# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:32:21 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cc2c3OCOc3ccc2c4ccc5cc6OCOc6cc5c14
#
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
 SAU  SAU  13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium  ligand  39  25  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SAU
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
 SAU  N     N  NR6   1  -0.495   0.3146   1.2959   0.5457
 SAU  C1    C  CH2   0   0.069  -6.1413   0.9984  -0.3899
 SAU  O1    O  O     0  -0.474  -4.9069   1.6985  -0.4898
 SAU  C2    C  CR56  0   0.327  -4.4882  -0.4504  -0.0320
 SAU  O2    O  O     0  -0.473  -5.8210  -0.3723  -0.1785
 SAU  C3    C  CR56  0   0.334  -3.9276   0.8221  -0.2058
 SAU  O3    O  O     0  -0.475   5.9330  -0.1164  -0.3615
 SAU  C4    C  CR16  0  -0.396  -3.7085  -1.5397   0.1775
 SAU  O4    O  O     0  -0.463   4.5381   1.6733  -0.0510
 SAU  C5    C  CR66  0   0.062  -2.3059  -1.3404   0.2509
 SAU  C6    C  CR66  0   0.098  -1.7356  -0.0412   0.1691
 SAU  C7    C  CR16  0  -0.390  -2.5927   1.0571  -0.1246
 SAU  C8    C  CR16  0  -0.283  -1.4604  -2.4717   0.3300
 SAU  C9    C  CR16  0  -0.366  -0.1127  -2.3475   0.2530
 SAU  C10   C  CR66  0   0.279  -0.3119   0.0663   0.3084
 SAU  C12   C  CR16  0   0.071   1.6120   1.4403   0.4236
 SAU  C13   C  CR66  0  -0.138   2.4613   0.3741   0.1228
 SAU  C14   C  CR66  0   0.292   1.9304  -0.9443   0.0944
 SAU  C15   C  CR66  0   0.017   0.5026  -1.0728   0.2206
 SAU  C18   C  CR16  0  -0.373   2.8021  -2.0220  -0.0875
 SAU  C19   C  CR16  0  -0.292   4.1682  -1.8339  -0.2501
 SAU  C20   C  CR56  0   0.306   4.6609  -0.5420  -0.2221
 SAU  C21   C  CR56  0   0.290   3.8351   0.5363  -0.0388
 SAU  C23   C  CH2   0   0.068   5.9158   1.2909  -0.1488
 SAU  C25   C  CH3   0  -0.589  -0.3925   2.4493   1.1375
 SAU  H1    H  HCH2  0   0.250  -6.7164   1.3790   0.4574
 SAU  H1A   H  HCH2  0   0.254  -6.7026   1.1072  -1.3182
 SAU  H4    H  HCR6  0   0.285  -4.1196  -2.5372   0.2557
 SAU  H7    H  HCR6  0   0.293  -2.2233   2.0448  -0.3416
 SAU  H8    H  HCR6  0   0.275  -1.9080  -3.4548   0.3976
 SAU  H9    H  HCR6  0   0.274   0.4972  -3.2382   0.2416
 SAU  H12   H  HCR6  0   0.350   2.0087   2.4250   0.6269
 SAU  H18   H  HCR6  0   0.279   2.4301  -3.0345  -0.1198
 SAU  H19   H  HCR6  0   0.304   4.8250  -2.6799  -0.3994
 SAU  H23   H  HCH2  0   0.255   6.4280   1.5367   0.7844
 SAU  H23A  H  HCH2  0   0.261   6.3741   1.8029  -0.9941
 SAU  H25   H  HCH3  0   0.307   0.2992   2.9629   1.7961
 SAU  H25A  H  HCH3  0   0.302  -0.7250   3.1377   0.3667
 SAU  H25B  H  HCH3  0   0.305  -1.2322   2.1022   1.7280

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
 SAU  N    C10   aromatic  1.400  0.020  1.400
 SAU  N    C12   aromatic  1.311  0.020  1.311
 SAU  N    C25   single    1.477  0.020  1.477
 SAU  C1   O1    single    1.423  0.020  1.423
 SAU  C1   O2    single    1.423  0.020  1.423
 SAU  O1   C3    single    1.345  0.020  1.345
 SAU  C2   O2    single    1.343  0.020  1.343
 SAU  C2   C3    aromatic  1.401  0.020  1.401
 SAU  C2   C4    aromatic  1.356  0.020  1.356
 SAU  C3   C7    aromatic  1.358  0.020  1.358
 SAU  O3   C20   single    1.349  0.020  1.349
 SAU  O3   C23   single    1.423  0.020  1.423
 SAU  C4   C5    aromatic  1.419  0.020  1.419
 SAU  O4   C21   single    1.337  0.020  1.337
 SAU  O4   C23   single    1.433  0.020  1.433
 SAU  C5   C6    aromatic  1.421  0.020  1.421
 SAU  C5   C8    aromatic  1.414  0.020  1.414
 SAU  C6   C7    aromatic  1.424  0.020  1.424
 SAU  C6   C10   aromatic  1.435  0.020  1.435
 SAU  C8   C9    aromatic  1.356  0.020  1.356
 SAU  C9   C15   aromatic  1.416  0.020  1.416
 SAU  C10  C15   aromatic  1.403  0.020  1.403
 SAU  C12  C13   aromatic  1.396  0.020  1.396
 SAU  C13  C14   aromatic  1.422  0.020  1.422
 SAU  C13  C21   aromatic  1.393  0.020  1.393
 SAU  C14  C15   aromatic  1.439  0.020  1.439
 SAU  C14  C18   aromatic  1.398  0.020  1.398
 SAU  C18  C19   aromatic  1.389  0.020  1.389
 SAU  C19  C20   aromatic  1.383  0.020  1.383
 SAU  C20  C21   aromatic  1.371  0.020  1.371
 SAU  C1   H1    single    0.970  0.020  1.090
 SAU  C1   H1A   single    0.970  0.020  1.090
 SAU  C4   H4    single    0.930  0.020  1.080
 SAU  C7   H7    single    0.930  0.020  1.080
 SAU  C8   H8    single    0.930  0.020  1.080
 SAU  C9   H9    single    0.930  0.020  1.080
 SAU  C12  H12   single    0.930  0.020  1.080
 SAU  C18  H18   single    0.930  0.020  1.080
 SAU  C19  H19   single    0.930  0.020  1.080
 SAU  C23  H23   single    0.970  0.020  1.090
 SAU  C23  H23A  single    0.970  0.020  1.090
 SAU  C25  H25   single    0.970  0.020  1.090
 SAU  C25  H25A  single    0.970  0.020  1.090
 SAU  C25  H25B  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
 SAU  C25   N    C12   115.16  3.000
 SAU  C25   N    C10   122.65  3.000
 SAU  C12   N    C10   121.58  3.000
 SAU  H1A   C1   H1    110.77  3.000
 SAU  H1A   C1   O2    109.78  3.000
 SAU  H1    C1   O2    109.80  3.000
 SAU  H1A   C1   O1    109.74  3.000
 SAU  H1    C1   O1    109.86  3.000
 SAU  O2    C1   O1    106.80  3.000
 SAU  C3    O1   C1    107.24  3.000
 SAU  C4    C2   C3    121.24  3.000
 SAU  C4    C2   O2    129.37  3.000
 SAU  C3    C2   O2    109.30  3.000
 SAU  C2    O2   C1    107.19  3.000
 SAU  C7    C3   C2    122.89  3.000
 SAU  C7    C3   O1    128.01  3.000
 SAU  C2    C3   O1    109.07  3.000
 SAU  C23   O3   C20   106.57  3.000
 SAU  H4    C4   C5    120.11  3.000
 SAU  H4    C4   C2    122.24  3.000
 SAU  C5    C4   C2    117.63  3.000
 SAU  C23   O4   C21   106.21  3.000
 SAU  C8    C5   C6    119.64  3.000
 SAU  C8    C5   C4    118.78  3.000
 SAU  C6    C5   C4    121.48  3.000
 SAU  C10   C6   C7    124.03  3.000
 SAU  C10   C6   C5    117.46  3.000
 SAU  C7    C6   C5    118.39  3.000
 SAU  H7    C7   C6    122.88  3.000
 SAU  H7    C7   C3    118.95  3.000
 SAU  C6    C7   C3    118.07  3.000
 SAU  H8    C8   C9    119.86  3.000
 SAU  H8    C8   C5    118.87  3.000
 SAU  C9    C8   C5    121.18  3.000
 SAU  H9    C9   C15   119.81  3.000
 SAU  H9    C9   C8    119.12  3.000
 SAU  C15   C9   C8    121.05  3.000
 SAU  C15   C10  C6    120.61  3.000
 SAU  C15   C10  N     117.63  3.000
 SAU  C6    C10  N     121.76  3.000
 SAU  H12   C12  C13   120.87  3.000
 SAU  H12   C12  N     116.49  3.000
 SAU  C13   C12  N     122.55  3.000
 SAU  C21   C13  C14   118.30  3.000
 SAU  C21   C13  C12   122.42  3.000
 SAU  C14   C13  C12   119.04  3.000
 SAU  C18   C14  C15   124.14  3.000
 SAU  C18   C14  C13   118.99  3.000
 SAU  C15   C14  C13   116.85  3.000
 SAU  C14   C15  C10   120.59  3.000
 SAU  C14   C15  C9    120.90  3.000
 SAU  C10   C15  C9    118.50  3.000
 SAU  H18   C18  C19   117.56  3.000
 SAU  H18   C18  C14   120.81  3.000
 SAU  C19   C18  C14   121.62  3.000
 SAU  H19   C19  C20   121.15  3.000
 SAU  H19   C19  C18   120.51  3.000
 SAU  C20   C19  C18   118.34  3.000
 SAU  C21   C20  C19   121.54  3.000
 SAU  C21   C20  O3    109.51  3.000
 SAU  C19   C20  O3    128.96  3.000
 SAU  C20   C21  C13   121.21  3.000
 SAU  C20   C21  O4    110.55  3.000
 SAU  C13   C21  O4    128.23  3.000
 SAU  H23A  C23  H23   111.09  3.000
 SAU  H23A  C23  O4    109.39  3.000
 SAU  H23   C23  O4    109.42  3.000
 SAU  H23A  C23  O3    110.10  3.000
 SAU  H23   C23  O3    110.14  3.000
 SAU  O4    C23  O3    106.60  3.000
 SAU  H25B  C25  H25A  110.65  3.000
 SAU  H25B  C25  H25   108.36  3.000
 SAU  H25A  C25  H25   109.04  3.000
 SAU  H25B  C25  N     109.84  3.000
 SAU  H25A  C25  N     110.94  3.000
 SAU  H25   C25  N     107.93  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
 SAU  CONST_01  C5   C6   C10  N     180.00   0.0  0
 SAU  CONST_03  C9   C15  C10  N     180.00   0.0  0
 SAU  CONST_04  C14  C15  C10  N       0.00   0.0  0
 SAU  CONST_05  C14  C13  C12  N       0.00   0.0  0
 SAU  CONST_06  C21  C13  C12  N     180.00   0.0  0
 SAU  CONST_07  C6   C7   C3   C2      0.00   0.0  0
 SAU  CONST_08  C6   C5   C4   C2      0.00   0.0  0
 SAU  CONST_09  C8   C5   C4   C2    180.00   0.0  0
 SAU  CONST_10  C5   C4   C2   C3      0.00   0.0  0
 SAU  CONST_11  C5   C6   C7   C3      0.00   0.0  0
 SAU  CONST_12  C10  C6   C7   C3    180.00   0.0  0
 SAU  CONST_13  C7   C3   C2   C4      0.00   0.0  0
 SAU  CONST_14  C7   C6   C5   C4      0.00   0.0  0
 SAU  CONST_15  C10  C6   C5   C4    180.00   0.0  0
 SAU  CONST_16  C9   C8   C5   C4    180.00   0.0  0
 SAU  CONST_17  C15  C10  C6   C5      0.00   0.0  0
 SAU  CONST_18  C15  C9   C8   C5      0.00   0.0  0
 SAU  CONST_19  C9   C8   C5   C6      0.00   0.0  0
 SAU  CONST_20  C12  N    C10  C6    180.00   0.0  0
 SAU  CONST_21  C9   C15  C10  C6      0.00   0.0  0
 SAU  CONST_22  C14  C15  C10  C6    180.00   0.0  0
 SAU  CONST_23  C8   C5   C6   C7    180.00   0.0  0
 SAU  CONST_25  C10  C6   C5   C8      0.00   0.0  0
 SAU  CONST_26  C10  C15  C9   C8      0.00   0.0  0
 SAU  CONST_27  C14  C15  C9   C8    180.00   0.0  0
 SAU  CONST_28  C13  C14  C15  C9    180.00   0.0  0
 SAU  CONST_29  C18  C14  C15  C9      0.00   0.0  0
 SAU  CONST_30  C13  C12  N    C10     0.00   0.0  0
 SAU  CONST_31  C13  C14  C15  C10     0.00   0.0  0
 SAU  CONST_32  C18  C14  C15  C10   180.00   0.0  0
 SAU  CONST_33  C15  C10  N    C12     0.00   0.0  0
 SAU  CONST_34  C15  C14  C13  C12     0.00   0.0  0
 SAU  CONST_35  C18  C14  C13  C12   180.00   0.0  0
 SAU  CONST_36  C20  C21  C13  C12   180.00   0.0  0
 SAU  CONST_37  C19  C18  C14  C13     0.00   0.0  0
 SAU  CONST_38  C19  C20  C21  C13     0.00   0.0  0
 SAU  CONST_39  C20  C21  C13  C14     0.00   0.0  0
 SAU  CONST_40  C20  C19  C18  C14     0.00   0.0  0
 SAU  CONST_41  C21  C13  C14  C15   180.00   0.0  0
 SAU  CONST_42  C19  C18  C14  C15   180.00   0.0  0
 SAU  CONST_43  C21  C13  C14  C18     0.00   0.0  0
 SAU  CONST_44  C21  C20  C19  C18     0.00   0.0  0
 SAU  CONST_46  C25  N    C12  C13   180.00   0.0  0
 SAU  CONST_48  H7   C7   C3   O1      0.00   0.0  0
 SAU  CONST_49  H4   C4   C2   O2      0.00   0.0  0
 SAU  CONST_50  H19  C19  C20  O3      0.00   0.0  0
 SAU  CONST_51  H8   C8   C5   C4      0.00   0.0  0
 SAU  CONST_52  H9   C9   C8   C5    180.00   0.0  0
 SAU  CONST_53  H12  C12  N    C10   180.00   0.0  0
 SAU  CONST_54  H18  C18  C14  C13   180.00   0.0  0
 SAU  Var_01    C2   C3   O1   C1      4.77  30.0  1
 SAU  Var_02    C3   C2   O2   C1     -2.79  30.0  1
 SAU  Var_03    H1   C1   O2   C2   -113.46  30.0  1
 SAU  Var_04    H23  C23  O3   C20   111.29  30.0  1
 SAU  Var_05    H25  C25  N    C10   142.80  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
 SAU  plan-1  N    0.020
 SAU  plan-1  O1   0.020
 SAU  plan-1  C2   0.020
 SAU  plan-1  O2   0.020
 SAU  plan-1  C3   0.020
 SAU  plan-1  O3   0.020
 SAU  plan-1  C4   0.020
 SAU  plan-1  O4   0.020
 SAU  plan-1  C5   0.020
 SAU  plan-1  C6   0.020
 SAU  plan-1  C7   0.020
 SAU  plan-1  C8   0.020
 SAU  plan-1  C9   0.020
 SAU  plan-1  C10  0.020
 SAU  plan-1  C12  0.020
 SAU  plan-1  C13  0.020
 SAU  plan-1  C14  0.020
 SAU  plan-1  C15  0.020
 SAU  plan-1  C18  0.020
 SAU  plan-1  C19  0.020
 SAU  plan-1  C20  0.020
 SAU  plan-1  C21  0.020
 SAU  plan-1  C25  0.020
 SAU  plan-1  H4   0.020
 SAU  plan-1  H7   0.020
 SAU  plan-1  H8   0.020
 SAU  plan-1  H9   0.020
 SAU  plan-1  H12  0.020
 SAU  plan-1  H18  0.020
 SAU  plan-1  H19  0.020

