# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 13:19:55 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 9-ammonio-4-bromo-5-{[2-(dimethylamino)ethyl]carbamoyl}acridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCNC(=O)c1cccc2c([NH3+])c3cccc(Br)c3[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
 DA5  DA5  9-ammonio-4-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_DA5
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
 DA5  C1    C   CR16  0  -0.316  -0.9721  -3.8625  -0.0455
 DA5  C2    C   CR16  0  -0.206   0.3670  -4.0739  -0.1209
 DA5  C3    C   CR16  0  -0.301   1.2673  -2.9874  -0.1763
 DA5  C4    C   CR6   0  -0.070   0.8418  -1.6872  -0.1491
 DA5  C5    C   CR6   0  -0.180  -2.7429   1.4897  -0.1338
 DA5  C6    C   CR16  0  -0.220  -4.0718   1.7869  -0.0451
 DA5  C7    C   CR16  0  -0.223  -5.0370   0.7640   0.0845
 DA5  C8    C   CR16  0  -0.315  -4.6705  -0.5442   0.1128
 DA5  C9    C   CR6   0   0.376  -2.8328  -2.2084   0.0031
 DA5  N9    N   NT3   1  -0.920  -3.8090  -3.2755   0.0612
 DA5  N10   N   NR16  1  -0.789  -1.0329  -0.2025  -0.1618
 DA5  C11   C   CR66  0   0.154  -1.4824  -2.5371  -0.0485
 DA5  C12   C   CR66  0   0.370  -0.5631  -1.4545  -0.1184
 DA5  C13   C   CR66  0   0.117  -3.2998  -0.8962   0.0139
 DA5  C14   C   CR66  0   0.450  -2.3245   0.1362  -0.0960
 DA5  BR    BR  BR    0   0.055  -1.4837   2.8652  -0.2940
 DA5  CD1   C   C     0   0.659   1.7789  -0.5202  -0.1743
 DA5  OD1   O   O     0  -0.520   1.3526   0.6091  -0.4435
 DA5  ND1   N   NH1   0  -0.655   3.0548  -0.7456   0.1057
 DA5  CD2   C   CH2   0  -0.264   4.0500   0.3116   0.1039
 DA5  CD3   C   CH2   0  -0.308   5.4424  -0.3030   0.1572
 DA5  ND2   N   NT    0  -0.411   6.4709   0.7124   0.2314
 DA5  CD7   C   CH3   0  -0.520   7.7289   0.1539   0.6812
 DA5  CD8   C   CH3   0  -0.528   6.6451   1.4220  -1.0199
 DA5  H1    H   HCR6  0   0.292  -1.6265  -4.7199   0.0188
 DA5  H2    H   HCR6  0   0.311   0.7565  -5.0812  -0.1344
 DA5  H3    H   HCR6  0   0.300   2.3202  -3.2216  -0.2503
 DA5  H6    H   HCR6  0   0.320  -4.4029   2.8162  -0.0685
 DA5  H7    H   HCR6  0   0.309  -6.0794   1.0364   0.1622
 DA5  H8    H   HCR6  0   0.295  -5.4377  -1.2967   0.2234
 DA5  HN91  H   HNT3  0   0.513  -4.0893  -3.4926   1.0251
 DA5  HN92  H   HNT3  0   0.506  -4.6639  -3.0579  -0.4580
 DA5  HN93  H   HNT3  0   0.505  -3.4736  -4.1510  -0.3460
 DA5  H10   H   HNR6  0   0.489  -0.2598   0.4963  -0.2890
 DA5  HND1  H   HNH1  0   0.425   3.3374  -1.6446   0.4622
 DA5  HD21  H   HCH2  0   0.253   3.9093   0.9702   0.9646
 DA5  HD22  H   HCH2  0   0.256   3.9177   0.9130  -0.7956
 DA5  HD31  H   HCH2  0   0.210   5.5799  -0.9795  -0.7035
 DA5  HD32  H   HCH2  0   0.246   5.5111  -0.9213   1.0571
 DA5  HD71  H   HCH3  0   0.235   8.4687   0.9481   0.7903
 DA5  HD72  H   HCH3  0   0.235   7.6049  -0.3193   1.6563
 DA5  HD73  H   HCH3  0   0.195   8.1448  -0.5969  -0.0077
 DA5  HD81  H   HCH3  0   0.237   5.7241   1.9204  -1.3221
 DA5  HD82  H   HCH3  0   0.238   7.4049   2.1946  -0.8994
 DA5  HD83  H   HCH3  0   0.196   6.9604   0.7658  -1.8462

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
 DA5  C1   C2    aromatic  1.358  0.020  1.358
 DA5  C1   C11   aromatic  1.420  0.020  1.420
 DA5  C1   H1    single    0.930  0.020  1.080
 DA5  C2   C3    aromatic  1.412  0.020  1.412
 DA5  C2   H2    single    0.930  0.020  1.080
 DA5  C3   C4    aromatic  1.368  0.020  1.368
 DA5  C3   H3    single    0.930  0.020  1.080
 DA5  C4   C12   aromatic  1.424  0.020  1.424
 DA5  C4   CD1   single    1.497  0.020  1.497
 DA5  C5   C6    aromatic  1.365  0.020  1.365
 DA5  C5   C14   aromatic  1.417  0.020  1.417
 DA5  C5   BR    single    1.872  0.020  1.872
 DA5  C6   C7    aromatic  1.412  0.020  1.412
 DA5  C6   H6    single    0.930  0.020  1.080
 DA5  C7   C8    aromatic  1.359  0.020  1.359
 DA5  C7   H7    single    0.930  0.020  1.080
 DA5  C8   C13   aromatic  1.419  0.020  1.419
 DA5  C8   H8    single    0.930  0.020  1.080
 DA5  C9   N9    single    1.447  0.020  1.447
 DA5  C9   C11   aromatic  1.391  0.020  1.391
 DA5  C9   C13   aromatic  1.393  0.020  1.393
 DA5  N9   HN91  single    0.890  0.020  1.040
 DA5  N9   HN92  single    0.890  0.020  1.040
 DA5  N9   HN93  single    0.890  0.020  1.040
 DA5  N10  C12   aromatic  1.338  0.020  1.338
 DA5  N10  C14   aromatic  1.337  0.020  1.337
 DA5  N10  H10   single    0.860  0.020  1.020
 DA5  C11  C12   aromatic  1.422  0.020  1.422
 DA5  C13  C14   aromatic  1.424  0.020  1.424
 DA5  CD1  OD1   double    1.237  0.020  1.237
 DA5  CD1  ND1   single    1.326  0.020  1.326
 DA5  ND1  CD2   single    1.452  0.020  1.452
 DA5  ND1  HND1  single    0.860  0.020  1.020
 DA5  CD2  CD3   single    1.523  0.020  1.523
 DA5  CD2  HD21  single    0.970  0.020  1.090
 DA5  CD2  HD22  single    0.970  0.020  1.090
 DA5  CD3  ND2   single    1.447  0.020  1.447
 DA5  CD3  HD31  single    0.970  0.020  1.090
 DA5  CD3  HD32  single    0.970  0.020  1.090
 DA5  ND2  CD7   single    1.448  0.020  1.448
 DA5  ND2  CD8   single    1.449  0.020  1.449
 DA5  CD7  HD71  single    0.970  0.020  1.090
 DA5  CD7  HD72  single    0.970  0.020  1.090
 DA5  CD7  HD73  single    0.970  0.020  1.090
 DA5  CD8  HD81  single    0.970  0.020  1.090
 DA5  CD8  HD82  single    0.970  0.020  1.090
 DA5  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
 DA5  H1    C1   C11   121.54  3.000
 DA5  H1    C1   C2    118.49  3.000
 DA5  C11   C1   C2    119.97  3.000
 DA5  H2    C2   C3    119.15  3.000
 DA5  H2    C2   C1    120.10  3.000
 DA5  C3    C2   C1    120.74  3.000
 DA5  H3    C3   C4    120.66  3.000
 DA5  H3    C3   C2    117.19  3.000
 DA5  C4    C3   C2    122.15  3.000
 DA5  CD1   C4   C12   119.37  3.000
 DA5  CD1   C4   C3    123.08  3.000
 DA5  C12   C4   C3    117.54  3.000
 DA5  BR    C5   C14   120.37  3.000
 DA5  BR    C5   C6    120.04  3.000
 DA5  C14   C5   C6    119.59  3.000
 DA5  H6    C6   C7    118.82  3.000
 DA5  H6    C6   C5    120.27  3.000
 DA5  C7    C6   C5    120.91  3.000
 DA5  H7    C7   C8    120.11  3.000
 DA5  H7    C7   C6    118.91  3.000
 DA5  C8    C7   C6    120.99  3.000
 DA5  H8    C8   C13   121.36  3.000
 DA5  H8    C8   C7    118.76  3.000
 DA5  C13   C8   C7    119.87  3.000
 DA5  C13   C9   C11   123.27  3.000
 DA5  C13   C9   N9    117.91  3.000
 DA5  C11   C9   N9    118.82  3.000
 DA5  HN93  N9   HN92  104.72  3.000
 DA5  HN93  N9   HN91  106.41  3.000
 DA5  HN92  N9   HN91  107.04  3.000
 DA5  HN93  N9   C9    113.22  3.000
 DA5  HN92  N9   C9    112.71  3.000
 DA5  HN91  N9   C9    112.18  3.000
 DA5  H10   N10  C14   123.29  3.000
 DA5  H10   N10  C12   111.61  3.000
 DA5  C14   N10  C12   125.08  3.000
 DA5  C12   C11  C9    116.72  3.000
 DA5  C12   C11  C1    118.58  3.000
 DA5  C9    C11  C1    124.71  3.000
 DA5  C11   C12  N10   119.15  3.000
 DA5  C11   C12  C4    120.95  3.000
 DA5  N10   C12  C4    119.90  3.000
 DA5  C14   C13  C9    116.91  3.000
 DA5  C14   C13  C8    119.15  3.000
 DA5  C9    C13  C8    123.94  3.000
 DA5  C13   C14  N10   118.79  3.000
 DA5  C13   C14  C5    119.48  3.000
 DA5  N10   C14  C5    121.72  3.000
 DA5  ND1   CD1  OD1   122.21  3.000
 DA5  ND1   CD1  C4    117.80  3.000
 DA5  OD1   CD1  C4    119.99  3.000
 DA5  HND1  ND1  CD2   117.25  3.000
 DA5  HND1  ND1  CD1   119.77  3.000
 DA5  CD2   ND1  CD1   122.39  3.000
 DA5  HD22  CD2  HD21  107.57  3.000
 DA5  HD22  CD2  CD3   111.25  3.000
 DA5  HD21  CD2  CD3   109.47  3.000
 DA5  HD22  CD2  ND1   108.64  3.000
 DA5  HD21  CD2  ND1   110.46  3.000
 DA5  CD3   CD2  ND1   109.44  3.000
 DA5  HD32  CD3  HD31  106.70  3.000
 DA5  HD32  CD3  ND2   108.04  3.000
 DA5  HD31  CD3  ND2   112.44  3.000
 DA5  HD32  CD3  CD2   108.32  3.000
 DA5  HD31  CD3  CD2   109.51  3.000
 DA5  ND2   CD3  CD2   111.62  3.000
 DA5  CD8   ND2  CD7   110.65  3.000
 DA5  CD8   ND2  CD3   112.63  3.000
 DA5  CD7   ND2  CD3   111.27  3.000
 DA5  HD73  CD7  HD72  107.85  3.000
 DA5  HD73  CD7  HD71  107.63  3.000
 DA5  HD72  CD7  HD71  107.67  3.000
 DA5  HD73  CD7  ND2   113.39  3.000
 DA5  HD72  CD7  ND2   110.26  3.000
 DA5  HD71  CD7  ND2   109.84  3.000
 DA5  HD83  CD8  HD82  107.80  3.000
 DA5  HD83  CD8  HD81  107.84  3.000
 DA5  HD82  CD8  HD81  107.19  3.000
 DA5  HD83  CD8  ND2   112.99  3.000
 DA5  HD82  CD8  ND2   109.59  3.000
 DA5  HD81  CD8  ND2   111.21  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
 DA5  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DA5  CONST_02  C13   C9   C11  C1    180.00   0.0  0
 DA5  CONST_03  C4    C12  C11  C1      0.00   0.0  0
 DA5  CONST_04  N10   C12  C11  C1    180.00   0.0  0
 DA5  CONST_05  C9    C11  C1   C2    180.00   0.0  0
 DA5  CONST_06  C12   C11  C1   C2      0.00   0.0  0
 DA5  CONST_07  C12   C4   C3   C2      0.00   0.0  0
 DA5  CONST_08  C11   C1   C2   C3      0.00   0.0  0
 DA5  CONST_09  N10   C12  C4   C3    180.00   0.0  0
 DA5  CONST_10  C11   C12  C4   C3      0.00   0.0  0
 DA5  CONST_11  C14   N10  C12  C4    180.00   0.0  0
 DA5  CONST_12  C9    C11  C12  C4    180.00   0.0  0
 DA5  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 DA5  CONST_14  C12   N10  C14  C5    180.00   0.0  0
 DA5  CONST_15  C8    C13  C14  C5      0.00   0.0  0
 DA5  CONST_16  C9    C13  C14  C5    180.00   0.0  0
 DA5  CONST_17  N10   C14  C5   C6    180.00   0.0  0
 DA5  CONST_18  C13   C14  C5   C6      0.00   0.0  0
 DA5  CONST_19  C13   C8   C7   C6      0.00   0.0  0
 DA5  CONST_20  C14   C5   C6   C7      0.00   0.0  0
 DA5  CONST_21  C9    C13  C8   C7    180.00   0.0  0
 DA5  CONST_22  C14   C13  C8   C7      0.00   0.0  0
 DA5  CONST_23  C11   C9   C13  C8    180.00   0.0  0
 DA5  CONST_24  N10   C14  C13  C8    180.00   0.0  0
 DA5  CONST_25  N10   C12  C11  C9      0.00   0.0  0
 DA5  CONST_26  N10   C14  C13  C9      0.00   0.0  0
 DA5  CONST_27  C14   C13  C9   C11     0.00   0.0  0
 DA5  CONST_28  C14   N10  C12  C11     0.00   0.0  0
 DA5  CONST_29  C13   C14  N10  C12     0.00   0.0  0
 DA5  CONST_30  C13   C9   C11  C12     0.00   0.0  0
 DA5  CONST_31  N9    C9   C11  C1      0.00   0.0  0
 DA5  CONST_32  CD1   C4   C3   C2    180.00   0.0  0
 DA5  CONST_33  BR    C5   C6   C7    180.00   0.0  0
 DA5  CONST_34  N9    C9   C13  C8      0.00   0.0  0
 DA5  CONST_35  C12   C11  C9   N9    180.00   0.0  0
 DA5  CONST_36  C14   C13  C9   N9    180.00   0.0  0
 DA5  CONST_37  CD1   C4   C12  N10     0.00   0.0  0
 DA5  CONST_38  BR    C5   C14  N10     0.00   0.0  0
 DA5  CONST_39  CD1   C4   C12  C11   180.00   0.0  0
 DA5  CONST_40  BR    C5   C14  C13   180.00   0.0  0
 DA5  CONST_41  H3    C3   C2   C1    180.00   0.0  0
 DA5  CONST_42  H1    C1   C2   C3    180.00   0.0  0
 DA5  CONST_43  H2    C2   C3   C4    180.00   0.0  0
 DA5  CONST_44  H10   N10  C12  C4      0.00   0.0  0
 DA5  CONST_45  H7    C7   C6   C5    180.00   0.0  0
 DA5  CONST_46  H8    C8   C7   C6    180.00   0.0  0
 DA5  CONST_47  H6    C6   C7   C8    180.00   0.0  0
 DA5  CONST_48  CD2   ND1  CD1  C4    180.00   0.0  0
 DA5  CONST_49  HND1  ND1  CD1  C4      0.00   0.0  0
 DA5  CONST_50  CD2   ND1  CD1  OD1     0.00   0.0  0
 DA5  Var_01    OD1   CD1  C4   C3    164.03  30.0  2
 DA5  Var_02    HN91  N9   C9   C11    94.80  30.0  2
 DA5  Var_03    CD3   CD2  ND1  CD1  -167.62  30.0  3
 DA5  Var_04    ND2   CD3  CD2  ND1  -176.85  30.0  3
 DA5  Var_05    CD7   ND2  CD3  CD2   162.71  30.0  3
 DA5  Var_06    HD71  CD7  ND2  CD3  -176.38  30.0  3
 DA5  Var_07    HD81  CD8  ND2  CD3    59.78  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
 DA5  plan-1  C1    0.020
 DA5  plan-1  C2    0.020
 DA5  plan-1  C3    0.020
 DA5  plan-1  C4    0.020
 DA5  plan-1  C5    0.020
 DA5  plan-1  C6    0.020
 DA5  plan-1  C7    0.020
 DA5  plan-1  C8    0.020
 DA5  plan-1  C9    0.020
 DA5  plan-1  N9    0.020
 DA5  plan-1  N10   0.020
 DA5  plan-1  C11   0.020
 DA5  plan-1  C12   0.020
 DA5  plan-1  C13   0.020
 DA5  plan-1  C14   0.020
 DA5  plan-1  BR    0.020
 DA5  plan-1  CD1   0.020
 DA5  plan-1  H1    0.020
 DA5  plan-1  H2    0.020
 DA5  plan-1  H3    0.020
 DA5  plan-1  H6    0.020
 DA5  plan-1  H7    0.020
 DA5  plan-1  H8    0.020
 DA5  plan-1  H10   0.020
 DA5  plan-2  C4    0.020
 DA5  plan-2  CD1   0.020
 DA5  plan-2  OD1   0.020
 DA5  plan-2  ND1   0.020
 DA5  plan-2  CD2   0.020
 DA5  plan-2  HND1  0.020

