# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:54:24 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 9-amino-4-bromo-5-{[2-(dimethylammonio)ethyl]carbamoyl}acridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+](C)CCNC(=O)c1cccc2c(N)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
 DAX  DAX  9-amino-4-bromo-5-{[2-(dimethylammonio)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 PERFECT
;

data_comp_DAX
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
 DAX  C1    C   CR16  0  -0.305  -1.0546  -3.8962   0.4290
 DAX  C2    C   CR16  0  -0.228   0.2688  -4.2120   0.5631
 DAX  C3    C   CR16  0  -0.305   1.2332  -3.2011   0.4973
 DAX  C4    C   CR6   0  -0.087   0.8907  -1.8845   0.2841
 DAX  C5    C   CR6   0  -0.202  -2.4436   1.4492  -0.6362
 DAX  C6    C   CR16  0  -0.230  -3.7486   1.8421  -0.7827
 DAX  C7    C   CR16  0  -0.243  -4.7877   0.9121  -0.6504
 DAX  C8    C   CR16  0  -0.307  -4.5044  -0.3970  -0.3767
 DAX  C9    C   CR6   0   0.522  -2.8418  -2.2046   0.0409
 DAX  N9    N   NH2   0  -0.818  -3.7870  -3.1081   0.1482
 DAX  N10   N   NR16  1  -0.825  -0.8444  -0.2957  -0.1981
 DAX  C11   C   CR66  0   0.024  -1.4614  -2.5695   0.1887
 DAX  C12   C   CR66  0   0.365  -0.4793  -1.5663   0.0817
 DAX  C13   C   CR66  0   0.014  -3.1735  -0.8322  -0.2255
 DAX  C14   C   CR66  0   0.441  -2.1259   0.1021  -0.3517
 DAX  CD1   C   C     0   0.609   1.9204  -0.8043   0.2492
 DAX  OD1   O   O     0  -0.500   1.7231   0.2480  -0.3567
 DAX  ND1   N   NH1   0  -0.646   3.0515  -1.0292   0.9282
 DAX  BR    BR  BR    0   0.016  -1.0767   2.7289  -0.8078
 DAX  CD2   C   CH2   0  -0.324   4.1118  -0.0545   1.0025
 DAX  CD3   C   CH2   0  -0.310   5.0748  -0.2265  -0.1677
 DAX  ND2   N   NT1   1  -0.512   6.3007   0.6094  -0.0152
 DAX  CD7   C   CH3   0  -0.536   7.3229   0.2352  -1.0259
 DAX  CD8   C   CH3   0  -0.546   6.0158   2.0656  -0.0709
 DAX  H1    H   HCR6  0   0.276  -1.7765  -4.6971   0.5015
 DAX  H2    H   HCR6  0   0.291   0.5723  -5.2352   0.7275
 DAX  H3    H   HCR6  0   0.288   2.2716  -3.4863   0.6037
 DAX  H6    H   HCR6  0   0.305  -3.9858   2.8747  -0.9998
 DAX  H7    H   HCR6  0   0.291  -5.8111   1.2374  -0.7670
 DAX  H8    H   HCR6  0   0.273  -5.3320  -1.0851  -0.2805
 DAX  H91   H   HNH2  0   0.446  -3.5939  -4.0791   0.3281
 DAX  H92   H   HNH2  0   0.446  -4.7631  -2.8860   0.0486
 DAX  H10   H   HNR6  0   0.458  -0.0624   0.3456  -0.3559
 DAX  HD1   H   HNH1  0   0.429   3.1492  -1.8582   1.4908
 DAX  HD21  H   HCH2  0   0.294   4.6372  -0.2104   1.9449
 DAX  HD22  H   HCH2  0   0.279   3.6796   0.9446   1.0266
 DAX  HD31  H   HCH2  0   0.304   4.6158   0.0463  -1.1173
 DAX  HD32  H   HCH2  0   0.310   5.4063  -1.2619  -0.2236
 DAX  HD2   H   HNT1  0   0.470   6.7003   0.4048   0.9019
 DAX  HD71  H   HCH3  0   0.296   8.2212   0.8171  -0.8435
 DAX  HD72  H   HCH3  0   0.296   7.5417  -0.8241  -0.9335
 DAX  HD73  H   HCH3  0   0.292   6.9320   0.4537  -2.0154
 DAX  HD81  H   HCH3  0   0.296   5.3339   2.3429   0.7260
 DAX  HD82  H   HCH3  0   0.301   6.9492   2.6062   0.0518
 DAX  HD83  H   HCH3  0   0.293   5.5767   2.2947  -1.0382

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
 DAX  C1   C2    aromatic  1.367  0.020  1.367
 DAX  C1   C11   aromatic  1.408  0.020  1.408
 DAX  C1   H1    single    0.930  0.020  1.080
 DAX  C2   C3    aromatic  1.399  0.020  1.399
 DAX  C2   H2    single    0.930  0.020  1.080
 DAX  C3   C4    aromatic  1.377  0.020  1.377
 DAX  C3   H3    single    0.930  0.020  1.080
 DAX  C4   C12   aromatic  1.421  0.020  1.421
 DAX  C4   CD1   single    1.493  0.020  1.493
 DAX  C5   C6    aromatic  1.371  0.020  1.371
 DAX  C5   C14   aromatic  1.413  0.020  1.413
 DAX  C5   BR    single    1.880  0.020  1.880
 DAX  C6   C7    aromatic  1.401  0.020  1.401
 DAX  C6   H6    single    0.930  0.020  1.080
 DAX  C7   C8    aromatic  1.367  0.020  1.367
 DAX  C7   H7    single    0.930  0.020  1.080
 DAX  C8   C13   aromatic  1.408  0.020  1.408
 DAX  C8   H8    single    0.930  0.020  1.080
 DAX  C9   N9    single    1.312  0.020  1.312
 DAX  C9   C11   aromatic  1.436  0.020  1.436
 DAX  C9   C13   aromatic  1.437  0.020  1.437
 DAX  N9   H91   single    0.860  0.020  1.020
 DAX  N9   H92   single    0.860  0.020  1.020
 DAX  N10  C12   aromatic  1.351  0.020  1.351
 DAX  N10  C14   aromatic  1.351  0.020  1.351
 DAX  N10  H10   single    0.860  0.020  1.020
 DAX  C11  C12   aromatic  1.408  0.020  1.408
 DAX  C13  C14   aromatic  1.409  0.020  1.409
 DAX  CD1  OD1   double    1.230  0.020  1.230
 DAX  CD1  ND1   single    1.338  0.020  1.338
 DAX  ND1  CD2   single    1.442  0.020  1.442
 DAX  ND1  HD1   single    0.860  0.020  1.020
 DAX  CD2  CD3   single    1.525  0.020  1.525
 DAX  CD2  HD21  single    0.970  0.020  1.090
 DAX  CD2  HD22  single    0.970  0.020  1.090
 DAX  CD3  ND2   single    1.492  0.020  1.492
 DAX  CD3  HD31  single    0.970  0.020  1.090
 DAX  CD3  HD32  single    0.970  0.020  1.090
 DAX  ND2  CD7   single    1.485  0.020  1.485
 DAX  ND2  CD8   single    1.485  0.020  1.485
 DAX  ND2  HD2   single    0.890  0.020  1.040
 DAX  CD7  HD71  single    0.970  0.020  1.090
 DAX  CD7  HD72  single    0.970  0.020  1.090
 DAX  CD7  HD73  single    0.970  0.020  1.090
 DAX  CD8  HD81  single    0.970  0.020  1.090
 DAX  CD8  HD82  single    0.970  0.020  1.090
 DAX  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
 DAX  H1    C1   C11   121.12  3.000
 DAX  H1    C1   C2    117.96  3.000
 DAX  C11   C1   C2    120.92  3.000
 DAX  H2    C2   C3    119.88  3.000
 DAX  H2    C2   C1    120.39  3.000
 DAX  C3    C2   C1    119.73  3.000
 DAX  H3    C3   C4    120.39  3.000
 DAX  H3    C3   C2    117.81  3.000
 DAX  C4    C3   C2    121.79  3.000
 DAX  CD1   C4   C12   119.98  3.000
 DAX  CD1   C4   C3    121.60  3.000
 DAX  C12   C4   C3    118.42  3.000
 DAX  BR    C5   C14   120.25  3.000
 DAX  BR    C5   C6    119.16  3.000
 DAX  C14   C5   C6    120.59  3.000
 DAX  H6    C6   C7    119.35  3.000
 DAX  H6    C6   C5    120.26  3.000
 DAX  C7    C6   C5    120.39  3.000
 DAX  H7    C7   C8    120.42  3.000
 DAX  H7    C7   C6    119.52  3.000
 DAX  C8    C7   C6    120.06  3.000
 DAX  H8    C8   C13   121.16  3.000
 DAX  H8    C8   C7    117.97  3.000
 DAX  C13   C8   C7    120.88  3.000
 DAX  C13   C9   C11   118.94  3.000
 DAX  C13   C9   N9    120.44  3.000
 DAX  C11   C9   N9    120.62  3.000
 DAX  H92   N9   H91   114.64  3.000
 DAX  H92   N9   C9    122.61  3.000
 DAX  H91   N9   C9    122.75  3.000
 DAX  H10   N10  C14   121.52  3.000
 DAX  H10   N10  C12   114.50  3.000
 DAX  C14   N10  C12   123.84  3.000
 DAX  C12   C11  C9    118.80  3.000
 DAX  C12   C11  C1    118.86  3.000
 DAX  C9    C11  C1    122.33  3.000
 DAX  C11   C12  N10   119.82  3.000
 DAX  C11   C12  C4    120.14  3.000
 DAX  N10   C12  C4    120.03  3.000
 DAX  C14   C13  C9    118.57  3.000
 DAX  C14   C13  C8    119.20  3.000
 DAX  C9    C13  C8    122.22  3.000
 DAX  C13   C14  N10   119.99  3.000
 DAX  C13   C14  C5    118.88  3.000
 DAX  N10   C14  C5    121.13  3.000
 DAX  ND1   CD1  OD1   121.95  3.000
 DAX  ND1   CD1  C4    116.72  3.000
 DAX  OD1   CD1  C4    121.33  3.000
 DAX  HD1   ND1  CD2   117.16  3.000
 DAX  HD1   ND1  CD1   120.26  3.000
 DAX  CD2   ND1  CD1   122.28  3.000
 DAX  HD22  CD2  HD21  107.66  3.000
 DAX  HD22  CD2  CD3   111.78  3.000
 DAX  HD21  CD2  CD3   110.05  3.000
 DAX  HD22  CD2  ND1   109.23  3.000
 DAX  HD21  CD2  ND1   107.60  3.000
 DAX  CD3   CD2  ND1   110.39  3.000
 DAX  HD32  CD3  HD31  108.77  3.000
 DAX  HD32  CD3  ND2   106.74  3.000
 DAX  HD31  CD3  ND2   107.16  3.000
 DAX  HD32  CD3  CD2   109.81  3.000
 DAX  HD31  CD3  CD2   111.99  3.000
 DAX  ND2   CD3  CD2   112.16  3.000
 DAX  HD2   ND2  CD8   107.77  3.000
 DAX  HD2   ND2  CD7   106.94  3.000
 DAX  CD8   ND2  CD7   110.70  3.000
 DAX  HD2   ND2  CD3   107.53  3.000
 DAX  CD8   ND2  CD3   112.83  3.000
 DAX  CD7   ND2  CD3   110.78  3.000
 DAX  HD73  CD7  HD72  110.27  3.000
 DAX  HD73  CD7  HD71  110.07  3.000
 DAX  HD72  CD7  HD71  110.00  3.000
 DAX  HD73  CD7  ND2   108.75  3.000
 DAX  HD72  CD7  ND2   109.05  3.000
 DAX  HD71  CD7  ND2   108.67  3.000
 DAX  HD83  CD8  HD82  110.06  3.000
 DAX  HD83  CD8  HD81  110.25  3.000
 DAX  HD82  CD8  HD81  109.28  3.000
 DAX  HD83  CD8  ND2   108.52  3.000
 DAX  HD82  CD8  ND2   108.61  3.000
 DAX  HD81  CD8  ND2   110.10  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
 DAX  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DAX  CONST_02  C13   C9   C11  C1    180.00   0.0  0
 DAX  CONST_03  C4    C12  C11  C1      0.00   0.0  0
 DAX  CONST_04  N10   C12  C11  C1    180.00   0.0  0
 DAX  CONST_05  C9    C11  C1   C2    180.00   0.0  0
 DAX  CONST_06  C12   C11  C1   C2      0.00   0.0  0
 DAX  CONST_07  C12   C4   C3   C2      0.00   0.0  0
 DAX  CONST_08  C11   C1   C2   C3      0.00   0.0  0
 DAX  CONST_09  N10   C12  C4   C3    180.00   0.0  0
 DAX  CONST_10  C11   C12  C4   C3      0.00   0.0  0
 DAX  CONST_11  C14   N10  C12  C4    180.00   0.0  0
 DAX  CONST_12  C9    C11  C12  C4    180.00   0.0  0
 DAX  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 DAX  CONST_14  C12   N10  C14  C5    180.00   0.0  0
 DAX  CONST_15  C8    C13  C14  C5      0.00   0.0  0
 DAX  CONST_16  C9    C13  C14  C5    180.00   0.0  0
 DAX  CONST_17  N10   C14  C5   C6    180.00   0.0  0
 DAX  CONST_18  C13   C14  C5   C6      0.00   0.0  0
 DAX  CONST_19  C13   C8   C7   C6      0.00   0.0  0
 DAX  CONST_20  C14   C5   C6   C7      0.00   0.0  0
 DAX  CONST_21  C9    C13  C8   C7    180.00   0.0  0
 DAX  CONST_22  C14   C13  C8   C7      0.00   0.0  0
 DAX  CONST_23  C11   C9   C13  C8    180.00   0.0  0
 DAX  CONST_24  N10   C14  C13  C8    180.00   0.0  0
 DAX  CONST_25  N10   C12  C11  C9      0.00   0.0  0
 DAX  CONST_26  N10   C14  C13  C9      0.00   0.0  0
 DAX  CONST_27  C14   C13  C9   C11     0.00   0.0  0
 DAX  CONST_28  C14   N10  C12  C11     0.00   0.0  0
 DAX  CONST_29  C13   C14  N10  C12     0.00   0.0  0
 DAX  CONST_30  C13   C9   C11  C12     0.00   0.0  0
 DAX  CONST_31  N9    C9   C11  C1      0.00   0.0  0
 DAX  CONST_32  CD1   C4   C3   C2    180.00   0.0  0
 DAX  CONST_33  BR    C5   C6   C7    180.00   0.0  0
 DAX  CONST_34  N9    C9   C13  C8      0.00   0.0  0
 DAX  CONST_35  C12   C11  C9   N9    180.00   0.0  0
 DAX  CONST_36  C14   C13  C9   N9    180.00   0.0  0
 DAX  CONST_37  CD1   C4   C12  N10     0.00   0.0  0
 DAX  CONST_38  BR    C5   C14  N10     0.00   0.0  0
 DAX  CONST_39  CD1   C4   C12  C11   180.00   0.0  0
 DAX  CONST_40  BR    C5   C14  C13   180.00   0.0  0
 DAX  CONST_41  H3    C3   C2   C1    180.00   0.0  0
 DAX  CONST_42  H1    C1   C2   C3    180.00   0.0  0
 DAX  CONST_43  H2    C2   C3   C4    180.00   0.0  0
 DAX  CONST_44  H10   N10  C12  C4      0.00   0.0  0
 DAX  CONST_45  H7    C7   C6   C5    180.00   0.0  0
 DAX  CONST_46  H8    C8   C7   C6    180.00   0.0  0
 DAX  CONST_47  H6    C6   C7   C8    180.00   0.0  0
 DAX  CONST_48  H91   N9   C9   C11     0.00   0.0  0
 DAX  CONST_49  H92   N9   C9   C11   180.00   0.0  0
 DAX  CONST_50  CD2   ND1  CD1  C4    180.00   0.0  0
 DAX  CONST_51  HD1   ND1  CD1  C4      0.00   0.0  0
 DAX  CONST_52  CD2   ND1  CD1  OD1     0.00   0.0  0
 DAX  Var_01    OD1   CD1  C4   C3    155.41  30.0  2
 DAX  Var_02    CD3   CD2  ND1  CD1   -88.35  30.0  3
 DAX  Var_03    ND2   CD3  CD2  ND1  -170.78  30.0  3
 DAX  Var_04    CD7   ND2  CD3  CD2   169.40  30.0  3
 DAX  Var_05    HD71  CD7  ND2  CD3  -176.35  30.0  3
 DAX  Var_06    HD81  CD8  ND2  CD3    60.09  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
 DAX  plan-1  C1   0.020
 DAX  plan-1  C2   0.020
 DAX  plan-1  C3   0.020
 DAX  plan-1  C4   0.020
 DAX  plan-1  C5   0.020
 DAX  plan-1  C6   0.020
 DAX  plan-1  C7   0.020
 DAX  plan-1  C8   0.020
 DAX  plan-1  C9   0.020
 DAX  plan-1  N9   0.020
 DAX  plan-1  N10  0.020
 DAX  plan-1  C11  0.020
 DAX  plan-1  C12  0.020
 DAX  plan-1  C13  0.020
 DAX  plan-1  C14  0.020
 DAX  plan-1  CD1  0.020
 DAX  plan-1  BR   0.020
 DAX  plan-1  H1   0.020
 DAX  plan-1  H2   0.020
 DAX  plan-1  H3   0.020
 DAX  plan-1  H6   0.020
 DAX  plan-1  H7   0.020
 DAX  plan-1  H8   0.020
 DAX  plan-1  H10  0.020
 DAX  plan-2  C4   0.020
 DAX  plan-2  CD1  0.020
 DAX  plan-2  OD1  0.020
 DAX  plan-2  ND1  0.020
 DAX  plan-2  CD2  0.020
 DAX  plan-2  HD1  0.020
 DAX  plan-3  C9   0.020
 DAX  plan-3  N9   0.020
 DAX  plan-3  H91  0.020
 DAX  plan-3  H92  0.020

