# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 23:01:55 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (5~{Z})-5-[[3-[6-[(4-azanylcyclohexyl)amino]pyrazin-2-yl]phenyl]methylidene]-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CC[C@@H](CC1)Nc2cncc(n2)c3cccc(/C=C/4SC(=O)NC/4=O)c3
#
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
 0F5  0F5  (5~{Z})-5-[[3-[6-[(4-azanylcyclohexyl)amino]pyrazin-2-yl]phenyl]methylidene]-1,3-thiazolidine-2,4-dione  ligand  49  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0F5
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
 0F5  C10  C  CR16  0  -0.323  -2.9204  -1.5802  -0.3785
 0F5  C13  C  C1    0  -0.249  -3.9672   0.7145  -0.4411
 0F5  C15  C  CR5   0   0.638  -6.2667   1.5652  -0.5683
 0F5  C17  C  CR5   0   0.427  -7.6999  -0.2553  -0.1316
 0F5  C21  C  CR16  0  -0.067   5.5867  -0.2296   0.2910
 0F5  C22  C  C     0  -0.447   6.5100  -1.4339   0.4418
 0F5  C24  C  CR16  0  -0.054   8.3989  -0.1391  -0.6287
 0F5  C26  C  C     0  -0.437   6.0137   0.6313  -0.8998
 0F5  O19  O  O     0  -0.406  -6.0101   2.7178  -0.8174
 0F5  N16  N  NR15  0  -0.683  -7.5400   1.0737  -0.4073
 0F5  O20  O  O     0  -0.391  -8.7368  -0.8338   0.0324
 0F5  S18  S  S2    0   0.095  -6.1076  -1.0416  -0.0521
 0F5  C14  C  CR5   0  -0.306  -5.2832   0.4695  -0.3857
 0F5  C12  C  CR6   0   0.187  -2.8399  -0.1879  -0.2746
 0F5  C11  C  CR16  0  -0.383  -1.5959   0.3921  -0.0095
 0F5  C08  C  CR16  0  -0.215  -1.7861  -2.3558  -0.2046
 0F5  C09  C  CR16  0  -0.288  -0.5637  -1.7676   0.0795
 0F5  C07  C  CR6   0   0.091  -0.4570  -0.3807   0.1870
 0F5  C03  C  CR6   0   0.201   0.8462   0.2432   0.4948
 0F5  N02  N  N     0  -0.453   1.9369  -0.4528   0.1925
 0F5  C01  C  CR16  0  -0.164   0.9388   1.4933   1.0965
 0F5  N05  N  N     0  -0.345   2.1256   2.0376   1.3500
 0F5  C06  C  CR16  0  -0.171   3.2092   1.3651   1.0396
 0F5  C04  C  CR6   0   0.460   3.1284   0.0729   0.4662
 0F5  N28  N  NH1   0  -0.676   4.2139  -0.6788   0.1920
 0F5  C23  C  C     0  -0.439   7.9658  -0.9973   0.5552
 0F5  N27  N  NH2   0  -0.806   9.7684   0.3144  -0.4309
 0F5  C25  C  C     0  -0.438   7.4701   1.0617  -0.7697
 0F5  H1   H  HCR6  0   0.262  -3.8465  -2.0761  -0.6354
 0F5  H2   H  H     0   0.290  -3.7042   1.7536  -0.6126
 0F5  H4   H  HCR6  0   0.236   5.6793   0.3692   1.2041
 0F5  H6   H  H     0   0.224   6.3872  -2.0917  -0.4263
 0F5  H7   H  HCR6  0   0.188   8.2894  -0.7532  -1.5389
 0F5  H8   H  H     0   0.221   5.8729   0.0535  -1.8197
 0F5  H9   H  H     0   0.238   5.3672   1.5092  -0.9795
 0F5  H10  H  HNR5  0   0.443  -8.3504   1.6742  -0.5020
 0F5  H11  H  HCR6  0   0.264  -1.5289   1.4722   0.0301
 0F5  H12  H  HCR6  0   0.271  -1.8566  -3.4312  -0.2948
 0F5  H13  H  HCR6  0   0.265   0.3129  -2.3857   0.2178
 0F5  H14  H  HCR6  0   0.261   0.0643   2.0587   1.3909
 0F5  H15  H  HCR6  0   0.272   4.1613   1.8382   1.2452
 0F5  H16  H  HNH1  0   0.382   4.0354  -1.5278  -0.3235
 0F5  H17  H  H     0   0.215   8.1109  -0.4245   1.4777
 0F5  H18  H  H     0   0.235   8.6081  -1.8795   0.6294
 0F5  H19  H  HNH2  0   0.341  10.3816  -0.4890  -0.3579
 0F5  H20  H  HNH2  0   0.340  10.0793   0.8158  -1.2545
 0F5  H22  H  H     0   0.214   7.5902   1.7044   0.1094
 0F5  H23  H  H     0   0.233   7.7583   1.6606  -1.6381
 0F5  H5   H  H     0   0.246   6.2205  -2.0117   1.3219

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
 0F5  C06  N05  aromatic  1.313  0.020  1.313
 0F5  C06  C04  aromatic  1.416  0.020  1.416
 0F5  N28  C04  single    1.349  0.020  1.349
 0F5  N28  C21  single    1.448  0.020  1.448
 0F5  C22  C21  single    1.525  0.020  1.525
 0F5  C22  C23  single    1.524  0.020  1.524
 0F5  N05  C01  aromatic  1.330  0.020  1.330
 0F5  C04  N02  aromatic  1.331  0.020  1.331
 0F5  C26  C21  single    1.530  0.020  1.530
 0F5  C26  C25  single    1.524  0.020  1.524
 0F5  C23  C24  single    1.525  0.020  1.525
 0F5  C24  C25  single    1.525  0.020  1.525
 0F5  C24  N27  single    1.456  0.020  1.456
 0F5  C01  C03  aromatic  1.390  0.020  1.390
 0F5  N02  C03  aromatic  1.329  0.020  1.329
 0F5  C03  C07  single    1.477  0.020  1.477
 0F5  C07  C11  aromatic  1.390  0.020  1.390
 0F5  C07  C09  aromatic  1.395  0.020  1.395
 0F5  O20  C17  double    1.199  0.020  1.199
 0F5  C11  C12  aromatic  1.398  0.020  1.398
 0F5  C09  C08  aromatic  1.386  0.020  1.386
 0F5  S18  C17  single    1.778  0.020  1.778
 0F5  S18  C14  single    1.753  0.020  1.753
 0F5  C17  N16  single    1.367  0.020  1.367
 0F5  C12  C13  single    1.454  0.020  1.454
 0F5  C12  C10  aromatic  1.398  0.020  1.398
 0F5  C08  C10  aromatic  1.385  0.020  1.385
 0F5  C14  C13  double    1.340  0.020  1.340
 0F5  C14  C15  single    1.484  0.020  1.484
 0F5  N16  C15  single    1.374  0.020  1.374
 0F5  C15  O19  double    1.207  0.020  1.207
 0F5  C10  H1   single    0.930  0.020  1.080
 0F5  C13  H2   single    0.930  0.020  1.080
 0F5  C21  H4   single    0.970  0.020  1.090
 0F5  C22  H5   single    0.970  0.020  1.090
 0F5  C22  H6   single    0.970  0.020  1.090
 0F5  C24  H7   single    0.970  0.020  1.090
 0F5  C26  H8   single    0.970  0.020  1.090
 0F5  C26  H9   single    0.970  0.020  1.090
 0F5  N16  H10  single    0.860  0.020  1.020
 0F5  C11  H11  single    0.930  0.020  1.080
 0F5  C08  H12  single    0.930  0.020  1.080
 0F5  C09  H13  single    0.930  0.020  1.080
 0F5  C01  H14  single    0.930  0.020  1.080
 0F5  C06  H15  single    0.930  0.020  1.080
 0F5  N28  H16  single    0.860  0.020  1.020
 0F5  C23  H17  single    0.970  0.020  1.090
 0F5  C23  H18  single    0.970  0.020  1.090
 0F5  N27  H19  single    0.890  0.020  1.040
 0F5  N27  H20  single    0.890  0.020  1.040
 0F5  C25  H22  single    0.970  0.020  1.090
 0F5  C25  H23  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
 0F5  H1   C10  C08  118.32  3.000
 0F5  H1   C10  C12  121.56  3.000
 0F5  C08  C10  C12  120.07  3.000
 0F5  H2   C13  C12  115.12  3.000
 0F5  H2   C13  C14  114.81  3.000
 0F5  C12  C13  C14  130.06  3.000
 0F5  C14  C15  N16  109.61  3.000
 0F5  N16  C15  O19  124.24  3.000
 0F5  C14  C15  O19  126.15  3.000
 0F5  S18  C17  O20  123.73  3.000
 0F5  S18  C17  N16  109.54  3.000
 0F5  O20  C17  N16  126.73  3.000
 0F5  H4   C21  N28  107.86  3.000
 0F5  H4   C21  C26  108.51  3.000
 0F5  N28  C21  C26  112.70  3.000
 0F5  H4   C21  C22  107.34  3.000
 0F5  C26  C21  C22  110.63  3.000
 0F5  N28  C21  C22  109.62  3.000
 0F5  H6   C22  H5   106.92  3.000
 0F5  H6   C22  C23  109.75  3.000
 0F5  H5   C22  C23  110.17  3.000
 0F5  H6   C22  C21  109.14  3.000
 0F5  H5   C22  C21  109.70  3.000
 0F5  C23  C22  C21  111.07  3.000
 0F5  H7   C24  C25  107.55  3.000
 0F5  H7   C24  N27  112.25  3.000
 0F5  C25  C24  N27  109.89  3.000
 0F5  H7   C24  C23  107.40  3.000
 0F5  N27  C24  C23  109.69  3.000
 0F5  C25  C24  C23  110.00  3.000
 0F5  H9   C26  H8   106.65  3.000
 0F5  H9   C26  C25  110.15  3.000
 0F5  H8   C26  C25  110.08  3.000
 0F5  H9   C26  C21  110.09  3.000
 0F5  H8   C26  C21  108.72  3.000
 0F5  C25  C26  C21  111.04  3.000
 0F5  H10  N16  C17  120.12  3.000
 0F5  H10  N16  C15  121.21  3.000
 0F5  C17  N16  C15  118.67  3.000
 0F5  C14  S18  C17   91.80  3.000
 0F5  S18  C14  C15  110.38  3.000
 0F5  C15  C14  C13  120.73  3.000
 0F5  S18  C14  C13  128.85  3.000
 0F5  C11  C12  C13  117.02  3.000
 0F5  C13  C12  C10  124.40  3.000
 0F5  C11  C12  C10  118.58  3.000
 0F5  H11  C11  C07  119.90  3.000
 0F5  H11  C11  C12  118.41  3.000
 0F5  C07  C11  C12  121.68  3.000
 0F5  H12  C08  C09  119.77  3.000
 0F5  H12  C08  C10  119.54  3.000
 0F5  C09  C08  C10  120.69  3.000
 0F5  H13  C09  C07  119.75  3.000
 0F5  H13  C09  C08  119.91  3.000
 0F5  C07  C09  C08  120.34  3.000
 0F5  C03  C07  C09  120.22  3.000
 0F5  C09  C07  C11  118.62  3.000
 0F5  C03  C07  C11  121.16  3.000
 0F5  C01  C03  N02  120.98  3.000
 0F5  N02  C03  C07  117.10  3.000
 0F5  C01  C03  C07  121.91  3.000
 0F5  C04  N02  C03  118.77  3.000
 0F5  H14  C01  N05  117.09  3.000
 0F5  H14  C01  C03  122.25  3.000
 0F5  N05  C01  C03  120.66  3.000
 0F5  C06  N05  C01  118.81  3.000
 0F5  H15  C06  C04  121.72  3.000
 0F5  H15  C06  N05  117.20  3.000
 0F5  C04  C06  N05  121.08  3.000
 0F5  N28  C04  C06  123.03  3.000
 0F5  N28  C04  N02  117.30  3.000
 0F5  C06  C04  N02  119.66  3.000
 0F5  H16  N28  C04  115.49  3.000
 0F5  H16  N28  C21  117.63  3.000
 0F5  C04  N28  C21  125.20  3.000
 0F5  H18  C23  H17  106.67  3.000
 0F5  H18  C23  C24  109.87  3.000
 0F5  H17  C23  C24  108.78  3.000
 0F5  H18  C23  C22  109.56  3.000
 0F5  H17  C23  C22  109.81  3.000
 0F5  C24  C23  C22  112.01  3.000
 0F5  H20  N27  H19  105.38  3.000
 0F5  H20  N27  C24  109.41  3.000
 0F5  H19  N27  C24  109.39  3.000
 0F5  H23  C25  H22  106.68  3.000
 0F5  H23  C25  C26  109.80  3.000
 0F5  H22  C25  C26  109.81  3.000
 0F5  H23  C25  C24  110.13  3.000
 0F5  H22  C25  C24  108.72  3.000
 0F5  C26  C25  C24  111.57  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
 0F5  CONST_01  C07  C11  C12  C10    0.00   0.0  0
 0F5  CONST_02  C07  C09  C08  C10    0.00   0.0  0
 0F5  CONST_03  C03  C07  C11  C12  180.00   0.0  0
 0F5  CONST_04  C09  C07  C11  C12    0.00   0.0  0
 0F5  CONST_05  C09  C08  C10  C12    0.00   0.0  0
 0F5  CONST_08  C08  C09  C07  C11    0.00   0.0  0
 0F5  CONST_09  C08  C10  C12  C11    0.00   0.0  0
 0F5  CONST_10  C03  C07  C09  C08  180.00   0.0  0
 0F5  CONST_13  N05  C01  C03  C07  180.00   0.0  0
 0F5  CONST_14  C04  N02  C03  C07  180.00   0.0  0
 0F5  CONST_15  C06  N05  C01  C03    0.00   0.0  0
 0F5  CONST_16  C06  C04  N02  C03    0.00   0.0  0
 0F5  CONST_17  N05  C06  C04  N02    0.00   0.0  0
 0F5  CONST_18  N05  C01  C03  N02    0.00   0.0  0
 0F5  CONST_19  C04  C06  N05  C01    0.00   0.0  0
 0F5  CONST_20  C04  N02  C03  C01    0.00   0.0  0
 0F5  CONST_21  C14  C15  N16  C17    0.00   0.0  0
 0F5  CONST_22  C07  C11  C12  C13  180.00   0.0  0
 0F5  CONST_23  C08  C10  C12  C13  180.00   0.0  0
 0F5  CONST_24  N28  C04  N02  C03  180.00   0.0  0
 0F5  CONST_25  N28  C04  C06  N05  180.00   0.0  0
 0F5  CONST_26  C06  C04  N28  C21    0.00   0.0  0
 0F5  CONST_27  N02  C04  N28  C21  180.00   0.0  0
 0F5  CONST_28  O19  C15  N16  C17  180.00   0.0  0
 0F5  CONST_29  H11  C11  C12  C10  180.00   0.0  0
 0F5  CONST_30  H13  C09  C08  C10  180.00   0.0  0
 0F5  CONST_31  H12  C08  C10  C12  180.00   0.0  0
 0F5  CONST_32  H1   C10  C12  C11  180.00   0.0  0
 0F5  CONST_33  H14  C01  C03  C07    0.00   0.0  0
 0F5  CONST_34  H15  C06  C04  N02  180.00   0.0  0
 0F5  CONST_35  H10  N16  C15  C14  180.00   0.0  0
 0F5  CONST_36  H16  N28  C04  N02    0.00   0.0  0
 0F5  Var_01    C24  C23  C22  C21  -55.99  30.0  1
 0F5  Var_02    C24  C25  C26  C21   56.66  30.0  1
 0F5  Var_03    C14  C13  C12  C10   18.46  30.0  2
 0F5  Var_04    C12  C13  C14  C15  179.03  30.0  2

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
 0F5  chir_01  C21  N28  C22  C26  negativ
 0F5  chir_02  C24  N27  C23  C25  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
 0F5  plan-1  C13  0.020
 0F5  plan-1  C15  0.020
 0F5  plan-1  C17  0.020
 0F5  plan-1  O19  0.020
 0F5  plan-1  N16  0.020
 0F5  plan-1  O20  0.020
 0F5  plan-1  S18  0.020
 0F5  plan-1  C14  0.020
 0F5  plan-1  H10  0.020
 0F5  plan-2  C10  0.020
 0F5  plan-2  C13  0.020
 0F5  plan-2  C12  0.020
 0F5  plan-2  C11  0.020
 0F5  plan-2  C08  0.020
 0F5  plan-2  C09  0.020
 0F5  plan-2  C07  0.020
 0F5  plan-2  C03  0.020
 0F5  plan-2  H1   0.020
 0F5  plan-2  H11  0.020
 0F5  plan-2  H12  0.020
 0F5  plan-2  H13  0.020
 0F5  plan-3  C07  0.020
 0F5  plan-3  C03  0.020
 0F5  plan-3  N02  0.020
 0F5  plan-3  C01  0.020
 0F5  plan-3  N05  0.020
 0F5  plan-3  C06  0.020
 0F5  plan-3  C04  0.020
 0F5  plan-3  N28  0.020
 0F5  plan-3  H14  0.020
 0F5  plan-3  H15  0.020
 0F5  plan-4  C21  0.020
 0F5  plan-4  C04  0.020
 0F5  plan-4  N28  0.020
 0F5  plan-4  H16  0.020

