# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:02:15 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: acridin-10-ium-9-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1c2ccccc2[nH+]c3ccccc13
#
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
 AA  AA  'acridin-10-ium-9-amine   '  ligand  26  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AA
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
 AA  C1   C  CR16  0  -0.305  -2.5011   1.1576   0.0019
 AA  C2   C  CR16  0  -0.243  -3.6543   0.4218  -0.0001
 AA  C3   C  CR16  0  -0.245  -3.5889  -0.9824   0.0005
 AA  C4   C  CR16  0  -0.309  -2.3809  -1.6261   0.0022
 AA  C5   C  CR16  0  -0.309   2.3821  -1.6201   0.0042
 AA  C6   C  CR16  0  -0.245   3.5884  -0.9734   0.0076
 AA  C7   C  CR16  0  -0.243   3.6502   0.4309   0.0144
 AA  C8   C  CR16  0  -0.305   2.4953   1.1638   0.0164
 AA  C9   C  CR6   0   0.505  -0.0031   1.2638   0.0096
 AA  N10  N  NR16  1  -0.783   0.0005  -1.5163   0.0042
 AA  C11  C  CR66  0   0.357   1.1915  -0.8735   0.0058
 AA  C12  C  CR66  0   0.011   1.2316   0.5337   0.0105
 AA  C13  C  CR66  0   0.010  -1.2360   0.5305   0.0057
 AA  C14  C  CR66  0   0.357  -1.1923  -0.8766   0.0046
 AA  N9   N  NH2   0  -0.820  -0.0047   2.5783   0.0120
 AA  H1   H  HCR6  0   0.266  -2.5862   2.2356  -0.0007
 AA  H2   H  HCR6  0   0.279  -4.6136   0.9194  -0.0028
 AA  H3   H  HCR6  0   0.285  -4.5012  -1.5633  -0.0014
 AA  H4   H  HCR6  0   0.293  -2.3277  -2.7071   0.0013
 AA  H5   H  HCR6  0   0.293   2.3315  -2.7013   0.0003
 AA  H6   H  HCR6  0   0.285   4.5021  -1.5521   0.0060
 AA  H7   H  HCR6  0   0.279   4.6082   0.9311   0.0194
 AA  H8   H  HCR6  0   0.266   2.5779   2.2419   0.0242
 AA  H10  H  HNR6  0   0.438   0.0020  -2.5272   0.0023
 AA  H91  H  HNH2  0   0.441   0.8425   3.1203   0.0086
 AA  H92  H  HNH2  0   0.441  -0.8535   3.1179   0.0179

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
 AA  C1   C2   aromatic  1.368  0.020  1.368
 AA  C1   C13  aromatic  1.412  0.020  1.412
 AA  C1   H1   single    0.930  0.020  1.080
 AA  C2   C3   aromatic  1.406  0.020  1.406
 AA  C2   H2   single    0.930  0.020  1.080
 AA  C3   C4   aromatic  1.369  0.020  1.369
 AA  C3   H3   single    0.930  0.020  1.080
 AA  C4   C14  aromatic  1.405  0.020  1.405
 AA  C4   H4   single    0.930  0.020  1.080
 AA  C5   C6   aromatic  1.369  0.020  1.369
 AA  C5   C11  aromatic  1.405  0.020  1.405
 AA  C5   H5   single    0.930  0.020  1.080
 AA  C6   C7   aromatic  1.406  0.020  1.406
 AA  C6   H6   single    0.930  0.020  1.080
 AA  C7   C8   aromatic  1.368  0.020  1.368
 AA  C7   H7   single    0.930  0.020  1.080
 AA  C8   C12  aromatic  1.412  0.020  1.412
 AA  C8   H8   single    0.930  0.020  1.080
 AA  C9   C12  aromatic  1.434  0.020  1.434
 AA  C9   C13  aromatic  1.435  0.020  1.435
 AA  C9   N9   single    1.314  0.020  1.314
 AA  N10  C11  aromatic  1.353  0.020  1.353
 AA  N10  C14  aromatic  1.354  0.020  1.354
 AA  N10  H10  single    0.860  0.020  1.020
 AA  C11  C12  aromatic  1.408  0.020  1.408
 AA  C13  C14  aromatic  1.408  0.020  1.408
 AA  N9   H91  single    0.860  0.020  1.020
 AA  N9   H92  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
 AA  H1   C1   C13  120.88  3.000
 AA  H1   C1   C2   118.03  3.000
 AA  C13  C1   C2   121.09  3.000
 AA  H2   C2   C3   120.08  3.000
 AA  H2   C2   C1   120.04  3.000
 AA  C3   C2   C1   119.88  3.000
 AA  H3   C3   C4   119.46  3.000
 AA  H3   C3   C2   119.82  3.000
 AA  C4   C3   C2   120.72  3.000
 AA  H4   C4   C14  119.41  3.000
 AA  H4   C4   C3   120.87  3.000
 AA  C14  C4   C3   119.71  3.000
 AA  H5   C5   C11  119.41  3.000
 AA  H5   C5   C6   120.88  3.000
 AA  C11  C5   C6   119.71  3.000
 AA  H6   C6   C7   119.83  3.000
 AA  H6   C6   C5   119.46  3.000
 AA  C7   C6   C5   120.71  3.000
 AA  H7   C7   C8   120.03  3.000
 AA  H7   C7   C6   120.09  3.000
 AA  C8   C7   C6   119.88  3.000
 AA  H8   C8   C12  120.88  3.000
 AA  H8   C8   C7   118.02  3.000
 AA  C12  C8   C7   121.10  3.000
 AA  N9   C9   C13  120.67  3.000
 AA  N9   C9   C12  120.67  3.000
 AA  C13  C9   C12  118.66  3.000
 AA  H10  N10  C14  118.29  3.000
 AA  H10  N10  C11  118.27  3.000
 AA  C14  N10  C11  123.44  3.000
 AA  C12  C11  N10  119.99  3.000
 AA  C12  C11  C5   120.46  3.000
 AA  N10  C11  C5   119.55  3.000
 AA  C11  C12  C9   118.96  3.000
 AA  C11  C12  C8   118.13  3.000
 AA  C9   C12  C8   122.90  3.000
 AA  C14  C13  C9   118.96  3.000
 AA  C14  C13  C1   118.15  3.000
 AA  C9   C13  C1   122.89  3.000
 AA  C13  C14  N10  119.99  3.000
 AA  C13  C14  C4   120.45  3.000
 AA  N10  C14  C4   119.56  3.000
 AA  H92  N9   H91  114.94  3.000
 AA  H92  N9   C9   122.52  3.000
 AA  H91  N9   C9   122.54  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
 AA  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 AA  CONST_02  C12  C9   C13  C1   180.00  0.0  0
 AA  CONST_03  C4   C14  C13  C1     0.00  0.0  0
 AA  CONST_04  N10  C14  C13  C1   180.00  0.0  0
 AA  CONST_05  C9   C13  C1   C2   180.00  0.0  0
 AA  CONST_06  C14  C13  C1   C2     0.00  0.0  0
 AA  CONST_07  C14  C4   C3   C2     0.00  0.0  0
 AA  CONST_08  C13  C1   C2   C3     0.00  0.0  0
 AA  CONST_09  N10  C14  C4   C3   180.00  0.0  0
 AA  CONST_10  C13  C14  C4   C3     0.00  0.0  0
 AA  CONST_11  C11  N10  C14  C4   180.00  0.0  0
 AA  CONST_12  C9   C13  C14  C4   180.00  0.0  0
 AA  CONST_13  C8   C7   C6   C5     0.00  0.0  0
 AA  CONST_14  C14  N10  C11  C5   180.00  0.0  0
 AA  CONST_15  C8   C12  C11  C5     0.00  0.0  0
 AA  CONST_16  C9   C12  C11  C5   180.00  0.0  0
 AA  CONST_17  N10  C11  C5   C6   180.00  0.0  0
 AA  CONST_18  C12  C11  C5   C6     0.00  0.0  0
 AA  CONST_19  C12  C8   C7   C6     0.00  0.0  0
 AA  CONST_20  C11  C5   C6   C7     0.00  0.0  0
 AA  CONST_21  C9   C12  C8   C7   180.00  0.0  0
 AA  CONST_22  C11  C12  C8   C7     0.00  0.0  0
 AA  CONST_23  C13  C9   C12  C8   180.00  0.0  0
 AA  CONST_24  N10  C11  C12  C8   180.00  0.0  0
 AA  CONST_25  N10  C11  C12  C9     0.00  0.0  0
 AA  CONST_26  N10  C14  C13  C9     0.00  0.0  0
 AA  CONST_27  C13  C14  N10  C11    0.00  0.0  0
 AA  CONST_28  C13  C9   C12  C11    0.00  0.0  0
 AA  CONST_29  C14  C13  C9   C12    0.00  0.0  0
 AA  CONST_30  C14  N10  C11  C12    0.00  0.0  0
 AA  CONST_31  N9   C9   C13  C1     0.00  0.0  0
 AA  CONST_32  N9   C9   C12  C8     0.00  0.0  0
 AA  CONST_33  N9   C9   C12  C11  180.00  0.0  0
 AA  CONST_34  N9   C9   C13  C14  180.00  0.0  0
 AA  CONST_35  H3   C3   C2   C1   180.00  0.0  0
 AA  CONST_36  H4   C4   C3   C2   180.00  0.0  0
 AA  CONST_37  H1   C1   C2   C3   180.00  0.0  0
 AA  CONST_38  H2   C2   C3   C4   180.00  0.0  0
 AA  CONST_39  H10  N10  C14  C4     0.00  0.0  0
 AA  CONST_40  H7   C7   C6   C5   180.00  0.0  0
 AA  CONST_41  H8   C8   C7   C6   180.00  0.0  0
 AA  CONST_42  H5   C5   C6   C7   180.00  0.0  0
 AA  CONST_43  H6   C6   C7   C8   180.00  0.0  0
 AA  CONST_44  H91  N9   C9   C12    0.00  0.0  0
 AA  CONST_45  H92  N9   C9   C12  180.00  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
 AA  plan-1  C1   0.020
 AA  plan-1  C2   0.020
 AA  plan-1  C3   0.020
 AA  plan-1  C4   0.020
 AA  plan-1  C5   0.020
 AA  plan-1  C6   0.020
 AA  plan-1  C7   0.020
 AA  plan-1  C8   0.020
 AA  plan-1  C9   0.020
 AA  plan-1  N10  0.020
 AA  plan-1  C11  0.020
 AA  plan-1  C12  0.020
 AA  plan-1  C13  0.020
 AA  plan-1  C14  0.020
 AA  plan-1  N9   0.020
 AA  plan-1  H1   0.020
 AA  plan-1  H2   0.020
 AA  plan-1  H3   0.020
 AA  plan-1  H4   0.020
 AA  plan-1  H5   0.020
 AA  plan-1  H6   0.020
 AA  plan-1  H7   0.020
 AA  plan-1  H8   0.020
 AA  plan-1  H10  0.020
 AA  plan-2  C9   0.020
 AA  plan-2  N9   0.020
 AA  plan-2  H91  0.020
 AA  plan-2  H92  0.020

