# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 15:46:34 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-{2-[5-methyl-1-(pyridin-4-yl)-1H-benzimidazol-2-yl]ethyl}-1H-benzo[de]isoquinoline-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(c3ccncc3)c(CCN4C(=O)c5cccc6cccc(C4=O)c56)nc2c1
#
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
 AEL  AEL  2-{2-[5-methyl-1-(pyridin-4-yl)-1H-benzimidazol-2-yl]ethyl}-1H-benzo[de]isoquinoline-1,3(2H)-dione  ligand  53  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AEL
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
 AEL  C11  C  CR6   0   0.568  -2.2602   0.5266  -0.7617
 AEL  C13  C  CR6   0   0.565  -2.4030  -1.7807   0.0890
 AEL  O15  O  O     0  -0.426  -1.5602   1.4362  -1.1563
 AEL  C18  C  CR5   0   0.457   1.9875  -0.6452   0.3765
 AEL  C20  C  CR56  0   0.306   4.1160  -0.1257   0.0738
 AEL  C1   C  CR66  0   0.117  -5.8765  -0.2671   0.0464
 AEL  C2   C  CR16  0  -0.299  -6.4793   0.9578  -0.3144
 AEL  C3   C  CR16  0  -0.249  -5.7223   1.9922  -0.7997
 AEL  C4   C  CR16  0  -0.290  -4.3334   1.8482  -0.9431
 AEL  C5   C  CR66  0  -0.146  -3.7166   0.6661  -0.6033
 AEL  C6   C  C     0   0.300  -4.4778  -0.4093  -0.1051
 AEL  C7   C  CR66  0  -0.143  -3.8570  -1.6225   0.2507
 AEL  C8   C  CR16  0  -0.290  -4.6092  -2.6624   0.7466
 AEL  C9   C  CR16  0  -0.249  -5.9982  -2.5270   0.8967
 AEL  C10  C  CR16  0  -0.300  -6.6205  -1.3550   0.5534
 AEL  N12  N  NR6   0  -0.617  -1.7035  -0.7065  -0.4464
 AEL  O14  O  O     0  -0.430  -1.8201  -2.7992   0.3981
 AEL  C16  C  CH2   0  -0.321  -0.2656  -0.8668  -0.6360
 AEL  C17  C  CH2   0  -0.569   0.5257  -0.4989   0.6225
 AEL  N19  N  NR5   0  -0.653   2.8626   0.4127   0.2972
 AEL  C21  C  CR56  0   0.147   3.9092  -1.5078   0.0155
 AEL  N22  N  N     0  -0.465   2.5791  -1.7924   0.2133
 AEL  C23  C  CR16  0  -0.283   5.3679   0.4427  -0.1182
 AEL  C24  C  CR16  0  -0.311   6.4167  -0.4285  -0.3549
 AEL  C25  C  CR6   0   0.080   6.2443  -1.8246  -0.4073
 AEL  C26  C  CR16  0  -0.380   4.9806  -2.3657  -0.2258
 AEL  C27  C  CR6   0   0.385   2.5816   1.7830   0.4555
 AEL  C28  C  CR16  0  -0.360   3.2731   2.5295   1.3998
 AEL  C29  C  CR16  0  -0.059   2.9733   3.8776   1.5130
 AEL  N30  N  N     0  -0.402   2.0532   4.4912   0.7783
 AEL  C31  C  CR16  0  -0.060   1.3979   3.7641  -0.1177
 AEL  C32  C  CR16  0  -0.354   1.6284   2.4135  -0.3301
 AEL  C33  C  CH3   0  -0.720   7.4328  -2.7160  -0.6353
 AEL  H1   H  HCR6  0   0.276  -7.5504   1.0704  -0.2016
 AEL  H2   H  HCR6  0   0.276  -6.1903   2.9268  -1.0762
 AEL  H3   H  HCR6  0   0.276  -3.7499   2.6748  -1.3252
 AEL  H4   H  HCR6  0   0.277  -4.1317  -3.5924   1.0238
 AEL  H5   H  HCR6  0   0.276  -6.5734  -3.3560   1.2853
 AEL  H6   H  HCR6  0   0.276  -7.6921  -1.2509   0.6697
 AEL  H7   H  HCH2  0   0.287  -0.0654  -1.8994  -0.9085
 AEL  H8   H  HCH2  0   0.286   0.0373  -0.2469  -1.4767
 AEL  H9   H  HCH2  0   0.294   0.2516  -1.1714   1.4368
 AEL  H10  H  HCH2  0   0.282   0.2807   0.5124   0.9461
 AEL  H11  H  HCR6  0   0.271   5.5280   1.5124  -0.0913
 AEL  H12  H  HCR6  0   0.250   7.4075  -0.0190  -0.5107
 AEL  H13  H  HCR6  0   0.249   4.8235  -3.4367  -0.2746
 AEL  H14  H  HCR6  0   0.296   4.0177   2.0785   2.0417
 AEL  H15  H  HCR6  0   0.276   3.4981   4.4829   2.2427
 AEL  H16  H  HCR6  0   0.276   0.6521   4.2788  -0.7117
 AEL  H17  H  HCR6  0   0.295   1.0761   1.8812  -1.0916
 AEL  H18  H  HCH3  0   0.246   7.9418  -2.9392   0.3049
 AEL  H19  H  HCH3  0   0.243   7.1399  -3.6667  -1.0801
 AEL  H20  H  HCH3  0   0.242   8.1644  -2.2482  -1.2938

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
 AEL  C3   C2   aromatic  1.371  0.020  1.371
 AEL  C3   C4   aromatic  1.404  0.020  1.404
 AEL  C2   C1   aromatic  1.412  0.020  1.412
 AEL  C4   C5   aromatic  1.376  0.020  1.376
 AEL  C1   C10  aromatic  1.412  0.020  1.412
 AEL  C1   C6   aromatic  1.414  0.020  1.414
 AEL  C10  C9   aromatic  1.371  0.020  1.371
 AEL  C5   C6   aromatic  1.409  0.020  1.409
 AEL  C5   C11  single    1.472  0.020  1.472
 AEL  C6   C7   aromatic  1.409  0.020  1.409
 AEL  C9   C8   aromatic  1.404  0.020  1.404
 AEL  O15  C11  double    1.214  0.020  1.214
 AEL  C11  N12  single    1.389  0.020  1.389
 AEL  C7   C8   aromatic  1.376  0.020  1.376
 AEL  C7   C13  single    1.472  0.020  1.472
 AEL  N12  C13  single    1.389  0.020  1.389
 AEL  N12  C16  single    1.459  0.020  1.459
 AEL  C13  O14  double    1.213  0.020  1.213
 AEL  C16  C17  single    1.532  0.020  1.532
 AEL  C17  C18  single    1.490  0.020  1.490
 AEL  N22  C18  aromatic  1.301  0.020  1.301
 AEL  N22  C21  aromatic  1.374  0.020  1.374
 AEL  C18  N19  aromatic  1.375  0.020  1.375
 AEL  C21  C26  aromatic  1.394  0.020  1.394
 AEL  C21  C20  aromatic  1.399  0.020  1.399
 AEL  C26  C25  aromatic  1.387  0.020  1.387
 AEL  C32  C31  aromatic  1.386  0.020  1.386
 AEL  C32  C27  aromatic  1.387  0.020  1.387
 AEL  N19  C20  aromatic  1.382  0.020  1.382
 AEL  N19  C27  single    1.408  0.020  1.408
 AEL  C20  C23  aromatic  1.388  0.020  1.388
 AEL  C25  C33  single    1.503  0.020  1.503
 AEL  C25  C24  aromatic  1.408  0.020  1.408
 AEL  C31  N30  aromatic  1.327  0.020  1.327
 AEL  C27  C28  aromatic  1.388  0.020  1.388
 AEL  C23  C24  aromatic  1.384  0.020  1.384
 AEL  N30  C29  aromatic  1.328  0.020  1.328
 AEL  C28  C29  aromatic  1.386  0.020  1.386
 AEL  C2   H1   single    0.930  0.020  1.080
 AEL  C3   H2   single    0.930  0.020  1.080
 AEL  C4   H3   single    0.930  0.020  1.080
 AEL  C8   H4   single    0.930  0.020  1.080
 AEL  C9   H5   single    0.930  0.020  1.080
 AEL  C10  H6   single    0.930  0.020  1.080
 AEL  C16  H7   single    0.970  0.020  1.090
 AEL  C16  H8   single    0.970  0.020  1.090
 AEL  C17  H9   single    0.970  0.020  1.090
 AEL  C17  H10  single    0.970  0.020  1.090
 AEL  C23  H11  single    0.930  0.020  1.080
 AEL  C24  H12  single    0.930  0.020  1.080
 AEL  C26  H13  single    0.930  0.020  1.080
 AEL  C28  H14  single    0.930  0.020  1.080
 AEL  C29  H15  single    0.930  0.020  1.080
 AEL  C31  H16  single    0.930  0.020  1.080
 AEL  C32  H17  single    0.930  0.020  1.080
 AEL  C33  H18  single    0.970  0.020  1.090
 AEL  C33  H19  single    0.970  0.020  1.090
 AEL  C33  H20  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
 AEL  N12  C11  C5   117.15  3.000
 AEL  N12  C11  O15  120.52  3.000
 AEL  C5   C11  O15  122.33  3.000
 AEL  O14  C13  N12  120.36  3.000
 AEL  O14  C13  C7   122.47  3.000
 AEL  N12  C13  C7   117.17  3.000
 AEL  N22  C18  N19  112.44  3.000
 AEL  N19  C18  C17  123.95  3.000
 AEL  N22  C18  C17  123.61  3.000
 AEL  C23  C20  C21  122.15  3.000
 AEL  C23  C20  N19  132.89  3.000
 AEL  C21  C20  N19  104.92  3.000
 AEL  C10  C1   C6   118.82  3.000
 AEL  C6   C1   C2   118.82  3.000
 AEL  C10  C1   C2   122.35  3.000
 AEL  H1   C2   C3   120.31  3.000
 AEL  H1   C2   C1   119.07  3.000
 AEL  C3   C2   C1   120.62  3.000
 AEL  H2   C3   C4   119.40  3.000
 AEL  H2   C3   C2   120.26  3.000
 AEL  C4   C3   C2   120.34  3.000
 AEL  H3   C4   C5   120.13  3.000
 AEL  H3   C4   C3   119.44  3.000
 AEL  C5   C4   C3   120.43  3.000
 AEL  C6   C5   C4   120.06  3.000
 AEL  C6   C5   C11  120.04  3.000
 AEL  C4   C5   C11  119.90  3.000
 AEL  C7   C6   C5   120.58  3.000
 AEL  C7   C6   C1   119.70  3.000
 AEL  C5   C6   C1   119.72  3.000
 AEL  C8   C7   C6   120.07  3.000
 AEL  C8   C7   C13  119.90  3.000
 AEL  C6   C7   C13  120.03  3.000
 AEL  H4   C8   C9   119.50  3.000
 AEL  H4   C8   C7   120.06  3.000
 AEL  C9   C8   C7   120.44  3.000
 AEL  H5   C9   C10  120.28  3.000
 AEL  H5   C9   C8   119.40  3.000
 AEL  C10  C9   C8   120.33  3.000
 AEL  H6   C10  C9   120.30  3.000
 AEL  H6   C10  C1   119.07  3.000
 AEL  C9   C10  C1   120.63  3.000
 AEL  C16  N12  C13  117.46  3.000
 AEL  C16  N12  C11  117.58  3.000
 AEL  C13  N12  C11  124.90  3.000
 AEL  H8   C16  H7   107.25  3.000
 AEL  H8   C16  C17  110.75  3.000
 AEL  H7   C16  C17  109.83  3.000
 AEL  H8   C16  N12  108.20  3.000
 AEL  H7   C16  N12  108.58  3.000
 AEL  C17  C16  N12  112.09  3.000
 AEL  H10  C17  H9   107.09  3.000
 AEL  H10  C17  C16  110.53  3.000
 AEL  H9   C17  C16  109.60  3.000
 AEL  H10  C17  C18  111.15  3.000
 AEL  H9   C17  C18  108.02  3.000
 AEL  C16  C17  C18  110.35  3.000
 AEL  C27  N19  C20  125.34  3.000
 AEL  C27  N19  C18  127.97  3.000
 AEL  C20  N19  C18  106.66  3.000
 AEL  C26  C21  N22  129.90  3.000
 AEL  C26  C21  C20  120.12  3.000
 AEL  N22  C21  C20  109.98  3.000
 AEL  C21  N22  C18  105.99  3.000
 AEL  H11  C23  C24  120.97  3.000
 AEL  H11  C23  C20  122.34  3.000
 AEL  C24  C23  C20  116.70  3.000
 AEL  H12  C24  C25  118.78  3.000
 AEL  H12  C24  C23  118.67  3.000
 AEL  C25  C24  C23  122.55  3.000
 AEL  C33  C25  C26  120.60  3.000
 AEL  C33  C25  C24  119.81  3.000
 AEL  C26  C25  C24  119.59  3.000
 AEL  H13  C26  C25  120.80  3.000
 AEL  H13  C26  C21  120.32  3.000
 AEL  C25  C26  C21  118.89  3.000
 AEL  C32  C27  C28  118.89  3.000
 AEL  C28  C27  N19  120.03  3.000
 AEL  C32  C27  N19  121.07  3.000
 AEL  H14  C28  C29  120.41  3.000
 AEL  H14  C28  C27  121.49  3.000
 AEL  C29  C28  C27  118.10  3.000
 AEL  H15  C29  N30  116.75  3.000
 AEL  H15  C29  C28  119.58  3.000
 AEL  N30  C29  C28  123.67  3.000
 AEL  C31  N30  C29  117.55  3.000
 AEL  H16  C31  C32  119.55  3.000
 AEL  H16  C31  N30  116.73  3.000
 AEL  C32  C31  N30  123.72  3.000
 AEL  H17  C32  C31  120.18  3.000
 AEL  H17  C32  C27  121.77  3.000
 AEL  C31  C32  C27  118.06  3.000
 AEL  H20  C33  H19  107.96  3.000
 AEL  H20  C33  H18  107.15  3.000
 AEL  H19  C33  H18  107.36  3.000
 AEL  H20  C33  C25  111.58  3.000
 AEL  H19  C33  C25  111.52  3.000
 AEL  H18  C33  C25  111.05  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
 AEL  CONST_01  C26  C21  N22  C18   180.00   0.0  0
 AEL  CONST_02  C20  C21  N22  C18     0.00   0.0  0
 AEL  CONST_03  C21  C20  N19  C18     0.00   0.0  0
 AEL  CONST_04  C23  C20  N19  C18   180.00   0.0  0
 AEL  CONST_07  C25  C26  C21  C20     0.00   0.0  0
 AEL  CONST_08  N22  C18  N19  C20     0.00   0.0  0
 AEL  CONST_11  C25  C24  C23  C20     0.00   0.0  0
 AEL  CONST_12  C4   C3   C2   C1      0.00   0.0  0
 AEL  CONST_13  C8   C9   C10  C1      0.00   0.0  0
 AEL  CONST_14  C4   C5   C6   C1      0.00   0.0  0
 AEL  CONST_15  C8   C7   C6   C1      0.00   0.0  0
 AEL  CONST_16  C5   C4   C3   C2      0.00   0.0  0
 AEL  CONST_17  C9   C10  C1   C2    180.00   0.0  0
 AEL  CONST_18  C5   C6   C1   C2      0.00   0.0  0
 AEL  CONST_19  C7   C6   C1   C2    180.00   0.0  0
 AEL  CONST_20  C10  C1   C2   C3    180.00   0.0  0
 AEL  CONST_21  C6   C1   C2   C3      0.00   0.0  0
 AEL  CONST_22  C6   C5   C4   C3      0.00   0.0  0
 AEL  CONST_23  C7   C6   C5   C4    180.00   0.0  0
 AEL  CONST_24  C10  C1   C6   C5    180.00   0.0  0
 AEL  CONST_25  C8   C7   C6   C5    180.00   0.0  0
 AEL  CONST_26  C9   C10  C1   C6      0.00   0.0  0
 AEL  CONST_27  C9   C8   C7   C6      0.00   0.0  0
 AEL  CONST_28  C10  C1   C6   C7      0.00   0.0  0
 AEL  CONST_29  C10  C9   C8   C7      0.00   0.0  0
 AEL  CONST_30  C21  N22  C18  N19     0.00   0.0  0
 AEL  CONST_31  N22  C21  C20  N19     0.00   0.0  0
 AEL  CONST_32  C26  C21  C20  N19   180.00   0.0  0
 AEL  CONST_33  C24  C23  C20  N19   180.00   0.0  0
 AEL  CONST_34  C31  C32  C27  N19   180.00   0.0  0
 AEL  CONST_35  C29  C28  C27  N19   180.00   0.0  0
 AEL  CONST_36  C24  C25  C26  C21     0.00   0.0  0
 AEL  CONST_37  C27  N19  C20  C21   180.00   0.0  0
 AEL  CONST_38  C24  C23  C20  C21     0.00   0.0  0
 AEL  CONST_39  C27  N19  C18  N22   180.00   0.0  0
 AEL  CONST_40  C25  C26  C21  N22   180.00   0.0  0
 AEL  CONST_41  C23  C20  C21  N22   180.00   0.0  0
 AEL  CONST_42  C26  C21  C20  C23     0.00   0.0  0
 AEL  CONST_43  C27  N19  C20  C23     0.00   0.0  0
 AEL  CONST_44  C26  C25  C24  C23     0.00   0.0  0
 AEL  CONST_45  N30  C31  C32  C27     0.00   0.0  0
 AEL  CONST_46  N30  C29  C28  C27     0.00   0.0  0
 AEL  CONST_47  C31  C32  C27  C28     0.00   0.0  0
 AEL  CONST_48  C31  N30  C29  C28     0.00   0.0  0
 AEL  CONST_49  C32  C31  N30  C29     0.00   0.0  0
 AEL  CONST_50  C32  C27  C28  C29     0.00   0.0  0
 AEL  CONST_51  C5   C11  N12  C13     0.00   0.0  0
 AEL  CONST_52  C17  C18  N19  C20   180.00   0.0  0
 AEL  CONST_53  C21  N22  C18  C17   180.00   0.0  0
 AEL  CONST_54  C27  N19  C18  C17     0.00   0.0  0
 AEL  CONST_55  C33  C25  C26  C21   180.00   0.0  0
 AEL  CONST_56  C33  C25  C24  C23   180.00   0.0  0
 AEL  CONST_57  O15  C11  N12  C13   180.00   0.0  0
 AEL  CONST_58  C16  N12  C11  C5    180.00   0.0  0
 AEL  CONST_59  H3   C4   C5   C11     0.00   0.0  0
 AEL  CONST_60  H4   C8   C7   C13     0.00   0.0  0
 AEL  CONST_61  H13  C26  C21  C20   180.00   0.0  0
 AEL  CONST_62  H12  C24  C23  C20   180.00   0.0  0
 AEL  CONST_63  H2   C3   C2   C1    180.00   0.0  0
 AEL  CONST_64  H5   C9   C10  C1    180.00   0.0  0
 AEL  CONST_65  H6   C10  C1   C2      0.00   0.0  0
 AEL  CONST_66  H1   C2   C3   C4    180.00   0.0  0
 AEL  CONST_67  H11  C23  C20  N19     0.00   0.0  0
 AEL  CONST_68  H17  C32  C27  N19     0.00   0.0  0
 AEL  CONST_69  H14  C28  C27  N19     0.00   0.0  0
 AEL  CONST_70  H16  C31  C32  C27   180.00   0.0  0
 AEL  CONST_71  H15  C29  C28  C27   180.00   0.0  0
 AEL  CONST_72  C16  N12  C11  O15     0.00   0.0  0
 AEL  Var_01    C17  C16  N12  C11    90.44  30.0  3
 AEL  Var_02    N12  C16  C17  C18  -178.66  30.0  1
 AEL  Var_03    N22  C18  C17  C16   -69.58  30.0  2
 AEL  Var_04    H18  C33  C25  C24    85.40  30.0  2

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
 AEL  plan-1  N19  0.020
 AEL  plan-1  C27  0.020
 AEL  plan-1  C28  0.020
 AEL  plan-1  C29  0.020
 AEL  plan-1  N30  0.020
 AEL  plan-1  C31  0.020
 AEL  plan-1  C32  0.020
 AEL  plan-1  H14  0.020
 AEL  plan-1  H15  0.020
 AEL  plan-1  H16  0.020
 AEL  plan-1  H17  0.020
 AEL  plan-2  C18  0.020
 AEL  plan-2  C20  0.020
 AEL  plan-2  C17  0.020
 AEL  plan-2  N19  0.020
 AEL  plan-2  C21  0.020
 AEL  plan-2  N22  0.020
 AEL  plan-2  C23  0.020
 AEL  plan-2  C24  0.020
 AEL  plan-2  C25  0.020
 AEL  plan-2  C26  0.020
 AEL  plan-2  C27  0.020
 AEL  plan-2  C33  0.020
 AEL  plan-2  H11  0.020
 AEL  plan-2  H12  0.020
 AEL  plan-2  H13  0.020
 AEL  plan-3  C11  0.020
 AEL  plan-3  C13  0.020
 AEL  plan-3  O15  0.020
 AEL  plan-3  C1   0.020
 AEL  plan-3  C2   0.020
 AEL  plan-3  C3   0.020
 AEL  plan-3  C4   0.020
 AEL  plan-3  C5   0.020
 AEL  plan-3  C6   0.020
 AEL  plan-3  C7   0.020
 AEL  plan-3  C8   0.020
 AEL  plan-3  C9   0.020
 AEL  plan-3  C10  0.020
 AEL  plan-3  N12  0.020
 AEL  plan-3  O14  0.020
 AEL  plan-3  C16  0.020
 AEL  plan-3  H1   0.020
 AEL  plan-3  H2   0.020
 AEL  plan-3  H3   0.020
 AEL  plan-3  H4   0.020
 AEL  plan-3  H5   0.020
 AEL  plan-3  H6   0.020

