# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:01:32 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 9-ammonio-3-bromo-5-{[2-(dimethylamino)ethyl]carbamoyl}acridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCNC(=O)c1cccc2c([NH3+])c3ccc(Br)cc3[nH+]c12
#
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
 DA6  DA6  9-ammonio-3-bromo-5-{[2-(dimethylamino)ethyl]carbamoyl}acridinium  ligand  45  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DA6
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
 DA6  C1    C   CR16  0  -0.315  -0.4818  -3.9797   0.0666
 DA6  C2    C   CR16  0  -0.207  -1.8321  -3.9207   0.2041
 DA6  C3    C   CR16  0  -0.307  -2.4939  -2.6780   0.2989
 DA6  C4    C   CR6   0  -0.061  -1.8216  -1.4860   0.2497
 DA6  C5    C   CR16  0  -0.259   2.2811   0.9098   0.0004
 DA6  C6    C   CR6   0  -0.120   3.6364   0.9465  -0.1482
 DA6  C7    C   CR16  0  -0.194   4.4033  -0.2382  -0.2961
 DA6  C8    C   CR16  0  -0.303   3.7922  -1.4509  -0.2842
 DA6  C9    C   CR6   0   0.381   1.6672  -2.7381  -0.0769
 DA6  N9    N   NT3   1  -0.920   2.3942  -3.9863  -0.1675
 DA6  N10   N   NR16  1  -0.778   0.3134  -0.4082   0.1383
 DA6  C11   C   CR66  0   0.136   0.2788  -2.7824   0.0382
 DA6  C12   C   CR66  0   0.362  -0.4029  -1.5385   0.1419
 DA6  C13   C   CR66  0   0.120   2.3839  -1.5488  -0.1249
 DA6  C14   C   CR66  0   0.390   1.6425  -0.3434   0.0051
 DA6  BR    BR  BR    0   0.055   4.5243   2.5873  -0.1629
 DA6  CD1   C   C     0   0.658  -2.5047  -0.1548   0.3301
 DA6  OD1   O   O     0  -0.522  -1.8482   0.8688   0.5544
 DA6  ND1   N   NH1   0  -0.658  -3.8167  -0.1214   0.1461
 DA6  CD2   C   CH2   0  -0.260  -4.5855   1.1057   0.2594
 DA6  CD3   C   CH2   0  -0.316  -6.0334   0.8260  -0.1194
 DA6  ND2   N   NT    0  -0.409  -6.8744   1.9882   0.0711
 DA6  CD7   C   CH3   0  -0.529  -6.6439   3.0113  -0.9292
 DA6  CD8   C   CH3   0  -0.520  -8.2747   1.6193   0.1056
 DA6  H1    H   HCR6  0   0.294  -0.0100  -4.9476  -0.0262
 DA6  H2    H   HCR6  0   0.310  -2.4149  -4.8292   0.2392
 DA6  H3    H   HCR6  0   0.298  -3.5677  -2.7062   0.4217
 DA6  H5    H   HCR6  0   0.329   1.6876   1.8074   0.1105
 DA6  H7    H   HCR6  0   0.317   5.4754  -0.1815  -0.4188
 DA6  H8    H   HCR6  0   0.297   4.4067  -2.3308  -0.4102
 DA6  HN91  H   HNT3  0   0.513   2.4906  -4.3075  -1.1385
 DA6  HN92  H   HNT3  0   0.505   3.3406  -3.9227   0.2153
 DA6  HN93  H   HNT3  0   0.506   1.9514  -4.7478   0.3529
 DA6  H10   H   HNR6  0   0.479  -0.2713   0.4431   0.2865
 DA6  HND1  H   HNH1  0   0.427  -4.3149  -0.9620  -0.0981
 DA6  HD21  H   HCH2  0   0.254  -4.1426   1.8658  -0.3859
 DA6  HD22  H   HCH2  0   0.253  -4.5446   1.4787   1.2849
 DA6  HD31  H   HCH2  0   0.248  -6.4065   0.0269   0.5275
 DA6  HD32  H   HCH2  0   0.210  -6.0790   0.4431  -1.1537
 DA6  HD71  H   HCH3  0   0.237  -5.6084   3.3504  -0.9162
 DA6  HD72  H   HCH3  0   0.196  -6.8742   2.6707  -1.9507
 DA6  HD73  H   HCH3  0   0.238  -7.2696   3.8789  -0.7173
 DA6  HD81  H   HCH3  0   0.195  -8.6326   1.1805  -0.8385
 DA6  HD82  H   HCH3  0   0.235  -8.4547   0.8945   0.9004
 DA6  HD83  H   HCH3  0   0.235  -8.8840   2.4999   0.3130

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
 DA6  C1   C2    aromatic  1.359  0.020  1.359
 DA6  C1   C11   aromatic  1.419  0.020  1.419
 DA6  C1   H1    single    0.930  0.020  1.080
 DA6  C2   C3    aromatic  1.411  0.020  1.411
 DA6  C2   H2    single    0.930  0.020  1.080
 DA6  C3   C4    aromatic  1.369  0.020  1.369
 DA6  C3   H3    single    0.930  0.020  1.080
 DA6  C4   C12   aromatic  1.424  0.020  1.424
 DA6  C4   CD1   single    1.498  0.020  1.498
 DA6  C5   C6    aromatic  1.364  0.020  1.364
 DA6  C5   C14   aromatic  1.407  0.020  1.407
 DA6  C5   H5    single    0.930  0.020  1.080
 DA6  C6   C7    aromatic  1.419  0.020  1.419
 DA6  C6   BR    single    1.866  0.020  1.866
 DA6  C7   C8    aromatic  1.358  0.020  1.358
 DA6  C7   H7    single    0.930  0.020  1.080
 DA6  C8   C13   aromatic  1.421  0.020  1.421
 DA6  C8   H8    single    0.930  0.020  1.080
 DA6  C9   N9    single    1.447  0.020  1.447
 DA6  C9   C11   aromatic  1.394  0.020  1.394
 DA6  C9   C13   aromatic  1.389  0.020  1.389
 DA6  N9   HN91  single    0.890  0.020  1.040
 DA6  N9   HN92  single    0.890  0.020  1.040
 DA6  N9   HN93  single    0.890  0.020  1.040
 DA6  N10  C12   aromatic  1.338  0.020  1.338
 DA6  N10  C14   aromatic  1.337  0.020  1.337
 DA6  N10  H10   single    0.860  0.020  1.020
 DA6  C11  C12   aromatic  1.422  0.020  1.422
 DA6  C13  C14   aromatic  1.421  0.020  1.421
 DA6  CD1  OD1   double    1.237  0.020  1.237
 DA6  CD1  ND1   single    1.325  0.020  1.325
 DA6  ND1  CD2   single    1.453  0.020  1.453
 DA6  ND1  HND1  single    0.860  0.020  1.020
 DA6  CD2  CD3   single    1.523  0.020  1.523
 DA6  CD2  HD21  single    0.970  0.020  1.090
 DA6  CD2  HD22  single    0.970  0.020  1.090
 DA6  CD3  ND2   single    1.447  0.020  1.447
 DA6  CD3  HD31  single    0.970  0.020  1.090
 DA6  CD3  HD32  single    0.970  0.020  1.090
 DA6  ND2  CD7   single    1.449  0.020  1.449
 DA6  ND2  CD8   single    1.448  0.020  1.448
 DA6  CD7  HD71  single    0.970  0.020  1.090
 DA6  CD7  HD72  single    0.970  0.020  1.090
 DA6  CD7  HD73  single    0.970  0.020  1.090
 DA6  CD8  HD81  single    0.970  0.020  1.090
 DA6  CD8  HD82  single    0.970  0.020  1.090
 DA6  CD8  HD83  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
 DA6  H1    C1   C11   121.33  3.000
 DA6  H1    C1   C2    118.78  3.000
 DA6  C11   C1   C2    119.88  3.000
 DA6  H2    C2   C3    119.05  3.000
 DA6  H2    C2   C1    120.21  3.000
 DA6  C3    C2   C1    120.74  3.000
 DA6  H3    C3   C4    120.96  3.000
 DA6  H3    C3   C2    116.77  3.000
 DA6  C4    C3   C2    122.27  3.000
 DA6  CD1   C4   C12   119.41  3.000
 DA6  CD1   C4   C3    123.21  3.000
 DA6  C12   C4   C3    117.37  3.000
 DA6  H5    C5   C14   119.33  3.000
 DA6  H5    C5   C6    122.28  3.000
 DA6  C14   C5   C6    118.39  3.000
 DA6  BR    C6   C7    118.44  3.000
 DA6  BR    C6   C5    119.83  3.000
 DA6  C7    C6   C5    121.73  3.000
 DA6  H7    C7   C8    119.63  3.000
 DA6  H7    C7   C6    120.28  3.000
 DA6  C8    C7   C6    120.09  3.000
 DA6  H8    C8   C13   121.38  3.000
 DA6  H8    C8   C7    118.04  3.000
 DA6  C13   C8   C7    120.57  3.000
 DA6  C13   C9   C11   122.95  3.000
 DA6  C13   C9   N9    118.49  3.000
 DA6  C11   C9   N9    118.56  3.000
 DA6  HN93  N9   HN92  104.85  3.000
 DA6  HN93  N9   HN91  106.78  3.000
 DA6  HN92  N9   HN91  106.64  3.000
 DA6  HN93  N9   C9    113.12  3.000
 DA6  HN92  N9   C9    112.82  3.000
 DA6  HN91  N9   C9    112.08  3.000
 DA6  H10   N10  C14   122.11  3.000
 DA6  H10   N10  C12   112.89  3.000
 DA6  C14   N10  C12   124.97  3.000
 DA6  C12   C11  C9    117.10  3.000
 DA6  C12   C11  C1    118.66  3.000
 DA6  C9    C11  C1    124.23  3.000
 DA6  C11   C12  N10   118.82  3.000
 DA6  C11   C12  C4    121.02  3.000
 DA6  N10   C12  C4    120.16  3.000
 DA6  C14   C13  C9    116.99  3.000
 DA6  C14   C13  C8    117.97  3.000
 DA6  C9    C13  C8    125.04  3.000
 DA6  C13   C14  N10   119.11  3.000
 DA6  C13   C14  C5    121.24  3.000
 DA6  N10   C14  C5    119.65  3.000
 DA6  ND1   CD1  OD1   122.00  3.000
 DA6  ND1   CD1  C4    117.79  3.000
 DA6  OD1   CD1  C4    120.21  3.000
 DA6  HND1  ND1  CD2   117.53  3.000
 DA6  HND1  ND1  CD1   120.16  3.000
 DA6  CD2   ND1  CD1   122.31  3.000
 DA6  HD22  CD2  HD21  107.59  3.000
 DA6  HD22  CD2  CD3   109.39  3.000
 DA6  HD21  CD2  CD3   111.52  3.000
 DA6  HD22  CD2  ND1   110.00  3.000
 DA6  HD21  CD2  ND1   109.12  3.000
 DA6  CD3   CD2  ND1   109.19  3.000
 DA6  HD32  CD3  HD31  106.66  3.000
 DA6  HD32  CD3  ND2   112.20  3.000
 DA6  HD31  CD3  ND2   108.10  3.000
 DA6  HD32  CD3  CD2   109.64  3.000
 DA6  HD31  CD3  CD2   108.15  3.000
 DA6  ND2   CD3  CD2   111.86  3.000
 DA6  CD8   ND2  CD7   110.49  3.000
 DA6  CD8   ND2  CD3   111.12  3.000
 DA6  CD7   ND2  CD3   112.56  3.000
 DA6  HD73  CD7  HD72  107.83  3.000
 DA6  HD73  CD7  HD71  107.18  3.000
 DA6  HD72  CD7  HD71  107.82  3.000
 DA6  HD73  CD7  ND2   109.65  3.000
 DA6  HD72  CD7  ND2   112.87  3.000
 DA6  HD71  CD7  ND2   111.26  3.000
 DA6  HD83  CD8  HD82  107.80  3.000
 DA6  HD83  CD8  HD81  107.66  3.000
 DA6  HD82  CD8  HD81  107.84  3.000
 DA6  HD83  CD8  ND2   109.81  3.000
 DA6  HD82  CD8  ND2   110.25  3.000
 DA6  HD81  CD8  ND2   113.29  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
 DA6  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 DA6  CONST_02  C13   C9   C11  C1   180.00   0.0  0
 DA6  CONST_03  C4    C12  C11  C1     0.00   0.0  0
 DA6  CONST_04  N10   C12  C11  C1   180.00   0.0  0
 DA6  CONST_05  C9    C11  C1   C2   180.00   0.0  0
 DA6  CONST_06  C12   C11  C1   C2     0.00   0.0  0
 DA6  CONST_07  C12   C4   C3   C2     0.00   0.0  0
 DA6  CONST_08  C11   C1   C2   C3     0.00   0.0  0
 DA6  CONST_09  N10   C12  C4   C3   180.00   0.0  0
 DA6  CONST_10  C11   C12  C4   C3     0.00   0.0  0
 DA6  CONST_11  C14   N10  C12  C4   180.00   0.0  0
 DA6  CONST_12  C9    C11  C12  C4   180.00   0.0  0
 DA6  CONST_13  C8    C7   C6   C5     0.00   0.0  0
 DA6  CONST_14  C12   N10  C14  C5   180.00   0.0  0
 DA6  CONST_15  C8    C13  C14  C5     0.00   0.0  0
 DA6  CONST_16  C9    C13  C14  C5   180.00   0.0  0
 DA6  CONST_17  N10   C14  C5   C6   180.00   0.0  0
 DA6  CONST_18  C13   C14  C5   C6     0.00   0.0  0
 DA6  CONST_19  C13   C8   C7   C6     0.00   0.0  0
 DA6  CONST_20  C14   C5   C6   C7     0.00   0.0  0
 DA6  CONST_21  C9    C13  C8   C7   180.00   0.0  0
 DA6  CONST_22  C14   C13  C8   C7     0.00   0.0  0
 DA6  CONST_23  C11   C9   C13  C8   180.00   0.0  0
 DA6  CONST_24  N10   C14  C13  C8   180.00   0.0  0
 DA6  CONST_25  N10   C12  C11  C9     0.00   0.0  0
 DA6  CONST_26  N10   C14  C13  C9     0.00   0.0  0
 DA6  CONST_27  C14   C13  C9   C11    0.00   0.0  0
 DA6  CONST_28  C14   N10  C12  C11    0.00   0.0  0
 DA6  CONST_29  C13   C14  N10  C12    0.00   0.0  0
 DA6  CONST_30  C13   C9   C11  C12    0.00   0.0  0
 DA6  CONST_31  N9    C9   C11  C1     0.00   0.0  0
 DA6  CONST_32  CD1   C4   C3   C2   180.00   0.0  0
 DA6  CONST_33  BR    C6   C7   C8   180.00   0.0  0
 DA6  CONST_34  N9    C9   C13  C8     0.00   0.0  0
 DA6  CONST_35  C12   C11  C9   N9   180.00   0.0  0
 DA6  CONST_36  C14   C13  C9   N9   180.00   0.0  0
 DA6  CONST_37  CD1   C4   C12  N10    0.00   0.0  0
 DA6  CONST_38  CD1   C4   C12  C11  180.00   0.0  0
 DA6  CONST_39  BR    C6   C5   C14  180.00   0.0  0
 DA6  CONST_40  H3    C3   C2   C1   180.00   0.0  0
 DA6  CONST_41  H1    C1   C2   C3   180.00   0.0  0
 DA6  CONST_42  H2    C2   C3   C4   180.00   0.0  0
 DA6  CONST_43  H10   N10  C12  C4     0.00   0.0  0
 DA6  CONST_44  H7    C7   C6   C5   180.00   0.0  0
 DA6  CONST_45  H8    C8   C7   C6   180.00   0.0  0
 DA6  CONST_46  H5    C5   C6   C7   180.00   0.0  0
 DA6  CONST_47  CD2   ND1  CD1  C4   180.00   0.0  0
 DA6  CONST_48  HND1  ND1  CD1  C4     0.00   0.0  0
 DA6  CONST_49  CD2   ND1  CD1  OD1    0.00   0.0  0
 DA6  Var_01    OD1   CD1  C4   C3   165.21  30.0  2
 DA6  Var_02    HN91  N9   C9   C11   88.73  30.0  2
 DA6  Var_03    CD3   CD2  ND1  CD1  175.43  30.0  3
 DA6  Var_04    ND2   CD3  CD2  ND1  175.62  30.0  3
 DA6  Var_05    CD7   ND2  CD3  CD2   72.89  30.0  3
 DA6  Var_06    HD71  CD7  ND2  CD3  -59.26  30.0  3
 DA6  Var_07    HD81  CD8  ND2  CD3  -63.18  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
 DA6  plan-1  C1    0.020
 DA6  plan-1  C2    0.020
 DA6  plan-1  C3    0.020
 DA6  plan-1  C4    0.020
 DA6  plan-1  C5    0.020
 DA6  plan-1  C6    0.020
 DA6  plan-1  C7    0.020
 DA6  plan-1  C8    0.020
 DA6  plan-1  C9    0.020
 DA6  plan-1  N9    0.020
 DA6  plan-1  N10   0.020
 DA6  plan-1  C11   0.020
 DA6  plan-1  C12   0.020
 DA6  plan-1  C13   0.020
 DA6  plan-1  C14   0.020
 DA6  plan-1  BR    0.020
 DA6  plan-1  CD1   0.020
 DA6  plan-1  H1    0.020
 DA6  plan-1  H2    0.020
 DA6  plan-1  H3    0.020
 DA6  plan-1  H5    0.020
 DA6  plan-1  H7    0.020
 DA6  plan-1  H8    0.020
 DA6  plan-1  H10   0.020
 DA6  plan-2  C4    0.020
 DA6  plan-2  CD1   0.020
 DA6  plan-2  OD1   0.020
 DA6  plan-2  ND1   0.020
 DA6  plan-2  CD2   0.020
 DA6  plan-2  HND1  0.020

