07  C06  C05     0.00   0.0  0
 GH1  CONST_13  C24  N23  C21  C20     0.00   0.0  0
 GH1  CONST_14  O12  C13  C14  C15   180.00   0.0  0
 GH1  CONST_15  O12  C13  C18  C17   180.00   0.0  0
 GH1  CONST_16  C09  C07  C08  C03   180.00   0.0  0
 GH1  CONST_17  O02  C03  C04  C05   180.00   0.0  0
 GH1  CONST_18  C09  C07  C06  C05   180.00   0.0  0
 GH1  CONST_19  O02  C03  C08  C07   180.00   0.0  0
 GH1  CONST_20  C19  C16  C15  C14   180.00   0.0  0
 GH1  CONST_21  C19  C16  C17  C18   180.00   0.0  0
 GH1  CONST_22  O22  C21  N23  C24   180.00   0.0  0
 GH1  CONST_23  H2   C17  C18  C13   180.00   0.0  0
 GH1  CONST_24  H1   C15  C14  C13   180.00   0.0  0
 GH1  CONST_25  H7   C05  C04  C03   180.00   0.0  0
 GH1  CONST_26  H8   C06  C05  C04   180.00   0.0  0
 GH1  CONST_27  H9   C08  C03  C04   180.00   0.0  0
 GH1  CONST_28  H6   C04  C05  C06   180.00   0.0  0
 GH1  CONST_29  H14  C18  C13  C14   180.00   0.0  0
 GH1  CONST_30  H13  C14  C15  C16   180.00   0.0  0
 GH1  CONST_31  H17  N23  C21  C20   180.00   0.0  0
 GH1  Var_01    N23  C24  S26  C20     0.38  30.0  1
 GH1  Var_02    S26  C24  N23  C21     0.32  30.0  1
 GH1  Var_03    C20  C19  C16  C15   105.96  30.0  2
 GH1  Var_04    C04  C03  O02  C01     0.42  30.0  3
 GH1  Var_05    O10  C09  C07  C06   179.48  30.0  2
 GH1  Var_06    C18  C13  O12  C11  -177.57  30.0  2
 GH1  Var_07    C09  C11  O12  C13   178.04  30.0  1
 GH1  Var_08    O12  C11  C09  C07  -179.08  30.0  3
 GH1  Var_09    H3   C01  O02  C03   -62.33  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
 GH1  chir_01  C20  C19  S26  C21  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
 GH1  plan-1  C13  0.020
 GH1  plan-1  C15  0.020
 GH1  plan-1  C17  0.020
 GH1  plan-1  C14  0.020
 GH1  plan-1  C16  0.020
 GH1  plan-1  C18  0.020
 GH1  plan-1  C19  0.020
 GH1  plan-1  O12  0.020
 GH1  plan-1  H1   0.020
 GH1  plan-1  H2   0.020
 GH1  plan-1  H13  0.020
 GH1  plan-1  H14  0.020
 GH1  plan-2  C03  0.020
 GH1  plan-2  C04  0.020
 GH1  plan-2  C05  0.020
 GH1  plan-2  C06  0.020
 GH1  plan-2  C07  0.020
 GH1  plan-2  C08  0.020
 GH1  plan-2  C09  0.020
 GH1  plan-2  H6   0.020
 GH1  plan-2  H7   0.020
 GH1  plan-2  H8   0.020
 GH1  plan-2  H9   0.020
 GH1  plan-2  O02  0.020
 GH1  plan-3  C20  0.020
 GH1  plan-3  C21  0.020
 GH1  plan-3  C24  0.020
 GH1  plan-3  N23  0.020
 GH1  plan-3  H17  0.020
 GH1  plan-3  O22  0.020
 GH1  plan-4  C24  0.020
 GH1  plan-4  N23  0.020
 GH1  plan-4  O25  0.020
 GH1  plan-4  S26  0.020
 GH1  plan-5  C07  0.020
 GH1  plan-5  C09  0.020
 GH1  plan-5  O10  0.020
 GH1  plan-5  C11  0.020

