# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 10:23:25 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (6~{Z})-3-[[2,5-bis(fluoranyl)phenyl]methylidene]-6-[(4-~{tert}-butyl-1~{H}-imidazol-5-yl)methylidene]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1nc[nH]c1\C=C2/NC(=O)\C(NC2=O)=C\c3cc(F)ccc3F
#
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
 PO7  PO7  (6~{Z})-3-[[2,5-bis(fluoranyl)phenyl]methylidene]-6-[(4-~{tert}-butyl-1~{H}-imidazol-5-yl)methylidene]piperazine-2,5-dione  ligand  45  27  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PO7
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
 PO7  FAG  F  F     0  -0.300   5.1681  -1.8143  -1.4677
 PO7  CAS  C  CR6   0   0.520   5.2064  -0.6958  -0.7295
 PO7  CAK  C  CR16  0  -0.387   6.3588   0.0615  -0.7263
 PO7  CAJ  C  CR16  0  -0.400   6.4053   1.2215   0.0328
 PO7  CAR  C  CR6   0   0.543   5.2891   1.5755   0.7656
 PO7  FAF  F  F     0  -0.311   5.3313   2.6851   1.5172
 PO7  CAM  C  CR16  0  -0.459   4.1345   0.8205   0.7632
 PO7  CAT  C  CR6   0  -0.091   4.0703  -0.3447  -0.0059
 PO7  CAH  C  C1    0  -0.330   2.8898  -1.2064  -0.0294
 PO7  CAY  C  CR6   0   0.226   1.6163  -0.7973  -0.1211
 PO7  CAW  C  CR6   0   0.544   0.5301  -1.8126  -0.0711
 PO7  OAD  O  O     0  -0.446   0.7503  -3.0088  -0.0793
 PO7  NAQ  N  NR16  0  -0.756  -0.7269  -1.3137  -0.0152
 PO7  NAP  N  NR16  0  -0.749   1.2360   0.5208  -0.3188
 PO7  CAX  C  CR6   0   0.548  -0.0269   1.0190  -0.2849
 PO7  OAE  O  O     0  -0.452  -0.2490   2.2031  -0.4597
 PO7  CAZ  C  CR6   0   0.218  -1.0908   0.0304  -0.0080
 PO7  CAI  C  C1    0  -0.397  -2.3468   0.4653   0.2029
 PO7  CAU  C  CR5   0   0.307  -3.5023  -0.3026   0.5802
 PO7  NAN  N  NR15  0  -0.636  -3.4537  -1.4651   1.3179
 PO7  CAL  C  CR15  0   0.101  -4.7122  -1.8881   1.4958
 PO7  NAO  N  N     0  -0.448  -5.5743  -1.0973   0.9049
 PO7  CAV  C  CR5   0   0.197  -4.8520  -0.0969   0.3330
 PO7  CBA  C  CT    0  -0.207  -5.5133   1.0229  -0.4366
 PO7  CAB  C  CH3   0  -0.637  -4.8861   1.1626  -1.8296
 PO7  CAC  C  CH3   0  -0.630  -7.0064   0.7374  -0.6034
 PO7  CAA  C  CH3   0  -0.639  -5.3507   2.3409   0.3351
 PO7  H1   H  HCR6  0   0.297   7.2138  -0.2469  -1.3128
 PO7  H2   H  HCR6  0   0.297   7.2981   1.8317   0.0552
 PO7  H3   H  HCR6  0   0.304   3.3011   1.1177   1.3871
 PO7  H4   H  H     0   0.290   3.0479  -2.2755   0.0224
 PO7  H6   H  HNR6  0   0.419  -1.4635  -2.0039  -0.0813
 PO7  H7   H  H     0   0.278  -2.4974   1.5272   0.0675
 PO7  H8   H  HNR5  0   0.422  -2.6487  -1.8487   1.7894
 PO7  H9   H  HCR5  0   0.286  -4.9483  -2.7715   2.0685
 PO7  H11  H  HCH3  0   0.230  -4.9738   0.2362  -2.3997
 PO7  H12  H  HCH3  0   0.230  -5.3923   1.9502  -2.3920
 PO7  H13  H  HCH3  0   0.228  -3.8294   1.4266  -1.7834
 PO7  H14  H  HCH3  0   0.226  -7.5195   0.6755   0.3564
 PO7  H15  H  HCH3  0   0.224  -7.4681   1.5421  -1.1781
 PO7  H16  H  HCH3  0   0.225  -7.1834  -0.1980  -1.1352
 PO7  H17  H  HCH3  0   0.230  -4.3044   2.6276   0.4502
 PO7  H18  H  HCH3  0   0.230  -5.8531   3.1547  -0.1917
 PO7  H19  H  HCH3  0   0.231  -5.7868   2.2669   1.3326
 PO7  H5   H  HNR6  0   0.426   1.9609   1.1952  -0.5314

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
 PO7  NAO  CAL  aromatic  1.311  0.020  1.311
 PO7  NAO  CAV  aromatic  1.360  0.020  1.360
 PO7  CAB  CBA  single    1.534  0.020  1.534
 PO7  CAL  NAN  aromatic  1.340  0.020  1.340
 PO7  CAV  CBA  single    1.511  0.020  1.511
 PO7  CAV  CAU  aromatic  1.388  0.020  1.388
 PO7  CBA  CAC  single    1.529  0.020  1.529
 PO7  CBA  CAA  single    1.536  0.020  1.536
 PO7  NAN  CAU  aromatic  1.378  0.020  1.378
 PO7  CAU  CAI  single    1.438  0.020  1.438
 PO7  CAI  CAZ  double    1.346  0.020  1.346
 PO7  NAQ  CAZ  single    1.393  0.020  1.393
 PO7  NAQ  CAW  single    1.354  0.020  1.354
 PO7  CAZ  CAX  single    1.478  0.020  1.478
 PO7  OAD  CAW  double    1.216  0.020  1.216
 PO7  CAW  CAY  single    1.488  0.020  1.488
 PO7  CAX  OAE  double    1.217  0.020  1.217
 PO7  CAX  NAP  single    1.358  0.020  1.358
 PO7  CAY  NAP  single    1.386  0.020  1.386
 PO7  CAY  CAH  double    1.341  0.020  1.341
 PO7  CAH  CAT  single    1.462  0.020  1.462
 PO7  CAT  CAM  aromatic  1.398  0.020  1.398
 PO7  CAT  CAS  aromatic  1.392  0.020  1.392
 PO7  CAM  CAR  aromatic  1.379  0.020  1.379
 PO7  FAG  CAS  single    1.341  0.020  1.341
 PO7  CAS  CAK  aromatic  1.379  0.020  1.379
 PO7  CAR  FAF  single    1.341  0.020  1.341
 PO7  CAR  CAJ  aromatic  1.381  0.020  1.381
 PO7  CAK  CAJ  aromatic  1.387  0.020  1.387
 PO7  CAK  H1   single    0.930  0.020  1.080
 PO7  CAJ  H2   single    0.930  0.020  1.080
 PO7  CAM  H3   single    0.930  0.020  1.080
 PO7  CAH  H4   single    0.930  0.020  1.080
 PO7  NAQ  H6   single    0.860  0.020  1.020
 PO7  CAI  H7   single    0.930  0.020  1.080
 PO7  NAN  H8   single    0.860  0.020  1.020
 PO7  CAL  H9   single    0.930  0.020  1.080
 PO7  CAB  H11  single    0.970  0.020  1.090
 PO7  CAB  H12  single    0.970  0.020  1.090
 PO7  CAB  H13  single    0.970  0.020  1.090
 PO7  CAC  H14  single    0.970  0.020  1.090
 PO7  CAC  H15  single    0.970  0.020  1.090
 PO7  CAC  H16  single    0.970  0.020  1.090
 PO7  CAA  H17  single    0.970  0.020  1.090
 PO7  CAA  H18  single    0.970  0.020  1.090
 PO7  CAA  H19  single    0.970  0.020  1.090
 PO7  NAP  H5   single    0.860  0.020  1.020

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
 PO7  CAT  CAS  CAK  122.84  3.000
 PO7  CAK  CAS  FAG  118.90  3.000
 PO7  CAT  CAS  FAG  118.26  3.000
 PO7  H1   CAK  CAJ  120.57  3.000
 PO7  H1   CAK  CAS  120.18  3.000
 PO7  CAJ  CAK  CAS  119.25  3.000
 PO7  H2   CAJ  CAR  120.76  3.000
 PO7  H2   CAJ  CAK  120.72  3.000
 PO7  CAR  CAJ  CAK  118.52  3.000
 PO7  CAM  CAR  FAF  118.70  3.000
 PO7  FAF  CAR  CAJ  118.94  3.000
 PO7  CAM  CAR  CAJ  122.35  3.000
 PO7  H3   CAM  CAT  120.71  3.000
 PO7  H3   CAM  CAR  119.53  3.000
 PO7  CAT  CAM  CAR  119.72  3.000
 PO7  CAH  CAT  CAM  122.51  3.000
 PO7  CAM  CAT  CAS  117.31  3.000
 PO7  CAH  CAT  CAS  120.14  3.000
 PO7  H4   CAH  CAY  116.33  3.000
 PO7  H4   CAH  CAT  117.63  3.000
 PO7  CAY  CAH  CAT  126.04  3.000
 PO7  NAP  CAY  CAW  116.97  3.000
 PO7  NAP  CAY  CAH  124.10  3.000
 PO7  CAW  CAY  CAH  118.88  3.000
 PO7  NAQ  CAW  OAD  122.07  3.000
 PO7  OAD  CAW  CAY  122.60  3.000
 PO7  NAQ  CAW  CAY  115.33  3.000
 PO7  H6   NAQ  CAZ  117.95  3.000
 PO7  H6   NAQ  CAW  114.96  3.000
 PO7  CAZ  NAQ  CAW  126.78  3.000
 PO7  H5   NAP  CAX  115.25  3.000
 PO7  H5   NAP  CAY  117.83  3.000
 PO7  CAX  NAP  CAY  126.91  3.000
 PO7  CAZ  CAX  OAE  123.09  3.000
 PO7  OAE  CAX  NAP  121.53  3.000
 PO7  CAZ  CAX  NAP  115.38  3.000
 PO7  CAI  CAZ  CAX  119.00  3.000
 PO7  CAX  CAZ  NAQ  117.16  3.000
 PO7  CAI  CAZ  NAQ  123.82  3.000
 PO7  H7   CAI  CAU  116.46  3.000
 PO7  H7   CAI  CAZ  115.32  3.000
 PO7  CAU  CAI  CAZ  128.21  3.000
 PO7  CAV  CAU  NAN  104.76  3.000
 PO7  NAN  CAU  CAI  124.26  3.000
 PO7  CAV  CAU  CAI  130.98  3.000
 PO7  H8   NAN  CAL  124.58  3.000
 PO7  H8   NAN  CAU  126.82  3.000
 PO7  CAL  NAN  CAU  107.73  3.000
 PO7  H9   CAL  NAO  126.11  3.000
 PO7  H9   CAL  NAN  122.32  3.000
 PO7  NAO  CAL  NAN  111.57  3.000
 PO7  CAV  NAO  CAL  106.51  3.000
 PO7  CBA  CAV  NAO  121.79  3.000
 PO7  CBA  CAV  CAU  128.78  3.000
 PO7  NAO  CAV  CAU  109.43  3.000
 PO7  CAA  CBA  CAC  108.56  3.000
 PO7  CAA  CBA  CAB  109.56  3.000
 PO7  CAC  CBA  CAB  108.49  3.000
 PO7  CAA  CBA  CAV  109.49  3.000
 PO7  CAC  CBA  CAV  110.15  3.000
 PO7  CAB  CBA  CAV  110.55  3.000
 PO7  H13  CAB  H12  107.24  3.000
 PO7  H13  CAB  H11  107.79  3.000
 PO7  H12  CAB  H11  107.82  3.000
 PO7  H13  CAB  CBA  112.32  3.000
 PO7  H12  CAB  CBA  110.11  3.000
 PO7  H11  CAB  CBA  111.36  3.000
 PO7  H16  CAC  H15  107.88  3.000
 PO7  H16  CAC  H14  107.71  3.000
 PO7  H15  CAC  H14  107.84  3.000
 PO7  H16  CAC  CBA  111.83  3.000
 PO7  H15  CAC  CBA  109.44  3.000
 PO7  H14  CAC  CBA  111.97  3.000
 PO7  H19  CAA  H18  107.92  3.000
 PO7  H19  CAA  H17  107.73  3.000
 PO7  H18  CAA  H17  107.23  3.000
 PO7  H19  CAA  CBA  111.03  3.000
 PO7  H18  CAA  CBA  110.40  3.000
 PO7  H17  CAA  CBA  112.34  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
 PO7  CONST_01  CAR  CAM  CAT  CAS     0.00   0.0  0
 PO7  CONST_02  CAR  CAJ  CAK  CAS     0.00   0.0  0
 PO7  CONST_03  CAM  CAT  CAS  CAK     0.00   0.0  0
 PO7  CONST_04  CAM  CAR  CAJ  CAK     0.00   0.0  0
 PO7  CONST_05  CAT  CAM  CAR  CAJ     0.00   0.0  0
 PO7  CONST_06  CAT  CAS  CAK  CAJ     0.00   0.0  0
 PO7  CONST_07  CAL  NAO  CAV  CAU     0.00   0.0  0
 PO7  CONST_08  NAO  CAL  NAN  CAU     0.00   0.0  0
 PO7  CONST_09  CAV  NAO  CAL  NAN     0.00   0.0  0
 PO7  CONST_10  NAO  CAV  CAU  NAN     0.00   0.0  0
 PO7  CONST_11  CAV  CAU  NAN  CAL     0.00   0.0  0
 PO7  CONST_12  CAZ  NAQ  CAW  CAY     0.00   0.0  0
 PO7  CONST_13  CAZ  CAX  NAP  CAY     0.00   0.0  0
 PO7  CONST_14  CAM  CAT  CAS  FAG   180.00   0.0  0
 PO7  CONST_15  CAJ  CAK  CAS  FAG   180.00   0.0  0
 PO7  CONST_16  CAH  CAT  CAS  CAK   180.00   0.0  0
 PO7  CONST_17  FAF  CAR  CAJ  CAK   180.00   0.0  0
 PO7  CONST_18  CAH  CAT  CAM  CAR   180.00   0.0  0
 PO7  CONST_19  CAT  CAM  CAR  FAF   180.00   0.0  0
 PO7  CONST_20  NAO  CAV  CAU  CAI   180.00   0.0  0
 PO7  CONST_21  CAL  NAN  CAU  CAI   180.00   0.0  0
 PO7  CONST_22  CBA  CAV  CAU  NAN   180.00   0.0  0
 PO7  CONST_23  CBA  CAV  NAO  CAL   180.00   0.0  0
 PO7  CONST_24  OAE  CAX  NAP  CAY   180.00   0.0  0
 PO7  CONST_25  CAZ  NAQ  CAW  OAD   180.00   0.0  0
 PO7  CONST_26  H3   CAM  CAT  CAS   180.00   0.0  0
 PO7  CONST_27  H2   CAJ  CAK  CAS   180.00   0.0  0
 PO7  CONST_28  H1   CAK  CAJ  CAR   180.00   0.0  0
 PO7  CONST_29  H9   CAL  NAN  CAU   180.00   0.0  0
 PO7  CONST_30  H8   NAN  CAL  NAO   180.00   0.0  0
 PO7  CONST_31  H6   NAQ  CAW  CAY   180.00   0.0  0
 PO7  CONST_32  H5   NAP  CAX  CAZ   180.00   0.0  0
 PO7  Var_01    CAY  CAH  CAT  CAS  -138.19  30.0  2
 PO7  Var_02    CAW  CAY  CAH  CAT  -177.34  30.0  2
 PO7  Var_03    CAU  CAI  CAZ  NAQ     6.57  30.0  2
 PO7  Var_04    CAV  CAU  CAI  CAZ  -151.68  30.0  3
 PO7  Var_05    CAB  CBA  CAV  CAU    52.71  30.0  2
 PO7  Var_06    H11  CAB  CBA  CAV    58.50  30.0  3
 PO7  Var_07    H14  CAC  CBA  CAV    61.65  30.0  3
 PO7  Var_08    H17  CAA  CBA  CAV    62.28  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
 PO7  plan-1  CAI  0.020
 PO7  plan-1  CAU  0.020
 PO7  plan-1  NAN  0.020
 PO7  plan-1  CAL  0.020
 PO7  plan-1  NAO  0.020
 PO7  plan-1  CAV  0.020
 PO7  plan-1  CBA  0.020
 PO7  plan-1  H8   0.020
 PO7  plan-1  H9   0.020
 PO7  plan-2  FAG  0.020
 PO7  plan-2  CAS  0.020
 PO7  plan-2  CAK  0.020
 PO7  plan-2  CAJ  0.020
 PO7  plan-2  CAR  0.020
 PO7  plan-2  FAF  0.020
 PO7  plan-2  CAM  0.020
 PO7  plan-2  CAT  0.020
 PO7  plan-2  CAH  0.020
 PO7  plan-2  H1   0.020
 PO7  plan-2  H2   0.020
 PO7  plan-2  H3   0.020
 PO7  plan-3  CAH  0.020
 PO7  plan-3  CAY  0.020
 PO7  plan-3  CAW  0.020
 PO7  plan-3  OAD  0.020
 PO7  plan-3  NAQ  0.020
 PO7  plan-3  NAP  0.020
 PO7  plan-3  CAX  0.020
 PO7  plan-3  OAE  0.020
 PO7  plan-3  CAZ  0.020
 PO7  plan-3  CAI  0.020
 PO7  plan-3  H6   0.020
 PO7  plan-3  H5   0.020

