# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:35:38 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-[(3aR,4S,7R,7aS)-1,3-dioxo-1,3,3a,4,7,7a-hexahydro-2H-4,7-methanoisoindol-2-yl]-N-(quinolin-8-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cccc2cccnc12)c3ccc(cc3)N4C(=O)[C@@H]5[C@H]6C[C@H](C=C6)[C@@H]5C4=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
 IWR  IWR  4-[(3aR,4S,7R,7aS)-1,3-dioxo-1,3,3a,4,7,7a-hexahydro-2H-4,7-methanoisoindol-2-yl]-N-(quinolin-8-yl)benzamide  ligand  50  31  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IWR
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
 IWR  CAF  C  CR66  0   0.147   5.1744  -0.3575   0.0555
 IWR  NAG  N  N     0  -0.457   4.4804  -1.5117  -0.0301
 IWR  CAH  C  CR16  0  -0.057   5.1371  -2.6416  -0.0451
 IWR  CAI  C  CR16  0  -0.335   6.5416  -2.7205   0.0238
 IWR  CAJ  C  CR16  0  -0.179   7.2600  -1.5610   0.1085
 IWR  CAA  C  CR66  0   0.084   6.5842  -0.3214   0.1273
 IWR  CAB  C  CR16  0  -0.330   7.2486   0.9217   0.2122
 IWR  CAC  C  CR16  0  -0.247   6.5144   2.0741   0.2241
 IWR  CAD  C  CR16  0  -0.332   5.1061   2.0595   0.1545
 IWR  CAE  C  CR6   0   0.345   4.4306   0.8640   0.0712
 IWR  NAK  N  NH1   0  -0.753   3.0538   0.7001  -0.0115
 IWR  CAL  C  C     0   0.534   2.0795   1.6392   0.0353
 IWR  OAM  O  O     0  -0.455   2.2839   2.8274   0.2123
 IWR  CAN  C  CR6   0  -0.033   0.6913   1.1100  -0.1277
 IWR  CAS  C  CR16  0  -0.271  -0.3509   1.8222   0.4613
 IWR  CAO  C  CR16  0  -0.261  -1.6567   1.3803   0.3450
 IWR  CAR  C  CR16  0  -0.301   0.4017  -0.0357  -0.8651
 IWR  CAQ  C  CR16  0  -0.254  -0.9067  -0.4693  -1.0038
 IWR  CAP  C  CR6   0   0.334  -1.9311   0.2354  -0.3906
 IWR  NAT  N  NR5   0  -0.650  -3.2659  -0.2171  -0.5117
 IWR  CAW  C  CR5   0   0.575  -4.2562   0.4979  -1.1722
 IWR  OBE  O  O     0  -0.411  -4.0671   1.5436  -1.7386
 IWR  CAV  C  CR15  0  -0.402  -5.5468  -0.2586  -1.0284
 IWR  CBB  C  CH1   0  -0.274  -6.6224   0.4587  -0.1504
 IWR  CBC  C  CH2   0  -0.421  -7.3569  -0.7775   0.3900
 IWR  CBA  C  C1    0  -0.228  -5.9190   0.9277   1.1036
 IWR  CAZ  C  C1    0  -0.224  -5.6107  -0.1538   1.8210
 IWR  CAY  C  CH1   0  -0.276  -6.1044  -1.3636   1.0593
 IWR  CAU  C  CR15  0  -0.400  -5.1939  -1.5020  -0.2024
 IWR  CAX  C  CR5   0   0.574  -3.7245  -1.3850   0.0824
 IWR  OBD  O  O     0  -0.412  -3.0303  -2.1315   0.7234
 IWR  H1   H  HCR6  0   0.272   4.5482  -3.5492  -0.1161
 IWR  H2   H  HCR6  0   0.277   7.0273  -3.6861   0.0074
 IWR  H3   H  HCR6  0   0.277   8.3415  -1.5787   0.1605
 IWR  H4   H  HCR6  0   0.263   8.3294   0.9475   0.2657
 IWR  H5   H  HCR6  0   0.266   7.0142   3.0316   0.2890
 IWR  H6   H  HCR6  0   0.286   4.5731   2.9959   0.1687
 IWR  H7   H  HNH1  0   0.419   2.7867  -0.2764  -0.0577
 IWR  H8   H  HCR6  0   0.272  -0.1407   2.7180   1.0294
 IWR  H9   H  HCR6  0   0.287  -2.4569   1.9196   0.8342
 IWR  H10  H  HCR6  0   0.269   1.1805  -0.5897  -1.3736
 IWR  H11  H  HCR6  0   0.280  -1.1262  -1.3461  -1.5975
 IWR  H12  H  HCR5  0   0.325  -5.9474  -0.4938  -2.0158
 IWR  H13  H  HCH1  0   0.259  -7.2055   1.1999  -0.6914
 IWR  H14  H  HCH2  0   0.261  -8.1395  -0.5258   1.1063
 IWR  H15  H  HCH2  0   0.249  -7.7741  -1.4154  -0.3926
 IWR  H17  H  H     0   0.261  -5.6386   1.9514   1.3118
 IWR  H18  H  H     0   0.261  -5.0273  -0.1902   2.7311
 IWR  H20  H  HCH1  0   0.260  -6.2135  -2.2859   1.6246
 IWR  H21  H  HCR5  0   0.326  -5.3953  -2.4403  -0.7218

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
 IWR  OBE  CAW  double    1.204  0.020  1.204
 IWR  CBB  CAV  single    1.563  0.020  1.563
 IWR  CBB  CBA  single    1.512  0.020  1.512
 IWR  CBB  CBC  single    1.536  0.020  1.536
 IWR  CAW  CAV  single    1.503  0.020  1.503
 IWR  CAW  NAT  single    1.389  0.020  1.389
 IWR  CAV  CAU  single    1.534  0.020  1.534
 IWR  CBA  CAZ  double    1.334  0.020  1.334
 IWR  CBC  CAY  single    1.536  0.020  1.536
 IWR  NAT  CAP  single    1.415  0.020  1.415
 IWR  NAT  CAX  single    1.388  0.020  1.388
 IWR  CAU  CAY  single    1.562  0.020  1.562
 IWR  CAU  CAX  single    1.501  0.020  1.501
 IWR  CAP  CAQ  aromatic  1.386  0.020  1.386
 IWR  CAP  CAO  aromatic  1.388  0.020  1.388
 IWR  CAQ  CAR  aromatic  1.385  0.020  1.385
 IWR  CAZ  CAY  single    1.513  0.020  1.513
 IWR  CAO  CAS  aromatic  1.384  0.020  1.384
 IWR  CAR  CAN  aromatic  1.393  0.020  1.393
 IWR  CAX  OBD  double    1.204  0.020  1.204
 IWR  OAM  CAL  double    1.219  0.020  1.219
 IWR  CAS  CAN  aromatic  1.393  0.020  1.393
 IWR  CAN  CAL  single    1.495  0.020  1.495
 IWR  CAL  NAK  single    1.354  0.020  1.354
 IWR  NAK  CAE  single    1.389  0.020  1.389
 IWR  CAD  CAE  aromatic  1.376  0.020  1.376
 IWR  CAD  CAC  aromatic  1.410  0.020  1.410
 IWR  CAE  CAF  aromatic  1.430  0.020  1.430
 IWR  CAC  CAB  aromatic  1.366  0.020  1.366
 IWR  CAF  NAG  aromatic  1.349  0.020  1.349
 IWR  CAF  CAA  aromatic  1.412  0.020  1.412
 IWR  CAB  CAA  aromatic  1.412  0.020  1.412
 IWR  NAG  CAH  aromatic  1.307  0.020  1.307
 IWR  CAA  CAJ  aromatic  1.412  0.020  1.412
 IWR  CAH  CAI  aromatic  1.408  0.020  1.408
 IWR  CAJ  CAI  aromatic  1.367  0.020  1.367
 IWR  CAH  H1   single    0.930  0.020  1.080
 IWR  CAI  H2   single    0.930  0.020  1.080
 IWR  CAJ  H3   single    0.930  0.020  1.080
 IWR  CAB  H4   single    0.930  0.020  1.080
 IWR  CAC  H5   single    0.930  0.020  1.080
 IWR  CAD  H6   single    0.930  0.020  1.080
 IWR  NAK  H7   single    0.860  0.020  1.020
 IWR  CAS  H8   single    0.930  0.020  1.080
 IWR  CAO  H9   single    0.930  0.020  1.080
 IWR  CAR  H10  single    0.930  0.020  1.080
 IWR  CAQ  H11  single    0.930  0.020  1.080
 IWR  CAV  H12  single    0.970  0.020  1.090
 IWR  CBB  H13  single    0.970  0.020  1.090
 IWR  CBC  H14  single    0.970  0.020  1.090
 IWR  CBC  H15  single    0.970  0.020  1.090
 IWR  CBA  H17  single    0.930  0.020  1.080
 IWR  CAZ  H18  single    0.930  0.020  1.080
 IWR  CAY  H20  single    0.970  0.020  1.090
 IWR  CAU  H21  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
 IWR  CAE  CAF  CAA  119.79  3.000
 IWR  CAA  CAF  NAG  122.58  3.000
 IWR  CAE  CAF  NAG  117.63  3.000
 IWR  CAH  NAG  CAF  118.80  3.000
 IWR  H1   CAH  CAI  119.86  3.000
 IWR  H1   CAH  NAG  116.85  3.000
 IWR  CAI  CAH  NAG  123.29  3.000
 IWR  H2   CAI  CAJ  121.51  3.000
 IWR  H2   CAI  CAH  119.83  3.000
 IWR  CAJ  CAI  CAH  118.66  3.000
 IWR  H3   CAJ  CAA  119.45  3.000
 IWR  H3   CAJ  CAI  120.94  3.000
 IWR  CAA  CAJ  CAI  119.61  3.000
 IWR  CAB  CAA  CAJ  123.26  3.000
 IWR  CAJ  CAA  CAF  117.05  3.000
 IWR  CAB  CAA  CAF  119.69  3.000
 IWR  H4   CAB  CAC  121.06  3.000
 IWR  H4   CAB  CAA  119.59  3.000
 IWR  CAC  CAB  CAA  119.35  3.000
 IWR  H5   CAC  CAD  118.26  3.000
 IWR  H5   CAC  CAB  119.91  3.000
 IWR  CAD  CAC  CAB  121.83  3.000
 IWR  H6   CAD  CAE  120.88  3.000
 IWR  H6   CAD  CAC  118.97  3.000
 IWR  CAE  CAD  CAC  120.16  3.000
 IWR  NAK  CAE  CAD  126.36  3.000
 IWR  CAD  CAE  CAF  119.18  3.000
 IWR  NAK  CAE  CAF  114.46  3.000
 IWR  H7   NAK  CAL  118.70  3.000
 IWR  H7   NAK  CAE  112.19  3.000
 IWR  CAL  NAK  CAE  129.00  3.000
 IWR  CAN  CAL  OAM  121.13  3.000
 IWR  CAN  CAL  NAK  114.77  3.000
 IWR  OAM  CAL  NAK  124.10  3.000
 IWR  CAR  CAN  CAS  119.27  3.000
 IWR  CAS  CAN  CAL  117.89  3.000
 IWR  CAR  CAN  CAL  122.82  3.000
 IWR  H8   CAS  CAO  119.49  3.000
 IWR  H8   CAS  CAN  120.02  3.000
 IWR  CAO  CAS  CAN  120.49  3.000
 IWR  H9   CAO  CAP  120.30  3.000
 IWR  H9   CAO  CAS  120.06  3.000
 IWR  CAP  CAO  CAS  119.64  3.000
 IWR  H10  CAR  CAQ  118.18  3.000
 IWR  H10  CAR  CAN  121.34  3.000
 IWR  CAQ  CAR  CAN  120.45  3.000
 IWR  H11  CAQ  CAP  120.33  3.000
 IWR  H11  CAQ  CAR  120.03  3.000
 IWR  CAP  CAQ  CAR  119.64  3.000
 IWR  NAT  CAP  CAQ  119.79  3.000
 IWR  CAQ  CAP  CAO  120.50  3.000
 IWR  NAT  CAP  CAO  119.71  3.000
 IWR  CAX  NAT  CAW  113.65  3.000
 IWR  CAX  NAT  CAP  122.96  3.000
 IWR  CAW  NAT  CAP  123.30  3.000
 IWR  CAV  CAW  OBE  128.10  3.000
 IWR  CAV  CAW  NAT  107.92  3.000
 IWR  OBE  CAW  NAT  123.97  3.000
 IWR  H12  CAV  CAU  113.39  3.000
 IWR  H12  CAV  CBB  110.78  3.000
 IWR  CAU  CAV  CBB  103.17  3.000
 IWR  H12  CAV  CAW  109.70  3.000
 IWR  CAU  CAV  CAW  105.19  3.000
 IWR  CBB  CAV  CAW  114.44  3.000
 IWR  H13  CBB  CBA  116.79  3.000
 IWR  H13  CBB  CBC  117.85  3.000
 IWR  CBA  CBB  CBC  100.38  3.000
 IWR  H13  CBB  CAV  113.73  3.000
 IWR  CBC  CBB  CAV   99.05  3.000
 IWR  CBA  CBB  CAV  106.74  3.000
 IWR  H15  CBC  H14  109.34  3.000
 IWR  H15  CBC  CAY  113.62  3.000
 IWR  H14  CBC  CAY  112.77  3.000
 IWR  H15  CBC  CBB  113.61  3.000
 IWR  H14  CBC  CBB  112.86  3.000
 IWR  CAY  CBC  CBB   94.04  3.000
 IWR  H17  CBA  CAZ  127.15  3.000
 IWR  H17  CBA  CBB  125.01  3.000
 IWR  CAZ  CBA  CBB  107.58  3.000
 IWR  H18  CAZ  CAY  124.95  3.000
 IWR  H18  CAZ  CBA  127.19  3.000
 IWR  CAY  CAZ  CBA  107.59  3.000
 IWR  H20  CAY  CAU  113.78  3.000
 IWR  H20  CAY  CAZ  116.71  3.000
 IWR  CAU  CAY  CAZ  106.70  3.000
 IWR  H20  CAY  CBC  117.93  3.000
 IWR  CAZ  CAY  CBC  100.39  3.000
 IWR  CAU  CAY  CBC   99.04  3.000
 IWR  H21  CAU  CAX  109.76  3.000
 IWR  H21  CAU  CAY  110.67  3.000
 IWR  CAX  CAU  CAY  114.22  3.000
 IWR  H21  CAU  CAV  113.47  3.000
 IWR  CAX  CAU  CAV  105.32  3.000
 IWR  CAY  CAU  CAV  103.23  3.000
 IWR  OBD  CAX  CAU  128.09  3.000
 IWR  OBD  CAX  NAT  123.98  3.000
 IWR  CAU  CAX  NAT  107.92  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
 IWR  CONST_01  CAC  CAD  CAE  CAF    0.00   0.0  0
 IWR  CONST_02  CAI  CAH  NAG  CAF    0.00   0.0  0
 IWR  CONST_03  CAC  CAB  CAA  CAF    0.00   0.0  0
 IWR  CONST_04  CAI  CAJ  CAA  CAF    0.00   0.0  0
 IWR  CONST_05  CAD  CAE  CAF  NAG  180.00   0.0  0
 IWR  CONST_06  CAB  CAA  CAF  NAG  180.00   0.0  0
 IWR  CONST_07  CAJ  CAA  CAF  NAG    0.00   0.0  0
 IWR  CONST_08  CAJ  CAI  CAH  NAG    0.00   0.0  0
 IWR  CONST_09  CAE  CAF  NAG  CAH  180.00   0.0  0
 IWR  CONST_10  CAA  CAF  NAG  CAH    0.00   0.0  0
 IWR  CONST_11  CAA  CAJ  CAI  CAH    0.00   0.0  0
 IWR  CONST_12  CAB  CAA  CAJ  CAI  180.00   0.0  0
 IWR  CONST_13  CAE  CAF  CAA  CAJ  180.00   0.0  0
 IWR  CONST_14  CAC  CAB  CAA  CAJ  180.00   0.0  0
 IWR  CONST_15  CAD  CAE  CAF  CAA    0.00   0.0  0
 IWR  CONST_16  CAD  CAC  CAB  CAA    0.00   0.0  0
 IWR  CONST_17  CAE  CAD  CAC  CAB    0.00   0.0  0
 IWR  CONST_18  CAE  CAF  CAA  CAB    0.00   0.0  0
 IWR  CONST_19  CAP  CAQ  CAR  CAN    0.00   0.0  0
 IWR  CONST_20  CAP  CAO  CAS  CAN    0.00   0.0  0
 IWR  CONST_21  CAQ  CAP  CAO  CAS    0.00   0.0  0
 IWR  CONST_22  CAQ  CAR  CAN  CAS    0.00   0.0  0
 IWR  CONST_23  CAR  CAQ  CAP  CAO    0.00   0.0  0
 IWR  CONST_24  CAR  CAN  CAS  CAO    0.00   0.0  0
 IWR  CONST_25  NAT  CAP  CAO  CAS  180.00   0.0  0
 IWR  CONST_26  NAT  CAP  CAQ  CAR  180.00   0.0  0
 IWR  CONST_27  CAV  CAW  NAT  CAP  180.00   0.0  0
 IWR  CONST_28  CAX  NAT  CAW  CAV    0.00   0.0  0
 IWR  CONST_29  NAK  CAE  CAF  NAG    0.00   0.0  0
 IWR  CONST_30  NAK  CAE  CAF  CAA  180.00   0.0  0
 IWR  CONST_31  NAK  CAE  CAD  CAC  180.00   0.0  0
 IWR  CONST_32  CAQ  CAR  CAN  CAL  180.00   0.0  0
 IWR  CONST_33  CAO  CAS  CAN  CAL  180.00   0.0  0
 IWR  CONST_34  OBE  CAW  NAT  CAP    0.00   0.0  0
 IWR  CONST_35  CAX  NAT  CAW  OBE  180.00   0.0  0
 IWR  CONST_36  H6   CAD  CAE  CAF  180.00   0.0  0
 IWR  CONST_37  H1   CAH  NAG  CAF  180.00   0.0  0
 IWR  CONST_38  H4   CAB  CAA  CAF  180.00   0.0  0
 IWR  CONST_39  H3   CAJ  CAA  CAF  180.00   0.0  0
 IWR  CONST_40  H2   CAI  CAH  NAG  180.00   0.0  0
 IWR  CONST_41  H5   CAC  CAB  CAA  180.00   0.0  0
 IWR  CONST_42  H11  CAQ  CAR  CAN  180.00   0.0  0
 IWR  CONST_43  H9   CAO  CAS  CAN  180.00   0.0  0
 IWR  CONST_44  H10  CAR  CAN  CAS  180.00   0.0  0
 IWR  CONST_45  H8   CAS  CAN  CAR  180.00   0.0  0
 IWR  CONST_46  CAN  CAL  NAK  CAE  180.00   0.0  0
 IWR  CONST_47  CAL  NAK  CAE  CAF  180.00   0.0  0
 IWR  CONST_48  CAL  NAK  CAE  CAD    0.00   0.0  0
 IWR  CONST_49  H7   NAK  CAE  CAF    0.00   0.0  0
 IWR  CONST_50  OAM  CAL  NAK  CAE    0.00   0.0  0
 IWR  Var_01    CAW  NAT  CAP  CAO   65.26  30.0  2
 IWR  Var_02    CAU  CAX  NAT  CAP  177.11  30.0  1
 IWR  Var_03    CAY  CAZ  CBA  CBB   -0.07  30.0  2
 IWR  Var_04    CAR  CAN  CAL  NAK  -29.16  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
 IWR  chir_01  CAV  CBB  CAW  CAU  negativ
 IWR  chir_02  CBB  CAV  CBA  CBC  positiv
 IWR  chir_03  CAY  CBC  CAU  CAZ  negativ
 IWR  chir_04  CAU  CAX  CAY  CAV  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
 IWR  plan-1  CAL  0.020
 IWR  plan-1  CAN  0.020
 IWR  plan-1  CAS  0.020
 IWR  plan-1  CAO  0.020
 IWR  plan-1  CAR  0.020
 IWR  plan-1  CAQ  0.020
 IWR  plan-1  CAP  0.020
 IWR  plan-1  NAT  0.020
 IWR  plan-1  H8   0.020
 IWR  plan-1  H9   0.020
 IWR  plan-1  H10  0.020
 IWR  plan-1  H11  0.020
 IWR  plan-2  CAF  0.020
 IWR  plan-2  NAG  0.020
 IWR  plan-2  CAH  0.020
 IWR  plan-2  CAI  0.020
 IWR  plan-2  CAJ  0.020
 IWR  plan-2  CAA  0.020
 IWR  plan-2  CAB  0.020
 IWR  plan-2  CAC  0.020
 IWR  plan-2  CAD  0.020
 IWR  plan-2  CAE  0.020
 IWR  plan-2  NAK  0.020
 IWR  plan-2  H1   0.020
 IWR  plan-2  H2   0.020
 IWR  plan-2  H3   0.020
 IWR  plan-2  H4   0.020
 IWR  plan-2  H5   0.020
 IWR  plan-2  H6   0.020
 IWR  plan-3  CAE  0.020
 IWR  plan-3  NAK  0.020
 IWR  plan-3  CAL  0.020
 IWR  plan-3  OAM  0.020
 IWR  plan-3  CAN  0.020
 IWR  plan-3  H7   0.020
 IWR  plan-4  NAT  0.020
 IWR  plan-4  CAU  0.020
 IWR  plan-4  CAX  0.020
 IWR  plan-4  OBD  0.020
 IWR  plan-5  CAP  0.020
 IWR  plan-5  NAT  0.020
 IWR  plan-5  CAW  0.020
 IWR  plan-5  OBE  0.020
 IWR  plan-5  CAV  0.020
 IWR  plan-5  CAX  0.020

