# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 10:10:52 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1Oc2cc3CC[n+]4cc5c6OCOc6ccc5cc4c3cc2O1
#
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
 KPT  KPT  6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium  ligand  38  24  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KPT
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
 KPT  C36  C  CH2   0   0.070  -6.0230   0.6811   0.0139
 KPT  O4   O  O     0  -0.476  -5.8835  -0.7279   0.1715
 KPT  O3   O  O     0  -0.466  -4.6986   1.2176  -0.0827
 KPT  C18  C  CR56  0   0.280  -3.8627   0.1770   0.0275
 KPT  C13  C  CR66  0  -0.112  -2.4674   0.1832  -0.0013
 KPT  C14  C  CR16  0   0.080  -1.6974   1.3346  -0.1526
 KPT  C17  C  CR56  0   0.312  -4.5607  -0.9886   0.1808
 KPT  C16  C  CR16  0  -0.304  -3.9298  -2.2205   0.3236
 KPT  C15  C  CR16  0  -0.335  -2.5494  -2.2511   0.3086
 KPT  C12  C  CR66  0   0.280  -1.8032  -1.0728   0.1416
 KPT  C11  C  CR16  0  -0.451  -0.3963  -1.0574   0.1159
 KPT  C10  C  CR66  0   0.401   0.3160   0.0967  -0.0580
 KPT  N    N  N     1  -0.501  -0.3819   1.2830  -0.1807
 KPT  C9   C  C     0  -0.320   0.3788   2.5283  -0.3883
 KPT  C8   C  C     0  -0.539   1.5830   2.5478   0.5229
 KPT  C6   C  CR66  0   0.060   1.7784   0.1525  -0.0913
 KPT  C5   C  CR66  0   0.101   2.4272   1.3425   0.2392
 KPT  C4   C  CR16  0  -0.399   3.8231   1.4094   0.2913
 KPT  C7   C  CR16  0  -0.422   2.5141  -1.0076  -0.4083
 KPT  C3   C  CR56  0   0.323   3.8754  -0.9167  -0.3477
 KPT  C2   C  CR56  0   0.323   4.5194   0.2640   0.0006
 KPT  O2   O  O     0  -0.476   5.8514   0.0797  -0.0449
 KPT  O1   O  O     0  -0.483   4.7970  -1.8642  -0.6279
 KPT  C1   C  CH2   0   0.069   6.0671  -1.3003  -0.3282
 KPT  H1   H  HCH2  0   0.256  -6.5734   0.9023  -0.9019
 KPT  H21  H  HCH2  0   0.256  -6.5257   1.1069   0.8838
 KPT  H2   H  HCR6  0   0.350  -2.1464   2.3120  -0.2570
 KPT  H3   H  HCR6  0   0.303  -4.5056  -3.1272   0.4498
 KPT  H4   H  HCR6  0   0.282  -2.0319  -3.1934   0.4232
 KPT  H5   H  HCR6  0   0.298   0.1350  -1.9878   0.2582
 KPT  H6   H  H     0   0.306   0.6826   2.5568  -1.4358
 KPT  H7   H  H     0   0.302  -0.2903   3.3623  -0.1969
 KPT  H8   H  H     0   0.293   2.1410   3.4652   0.3381
 KPT  H9   H  H     0   0.284   1.2637   2.5707   1.5691
 KPT  H10  H  HCR6  0   0.282   4.3262   2.3332   0.5450
 KPT  H11  H  HCR6  0   0.281   2.0331  -1.9269  -0.7128
 KPT  H12  H  HCH2  0   0.250   6.7290  -1.3993  -1.1889
 KPT  H14  H  HCH2  0   0.244   6.4975  -1.7929   0.5478

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
 KPT  O4   C36  single    1.425  0.020  1.425
 KPT  O3   C36  single    1.432  0.020  1.432
 KPT  C18  O3   single    1.339  0.020  1.339
 KPT  C13  C14  aromatic  1.393  0.020  1.393
 KPT  C13  C18  aromatic  1.396  0.020  1.396
 KPT  C17  C18  aromatic  1.367  0.020  1.367
 KPT  C17  O4   single    1.348  0.020  1.348
 KPT  C16  C17  aromatic  1.391  0.020  1.391
 KPT  C15  C12  aromatic  1.405  0.020  1.405
 KPT  C15  C16  aromatic  1.381  0.020  1.381
 KPT  C12  C13  aromatic  1.428  0.020  1.428
 KPT  C11  C10  aromatic  1.367  0.020  1.367
 KPT  C11  C12  aromatic  1.407  0.020  1.407
 KPT  C10  N    aromatic  1.382  0.020  1.382
 KPT  N    C9   single    1.474  0.020  1.474
 KPT  N    C14  aromatic  1.317  0.020  1.317
 KPT  C8   C9   single    1.510  0.020  1.510
 KPT  C6   C5   aromatic  1.395  0.020  1.395
 KPT  C6   C10  aromatic  1.464  0.020  1.464
 KPT  C5   C8   single    1.499  0.020  1.499
 KPT  C4   C5   aromatic  1.398  0.020  1.398
 KPT  C7   C6   aromatic  1.410  0.020  1.410
 KPT  C3   C2   aromatic  1.389  0.020  1.389
 KPT  C3   C7   aromatic  1.366  0.020  1.366
 KPT  C2   C4   aromatic  1.372  0.020  1.372
 KPT  O2   C2   single    1.345  0.020  1.345
 KPT  O1   C3   single    1.351  0.020  1.351
 KPT  C1   O1   single    1.422  0.020  1.422
 KPT  C1   O2   single    1.425  0.020  1.425
 KPT  C36  H1   single    0.970  0.020  1.090
 KPT  C36  H21  single    0.970  0.020  1.090
 KPT  C14  H2   single    0.930  0.020  1.080
 KPT  C16  H3   single    0.930  0.020  1.080
 KPT  C15  H4   single    0.930  0.020  1.080
 KPT  C11  H5   single    0.930  0.020  1.080
 KPT  C9   H6   single    0.970  0.020  1.090
 KPT  C9   H7   single    0.970  0.020  1.090
 KPT  C8   H8   single    0.970  0.020  1.090
 KPT  C8   H9   single    0.970  0.020  1.090
 KPT  C4   H10  single    0.930  0.020  1.080
 KPT  C7   H11  single    0.930  0.020  1.080
 KPT  C1   H12  single    0.970  0.020  1.090
 KPT  C1   H14  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
 KPT  H21  C36  H1   110.95  3.000
 KPT  H21  C36  O3   109.49  3.000
 KPT  H1   C36  O3   109.51  3.000
 KPT  H21  C36  O4   110.05  3.000
 KPT  H1   C36  O4   110.05  3.000
 KPT  O3   C36  O4   106.70  3.000
 KPT  C17  O4   C36  106.74  3.000
 KPT  C18  O3   C36  106.30  3.000
 KPT  C17  C18  C13  121.10  3.000
 KPT  C17  C18  O3   110.67  3.000
 KPT  C13  C18  O3   128.23  3.000
 KPT  C12  C13  C14  118.73  3.000
 KPT  C12  C13  C18  117.32  3.000
 KPT  C14  C13  C18  123.95  3.000
 KPT  H2   C14  N    116.64  3.000
 KPT  H2   C14  C13  121.89  3.000
 KPT  N    C14  C13  121.47  3.000
 KPT  C16  C17  C18  122.33  3.000
 KPT  C16  C17  O4   128.08  3.000
 KPT  C18  C17  O4   109.59  3.000
 KPT  H3   C16  C15  121.00  3.000
 KPT  H3   C16  C17  120.86  3.000
 KPT  C15  C16  C17  118.14  3.000
 KPT  H4   C15  C12  119.31  3.000
 KPT  H4   C15  C16  119.78  3.000
 KPT  C12  C15  C16  120.92  3.000
 KPT  C11  C12  C15  122.85  3.000
 KPT  C11  C12  C13  116.97  3.000
 KPT  C15  C12  C13  120.18  3.000
 KPT  H5   C11  C10  119.16  3.000
 KPT  H5   C11  C12  118.66  3.000
 KPT  C10  C11  C12  122.16  3.000
 KPT  C6   C10  N    118.02  3.000
 KPT  C6   C10  C11  123.74  3.000
 KPT  N    C10  C11  118.22  3.000
 KPT  C9   N    C10  118.50  3.000
 KPT  C9   N    C14  119.05  3.000
 KPT  C10  N    C14  122.43  3.000
 KPT  H7   C9   H6   108.70  3.000
 KPT  H7   C9   C8   112.02  3.000
 KPT  H6   C9   C8   110.91  3.000
 KPT  H7   C9   N    107.82  3.000
 KPT  H6   C9   N    107.52  3.000
 KPT  C8   C9   N    109.72  3.000
 KPT  H9   C8   H8   107.10  3.000
 KPT  H9   C8   C5   111.25  3.000
 KPT  H8   C8   C5   110.89  3.000
 KPT  H9   C8   C9   110.15  3.000
 KPT  H8   C8   C9   108.47  3.000
 KPT  C5   C8   C9   108.94  3.000
 KPT  C7   C6   C5   120.83  3.000
 KPT  C7   C6   C10  119.67  3.000
 KPT  C5   C6   C10  119.45  3.000
 KPT  C4   C5   C6   120.92  3.000
 KPT  C4   C5   C8   121.12  3.000
 KPT  C6   C5   C8   117.96  3.000
 KPT  H10  C4   C2   121.77  3.000
 KPT  H10  C4   C5   120.91  3.000
 KPT  C2   C4   C5   117.32  3.000
 KPT  H11  C7   C3   120.83  3.000
 KPT  H11  C7   C6   122.06  3.000
 KPT  C3   C7   C6   117.09  3.000
 KPT  O1   C3   C2   109.38  3.000
 KPT  O1   C3   C7   128.61  3.000
 KPT  C2   C3   C7   121.99  3.000
 KPT  O2   C2   C3   109.51  3.000
 KPT  O2   C2   C4   128.62  3.000
 KPT  C3   C2   C4   121.83  3.000
 KPT  C1   O2   C2   106.82  3.000
 KPT  C1   O1   C3   106.71  3.000
 KPT  H14  C1   H12  110.65  3.000
 KPT  H14  C1   O1   109.99  3.000
 KPT  H12  C1   O1   109.87  3.000
 KPT  H14  C1   O2   109.67  3.000
 KPT  H12  C1   O2   109.68  3.000
 KPT  O1   C1   O2   106.90  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
 KPT  CONST_01  N    C14  C13  C18   180.00   0.0  0
 KPT  CONST_02  C15  C12  C13  C18     0.00   0.0  0
 KPT  CONST_03  C11  C12  C13  C18   180.00   0.0  0
 KPT  CONST_04  C15  C16  C17  C18     0.00   0.0  0
 KPT  CONST_05  C10  N    C14  C13     0.00   0.0  0
 KPT  CONST_06  C16  C17  C18  C13     0.00   0.0  0
 KPT  CONST_07  C16  C15  C12  C13     0.00   0.0  0
 KPT  CONST_08  C10  C11  C12  C13     0.00   0.0  0
 KPT  CONST_09  C17  C18  C13  C14   180.00   0.0  0
 KPT  CONST_10  C15  C12  C13  C14   180.00   0.0  0
 KPT  CONST_11  C11  C12  C13  C14     0.00   0.0  0
 KPT  CONST_12  C11  C10  N    C14     0.00   0.0  0
 KPT  CONST_13  C6   C10  N    C14   180.00   0.0  0
 KPT  CONST_14  C12  C13  C18  C17     0.00   0.0  0
 KPT  CONST_15  C12  C15  C16  C17     0.00   0.0  0
 KPT  CONST_16  C11  C12  C15  C16   180.00   0.0  0
 KPT  CONST_17  C10  C11  C12  C15   180.00   0.0  0
 KPT  CONST_18  N    C14  C13  C12     0.00   0.0  0
 KPT  CONST_19  N    C10  C11  C12     0.00   0.0  0
 KPT  CONST_20  C6   C10  C11  C12   180.00   0.0  0
 KPT  CONST_23  C4   C5   C6   C10   180.00   0.0  0
 KPT  CONST_24  C3   C7   C6   C10   180.00   0.0  0
 KPT  CONST_27  C2   C4   C5   C6      0.00   0.0  0
 KPT  CONST_28  C2   C3   C7   C6      0.00   0.0  0
 KPT  CONST_29  C3   C7   C6   C5      0.00   0.0  0
 KPT  CONST_30  C3   C2   C4   C5      0.00   0.0  0
 KPT  CONST_31  C7   C6   C5   C4      0.00   0.0  0
 KPT  CONST_32  C7   C3   C2   C4      0.00   0.0  0
 KPT  CONST_33  H3   C16  C17  O4      0.00   0.0  0
 KPT  CONST_34  H2   C14  C13  C18     0.00   0.0  0
 KPT  CONST_35  H4   C15  C12  C13   180.00   0.0  0
 KPT  CONST_36  H5   C11  C12  C13   180.00   0.0  0
 KPT  CONST_37  H11  C7   C6   C10     0.00   0.0  0
 KPT  CONST_38  H10  C4   C5   C8      0.00   0.0  0
 KPT  Var_01    C18  C17  O4   C36    -0.46  30.0  1
 KPT  Var_02    C13  C18  O3   C36  -179.81  30.0  1
 KPT  Var_03    C8   C9   N    C14   138.81  30.0  1
 KPT  Var_04    C5   C8   C9   N      58.02  30.0  1
 KPT  Var_05    C6   C5   C8   C9    -35.88  30.0  1
 KPT  Var_06    O2   C1   O1   C3     -8.18  30.0  1
 KPT  Var_07    O1   C1   O2   C2      7.95  30.0  1
 KPT  Var_08    H1   C36  O3   C18  -119.66  30.0  1

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
 KPT  plan-1  O4   0.020
 KPT  plan-1  O3   0.020
 KPT  plan-1  C18  0.020
 KPT  plan-1  C13  0.020
 KPT  plan-1  C14  0.020
 KPT  plan-1  C17  0.020
 KPT  plan-1  C16  0.020
 KPT  plan-1  C15  0.020
 KPT  plan-1  C12  0.020
 KPT  plan-1  C11  0.020
 KPT  plan-1  C10  0.020
 KPT  plan-1  N    0.020
 KPT  plan-1  C9   0.020
 KPT  plan-1  C6   0.020
 KPT  plan-1  H2   0.020
 KPT  plan-1  H3   0.020
 KPT  plan-1  H4   0.020
 KPT  plan-1  H5   0.020
 KPT  plan-2  C10  0.020
 KPT  plan-2  C8   0.020
 KPT  plan-2  C6   0.020
 KPT  plan-2  C5   0.020
 KPT  plan-2  C4   0.020
 KPT  plan-2  C7   0.020
 KPT  plan-2  C3   0.020
 KPT  plan-2  C2   0.020
 KPT  plan-2  O2   0.020
 KPT  plan-2  O1   0.020
 KPT  plan-2  H10  0.020
 KPT  plan-2  H11  0.020

