# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:28:19 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-[(3aR,4R,7S,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
 2XS  2XS  4-[(3aR,4R,7S,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  .  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_2XS
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
 2XS  CAF  C  CR66  0   0.147   5.2671   0.3592  -0.0266
 2XS  NAG  N  N     0  -0.457   4.5667   1.5050  -0.1608
 2XS  CAH  C  CR16  0  -0.057   5.2184   2.6334  -0.2606
 2XS  CAI  C  CR16  0  -0.335   6.6239   2.7194  -0.2344
 2XS  CAJ  C  CR16  0  -0.179   7.3487   1.5686  -0.1004
 2XS  CAA  C  CR66  0   0.084   6.6786   0.3307   0.0092
 2XS  CAB  C  CR16  0  -0.330   7.3498  -0.9039   0.1480
 2XS  CAC  C  CR16  0  -0.247   6.6206  -2.0554   0.2457
 2XS  CAD  C  CR16  0  -0.332   5.2109  -2.0481   0.2138
 2XS  CAE  C  CR6   0   0.345   4.5287  -0.8610   0.0798
 2XS  NAK  N  NH1   0  -0.754   3.1495  -0.7049   0.0267
 2XS  CAL  C  C     0   0.537   2.1814  -1.6458   0.1292
 2XS  OAM  O  O     0  -0.455   2.3968  -2.8255   0.3460
 2XS  CAN  C  CR6   0  -0.032   0.7854  -1.1329  -0.0247
 2XS  CAS  C  CR16  0  -0.270  -0.2418  -1.8541   0.5794
 2XS  CAO  C  CR16  0  -0.253  -1.5550  -1.4326   0.4695
 2XS  CAR  C  CR16  0  -0.301   0.4728   0.0030  -0.7682
 2XS  CAQ  C  CR16  0  -0.252  -0.8425   0.4180  -0.8977
 2XS  CAP  C  CR6   0   0.336  -1.8516  -0.2976  -0.2720
 2XS  NAT  N  NR5   0  -0.654  -3.1951   0.1314  -0.3908
 2XS  CAW  C  CR5   0   0.570  -3.6780   1.2951   0.1925
 2XS  OBE  O  O     0  -0.410  -3.0022   2.0534   0.8385
 2XS  CAV  C  CR15  0  -0.389  -5.1487   1.4004  -0.1119
 2XS  CBB  C  CH1   0  -0.304  -6.0429   1.2207   1.1545
 2XS  CBC  C  CH2   0  -0.443  -5.9794  -0.3011   1.3403
 2XS  CBA  C  C1    0  -0.193  -7.4617   1.3682   0.6465
 2XS  CAZ  C  C1    0  -0.193  -7.7425   0.2859  -0.0787
 2XS  CAY  C  CH1   0  -0.304  -6.5162  -0.6017  -0.0656
 2XS  CAU  C  CR15  0  -0.390  -5.4741   0.1534  -0.9485
 2XS  CAX  C  CR5   0   0.569  -4.1685  -0.5868  -1.0719
 2XS  OBD  O  O     0  -0.410  -3.9620  -1.6269  -1.6417
 2XS  H1   H  HCR6  0   0.272   4.6244   3.5338  -0.3695
 2XS  H2   H  HCR6  0   0.277   7.1052   3.6834  -0.3222
 2XS  H3   H  HCR6  0   0.277   8.4312   1.5919  -0.0779
 2XS  H4   H  HCR6  0   0.263   8.4317  -0.9240   0.1747
 2XS  H5   H  HCR6  0   0.266   7.1253  -3.0065   0.3529
 2XS  H6   H  HCR6  0   0.286   4.6826  -2.9832   0.2980
 2XS  H7   H  HNH1  0   0.420   2.8776   0.2673  -0.0612
 2XS  H8   H  HCR6  0   0.272  -0.0147  -2.7423   1.1526
 2XS  H9   H  HCR6  0   0.277  -2.3432  -1.9816   0.9677
 2XS  H10  H  HCR6  0   0.269   1.2383   0.5643  -1.2885
 2XS  H11  H  HCR6  0   0.282  -1.0789   1.2885  -1.4946
 2XS  H12  H  HCR5  0   0.325  -5.3417   2.3480  -0.6164
 2XS  H13  H  HCH1  0   0.264  -5.7584   1.8513   1.9942
 2XS  H14  H  HCH2  0   0.243  -4.9792  -0.6935   1.5437
 2XS  H15  H  HCH2  0   0.267  -6.6468  -0.6546   2.1255
 2XS  H16  H  H     0   0.254  -8.0739   2.2497   0.7783
 2XS  H18  H  H     0   0.254  -8.6315   0.0977  -0.6646
 2XS  H20  H  HCH1  0   0.264  -6.6659  -1.6425  -0.3447
 2XS  H21  H  HCR5  0   0.324  -5.8601   0.3657  -1.9461

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
 2XS  CAZ  CBA  double    1.333  0.020  1.333
 2XS  CAZ  CAY  single    1.514  0.020  1.514
 2XS  CBA  CBB  single    1.514  0.020  1.514
 2XS  CAY  CAU  single    1.561  0.020  1.561
 2XS  CAY  CBC  single    1.535  0.020  1.535
 2XS  CAU  CAV  single    1.537  0.020  1.537
 2XS  CAU  CAX  single    1.506  0.020  1.506
 2XS  CBC  CBB  single    1.534  0.020  1.534
 2XS  CBB  CAV  single    1.561  0.020  1.561
 2XS  OBD  CAX  double    1.204  0.020  1.204
 2XS  CAV  CAW  single    1.506  0.020  1.506
 2XS  CAX  NAT  single    1.388  0.020  1.388
 2XS  NAT  CAW  single    1.388  0.020  1.388
 2XS  NAT  CAP  single    1.415  0.020  1.415
 2XS  CAW  OBE  double    1.204  0.020  1.204
 2XS  CAP  CAQ  aromatic  1.386  0.020  1.386
 2XS  CAP  CAO  aromatic  1.388  0.020  1.388
 2XS  CAQ  CAR  aromatic  1.385  0.020  1.385
 2XS  CAO  CAS  aromatic  1.383  0.020  1.383
 2XS  CAR  CAN  aromatic  1.393  0.020  1.393
 2XS  CAS  CAN  aromatic  1.393  0.020  1.393
 2XS  CAH  NAG  aromatic  1.307  0.020  1.307
 2XS  CAH  CAI  aromatic  1.408  0.020  1.408
 2XS  CAN  CAL  single    1.495  0.020  1.495
 2XS  NAG  CAF  aromatic  1.350  0.020  1.350
 2XS  CAI  CAJ  aromatic  1.367  0.020  1.367
 2XS  NAK  CAL  single    1.354  0.020  1.354
 2XS  NAK  CAE  single    1.389  0.020  1.389
 2XS  CAL  OAM  double    1.219  0.020  1.219
 2XS  CAF  CAE  aromatic  1.430  0.020  1.430
 2XS  CAF  CAA  aromatic  1.412  0.020  1.412
 2XS  CAJ  CAA  aromatic  1.412  0.020  1.412
 2XS  CAE  CAD  aromatic  1.376  0.020  1.376
 2XS  CAA  CAB  aromatic  1.412  0.020  1.412
 2XS  CAD  CAC  aromatic  1.410  0.020  1.410
 2XS  CAB  CAC  aromatic  1.366  0.020  1.366
 2XS  CAH  H1   single    0.930  0.020  1.080
 2XS  CAI  H2   single    0.930  0.020  1.080
 2XS  CAJ  H3   single    0.930  0.020  1.080
 2XS  CAB  H4   single    0.930  0.020  1.080
 2XS  CAC  H5   single    0.930  0.020  1.080
 2XS  CAD  H6   single    0.930  0.020  1.080
 2XS  NAK  H7   single    0.860  0.020  1.020
 2XS  CAS  H8   single    0.930  0.020  1.080
 2XS  CAO  H9   single    0.930  0.020  1.080
 2XS  CAR  H10  single    0.930  0.020  1.080
 2XS  CAQ  H11  single    0.930  0.020  1.080
 2XS  CAV  H12  single    0.970  0.020  1.090
 2XS  CBB  H13  single    0.970  0.020  1.090
 2XS  CBC  H14  single    0.970  0.020  1.090
 2XS  CBC  H15  single    0.970  0.020  1.090
 2XS  CBA  H16  single    0.930  0.020  1.080
 2XS  CAZ  H18  single    0.930  0.020  1.080
 2XS  CAY  H20  single    0.970  0.020  1.090
 2XS  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
 2XS  CAE  CAF  CAA  119.79  3.000
 2XS  CAA  CAF  NAG  122.57  3.000
 2XS  CAE  CAF  NAG  117.63  3.000
 2XS  CAH  NAG  CAF  118.81  3.000
 2XS  H1   CAH  CAI  119.86  3.000
 2XS  H1   CAH  NAG  116.85  3.000
 2XS  CAI  CAH  NAG  123.30  3.000
 2XS  H2   CAI  CAJ  121.51  3.000
 2XS  H2   CAI  CAH  119.82  3.000
 2XS  CAJ  CAI  CAH  118.66  3.000
 2XS  H3   CAJ  CAA  119.45  3.000
 2XS  H3   CAJ  CAI  120.94  3.000
 2XS  CAA  CAJ  CAI  119.61  3.000
 2XS  CAB  CAA  CAJ  123.27  3.000
 2XS  CAB  CAA  CAF  119.68  3.000
 2XS  CAJ  CAA  CAF  117.05  3.000
 2XS  H4   CAB  CAC  121.06  3.000
 2XS  H4   CAB  CAA  119.59  3.000
 2XS  CAC  CAB  CAA  119.35  3.000
 2XS  H5   CAC  CAD  118.23  3.000
 2XS  H5   CAC  CAB  119.93  3.000
 2XS  CAD  CAC  CAB  121.83  3.000
 2XS  H6   CAD  CAE  120.90  3.000
 2XS  H6   CAD  CAC  118.94  3.000
 2XS  CAE  CAD  CAC  120.16  3.000
 2XS  NAK  CAE  CAD  126.37  3.000
 2XS  CAD  CAE  CAF  119.17  3.000
 2XS  NAK  CAE  CAF  114.45  3.000
 2XS  H7   NAK  CAL  118.78  3.000
 2XS  H7   NAK  CAE  112.18  3.000
 2XS  CAL  NAK  CAE  128.98  3.000
 2XS  CAN  CAL  OAM  121.02  3.000
 2XS  OAM  CAL  NAK  124.04  3.000
 2XS  CAN  CAL  NAK  114.93  3.000
 2XS  CAR  CAN  CAS  119.22  3.000
 2XS  CAS  CAN  CAL  117.79  3.000
 2XS  CAR  CAN  CAL  122.96  3.000
 2XS  H8   CAS  CAO  119.45  3.000
 2XS  H8   CAS  CAN  120.02  3.000
 2XS  CAO  CAS  CAN  120.52  3.000
 2XS  H9   CAO  CAP  120.35  3.000
 2XS  H9   CAO  CAS  120.02  3.000
 2XS  CAP  CAO  CAS  119.63  3.000
 2XS  H10  CAR  CAQ  118.11  3.000
 2XS  H10  CAR  CAN  121.38  3.000
 2XS  CAQ  CAR  CAN  120.48  3.000
 2XS  H11  CAQ  CAP  120.35  3.000
 2XS  H11  CAQ  CAR  120.02  3.000
 2XS  CAP  CAQ  CAR  119.62  3.000
 2XS  NAT  CAP  CAQ  119.78  3.000
 2XS  CAQ  CAP  CAO  120.51  3.000
 2XS  NAT  CAP  CAO  119.71  3.000
 2XS  CAX  NAT  CAW  113.32  3.000
 2XS  CAW  NAT  CAP  123.29  3.000
 2XS  CAX  NAT  CAP  123.37  3.000
 2XS  CAV  CAW  OBE  127.79  3.000
 2XS  OBE  CAW  NAT  123.93  3.000
 2XS  CAV  CAW  NAT  108.27  3.000
 2XS  H12  CAV  CAU  114.57  3.000
 2XS  H12  CAV  CBB  111.96  3.000
 2XS  CAU  CAV  CBB  103.12  3.000
 2XS  H12  CAV  CAW  109.10  3.000
 2XS  CBB  CAV  CAW  112.80  3.000
 2XS  CAU  CAV  CAW  105.08  3.000
 2XS  H13  CBB  CBA  116.59  3.000
 2XS  H13  CBB  CBC  118.07  3.000
 2XS  CBA  CBB  CBC  100.14  3.000
 2XS  H13  CBB  CAV  114.19  3.000
 2XS  CBC  CBB  CAV  100.88  3.000
 2XS  CBA  CBB  CAV  104.68  3.000
 2XS  H15  CBC  H14  108.05  3.000
 2XS  H15  CBC  CAY  112.48  3.000
 2XS  H14  CBC  CAY  114.83  3.000
 2XS  H15  CBC  CBB  112.57  3.000
 2XS  H14  CBC  CBB  114.60  3.000
 2XS  CAY  CBC  CBB   93.95  3.000
 2XS  H16  CBA  CAZ  127.53  3.000
 2XS  H16  CBA  CBB  124.68  3.000
 2XS  CAZ  CBA  CBB  107.51  3.000
 2XS  H18  CAZ  CAY  124.65  3.000
 2XS  H18  CAZ  CBA  127.55  3.000
 2XS  CAY  CAZ  CBA  107.51  3.000
 2XS  H20  CAY  CAU  114.18  3.000
 2XS  H20  CAY  CAZ  116.57  3.000
 2XS  CAU  CAY  CAZ  104.61  3.000
 2XS  H20  CAY  CBC  118.07  3.000
 2XS  CAU  CAY  CBC  100.95  3.000
 2XS  CAZ  CAY  CBC  100.16  3.000
 2XS  H21  CAU  CAX  109.12  3.000
 2XS  H21  CAU  CAY  112.05  3.000
 2XS  CAX  CAU  CAY  112.80  3.000
 2XS  H21  CAU  CAV  114.52  3.000
 2XS  CAX  CAU  CAV  105.07  3.000
 2XS  CAY  CAU  CAV  103.07  3.000
 2XS  OBD  CAX  CAU  127.75  3.000
 2XS  OBD  CAX  NAT  123.98  3.000
 2XS  CAU  CAX  NAT  108.26  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
 2XS  CONST_01  CAI  CAH  NAG  CAF    0.00   0.0  0
 2XS  CONST_02  CAC  CAD  CAE  CAF    0.00   0.0  0
 2XS  CONST_03  CAI  CAJ  CAA  CAF    0.00   0.0  0
 2XS  CONST_04  CAC  CAB  CAA  CAF    0.00   0.0  0
 2XS  CONST_05  CAJ  CAI  CAH  NAG    0.00   0.0  0
 2XS  CONST_06  CAD  CAE  CAF  NAG  180.00   0.0  0
 2XS  CONST_07  CAJ  CAA  CAF  NAG    0.00   0.0  0
 2XS  CONST_08  CAB  CAA  CAF  NAG  180.00   0.0  0
 2XS  CONST_09  CAE  CAF  NAG  CAH  180.00   0.0  0
 2XS  CONST_10  CAA  CAF  NAG  CAH    0.00   0.0  0
 2XS  CONST_11  CAA  CAJ  CAI  CAH    0.00   0.0  0
 2XS  CONST_12  CAB  CAA  CAJ  CAI  180.00   0.0  0
 2XS  CONST_13  CAE  CAF  CAA  CAJ  180.00   0.0  0
 2XS  CONST_14  CAC  CAB  CAA  CAJ  180.00   0.0  0
 2XS  CONST_15  CAD  CAE  CAF  CAA    0.00   0.0  0
 2XS  CONST_16  CAD  CAC  CAB  CAA    0.00   0.0  0
 2XS  CONST_17  CAE  CAF  CAA  CAB    0.00   0.0  0
 2XS  CONST_18  CAE  CAD  CAC  CAB    0.00   0.0  0
 2XS  CONST_19  CAP  CAQ  CAR  CAN    0.00   0.0  0
 2XS  CONST_20  CAP  CAO  CAS  CAN    0.00   0.0  0
 2XS  CONST_21  CAQ  CAP  CAO  CAS    0.00   0.0  0
 2XS  CONST_22  CAQ  CAR  CAN  CAS    0.00   0.0  0
 2XS  CONST_23  CAR  CAQ  CAP  CAO    0.00   0.0  0
 2XS  CONST_24  CAR  CAN  CAS  CAO    0.00   0.0  0
 2XS  CONST_25  NAT  CAP  CAO  CAS  180.00   0.0  0
 2XS  CONST_26  NAT  CAP  CAQ  CAR  180.00   0.0  0
 2XS  CONST_27  CAV  CAW  NAT  CAP  180.00   0.0  0
 2XS  CONST_28  CAX  NAT  CAW  CAV    0.00   0.0  0
 2XS  CONST_29  NAK  CAE  CAF  NAG    0.00   0.0  0
 2XS  CONST_30  NAK  CAE  CAF  CAA  180.00   0.0  0
 2XS  CONST_31  NAK  CAE  CAD  CAC  180.00   0.0  0
 2XS  CONST_32  CAQ  CAR  CAN  CAL  180.00   0.0  0
 2XS  CONST_33  CAO  CAS  CAN  CAL  180.00   0.0  0
 2XS  CONST_34  OBE  CAW  NAT  CAP    0.00   0.0  0
 2XS  CONST_35  CAX  NAT  CAW  OBE  180.00   0.0  0
 2XS  CONST_36  H1   CAH  NAG  CAF  180.00   0.0  0
 2XS  CONST_37  H6   CAD  CAE  CAF  180.00   0.0  0
 2XS  CONST_38  H3   CAJ  CAA  CAF  180.00   0.0  0
 2XS  CONST_39  H4   CAB  CAA  CAF  180.00   0.0  0
 2XS  CONST_40  H2   CAI  CAH  NAG  180.00   0.0  0
 2XS  CONST_41  H5   CAC  CAB  CAA  180.00   0.0  0
 2XS  CONST_42  H11  CAQ  CAR  CAN  180.00   0.0  0
 2XS  CONST_43  H9   CAO  CAS  CAN  180.00   0.0  0
 2XS  CONST_44  H10  CAR  CAN  CAS  180.00   0.0  0
 2XS  CONST_45  H8   CAS  CAN  CAR  180.00   0.0  0
 2XS  CONST_46  CAN  CAL  NAK  CAE  180.00   0.0  0
 2XS  CONST_47  CAL  NAK  CAE  CAF  180.00   0.0  0
 2XS  CONST_48  CAL  NAK  CAE  CAD    0.00   0.0  0
 2XS  CONST_49  H7   NAK  CAE  CAF    0.00   0.0  0
 2XS  CONST_50  OAM  CAL  NAK  CAE    0.00   0.0  0
 2XS  Var_01    CAX  NAT  CAP  CAO  -66.98  30.0  2
 2XS  Var_02    CAU  CAX  NAT  CAP  178.25  30.0  1
 2XS  Var_03    CAY  CAZ  CBA  CBB    0.04  30.0  2
 2XS  Var_04    CAR  CAN  CAL  NAK   27.32  30.0  3

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
 2XS  chir_01  CAV  CAU  CBB  CAW  negativ
 2XS  chir_02  CBB  CBA  CBC  CAV  negativ
 2XS  chir_03  CAY  CBC  CAU  CAZ  positiv
 2XS  chir_04  CAU  CAY  CAV  CAX  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
 2XS  plan-1  CAL  0.020
 2XS  plan-1  CAN  0.020
 2XS  plan-1  CAS  0.020
 2XS  plan-1  CAO  0.020
 2XS  plan-1  CAR  0.020
 2XS  plan-1  CAQ  0.020
 2XS  plan-1  CAP  0.020
 2XS  plan-1  NAT  0.020
 2XS  plan-1  H8   0.020
 2XS  plan-1  H9   0.020
 2XS  plan-1  H10  0.020
 2XS  plan-1  H11  0.020
 2XS  plan-2  CAF  0.020
 2XS  plan-2  NAG  0.020
 2XS  plan-2  CAH  0.020
 2XS  plan-2  CAI  0.020
 2XS  plan-2  CAJ  0.020
 2XS  plan-2  CAA  0.020
 2XS  plan-2  CAB  0.020
 2XS  plan-2  CAC  0.020
 2XS  plan-2  CAD  0.020
 2XS  plan-2  CAE  0.020
 2XS  plan-2  NAK  0.020
 2XS  plan-2  H1   0.020
 2XS  plan-2  H2   0.020
 2XS  plan-2  H3   0.020
 2XS  plan-2  H4   0.020
 2XS  plan-2  H5   0.020
 2XS  plan-2  H6   0.020
 2XS  plan-3  CAE  0.020
 2XS  plan-3  NAK  0.020
 2XS  plan-3  CAL  0.020
 2XS  plan-3  OAM  0.020
 2XS  plan-3  CAN  0.020
 2XS  plan-3  H7   0.020
 2XS  plan-4  NAT  0.020
 2XS  plan-4  CAU  0.020
 2XS  plan-4  CAX  0.020
 2XS  plan-4  OBD  0.020
 2XS  plan-5  CAP  0.020
 2XS  plan-5  NAT  0.020
 2XS  plan-5  CAW  0.020
 2XS  plan-5  OBE  0.020
 2XS  plan-5  CAV  0.020
 2XS  plan-5  CAX  0.020

