# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 19:00:26 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC[C@@H](N2C(=O)c3ccccc3C2=O)C(=O)N1
#
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
 6EL  6EL  2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]isoindole-1,3-dione  ligand  29  19  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6EL
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
 6EL  O    O  O     0  -0.415  -1.2500   0.3609   2.0290
 6EL  C    C  C     0   0.587  -1.8550   0.1023   1.0174
 6EL  NE2  N  NH1   0  -0.690  -3.1925   0.3828   0.8908
 6EL  CD   C  C     0   0.556  -4.0262   0.1097  -0.1785
 6EL  OE1  O  O     0  -0.427  -5.1997   0.3930  -0.1169
 6EL  CG   C  CH2   0  -0.597  -3.3861  -0.5631  -1.3587
 6EL  CB   C  CH2   0  -0.460  -1.9056  -0.2471  -1.4845
 6EL  CA   C  CH1   0  -0.240  -1.2121  -0.5906  -0.1737
 6EL  N    N  NR5   0  -0.617   0.2014  -0.3318  -0.1752
 6EL  CAN  C  CR5   0   0.598   0.7516   0.9429  -0.2205
 6EL  OAC  O  O     0  -0.396   0.1210   1.9655  -0.2970
 6EL  CAO  C  CR5   0   0.591   1.1745  -1.3180  -0.0636
 6EL  OAD  O  O     0  -0.394   0.9620  -2.5000   0.0145
 6EL  CAQ  C  CR56  0  -0.036   2.4717  -0.6051  -0.0633
 6EL  CAP  C  CR56  0  -0.022   2.2174   0.7538  -0.1554
 6EL  CAH  C  CR16  0  -0.293   3.7562  -1.0988   0.0163
 6EL  CAF  C  CR16  0  -0.239   4.7957  -0.1704  -0.0002
 6EL  CAE  C  CR16  0  -0.239   4.5400   1.1949  -0.0923
 6EL  CAG  C  CR16  0  -0.294   3.2365   1.6816  -0.1714
 6EL  H1   H  HNH1  0   0.421  -3.6303   0.8143   1.6978
 6EL  H2   H  HCH2  0   0.297  -3.5350  -1.6411  -1.2363
 6EL  H3   H  HCH2  0   0.300  -3.9306  -0.2702  -2.2553
 6EL  H4   H  HCH2  0   0.284  -1.4665  -0.8345  -2.2899
 6EL  H5   H  HCH2  0   0.270  -1.7655   0.8056  -1.7321
 6EL  H6   H  HCH1  0   0.338  -1.3335  -1.6656   0.0059
 6EL  H7   H  HCR6  0   0.278   3.9538  -2.1598   0.0891
 6EL  H8   H  HCR6  0   0.281   5.8194  -0.5142   0.0614
 6EL  H9   H  HCR6  0   0.281   5.3686   1.8898  -0.1018
 6EL  H10  H  HCR6  0   0.277   3.0399   2.7431  -0.2403

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
 6EL  OE1  CD   double    1.209  0.020  1.209
 6EL  NE2  CD   single    1.383  0.020  1.383
 6EL  NE2  C    single    1.373  0.020  1.373
 6EL  O    C    double    1.207  0.020  1.207
 6EL  CD   CG   single    1.502  0.020  1.502
 6EL  C    CA   single    1.521  0.020  1.521
 6EL  CG   CB   single    1.519  0.020  1.519
 6EL  CA   CB   single    1.522  0.020  1.522
 6EL  CA   N    single    1.437  0.020  1.437
 6EL  OAD  CAO  double    1.203  0.020  1.203
 6EL  N    CAO  single    1.390  0.020  1.390
 6EL  N    CAN  single    1.389  0.020  1.389
 6EL  CAO  CAQ  single    1.480  0.020  1.480
 6EL  CAN  OAC  double    1.204  0.020  1.204
 6EL  CAN  CAP  single    1.479  0.020  1.479
 6EL  CAQ  CAP  aromatic  1.386  0.020  1.386
 6EL  CAQ  CAH  aromatic  1.378  0.020  1.378
 6EL  CAP  CAG  aromatic  1.378  0.020  1.378
 6EL  CAH  CAF  aromatic  1.394  0.020  1.394
 6EL  CAG  CAE  aromatic  1.394  0.020  1.394
 6EL  CAF  CAE  aromatic  1.392  0.020  1.392
 6EL  NE2  H1   single    0.860  0.020  1.020
 6EL  CG   H2   single    0.970  0.020  1.090
 6EL  CG   H3   single    0.970  0.020  1.090
 6EL  CB   H4   single    0.970  0.020  1.090
 6EL  CB   H5   single    0.970  0.020  1.090
 6EL  CA   H6   single    0.970  0.020  1.090
 6EL  CAH  H7   single    0.930  0.020  1.080
 6EL  CAF  H8   single    0.930  0.020  1.080
 6EL  CAE  H9   single    0.930  0.020  1.080
 6EL  CAG  H10  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
 6EL  CA   C    NE2  115.65  3.000
 6EL  CA   C    O    122.85  3.000
 6EL  NE2  C    O    121.47  3.000
 6EL  H1   NE2  CD   116.03  3.000
 6EL  H1   NE2  C    115.73  3.000
 6EL  CD   NE2  C    128.19  3.000
 6EL  CG   CD   OE1  123.98  3.000
 6EL  CG   CD   NE2  116.05  3.000
 6EL  OE1  CD   NE2  119.96  3.000
 6EL  H3   CG   H2   106.78  3.000
 6EL  H3   CG   CB   111.29  3.000
 6EL  H2   CG   CB   110.28  3.000
 6EL  H3   CG   CD   108.27  3.000
 6EL  H2   CG   CD   107.17  3.000
 6EL  CB   CG   CD   112.79  3.000
 6EL  H5   CB   H4   107.51  3.000
 6EL  H5   CB   CA   110.78  3.000
 6EL  H4   CB   CA   109.35  3.000
 6EL  H5   CB   CG   110.17  3.000
 6EL  H4   CB   CG   110.00  3.000
 6EL  CA   CB   CG   109.01  3.000
 6EL  H6   CA   N    106.59  3.000
 6EL  H6   CA   CB   108.17  3.000
 6EL  N    CA   CB   113.99  3.000
 6EL  H6   CA   C    105.76  3.000
 6EL  N    CA   C    109.55  3.000
 6EL  CB   CA   C    112.27  3.000
 6EL  CAO  N    CAN  112.11  3.000
 6EL  CAN  N    CA   123.70  3.000
 6EL  CAO  N    CA   124.11  3.000
 6EL  CAP  CAN  OAC  129.08  3.000
 6EL  CAP  CAN  N    105.88  3.000
 6EL  OAC  CAN  N    125.03  3.000
 6EL  CAQ  CAO  OAD  128.88  3.000
 6EL  CAQ  CAO  N    105.77  3.000
 6EL  OAD  CAO  N    125.34  3.000
 6EL  CAH  CAQ  CAP  121.74  3.000
 6EL  CAH  CAQ  CAO  130.11  3.000
 6EL  CAP  CAQ  CAO  108.15  3.000
 6EL  CAG  CAP  CAQ  121.69  3.000
 6EL  CAG  CAP  CAN  130.24  3.000
 6EL  CAQ  CAP  CAN  108.06  3.000
 6EL  H7   CAH  CAF  121.19  3.000
 6EL  H7   CAH  CAQ  121.70  3.000
 6EL  CAF  CAH  CAQ  117.12  3.000
 6EL  H8   CAF  CAE  119.29  3.000
 6EL  H8   CAF  CAH  119.57  3.000
 6EL  CAE  CAF  CAH  121.13  3.000
 6EL  H9   CAE  CAG  119.45  3.000
 6EL  H9   CAE  CAF  119.35  3.000
 6EL  CAG  CAE  CAF  121.20  3.000
 6EL  H10  CAG  CAE  121.08  3.000
 6EL  H10  CAG  CAP  121.79  3.000
 6EL  CAE  CAG  CAP  117.12  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
 6EL  CONST_01  CAE  CAG  CAP  CAQ    0.00   0.0  0
 6EL  CONST_02  CAE  CAF  CAH  CAQ    0.00   0.0  0
 6EL  CONST_03  CAF  CAH  CAQ  CAP    0.00   0.0  0
 6EL  CONST_04  CAF  CAE  CAG  CAP    0.00   0.0  0
 6EL  CONST_05  CAG  CAP  CAQ  CAH    0.00   0.0  0
 6EL  CONST_06  CAG  CAE  CAF  CAH    0.00   0.0  0
 6EL  CONST_07  CA   C    NE2  CD     0.00   0.0  0
 6EL  CONST_08  CAP  CAN  N    CA   180.00   0.0  0
 6EL  CONST_09  CAP  CAN  N    CAO    0.00   0.0  0
 6EL  CONST_10  CD   NE2  C    O    180.00   0.0  0
 6EL  CONST_11  OAC  CAN  N    CA     0.00   0.0  0
 6EL  CONST_12  CAO  N    CAN  OAC  180.00   0.0  0
 6EL  CONST_13  H10  CAG  CAP  CAN    0.00   0.0  0
 6EL  CONST_14  H7   CAH  CAQ  CAO    0.00   0.0  0
 6EL  CONST_15  H8   CAF  CAH  CAQ  180.00   0.0  0
 6EL  CONST_16  H9   CAE  CAG  CAP  180.00   0.0  0
 6EL  CONST_17  H1   NE2  C    CA   180.00   0.0  0
 6EL  Var_01    CG   CD   NE2  C     -0.86  30.0  1
 6EL  Var_02    CB   CG   CD   NE2  -27.52  30.0  1
 6EL  Var_03    CA   CB   CG   CD    54.38  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
 6EL  chir_01  CA  C  CB  N  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
 6EL  plan-1  CA   0.020
 6EL  plan-1  N    0.020
 6EL  plan-1  CAN  0.020
 6EL  plan-1  OAC  0.020
 6EL  plan-1  CAO  0.020
 6EL  plan-1  OAD  0.020
 6EL  plan-1  CAQ  0.020
 6EL  plan-1  CAP  0.020
 6EL  plan-1  CAH  0.020
 6EL  plan-1  CAF  0.020
 6EL  plan-1  CAE  0.020
 6EL  plan-1  CAG  0.020
 6EL  plan-1  H7   0.020
 6EL  plan-1  H8   0.020
 6EL  plan-1  H9   0.020
 6EL  plan-1  H10  0.020
 6EL  plan-2  O    0.020
 6EL  plan-2  C    0.020
 6EL  plan-2  NE2  0.020
 6EL  plan-2  CD   0.020
 6EL  plan-2  CA   0.020
 6EL  plan-2  H1   0.020
 6EL  plan-3  NE2  0.020
 6EL  plan-3  CD   0.020
 6EL  plan-3  OE1  0.020
 6EL  plan-3  CG   0.020

