# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:38:42 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc2C(=O)N([C@H]3CCC(=O)NC3=O)C(=O)c2c1
#
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
 F4U  F4U  2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione  ligand  30  20  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F4U
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
 F4U  N    N  NR5   0  -0.619  -28.5222  -17.9568   -8.1061
 F4U  CA   C  CR16  0  -0.238  -28.7199  -18.6260   -6.8508
 F4U  C    C  CR6   0   0.587  -28.9152  -20.1149   -7.0918
 F4U  O    O  O     0  -0.415  -28.4664  -20.6862   -8.0554
 F4U  CB   C  C     0  -0.457  -29.8308  -18.0263   -5.9996
 F4U  CG   C  C     0  -0.597  -29.9546  -18.8186   -4.7100
 F4U  CD   C  CR6   0   0.556  -30.1414  -20.2896   -4.9440
 F4U  OE1  O  O     0  -0.428  -30.6977  -21.0320   -4.1690
 F4U  NE2  N  NR16  0  -0.690  -29.6066  -20.7904   -6.1172
 F4U  CAA  C  CR16  0  -0.437  -29.3078  -16.9567  -11.5091
 F4U  CAB  C  CR6   0   0.392  -28.5041  -16.1812  -12.3540
 F4U  CAC  C  CR16  0  -0.331  -27.2573  -15.7120  -11.9197
 F4U  CAD  C  CR16  0  -0.279  -26.7862  -16.0019  -10.6489
 F4U  CAE  C  CR56  0  -0.074  -27.5848  -16.7671   -9.8200
 F4U  CAF  C  CR56  0   0.005  -28.8162  -17.2259  -10.2544
 F4U  CAG  C  CR5   0   0.589  -27.3736  -17.2393   -8.4420
 F4U  CAI  C  CR5   0   0.599  -29.4290  -18.0046   -9.1524
 F4U  OAR  O  O     0  -0.397  -30.4904  -18.5733   -9.1285
 F4U  OAS  O  O     0  -0.400  -26.4295  -17.0693   -7.7137
 F4U  OAT  O  OH1   0  -0.612  -28.8801  -15.8547  -13.5942
 F4U  H1   H  HCR6  0   0.336  -27.7795  -18.5381   -6.2939
 F4U  H2   H  H     0   0.283  -29.5906  -16.9882   -5.7747
 F4U  H3   H  H     0   0.269  -30.7783  -18.0349   -6.5394
 F4U  H4   H  H     0   0.296  -29.0499  -18.7023   -4.1032
 F4U  H5   H  H     0   0.300  -30.7857  -18.4600   -4.1045
 F4U  H6   H  HNR6  0   0.420  -29.7114  -21.7889   -6.2638
 F4U  H7   H  HCR6  0   0.292  -30.2729  -17.3288  -11.8320
 F4U  H8   H  HCR6  0   0.287  -26.6613  -15.1121  -12.5952
 F4U  H9   H  HCR6  0   0.278  -25.8213  -15.6333  -10.3275
 F4U  H10  H  HOH1  0   0.485  -29.7540  -16.2085  -13.7984

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
 F4U  OAT  CAB  single    1.336  0.020  1.336
 F4U  CAB  CAC  aromatic  1.401  0.020  1.401
 F4U  CAB  CAA  aromatic  1.400  0.020  1.400
 F4U  CAC  CAD  aromatic  1.386  0.020  1.386
 F4U  CAA  CAF  aromatic  1.374  0.020  1.374
 F4U  CAD  CAE  aromatic  1.382  0.020  1.382
 F4U  CAF  CAE  aromatic  1.384  0.020  1.384
 F4U  CAF  CAI  single    1.482  0.020  1.482
 F4U  CAE  CAG  single    1.472  0.020  1.472
 F4U  OAR  CAI  double    1.204  0.020  1.204
 F4U  CAI  N    single    1.385  0.020  1.385
 F4U  CAG  N    single    1.395  0.020  1.395
 F4U  CAG  OAS  double    1.204  0.020  1.204
 F4U  N    CA   single    1.436  0.020  1.436
 F4U  O    C    double    1.207  0.020  1.207
 F4U  C    CA   single    1.521  0.020  1.521
 F4U  C    NE2  single    1.373  0.020  1.373
 F4U  CA   CB   single    1.523  0.020  1.523
 F4U  NE2  CD   single    1.383  0.020  1.383
 F4U  CB   CG   single    1.519  0.020  1.519
 F4U  CD   CG   single    1.501  0.020  1.501
 F4U  CD   OE1  double    1.209  0.020  1.209
 F4U  CA   H1   single    0.970  0.020  1.090
 F4U  CB   H2   single    0.970  0.020  1.090
 F4U  CB   H3   single    0.970  0.020  1.090
 F4U  CG   H4   single    0.970  0.020  1.090
 F4U  CG   H5   single    0.970  0.020  1.090
 F4U  NE2  H6   single    0.860  0.020  1.020
 F4U  CAA  H7   single    0.930  0.020  1.080
 F4U  CAC  H8   single    0.930  0.020  1.080
 F4U  CAD  H9   single    0.930  0.020  1.080
 F4U  OAT  H10  single    0.850  0.020  0.980

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
 F4U  CAI  N    CAG  112.01  3.000
 F4U  CAG  N    CA   124.28  3.000
 F4U  CAI  N    CA   123.64  3.000
 F4U  H1   CA   CB   108.08  3.000
 F4U  H1   CA   C    105.61  3.000
 F4U  CB   CA   C    112.36  3.000
 F4U  H1   CA   N    106.77  3.000
 F4U  CB   CA   N    113.93  3.000
 F4U  C    CA   N    109.59  3.000
 F4U  NE2  C    O    121.41  3.000
 F4U  NE2  C    CA   115.72  3.000
 F4U  O    C    CA   122.84  3.000
 F4U  H3   CB   H2   107.54  3.000
 F4U  H3   CB   CG   110.21  3.000
 F4U  H2   CB   CG   109.87  3.000
 F4U  H3   CB   CA   110.74  3.000
 F4U  H2   CB   CA   109.26  3.000
 F4U  CG   CB   CA   109.19  3.000
 F4U  H5   CG   H4   106.70  3.000
 F4U  H5   CG   CD   108.32  3.000
 F4U  H4   CG   CD   107.04  3.000
 F4U  H5   CG   CB   111.26  3.000
 F4U  H4   CG   CB   110.35  3.000
 F4U  CD   CG   CB   112.89  3.000
 F4U  NE2  CD   OE1  119.96  3.000
 F4U  OE1  CD   CG   123.99  3.000
 F4U  NE2  CD   CG   116.03  3.000
 F4U  H6   NE2  CD   116.03  3.000
 F4U  H6   NE2  C    115.71  3.000
 F4U  CD   NE2  C    128.22  3.000
 F4U  H7   CAA  CAF  121.56  3.000
 F4U  H7   CAA  CAB  121.44  3.000
 F4U  CAF  CAA  CAB  117.00  3.000
 F4U  OAT  CAB  CAC  117.14  3.000
 F4U  CAC  CAB  CAA  120.61  3.000
 F4U  OAT  CAB  CAA  122.25  3.000
 F4U  H8   CAC  CAD  120.07  3.000
 F4U  H8   CAC  CAB  118.83  3.000
 F4U  CAD  CAC  CAB  121.10  3.000
 F4U  H9   CAD  CAE  121.73  3.000
 F4U  H9   CAD  CAC  120.28  3.000
 F4U  CAE  CAD  CAC  117.99  3.000
 F4U  CAG  CAE  CAF  108.37  3.000
 F4U  CAG  CAE  CAD  131.01  3.000
 F4U  CAF  CAE  CAD  120.62  3.000
 F4U  CAI  CAF  CAE  107.98  3.000
 F4U  CAI  CAF  CAA  129.34  3.000
 F4U  CAE  CAF  CAA  122.68  3.000
 F4U  OAS  CAG  CAE  129.30  3.000
 F4U  OAS  CAG  N    124.91  3.000
 F4U  CAE  CAG  N    105.79  3.000
 F4U  OAR  CAI  CAF  128.85  3.000
 F4U  OAR  CAI  N    125.32  3.000
 F4U  CAF  CAI  N    105.84  3.000
 F4U  H10  OAT  CAB  111.20  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
 F4U  CONST_01  CAD  CAC  CAB  CAA    0.00   0.0  0
 F4U  CONST_02  CAD  CAE  CAF  CAA    0.00   0.0  0
 F4U  CONST_03  CAE  CAD  CAC  CAB    0.00   0.0  0
 F4U  CONST_04  CAE  CAF  CAA  CAB    0.00   0.0  0
 F4U  CONST_05  CAF  CAA  CAB  CAC    0.00   0.0  0
 F4U  CONST_06  CAF  CAE  CAD  CAC    0.00   0.0  0
 F4U  CONST_07  CAE  CAG  N    CA   180.00   0.0  0
 F4U  CONST_08  CD   NE2  C    CA     0.00   0.0  0
 F4U  CONST_09  CAI  N    CAG  CAE    0.00   0.0  0
 F4U  CONST_10  OAT  CAB  CAC  CAD  180.00   0.0  0
 F4U  CONST_11  OAT  CAB  CAA  CAF  180.00   0.0  0
 F4U  CONST_12  OAS  CAG  N    CA     0.00   0.0  0
 F4U  CONST_13  CD   NE2  C    O    180.00   0.0  0
 F4U  CONST_14  OAS  CAG  N    CAI  180.00   0.0  0
 F4U  CONST_15  H8   CAC  CAB  CAA  180.00   0.0  0
 F4U  CONST_16  H9   CAD  CAC  CAB  180.00   0.0  0
 F4U  CONST_17  H7   CAA  CAB  CAC  180.00   0.0  0
 F4U  CONST_18  H6   NE2  C    CA   180.00   0.0  0
 F4U  Var_01    CD   CG   CB   CA   -54.10  30.0  1
 F4U  Var_02    CG   CD   NE2  C      0.62  30.0  1
 F4U  Var_03    NE2  CD   CG   CB    27.59  30.0  1

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
 F4U  chir_01  CA  N  C  CB  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
 F4U  plan-1  N    0.020
 F4U  plan-1  CA   0.020
 F4U  plan-1  CAA  0.020
 F4U  plan-1  CAB  0.020
 F4U  plan-1  CAC  0.020
 F4U  plan-1  CAD  0.020
 F4U  plan-1  CAE  0.020
 F4U  plan-1  CAF  0.020
 F4U  plan-1  CAG  0.020
 F4U  plan-1  CAI  0.020
 F4U  plan-1  OAR  0.020
 F4U  plan-1  OAS  0.020
 F4U  plan-1  OAT  0.020
 F4U  plan-1  H7   0.020
 F4U  plan-1  H8   0.020
 F4U  plan-1  H9   0.020
 F4U  plan-2  CA   0.020
 F4U  plan-2  C    0.020
 F4U  plan-2  O    0.020
 F4U  plan-2  CD   0.020
 F4U  plan-2  NE2  0.020
 F4U  plan-2  H6   0.020
 F4U  plan-3  CG   0.020
 F4U  plan-3  CD   0.020
 F4U  plan-3  OE1  0.020
 F4U  plan-3  NE2  0.020

