# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 05:53:09 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[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
 AR6  AR6  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AR6
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
 AR6  N1    N  N      0  -0.475  -7.3523   2.7445  -1.2741
 AR6  C2    C  CR16   0   0.041  -7.5528   2.0708  -0.1439
 AR6  N3    N  N      0  -0.454  -6.7492   1.2077   0.4516
 AR6  C4    C  CR56   0   0.487  -5.6128   1.0451  -0.2229
 AR6  C5    C  CR56   0  -0.011  -5.2608   1.6766  -1.4060
 AR6  C6    C  CR6    0   0.447  -6.2046   2.5723  -1.9388
 AR6  N6    N  NH2    0  -0.817  -6.0057   3.2356  -3.0820
 AR6  N7    N  N      0  -0.459  -4.0134   1.2830  -1.8149
 AR6  C8    C  CR15   0   0.068  -3.6224   0.4336  -0.9087
 AR6  N9    N  NR5    0  -0.542  -4.5490   0.2478   0.0846
 AR6  PA    P  P      0   1.358   0.2919  -1.1942  -0.3115
 AR6  PB    P  P      0   1.342   2.1403   1.0064  -0.6435
 AR6  C1'   C  CH1    0   0.225  -4.4556  -0.6417   1.2185
 AR6  O1A   O  OP    -1  -0.790   1.1124  -2.4250  -0.5271
 AR6  O1B   O  OP    -1  -0.792   1.5825   2.3946  -0.6117
 AR6  C1D   C  CH1    0   0.277   7.5446  -0.0709  -0.1175
 AR6  O1D   O  OH1    0  -0.664   8.0975  -1.2376   0.3764
 AR6  C2'   C  CH1    0  -0.048  -4.7094  -2.1098   0.8735
 AR6  O2'   O  OH1    0  -0.652  -6.0790  -2.3779   0.8918
 AR6  O2A   O  O      0  -0.781  -0.6171  -0.6929  -1.3939
 AR6  O2B   O  O      0  -0.794   2.4539   0.3433  -1.9467
 AR6  C2D   C  CH1    0  -0.088   8.1507   1.1418   0.5902
 AR6  O2D   O  OH1    0  -0.667   8.3924   0.8974   1.9491
 AR6  C3'   C  CH1    0  -0.032  -3.8948  -2.8143   1.9625
 AR6  O3'   O  OH1    0  -0.668  -4.5718  -2.7924   3.1920
 AR6  O3A   O  O2     0  -0.734   1.2078   0.0265   0.2875
 AR6  C3D   C  CH1    0   0.002   6.9995   2.1350   0.4775
 AR6  O3D   O  OH1    0  -0.661   7.0042   3.1887   1.3931
 AR6  C4'   C  CH1    0  -0.045  -2.6817  -1.9000   2.0498
 AR6  O4'   O  O2     0  -0.491  -3.1608  -0.5877   1.7381
 AR6  C4D   C  CH1    0   0.007   5.7863   1.2320   0.7046
 AR6  O4D   O  O2     0  -0.510   6.1522  -0.0173   0.1429
 AR6  C5'   C  CH2    0  -0.149  -1.5925  -2.3237   1.0825
 AR6  O5'   O  O2     0  -0.617  -0.5702  -1.3559   1.0853
 AR6  C5D   C  CH2    0  -0.147   4.5382   1.7658   0.0436
 AR6  O5D   O  O2     0  -0.620   3.4462   0.9253   0.3545
 AR6  H2    H  HCR6   0   0.250  -8.5014   2.2595   0.3479
 AR6  HN6   H  HNH2   0   0.401  -6.6590   3.9455  -3.3655
 AR6  HN6A  H  HNH2   0   0.409  -5.1047   3.2256  -3.5273
 AR6  H8    H  HCR5   0   0.328  -2.6584  -0.0631  -0.9099
 AR6  H1'   H  HCH1   0   0.257  -5.1983  -0.2927   1.9450
 AR6  H2'   H  HCH1   0   0.248  -4.2693  -2.3335  -0.1062
 AR6  HO2'  H  HOH1   0   0.469  -6.2426  -3.1825   0.3898
 AR6  HO2D  H  HOH1   0   0.452   8.9406   0.1086   2.0201
 AR6  H3'   H  HCH1   0   0.252  -3.6164  -3.8356   1.6693
 AR6  HO3'  H  HOH1   0   0.449  -5.4761  -3.0901   3.0389
 AR6  H3D   H  HCH1   0   0.228   6.9780   2.5039  -0.5590
 AR6  HO3D  H  HOH1   0   0.459   7.6316   3.8536   1.0941
 AR6  H4'   H  HCH1   0   0.263  -2.2766  -1.8791   3.0660
 AR6  H4D   H  HCH1   0   0.222   5.6097   1.1246   1.7842
 AR6  H5'   H  HCH2   0   0.229  -1.2121  -3.3004   1.4028
 AR6  H5'A  H  HCH2   0   0.204  -2.0167  -2.4601   0.0795
 AR6  H5D   H  HCH2   0   0.215   4.3602   2.7857   0.4034
 AR6  H5DA  H  HCH2   0   0.204   4.7086   1.8237  -1.0387
 AR6  HD1   H  HOH1   0   0.470   7.9761  -1.9499  -0.2592
 AR6  H1D   H  HCH1   0   0.207   7.6996   0.0060  -1.2015
 AR6  H2D   H  HCH1   0   0.239   9.0556   1.4835   0.0708

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
 AR6  N1   C2    aromatic  1.331  0.020  1.331
 AR6  N1   C6    aromatic  1.337  0.020  1.337
 AR6  C2   N3    aromatic  1.321  0.020  1.321
 AR6  N3   C4    aromatic  1.331  0.020  1.331
 AR6  C4   C5    aromatic  1.386  0.020  1.386
 AR6  C4   N9    aromatic  1.365  0.020  1.365
 AR6  C5   C6    aromatic  1.406  0.020  1.406
 AR6  C5   N7    aromatic  1.370  0.020  1.370
 AR6  C6   N6    single    1.337  0.020  1.337
 AR6  N7   C8    aromatic  1.302  0.020  1.302
 AR6  C8   N9    aromatic  1.371  0.020  1.371
 AR6  N9   C1'   single    1.444  0.020  1.444
 AR6  PA   O1A   deloc     1.495  0.020  1.495
 AR6  PA   O2A   deloc     1.500  0.020  1.500
 AR6  PA   O3A   single    1.639  0.020  1.639
 AR6  PA   O5'   single    1.649  0.020  1.649
 AR6  PB   O1B   deloc     1.496  0.020  1.496
 AR6  PB   O2B   deloc     1.495  0.020  1.495
 AR6  PB   O3A   single    1.642  0.020  1.642
 AR6  PB   O5D   single    1.645  0.020  1.645
 AR6  C1'  C2'   single    1.529  0.020  1.529
 AR6  C1'  O4'   single    1.396  0.020  1.396
 AR6  C1D  O1D   single    1.382  0.020  1.382
 AR6  C1D  C2D   single    1.529  0.020  1.529
 AR6  C1D  O4D   single    1.417  0.020  1.417
 AR6  C2'  O2'   single    1.396  0.020  1.396
 AR6  C2'  C3'   single    1.532  0.020  1.532
 AR6  C2D  O2D   single    1.402  0.020  1.402
 AR6  C2D  C3D   single    1.525  0.020  1.525
 AR6  C3'  O3'   single    1.404  0.020  1.404
 AR6  C3'  C4'   single    1.522  0.020  1.522
 AR6  C3D  O3D   single    1.396  0.020  1.396
 AR6  C3D  C4D   single    1.529  0.020  1.529
 AR6  C4'  O4'   single    1.431  0.020  1.431
 AR6  C4'  C5'   single    1.517  0.020  1.517
 AR6  C4D  O4D   single    1.418  0.020  1.418
 AR6  C4D  C5D   single    1.510  0.020  1.510
 AR6  C5'  O5'   single    1.408  0.020  1.408
 AR6  C5D  O5D   single    1.413  0.020  1.413
 AR6  C2   H2    single    0.930  0.020  1.080
 AR6  N6   HN6   single    0.860  0.020  1.020
 AR6  N6   HN6A  single    0.860  0.020  1.020
 AR6  C8   H8    single    0.930  0.020  1.080
 AR6  C1'  H1'   single    0.970  0.020  1.090
 AR6  C1D  H1D   single    0.970  0.020  1.090
 AR6  C2'  H2'   single    0.970  0.020  1.090
 AR6  O2'  HO2'  single    0.850  0.020  0.980
 AR6  C2D  H2D   single    0.970  0.020  1.090
 AR6  O2D  HO2D  single    0.850  0.020  0.980
 AR6  C3'  H3'   single    0.970  0.020  1.090
 AR6  O3'  HO3'  single    0.850  0.020  0.980
 AR6  C3D  H3D   single    0.970  0.020  1.090
 AR6  O3D  HO3D  single    0.850  0.020  0.980
 AR6  C4'  H4'   single    0.970  0.020  1.090
 AR6  C4D  H4D   single    0.970  0.020  1.090
 AR6  C5'  H5'   single    0.970  0.020  1.090
 AR6  C5'  H5'A  single    0.970  0.020  1.090
 AR6  C5D  H5D   single    0.970  0.020  1.090
 AR6  C5D  H5DA  single    0.970  0.020  1.090
 AR6  O1D  HD1   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
 AR6  C6    N1   C2   119.09  3.000
 AR6  H2    C2   N3   116.17  3.000
 AR6  H2    C2   N1   115.38  3.000
 AR6  N3    C2   N1   128.45  3.000
 AR6  C4    N3   C2   111.75  3.000
 AR6  N9    C4   C5   105.10  3.000
 AR6  N9    C4   N3   128.50  3.000
 AR6  C5    C4   N3   126.40  3.000
 AR6  N7    C5   C6   132.92  3.000
 AR6  N7    C5   C4   110.79  3.000
 AR6  C6    C5   C4   116.30  3.000
 AR6  N6    C6   C5   122.70  3.000
 AR6  N6    C6   N1   119.27  3.000
 AR6  C5    C6   N1   118.02  3.000
 AR6  HN6A  N6   HN6  117.68  3.000
 AR6  HN6A  N6   C6   120.50  3.000
 AR6  HN6   N6   C6   119.65  3.000
 AR6  C8    N7   C5   104.65  3.000
 AR6  H8    C8   N9   122.65  3.000
 AR6  H8    C8   N7   124.39  3.000
 AR6  N9    C8   N7   112.94  3.000
 AR6  C1'   N9   C8   127.49  3.000
 AR6  C1'   N9   C4   125.97  3.000
 AR6  C8    N9   C4   106.52  3.000
 AR6  O5'   PA   O3A   93.19  3.000
 AR6  O5'   PA   O2A  109.10  3.000
 AR6  O3A   PA   O2A  110.70  3.000
 AR6  O5'   PA   O1A  109.16  3.000
 AR6  O3A   PA   O1A  111.05  3.000
 AR6  O2A   PA   O1A  120.25  3.000
 AR6  O5D   PB   O3A   94.44  3.000
 AR6  O5D   PB   O2B  109.89  3.000
 AR6  O3A   PB   O2B  110.40  3.000
 AR6  O5D   PB   O1B  109.19  3.000
 AR6  O3A   PB   O1B  109.26  3.000
 AR6  O2B   PB   O1B  120.53  3.000
 AR6  H1'   C1'  O4'  111.68  3.000
 AR6  H1'   C1'  C2'  110.04  3.000
 AR6  O4'   C1'  C2'  105.97  3.000
 AR6  H1'   C1'  N9   106.29  3.000
 AR6  O4'   C1'  N9   109.17  3.000
 AR6  C2'   C1'  N9   113.79  3.000
 AR6  H1D   C1D  O4D  108.51  3.000
 AR6  H1D   C1D  C2D  110.21  3.000
 AR6  O4D   C1D  C2D  105.92  3.000
 AR6  H1D   C1D  O1D  110.82  3.000
 AR6  O4D   C1D  O1D  111.05  3.000
 AR6  C2D   C1D  O1D  110.21  3.000
 AR6  HD1   O1D  C1D  109.77  3.000
 AR6  H2'   C2'  C3'  109.13  3.000
 AR6  H2'   C2'  O2'  111.48  3.000
 AR6  C3'   C2'  O2'  115.10  3.000
 AR6  H2'   C2'  C1'  109.31  3.000
 AR6  C3'   C2'  C1'  101.12  3.000
 AR6  O2'   C2'  C1'  110.14  3.000
 AR6  HO2'  O2'  C2'  108.70  3.000
 AR6  H2D   C2D  C3D  112.62  3.000
 AR6  H2D   C2D  O2D  111.76  3.000
 AR6  C3D   C2D  O2D  108.39  3.000
 AR6  H2D   C2D  C1D  110.76  3.000
 AR6  C3D   C2D  C1D  100.55  3.000
 AR6  O2D   C2D  C1D  112.25  3.000
 AR6  HO2D  O2D  C2D  108.20  3.000
 AR6  H3'   C3'  C4'  111.83  3.000
 AR6  H3'   C3'  O3'  111.75  3.000
 AR6  C4'   C3'  O3'  108.96  3.000
 AR6  H3'   C3'  C2'  111.88  3.000
 AR6  C4'   C3'  C2'  100.86  3.000
 AR6  O3'   C3'  C2'  111.04  3.000
 AR6  HO3'  O3'  C3'  107.97  3.000
 AR6  PB    O3A  PA   123.67  3.000
 AR6  H3D   C3D  C4D  108.80  3.000
 AR6  H3D   C3D  O3D  111.40  3.000
 AR6  C4D   C3D  O3D  110.55  3.000
 AR6  H3D   C3D  C2D  107.62  3.000
 AR6  C4D   C3D  C2D  101.73  3.000
 AR6  O3D   C3D  C2D  116.15  3.000
 AR6  HO3D  O3D  C3D  108.67  3.000
 AR6  H4'   C4'  C5'  109.37  3.000
 AR6  H4'   C4'  O4'  107.97  3.000
 AR6  C5'   C4'  O4'  110.95  3.000
 AR6  H4'   C4'  C3'  111.10  3.000
 AR6  C5'   C4'  C3'  111.59  3.000
 AR6  O4'   C4'  C3'  105.76  3.000
 AR6  C4'   O4'  C1'  110.85  3.000
 AR6  H4D   C4D  C5D  109.37  3.000
 AR6  H4D   C4D  O4D  110.15  3.000
 AR6  C5D   C4D  O4D  110.57  3.000
 AR6  H4D   C4D  C3D  109.33  3.000
 AR6  C5D   C4D  C3D  112.46  3.000
 AR6  O4D   C4D  C3D  104.88  3.000
 AR6  C4D   O4D  C1D  111.07  3.000
 AR6  H5'A  C5'  H5'  106.88  3.000
 AR6  H5'A  C5'  O5'  111.59  3.000
 AR6  H5'   C5'  O5'  111.10  3.000
 AR6  H5'A  C5'  C4'  109.87  3.000
 AR6  H5'   C5'  C4'  108.16  3.000
 AR6  O5'   C5'  C4'  109.16  3.000
 AR6  C5'   O5'  PA   116.44  3.000
 AR6  H5DA  C5D  H5D  107.45  3.000
 AR6  H5DA  C5D  O5D  111.63  3.000
 AR6  H5D   C5D  O5D  110.85  3.000
 AR6  H5DA  C5D  C4D  108.79  3.000
 AR6  H5D   C5D  C4D  108.63  3.000
 AR6  O5D   C5D  C4D  109.42  3.000
 AR6  C5D   O5D  PB   116.79  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
 AR6  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 AR6  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 AR6  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 AR6  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 AR6  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 AR6  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 AR6  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 AR6  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 AR6  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 AR6  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 AR6  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 AR6  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 AR6  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 AR6  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 AR6  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 AR6  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 AR6  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 AR6  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 AR6  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 AR6  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 AR6  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 AR6  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 AR6  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 AR6  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 AR6  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 AR6  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 AR6  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 AR6  Var_01    C4'   C5'  O5'  PA  -151.28  30.0  2
 AR6  Var_02    C4D   C5D  O5D  PB  -159.60  30.0  2
 AR6  Var_03    O1B   PB   O3A  PA   113.03  30.0  1
 AR6  Var_04    O1A   PA   O3A  PB    82.51  30.0  1

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
 AR6  chir_03  C1'  N9   C2'  O4'  negativ
 AR6  chir_04  C1D  O1D  C2D  O4D  positiv
 AR6  chir_05  C2'  C1'  O2'  C3'  positiv
 AR6  chir_06  C2D  C1D  O2D  C3D  positiv
 AR6  chir_07  C3'  C2'  O3'  C4'  positiv
 AR6  chir_08  C3D  C2D  O3D  C4D  positiv
 AR6  chir_09  C4'  O4'  C3'  C5'  negativ
 AR6  chir_10  C4D  C3D  O4D  C5D  positiv

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
 AR6  plan-1  C6    0.020
 AR6  plan-1  N6    0.020
 AR6  plan-1  HN6   0.020
 AR6  plan-1  HN6A  0.020
 AR6  plan-2  N1    0.020
 AR6  plan-2  C2    0.020
 AR6  plan-2  N3    0.020
 AR6  plan-2  C4    0.020
 AR6  plan-2  C5    0.020
 AR6  plan-2  C6    0.020
 AR6  plan-2  N6    0.020
 AR6  plan-2  N7    0.020
 AR6  plan-2  C8    0.020
 AR6  plan-2  N9    0.020
 AR6  plan-2  C1'   0.020
 AR6  plan-2  H2    0.020
 AR6  plan-2  H8    0.020

