# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 22:58:37 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 2,3-dimethoxy-12H-[1,3]dioxolo[5,6]indeno[1,2-c]isoquinolin-6-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2c[nH+]c3c(Cc4cc5OCOc5cc34)c2cc1OC
#
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
 AI3  AI3  2,3-dimethoxy-12H-[1,3]dioxolo[5,6]indeno[1,2-c]isoquinolin-6-ium  ligand  40  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AI3
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
 AI3  C1    C  CR16  0  -0.513   2.3051  -1.1317   0.0127
 AI3  C2    C  CR66  0   0.314   1.4158  -0.0397   0.0036
 AI3  C3    C  CR66  0  -0.036   1.9422   1.2847  -0.0109
 AI3  C4    C  CR16  0  -0.456   3.3464   1.4911  -0.0145
 AI3  C5    C  CR6   0   0.340   4.1940   0.4244  -0.0065
 AI3  C6    C  CR6   0   0.392   3.6599  -0.9173   0.0066
 AI3  C13   C  CR16  0   0.012   1.0674   2.3621  -0.0241
 AI3  N14   N  NR16  1  -0.656  -0.2481   2.1728  -0.0233
 AI3  C15   C  CR56  0   0.306  -0.7879   0.9366  -0.0089
 AI3  C16   C  CR56  0  -0.046   0.0224  -0.1755   0.0056
 AI3  C22   C  CH2   0  -0.547  -0.8337  -1.4018   0.0178
 AI3  C23   C  CR56  0   0.019  -2.2248  -0.8325   0.0068
 AI3  C24   C  CR56  0   0.137  -2.1841   0.5645  -0.0091
 AI3  C29   C  CR16  0  -0.394  -3.3394   1.3571  -0.0291
 AI3  C30   C  CR56  0   0.310  -4.5175   0.6584  -0.0356
 AI3  C31   C  CR56  0   0.320  -4.5643  -0.7358  -0.0218
 AI3  C32   C  CR16  0  -0.399  -3.4353  -1.5209   0.0029
 AI3  O38   O  O     0  -0.477  -5.8512  -1.1362  -0.0160
 AI3  C39   C  CH2   0   0.067  -6.6407   0.0301  -0.2196
 AI3  O40   O  O     0  -0.483  -5.7789   1.1444  -0.0344
 AI3  O45   O  O2    0  -0.438   4.5815  -1.8657   0.0105
 AI3  C47   C  CH3   0  -0.449   4.1658  -3.2242   0.0163
 AI3  O49   O  O2    0  -0.447   5.5242   0.4851  -0.0111
 AI3  C51   C  CH3   0  -0.447   6.1308   1.7665  -0.0292
 AI3  H1    H  HCR6  0   0.301   1.9027  -2.1351   0.0235
 AI3  H4    H  HCR6  0   0.303   3.7189   2.5065  -0.0254
 AI3  H13   H  HCR6  0   0.343   1.4053   3.3877  -0.0370
 AI3  H14   H  HNR6  0   0.457  -0.8492   2.9873  -0.0356
 AI3  H221  H  HCH2  0   0.301  -0.6471  -2.0388  -0.8517
 AI3  H222  H  HCH2  0   0.301  -0.6510  -2.0188   0.9024
 AI3  H29   H  HCR6  0   0.278  -3.3152   2.4389  -0.0375
 AI3  H32   H  HCR6  0   0.280  -3.4869  -2.6014   0.0165
 AI3  H391  H  HCH2  0   0.241  -7.0408   0.0322  -1.2384
 AI3  H392  H  HCH2  0   0.252  -7.4474   0.0607   0.5114
 AI3  H471  H  HCH3  0   0.244   3.5801  -3.4646  -0.8733
 AI3  H472  H  HCH3  0   0.274   5.0743  -3.8190   0.0179
 AI3  H473  H  HCH3  0   0.244   3.5815  -3.4578   0.9085
 AI3  H511  H  HCH3  0   0.271   7.2039   1.5983  -0.0344
 AI3  H512  H  HCH3  0   0.239   5.8512   2.3280  -0.9235
 AI3  H513  H  HCH3  0   0.239   5.8630   2.3482   0.8558

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
 AI3  C1   C2    aromatic  1.408  0.020  1.408
 AI3  C1   C6    aromatic  1.372  0.020  1.372
 AI3  C1   H1    single    0.930  0.020  1.080
 AI3  C2   C3    aromatic  1.425  0.020  1.425
 AI3  C2   C16   aromatic  1.400  0.020  1.400
 AI3  C3   C4    aromatic  1.419  0.020  1.419
 AI3  C3   C13   aromatic  1.388  0.020  1.388
 AI3  C4   C5    aromatic  1.362  0.020  1.362
 AI3  C4   H4    single    0.930  0.020  1.080
 AI3  C5   C6    aromatic  1.444  0.020  1.444
 AI3  C5   O49   single    1.332  0.020  1.332
 AI3  C6   O45   single    1.322  0.020  1.322
 AI3  C13  N14   aromatic  1.329  0.020  1.329
 AI3  C13  H13   single    0.930  0.020  1.080
 AI3  N14  C15   aromatic  1.349  0.020  1.349
 AI3  N14  H14   single    0.860  0.020  1.020
 AI3  C15  C16   aromatic  1.376  0.020  1.376
 AI3  C15  C24   aromatic  1.445  0.020  1.445
 AI3  C16  C22   single    1.496  0.020  1.496
 AI3  C22  C23   single    1.503  0.020  1.503
 AI3  C22  H221  single    0.970  0.020  1.090
 AI3  C22  H222  single    0.970  0.020  1.090
 AI3  C23  C24   aromatic  1.398  0.020  1.398
 AI3  C23  C32   aromatic  1.393  0.020  1.393
 AI3  C24  C29   aromatic  1.401  0.020  1.401
 AI3  C29  C30   aromatic  1.370  0.020  1.370
 AI3  C29  H29   single    0.930  0.020  1.080
 AI3  C30  C31   aromatic  1.395  0.020  1.395
 AI3  C30  O40   single    1.352  0.020  1.352
 AI3  C31  C32   aromatic  1.375  0.020  1.375
 AI3  C31  O38   single    1.348  0.020  1.348
 AI3  C32  H32   single    0.930  0.020  1.080
 AI3  O38  C39   single    1.423  0.020  1.423
 AI3  C39  O40   single    1.421  0.020  1.421
 AI3  C39  H391  single    0.970  0.020  1.090
 AI3  C39  H392  single    0.970  0.020  1.090
 AI3  O45  C47   single    1.421  0.020  1.421
 AI3  C47  H471  single    0.970  0.020  1.090
 AI3  C47  H472  single    0.970  0.020  1.090
 AI3  C47  H473  single    0.970  0.020  1.090
 AI3  O49  C51   single    1.418  0.020  1.418
 AI3  C51  H511  single    0.970  0.020  1.090
 AI3  C51  H512  single    0.970  0.020  1.090
 AI3  C51  H513  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
 AI3  H1    C1   C6    120.84  3.000
 AI3  H1    C1   C2    118.99  3.000
 AI3  C6    C1   C2    120.16  3.000
 AI3  C16   C2   C3    117.24  3.000
 AI3  C16   C2   C1    123.59  3.000
 AI3  C3    C2   C1    119.17  3.000
 AI3  C13   C3   C4    120.71  3.000
 AI3  C13   C3   C2    119.26  3.000
 AI3  C4    C3   C2    120.04  3.000
 AI3  H4    C4   C5    121.38  3.000
 AI3  H4    C4   C3    118.51  3.000
 AI3  C5    C4   C3    120.11  3.000
 AI3  O49   C5   C6    114.32  3.000
 AI3  O49   C5   C4    125.86  3.000
 AI3  C6    C5   C4    119.82  3.000
 AI3  O45   C6   C5    114.11  3.000
 AI3  O45   C6   C1    125.18  3.000
 AI3  C5    C6   C1    120.70  3.000
 AI3  H13   C13  N14   116.42  3.000
 AI3  H13   C13  C3    122.70  3.000
 AI3  N14   C13  C3    120.88  3.000
 AI3  H14   N14  C15   119.98  3.000
 AI3  H14   N14  C13   118.24  3.000
 AI3  C15   N14  C13   121.78  3.000
 AI3  C24   C15  C16   111.15  3.000
 AI3  C24   C15  N14   128.51  3.000
 AI3  C16   C15  N14   120.34  3.000
 AI3  C22   C16  C15   109.01  3.000
 AI3  C22   C16  C2    130.48  3.000
 AI3  C15   C16  C2    120.51  3.000
 AI3  H222  C22  H221  106.61  3.000
 AI3  H222  C22  C23   111.97  3.000
 AI3  H221  C22  C23   111.87  3.000
 AI3  H222  C22  C16   111.93  3.000
 AI3  H221  C22  C16   111.92  3.000
 AI3  C23   C22  C16   102.66  3.000
 AI3  C32   C23  C24   121.29  3.000
 AI3  C32   C23  C22   128.12  3.000
 AI3  C24   C23  C22   110.59  3.000
 AI3  C29   C24  C23   122.79  3.000
 AI3  C29   C24  C15   130.62  3.000
 AI3  C23   C24  C15   106.59  3.000
 AI3  H29   C29  C30   121.95  3.000
 AI3  H29   C29  C24   123.17  3.000
 AI3  C30   C29  C24   114.88  3.000
 AI3  O40   C30  C31   109.15  3.000
 AI3  O40   C30  C29   128.25  3.000
 AI3  C31   C30  C29   122.59  3.000
 AI3  O38   C31  C32   127.90  3.000
 AI3  O38   C31  C30   109.20  3.000
 AI3  C32   C31  C30   122.89  3.000
 AI3  H32   C32  C31   122.08  3.000
 AI3  H32   C32  C23   122.36  3.000
 AI3  C31   C32  C23   115.56  3.000
 AI3  C39   O38  C31   106.60  3.000
 AI3  H392  C39  H391  110.73  3.000
 AI3  H392  C39  O40   109.86  3.000
 AI3  H391  C39  O40   109.97  3.000
 AI3  H392  C39  O38   109.75  3.000
 AI3  H391  C39  O38   109.73  3.000
 AI3  O40   C39  O38   106.72  3.000
 AI3  C39   O40  C30   106.49  3.000
 AI3  C47   O45  C6    118.81  3.000
 AI3  H473  C47  H472  109.22  3.000
 AI3  H473  C47  H471  109.36  3.000
 AI3  H472  C47  H471  109.24  3.000
 AI3  H473  C47  O45   111.38  3.000
 AI3  H472  C47  O45   106.20  3.000
 AI3  H471  C47  O45   111.36  3.000
 AI3  C51   O49  C5    117.94  3.000
 AI3  H513  C51  H512  109.08  3.000
 AI3  H513  C51  H511  109.18  3.000
 AI3  H512  C51  H511  109.18  3.000
 AI3  H513  C51  O49   111.47  3.000
 AI3  H512  C51  O49   111.44  3.000
 AI3  H511  C51  O49   106.42  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
 AI3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 AI3  CONST_02  C13   C3   C2   C1    180.00   0.0  0
 AI3  CONST_03  C15   C16  C2   C1    180.00   0.0  0
 AI3  CONST_04  C4    C5   C6   C1      0.00   0.0  0
 AI3  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 AI3  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 AI3  CONST_07  N14   C13  C3   C2      0.00   0.0  0
 AI3  CONST_08  N14   C15  C16  C2      0.00   0.0  0
 AI3  CONST_09  C24   C15  C16  C2    180.00   0.0  0
 AI3  CONST_10  C6    C1   C2   C3      0.00   0.0  0
 AI3  CONST_11  C15   C16  C2   C3      0.00   0.0  0
 AI3  CONST_12  C6    C5   C4   C3      0.00   0.0  0
 AI3  CONST_13  C15   N14  C13  C3      0.00   0.0  0
 AI3  CONST_14  C16   C2   C3   C4    180.00   0.0  0
 AI3  CONST_15  N14   C13  C3   C4    180.00   0.0  0
 AI3  CONST_16  C13   C3   C4   C5    180.00   0.0  0
 AI3  CONST_17  C16   C2   C1   C6    180.00   0.0  0
 AI3  CONST_18  C16   C2   C3   C13     0.00   0.0  0
 AI3  CONST_19  C16   C15  N14  C13     0.00   0.0  0
 AI3  CONST_20  C24   C15  N14  C13   180.00   0.0  0
 AI3  CONST_21  C23   C24  C15  N14   180.00   0.0  0
 AI3  CONST_22  C29   C24  C15  N14     0.00   0.0  0
 AI3  CONST_23  C32   C23  C24  C15   180.00   0.0  0
 AI3  CONST_24  C30   C29  C24  C15   180.00   0.0  0
 AI3  CONST_25  C23   C24  C15  C16     0.00   0.0  0
 AI3  CONST_26  C29   C24  C15  C16   180.00   0.0  0
 AI3  CONST_27  C30   C29  C24  C23     0.00   0.0  0
 AI3  CONST_28  C30   C31  C32  C23     0.00   0.0  0
 AI3  CONST_29  C31   C32  C23  C24     0.00   0.0  0
 AI3  CONST_30  C31   C30  C29  C24     0.00   0.0  0
 AI3  CONST_31  C32   C23  C24  C29     0.00   0.0  0
 AI3  CONST_32  C32   C31  C30  C29     0.00   0.0  0
 AI3  CONST_33  O49   C5   C6   C1    180.00   0.0  0
 AI3  CONST_34  O45   C6   C1   C2    180.00   0.0  0
 AI3  CONST_35  O49   C5   C4   C3    180.00   0.0  0
 AI3  CONST_36  O45   C6   C5   C4    180.00   0.0  0
 AI3  CONST_37  H4    C4   C3   C2    180.00   0.0  0
 AI3  CONST_38  H13   C13  C3   C2    180.00   0.0  0
 AI3  CONST_39  H1    C1   C2   C3    180.00   0.0  0
 AI3  CONST_40  H14   N14  C13  C3    180.00   0.0  0
 AI3  CONST_41  H29   C29  C24  C15     0.00   0.0  0
 AI3  CONST_42  H32   C32  C23  C22     0.00   0.0  0
 AI3  Var_01    O38   C39  O40  C30    13.25  30.0  1
 AI3  Var_02    O40   C39  O38  C31   -13.16  30.0  1
 AI3  Var_03    H221  C22  C16  C2    -59.63  30.0  1
 AI3  Var_04    H511  C51  O49  C5   -179.76  30.0  3
 AI3  Var_05    H471  C47  O45  C6     61.14  30.0  3

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
 AI3  plan-1  C1   0.020
 AI3  plan-1  C2   0.020
 AI3  plan-1  C3   0.020
 AI3  plan-1  C4   0.020
 AI3  plan-1  C5   0.020
 AI3  plan-1  C6   0.020
 AI3  plan-1  C13  0.020
 AI3  plan-1  N14  0.020
 AI3  plan-1  C15  0.020
 AI3  plan-1  C16  0.020
 AI3  plan-1  C22  0.020
 AI3  plan-1  C23  0.020
 AI3  plan-1  C24  0.020
 AI3  plan-1  C29  0.020
 AI3  plan-1  C30  0.020
 AI3  plan-1  C31  0.020
 AI3  plan-1  C32  0.020
 AI3  plan-1  O38  0.020
 AI3  plan-1  O40  0.020
 AI3  plan-1  O45  0.020
 AI3  plan-1  O49  0.020
 AI3  plan-1  H1   0.020
 AI3  plan-1  H4   0.020
 AI3  plan-1  H13  0.020
 AI3  plan-1  H14  0.020
 AI3  plan-1  H29  0.020
 AI3  plan-1  H32  0.020

