# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 22:54:52 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-(4-{[(5R)-2,4-dioxo-1,3-thiazolidin-5-yl]methyl}-2-methoxyphenoxy)-3-(trifluoromethyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C[C@H]2SC(=O)NC2=O)ccc1Oc3ccc(cc3C(F)(F)F)C#N
#
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
 5FB  5FB  4-(4-{[(5R)-2,4-dioxo-1,3-thiazolidin-5-yl]methyl}-2-methoxyphenoxy)-3-(trifluoromethyl)benzonitrile  ligand  42  29  .  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_5FB
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
 5FB  C15   C  CR16  0  -0.288  -0.4412   0.3837  -1.4435
 5FB  C20   C  CR16  0  -0.226   3.7941  -2.1277  -0.8343
 5FB  C21   C  CR6   0   0.007   5.0245  -1.5411  -0.5463
 5FB  C22   C  CSP   0   0.056   6.2216  -2.3092  -0.6273
 5FB  C24   C  CR16  0  -0.282   5.0873  -0.1996  -0.1771
 5FB  C26   C  CT    0   1.077   3.9875   1.9931   0.3176
 5FB  C01   C  CH3   0  -0.440   0.3535  -1.3799   2.9349
 5FB  O02   O  O2    0  -0.454   0.7492  -0.6297   1.8006
 5FB  C03   C  CR6   0   0.379  -0.1144  -0.4990   0.7869
 5FB  C04   C  CR16  0  -0.432  -1.4078  -1.0032   0.7581
 5FB  C05   C  CR6   0   0.127  -2.2225  -0.8164  -0.3593
 5FB  C06   C  CH2   0  -0.502  -3.6333  -1.3347  -0.3384
 5FB  C07   C  CH1   0  -0.554  -4.5437  -0.4372   0.5009
 5FB  S08   S  S2    0   0.088  -4.6154   1.2640  -0.1374
 5FB  C09   C  C     0   0.404  -6.3753   1.2351  -0.2632
 5FB  O10   O  O     0  -0.400  -7.0435   2.1568  -0.6424
 5FB  N11   N  NH1   0  -0.659  -6.8566   0.0095   0.1293
 5FB  C12   C  C     0   0.625  -5.9716  -0.9506   0.5308
 5FB  O13   O  O     0  -0.409  -6.2766  -2.0670   0.8644
 5FB  C14   C  CR16  0  -0.328  -1.7374  -0.1199  -1.4560
 5FB  C16   C  CR6   0   0.218   0.3541   0.1973  -0.3353
 5FB  O17   O  O2    0  -0.492   1.6145   0.7484  -0.3000
 5FB  C18   C  CR6   0   0.429   2.6948  -0.0449  -0.3792
 5FB  C19   C  CR16  0  -0.326   2.6352  -1.3839  -0.7527
 5FB  N23   N  NS    0  -0.250   7.1895  -2.9315  -0.6905
 5FB  C25   C  CR6   0  -0.284   3.9301   0.5511  -0.0910
 5FB  F27   F  F     0  -0.307   3.2820   2.2283   1.4293
 5FB  F28   F  F     0  -0.300   5.2406   2.3854   0.5655
 5FB  F29   F  F     0  -0.308   3.5084   2.8046  -0.6322
 5FB  H15   H  HCR6  0   0.279  -0.0503   0.9248  -2.2957
 5FB  H20   H  HCR6  0   0.297   3.7408  -3.1676  -1.1255
 5FB  H24   H  HCR6  0   0.299   6.0490   0.2410   0.0432
 5FB  H01   H  HCH3  0   0.234  -0.4952  -0.9216   3.4483
 5FB  H01A  H  HCH3  0   0.234   0.0973  -2.4084   2.6704
 5FB  H01B  H  HCH3  0   0.267   1.2068  -1.3902   3.6072
 5FB  H04   H  HCR6  0   0.286  -1.8005  -1.5498   1.6066
 5FB  H06   H  HCH2  0   0.284  -4.0260  -1.4079  -1.3538
 5FB  H06A  H  HCH2  0   0.288  -3.6596  -2.3368   0.0942
 5FB  H07   H  HCH1  0   0.355  -4.1844  -0.4008   1.5326
 5FB  HN11  H  HNH1  0   0.441  -7.8527  -0.1763   0.0974
 5FB  H14   H  HCR6  0   0.260  -2.3624   0.0278  -2.3270
 5FB  H19   H  HCR6  0   0.304   1.6889  -1.8509  -0.9890

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
 5FB  C14  C15   aromatic  1.391  0.020  1.391
 5FB  C15  C16   aromatic  1.377  0.020  1.377
 5FB  C15  H15   single    0.930  0.020  1.080
 5FB  C21  C20   aromatic  1.393  0.020  1.393
 5FB  C19  C20   aromatic  1.379  0.020  1.379
 5FB  C20  H20   single    0.930  0.020  1.080
 5FB  C24  C21   aromatic  1.393  0.020  1.393
 5FB  C21  C22   single    1.425  0.020  1.425
 5FB  C22  N23   triple    1.152  0.020  1.152
 5FB  C25  C24   aromatic  1.382  0.020  1.382
 5FB  C24  H24   single    0.930  0.020  1.080
 5FB  F27  C26   single    1.337  0.020  1.337
 5FB  F29  C26   single    1.338  0.020  1.338
 5FB  C26  C25   single    1.500  0.020  1.500
 5FB  C26  F28   single    1.336  0.020  1.336
 5FB  O02  C01   single    1.416  0.020  1.416
 5FB  C01  H01   single    0.970  0.020  1.090
 5FB  C01  H01A  single    0.970  0.020  1.090
 5FB  C01  H01B  single    0.970  0.020  1.090
 5FB  C03  O02   single    1.338  0.020  1.338
 5FB  C16  C03   aromatic  1.401  0.020  1.401
 5FB  C04  C03   aromatic  1.388  0.020  1.388
 5FB  C05  C04   aromatic  1.395  0.020  1.395
 5FB  C04  H04   single    0.930  0.020  1.080
 5FB  C14  C05   aromatic  1.387  0.020  1.387
 5FB  C06  C05   single    1.503  0.020  1.503
 5FB  C07  C06   single    1.529  0.020  1.529
 5FB  C06  H06   single    0.970  0.020  1.090
 5FB  C06  H06A  single    0.970  0.020  1.090
 5FB  C12  C07   single    1.518  0.020  1.518
 5FB  C07  S08   single    1.818  0.020  1.818
 5FB  C07  H07   single    0.970  0.020  1.090
 5FB  C09  S08   single    1.765  0.020  1.765
 5FB  N11  C09   single    1.374  0.020  1.374
 5FB  C09  O10   double    1.200  0.020  1.200
 5FB  C12  N11   single    1.366  0.020  1.366
 5FB  N11  HN11  single    0.860  0.020  1.020
 5FB  O13  C12   double    1.205  0.020  1.205
 5FB  C14  H14   single    0.930  0.020  1.080
 5FB  C16  O17   single    1.376  0.020  1.376
 5FB  O17  C18   single    1.343  0.020  1.343
 5FB  C25  C18   aromatic  1.402  0.020  1.402
 5FB  C18  C19   aromatic  1.391  0.020  1.391
 5FB  C19  H19   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
 5FB  H15   C15  C16   119.52  3.000
 5FB  H15   C15  C14   120.70  3.000
 5FB  C16   C15  C14   119.78  3.000
 5FB  H20   C20  C19   119.55  3.000
 5FB  H20   C20  C21   120.27  3.000
 5FB  C19   C20  C21   120.18  3.000
 5FB  C24   C21  C22   119.77  3.000
 5FB  C22   C21  C20   120.22  3.000
 5FB  C24   C21  C20   120.01  3.000
 5FB  N23   C22  C21   180.00  3.000
 5FB  H24   C24  C25   120.73  3.000
 5FB  H24   C24  C21   119.14  3.000
 5FB  C25   C24  C21   120.13  3.000
 5FB  F29   C26  F28   106.82  3.000
 5FB  F28   C26  F27   106.79  3.000
 5FB  F29   C26  F27   107.13  3.000
 5FB  F28   C26  C25   111.63  3.000
 5FB  F29   C26  C25   112.09  3.000
 5FB  F27   C26  C25   112.04  3.000
 5FB  H01B  C01  H01A  108.97  3.000
 5FB  H01B  C01  H01   108.87  3.000
 5FB  H01A  C01  H01   109.05  3.000
 5FB  H01B  C01  O02   106.33  3.000
 5FB  H01A  C01  O02   111.74  3.000
 5FB  H01   C01  O02   111.78  3.000
 5FB  C03   O02  C01   118.56  3.000
 5FB  C16   C03  C04   118.37  3.000
 5FB  C04   C03  O02   125.55  3.000
 5FB  C16   C03  O02   116.07  3.000
 5FB  H04   C04  C05   118.89  3.000
 5FB  H04   C04  C03   120.32  3.000
 5FB  C05   C04  C03   120.79  3.000
 5FB  C14   C05  C06   120.83  3.000
 5FB  C06   C05  C04   119.39  3.000
 5FB  C14   C05  C04   119.75  3.000
 5FB  H06A  C06  H06   107.36  3.000
 5FB  H06A  C06  C07   107.87  3.000
 5FB  H06   C06  C07   109.62  3.000
 5FB  H06A  C06  C05   110.16  3.000
 5FB  H06   C06  C05   110.37  3.000
 5FB  C07   C06  C05   111.35  3.000
 5FB  H07   C07  C12   107.57  3.000
 5FB  H07   C07  S08   108.25  3.000
 5FB  C12   C07  S08   106.64  3.000
 5FB  H07   C07  C06   109.99  3.000
 5FB  S08   C07  C06   112.33  3.000
 5FB  C12   C07  C06   111.86  3.000
 5FB  C09   S08  C07    92.81  3.000
 5FB  N11   C09  O10   125.48  3.000
 5FB  O10   C09  S08   124.42  3.000
 5FB  N11   C09  S08   110.10  3.000
 5FB  HN11  N11  C12   121.14  3.000
 5FB  HN11  N11  C09   119.91  3.000
 5FB  C12   N11  C09   118.94  3.000
 5FB  O13   C12  N11   124.66  3.000
 5FB  O13   C12  C07   123.87  3.000
 5FB  N11   C12  C07   111.47  3.000
 5FB  H14   C14  C05   120.20  3.000
 5FB  H14   C14  C15   119.75  3.000
 5FB  C05   C14  C15   120.05  3.000
 5FB  O17   C16  C03   118.99  3.000
 5FB  O17   C16  C15   119.71  3.000
 5FB  C03   C16  C15   121.25  3.000
 5FB  C18   O17  C16   119.93  3.000
 5FB  C25   C18  C19   120.14  3.000
 5FB  C19   C18  O17   123.36  3.000
 5FB  C25   C18  O17   116.48  3.000
 5FB  H19   C19  C18   120.78  3.000
 5FB  H19   C19  C20   119.30  3.000
 5FB  C18   C19  C20   119.92  3.000
 5FB  C18   C25  C26   119.91  3.000
 5FB  C18   C25  C24   119.62  3.000
 5FB  C26   C25  C24   120.48  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
 5FB  CONST_01  C04   C05  C14  C15     0.00   0.0  0
 5FB  CONST_02  C04   C03  C16  C15     0.00   0.0  0
 5FB  CONST_03  C25   C24  C21  C20     0.00   0.0  0
 5FB  CONST_04  C25   C18  C19  C20     0.00   0.0  0
 5FB  CONST_05  C18   C19  C20  C21     0.00   0.0  0
 5FB  CONST_06  C18   C25  C24  C21     0.00   0.0  0
 5FB  CONST_07  C19   C20  C21  C24     0.00   0.0  0
 5FB  CONST_08  C19   C18  C25  C24     0.00   0.0  0
 5FB  CONST_09  C14   C15  C16  C03     0.00   0.0  0
 5FB  CONST_10  C14   C05  C04  C03     0.00   0.0  0
 5FB  CONST_11  C16   C03  C04  C05     0.00   0.0  0
 5FB  CONST_12  C16   C15  C14  C05     0.00   0.0  0
 5FB  CONST_13  C09   N11  C12  C07     0.00   0.0  0
 5FB  CONST_14  C06   C05  C14  C15   180.00   0.0  0
 5FB  CONST_15  O02   C03  C16  C15   180.00   0.0  0
 5FB  CONST_16  O17   C18  C19  C20   180.00   0.0  0
 5FB  CONST_17  C26   C25  C24  C21   180.00   0.0  0
 5FB  CONST_18  C19   C20  C21  C22   180.00   0.0  0
 5FB  CONST_19  C25   C24  C21  C22   180.00   0.0  0
 5FB  CONST_20  O17   C18  C25  C24   180.00   0.0  0
 5FB  CONST_21  C19   C18  C25  C26   180.00   0.0  0
 5FB  CONST_22  C05   C04  C03  O02   180.00   0.0  0
 5FB  CONST_23  C06   C05  C04  C03   180.00   0.0  0
 5FB  CONST_24  O17   C16  C03  C04   180.00   0.0  0
 5FB  CONST_25  O17   C16  C15  C14   180.00   0.0  0
 5FB  CONST_26  O13   C12  N11  C09   180.00   0.0  0
 5FB  CONST_27  H24   C24  C21  C20   180.00   0.0  0
 5FB  CONST_28  H19   C19  C20  C21   180.00   0.0  0
 5FB  CONST_29  H20   C20  C21  C24   180.00   0.0  0
 5FB  CONST_30  H15   C15  C16  C03   180.00   0.0  0
 5FB  CONST_31  H14   C14  C05  C04   180.00   0.0  0
 5FB  CONST_32  H04   C04  C05  C14   180.00   0.0  0
 5FB  CONST_33  HN11  N11  C12  C07   180.00   0.0  0
 5FB  Var_01    N11   C09  S08  C07    -1.08  30.0  1
 5FB  Var_02    C12   N11  C09  S08    -0.15  30.0  1
 5FB  Var_03    C07   C06  C05  C04    76.32  30.0  3
 5FB  Var_04    C25   C18  O17  C16  -168.61  30.0  2
 5FB  Var_05    F27   C26  C25  C24  -119.93  30.0  2
 5FB  Var_06    C16   C03  O02  C01  -176.98  30.0  2
 5FB  Var_07    H01   C01  O02  C03   -63.51  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
 5FB  chir_01  C07  C06  C12  S08  positiv

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
 5FB  plan-1  C20   0.020
 5FB  plan-1  C21   0.020
 5FB  plan-1  C22   0.020
 5FB  plan-1  C24   0.020
 5FB  plan-1  C26   0.020
 5FB  plan-1  O17   0.020
 5FB  plan-1  C18   0.020
 5FB  plan-1  C19   0.020
 5FB  plan-1  N23   0.020
 5FB  plan-1  C25   0.020
 5FB  plan-1  H20   0.020
 5FB  plan-1  H24   0.020
 5FB  plan-1  H19   0.020
 5FB  plan-2  C15   0.020
 5FB  plan-2  O02   0.020
 5FB  plan-2  C03   0.020
 5FB  plan-2  C04   0.020
 5FB  plan-2  C05   0.020
 5FB  plan-2  C06   0.020
 5FB  plan-2  C14   0.020
 5FB  plan-2  C16   0.020
 5FB  plan-2  O17   0.020
 5FB  plan-2  H15   0.020
 5FB  plan-2  H04   0.020
 5FB  plan-2  H14   0.020
 5FB  plan-3  S08   0.020
 5FB  plan-3  C09   0.020
 5FB  plan-3  O10   0.020
 5FB  plan-3  N11   0.020
 5FB  plan-4  C07   0.020
 5FB  plan-4  C09   0.020
 5FB  plan-4  N11   0.020
 5FB  plan-4  C12   0.020
 5FB  plan-4  O13   0.020
 5FB  plan-4  HN11  0.020

