# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 23:22:58 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: [dibromo-[[[(2R,3S,4R,5R)-5-[6-(diethylamino)purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)c1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)C(Br)(Br)[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 ARU  ARU  '[dibromo-[[[(2R,3S,4R,5R)-5-[6-(diethylamino)purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]methyl]phosphonic acid'  ligand  57  37  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ARU
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
 ARU  N1    N   N      0  -0.460  -6.3880   1.4456   1.6706
 ARU  C2    C   CR16   0   0.031  -6.2734   0.2551   2.2417
 ARU  N3    N   N      0  -0.406  -5.4917  -0.7484   1.8877
 ARU  C4    C   CR56   0   0.571  -4.7615  -0.4411   0.8188
 ARU  C5    C   CR56   0  -0.054  -4.7657   0.7593   0.1121
 ARU  C6    C   CR6    0   0.459  -5.6432   1.7601   0.5979
 ARU  N6    N   NT     0  -0.462  -5.7766   2.9963   0.0864
 ARU  N7    N   N      0  -0.480  -3.8687   0.6883  -0.9277
 ARU  C8    C   CR15   0   0.151  -3.3418  -0.4973  -0.8485
 ARU  N9    N   NR5    0  -0.618  -3.8467  -1.2325   0.1887
 ARU  C1'   C   CH1    0   0.191  -3.5343  -2.5970   0.5287
 ARU  C2'   C   CH1    0   0.058  -4.0836  -3.6191  -0.4646
 ARU  O2'   O   OH1    0  -0.639  -5.4252  -3.8898  -0.1868
 ARU  C3'   C   CH1    0  -0.100  -3.1228  -4.7876  -0.2368
 ARU  O3'   O   OH1    0  -0.682  -3.4387  -5.4754   0.9469
 ARU  C4'   C   CH1    0  -0.025  -1.8073  -4.0431  -0.0445
 ARU  O4'   O   O2     0  -0.477  -2.1493  -2.7768   0.5274
 ARU  C5'   C   CH2    0  -0.137  -1.0679  -3.8676  -1.3591
 ARU  O5'   O   O2     0  -0.605   0.1264  -3.1552  -1.1669
 ARU  CAA   C   CH3    0  -0.674  -8.1879   3.6549   0.1989
 ARU  CAB   C   CH2    0  -0.333  -6.7588   3.9098   0.6555
 ARU  CAD   C   CH2    0  -0.287  -5.0477   3.4210  -1.1001
 ARU  CAE   C   CH3    0  -0.664  -5.6760   2.9800  -2.4131
 ARU  OAF   O   OP    -1  -0.865   3.2032   2.7908   1.4802
 ARU  BRAG  BR  BR     0  -0.231   1.1040   0.2704   2.3348
 ARU  OAH   O   OP    -1  -0.806   3.1754   0.0542  -0.2547
 ARU  OAI   O   O      0  -0.848   1.7232  -2.0084  -2.7710
 ARU  OAJ   O   O      0  -0.928   1.5384   3.9078  -0.1227
 ARU  PAK   P   P      0   1.222   1.7504   3.1127   1.1584
 ARU  CAL   C   CT     0  -0.648   1.0051   1.3997   0.7301
 ARU  PAM   P   P      0   1.284   1.7980   0.4717  -0.6689
 ARU  OAN   O   O2     0  -0.661   0.8299  -0.8760  -0.6596
 ARU  PAO   P   P      0   1.368   0.4765  -1.7592  -1.9770
 ARU  OAV   O   OP    -1  -0.889   0.9212   3.5845   2.3465
 ARU  BRAW  BR  BR     0  -0.043  -0.8866   1.6262   0.3102
 ARU  OAX   O   O      0  -0.847   1.5783   1.2197  -1.9486
 ARU  OAY   O   OP    -1  -0.790  -0.7578  -1.2620  -2.6738
 ARU  H2    H   HCR6   0   0.266  -6.9058   0.0895   3.1083
 ARU  H8    H   HCR5   0   0.294  -2.5493  -0.8705  -1.4877
 ARU  H1'   H   HCH1   0   0.292  -3.9684  -2.7698   1.5206
 ARU  H2'   H   HCH1   0   0.270  -3.9492  -3.2406  -1.4863
 ARU  HO2'  H   HOH1   0   0.473  -5.8288  -4.2854  -0.9657
 ARU  H3'   H   HCH1   0   0.268  -3.0869  -5.4643  -1.1009
 ARU  HO3'  H   HOH1   0   0.434  -4.3827  -5.6716   0.9320
 ARU  H4'   H   HCH1   0   0.236  -1.1623  -4.5760   0.6617
 ARU  H5'   H   HCH2   0   0.256  -0.8337  -4.8672  -1.7431
 ARU  H5'A  H   HCH2   0   0.204  -1.7136  -3.3818  -2.0963
 ARU  HAA   H   HCH3   0   0.202  -8.2943   3.7783  -0.8785
 ARU  HAAA  H   HCH3   0   0.214  -8.5132   2.6499   0.4644
 ARU  HAAB  H   HCH3   0   0.270  -8.8619   4.3646   0.6806
 ARU  HAB   H   HCH2   0   0.277  -6.7054   3.8565   1.7421
 ARU  HABA  H   HCH2   0   0.218  -6.4552   4.9177   0.3728
 ARU  HAD   H   HCH2   0   0.182  -4.9903   4.5091  -1.0663
 ARU  HADA  H   HCH2   0   0.283  -4.0246   3.0550  -1.0440
 ARU  HAE   H   HCH3   0   0.213  -5.7241   1.8941  -2.4840
 ARU  HAEA  H   HCH3   0   0.266  -6.6822   3.3804  -2.5376
 ARU  HAEB  H   HCH3   0   0.203  -5.0720   3.3401  -3.2470

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
 ARU  N1    C2    aromatic  1.325  0.020  1.325
 ARU  N1    C6    aromatic  1.343  0.020  1.343
 ARU  C2    N3    aromatic  1.320  0.020  1.320
 ARU  N3    C4    aromatic  1.331  0.020  1.331
 ARU  C4    C5    aromatic  1.393  0.020  1.393
 ARU  C4    N9    aromatic  1.364  0.020  1.364
 ARU  C5    C6    aromatic  1.417  0.020  1.417
 ARU  C5    N7    aromatic  1.375  0.020  1.375
 ARU  C6    N6    single    1.345  0.020  1.345
 ARU  N6    CAB   single    1.457  0.020  1.457
 ARU  N6    CAD   single    1.456  0.020  1.456
 ARU  N7    C8    aromatic  1.300  0.020  1.300
 ARU  C8    N9    aromatic  1.368  0.020  1.368
 ARU  N9    C1'   single    1.441  0.020  1.441
 ARU  C1'   C2'   single    1.527  0.020  1.527
 ARU  C1'   O4'   single    1.397  0.020  1.397
 ARU  C2'   O2'   single    1.396  0.020  1.396
 ARU  C2'   C3'   single    1.530  0.020  1.530
 ARU  C3'   O3'   single    1.405  0.020  1.405
 ARU  C3'   C4'   single    1.524  0.020  1.524
 ARU  C4'   O4'   single    1.431  0.020  1.431
 ARU  C4'   C5'   single    1.518  0.020  1.518
 ARU  C5'   O5'   single    1.404  0.020  1.404
 ARU  O5'   PAO   single    1.652  0.020  1.652
 ARU  CAA   CAB   single    1.522  0.020  1.522
 ARU  CAD   CAE   single    1.521  0.020  1.521
 ARU  OAF   PAK   deloc     1.522  0.020  1.522
 ARU  BRAG  CAL   single    1.965  0.020  1.965
 ARU  OAH   PAM   deloc     1.498  0.020  1.498
 ARU  OAI   PAO   deloc     1.499  0.020  1.499
 ARU  OAJ   PAK   deloc     1.523  0.020  1.523
 ARU  PAK   CAL   single    1.917  0.020  1.917
 ARU  PAK   OAV   deloc     1.524  0.020  1.524
 ARU  CAL   PAM   single    1.857  0.020  1.857
 ARU  CAL   BRAW  single    1.951  0.020  1.951
 ARU  PAM   OAN   single    1.659  0.020  1.659
 ARU  PAM   OAX   deloc     1.498  0.020  1.498
 ARU  OAN   PAO   single    1.625  0.020  1.625
 ARU  PAO   OAY   deloc     1.502  0.020  1.502
 ARU  C2    H2    single    0.930  0.020  1.080
 ARU  C8    H8    single    0.930  0.020  1.080
 ARU  C1'   H1'   single    0.970  0.020  1.090
 ARU  C2'   H2'   single    0.970  0.020  1.090
 ARU  O2'   HO2'  single    0.850  0.020  0.980
 ARU  C3'   H3'   single    0.970  0.020  1.090
 ARU  O3'   HO3'  single    0.850  0.020  0.980
 ARU  C4'   H4'   single    0.970  0.020  1.090
 ARU  C5'   H5'   single    0.970  0.020  1.090
 ARU  C5'   H5'A  single    0.970  0.020  1.090
 ARU  CAA   HAA   single    0.970  0.020  1.090
 ARU  CAA   HAAA  single    0.970  0.020  1.090
 ARU  CAA   HAAB  single    0.970  0.020  1.090
 ARU  CAB   HAB   single    0.970  0.020  1.090
 ARU  CAB   HABA  single    0.970  0.020  1.090
 ARU  CAD   HAD   single    0.970  0.020  1.090
 ARU  CAD   HADA  single    0.970  0.020  1.090
 ARU  CAE   HAE   single    0.970  0.020  1.090
 ARU  CAE   HAEA  single    0.970  0.020  1.090
 ARU  CAE   HAEB  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
 ARU  C6    N1   C2    120.43  3.000
 ARU  H2    C2   N3    116.30  3.000
 ARU  H2    C2   N1    115.51  3.000
 ARU  N3    C2   N1    128.20  3.000
 ARU  C4    N3   C2    111.39  3.000
 ARU  N9    C4   C5    105.52  3.000
 ARU  N9    C4   N3    127.25  3.000
 ARU  C5    C4   N3    127.23  3.000
 ARU  N7    C5   C6    134.40  3.000
 ARU  N7    C5   C4    109.71  3.000
 ARU  C6    C5   C4    115.89  3.000
 ARU  N6    C6   C5    125.48  3.000
 ARU  N6    C6   N1    117.65  3.000
 ARU  C5    C6   N1    116.86  3.000
 ARU  CAD   N6   CAB   118.23  3.000
 ARU  CAD   N6   C6    121.91  3.000
 ARU  CAB   N6   C6    119.65  3.000
 ARU  C8    N7   C5    105.39  3.000
 ARU  H8    C8   N9    122.12  3.000
 ARU  H8    C8   N7    125.05  3.000
 ARU  N9    C8   N7    112.76  3.000
 ARU  C1'   N9   C8    127.44  3.000
 ARU  C1'   N9   C4    125.88  3.000
 ARU  C8    N9   C4    106.62  3.000
 ARU  H1'   C1'  O4'   111.91  3.000
 ARU  H1'   C1'  C2'   109.90  3.000
 ARU  O4'   C1'  C2'   105.66  3.000
 ARU  H1'   C1'  N9    106.08  3.000
 ARU  O4'   C1'  N9    109.69  3.000
 ARU  C2'   C1'  N9    113.73  3.000
 ARU  H2'   C2'  C3'   108.97  3.000
 ARU  H2'   C2'  O2'   111.69  3.000
 ARU  C3'   C2'  O2'   115.19  3.000
 ARU  H2'   C2'  C1'   109.29  3.000
 ARU  C3'   C2'  C1'   100.86  3.000
 ARU  O2'   C2'  C1'   110.23  3.000
 ARU  HO2'  O2'  C2'   108.76  3.000
 ARU  H3'   C3'  C4'   111.85  3.000
 ARU  H3'   C3'  O3'   111.63  3.000
 ARU  C4'   C3'  O3'   109.08  3.000
 ARU  H3'   C3'  C2'   111.96  3.000
 ARU  C4'   C3'  C2'   100.83  3.000
 ARU  O3'   C3'  C2'   110.99  3.000
 ARU  HO3'  O3'  C3'   107.86  3.000
 ARU  H4'   C4'  C5'   109.13  3.000
 ARU  H4'   C4'  O4'   108.28  3.000
 ARU  C5'   C4'  O4'   111.10  3.000
 ARU  H4'   C4'  C3'   110.63  3.000
 ARU  C5'   C4'  C3'   111.57  3.000
 ARU  O4'   C4'  C3'   106.05  3.000
 ARU  C4'   O4'  C1'   110.57  3.000
 ARU  H5'A  C5'  H5'   107.15  3.000
 ARU  H5'A  C5'  O5'   111.66  3.000
 ARU  H5'   C5'  O5'   109.21  3.000
 ARU  H5'A  C5'  C4'   110.33  3.000
 ARU  H5'   C5'  C4'   107.57  3.000
 ARU  O5'   C5'  C4'   110.76  3.000
 ARU  PAO   O5'  C5'   122.83  3.000
 ARU  HAAB  CAA  HAAA  107.94  3.000
 ARU  HAAB  CAA  HAA   107.61  3.000
 ARU  HAAA  CAA  HAA   108.44  3.000
 ARU  HAAB  CAA  CAB   109.81  3.000
 ARU  HAAA  CAA  CAB   111.22  3.000
 ARU  HAA   CAA  CAB   111.68  3.000
 ARU  HABA  CAB  HAB   106.88  3.000
 ARU  HABA  CAB  CAA   109.79  3.000
 ARU  HAB   CAB  CAA   109.71  3.000
 ARU  HABA  CAB  N6    106.90  3.000
 ARU  HAB   CAB  N6    109.02  3.000
 ARU  CAA   CAB  N6    114.26  3.000
 ARU  HADA  CAD  HAD   106.54  3.000
 ARU  HADA  CAD  CAE   109.60  3.000
 ARU  HAD   CAD  CAE   109.75  3.000
 ARU  HADA  CAD  N6    109.31  3.000
 ARU  HAD   CAD  N6    106.99  3.000
 ARU  CAE   CAD  N6    114.34  3.000
 ARU  HAEB  CAE  HAEA  107.61  3.000
 ARU  HAEB  CAE  HAE   107.69  3.000
 ARU  HAEA  CAE  HAE   108.54  3.000
 ARU  HAEB  CAE  CAD   109.61  3.000
 ARU  HAEA  CAE  CAD   111.92  3.000
 ARU  HAE   CAE  CAD   111.31  3.000
 ARU  OAV   PAK  CAL   103.85  3.000
 ARU  OAV   PAK  OAJ   114.75  3.000
 ARU  CAL   PAK  OAJ   102.98  3.000
 ARU  OAV   PAK  OAF   114.83  3.000
 ARU  CAL   PAK  OAF   103.25  3.000
 ARU  OAJ   PAK  OAF   114.90  3.000
 ARU  BRAW  CAL  PAM   108.06  3.000
 ARU  BRAW  CAL  PAK   108.75  3.000
 ARU  PAM   CAL  PAK   116.69  3.000
 ARU  BRAW  CAL  BRAG  106.94  3.000
 ARU  PAM   CAL  BRAG  107.86  3.000
 ARU  PAK   CAL  BRAG  108.16  3.000
 ARU  OAX   PAM  OAN   108.94  3.000
 ARU  OAX   PAM  CAL   109.35  3.000
 ARU  OAN   PAM  CAL    98.78  3.000
 ARU  OAX   PAM  OAH   120.68  3.000
 ARU  OAN   PAM  OAH   107.97  3.000
 ARU  CAL   PAM  OAH   108.89  3.000
 ARU  PAO   OAN  PAM   124.32  3.000
 ARU  OAY   PAO  OAN   112.02  3.000
 ARU  OAY   PAO  OAI   119.52  3.000
 ARU  OAN   PAO  OAI   109.81  3.000
 ARU  OAY   PAO  O5'   109.46  3.000
 ARU  OAN   PAO  O5'    96.19  3.000
 ARU  OAI   PAO  O5'   107.19  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
 ARU  CONST_01  C4    N3   C2   N1       0.00   0.0  0
 ARU  CONST_02  C4    C5   C6   N1       0.00   0.0  0
 ARU  CONST_03  N7    C5   C6   N1     180.00   0.0  0
 ARU  CONST_04  C5    C6   N1   C2       0.00   0.0  0
 ARU  CONST_05  C5    C4   N3   C2       0.00   0.0  0
 ARU  CONST_06  N9    C4   N3   C2     180.00   0.0  0
 ARU  CONST_07  C6    N1   C2   N3       0.00   0.0  0
 ARU  CONST_08  C6    C5   C4   N3       0.00   0.0  0
 ARU  CONST_09  N7    C5   C4   N3     180.00   0.0  0
 ARU  CONST_10  C8    N9   C4   N3     180.00   0.0  0
 ARU  CONST_11  C8    N7   C5   C4       0.00   0.0  0
 ARU  CONST_12  N7    C8   N9   C4       0.00   0.0  0
 ARU  CONST_13  C8    N9   C4   C5       0.00   0.0  0
 ARU  CONST_14  N9    C8   N7   C5       0.00   0.0  0
 ARU  CONST_15  N9    C4   C5   C6     180.00   0.0  0
 ARU  CONST_16  C8    N7   C5   C6     180.00   0.0  0
 ARU  CONST_17  N9    C4   C5   N7       0.00   0.0  0
 ARU  CONST_18  C1'   N9   C4   N3       0.00   0.0  0
 ARU  CONST_19  C1'   N9   C4   C5     180.00   0.0  0
 ARU  CONST_20  C1'   N9   C8   N7     180.00   0.0  0
 ARU  CONST_21  N6    C6   N1   C2     180.00   0.0  0
 ARU  CONST_22  N6    C6   C5   C4     180.00   0.0  0
 ARU  CONST_23  N7    C5   C6   N6       0.00   0.0  0
 ARU  CONST_24  H2    C2   N3   C4     180.00   0.0  0
 ARU  CONST_25  H8    C8   N9   C4     180.00   0.0  0
 ARU  CONST_26  CAB   N6   C6   N1       0.00   0.0  0
 ARU  CONST_27  CAD   N6   C6   N1     180.00   0.0  0
 ARU  CONST_28  CAB   N6   C6   C5     180.00   0.0  0
 ARU  CONST_29  CAD   N6   C6   C5       0.00   0.0  0
 ARU  Var_01    CAA   CAB  N6   C6     -79.10  30.0  3
 ARU  Var_02    CAE   CAD  N6   C6      81.45  30.0  3
 ARU  Var_03    OAI   PAO  O5'  C5'   -119.10  30.0  3
 ARU  Var_04    BRAG  CAL  PAK  OAF     63.43  30.0  3
 ARU  Var_05    OAH   PAM  CAL  BRAG   -53.82  30.0  3
 ARU  Var_06    HAA   CAA  CAB  N6     -61.74  30.0  3
 ARU  Var_07    HAE   CAE  CAD  N6     -61.14  30.0  3
 ARU  Var_08    H5'   C5'  O5'  PAO    118.23  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ARU  chir_01  C1'  N9   C2'  O4'  negativ
 ARU  chir_02  C2'  O2'  C3'  C1'  positiv
 ARU  chir_03  C3'  O3'  C4'  C2'  positiv
 ARU  chir_04  C4'  O4'  C3'  C5'  negativ

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
 ARU  plan-1  N1   0.020
 ARU  plan-1  C2   0.020
 ARU  plan-1  N3   0.020
 ARU  plan-1  C4   0.020
 ARU  plan-1  C5   0.020
 ARU  plan-1  C6   0.020
 ARU  plan-1  N6   0.020
 ARU  plan-1  N7   0.020
 ARU  plan-1  C8   0.020
 ARU  plan-1  N9   0.020
 ARU  plan-1  C1'  0.020
 ARU  plan-1  H2   0.020
 ARU  plan-1  H8   0.020
 ARU  plan-2  C6   0.020
 ARU  plan-2  N6   0.020
 ARU  plan-2  CAB  0.020
 ARU  plan-2  CAD  0.020

