# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 22:17:00 2021
#   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  61  37  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.495  35.3852  27.1544  33.3032
 ARU  C2    C   CR16  0   0.045  34.1298  27.0185  33.7028
 ARU  N3    N   N     0  -0.461  33.0295  27.4259  33.0953
 ARU  C4    C   CR56  0   0.490  33.3081  28.0265  31.9426
 ARU  C5    C   CR56  0  -0.011  34.5643  28.2431  31.3870
 ARU  C6    C   CR6   0   0.526  35.6672  27.7696  32.1425
 ARU  N6    N   NT    0  -0.461  36.9548  27.8817  31.7919
 ARU  N7    N   N     0  -0.451  34.4335  28.8741  30.1713
 ARU  C8    C   CR15  0   0.119  33.1575  29.0357  30.0077
 ARU  N9    N   NR5   0  -0.548  32.4142  28.5505  31.0510
 ARU  C1'   C   CH1   0   0.207  30.9843  28.5200  31.1875
 ARU  C2'   C   CH1   0  -0.016  30.3066  29.8772  30.9967
 ARU  O2'   O   OH1   0  -0.645  30.4082  30.6094  32.1750
 ARU  C3'   C   CH1   0  -0.050  28.9019  29.4449  30.5749
 ARU  O3'   O   OH1   0  -0.663  28.1912  29.1288  31.7413
 ARU  C4'   C   CH1   0  -0.015  29.2018  28.1967  29.7301
 ARU  O4'   O   O2    0  -0.490  30.4313  27.6691  30.2189
 ARU  C5'   C   CH2   0  -0.213  29.2888  28.4213  28.2366
 ARU  O5'   O   O2    0  -0.576  30.4000  29.2754  27.9344
 ARU  CAA   C   CH3   0  -0.657  37.4828  27.6855  29.3779
 ARU  CAB   C   CH2   0  -0.327  37.3934  28.5878  30.5980
 ARU  CAD   C   CH2   0  -0.317  37.9987  27.2871  32.6155
 ARU  CAE   C   CH3   0  -0.657  38.4551  28.2026  33.7402
 ARU  OAF   O   OH1   0  -0.724  28.8814  36.0764  26.8487
 ARU  BRAG  BR  BR    0   0.051  28.1779  33.3580  30.2024
 ARU  OAH   O   OH1   0  -0.720  29.5252  33.2889  25.9979
 ARU  OAI   O   O     0  -0.656  31.7289  31.0156  26.6863
 ARU  OAJ   O   O     0  -0.655  28.8665  36.6433  29.4266
 ARU  PAK   P   P     0   1.430  28.4244  35.7580  28.3374
 ARU  CAL   C   CT    0  -0.768  29.0318  34.0165  28.5927
 ARU  PAM   P   P     0   1.467  28.6185  32.8489  27.2211
 ARU  OAN   O   O2    0  -0.711  29.3806  31.5214  27.7259
 ARU  PAO   P   P     0   1.517  30.3785  30.5028  26.9374
 ARU  OAV   O   OH1   0  -0.714  26.8722  35.5877  28.0681
 ARU  BRAW  BR  BR    0   0.064  30.9434  34.1000  28.8341
 ARU  OAX   O   O     0  -0.626  27.1728  32.6987  27.0130
 ARU  OAY   O   OH1   0  -0.731  29.4472  30.1383  25.7070
 ARU  H2    H   HCR6  0   0.249  33.9929  26.5085  34.6509
 ARU  H8    H   HCR5  0   0.284  32.7061  29.4954  29.1421
 ARU  H1'   H   HCH1  0   0.265  30.7859  28.1491  32.1987
 ARU  H2'   H   HCH1  0   0.228  30.7707  30.4053  30.1556
 ARU  HO2'  H   HOH1  0   0.455  30.1769  31.5264  32.0003
 ARU  H3'   H   HCH1  0   0.248  28.3823  30.2087  29.9846
 ARU  HO3'  H   HOH1  0   0.459  27.3096  28.8347  31.4909
 ARU  H4'   H   HCH1  0   0.273  28.4053  27.4575  29.8733
 ARU  H5'   H   HCH2  0   0.278  29.4546  27.4750  27.7213
 ARU  H5'A  H   HCH2  0   0.258  28.3418  28.8349  27.8835
 ARU  HAA   H   HCH3  0   0.231  37.8699  28.2447  28.5256
 ARU  HAAA  H   HCH3  0   0.226  38.1532  26.8436  29.5550
 ARU  HAAB  H   HCH3  0   0.233  36.5022  27.2958  29.1072
 ARU  HAB   H   HCH2  0   0.262  36.7310  29.4261  30.3985
 ARU  HABA  H   HCH2  0   0.255  38.3731  29.0144  30.8208
 ARU  HAD   H   HCH2  0   0.252  37.6491  26.3384  33.0183
 ARU  HADA  H   HCH2  0   0.248  38.8373  27.0604  31.9547
 ARU  HAE   H   HCH3  0   0.230  39.2820  27.7455  34.2848
 ARU  HAEA  H   HCH3  0   0.225  38.8010  29.1629  33.3549
 ARU  HAEB  H   HCH3  0   0.232  37.6453  28.3870  34.4454
 ARU  HOAF  H   HOH1  0   0.513  29.7537  36.4854  26.7591
 ARU  HOAH  H   HOH1  0   0.514  29.0688  33.7784  25.2981
 ARU  HOAV  H   HOH1  0   0.513  26.3031  35.6547  28.8469
 ARU  HOAY  H   HOH1  0   0.514  29.8949  29.7061  24.9652

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  1.324  0.020  1.324
 ARU  N1    C6    aromatic  1.344  0.020  1.344
 ARU  C2    N3    aromatic  1.321  0.020  1.321
 ARU  N3    C4    aromatic  1.329  0.020  1.329
 ARU  C4    C5    aromatic  1.391  0.020  1.391
 ARU  C4    N9    aromatic  1.367  0.020  1.367
 ARU  C5    C6    aromatic  1.418  0.020  1.418
 ARU  C5    N7    aromatic  1.376  0.020  1.376
 ARU  C6    N6    single    1.339  0.020  1.339
 ARU  N6    CAB   single    1.455  0.020  1.455
 ARU  N6    CAD   single    1.457  0.020  1.457
 ARU  N7    C8    aromatic  1.297  0.020  1.297
 ARU  C8    N9    aromatic  1.370  0.020  1.370
 ARU  N9    C1'   single    1.437  0.020  1.437
 ARU  C1'   C2'   single    1.529  0.020  1.529
 ARU  C1'   O4'   single    1.403  0.020  1.403
 ARU  C2'   O2'   single    1.391  0.020  1.391
 ARU  C2'   C3'   single    1.529  0.020  1.529
 ARU  C3'   O3'   single    1.402  0.020  1.402
 ARU  C3'   C4'   single    1.537  0.020  1.537
 ARU  C4'   O4'   single    1.424  0.020  1.424
 ARU  C4'   C5'   single    1.513  0.020  1.513
 ARU  C5'   O5'   single    1.434  0.020  1.434
 ARU  O5'   PAO   single    1.581  0.020  1.581
 ARU  CAA   CAB   single    1.520  0.020  1.520
 ARU  CAD   CAE   single    1.520  0.020  1.520
 ARU  OAF   PAK   single    1.589  0.020  1.589
 ARU  BRAG  CAL   single    1.937  0.020  1.937
 ARU  OAH   PAM   single    1.585  0.020  1.585
 ARU  OAI   PAO   double    1.466  0.020  1.466
 ARU  OAJ   PAK   double    1.472  0.020  1.472
 ARU  PAK   CAL   single    1.862  0.020  1.862
 ARU  PAK   OAV   single    1.585  0.020  1.585
 ARU  CAL   PAM   single    1.848  0.020  1.848
 ARU  CAL   BRAW  single    1.929  0.020  1.929
 ARU  PAM   OAN   single    1.612  0.020  1.612
 ARU  PAM   OAX   double    1.468  0.020  1.468
 ARU  OAN   PAO   single    1.629  0.020  1.629
 ARU  PAO   OAY   single    1.586  0.020  1.586
 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
 ARU  OAF   HOAF  single    0.850  0.020  0.980
 ARU  OAH   HOAH  single    0.850  0.020  0.980
 ARU  OAV   HOAV  single    0.850  0.020  0.980
 ARU  OAY   HOAY  single    0.850  0.020  0.980

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    120.44  3.000
 ARU  H2    C2   N3    116.20  3.000
 ARU  H2    C2   N1    115.56  3.000
 ARU  N3    C2   N1    128.24  3.000
 ARU  C4    N3   C2    111.32  3.000
 ARU  N9    C4   C5    105.69  3.000
 ARU  N9    C4   N3    126.99  3.000
 ARU  C5    C4   N3    127.31  3.000
 ARU  N7    C5   C6    134.24  3.000
 ARU  N7    C5   C4    109.79  3.000
 ARU  C6    C5   C4    115.96  3.000
 ARU  N6    C6   C5    125.48  3.000
 ARU  N6    C6   N1    117.79  3.000
 ARU  C5    C6   N1    116.73  3.000
 ARU  CAD   N6   CAB   116.49  3.000
 ARU  CAD   N6   C6    120.46  3.000
 ARU  CAB   N6   C6    123.05  3.000
 ARU  C8    N7   C5    105.20  3.000
 ARU  H8    C8   N9    122.33  3.000
 ARU  H8    C8   N7    124.47  3.000
 ARU  N9    C8   N7    113.19  3.000
 ARU  C1'   N9   C8    128.31  3.000
 ARU  C1'   N9   C4    125.50  3.000
 ARU  C8    N9   C4    106.12  3.000
 ARU  H1'   C1'  O4'   111.14  3.000
 ARU  H1'   C1'  C2'   109.61  3.000
 ARU  O4'   C1'  C2'   106.11  3.000
 ARU  H1'   C1'  N9    105.98  3.000
 ARU  O4'   C1'  N9    109.86  3.000
 ARU  C2'   C1'  N9    114.23  3.000
 ARU  H2'   C2'  C3'   108.27  3.000
 ARU  H2'   C2'  O2'   111.43  3.000
 ARU  C3'   C2'  O2'   116.72  3.000
 ARU  H2'   C2'  C1'   109.62  3.000
 ARU  C3'   C2'  C1'   100.99  3.000
 ARU  O2'   C2'  C1'   109.22  3.000
 ARU  HO2'  O2'  C2'   109.30  3.000
 ARU  H3'   C3'  C4'   111.25  3.000
 ARU  H3'   C3'  O3'   111.39  3.000
 ARU  C4'   C3'  O3'   111.91  3.000
 ARU  H3'   C3'  C2'   112.77  3.000
 ARU  C4'   C3'  C2'   101.66  3.000
 ARU  O3'   C3'  C2'   107.45  3.000
 ARU  HO3'  O3'  C3'   108.46  3.000
 ARU  H4'   C4'  C5'   105.72  3.000
 ARU  H4'   C4'  O4'   109.43  3.000
 ARU  C5'   C4'  O4'   110.13  3.000
 ARU  H4'   C4'  C3'   109.52  3.000
 ARU  C5'   C4'  C3'   115.68  3.000
 ARU  O4'   C4'  C3'   106.30  3.000
 ARU  C4'   O4'  C1'   110.64  3.000
 ARU  H5'A  C5'  H5'   107.92  3.000
 ARU  H5'A  C5'  O5'   112.23  3.000
 ARU  H5'   C5'  O5'   107.44  3.000
 ARU  H5'A  C5'  C4'   109.00  3.000
 ARU  H5'   C5'  C4'   110.27  3.000
 ARU  O5'   C5'  C4'   109.95  3.000
 ARU  PAO   O5'  C5'   125.78  3.000
 ARU  HAAB  CAA  HAAA  108.51  3.000
 ARU  HAAB  CAA  HAA   107.98  3.000
 ARU  HAAA  CAA  HAA   107.73  3.000
 ARU  HAAB  CAA  CAB   111.03  3.000
 ARU  HAAA  CAA  CAB   111.35  3.000
 ARU  HAA   CAA  CAB   110.11  3.000
 ARU  HABA  CAB  HAB   106.44  3.000
 ARU  HABA  CAB  CAA   110.06  3.000
 ARU  HAB   CAB  CAA   110.26  3.000
 ARU  HABA  CAB  N6    107.02  3.000
 ARU  HAB   CAB  N6    109.95  3.000
 ARU  CAA   CAB  N6    112.85  3.000
 ARU  HADA  CAD  HAD   106.85  3.000
 ARU  HADA  CAD  CAE   110.02  3.000
 ARU  HAD   CAD  CAE   110.34  3.000
 ARU  HADA  CAD  N6    107.05  3.000
 ARU  HAD   CAD  N6    109.56  3.000
 ARU  CAE   CAD  N6    112.80  3.000
 ARU  HAEB  CAE  HAEA  108.38  3.000
 ARU  HAEB  CAE  HAE   108.13  3.000
 ARU  HAEA  CAE  HAE   107.75  3.000
 ARU  HAEB  CAE  CAD   110.95  3.000
 ARU  HAEA  CAE  CAD   111.34  3.000
 ARU  HAE   CAE  CAD   110.16  3.000
 ARU  HOAF  OAF  PAK   115.50  3.000
 ARU  HOAH  OAH  PAM   115.36  3.000
 ARU  OAV   PAK  CAL   104.02  3.000
 ARU  OAV   PAK  OAJ   119.00  3.000
 ARU  CAL   PAK  OAJ   111.29  3.000
 ARU  OAV   PAK  OAF    98.28  3.000
 ARU  CAL   PAK  OAF   102.82  3.000
 ARU  OAJ   PAK  OAF   119.10  3.000
 ARU  BRAW  CAL  PAM   109.99  3.000
 ARU  BRAW  CAL  PAK   107.46  3.000
 ARU  PAM   CAL  PAK   114.59  3.000
 ARU  BRAW  CAL  BRAG  110.34  3.000
 ARU  PAM   CAL  BRAG  107.66  3.000
 ARU  PAK   CAL  BRAG  106.74  3.000
 ARU  OAX   PAM  OAN   115.20  3.000
 ARU  OAX   PAM  CAL   112.95  3.000
 ARU  OAN   PAM  CAL   100.49  3.000
 ARU  OAX   PAM  OAH   118.84  3.000
 ARU  OAN   PAM  OAH   101.53  3.000
 ARU  CAL   PAM  OAH   105.63  3.000
 ARU  PAO   OAN  PAM   130.76  3.000
 ARU  OAY   PAO  OAN    99.18  3.000
 ARU  OAY   PAO  OAI   119.24  3.000
 ARU  OAN   PAO  OAI   115.36  3.000
 ARU  OAY   PAO  O5'   108.59  3.000
 ARU  OAN   PAO  O5'   100.86  3.000
 ARU  OAI   PAO  O5'   111.52  3.000
 ARU  HOAV  OAV  PAK   115.60  3.000
 ARU  HOAY  OAY  PAO   115.19  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     180.00   0.0  0
 ARU  CONST_27  CAD   N6   C6   N1       0.00   0.0  0
 ARU  CONST_28  CAB   N6   C6   C5       0.00   0.0  0
 ARU  CONST_29  CAD   N6   C6   C5     180.00   0.0  0
 ARU  Var_01    CAA   CAB  N6   C6     -90.39  30.0  3
 ARU  Var_02    CAE   CAD  N6   C6     -86.31  30.0  3
 ARU  Var_03    OAI   PAO  O5'  C5'   -170.26  30.0  3
 ARU  Var_04    BRAG  CAL  PAK  OAF   -166.78  30.0  3
 ARU  Var_05    OAH   PAM  CAL  BRAG  -170.84  30.0  3
 ARU  Var_06    HAA   CAA  CAB  N6    -176.71  30.0  3
 ARU  Var_07    HAE   CAE  CAD  N6    -176.07  30.0  3
 ARU  Var_08    H5'   C5'  O5'  PAO    105.17  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
 ARU  chir_05  PAM  CAL  OAN  OAX  both
 ARU  chir_06  PAO  OAI  OAN  OAY  both

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

