# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:41:52 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (5Z)-5-({4-[2-(thiophen-2-yl)ethoxy]phenyl}methylidene)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)/C(S1)=C/c2ccc(OCCc3sccc3)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
 GDY  GDY  (5Z)-5-({4-[2-(thiophen-2-yl)ethoxy]phenyl}methylidene)-1,3-thiazolidine-2,4-dione  ligand  35  22  .  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_GDY
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
 GDY  C10  C  CR16  0  -0.321  -0.1812   1.2895  -0.6351
 GDY  C13  C  CR16  0  -0.282  -0.6322  -1.3145   0.1578
 GDY  C15  C  C1    0  -0.247  -3.0474  -1.0549   0.1142
 GDY  C17  C  CR5   0   0.633  -5.4793  -1.3249   0.2957
 GDY  C20  C  CR5   0   0.430  -6.4504   0.7833  -0.1269
 GDY  C01  C  CR15  0  -0.182   7.6761  -0.9931  -0.6854
 GDY  C02  C  CR15  0  -0.233   6.5771  -0.3015  -1.2669
 GDY  C03  C  CR5   0  -0.164   5.7536   0.2720  -0.3443
 GDY  C05  C  CR15  0  -0.470   7.6681  -0.9373   0.6738
 GDY  C06  C  CH2   0  -0.530   4.4927   1.0382  -0.5799
 GDY  C09  C  CR6   0   0.395   0.9061   0.4443  -0.3841
 GDY  C11  C  CR16  0  -0.297  -1.4710   0.8337  -0.4840
 GDY  C12  C  CR6   0   0.146  -1.7335  -0.4846  -0.0783
 GDY  C14  C  CR16  0  -0.369   0.6699  -0.8709   0.0150
 GDY  C16  C  CR5   0  -0.322  -4.2728  -0.5086   0.0428
 GDY  N19  N  NR15  0  -0.684  -6.6032  -0.5386   0.1807
 GDY  O08  O  O2    0  -0.464   2.1210   0.9777  -0.5519
 GDY  O21  O  O     0  -0.396  -7.3234   1.5953  -0.2591
 GDY  S04  S  S2    0   0.204   6.3258  -0.0414   1.2532
 GDY  S22  S  S2    0   0.076  -4.7227   1.1511  -0.3097
 GDY  H1   H  HCR6  0   0.276   0.0008   2.3090  -0.9505
 GDY  H2   H  HCR6  0   0.272  -0.7987  -2.3399   0.4646
 GDY  H3   H  H     0   0.285  -3.0459  -2.1110   0.3667
 GDY  H6   H  HCR5  0   0.263   6.4023  -0.2296  -2.3320
 GDY  H7   H  HCR5  0   0.295   8.3791  -1.3648   1.3639
 GDY  H8   H  HCH2  0   0.268   4.4585   1.9286   0.0526
 GDY  H9   H  HCH2  0   0.272   4.4812   1.3782  -1.6173
 GDY  H12  H  HCR6  0   0.259  -2.2687   1.5302  -0.7000
 GDY  H13  H  HCR6  0   0.290   1.4801  -1.5582   0.2141
 GDY  H14  H  HNR5  0   0.441  -7.5295  -0.9228   0.3243
 GDY  O18  O  O     0  -0.414  -5.5056  -2.5026   0.5654
 GDY  C07  C  CH2   0  -0.168   3.2688   0.1769  -0.3115
 GDY  H5   H  HCR5  0   0.266   8.4390  -1.5040  -1.2552
 GDY  H10  H  HCH2  0   0.241   3.2714  -0.6974  -0.9704
 GDY  H11  H  HCH2  0   0.234   3.2716  -0.1815   0.7234

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
 GDY  C01  C02  aromatic  1.423  0.020  1.423
 GDY  C01  C05  aromatic  1.360  0.020  1.360
 GDY  C02  C03  aromatic  1.363  0.020  1.363
 GDY  C05  S04  aromatic  1.715  0.020  1.715
 GDY  C03  S04  aromatic  1.726  0.020  1.726
 GDY  C03  C06  single    1.494  0.020  1.494
 GDY  C06  C07  single    1.521  0.020  1.521
 GDY  C07  O08  single    1.420  0.020  1.420
 GDY  O08  C09  single    1.337  0.020  1.337
 GDY  C09  C10  aromatic  1.400  0.020  1.400
 GDY  C09  C14  aromatic  1.395  0.020  1.395
 GDY  C10  C11  aromatic  1.376  0.020  1.376
 GDY  C14  C13  aromatic  1.383  0.020  1.383
 GDY  C11  C12  aromatic  1.404  0.020  1.404
 GDY  C13  C12  aromatic  1.399  0.020  1.399
 GDY  C12  C15  single    1.445  0.020  1.445
 GDY  C15  C16  double    1.344  0.020  1.344
 GDY  S22  C16  single    1.755  0.020  1.755
 GDY  S22  C20  single    1.776  0.020  1.776
 GDY  C16  C17  single    1.478  0.020  1.478
 GDY  C20  O21  double    1.200  0.020  1.200
 GDY  C20  N19  single    1.366  0.020  1.366
 GDY  C17  N19  single    1.376  0.020  1.376
 GDY  C17  O18  double    1.209  0.020  1.209
 GDY  C10  H1   single    0.930  0.020  1.080
 GDY  C13  H2   single    0.930  0.020  1.080
 GDY  C15  H3   single    0.930  0.020  1.080
 GDY  C01  H5   single    0.930  0.020  1.080
 GDY  C02  H6   single    0.930  0.020  1.080
 GDY  C05  H7   single    0.930  0.020  1.080
 GDY  C06  H8   single    0.970  0.020  1.090
 GDY  C06  H9   single    0.970  0.020  1.090
 GDY  C07  H10  single    0.970  0.020  1.090
 GDY  C07  H11  single    0.970  0.020  1.090
 GDY  C11  H12  single    0.930  0.020  1.080
 GDY  C14  H13  single    0.930  0.020  1.080
 GDY  N19  H14  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
 GDY  H1   C10  C11  120.10  3.000
 GDY  H1   C10  C09  119.35  3.000
 GDY  C11  C10  C09  120.55  3.000
 GDY  H2   C13  C14  118.53  3.000
 GDY  H2   C13  C12  119.23  3.000
 GDY  C14  C13  C12  122.24  3.000
 GDY  H3   C15  C16  114.15  3.000
 GDY  H3   C15  C12  114.43  3.000
 GDY  C16  C15  C12  131.42  3.000
 GDY  O18  C17  N19  123.89  3.000
 GDY  O18  C17  C16  126.44  3.000
 GDY  N19  C17  C16  109.68  3.000
 GDY  S22  C20  O21  123.82  3.000
 GDY  O21  C20  N19  126.76  3.000
 GDY  S22  C20  N19  109.42  3.000
 GDY  H5   C01  C05  123.39  3.000
 GDY  H5   C01  C02  124.03  3.000
 GDY  C05  C01  C02  112.57  3.000
 GDY  H6   C02  C03  122.74  3.000
 GDY  H6   C02  C01  124.03  3.000
 GDY  C03  C02  C01  113.24  3.000
 GDY  S04  C03  C06  121.26  3.000
 GDY  C06  C03  C02  128.23  3.000
 GDY  S04  C03  C02  110.48  3.000
 GDY  H7   C05  S04  120.44  3.000
 GDY  H7   C05  C01  128.23  3.000
 GDY  S04  C05  C01  111.33  3.000
 GDY  H9   C06  H8   107.21  3.000
 GDY  H9   C06  C07  109.62  3.000
 GDY  H8   C06  C07  109.52  3.000
 GDY  H9   C06  C03  108.57  3.000
 GDY  H8   C06  C03  110.67  3.000
 GDY  C07  C06  C03  111.16  3.000
 GDY  O08  C09  C14  124.47  3.000
 GDY  C14  C09  C10  119.29  3.000
 GDY  O08  C09  C10  116.25  3.000
 GDY  H12  C11  C12  121.65  3.000
 GDY  H12  C11  C10  117.15  3.000
 GDY  C12  C11  C10  121.19  3.000
 GDY  C11  C12  C15  125.38  3.000
 GDY  C15  C12  C13  117.33  3.000
 GDY  C11  C12  C13  117.29  3.000
 GDY  H13  C14  C09  121.70  3.000
 GDY  H13  C14  C13  118.86  3.000
 GDY  C09  C14  C13  119.44  3.000
 GDY  S22  C16  C17  110.32  3.000
 GDY  C17  C16  C15  120.71  3.000
 GDY  S22  C16  C15  128.97  3.000
 GDY  H14  N19  C20  120.09  3.000
 GDY  H14  N19  C17  121.21  3.000
 GDY  C20  N19  C17  118.70  3.000
 GDY  C09  O08  C07  119.21  3.000
 GDY  C05  S04  C03   92.39  3.000
 GDY  C16  S22  C20   91.88  3.000
 GDY  H11  C07  H10  107.90  3.000
 GDY  H11  C07  O08  110.28  3.000
 GDY  H10  C07  O08  110.51  3.000
 GDY  H11  C07  C06  110.50  3.000
 GDY  H10  C07  C06  110.13  3.000
 GDY  O08  C07  C06  107.53  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
 GDY  CONST_01  C13  C14  C09  C10     0.00   0.0  0
 GDY  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 GDY  CONST_03  S04  C03  C02  C01     0.00   0.0  0
 GDY  CONST_04  C03  S04  C05  C01     0.00   0.0  0
 GDY  CONST_05  S04  C05  C01  C02     0.00   0.0  0
 GDY  CONST_06  C05  S04  C03  C02     0.00   0.0  0
 GDY  CONST_07  C05  C01  C02  C03     0.00   0.0  0
 GDY  CONST_08  C12  C11  C10  C09     0.00   0.0  0
 GDY  CONST_09  C12  C13  C14  C09     0.00   0.0  0
 GDY  CONST_10  C14  C09  C10  C11     0.00   0.0  0
 GDY  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 GDY  CONST_12  C16  C17  N19  C20     0.00   0.0  0
 GDY  CONST_13  C15  C12  C11  C10   180.00   0.0  0
 GDY  CONST_14  O08  C09  C14  C13   180.00   0.0  0
 GDY  CONST_15  C14  C13  C12  C15   180.00   0.0  0
 GDY  CONST_16  C06  C03  C02  C01   180.00   0.0  0
 GDY  CONST_17  C06  C03  S04  C05   180.00   0.0  0
 GDY  CONST_18  O08  C09  C10  C11   180.00   0.0  0
 GDY  CONST_19  O18  C17  N19  C20   180.00   0.0  0
 GDY  CONST_20  H13  C14  C09  C10   180.00   0.0  0
 GDY  CONST_21  H12  C11  C12  C13   180.00   0.0  0
 GDY  CONST_22  H7   C05  C01  C02   180.00   0.0  0
 GDY  CONST_23  H5   C01  C02  C03   180.00   0.0  0
 GDY  CONST_24  H6   C02  C01  C05   180.00   0.0  0
 GDY  CONST_25  H2   C13  C14  C09   180.00   0.0  0
 GDY  CONST_26  H1   C10  C11  C12   180.00   0.0  0
 GDY  CONST_27  H14  N19  C17  C16   180.00   0.0  0
 GDY  Var_01    C16  C15  C12  C13   175.83  30.0  2
 GDY  Var_02    C12  C15  C16  C17  -179.64  30.0  2
 GDY  Var_03    C07  C06  C03  C02   101.35  30.0  2
 GDY  Var_04    C14  C09  O08  C07    -0.19  30.0  2
 GDY  Var_05    O08  C07  C06  C03   179.75  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
 GDY  plan-1  C01  0.020
 GDY  plan-1  C02  0.020
 GDY  plan-1  C03  0.020
 GDY  plan-1  C05  0.020
 GDY  plan-1  C06  0.020
 GDY  plan-1  S04  0.020
 GDY  plan-1  H6   0.020
 GDY  plan-1  H7   0.020
 GDY  plan-1  H5   0.020
 GDY  plan-2  C15  0.020
 GDY  plan-2  C17  0.020
 GDY  plan-2  C20  0.020
 GDY  plan-2  C16  0.020
 GDY  plan-2  N19  0.020
 GDY  plan-2  O21  0.020
 GDY  plan-2  S22  0.020
 GDY  plan-2  H14  0.020
 GDY  plan-2  O18  0.020
 GDY  plan-3  C10  0.020
 GDY  plan-3  C13  0.020
 GDY  plan-3  C15  0.020
 GDY  plan-3  C09  0.020
 GDY  plan-3  C11  0.020
 GDY  plan-3  C12  0.020
 GDY  plan-3  C14  0.020
 GDY  plan-3  O08  0.020
 GDY  plan-3  H1   0.020
 GDY  plan-3  H2   0.020
 GDY  plan-3  H12  0.020
 GDY  plan-3  H13  0.020

