# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:57:30 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: {(5Z)-5-[(4-methoxyphenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)/C=C/2SC(=O)N(CC(O)=O)C/2=O
#
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
 YXP  YXP  '{(5Z)-5-[(4-methoxyphenyl)methylidene]-2,4-dioxo-1,3-thiazolidin-3-yl}acetic acid'  ligand  30  20  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YXP
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
 YXP  C4   C  C1     0  -0.283  -36.9902   -8.0332  18.1520
 YXP  C5   C  C      0   0.145  -36.6288   -8.8753  17.0950
 YXP  C6   C  C1     0  -0.256  -35.2200   -9.1460  16.9085
 YXP  C11  C  CR5    0   0.651  -33.0948   -9.9795  16.0058
 YXP  C7   C  CR5    0  -0.323  -34.5665   -9.8368  15.9603
 YXP  C8   C  CR5    0   0.420  -33.5788  -11.1560  14.0457
 YXP  C10  C  C      0   0.420  -31.0196  -12.4407  15.5410
 YXP  C12  C  C1     0  -0.299  -37.6671   -9.3990  16.3080
 YXP  C13  C  C1     0  -0.316  -38.9838   -9.0937  16.5683
 YXP  N1   N  NR5    0  -0.514  -32.6351  -10.6566  14.8990
 YXP  C3   C  C1     0  -0.368  -38.3081   -7.7115  18.4233
 YXP  C1   C  CH3    0  -0.439  -41.0317   -7.1273  18.8351
 YXP  C2   C  C      0   0.387  -39.3228   -8.2448  17.6287
 YXP  S1   S  S2     0   0.076  -35.2064  -10.6574  14.5522
 YXP  O2   O  O      0  -0.404  -33.3751  -11.8247  13.0693
 YXP  O3   O  OC    -1  -0.585  -32.0007  -12.9614  16.0938
 YXP  O4   O  O      0  -0.599  -29.8469  -12.8464  15.4870
 YXP  H1   H  H      0   0.269  -36.2156   -7.6150  18.7836
 YXP  H2   H  H      0   0.280  -34.5751   -8.7147  17.6684
 YXP  H4   H  HCH2   0   0.272  -30.9926  -11.1892  13.7527
 YXP  H5   H  HCH2   0   0.272  -30.6225  -10.3190  15.2258
 YXP  H6   H  H      0   0.259  -37.4688  -10.0668  15.4814
 YXP  H7   H  H      0   0.272  -39.7692   -9.5122  15.9519
 YXP  H8   H  H      0   0.286  -38.5247   -7.0535  19.2534
 YXP  H9   H  HCH3   0   0.263  -42.1160   -7.0745  18.7854
 YXP  H10  H  HCH3   0   0.234  -40.7409   -7.4954  19.8218
 YXP  H11  H  HCH3   0   0.234  -40.6216   -6.1243  18.6946
 YXP  C9   C  CH2    0  -0.473  -31.2591  -11.0969  14.8051
 YXP  O1   O  O2     0  -0.456  -40.6271   -8.0089  17.8036
 YXP  O5   O  O      0  -0.421  -32.3717   -9.5538  16.8772

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
 YXP  O2   C8   double    1.201  0.020  1.201
 YXP  C8   S1   single    1.776  0.020  1.776
 YXP  C8   N1   single    1.367  0.020  1.367
 YXP  C9   N1   single    1.448  0.020  1.448
 YXP  C9   C10  single    1.551  0.020  1.551
 YXP  S1   C7   single    1.751  0.020  1.751
 YXP  N1   C11  single    1.377  0.020  1.377
 YXP  O4   C10  deloc     1.242  0.020  1.242
 YXP  C10  O3   deloc     1.241  0.020  1.241
 YXP  C11  C7   single    1.479  0.020  1.479
 YXP  C11  O5   double    1.210  0.020  1.210
 YXP  C7   C6   double    1.343  0.020  1.343
 YXP  C12  C13  aromatic  1.376  0.020  1.376
 YXP  C12  C5   aromatic  1.404  0.020  1.404
 YXP  C13  C2   aromatic  1.400  0.020  1.400
 YXP  C6   C5   single    1.447  0.020  1.447
 YXP  C5   C4   aromatic  1.399  0.020  1.399
 YXP  C2   O1   single    1.337  0.020  1.337
 YXP  C2   C3   aromatic  1.395  0.020  1.395
 YXP  O1   C1   single    1.416  0.020  1.416
 YXP  C4   C3   aromatic  1.383  0.020  1.383
 YXP  C4   H1   single    0.930  0.020  1.080
 YXP  C6   H2   single    0.930  0.020  1.080
 YXP  C9   H4   single    0.970  0.020  1.090
 YXP  C9   H5   single    0.970  0.020  1.090
 YXP  C12  H6   single    0.930  0.020  1.080
 YXP  C13  H7   single    0.930  0.020  1.080
 YXP  C3   H8   single    0.930  0.020  1.080
 YXP  C1   H9   single    0.970  0.020  1.090
 YXP  C1   H10  single    0.970  0.020  1.090
 YXP  C1   H11  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
 YXP  H1   C4   C3   118.49  3.000
 YXP  H1   C4   C5   119.22  3.000
 YXP  C3   C4   C5   122.29  3.000
 YXP  C12  C5   C6   125.31  3.000
 YXP  C6   C5   C4   117.49  3.000
 YXP  C12  C5   C4   117.19  3.000
 YXP  H2   C6   C7   114.17  3.000
 YXP  H2   C6   C5   114.44  3.000
 YXP  C7   C6   C5   131.39  3.000
 YXP  O5   C11  N1   123.55  3.000
 YXP  O5   C11  C7   125.65  3.000
 YXP  N1   C11  C7   110.79  3.000
 YXP  S1   C7   C11  110.07  3.000
 YXP  C11  C7   C6   120.80  3.000
 YXP  S1   C7   C6   129.13  3.000
 YXP  O2   C8   S1   122.94  3.000
 YXP  S1   C8   N1   110.62  3.000
 YXP  O2   C8   N1   126.44  3.000
 YXP  O4   C10  O3   128.97  3.000
 YXP  O3   C10  C9   116.94  3.000
 YXP  O4   C10  C9   114.10  3.000
 YXP  H6   C12  C13  117.21  3.000
 YXP  H6   C12  C5   121.55  3.000
 YXP  C13  C12  C5   121.24  3.000
 YXP  H7   C13  C2   119.34  3.000
 YXP  H7   C13  C12  120.04  3.000
 YXP  C2   C13  C12  120.62  3.000
 YXP  C9   N1   C8   120.30  3.000
 YXP  C9   N1   C11  121.28  3.000
 YXP  C8   N1   C11  116.82  3.000
 YXP  H8   C3   C2   121.63  3.000
 YXP  H8   C3   C4   118.87  3.000
 YXP  C2   C3   C4   119.50  3.000
 YXP  H11  C1   H10  109.00  3.000
 YXP  H11  C1   H9   108.90  3.000
 YXP  H10  C1   H9   108.86  3.000
 YXP  H11  C1   O1   111.75  3.000
 YXP  H10  C1   O1   111.84  3.000
 YXP  H9   C1   O1   106.38  3.000
 YXP  O1   C2   C3   124.59  3.000
 YXP  C3   C2   C13  119.16  3.000
 YXP  O1   C2   C13  116.25  3.000
 YXP  C8   S1   C7    91.49  3.000
 YXP  H5   C9   H4   106.89  3.000
 YXP  H5   C9   N1   108.25  3.000
 YXP  H4   C9   N1   108.71  3.000
 YXP  H5   C9   C10  110.19  3.000
 YXP  H4   C9   C10  110.32  3.000
 YXP  N1   C9   C10  112.31  3.000
 YXP  C2   O1   C1   118.94  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
 YXP  CONST_01  C13  C12  C5   C4      0.00   0.0  0
 YXP  CONST_02  C13  C2   C3   C4      0.00   0.0  0
 YXP  CONST_03  C2   C13  C12  C5      0.00   0.0  0
 YXP  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 YXP  CONST_05  C3   C2   C13  C12     0.00   0.0  0
 YXP  CONST_06  C3   C4   C5   C12     0.00   0.0  0
 YXP  CONST_07  C8   N1   C11  C7      0.00   0.0  0
 YXP  CONST_08  O1   C2   C3   C4    180.00   0.0  0
 YXP  CONST_09  C13  C12  C5   C6    180.00   0.0  0
 YXP  CONST_10  C3   C4   C5   C6    180.00   0.0  0
 YXP  CONST_11  O1   C2   C13  C12   180.00   0.0  0
 YXP  CONST_12  C9   N1   C11  C7    180.00   0.0  0
 YXP  CONST_13  O5   C11  N1   C8    180.00   0.0  0
 YXP  CONST_14  H6   C12  C5   C4    180.00   0.0  0
 YXP  CONST_15  H7   C13  C12  C5    180.00   0.0  0
 YXP  CONST_16  H8   C3   C4   C5    180.00   0.0  0
 YXP  CONST_17  H1   C4   C5   C12   180.00   0.0  0
 YXP  CONST_18  O5   C11  N1   C9      0.00   0.0  0
 YXP  Var_01    S1   C7   C6   C5      1.24   0.0  2
 YXP  Var_02    C7   C6   C5   C4   -175.73  30.0  2
 YXP  Var_03    C10  C9   N1   C11    82.68  30.0  1
 YXP  Var_04    O4   C10  C9   N1   -179.66  30.0  3
 YXP  Var_05    H9   C1   O1   C2    179.23  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
 YXP  plan-1  C5   0.020
 YXP  plan-1  C6   0.020
 YXP  plan-1  C11  0.020
 YXP  plan-1  C7   0.020
 YXP  plan-1  C8   0.020
 YXP  plan-1  N1   0.020
 YXP  plan-1  S1   0.020
 YXP  plan-1  O2   0.020
 YXP  plan-1  H2   0.020
 YXP  plan-1  C9   0.020
 YXP  plan-1  O5   0.020
 YXP  plan-2  C4   0.020
 YXP  plan-2  C5   0.020
 YXP  plan-2  C6   0.020
 YXP  plan-2  C12  0.020
 YXP  plan-2  C13  0.020
 YXP  plan-2  C3   0.020
 YXP  plan-2  C2   0.020
 YXP  plan-2  H1   0.020
 YXP  plan-2  H6   0.020
 YXP  plan-2  H7   0.020
 YXP  plan-2  H8   0.020
 YXP  plan-2  O1   0.020
 YXP  plan-3  C10  0.020
 YXP  plan-3  O3   0.020
 YXP  plan-3  O4   0.020
 YXP  plan-3  C9   0.020

