# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:52:58 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-[(1R)-1-carboxy-2-naphthalen-1-ylethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1cccc2ccccc12)N3C(=O)c4ccc(cc4C3=O)C(O)=O
#
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
 23C  23C  '2-[(1R)-1-carboxy-2-naphthalen-1-ylethyl]-1,3-dioxo-2,3-dihydro-1H-isoindole-5-carboxylic acid'  ligand  44  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_23C
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
 23C  CD2  C  CR66  0   0.107  -2.9617   0.8771   0.2497
 23C  CAN  C  CR16  0  -0.338  -3.7621   0.4561  -0.8399
 23C  CAH  C  CR16  0  -0.249  -4.3537   1.3633  -1.6767
 23C  CAG  C  CR16  0  -0.261  -4.1776   2.7459  -1.4711
 23C  CAL  C  CR16  0  -0.309  -3.4193   3.1876  -0.4223
 23C  CAX  C  CR66  0   0.111  -2.7978   2.2733   0.4604
 23C  CAM  C  CR16  0  -0.332  -2.0206   2.7285   1.5508
 23C  CAI  C  CR16  0  -0.241  -1.4325   1.8347   2.3991
 23C  CD1  C  CR16  0  -0.342  -1.5871   0.4508   2.1854
 23C  CG   C  CR6   0   0.128  -2.3258  -0.0388   1.1376
 23C  CB   C  CH2   0  -0.573  -2.4058  -1.5243   0.9209
 23C  CA   C  CH1   0  -0.239  -1.4878  -1.9750  -0.2346
 23C  C    C  C     0   0.576  -1.3785  -3.4833  -0.4020
 23C  OXT  O  OH1   0  -0.583  -2.5437  -4.0738  -0.2071
 23C  O    O  O     0  -0.420  -0.3693  -4.0524  -0.7197
 23C  N    N  NR5   0  -0.607  -0.1707  -1.4040  -0.1438
 23C  CAW  C  CR5   0   0.593   0.3235  -0.4606  -1.0374
 23C  OAD  O  O     0  -0.382  -0.2546  -0.0465  -2.0064
 23C  CBA  C  CR56  0  -0.011   1.6696  -0.1005  -0.5361
 23C  CAP  C  CR16  0  -0.306   2.5904   0.7879  -1.0379
 23C  CAT  C  CR6   0  -0.075   3.7944   0.9258  -0.3420
 23C  CAR  C  C     0   0.553   4.7939   1.8889  -0.8830
 23C  OAE  O  O     0  -0.426   4.6100   2.5348  -1.8847
 23C  OAA  O  OH1   0  -0.588   5.8923   1.9587  -0.1518
 23C  CAK  C  CR16  0  -0.244   4.0391   0.1828   0.8144
 23C  CAO  C  CR16  0  -0.279   3.0950  -0.7138   1.3080
 23C  CAZ  C  CR56  0  -0.017   1.9147  -0.8362   0.6105
 23C  CAV  C  CR5   0   0.601   0.7259  -1.6825   0.8753
 23C  OAC  O  O     0  -0.391   0.5383  -2.4500   1.7829
 23C  HAN  H  HCR6  0   0.248  -3.9262  -0.5988  -1.0159
 23C  HAH  H  HCR6  0   0.260  -4.9620   1.0173  -2.5021
 23C  HAG  H  HCR6  0   0.259  -4.6477   3.4534  -2.1415
 23C  HAL  H  HCR6  0   0.256  -3.2846   4.2490  -0.2515
 23C  HAM  H  HCR6  0   0.255  -1.9031   3.7944   1.7047
 23C  HAI  H  HCR6  0   0.258  -0.8442   2.1816   3.2384
 23C  HD1  H  HCR6  0   0.256  -1.1061  -0.2401   2.8677
 23C  HB   H  HCH2  0   0.288  -2.1234  -2.0371   1.8400
 23C  HBA  H  HCH2  0   0.283  -3.4259  -1.8364   0.6945
 23C  HA   H  HCH1  0   0.335  -1.9087  -1.6066  -1.1766
 23C  HAP  H  HCR6  0   0.285   2.3944   1.3585  -1.9358
 23C  HAK  H  HCR6  0   0.290   4.9734   0.2937   1.3458
 23C  HAO  H  HCR6  0   0.284   3.2913  -1.2837   2.2056
 23C  H14  H  HOH1  0   0.493  -2.4682  -5.0286  -0.3586
 23C  H15  H  HOH1  0   0.494   6.5141   2.5912  -0.5421

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
 23C  CD2  CAN  aromatic  1.416  0.020  1.416
 23C  CD2  CAX  aromatic  1.421  0.020  1.421
 23C  CD2  CG   aromatic  1.425  0.020  1.425
 23C  CAN  CAH  aromatic  1.369  0.020  1.369
 23C  CAN  HAN  single    0.930  0.020  1.080
 23C  CAH  CAG  aromatic  1.409  0.020  1.409
 23C  CAH  HAH  single    0.930  0.020  1.080
 23C  CAG  CAL  aromatic  1.367  0.020  1.367
 23C  CAG  HAG  single    0.930  0.020  1.080
 23C  CAL  CAX  aromatic  1.415  0.020  1.415
 23C  CAL  HAL  single    0.930  0.020  1.080
 23C  CAX  CAM  aromatic  1.414  0.020  1.414
 23C  CAM  CAI  aromatic  1.365  0.020  1.365
 23C  CAM  HAM  single    0.930  0.020  1.080
 23C  CAI  CD1  aromatic  1.409  0.020  1.409
 23C  CAI  HAI  single    0.930  0.020  1.080
 23C  CD1  CG   aromatic  1.372  0.020  1.372
 23C  CD1  HD1  single    0.930  0.020  1.080
 23C  CG   CB   single    1.503  0.020  1.503
 23C  CB   CA   single    1.543  0.020  1.543
 23C  CB   HB   single    0.970  0.020  1.090
 23C  CB   HBA  single    0.970  0.020  1.090
 23C  CA   C    single    1.521  0.020  1.521
 23C  CA   N    single    1.438  0.020  1.438
 23C  CA   HA   single    0.970  0.020  1.090
 23C  C    OXT  single    1.321  0.020  1.321
 23C  C    O    double    1.201  0.020  1.201
 23C  N    CAW  single    1.390  0.020  1.390
 23C  N    CAV  single    1.386  0.020  1.386
 23C  CAW  OAD  double    1.202  0.020  1.202
 23C  CAW  CBA  single    1.481  0.020  1.481
 23C  CBA  CAP  aromatic  1.374  0.020  1.374
 23C  CBA  CAZ  aromatic  1.384  0.020  1.384
 23C  CAP  CAT  aromatic  1.397  0.020  1.397
 23C  CAP  HAP  single    0.930  0.020  1.080
 23C  CAT  CAR  single    1.490  0.020  1.490
 23C  CAT  CAK  aromatic  1.396  0.020  1.396
 23C  CAR  OAE  double    1.206  0.020  1.206
 23C  CAR  OAA  single    1.321  0.020  1.321
 23C  CAK  CAO  aromatic  1.392  0.020  1.392
 23C  CAK  HAK  single    0.930  0.020  1.080
 23C  CAO  CAZ  aromatic  1.376  0.020  1.376
 23C  CAO  HAO  single    0.930  0.020  1.080
 23C  CAZ  CAV  single    1.483  0.020  1.483
 23C  CAV  OAC  double    1.203  0.020  1.203
 23C  OXT  H14  single    0.850  0.020  0.980
 23C  OAA  H15  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
 23C  CG   CD2  CAX  119.16  3.000
 23C  CG   CD2  CAN  122.71  3.000
 23C  CAX  CD2  CAN  118.12  3.000
 23C  HAN  CAN  CAH  118.76  3.000
 23C  HAN  CAN  CD2  120.06  3.000
 23C  CAH  CAN  CD2  121.17  3.000
 23C  HAH  CAH  CAG  119.69  3.000
 23C  HAH  CAH  CAN  119.83  3.000
 23C  CAG  CAH  CAN  120.48  3.000
 23C  HAG  CAG  CAL  120.33  3.000
 23C  HAG  CAG  CAH  119.79  3.000
 23C  CAL  CAG  CAH  119.88  3.000
 23C  HAL  CAL  CAX  118.70  3.000
 23C  HAL  CAL  CAG  120.41  3.000
 23C  CAX  CAL  CAG  120.89  3.000
 23C  CAM  CAX  CAL  120.96  3.000
 23C  CAM  CAX  CD2  119.59  3.000
 23C  CAL  CAX  CD2  119.45  3.000
 23C  HAM  CAM  CAI  120.60  3.000
 23C  HAM  CAM  CAX  119.07  3.000
 23C  CAI  CAM  CAX  120.33  3.000
 23C  HAI  CAI  CD1  119.49  3.000
 23C  HAI  CAI  CAM  120.42  3.000
 23C  CD1  CAI  CAM  120.10  3.000
 23C  HD1  CD1  CG   119.49  3.000
 23C  HD1  CD1  CAI  118.82  3.000
 23C  CG   CD1  CAI  121.69  3.000
 23C  CB   CG   CD1  119.42  3.000
 23C  CB   CG   CD2  121.43  3.000
 23C  CD1  CG   CD2  119.11  3.000
 23C  HBA  CB   HB   106.44  3.000
 23C  HBA  CB   CA   108.51  3.000
 23C  HB   CB   CA   109.87  3.000
 23C  HBA  CB   CG   111.25  3.000
 23C  HB   CB   CG   109.25  3.000
 23C  CA   CB   CG   111.40  3.000
 23C  HA   CA   N    105.81  3.000
 23C  HA   CA   C    105.45  3.000
 23C  N    CA   C    109.56  3.000
 23C  HA   CA   CB   108.49  3.000
 23C  N    CA   CB   112.43  3.000
 23C  C    CA   CB   114.50  3.000
 23C  O    C    OXT  124.63  3.000
 23C  O    C    CA   123.99  3.000
 23C  OXT  C    CA   111.32  3.000
 23C  H14  OXT  C    110.40  3.000
 23C  CAV  N    CAW  112.28  3.000
 23C  CAV  N    CA   123.99  3.000
 23C  CAW  N    CA   123.67  3.000
 23C  CBA  CAW  OAD  128.78  3.000
 23C  CBA  CAW  N    105.70  3.000
 23C  OAD  CAW  N    125.52  3.000
 23C  CAZ  CBA  CAP  121.82  3.000
 23C  CAZ  CBA  CAW  108.19  3.000
 23C  CAP  CBA  CAW  129.98  3.000
 23C  HAP  CAP  CAT  121.16  3.000
 23C  HAP  CAP  CBA  121.51  3.000
 23C  CAT  CAP  CBA  117.33  3.000
 23C  CAK  CAT  CAR  121.82  3.000
 23C  CAK  CAT  CAP  120.73  3.000
 23C  CAR  CAT  CAP  117.45  3.000
 23C  OAA  CAR  OAE  123.93  3.000
 23C  OAA  CAR  CAT  113.01  3.000
 23C  OAE  CAR  CAT  123.06  3.000
 23C  H15  OAA  CAR  110.18  3.000
 23C  HAK  CAK  CAO  118.55  3.000
 23C  HAK  CAK  CAT  120.28  3.000
 23C  CAO  CAK  CAT  121.16  3.000
 23C  HAO  CAO  CAZ  121.97  3.000
 23C  HAO  CAO  CAK  120.71  3.000
 23C  CAZ  CAO  CAK  117.32  3.000
 23C  CAV  CAZ  CAO  130.36  3.000
 23C  CAV  CAZ  CBA  108.01  3.000
 23C  CAO  CAZ  CBA  121.63  3.000
 23C  OAC  CAV  CAZ  128.58  3.000
 23C  OAC  CAV  N    125.60  3.000
 23C  CAZ  CAV  N    105.82  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
 23C  CONST_01  CAG  CAH  CAN  CD2    0.00   0.0  0
 23C  CONST_02  CAG  CAL  CAX  CD2    0.00   0.0  0
 23C  CONST_03  CAI  CAM  CAX  CD2    0.00   0.0  0
 23C  CONST_04  CAI  CD1  CG   CD2    0.00   0.0  0
 23C  CONST_05  CAL  CAX  CD2  CAN    0.00   0.0  0
 23C  CONST_06  CAM  CAX  CD2  CAN  180.00   0.0  0
 23C  CONST_07  CD1  CG   CD2  CAN  180.00   0.0  0
 23C  CONST_08  CAL  CAG  CAH  CAN    0.00   0.0  0
 23C  CONST_09  CAX  CD2  CAN  CAH    0.00   0.0  0
 23C  CONST_10  CG   CD2  CAN  CAH  180.00   0.0  0
 23C  CONST_11  CAX  CAL  CAG  CAH    0.00   0.0  0
 23C  CONST_12  CAM  CAX  CAL  CAG  180.00   0.0  0
 23C  CONST_13  CG   CD2  CAX  CAL  180.00   0.0  0
 23C  CONST_14  CAI  CAM  CAX  CAL  180.00   0.0  0
 23C  CONST_15  CD1  CG   CD2  CAX    0.00   0.0  0
 23C  CONST_16  CD1  CAI  CAM  CAX    0.00   0.0  0
 23C  CONST_17  CG   CD2  CAX  CAM    0.00   0.0  0
 23C  CONST_18  CG   CD1  CAI  CAM    0.00   0.0  0
 23C  CONST_19  CAK  CAT  CAP  CBA    0.00   0.0  0
 23C  CONST_20  CAK  CAO  CAZ  CBA    0.00   0.0  0
 23C  CONST_21  CAO  CAZ  CBA  CAP    0.00   0.0  0
 23C  CONST_22  CAO  CAK  CAT  CAP    0.00   0.0  0
 23C  CONST_23  CAZ  CBA  CAP  CAT    0.00   0.0  0
 23C  CONST_24  CAZ  CAO  CAK  CAT    0.00   0.0  0
 23C  CONST_25  CAV  N    CAW  CBA    0.00   0.0  0
 23C  CONST_26  CB   CG   CD2  CAN    0.00   0.0  0
 23C  CONST_27  CB   CG   CD2  CAX  180.00   0.0  0
 23C  CONST_28  CB   CG   CD1  CAI  180.00   0.0  0
 23C  CONST_29  CAR  CAT  CAP  CBA  180.00   0.0  0
 23C  CONST_30  CAO  CAK  CAT  CAR  180.00   0.0  0
 23C  CONST_31  CBA  CAW  N    CA   180.00   0.0  0
 23C  CONST_32  CAV  N    CAW  OAD  180.00   0.0  0
 23C  CONST_33  HAH  CAH  CAN  CD2  180.00   0.0  0
 23C  CONST_34  HAL  CAL  CAX  CD2  180.00   0.0  0
 23C  CONST_35  HAM  CAM  CAX  CD2  180.00   0.0  0
 23C  CONST_36  HD1  CD1  CG   CD2  180.00   0.0  0
 23C  CONST_37  HAG  CAG  CAH  CAN  180.00   0.0  0
 23C  CONST_38  HAN  CAN  CAH  CAG  180.00   0.0  0
 23C  CONST_39  HAI  CAI  CAM  CAX  180.00   0.0  0
 23C  CONST_40  HAP  CAP  CBA  CAW    0.00   0.0  0
 23C  CONST_41  HAO  CAO  CAZ  CBA  180.00   0.0  0
 23C  CONST_42  HAK  CAK  CAT  CAP  180.00   0.0  0
 23C  CONST_43  OAD  CAW  N    CA     0.00   0.0  0
 23C  CONST_44  H15  OAA  CAR  CAT  180.00   0.0  0
 23C  CONST_45  H14  OXT  C    CA   180.00   0.0  0
 23C  Var_01    CA   CB   CG   CD2   75.15  30.0  2
 23C  Var_02    OAE  CAR  CAT  CAP   -0.50  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
 23C  chir_01  CA  CB  C  N  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
 23C  plan-1  CA   0.020
 23C  plan-1  N    0.020
 23C  plan-1  CAW  0.020
 23C  plan-1  OAD  0.020
 23C  plan-1  CBA  0.020
 23C  plan-1  CAP  0.020
 23C  plan-1  CAT  0.020
 23C  plan-1  CAR  0.020
 23C  plan-1  CAK  0.020
 23C  plan-1  CAO  0.020
 23C  plan-1  CAZ  0.020
 23C  plan-1  CAV  0.020
 23C  plan-1  OAC  0.020
 23C  plan-1  HAP  0.020
 23C  plan-1  HAK  0.020
 23C  plan-1  HAO  0.020
 23C  plan-2  CD2  0.020
 23C  plan-2  CAN  0.020
 23C  plan-2  CAH  0.020
 23C  plan-2  CAG  0.020
 23C  plan-2  CAL  0.020
 23C  plan-2  CAX  0.020
 23C  plan-2  CAM  0.020
 23C  plan-2  CAI  0.020
 23C  plan-2  CD1  0.020
 23C  plan-2  CG   0.020
 23C  plan-2  CB   0.020
 23C  plan-2  HAN  0.020
 23C  plan-2  HAH  0.020
 23C  plan-2  HAG  0.020
 23C  plan-2  HAL  0.020
 23C  plan-2  HAM  0.020
 23C  plan-2  HAI  0.020
 23C  plan-2  HD1  0.020
 23C  plan-3  CA   0.020
 23C  plan-3  C    0.020
 23C  plan-3  OXT  0.020
 23C  plan-3  O    0.020
 23C  plan-3  H14  0.020
 23C  plan-4  CAT  0.020
 23C  plan-4  CAR  0.020
 23C  plan-4  OAE  0.020
 23C  plan-4  OAA  0.020
 23C  plan-4  H15  0.020

