# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:56:06 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: methyl (2Z)-cyano[3-(3-fluoro-4'-methoxybiphenyl-4-yl)-4-oxo-1,3-thiazolidin-2-ylidene]acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)/C(C#N)=C/1SCC(=O)N/1c2ccc(cc2F)c3ccc(OC)cc3
#
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
 52Y  52Y  'methyl (2Z)-cyano[3-(3-fluoro-4'-methoxybiphenyl-4-yl)-4-oxo-1,3-thiazolidin-2-ylidene]acetate'  ligand  43  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_52Y
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
 52Y  C1   C  CH3   0  -0.438   8.3610  -0.5784  -0.8460
 52Y  O1   O  O2    0  -0.467   7.4728  -0.8348   0.2251
 52Y  C2   C  CR6   0   0.379   6.1774  -0.5134   0.0762
 52Y  C3   C  CR16  0  -0.327   5.3327  -0.8218   1.1458
 52Y  C4   C  CR16  0  -0.288   3.9860  -0.5290   1.0768
 52Y  C5   C  CR6   0   0.063   3.4299   0.0760  -0.0547
 52Y  C6   C  CR16  0  -0.291   4.2845   0.3796  -1.1109
 52Y  C7   C  CR16  0  -0.368   5.6416   0.0964  -1.0564
 52Y  C8   C  CR6   0   0.137   1.9907   0.3818  -0.1251
 52Y  C9   C  CR16  0  -0.500   1.2985   0.7702   1.0235
 52Y  C10  C  CR6   0   0.620  -0.0476   1.0415   0.9438
 52Y  C11  C  CR6   0   0.002  -0.7400   0.9382  -0.2496
 52Y  C12  C  CR16  0  -0.191  -0.0551   0.5787  -1.3986
 52Y  C13  C  CR16  0  -0.334   1.2956   0.2942  -1.3348
 52Y  N14  N  NT    0  -0.636  -2.1281   1.2274  -0.2849
 52Y  C15  C  C     0   0.593  -2.5290   2.5501  -0.4589
 52Y  C16  C  CH2   0  -0.710  -4.0204   2.6475  -0.5296
 52Y  S17  S  S2    0   0.224  -4.6931   0.9815  -0.3459
 52Y  C18  C  C     0   0.261  -3.1102   0.2841  -0.1789
 52Y  O19  O  O     0  -0.388  -1.7499   3.4579  -0.5420
 52Y  F20  F  F     0  -0.293  -0.7193   1.4052   2.0388
 52Y  C21  C  C     0  -0.233  -2.9099  -1.0582   0.0328
 52Y  C22  C  C     0   0.628  -4.0701  -1.9500   0.0892
 52Y  C23  C  CSP   0   0.055  -1.6400  -1.6557   0.2271
 52Y  N24  N  NS    0  -0.244  -0.6535  -2.2270   0.4083
 52Y  O25  O  O2    0  -0.457  -3.7247  -3.2070   0.2893
 52Y  O26  O  O     0  -0.453  -5.2124  -1.5679  -0.0388
 52Y  C27  C  CH3   0  -0.427  -4.7692  -4.1816   0.3405
 52Y  H1   H  HCH3  0   0.262   9.3366  -0.9389  -0.5309
 52Y  H2   H  HCH3  0   0.231   8.0660  -1.1091  -1.7546
 52Y  H3   H  HCH3  0   0.231   8.4348   0.4890  -1.0683
 52Y  H4   H  HCR6  0   0.267   5.7405  -1.3004   2.0271
 52Y  H5   H  HCR6  0   0.260   3.3545  -0.7994   1.9141
 52Y  H6   H  HCR6  0   0.262   3.9010   0.8706  -1.9963
 52Y  H7   H  HCR6  0   0.283   6.2614   0.3650  -1.9009
 52Y  H8   H  HCR6  0   0.286   1.8051   0.8781   1.9741
 52Y  H9   H  HCR6  0   0.290  -0.5916   0.4982  -2.3352
 52Y  H10  H  HCR6  0   0.268   1.8072  -0.0222  -2.2334
 52Y  H11  H  HCH2  0   0.347  -4.3910   3.2941   0.2662
 52Y  H12  H  HCH2  0   0.347  -4.3189   3.0726  -1.4882
 52Y  H13  H  HCH3  0   0.246  -5.3491  -4.1898  -0.5814
 52Y  H14  H  HCH3  0   0.259  -4.2723  -5.1388   0.4636
 52Y  H15  H  HCH3  0   0.246  -5.4328  -4.0057   1.1863

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
 52Y  C1   O1   single    1.415  0.020  1.415
 52Y  C7   C6   aromatic  1.387  0.020  1.387
 52Y  C7   C2   aromatic  1.394  0.020  1.394
 52Y  O1   C2   single    1.343  0.020  1.343
 52Y  C6   C5   aromatic  1.392  0.020  1.392
 52Y  C2   C3   aromatic  1.397  0.020  1.397
 52Y  F20  C10  single    1.335  0.020  1.335
 52Y  C9   C10  aromatic  1.376  0.020  1.376
 52Y  C9   C8   aromatic  1.396  0.020  1.396
 52Y  C5   C8   single    1.473  0.020  1.473
 52Y  C5   C4   aromatic  1.398  0.020  1.398
 52Y  C3   C4   aromatic  1.380  0.020  1.380
 52Y  C10  C11  aromatic  1.384  0.020  1.384
 52Y  C8   C13  aromatic  1.398  0.020  1.398
 52Y  O19  C15  double    1.199  0.020  1.199
 52Y  C11  N14  single    1.418  0.020  1.418
 52Y  C11  C12  aromatic  1.385  0.020  1.385
 52Y  C15  N14  single    1.393  0.020  1.393
 52Y  C15  C16  single    1.496  0.020  1.496
 52Y  C13  C12  aromatic  1.382  0.020  1.382
 52Y  N14  C18  single    1.366  0.020  1.366
 52Y  C16  S17  single    1.806  0.020  1.806
 52Y  N24  C23  triple    1.154  0.020  1.154
 52Y  C18  S17  single    1.738  0.020  1.738
 52Y  C18  C21  double    1.374  0.020  1.374
 52Y  C23  C21  single    1.417  0.020  1.417
 52Y  C21  C22  single    1.464  0.020  1.464
 52Y  C22  O26  double    1.211  0.020  1.211
 52Y  C22  O25  single    1.319  0.020  1.319
 52Y  O25  C27  single    1.429  0.020  1.429
 52Y  C1   H1   single    0.970  0.020  1.090
 52Y  C1   H2   single    0.970  0.020  1.090
 52Y  C1   H3   single    0.970  0.020  1.090
 52Y  C3   H4   single    0.930  0.020  1.080
 52Y  C4   H5   single    0.930  0.020  1.080
 52Y  C6   H6   single    0.930  0.020  1.080
 52Y  C7   H7   single    0.930  0.020  1.080
 52Y  C9   H8   single    0.930  0.020  1.080
 52Y  C12  H9   single    0.930  0.020  1.080
 52Y  C13  H10  single    0.930  0.020  1.080
 52Y  C16  H11  single    0.970  0.020  1.090
 52Y  C16  H12  single    0.970  0.020  1.090
 52Y  C27  H13  single    0.970  0.020  1.090
 52Y  C27  H14  single    0.970  0.020  1.090
 52Y  C27  H15  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
 52Y  H3   C1   H2   108.87  3.000
 52Y  H3   C1   H1   108.80  3.000
 52Y  H2   C1   H1   108.80  3.000
 52Y  H3   C1   O1   111.93  3.000
 52Y  H2   C1   O1   111.84  3.000
 52Y  H1   C1   O1   106.50  3.000
 52Y  C2   O1   C1   118.57  3.000
 52Y  C7   C2   C3   119.10  3.000
 52Y  C3   C2   O1   116.45  3.000
 52Y  C7   C2   O1   124.45  3.000
 52Y  H4   C3   C4   120.14  3.000
 52Y  H4   C3   C2   119.53  3.000
 52Y  C4   C3   C2   120.32  3.000
 52Y  H5   C4   C5   120.12  3.000
 52Y  H5   C4   C3   118.51  3.000
 52Y  C5   C4   C3   121.35  3.000
 52Y  C8   C5   C6   121.21  3.000
 52Y  C8   C5   C4   121.13  3.000
 52Y  C6   C5   C4   117.66  3.000
 52Y  H6   C6   C7   118.11  3.000
 52Y  H6   C6   C5   120.13  3.000
 52Y  C7   C6   C5   121.74  3.000
 52Y  H7   C7   C6   118.64  3.000
 52Y  H7   C7   C2   121.54  3.000
 52Y  C6   C7   C2   119.82  3.000
 52Y  C13  C8   C9   118.87  3.000
 52Y  C13  C8   C5   120.95  3.000
 52Y  C9   C8   C5   120.18  3.000
 52Y  H8   C9   C10  119.29  3.000
 52Y  H8   C9   C8   121.21  3.000
 52Y  C10  C9   C8   119.50  3.000
 52Y  F20  C10  C11  118.43  3.000
 52Y  C11  C10  C9   121.67  3.000
 52Y  F20  C10  C9   119.90  3.000
 52Y  N14  C11  C12  121.07  3.000
 52Y  C12  C11  C10  119.18  3.000
 52Y  N14  C11  C10  119.74  3.000
 52Y  H9   C12  C13  120.61  3.000
 52Y  H9   C12  C11  119.48  3.000
 52Y  C13  C12  C11  119.89  3.000
 52Y  H10  C13  C12  118.96  3.000
 52Y  H10  C13  C8   120.15  3.000
 52Y  C12  C13  C8   120.87  3.000
 52Y  C18  N14  C15  117.29  3.000
 52Y  C18  N14  C11  124.12  3.000
 52Y  C15  N14  C11  118.58  3.000
 52Y  O19  C15  C16  126.51  3.000
 52Y  C16  C15  N14  110.77  3.000
 52Y  O19  C15  N14  122.72  3.000
 52Y  H12  C16  H11  108.51  3.000
 52Y  H12  C16  S17  110.32  3.000
 52Y  H11  C16  S17  110.26  3.000
 52Y  H12  C16  C15  109.86  3.000
 52Y  H11  C16  C15  110.05  3.000
 52Y  S17  C16  C15  107.84  3.000
 52Y  C18  S17  C16   92.33  3.000
 52Y  C21  C18  S17  122.67  3.000
 52Y  C21  C18  N14  125.59  3.000
 52Y  S17  C18  N14  111.74  3.000
 52Y  C23  C21  C22  116.61  3.000
 52Y  C22  C21  C18  119.04  3.000
 52Y  C23  C21  C18  124.34  3.000
 52Y  O26  C22  O25  124.31  3.000
 52Y  O25  C22  C21  112.26  3.000
 52Y  O26  C22  C21  123.43  3.000
 52Y  N24  C23  C21  180.00  3.000
 52Y  C27  O25  C22  117.64  3.000
 52Y  H15  C27  H14  109.46  3.000
 52Y  H15  C27  H13  109.52  3.000
 52Y  H14  C27  H13  109.45  3.000
 52Y  H15  C27  O25  111.28  3.000
 52Y  H14  C27  O25  105.71  3.000
 52Y  H13  C27  O25  111.34  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
 52Y  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 52Y  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 52Y  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 52Y  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 52Y  CONST_05  C8   C5   C4   C3    180.00   0.0  0
 52Y  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 52Y  CONST_09  C7   C2   C3   C4      0.00   0.0  0
 52Y  CONST_10  C10  C9   C8   C5    180.00   0.0  0
 52Y  CONST_11  C12  C13  C8   C5    180.00   0.0  0
 52Y  CONST_14  C8   C5   C6   C7    180.00   0.0  0
 52Y  CONST_15  C11  C10  C9   C8      0.00   0.0  0
 52Y  CONST_16  C11  C12  C13  C8      0.00   0.0  0
 52Y  CONST_17  C12  C11  C10  C9      0.00   0.0  0
 52Y  CONST_18  C12  C13  C8   C9      0.00   0.0  0
 52Y  CONST_19  C13  C8   C9   C10     0.00   0.0  0
 52Y  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 52Y  CONST_21  N14  C11  C10  C9    180.00   0.0  0
 52Y  CONST_22  N14  C11  C12  C13   180.00   0.0  0
 52Y  CONST_23  C16  C15  N14  C11   180.00   0.0  0
 52Y  CONST_24  C18  N14  C15  C16     0.00   0.0  0
 52Y  CONST_25  C6   C7   C2   O1    180.00   0.0  0
 52Y  CONST_26  C4   C3   C2   O1    180.00   0.0  0
 52Y  CONST_27  F20  C10  C9   C8    180.00   0.0  0
 52Y  CONST_28  F20  C10  C11  C12   180.00   0.0  0
 52Y  CONST_29  F20  C10  C11  N14     0.00   0.0  0
 52Y  CONST_30  O19  C15  N14  C11     0.00   0.0  0
 52Y  CONST_31  O19  C15  N14  C18   180.00   0.0  0
 52Y  CONST_32  H6   C6   C7   C2    180.00   0.0  0
 52Y  CONST_33  H5   C4   C3   C2    180.00   0.0  0
 52Y  CONST_34  H7   C7   C2   C3    180.00   0.0  0
 52Y  CONST_35  H8   C9   C8   C5      0.00   0.0  0
 52Y  CONST_36  H10  C13  C8   C5      0.00   0.0  0
 52Y  CONST_37  H4   C3   C4   C5    180.00   0.0  0
 52Y  CONST_38  H9   C12  C13  C8    180.00   0.0  0
 52Y  Var_01    C15  N14  C11  C10    85.75  30.0  2
 52Y  Var_02    S17  C18  N14  C11  -177.01  30.0  1
 52Y  Var_03    S17  C16  C15  N14     0.37  30.0  1
 52Y  Var_04    C7   C2   O1   C1     -1.89  30.0  2
 52Y  Var_05    C23  C21  C18  N14     2.66  30.0  2
 52Y  Var_06    O26  C22  C21  C18    -0.17  30.0  2
 52Y  Var_07    H1   C1   O1   C2   -178.20  30.0  3
 52Y  Var_08    H13  C27  O25  C22    58.64  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
 52Y  plan-1  O1   0.020
 52Y  plan-1  C2   0.020
 52Y  plan-1  C3   0.020
 52Y  plan-1  C4   0.020
 52Y  plan-1  C5   0.020
 52Y  plan-1  C6   0.020
 52Y  plan-1  C7   0.020
 52Y  plan-1  C8   0.020
 52Y  plan-1  H4   0.020
 52Y  plan-1  H5   0.020
 52Y  plan-1  H6   0.020
 52Y  plan-1  H7   0.020
 52Y  plan-2  C5   0.020
 52Y  plan-2  C8   0.020
 52Y  plan-2  C9   0.020
 52Y  plan-2  C10  0.020
 52Y  plan-2  C11  0.020
 52Y  plan-2  C12  0.020
 52Y  plan-2  C13  0.020
 52Y  plan-2  N14  0.020
 52Y  plan-2  F20  0.020
 52Y  plan-2  H8   0.020
 52Y  plan-2  H9   0.020
 52Y  plan-2  H10  0.020
 52Y  plan-3  C11  0.020
 52Y  plan-3  N14  0.020
 52Y  plan-3  C15  0.020
 52Y  plan-3  C16  0.020
 52Y  plan-3  C18  0.020
 52Y  plan-3  O19  0.020
 52Y  plan-4  C21  0.020
 52Y  plan-4  C22  0.020
 52Y  plan-4  O25  0.020
 52Y  plan-4  O26  0.020

