# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 01:23:06 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: (5~{S})-5-[[4-[2-[[7-(diethylamino)-2-oxidanylidene-chromen-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)c1ccc2c(OC(=O)C=C2N(C)CCOc3ccc(C[C@@H]4SC(=O)NC4=O)cc3)c1
#
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
 J3F  J3F  (5~{S})-5-[[4-[2-[[7-(diethylamino)-2-oxidanylidene-chromen-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione  ligand  64  35  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J3F
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
 J3F  N1   N  NH1   0  -0.659  20.4641  16.8854  20.9791
 J3F  C4   C  CH2   0  -0.494  19.5958  15.8141  17.7476
 J3F  C5   C  CR6   0   0.088  18.9043  16.3889  16.5440
 J3F  C6   C  CR16  0  -0.287  19.5556  17.2582  15.6809
 J3F  C7   C  CR16  0  -0.364  18.9123  17.8132  14.5787
 J3F  C8   C  CR6   0   0.376  17.5817  17.4956  14.3278
 J3F  C10  C  CR16  0  -0.277  17.5678  16.0849  16.2789
 J3F  C15  C  CR16  0  -0.623  14.7554  20.3893   9.4654
 J3F  C17  C  CR66  0   0.402  15.6811  22.4433   7.8856
 J3F  C20  C  CR6   0   0.417  17.3630  24.0017   7.0998
 J3F  C21  C  CR16  0  -0.342  18.2631  23.3791   8.0035
 J3F  C22  C  CR16  0  -0.289  17.8809  22.3005   8.7588
 J3F  C24  C  CH3   0  -0.661  19.0117  26.6913   7.6303
 J3F  C26  C  CH3   0  -0.708  17.2501  26.7055   4.4841
 J3F  C1   C  C     0   0.400  20.4152  18.1842  20.5310
 J3F  C2   C  C     0   0.618  19.8277  15.9120  20.2605
 J3F  C3   C  CH1   0  -0.551  19.1320  16.4884  19.0411
 J3F  S1   S  S2    0   0.083  19.4726  18.2749  19.0411
 J3F  O1   O  O     0  -0.393  20.9362  19.1240  21.0639
 J3F  O2   O  O     0  -0.403  19.8220  14.7426  20.5479
 J3F  C9   C  CR16  0  -0.329  16.9111  16.6263  15.1916
 J3F  O3   O  O2    0  -0.473  16.8651  17.9701  13.2898
 J3F  C11  C  CH2   0  -0.183  17.5120  18.7566  12.3091
 J3F  C12  C  CH2   0  -0.339  16.4686  19.0131  11.2314
 J3F  N2   N  NT    0  -0.501  16.9888  19.8816  10.1941
 J3F  C14  C  CR6   0   0.507  16.1058  20.6313   9.4661
 J3F  C16  C  CR6   0   0.525  13.8463  21.1323   8.6553
 J3F  O4   O  O     0  -0.473  14.3729  22.1058   7.8541
 J3F  C18  C  CR66  0  -0.106  16.5895  21.7552   8.6915
 J3F  O5   O  O     0  -0.459  12.6504  20.9582   8.5694
 J3F  C19  C  CR16  0  -0.477  16.0426  23.5238   7.1000
 J3F  C23  C  CH2   0  -0.347  19.0266  25.6795   6.4928
 J3F  C25  C  CH2   0  -0.289  16.7277  25.6914   5.4846
 J3F  H1   H  HNH1  0   0.437  20.9823  16.6619  21.8214
 J3F  H4   H  HCH2  0   0.281  19.3793  14.7471  17.8349
 J3F  H3   H  HCH2  0   0.277  20.6780  15.9205  17.6516
 J3F  H5   H  HCR6  0   0.255  20.5930  17.5135  15.8612
 J3F  H6   H  HCR6  0   0.279  19.4654  18.4844  13.9357
 J3F  H8   H  HCR6  0   0.254  17.0310  15.4064  16.9324
 J3F  H13  H  HCH3  0   0.260  18.1379  18.2867   9.4633
 J3F  H14  H  HCH3  0   0.275  18.3041  19.7684   8.5437
 J3F  H15  H  HCH3  0   0.253  19.0988  19.6253  10.1110
 J3F  H16  H  HCR6  0   0.282  14.3220  19.5655  10.0122
 J3F  H18  H  HCR6  0   0.269  19.2712  23.7433   8.1278
 J3F  H19  H  HCR6  0   0.279  18.6073  21.8825   9.4416
 J3F  H22  H  HCH3  0   0.233  19.9926  27.1557   7.7349
 J3F  H23  H  HCH3  0   0.231  18.2859  27.4830   7.4403
 J3F  H24  H  HCH3  0   0.230  18.7594  26.2233   8.5825
 J3F  H27  H  HCH3  0   0.253  16.4042  27.0694   3.9016
 J3F  H28  H  HCH3  0   0.238  17.7135  27.5701   4.9581
 J3F  H29  H  HCH3  0   0.237  17.9635  26.2640   3.7883
 J3F  H2   H  HCH1  0   0.351  18.0563  16.3431  19.1692
 J3F  H7   H  HCR6  0   0.261  15.8762  16.3744  14.9959
 J3F  H10  H  HCH2  0   0.238  18.3818  18.2233  11.9122
 J3F  H9   H  HCH2  0   0.234  17.8599  19.7082  12.7269
 J3F  H12  H  HCH2  0   0.270  15.6135  19.4975  11.7033
 J3F  H11  H  HCH2  0   0.242  16.1262  18.0547  10.8184
 J3F  H17  H  HCR6  0   0.283  15.2670  23.9914   6.5120
 J3F  H21  H  HCH2  0   0.270  19.3182  26.1712   5.5677
 J3F  H20  H  HCH2  0   0.256  19.7972  24.9275   6.6604
 J3F  H25  H  HCH2  0   0.243  16.1777  24.9323   4.9241
 J3F  H26  H  HCH2  0   0.228  15.9973  26.1813   6.1405
 J3F  N3   N  NT    0  -0.503  17.7512  25.0186   6.2784
 J3F  C13  C  CH3   0  -0.584  18.1982  19.3750   9.5500

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
 J3F  C23  C24  single    1.522  0.020  1.522
 J3F  C23  N3   single    1.452  0.020  1.452
 J3F  N3   C20  single    1.364  0.020  1.364
 J3F  N3   C25  single    1.460  0.020  1.460
 J3F  C26  C25  single    1.517  0.020  1.517
 J3F  C20  C21  aromatic  1.419  0.020  1.419
 J3F  C20  C19  aromatic  1.404  0.020  1.404
 J3F  C21  C22  aromatic  1.371  0.020  1.371
 J3F  C19  C17  aromatic  1.384  0.020  1.384
 J3F  C22  C18  aromatic  1.403  0.020  1.403
 J3F  C17  C18  aromatic  1.396  0.020  1.396
 J3F  C17  O4   single    1.351  0.020  1.351
 J3F  C13  N2   single    1.461  0.020  1.461
 J3F  C18  C14  single    1.448  0.020  1.448
 J3F  O4   C16  single    1.366  0.020  1.366
 J3F  C14  N2   single    1.368  0.020  1.368
 J3F  C14  C15  double    1.372  0.020  1.372
 J3F  N2   C12  single    1.449  0.020  1.449
 J3F  C16  C15  single    1.426  0.020  1.426
 J3F  C16  O5   double    1.212  0.020  1.212
 J3F  C12  C11  single    1.522  0.020  1.522
 J3F  C11  O3   single    1.414  0.020  1.414
 J3F  O3   C8   single    1.348  0.020  1.348
 J3F  C8   C7   aromatic  1.391  0.020  1.391
 J3F  C8   C9   aromatic  1.397  0.020  1.397
 J3F  C7   C6   aromatic  1.392  0.020  1.392
 J3F  C9   C10  aromatic  1.381  0.020  1.381
 J3F  C6   C5   aromatic  1.387  0.020  1.387
 J3F  C10  C5   aromatic  1.396  0.020  1.396
 J3F  C5   C4   single    1.502  0.020  1.502
 J3F  S1   C3   single    1.819  0.020  1.819
 J3F  S1   C1   single    1.765  0.020  1.765
 J3F  C4   C3   single    1.531  0.020  1.531
 J3F  C3   C2   single    1.518  0.020  1.518
 J3F  C1   O1   double    1.199  0.020  1.199
 J3F  C1   N1   single    1.375  0.020  1.375
 J3F  C2   N1   single    1.367  0.020  1.367
 J3F  C2   O2   double    1.204  0.020  1.204
 J3F  N1   H1   single    0.860  0.020  1.020
 J3F  C4   H4   single    0.970  0.020  1.090
 J3F  C4   H3   single    0.970  0.020  1.090
 J3F  C6   H5   single    0.930  0.020  1.080
 J3F  C7   H6   single    0.930  0.020  1.080
 J3F  C10  H8   single    0.930  0.020  1.080
 J3F  C13  H13  single    0.970  0.020  1.090
 J3F  C13  H14  single    0.970  0.020  1.090
 J3F  C13  H15  single    0.970  0.020  1.090
 J3F  C15  H16  single    0.930  0.020  1.080
 J3F  C21  H18  single    0.930  0.020  1.080
 J3F  C22  H19  single    0.930  0.020  1.080
 J3F  C24  H22  single    0.970  0.020  1.090
 J3F  C24  H23  single    0.970  0.020  1.090
 J3F  C24  H24  single    0.970  0.020  1.090
 J3F  C26  H27  single    0.970  0.020  1.090
 J3F  C26  H28  single    0.970  0.020  1.090
 J3F  C26  H29  single    0.970  0.020  1.090
 J3F  C3   H2   single    0.970  0.020  1.090
 J3F  C9   H7   single    0.930  0.020  1.080
 J3F  C11  H10  single    0.970  0.020  1.090
 J3F  C11  H9   single    0.970  0.020  1.090
 J3F  C12  H12  single    0.970  0.020  1.090
 J3F  C12  H11  single    0.970  0.020  1.090
 J3F  C19  H17  single    0.930  0.020  1.080
 J3F  C23  H21  single    0.970  0.020  1.090
 J3F  C23  H20  single    0.970  0.020  1.090
 J3F  C25  H25  single    0.970  0.020  1.090
 J3F  C25  H26  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
 J3F  H1   N1   C2   121.17  3.000
 J3F  H1   N1   C1   119.82  3.000
 J3F  C2   N1   C1   119.00  3.000
 J3F  H3   C4   H4   107.38  3.000
 J3F  H3   C4   C3   109.38  3.000
 J3F  H4   C4   C3   107.62  3.000
 J3F  H3   C4   C5   110.40  3.000
 J3F  H4   C4   C5   110.28  3.000
 J3F  C3   C4   C5   111.65  3.000
 J3F  C10  C5   C6   117.89  3.000
 J3F  C10  C5   C4   120.63  3.000
 J3F  C6   C5   C4   121.47  3.000
 J3F  H5   C6   C7   118.71  3.000
 J3F  H5   C6   C5   119.58  3.000
 J3F  C7   C6   C5   121.71  3.000
 J3F  H6   C7   C8   121.58  3.000
 J3F  H6   C7   C6   118.81  3.000
 J3F  C8   C7   C6   119.61  3.000
 J3F  O3   C8   C9   116.11  3.000
 J3F  C9   C8   C7   119.33  3.000
 J3F  O3   C8   C7   124.56  3.000
 J3F  H8   C10  C9   118.98  3.000
 J3F  H8   C10  C5   119.72  3.000
 J3F  C9   C10  C5   121.30  3.000
 J3F  H16  C15  C16  115.42  3.000
 J3F  H16  C15  C14  121.97  3.000
 J3F  C16  C15  C14  122.39  3.000
 J3F  C19  C17  C18  122.86  3.000
 J3F  C18  C17  O4   121.36  3.000
 J3F  C19  C17  O4   115.76  3.000
 J3F  C19  C20  C21  116.54  3.000
 J3F  C19  C20  N3   121.44  3.000
 J3F  C21  C20  N3   122.02  3.000
 J3F  H18  C21  C22  117.55  3.000
 J3F  H18  C21  C20  121.18  3.000
 J3F  C22  C21  C20  121.27  3.000
 J3F  H19  C22  C18  119.89  3.000
 J3F  H19  C22  C21  117.70  3.000
 J3F  C18  C22  C21  122.39  3.000
 J3F  H24  C24  H23  108.03  3.000
 J3F  H24  C24  H22  107.89  3.000
 J3F  H23  C24  H22  107.83  3.000
 J3F  H24  C24  C23  111.68  3.000
 J3F  H23  C24  C23  111.03  3.000
 J3F  H22  C24  C23  110.24  3.000
 J3F  H29  C26  H28  108.71  3.000
 J3F  H29  C26  H27  107.58  3.000
 J3F  H28  C26  H27  107.32  3.000
 J3F  H29  C26  C25  112.06  3.000
 J3F  H28  C26  C25  112.95  3.000
 J3F  H27  C26  C25  107.96  3.000
 J3F  O1   C1   S1   124.51  3.000
 J3F  O1   C1   N1   125.45  3.000
 J3F  S1   C1   N1   110.04  3.000
 J3F  O2   C2   C3   123.95  3.000
 J3F  O2   C2   N1   124.62  3.000
 J3F  C3   C2   N1   111.43  3.000
 J3F  H2   C3   S1   108.35  3.000
 J3F  H2   C3   C2   107.85  3.000
 J3F  S1   C3   C2   106.69  3.000
 J3F  H2   C3   C4   109.80  3.000
 J3F  C2   C3   C4   111.89  3.000
 J3F  S1   C3   C4   112.09  3.000
 J3F  C3   S1   C1    92.84  3.000
 J3F  H7   C9   C10  120.38  3.000
 J3F  H7   C9   C8   119.45  3.000
 J3F  C10  C9   C8   120.17  3.000
 J3F  C11  O3   C8   119.13  3.000
 J3F  H9   C11  H10  108.00  3.000
 J3F  H9   C11  C12  109.95  3.000
 J3F  H10  C11  C12  111.72  3.000
 J3F  H9   C11  O3   111.33  3.000
 J3F  H10  C11  O3   110.13  3.000
 J3F  C12  C11  O3   105.74  3.000
 J3F  H11  C12  H12  107.82  3.000
 J3F  H11  C12  N2   111.45  3.000
 J3F  H12  C12  N2   108.97  3.000
 J3F  H11  C12  C11  109.44  3.000
 J3F  H12  C12  C11  107.83  3.000
 J3F  N2   C12  C11  111.21  3.000
 J3F  C14  N2   C12  118.53  3.000
 J3F  C12  N2   C13  113.88  3.000
 J3F  C14  N2   C13  119.32  3.000
 J3F  C18  C14  N2   119.63  3.000
 J3F  N2   C14  C15  122.61  3.000
 J3F  C18  C14  C15  117.74  3.000
 J3F  O5   C16  O4   116.18  3.000
 J3F  O5   C16  C15  126.48  3.000
 J3F  O4   C16  C15  117.29  3.000
 J3F  C16  O4   C17  122.50  3.000
 J3F  C14  C18  C22  125.68  3.000
 J3F  C14  C18  C17  118.30  3.000
 J3F  C22  C18  C17  115.79  3.000
 J3F  H17  C19  C20  121.86  3.000
 J3F  H17  C19  C17  117.36  3.000
 J3F  C20  C19  C17  120.76  3.000
 J3F  H20  C23  H21  104.67  3.000
 J3F  H20  C23  C24  110.53  3.000
 J3F  H21  C23  C24  109.73  3.000
 J3F  H20  C23  N3   109.25  3.000
 J3F  H21  C23  N3   108.40  3.000
 J3F  C24  C23  N3   113.84  3.000
 J3F  H26  C25  H25  106.37  3.000
 J3F  H26  C25  C26  108.97  3.000
 J3F  H25  C25  C26  107.43  3.000
 J3F  H26  C25  N3   110.33  3.000
 J3F  H25  C25  N3   108.16  3.000
 J3F  C26  C25  N3   115.17  3.000
 J3F  C25  N3   C23  119.10  3.000
 J3F  C25  N3   C20  118.15  3.000
 J3F  C23  N3   C20  120.02  3.000
 J3F  H15  C13  H14  108.25  3.000
 J3F  H15  C13  H13  108.35  3.000
 J3F  H14  C13  H13  107.01  3.000
 J3F  H15  C13  N2   112.18  3.000
 J3F  H14  C13  N2   111.33  3.000
 J3F  H13  C13  N2   109.54  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
 J3F  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 J3F  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 J3F  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 J3F  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 J3F  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 J3F  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 J3F  CONST_07  C21  C20  C19  C17     0.00   0.0  0
 J3F  CONST_08  C21  C22  C18  C17     0.00   0.0  0
 J3F  CONST_09  C18  C22  C21  C20     0.00   0.0  0
 J3F  CONST_10  C18  C17  C19  C20     0.00   0.0  0
 J3F  CONST_11  C19  C20  C21  C22     0.00   0.0  0
 J3F  CONST_12  C19  C17  C18  C22     0.00   0.0  0
 J3F  CONST_13  C3   C2   N1   C1      0.00   0.0  0
 J3F  CONST_14  C22  C21  C20  N3    180.00   0.0  0
 J3F  CONST_15  C17  C19  C20  N3    180.00   0.0  0
 J3F  CONST_16  C7   C6   C5   C4    180.00   0.0  0
 J3F  CONST_17  C9   C10  C5   C4    180.00   0.0  0
 J3F  CONST_18  O3   C8   C7   C6    180.00   0.0  0
 J3F  CONST_19  O3   C8   C9   C10   180.00   0.0  0
 J3F  CONST_20  O2   C2   N1   C1    180.00   0.0  0
 J3F  CONST_21  H6   C7   C6   C5    180.00   0.0  0
 J3F  CONST_22  H7   C9   C10  C5    180.00   0.0  0
 J3F  CONST_23  H8   C10  C5   C6    180.00   0.0  0
 J3F  CONST_24  H5   C6   C7   C8    180.00   0.0  0
 J3F  CONST_25  H19  C22  C18  C17   180.00   0.0  0
 J3F  CONST_26  H17  C19  C20  C21   180.00   0.0  0
 J3F  CONST_27  H18  C21  C22  C18   180.00   0.0  0
 J3F  CONST_28  H1   N1   C2   C3    180.00   0.0  0
 J3F  CONST_29  C23  N3   C20  C21     0.00   0.0  0
 J3F  CONST_30  C25  N3   C20  C21   180.00   0.0  0
 J3F  CONST_31  C23  N3   C20  C19   180.00   0.0  0
 J3F  CONST_32  C25  N3   C20  C19     0.00   0.0  0
 J3F  Var_01    C22  C18  C14  C15   167.86  30.0  1
 J3F  Var_02    S1   C1   N1   C2      0.24  30.0  1
 J3F  Var_03    O4   C16  C15  C14     0.55  30.0  1
 J3F  Var_04    C19  C17  O4   C16  -174.66  30.0  1
 J3F  Var_05    C18  C14  C15  C16     5.04  30.0  1
 J3F  Var_06    C3   C4   C5   C6    104.57  30.0  2
 J3F  Var_07    O5   C16  O4   C17   177.28  30.0  1
 J3F  Var_08    C12  C11  O3   C8    174.84  30.0  2
 J3F  Var_09    C24  C23  N3   C20   -78.38  30.0  3
 J3F  Var_10    C26  C25  N3   C20  -173.56  30.0  3
 J3F  Var_11    C14  N2   C12  C11  -154.45  30.0  2
 J3F  Var_12    H13  C13  N2   C14  -111.70  30.0  3
 J3F  Var_13    N2   C12  C11  O3    176.70  30.0  2
 J3F  Var_14    H22  C24  C23  N3   -179.59  30.0  3
 J3F  Var_15    H27  C26  C25  N3    175.18  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
 J3F  chir_01  C3  S1  C4  C2  negativ

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
 J3F  plan-1  C4   0.020
 J3F  plan-1  C5   0.020
 J3F  plan-1  C6   0.020
 J3F  plan-1  C7   0.020
 J3F  plan-1  C8   0.020
 J3F  plan-1  C10  0.020
 J3F  plan-1  C9   0.020
 J3F  plan-1  O3   0.020
 J3F  plan-1  H5   0.020
 J3F  plan-1  H6   0.020
 J3F  plan-1  H8   0.020
 J3F  plan-1  H7   0.020
 J3F  plan-2  C17  0.020
 J3F  plan-2  C20  0.020
 J3F  plan-2  C21  0.020
 J3F  plan-2  C22  0.020
 J3F  plan-2  C14  0.020
 J3F  plan-2  O4   0.020
 J3F  plan-2  C18  0.020
 J3F  plan-2  C19  0.020
 J3F  plan-2  H18  0.020
 J3F  plan-2  H19  0.020
 J3F  plan-2  H17  0.020
 J3F  plan-2  N3   0.020
 J3F  plan-3  C20  0.020
 J3F  plan-3  C23  0.020
 J3F  plan-3  C25  0.020
 J3F  plan-3  N3   0.020
 J3F  plan-4  N1   0.020
 J3F  plan-4  C1   0.020
 J3F  plan-4  C2   0.020
 J3F  plan-4  C3   0.020
 J3F  plan-4  O2   0.020
 J3F  plan-4  H1   0.020
 J3F  plan-5  N1   0.020
 J3F  plan-5  C1   0.020
 J3F  plan-5  S1   0.020
 J3F  plan-5  O1   0.020
 J3F  plan-6  C15  0.020
 J3F  plan-6  C16  0.020
 J3F  plan-6  O4   0.020
 J3F  plan-6  O5   0.020

