# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 14:14:48 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-ethyl-6-[(3aR,6aS)-hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-1-phenyl-1H-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nn(c2ccccc2)c3cc(ccc13)N4C[C@@H]5CNC[C@@H]5C4
#
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
 LJ9  LJ9  3-ethyl-6-[(3aR,6aS)-hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-1-phenyl-1H-indazole  ligand  49  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LJ9
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
 LJ9  C01   C  CH3   0  -0.664  -3.5744  -3.9424   1.3410
 LJ9  C02   C  CH2   0  -0.521  -3.7684  -3.1699   0.0372
 LJ9  C03   C  CR5   0   0.272  -2.9412  -1.9318  -0.0250
 LJ9  N04   N  N     0  -0.281  -3.4754  -0.7415   0.0108
 LJ9  N05   N  NR5   0  -0.533  -2.4638   0.1602  -0.0190
 LJ9  C06   C  CR56  0   0.504  -1.2470  -0.4587  -0.0934
 LJ9  C07   C  CR16  0  -0.461   0.0468   0.0515  -0.2135
 LJ9  C08   C  CR6   0   0.402   1.1053  -0.8562  -0.2913
 LJ9  C09   C  CR16  0  -0.356   0.8242  -2.2549  -0.2873
 LJ9  C10   C  CR16  0  -0.324  -0.4569  -2.7350  -0.1938
 LJ9  C11   C  CR56  0  -0.177  -1.5207  -1.8326  -0.0926
 LJ9  N12   N  NT    0  -0.521   2.4047  -0.4225  -0.3549
 LJ9  C13   C  CH2   0  -0.296   3.4636  -1.2516  -0.9089
 LJ9  C14   C  CH1   0  -0.269   4.7247  -0.4144  -0.7331
 LJ9  C15   C  CH2   0  -0.280   5.5112  -0.7266   0.5450
 LJ9  N16   N  NH1   0  -0.608   5.9628   0.5814   0.9828
 LJ9  C17   C  CH2   0  -0.281   4.7919   1.4289   0.8488
 LJ9  C18   C  CH1   0  -0.267   4.2359   1.0419  -0.5273
 LJ9  C19   C  CH2   0  -0.298   2.7145   0.9742  -0.5939
 LJ9  C20   C  CR6   0   0.343  -2.7625   1.5310  -0.0282
 LJ9  C21   C  CR16  0  -0.316  -1.9650   2.4341   0.6687
 LJ9  C22   C  CR16  0  -0.252  -2.2682   3.7881   0.6385
 LJ9  C23   C  CR16  0  -0.262  -3.3747   4.2473  -0.0615
 LJ9  C24   C  CR16  0  -0.251  -4.1803   3.3384  -0.7367
 LJ9  C25   C  CR16  0  -0.294  -3.8767   1.9862  -0.7300
 LJ9  H01   H  HCH3  0   0.229  -3.8497  -3.3333   2.2023
 LJ9  H01A  H  HCH3  0   0.236  -4.1974  -4.8368   1.3505
 LJ9  H01B  H  HCH3  0   0.227  -2.5395  -4.2593   1.4723
 LJ9  H02   H  HCH2  0   0.244  -3.5178  -3.8171  -0.8076
 LJ9  H02A  H  HCH2  0   0.249  -4.8188  -2.8981  -0.0790
 LJ9  H07   H  HCR6  0   0.275   0.2161   1.1161  -0.2614
 LJ9  H09   H  HCR6  0   0.264   1.6351  -2.9648  -0.3574
 LJ9  H10   H  HCR6  0   0.253  -0.6309  -3.8037  -0.2064
 LJ9  H13   H  HCH2  0   0.248   3.5440  -2.2023  -0.3795
 LJ9  H13A  H  HCH2  0   0.231   3.2757  -1.4806  -1.9657
 LJ9  H14   H  HCH1  0   0.261   5.3712  -0.5008  -1.6064
 LJ9  H15   H  HCH2  0   0.200   4.8456  -1.2148   1.2750
 LJ9  H15A  H  HCH2  0   0.231   6.3504  -1.4023   0.3699
 LJ9  HN16  H  HNH1  0   0.349   6.3108   0.5632   1.9328
 LJ9  H17   H  HCH2  0   0.200   4.0314   1.2309   1.6211
 LJ9  H17A  H  HCH2  0   0.231   5.0548   2.4863   0.9158
 LJ9  H18   H  HCH1  0   0.260   4.6258   1.7086  -1.2964
 LJ9  H19   H  HCH2  0   0.231   2.3409   1.3046  -1.5729
 LJ9  H19A  H  HCH2  0   0.244   2.2493   1.6130   0.1608
 LJ9  H21   H  HCR6  0   0.276  -1.1239   2.0879   1.2540
 LJ9  H22   H  HCR6  0   0.263  -1.6415   4.4821   1.1830
 LJ9  H23   H  HCR6  0   0.259  -3.6129   5.3025  -0.0756
 LJ9  H24   H  HCR6  0   0.262  -5.0485   3.6840  -1.2824
 LJ9  H25   H  HCR6  0   0.268  -4.4996   1.2846  -1.2677

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
 LJ9  C01  C02   single    1.528  0.020  1.528
 LJ9  C01  H01   single    0.970  0.020  1.090
 LJ9  C01  H01A  single    0.970  0.020  1.090
 LJ9  C01  H01B  single    0.970  0.020  1.090
 LJ9  C02  C03   single    1.490  0.020  1.490
 LJ9  C02  H02   single    0.970  0.020  1.090
 LJ9  C02  H02A  single    0.970  0.020  1.090
 LJ9  C03  C11   aromatic  1.426  0.020  1.426
 LJ9  C03  N04   aromatic  1.305  0.020  1.305
 LJ9  N04  N05   aromatic  1.355  0.020  1.355
 LJ9  N05  C06   aromatic  1.367  0.020  1.367
 LJ9  N05  C20   single    1.403  0.020  1.403
 LJ9  C11  C06   aromatic  1.401  0.020  1.401
 LJ9  C06  C07   aromatic  1.396  0.020  1.396
 LJ9  C08  C07   aromatic  1.397  0.020  1.397
 LJ9  C07  H07   single    0.930  0.020  1.080
 LJ9  C09  C08   aromatic  1.427  0.020  1.427
 LJ9  C08  N12   single    1.371  0.020  1.371
 LJ9  C10  C09   aromatic  1.371  0.020  1.371
 LJ9  C09  H09   single    0.930  0.020  1.080
 LJ9  C10  C11   aromatic  1.399  0.020  1.399
 LJ9  C10  H10   single    0.930  0.020  1.080
 LJ9  C13  N12   single    1.455  0.020  1.455
 LJ9  N12  C19   single    1.451  0.020  1.451
 LJ9  C13  C14   single    1.524  0.020  1.524
 LJ9  C13  H13   single    0.970  0.020  1.090
 LJ9  C13  H13A  single    0.970  0.020  1.090
 LJ9  C14  C18   single    1.550  0.020  1.550
 LJ9  C14  C15   single    1.533  0.020  1.533
 LJ9  C14  H14   single    0.970  0.020  1.090
 LJ9  C15  N16   single    1.451  0.020  1.451
 LJ9  C15  H15   single    0.970  0.020  1.090
 LJ9  C15  H15A  single    0.970  0.020  1.090
 LJ9  C17  N16   single    1.452  0.020  1.452
 LJ9  N16  HN16  single    0.890  0.020  1.040
 LJ9  C18  C17   single    1.534  0.020  1.534
 LJ9  C17  H17   single    0.970  0.020  1.090
 LJ9  C17  H17A  single    0.970  0.020  1.090
 LJ9  C19  C18   single    1.524  0.020  1.524
 LJ9  C18  H18   single    0.970  0.020  1.090
 LJ9  C19  H19   single    0.970  0.020  1.090
 LJ9  C19  H19A  single    0.970  0.020  1.090
 LJ9  C21  C20   aromatic  1.392  0.020  1.392
 LJ9  C20  C25   aromatic  1.393  0.020  1.393
 LJ9  C21  C22   aromatic  1.388  0.020  1.388
 LJ9  C21  H21   single    0.930  0.020  1.080
 LJ9  C22  C23   aromatic  1.388  0.020  1.388
 LJ9  C22  H22   single    0.930  0.020  1.080
 LJ9  C23  C24   aromatic  1.390  0.020  1.390
 LJ9  C23  H23   single    0.930  0.020  1.080
 LJ9  C25  C24   aromatic  1.386  0.020  1.386
 LJ9  C24  H24   single    0.930  0.020  1.080
 LJ9  C25  H25   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
 LJ9  H01B  C01  H01A  107.63  3.000
 LJ9  H01B  C01  H01   107.88  3.000
 LJ9  H01A  C01  H01   107.89  3.000
 LJ9  H01B  C01  C02   111.73  3.000
 LJ9  H01A  C01  C02   110.47  3.000
 LJ9  H01   C01  C02   111.08  3.000
 LJ9  H02A  C02  H02   106.61  3.000
 LJ9  H02A  C02  C03   108.84  3.000
 LJ9  H02   C02  C03   109.41  3.000
 LJ9  H02A  C02  C01   109.82  3.000
 LJ9  H02   C02  C01   109.33  3.000
 LJ9  C03   C02  C01   112.65  3.000
 LJ9  C11   C03  N04   110.23  3.000
 LJ9  N04   C03  C02   121.96  3.000
 LJ9  C11   C03  C02   127.79  3.000
 LJ9  N05   N04  C03   107.49  3.000
 LJ9  C20   N05  C06   129.15  3.000
 LJ9  C20   N05  N04   119.42  3.000
 LJ9  C06   N05  N04   111.37  3.000
 LJ9  C11   C06  C07   122.66  3.000
 LJ9  C07   C06  N05   131.62  3.000
 LJ9  C11   C06  N05   105.66  3.000
 LJ9  H07   C07  C08   121.33  3.000
 LJ9  H07   C07  C06   120.65  3.000
 LJ9  C08   C07  C06   118.01  3.000
 LJ9  N12   C08  C09   119.79  3.000
 LJ9  N12   C08  C07   121.01  3.000
 LJ9  C09   C08  C07   119.19  3.000
 LJ9  H09   C09  C10   118.41  3.000
 LJ9  H09   C09  C08   119.76  3.000
 LJ9  C10   C09  C08   121.83  3.000
 LJ9  H10   C10  C11   121.02  3.000
 LJ9  H10   C10  C09   119.66  3.000
 LJ9  C11   C10  C09   119.32  3.000
 LJ9  C10   C11  C06   118.95  3.000
 LJ9  C10   C11  C03   135.76  3.000
 LJ9  C06   C11  C03   105.24  3.000
 LJ9  C19   N12  C13   109.31  3.000
 LJ9  C19   N12  C08   120.97  3.000
 LJ9  C13   N12  C08   121.82  3.000
 LJ9  H13A  C13  H13   107.34  3.000
 LJ9  H13A  C13  C14   111.55  3.000
 LJ9  H13   C13  C14   111.21  3.000
 LJ9  H13A  C13  N12   111.16  3.000
 LJ9  H13   C13  N12   111.44  3.000
 LJ9  C14   C13  N12   104.20  3.000
 LJ9  H14   C14  C18   111.59  3.000
 LJ9  H14   C14  C15   110.34  3.000
 LJ9  C18   C14  C15   104.03  3.000
 LJ9  H14   C14  C13   110.78  3.000
 LJ9  C15   C14  C13   114.13  3.000
 LJ9  C18   C14  C13   105.70  3.000
 LJ9  H15A  C15  H15   107.24  3.000
 LJ9  H15A  C15  N16   111.54  3.000
 LJ9  H15   C15  N16   112.79  3.000
 LJ9  H15A  C15  C14   112.76  3.000
 LJ9  H15   C15  C14   109.43  3.000
 LJ9  N16   C15  C14   103.16  3.000
 LJ9  HN16  N16  C17   112.00  3.000
 LJ9  HN16  N16  C15   111.96  3.000
 LJ9  C17   N16  C15   104.32  3.000
 LJ9  H17A  C17  H17   107.29  3.000
 LJ9  H17A  C17  C18   112.76  3.000
 LJ9  H17   C17  C18   109.47  3.000
 LJ9  H17A  C17  N16   111.44  3.000
 LJ9  H17   C17  N16   112.77  3.000
 LJ9  C18   C17  N16   103.17  3.000
 LJ9  H18   C18  C19   110.69  3.000
 LJ9  H18   C18  C17   110.43  3.000
 LJ9  C19   C18  C17   114.35  3.000
 LJ9  H18   C18  C14   111.60  3.000
 LJ9  C19   C18  C14   105.50  3.000
 LJ9  C17   C18  C14   104.00  3.000
 LJ9  H19A  C19  H19   107.16  3.000
 LJ9  H19A  C19  C18   111.64  3.000
 LJ9  H19   C19  C18   111.40  3.000
 LJ9  H19A  C19  N12   110.99  3.000
 LJ9  H19   C19  N12   111.34  3.000
 LJ9  C18   C19  N12   104.40  3.000
 LJ9  C25   C20  C21   119.90  3.000
 LJ9  C25   C20  N05   119.52  3.000
 LJ9  C21   C20  N05   120.58  3.000
 LJ9  H21   C21  C22   119.60  3.000
 LJ9  H21   C21  C20   120.59  3.000
 LJ9  C22   C21  C20   119.80  3.000
 LJ9  H22   C22  C23   120.23  3.000
 LJ9  H22   C22  C21   119.23  3.000
 LJ9  C23   C22  C21   120.53  3.000
 LJ9  H23   C23  C24   120.27  3.000
 LJ9  H23   C23  C22   120.32  3.000
 LJ9  C24   C23  C22   119.41  3.000
 LJ9  H24   C24  C25   119.33  3.000
 LJ9  H24   C24  C23   120.08  3.000
 LJ9  C25   C24  C23   120.59  3.000
 LJ9  H25   C25  C24   120.29  3.000
 LJ9  H25   C25  C20   119.95  3.000
 LJ9  C24   C25  C20   119.76  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
 LJ9  CONST_01  N05  C06  C11  C03     0.00   0.0  0
 LJ9  CONST_02  C07  C06  C11  C03   180.00   0.0  0
 LJ9  CONST_03  C09  C10  C11  C03   180.00   0.0  0
 LJ9  CONST_04  C06  N05  N04  C03     0.00   0.0  0
 LJ9  CONST_05  C20  N05  N04  C03   180.00   0.0  0
 LJ9  CONST_06  C06  C11  C03  N04     0.00   0.0  0
 LJ9  CONST_07  C10  C11  C03  N04   180.00   0.0  0
 LJ9  CONST_08  C11  C06  N05  N04     0.00   0.0  0
 LJ9  CONST_09  C07  C06  N05  N04   180.00   0.0  0
 LJ9  CONST_12  C11  C03  N04  N05     0.00   0.0  0
 LJ9  CONST_13  C10  C11  C06  N05   180.00   0.0  0
 LJ9  CONST_14  C08  C07  C06  N05   180.00   0.0  0
 LJ9  CONST_15  C22  C21  C20  N05   180.00   0.0  0
 LJ9  CONST_16  C24  C25  C20  N05   180.00   0.0  0
 LJ9  CONST_19  C09  C10  C11  C06     0.00   0.0  0
 LJ9  CONST_20  C09  C08  C07  C06     0.00   0.0  0
 LJ9  CONST_21  C20  N05  C06  C07     0.00   0.0  0
 LJ9  CONST_22  C10  C11  C06  C07     0.00   0.0  0
 LJ9  CONST_23  C10  C09  C08  C07     0.00   0.0  0
 LJ9  CONST_24  C11  C06  C07  C08     0.00   0.0  0
 LJ9  CONST_25  C11  C10  C09  C08     0.00   0.0  0
 LJ9  CONST_26  C20  N05  C06  C11   180.00   0.0  0
 LJ9  CONST_27  C23  C22  C21  C20     0.00   0.0  0
 LJ9  CONST_28  C23  C24  C25  C20     0.00   0.0  0
 LJ9  CONST_29  C24  C25  C20  C21     0.00   0.0  0
 LJ9  CONST_30  C24  C23  C22  C21     0.00   0.0  0
 LJ9  CONST_31  C25  C20  C21  C22     0.00   0.0  0
 LJ9  CONST_32  C25  C24  C23  C22     0.00   0.0  0
 LJ9  CONST_33  N12  C08  C07  C06   180.00   0.0  0
 LJ9  CONST_34  N12  C08  C09  C10   180.00   0.0  0
 LJ9  CONST_35  C06  C11  C03  C02   180.00   0.0  0
 LJ9  CONST_36  C10  C11  C03  C02     0.00   0.0  0
 LJ9  CONST_37  N05  N04  C03  C02   180.00   0.0  0
 LJ9  CONST_38  H10  C10  C11  C03     0.00   0.0  0
 LJ9  CONST_39  H07  C07  C06  N05     0.00   0.0  0
 LJ9  CONST_40  H21  C21  C20  N05     0.00   0.0  0
 LJ9  CONST_41  H25  C25  C20  N05     0.00   0.0  0
 LJ9  CONST_42  H09  C09  C08  C07   180.00   0.0  0
 LJ9  CONST_43  H22  C22  C21  C20   180.00   0.0  0
 LJ9  CONST_44  H24  C24  C25  C20   180.00   0.0  0
 LJ9  CONST_45  H23  C23  C22  C21   180.00   0.0  0
 LJ9  Var_01    C13  N12  C08  C07  -157.30  30.0  2
 LJ9  Var_02    C14  C13  N12  C08  -177.87  30.0  1
 LJ9  Var_03    C18  C19  N12  C08   177.52  30.0  1
 LJ9  Var_04    C17  N16  C15  C14    45.09  30.0  1
 LJ9  Var_05    C18  C17  N16  C15   -44.99  30.0  1
 LJ9  Var_06    C11  C03  C02  C01    66.83  30.0  2
 LJ9  Var_07    H01  C01  C02  C03    60.08  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
 LJ9  chir_01  C14  C13  C18  C15  negativ
 LJ9  chir_02  C18  C14  C17  C19  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
 LJ9  plan-1  N05  0.020
 LJ9  plan-1  C20  0.020
 LJ9  plan-1  C21  0.020
 LJ9  plan-1  C22  0.020
 LJ9  plan-1  C23  0.020
 LJ9  plan-1  C24  0.020
 LJ9  plan-1  C25  0.020
 LJ9  plan-1  H21  0.020
 LJ9  plan-1  H22  0.020
 LJ9  plan-1  H23  0.020
 LJ9  plan-1  H24  0.020
 LJ9  plan-1  H25  0.020
 LJ9  plan-2  C02  0.020
 LJ9  plan-2  C03  0.020
 LJ9  plan-2  N04  0.020
 LJ9  plan-2  N05  0.020
 LJ9  plan-2  C06  0.020
 LJ9  plan-2  C07  0.020
 LJ9  plan-2  C08  0.020
 LJ9  plan-2  C09  0.020
 LJ9  plan-2  C10  0.020
 LJ9  plan-2  C11  0.020
 LJ9  plan-2  N12  0.020
 LJ9  plan-2  C20  0.020
 LJ9  plan-2  H07  0.020
 LJ9  plan-2  H09  0.020
 LJ9  plan-2  H10  0.020

