# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 19:31:31 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (5Z)-5-[(2,2-difluoro-1,3-benzodioxol-5-yl)methylidene]-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC1(F)Oc2ccc(cc2O1)/C=C/3SC(=O)NC/3=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
 BYM  BYM  (5Z)-5-[(2,2-difluoro-1,3-benzodioxol-5-yl)methylidene]-1,3-thiazolidine-2,4-dione  ligand  24  19  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYM
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
 BYM  C1   C  CR5   0   0.638   3.7713   1.3320   0.0793
 BYM  C3   C  CR5   0   0.429   4.7446  -0.8154   0.0979
 BYM  C8   C  CR56  0   0.324  -2.3014   0.6245   0.0573
 BYM  C9   C  CR56  0   0.307  -2.4863  -0.6778  -0.3558
 BYM  C11  C  CR16  0  -0.375  -1.0675   1.2022   0.1375
 BYM  C13  C  CR16  0  -0.303  -1.4393  -1.4845  -0.7208
 BYM  C14  C  CR5   0   1.039  -4.4562   0.1915   0.0918
 BYM  C15  C  CR6   0   0.146   0.0369   0.3963  -0.2066
 BYM  C16  C  CR16  0  -0.322  -0.1682  -0.9198  -0.6356
 BYM  N2   N  NR15  0  -0.684   4.8930   0.5418   0.1590
 BYM  S4   S  S2    0   0.093   3.0221  -1.2176  -0.0806
 BYM  C5   C  CR5   0  -0.309   2.5674   0.4752  -0.0564
 BYM  O6   O  O     0  -0.390   5.6168  -1.6359   0.1487
 BYM  O7   O  O     0  -0.405   3.7861   2.5380   0.1199
 BYM  O10  O  O     0  -0.491  -3.5242   1.1685   0.3274
 BYM  O12  O  O     0  -0.488  -3.8214  -0.9473  -0.3387
 BYM  C18  C  C1    0  -0.242   1.3441   1.0203  -0.0981
 BYM  F19  F  F     0  -0.285  -5.3363   0.6007  -0.8208
 BYM  H11  H  HCR6  0   0.298  -0.9381   2.2283   0.4551
 BYM  H13  H  HCR6  0   0.300  -1.5836  -2.4989  -1.0639
 BYM  H16  H  HCR6  0   0.270   0.6618  -1.5322  -0.9573
 BYM  HN2  H  HNR5  0   0.443   5.8156   0.9479   0.2616
 BYM  H18  H  H     0   0.293   1.3267   2.1022  -0.0136
 BYM  F17  F  F     0  -0.287  -5.1522  -0.0613   1.2003

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
 BYM  C1   N2   single    1.374  0.020  1.374
 BYM  C1   C5   single    1.484  0.020  1.484
 BYM  C1   O7   double    1.207  0.020  1.207
 BYM  C3   N2   single    1.367  0.020  1.367
 BYM  C3   S4   single    1.778  0.020  1.778
 BYM  C3   O6   double    1.199  0.020  1.199
 BYM  C8   C9   aromatic  1.379  0.020  1.379
 BYM  C8   C11  aromatic  1.365  0.020  1.365
 BYM  C8   O10  single    1.365  0.020  1.365
 BYM  C9   C13  aromatic  1.371  0.020  1.371
 BYM  C9   O12  single    1.362  0.020  1.362
 BYM  C11  C15  aromatic  1.410  0.020  1.410
 BYM  C11  H11  single    0.930  0.020  1.080
 BYM  C13  C16  aromatic  1.393  0.020  1.393
 BYM  C13  H13  single    0.930  0.020  1.080
 BYM  C14  O10  single    1.371  0.020  1.371
 BYM  C14  O12  single    1.373  0.020  1.373
 BYM  C14  F17  single    1.333  0.020  1.333
 BYM  C14  F19  single    1.332  0.020  1.332
 BYM  C15  C16  aromatic  1.399  0.020  1.399
 BYM  C15  C18  single    1.453  0.020  1.453
 BYM  C16  H16  single    0.930  0.020  1.080
 BYM  N2   HN2  single    0.860  0.020  1.020
 BYM  S4   C5   single    1.753  0.020  1.753
 BYM  C5   C18  double    1.340  0.020  1.340
 BYM  C18  H18  single    0.930  0.020  1.080

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
 BYM  O7   C1   C5   126.16  3.000
 BYM  O7   C1   N2   124.24  3.000
 BYM  C5   C1   N2   109.60  3.000
 BYM  O6   C3   S4   123.68  3.000
 BYM  O6   C3   N2   126.79  3.000
 BYM  S4   C3   N2   109.53  3.000
 BYM  O10  C8   C11  129.00  3.000
 BYM  O10  C8   C9   108.39  3.000
 BYM  C11  C8   C9   122.60  3.000
 BYM  O12  C9   C13  129.45  3.000
 BYM  O12  C9   C8   108.34  3.000
 BYM  C13  C9   C8   122.21  3.000
 BYM  H11  C11  C15  121.34  3.000
 BYM  H11  C11  C8   121.80  3.000
 BYM  C15  C11  C8   116.86  3.000
 BYM  H13  C13  C16  121.45  3.000
 BYM  H13  C13  C9   122.33  3.000
 BYM  C16  C13  C9   116.22  3.000
 BYM  F19  C14  F17  106.44  3.000
 BYM  F19  C14  O12  110.20  3.000
 BYM  F17  C14  O12  110.17  3.000
 BYM  F19  C14  O10  110.37  3.000
 BYM  F17  C14  O10  110.32  3.000
 BYM  O12  C14  O10  109.31  3.000
 BYM  C18  C15  C16  123.97  3.000
 BYM  C18  C15  C11  116.18  3.000
 BYM  C16  C15  C11  119.84  3.000
 BYM  H16  C16  C15  120.78  3.000
 BYM  H16  C16  C13  116.93  3.000
 BYM  C15  C16  C13  122.25  3.000
 BYM  HN2  N2   C3   120.09  3.000
 BYM  HN2  N2   C1   121.23  3.000
 BYM  C3   N2   C1   118.67  3.000
 BYM  C5   S4   C3    91.80  3.000
 BYM  C18  C5   S4   128.99  3.000
 BYM  C18  C5   C1   120.58  3.000
 BYM  S4   C5   C1   110.39  3.000
 BYM  C14  O10  C8   106.92  3.000
 BYM  C14  O12  C9   107.04  3.000
 BYM  H18  C18  C5   114.69  3.000
 BYM  H18  C18  C15  114.81  3.000
 BYM  C5   C18  C15  130.48  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
 BYM  CONST_01  C16  C13  C9   C8      0.00   0.0  0
 BYM  CONST_02  C16  C15  C11  C8      0.00   0.0  0
 BYM  CONST_03  C15  C11  C8   C9      0.00   0.0  0
 BYM  CONST_04  C15  C16  C13  C9      0.00   0.0  0
 BYM  CONST_05  C13  C9   C8   C11     0.00   0.0  0
 BYM  CONST_06  C13  C16  C15  C11     0.00   0.0  0
 BYM  CONST_07  C5   C1   N2   C3      0.00   0.0  0
 BYM  CONST_08  C18  C15  C11  C8    180.00   0.0  0
 BYM  CONST_09  C18  C15  C16  C13   180.00   0.0  0
 BYM  CONST_10  O7   C1   N2   C3    180.00   0.0  0
 BYM  CONST_11  H13  C13  C9   C8    180.00   0.0  0
 BYM  CONST_12  H11  C11  C8   C9    180.00   0.0  0
 BYM  CONST_13  H16  C16  C13  C9    180.00   0.0  0
 BYM  CONST_14  HN2  N2   C1   C5    180.00   0.0  0
 BYM  Var_01    O12  C14  O10  C8     -0.78  30.0  1
 BYM  Var_02    O10  C14  O12  C9      0.65  30.0  1
 BYM  Var_03    C15  C18  C5   C1   -179.07  30.0  2
 BYM  Var_04    C5   C18  C15  C11   163.28  30.0  2

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
 BYM  plan-1  C1   0.020
 BYM  plan-1  C3   0.020
 BYM  plan-1  N2   0.020
 BYM  plan-1  S4   0.020
 BYM  plan-1  C5   0.020
 BYM  plan-1  O6   0.020
 BYM  plan-1  O7   0.020
 BYM  plan-1  C18  0.020
 BYM  plan-1  HN2  0.020
 BYM  plan-2  C8   0.020
 BYM  plan-2  C9   0.020
 BYM  plan-2  C11  0.020
 BYM  plan-2  C13  0.020
 BYM  plan-2  C15  0.020
 BYM  plan-2  C16  0.020
 BYM  plan-2  O10  0.020
 BYM  plan-2  O12  0.020
 BYM  plan-2  C18  0.020
 BYM  plan-2  H11  0.020
 BYM  plan-2  H13  0.020
 BYM  plan-2  H16  0.020

