# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 15:38:36 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 3,6-diaminoacridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2cc3ccc(N)cc3[nH+]c2c1
#
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
 PF  PF  '3,6-diaminoacridinium    '  ligand  28  16  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PF
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
 PF  C1    C  CR16  0  -0.294   2.4505   1.6415  -0.0242
 PF  C2    C  CR16  0  -0.325   3.6166   0.9500  -0.0294
 PF  C3    C  CR6   0   0.408   3.6122  -0.4813  -0.0317
 PF  C4    C  CR16  0  -0.437   2.3938  -1.1628  -0.0288
 PF  C5    C  CR16  0  -0.437  -2.3777  -1.2106  -0.0114
 PF  C6    C  CR6   0   0.408  -3.6094  -0.5537  -0.0059
 PF  C7    C  CR16  0  -0.325  -3.6423   0.8772  -0.0045
 PF  C8    C  CR16  0  -0.294  -2.4902   1.5919  -0.0077
 PF  C9    C  CR16  0  -0.174  -0.0201   1.6396  -0.0152
 PF  N10   N  NR16  1  -0.783   0.0071  -1.0888  -0.0196
 PF  C11   C  CR66  0   0.422   1.2050  -0.4490  -0.0228
 PF  C12   C  CR66  0   0.024  -1.2244   0.9496  -0.0120
 PF  C13   C  CR66  0   0.025   1.1978   0.9739  -0.0205
 PF  C14   C  CR66  0   0.422  -1.2032  -0.4729  -0.0143
 PF  N15   N  NH2   0  -0.849   4.7766  -1.1370  -0.0337
 PF  N16   N  NH2   0  -0.849  -4.7603  -1.2329   0.0004
 PF  H1    H  HCR6  0   0.278   2.4618   2.7238  -0.0222
 PF  H2    H  HCR6  0   0.281   4.5636   1.4742  -0.0324
 PF  H4    H  HCR6  0   0.285   2.3772  -2.2459  -0.0300
 PF  H5    H  HCR6  0   0.284  -2.3387  -2.2932  -0.0139
 PF  H7    H  HCR6  0   0.281  -4.5997   1.3822  -0.0011
 PF  H8    H  HCR6  0   0.278  -2.5236   2.6738  -0.0069
 PF  H9    H  HCR6  0   0.289  -0.0310   2.7237  -0.0136
 PF  H10   H  HNR6  0   0.433   0.0179  -2.1004  -0.0183
 PF  H151  H  HNH2  0   0.412   5.6534  -0.6462  -0.0503
 PF  H152  H  HNH2  0   0.412   4.8139  -2.1416  -0.0477
 PF  H161  H  HNH2  0   0.412  -5.6473  -0.7608  -0.0149
 PF  H162  H  HNH2  0   0.412  -4.7767  -2.2381  -0.0063

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
 PF  C1   C2    aromatic  1.356  0.020  1.356
 PF  C1   C13   aromatic  1.420  0.020  1.420
 PF  C1   H1    single    0.930  0.020  1.080
 PF  C2   C3    aromatic  1.431  0.020  1.431
 PF  C2   H2    single    0.930  0.020  1.080
 PF  C3   C4    aromatic  1.396  0.020  1.396
 PF  C3   N15   single    1.336  0.020  1.336
 PF  C4   C11   aromatic  1.387  0.020  1.387
 PF  C4   H4    single    0.930  0.020  1.080
 PF  C5   C6    aromatic  1.396  0.020  1.396
 PF  C5   C14   aromatic  1.387  0.020  1.387
 PF  C5   H5    single    0.930  0.020  1.080
 PF  C6   C7    aromatic  1.431  0.020  1.431
 PF  C6   N16   single    1.336  0.020  1.336
 PF  C7   C8    aromatic  1.356  0.020  1.356
 PF  C7   H7    single    0.930  0.020  1.080
 PF  C8   C12   aromatic  1.419  0.020  1.419
 PF  C8   H8    single    0.930  0.020  1.080
 PF  C9   C12   aromatic  1.388  0.020  1.388
 PF  C9   C13   aromatic  1.388  0.020  1.388
 PF  C9   H9    single    0.930  0.020  1.080
 PF  N10  C11   aromatic  1.358  0.020  1.358
 PF  N10  C14   aromatic  1.358  0.020  1.358
 PF  N10  H10   single    0.860  0.020  1.020
 PF  C11  C13   aromatic  1.423  0.020  1.423
 PF  C12  C14   aromatic  1.423  0.020  1.423
 PF  N15  H151  single    0.860  0.020  1.020
 PF  N15  H152  single    0.860  0.020  1.020
 PF  N16  H161  single    0.860  0.020  1.020
 PF  N16  H162  single    0.860  0.020  1.020

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
 PF  H1    C1   C13   118.64  3.000
 PF  H1    C1   C2    120.07  3.000
 PF  C13   C1   C2    121.28  3.000
 PF  H2    C2   C3    119.14  3.000
 PF  H2    C2   C1    120.37  3.000
 PF  C3    C2   C1    120.49  3.000
 PF  N15   C3   C4    121.39  3.000
 PF  N15   C3   C2    119.21  3.000
 PF  C4    C3   C2    119.40  3.000
 PF  H4    C4   C11   120.10  3.000
 PF  H4    C4   C3    120.10  3.000
 PF  C11   C4   C3    119.80  3.000
 PF  H5    C5   C14   120.07  3.000
 PF  H5    C5   C6    120.13  3.000
 PF  C14   C5   C6    119.80  3.000
 PF  N16   C6   C7    119.23  3.000
 PF  N16   C6   C5    121.38  3.000
 PF  C7    C6   C5    119.39  3.000
 PF  H7    C7   C8    120.38  3.000
 PF  H7    C7   C6    119.12  3.000
 PF  C8    C7   C6    120.50  3.000
 PF  H8    C8   C12   118.67  3.000
 PF  H8    C8   C7    120.05  3.000
 PF  C12   C8   C7    121.28  3.000
 PF  H9    C9   C13   119.24  3.000
 PF  H9    C9   C12   119.23  3.000
 PF  C13   C9   C12   121.53  3.000
 PF  H10   N10  C14   117.59  3.000
 PF  H10   N10  C11   117.49  3.000
 PF  C14   N10  C11   124.92  3.000
 PF  C13   C11  N10   117.82  3.000
 PF  C13   C11  C4    121.27  3.000
 PF  N10   C11  C4    120.91  3.000
 PF  C14   C12  C9    118.95  3.000
 PF  C14   C12  C8    117.76  3.000
 PF  C9    C12  C8    123.29  3.000
 PF  C11   C13  C9    118.95  3.000
 PF  C11   C13  C1    117.76  3.000
 PF  C9    C13  C1    123.29  3.000
 PF  C12   C14  N10   117.83  3.000
 PF  C12   C14  C5    121.28  3.000
 PF  N10   C14  C5    120.90  3.000
 PF  H152  N15  H151  117.09  3.000
 PF  H152  N15  C3    121.51  3.000
 PF  H151  N15  C3    121.37  3.000
 PF  H162  N16  H161  117.08  3.000
 PF  H162  N16  C6    121.48  3.000
 PF  H161  N16  C6    121.42  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
 PF  CONST_01  C4    C3   C2   C1     0.00  0.0  0
 PF  CONST_02  C12   C9   C13  C1   180.00  0.0  0
 PF  CONST_03  C4    C11  C13  C1     0.00  0.0  0
 PF  CONST_04  N10   C11  C13  C1   180.00  0.0  0
 PF  CONST_05  C9    C13  C1   C2   180.00  0.0  0
 PF  CONST_06  C11   C13  C1   C2     0.00  0.0  0
 PF  CONST_07  C11   C4   C3   C2     0.00  0.0  0
 PF  CONST_08  C13   C1   C2   C3     0.00  0.0  0
 PF  CONST_09  N10   C11  C4   C3   180.00  0.0  0
 PF  CONST_10  C13   C11  C4   C3     0.00  0.0  0
 PF  CONST_11  C14   N10  C11  C4   180.00  0.0  0
 PF  CONST_12  C9    C13  C11  C4   180.00  0.0  0
 PF  CONST_13  C8    C7   C6   C5     0.00  0.0  0
 PF  CONST_14  C11   N10  C14  C5   180.00  0.0  0
 PF  CONST_15  C8    C12  C14  C5     0.00  0.0  0
 PF  CONST_16  C9    C12  C14  C5   180.00  0.0  0
 PF  CONST_17  N10   C14  C5   C6   180.00  0.0  0
 PF  CONST_18  C12   C14  C5   C6     0.00  0.0  0
 PF  CONST_19  C12   C8   C7   C6     0.00  0.0  0
 PF  CONST_20  C14   C5   C6   C7     0.00  0.0  0
 PF  CONST_21  C9    C12  C8   C7   180.00  0.0  0
 PF  CONST_22  C14   C12  C8   C7     0.00  0.0  0
 PF  CONST_23  C13   C9   C12  C8   180.00  0.0  0
 PF  CONST_24  N10   C14  C12  C8   180.00  0.0  0
 PF  CONST_25  N10   C14  C12  C9     0.00  0.0  0
 PF  CONST_26  N10   C11  C13  C9     0.00  0.0  0
 PF  CONST_27  C12   C14  N10  C11    0.00  0.0  0
 PF  CONST_28  C12   C9   C13  C11    0.00  0.0  0
 PF  CONST_29  C14   C12  C9   C13    0.00  0.0  0
 PF  CONST_30  C14   N10  C11  C13    0.00  0.0  0
 PF  CONST_31  N15   C3   C2   C1   180.00  0.0  0
 PF  CONST_32  N16   C6   C7   C8   180.00  0.0  0
 PF  CONST_33  N15   C3   C4   C11  180.00  0.0  0
 PF  CONST_34  N16   C6   C5   C14  180.00  0.0  0
 PF  CONST_35  H9    C9   C13  C1     0.00  0.0  0
 PF  CONST_36  H4    C4   C3   C2   180.00  0.0  0
 PF  CONST_37  H1    C1   C2   C3   180.00  0.0  0
 PF  CONST_38  H2    C2   C3   C4   180.00  0.0  0
 PF  CONST_39  H10   N10  C11  C4     0.00  0.0  0
 PF  CONST_40  H7    C7   C6   C5   180.00  0.0  0
 PF  CONST_41  H8    C8   C7   C6   180.00  0.0  0
 PF  CONST_42  H5    C5   C6   C7   180.00  0.0  0
 PF  CONST_43  H151  N15  C3   C2     0.00  0.0  0
 PF  CONST_44  H152  N15  C3   C2   180.00  0.0  0
 PF  CONST_45  H161  N16  C6   C5   180.00  0.0  0
 PF  CONST_46  H162  N16  C6   C5     0.00  0.0  0

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
 PF  plan-1  C1    0.020
 PF  plan-1  C2    0.020
 PF  plan-1  C3    0.020
 PF  plan-1  C4    0.020
 PF  plan-1  C5    0.020
 PF  plan-1  C6    0.020
 PF  plan-1  C7    0.020
 PF  plan-1  C8    0.020
 PF  plan-1  C9    0.020
 PF  plan-1  N10   0.020
 PF  plan-1  C11   0.020
 PF  plan-1  C12   0.020
 PF  plan-1  C13   0.020
 PF  plan-1  C14   0.020
 PF  plan-1  N15   0.020
 PF  plan-1  N16   0.020
 PF  plan-1  H1    0.020
 PF  plan-1  H2    0.020
 PF  plan-1  H4    0.020
 PF  plan-1  H5    0.020
 PF  plan-1  H7    0.020
 PF  plan-1  H8    0.020
 PF  plan-1  H9    0.020
 PF  plan-1  H10   0.020
 PF  plan-2  C3    0.020
 PF  plan-2  N15   0.020
 PF  plan-2  H151  0.020
 PF  plan-2  H152  0.020
 PF  plan-3  C6    0.020
 PF  plan-3  N16   0.020
 PF  plan-3  H161  0.020
 PF  plan-3  H162  0.020

