# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 27 06:03:49 2022
#   Inital geometry file: a 160 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@@H]([C@H](O)CO)[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
 YO7  YO7  '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  66  41  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YO7
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
 YO7  O3B  O  OP    -1  -0.776  11.3269  -28.5973  25.3826
 YO7  PB   P  P      0   1.363  11.2344  -27.3245  24.6108
 YO7  O2B  O  O      0  -0.777  12.3081  -26.2879  24.6005
 YO7  O1B  O  O2     0  -0.632  10.8904  -27.7907  23.0617
 YO7  C11  C  CH1    0   0.262  10.8002  -26.8600  22.0390
 YO7  C21  C  CH1    0  -0.012   9.5846  -27.1665  21.1661
 YO7  O21  O  OH1    0  -0.714   8.3703  -26.9917  21.8360
 YO7  C31  C  CH1    0   0.004   9.5667  -26.2160  19.9688
 YO7  O31  O  OH1    0  -0.669   8.5423  -26.5518  19.0655
 YO7  C41  C  CH1    0   0.031  10.8980  -26.2472  19.2338
 YO7  O41  O  OH1    0  -0.670  10.8746  -25.2546  18.2351
 YO7  C51  C  CH1    0  -0.002  12.0181  -25.9907  20.2543
 YO7  C61  C  CH1    0  -0.028  13.4110  -25.9699  19.6434
 YO7  C71  C  CH2    0  -0.173  14.5090  -25.8327  20.6960
 YO7  O71  O  OH1    0  -0.668  14.2989  -24.6449  21.4223
 YO7  O6A  O  OH1    0  -0.672  13.6042  -27.1500  18.8960
 YO7  O51  O  O2     0  -0.503  11.9655  -26.9752  21.2644
 YO7  O3A  O  O2     0  -0.749   9.8599  -26.5089  25.0279
 YO7  PA   P  P      0   1.388   8.3783  -27.1582  25.3060
 YO7  O1A  O  O      0  -0.782   8.0687  -28.1546  24.2187
 YO7  O2A  O  OP    -1  -0.765   8.2302  -27.5147  26.7466
 YO7  O5'  O  O2     0  -0.618   7.4909  -25.8257  24.9555
 YO7  C5'  C  CH2    0  -0.165   6.9531  -24.9892  25.9537
 YO7  C4'  C  CH1    0  -0.032   6.2218  -23.8338  25.3027
 YO7  C3'  C  CH1    0  -0.042   5.2672  -24.2321  24.1697
 YO7  O3'  O  OH1    0  -0.665   4.1865  -23.3416  24.0525
 YO7  C2'  C  CH1    0  -0.019   6.1568  -24.0486  22.9367
 YO7  O2'  O  OH1    0  -0.654   5.4968  -23.7844  21.7368
 YO7  O4'  O  O2     0  -0.497   7.1379  -22.8961  24.7268
 YO7  C1'  C  CH1    0   0.218   6.9952  -22.8342  23.3420
 YO7  N9   N  NR5    0  -0.538   8.3159  -22.8160  22.7458
 YO7  C4   C  CR5    0   0.502   8.6760  -22.1837  21.5960
 YO7  N3   N  N      0  -0.510   7.8864  -21.4323  20.8157
 YO7  C2   C  C      0   0.684   8.5004  -20.9578  19.7610
 YO7  N2   N  NH2    0  -0.831   7.8198  -20.2174  18.8725
 YO7  C8   C  CR15   0   0.089   9.4389  -23.4562  23.2081
 YO7  N7   N  N      0  -0.451  10.4736  -23.2653  22.4474
 YO7  C5   C  CR5    0  -0.087  10.0165  -22.4771  21.4242
 YO7  C6   C  C      0   0.502  10.6880  -21.9769  20.2723
 YO7  O6   O  O      0  -0.467  11.8482  -22.1387  19.9327
 YO7  N1   N  NH1    0  -0.726   9.8152  -21.2109  19.4872
 YO7  H2   H  HCH1   0   0.200  10.7172  -25.8326  22.4234
 YO7  H3   H  HCH1   0   0.192   9.6982  -28.1974  20.7885
 YO7  H4   H  HOH1   0   0.463   8.3213  -27.5318  22.6620
 YO7  H5   H  HCH1   0   0.204   9.4194  -25.1930  20.3584
 YO7  H6   H  HOH1   0   0.444   7.7165  -26.5749  19.5607
 YO7  H7   H  HCH1   0   0.218  11.0304  -27.2472  18.8003
 YO7  H8   H  HOH1   0   0.454  11.5436  -25.4647  17.5768
 YO7  H9   H  HCH1   0   0.232  11.8487  -24.9953  20.6907
 YO7  H10  H  HCH1   0   0.217  13.4545  -25.0825  18.9959
 YO7  H11  H  HCH2   0   0.200  15.4783  -25.8181  20.1767
 YO7  H12  H  HCH2   0   0.204  14.5047  -26.7180  21.3406
 YO7  H13  H  HOH1   0   0.456  14.8747  -24.6532  22.1913
 YO7  H14  H  HOH1   0   0.454  14.3843  -27.0398  18.3439
 YO7  H16  H  HCH2   0   0.222   6.2352  -25.5301  26.5790
 YO7  H17  H  HCH2   0   0.228   7.7291  -24.5933  26.6175
 YO7  H18  H  HCH1   0   0.257   5.6714  -23.3210  26.0996
 YO7  H19  H  HCH1   0   0.247   4.9231  -25.2678  24.2798
 YO7  H20  H  HOH1   0   0.453   3.6334  -23.4314  24.8351
 YO7  H21  H  HCH1   0   0.254   6.8167  -24.9165  22.8487
 YO7  H22  H  HOH1   0   0.458   5.1826  -24.6165  21.3702
 YO7  H23  H  HCH1   0   0.252   6.4982  -21.9096  23.0254
 YO7  H24  H  HNH2   0   0.410   6.8983  -19.9111  19.1357
 YO7  H25  H  HNH2   0   0.413   8.2954  -19.6611  18.1824
 YO7  H26  H  HCR5   0   0.297   9.4293  -24.0477  24.1092
 YO7  H27  H  HNH1   0   0.424  10.2148  -20.8298  18.6382

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
 YO7  O31  C31  single    1.406  0.020  1.406
 YO7  O41  C41  single    1.408  0.020  1.408
 YO7  O6   C6   double    1.220  0.020  1.220
 YO7  C31  C41  single    1.521  0.020  1.521
 YO7  C31  C21  single    1.529  0.020  1.529
 YO7  C41  C51  single    1.537  0.020  1.537
 YO7  C6   N1   single    1.402  0.020  1.402
 YO7  C6   C5   single    1.424  0.020  1.424
 YO7  O21  C21  single    1.398  0.020  1.398
 YO7  C51  C61  single    1.521  0.020  1.521
 YO7  C51  O51  single    1.412  0.020  1.412
 YO7  N1   C2   single    1.367  0.020  1.367
 YO7  C21  C11  single    1.528  0.020  1.528
 YO7  N7   C5   aromatic  1.370  0.020  1.370
 YO7  N7   C8   aromatic  1.298  0.020  1.298
 YO7  O71  C71  single    1.408  0.020  1.408
 YO7  C5   C4   aromatic  1.383  0.020  1.383
 YO7  C61  O6A  single    1.410  0.020  1.410
 YO7  C61  C71  single    1.527  0.020  1.527
 YO7  C11  O51  single    1.404  0.020  1.404
 YO7  C11  O1B  single    1.386  0.020  1.386
 YO7  C8   N9   aromatic  1.373  0.020  1.373
 YO7  C2   N2   single    1.342  0.020  1.342
 YO7  C2   N3   double    1.309  0.020  1.309
 YO7  C4   N3   single    1.341  0.020  1.341
 YO7  C4   N9   aromatic  1.361  0.020  1.361
 YO7  O1A  PA   deloc     1.507  0.020  1.507
 YO7  N9   C1'  single    1.449  0.020  1.449
 YO7  O1B  PB   single    1.654  0.020  1.654
 YO7  O2'  C2'  single    1.395  0.020  1.395
 YO7  C2'  C1'  single    1.530  0.020  1.530
 YO7  C2'  C3'  single    1.531  0.020  1.531
 YO7  C1'  O4'  single    1.393  0.020  1.393
 YO7  PA   O3A  single    1.641  0.020  1.641
 YO7  PA   O5'  single    1.639  0.020  1.639
 YO7  PA   O2A  deloc     1.491  0.020  1.491
 YO7  O2B  PB   deloc     1.493  0.020  1.493
 YO7  O3A  PB   single    1.652  0.020  1.652
 YO7  O5'  C5'  single    1.409  0.020  1.409
 YO7  PB   O3B  deloc     1.491  0.020  1.491
 YO7  O4'  C4'  single    1.432  0.020  1.432
 YO7  C3'  C4'  single    1.534  0.020  1.534
 YO7  C3'  O3'  single    1.405  0.020  1.405
 YO7  C5'  C4'  single    1.514  0.020  1.514
 YO7  C11  H2   single    0.970  0.020  1.090
 YO7  C21  H3   single    0.970  0.020  1.090
 YO7  O21  H4   single    0.850  0.020  0.980
 YO7  C31  H5   single    0.970  0.020  1.090
 YO7  O31  H6   single    0.850  0.020  0.980
 YO7  C41  H7   single    0.970  0.020  1.090
 YO7  O41  H8   single    0.850  0.020  0.980
 YO7  C51  H9   single    0.970  0.020  1.090
 YO7  C61  H10  single    0.970  0.020  1.090
 YO7  C71  H11  single    0.970  0.020  1.090
 YO7  C71  H12  single    0.970  0.020  1.090
 YO7  O71  H13  single    0.850  0.020  0.980
 YO7  O6A  H14  single    0.850  0.020  0.980
 YO7  C5'  H16  single    0.970  0.020  1.090
 YO7  C5'  H17  single    0.970  0.020  1.090
 YO7  C4'  H18  single    0.970  0.020  1.090
 YO7  C3'  H19  single    0.970  0.020  1.090
 YO7  O3'  H20  single    0.850  0.020  0.980
 YO7  C2'  H21  single    0.970  0.020  1.090
 YO7  O2'  H22  single    0.850  0.020  0.980
 YO7  C1'  H23  single    0.970  0.020  1.090
 YO7  N2   H24  single    0.890  0.020  1.040
 YO7  N2   H25  single    0.890  0.020  1.040
 YO7  C8   H26  single    0.930  0.020  1.080
 YO7  N1   H27  single    0.860  0.020  1.020

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
 YO7  O3A  PB   O1B  101.69  3.000
 YO7  O3A  PB   O2B  104.92  3.000
 YO7  O1B  PB   O2B  109.81  3.000
 YO7  O3A  PB   O3B  110.02  3.000
 YO7  O2B  PB   O3B  123.48  3.000
 YO7  O1B  PB   O3B  104.89  3.000
 YO7  C11  O1B  PB   121.03  3.000
 YO7  H2   C11  O51  109.39  3.000
 YO7  H2   C11  C21  109.09  3.000
 YO7  O51  C11  C21  109.20  3.000
 YO7  H2   C11  O1B  111.98  3.000
 YO7  O51  C11  O1B  107.34  3.000
 YO7  C21  C11  O1B  109.80  3.000
 YO7  H3   C21  C31  108.30  3.000
 YO7  H3   C21  O21  111.72  3.000
 YO7  C31  C21  O21  106.70  3.000
 YO7  H3   C21  C11  107.52  3.000
 YO7  O21  C21  C11  113.10  3.000
 YO7  C31  C21  C11  109.39  3.000
 YO7  H4   O21  C21  112.05  3.000
 YO7  H5   C31  C41  107.83  3.000
 YO7  H5   C31  O31  110.52  3.000
 YO7  C41  C31  O31  108.79  3.000
 YO7  H5   C31  C21  107.53  3.000
 YO7  C41  C31  C21  110.82  3.000
 YO7  O31  C31  C21  111.29  3.000
 YO7  H6   O31  C31  107.46  3.000
 YO7  H7   C41  C51  109.05  3.000
 YO7  H7   C41  O41  111.35  3.000
 YO7  C51  C41  O41  111.43  3.000
 YO7  H7   C41  C31  108.37  3.000
 YO7  C51  C41  C31  108.27  3.000
 YO7  O41  C41  C31  108.28  3.000
 YO7  H8   O41  C41  108.66  3.000
 YO7  H9   C51  O51  109.97  3.000
 YO7  H9   C51  C61  106.74  3.000
 YO7  O51  C51  C61  109.33  3.000
 YO7  H9   C51  C41  107.59  3.000
 YO7  O51  C51  C41  109.37  3.000
 YO7  C61  C51  C41  113.76  3.000
 YO7  H10  C61  O6A  110.97  3.000
 YO7  H10  C61  C71  107.76  3.000
 YO7  O6A  C61  C71  110.00  3.000
 YO7  H10  C61  C51  106.49  3.000
 YO7  C71  C61  C51  112.51  3.000
 YO7  O6A  C61  C51  109.08  3.000
 YO7  H12  C71  H11  106.98  3.000
 YO7  H12  C71  O71  112.20  3.000
 YO7  H11  C71  O71  111.34  3.000
 YO7  H12  C71  C61  109.28  3.000
 YO7  H11  C71  C61  108.03  3.000
 YO7  O71  C71  C61  108.90  3.000
 YO7  H13  O71  C71  108.43  3.000
 YO7  H14  O6A  C61  108.63  3.000
 YO7  C51  O51  C11  111.62  3.000
 YO7  PA   O3A  PB   126.77  3.000
 YO7  O5'  PA   O2A  110.31  3.000
 YO7  O2A  PA   O1A  121.23  3.000
 YO7  O5'  PA   O1A  105.78  3.000
 YO7  O2A  PA   O3A  110.36  3.000
 YO7  O5'  PA   O3A   97.52  3.000
 YO7  O1A  PA   O3A  108.95  3.000
 YO7  C5'  O5'  PA   122.54  3.000
 YO7  H17  C5'  H16  107.27  3.000
 YO7  H17  C5'  C4'  109.08  3.000
 YO7  H16  C5'  C4'  107.80  3.000
 YO7  H17  C5'  O5'  111.94  3.000
 YO7  H16  C5'  O5'  111.20  3.000
 YO7  C4'  C5'  O5'  109.44  3.000
 YO7  H18  C4'  O4'  107.90  3.000
 YO7  H18  C4'  C3'  110.25  3.000
 YO7  O4'  C4'  C3'  105.73  3.000
 YO7  H18  C4'  C5'  106.68  3.000
 YO7  C3'  C4'  C5'  114.82  3.000
 YO7  O4'  C4'  C5'  111.32  3.000
 YO7  H19  C3'  C2'  112.10  3.000
 YO7  H19  C3'  O3'  111.43  3.000
 YO7  C2'  C3'  O3'  107.68  3.000
 YO7  H19  C3'  C4'  111.48  3.000
 YO7  O3'  C3'  C4'  112.06  3.000
 YO7  C2'  C3'  C4'  101.66  3.000
 YO7  H20  O3'  C3'  108.36  3.000
 YO7  H21  C2'  C1'  108.69  3.000
 YO7  H21  C2'  O2'  111.50  3.000
 YO7  C1'  C2'  O2'  109.68  3.000
 YO7  H21  C2'  C3'  108.67  3.000
 YO7  C1'  C2'  C3'  101.54  3.000
 YO7  O2'  C2'  C3'  116.13  3.000
 YO7  H22  O2'  C2'  108.57  3.000
 YO7  C1'  O4'  C4'  111.30  3.000
 YO7  H23  C1'  N9   106.48  3.000
 YO7  H23  C1'  O4'  111.77  3.000
 YO7  N9   C1'  O4'  108.43  3.000
 YO7  H23  C1'  C2'  110.15  3.000
 YO7  O4'  C1'  C2'  106.50  3.000
 YO7  N9   C1'  C2'  113.60  3.000
 YO7  C8   N9   C4   106.54  3.000
 YO7  C4   N9   C1'  126.49  3.000
 YO7  C8   N9   C1'  126.95  3.000
 YO7  C5   C4   N3   128.14  3.000
 YO7  N3   C4   N9   126.61  3.000
 YO7  C5   C4   N9   105.24  3.000
 YO7  C2   N3   C4   113.31  3.000
 YO7  N1   C2   N2   117.22  3.000
 YO7  N2   C2   N3   119.70  3.000
 YO7  N1   C2   N3   123.05  3.000
 YO7  H25  N2   H24  116.36  3.000
 YO7  H25  N2   C2   121.31  3.000
 YO7  H24  N2   C2   117.34  3.000
 YO7  H26  C8   N7   125.28  3.000
 YO7  H26  C8   N9   122.01  3.000
 YO7  N7   C8   N9   112.71  3.000
 YO7  C5   N7   C8   104.85  3.000
 YO7  C6   C5   N7   130.46  3.000
 YO7  N7   C5   C4   110.65  3.000
 YO7  C6   C5   C4   118.88  3.000
 YO7  N1   C6   O6   120.58  3.000
 YO7  N1   C6   C5   110.58  3.000
 YO7  O6   C6   C5   128.84  3.000
 YO7  H27  N1   C6   115.44  3.000
 YO7  H27  N1   C2   118.54  3.000
 YO7  C6   N1   C2   126.02  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
 YO7  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 YO7  CONST_02  N7   C5   C4   N9     0.00   0.0  0
 YO7  CONST_03  C8   N7   C5   C4     0.00   0.0  0
 YO7  CONST_04  N7   C8   N9   C4     0.00   0.0  0
 YO7  CONST_05  C5   C4   N9   C8     0.00   0.0  0
 YO7  CONST_06  N7   C8   N9   C1'  180.00   0.0  0
 YO7  CONST_07  C5   C4   N9   C1'  180.00   0.0  0
 YO7  CONST_08  N3   C4   N9   C1'    0.00   0.0  0
 YO7  CONST_09  N1   C2   N3   C4     0.00   0.0  0
 YO7  CONST_10  C6   N1   C2   N3     0.00   0.0  0
 YO7  CONST_11  C5   C6   N1   C2     0.00   0.0  0
 YO7  CONST_12  N2   C2   N3   C4   180.00   0.0  0
 YO7  CONST_13  O6   C6   N1   C2   180.00   0.0  0
 YO7  CONST_14  C6   N1   C2   N2   180.00   0.0  0
 YO7  CONST_15  H26  C8   N9   C1'    0.00   0.0  0
 YO7  CONST_16  H27  N1   C2   N3   180.00   0.0  0
 YO7  CONST_17  H24  N2   C2   N3     0.00   0.0  0
 YO7  CONST_18  H25  N2   C2   N3   180.00   0.0  0
 YO7  Var_01    O3A  PB   O1B  C11   68.77  30.0  3
 YO7  Var_02    C4'  C5'  O5'  PA   178.54  30.0  3
 YO7  Var_03    O1A  PA   O3A  PB   -45.39  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
 YO7  chir_02  C11  C21  O51  O1B  positiv
 YO7  chir_03  C21  O21  C11  C31  positiv
 YO7  chir_04  C31  O31  C21  C41  negativ
 YO7  chir_05  C41  O41  C51  C31  negativ
 YO7  chir_06  C51  O51  C61  C41  negativ
 YO7  chir_07  C61  O6A  C51  C71  negativ
 YO7  chir_09  C4'  O4'  C3'  C5'  negativ
 YO7  chir_10  C3'  O3'  C4'  C2'  positiv
 YO7  chir_11  C2'  O2'  C3'  C1'  positiv
 YO7  chir_12  C1'  O4'  N9   C2'  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
 YO7  plan-1  C1'  0.020
 YO7  plan-1  N9   0.020
 YO7  plan-1  C4   0.020
 YO7  plan-1  N3   0.020
 YO7  plan-1  C2   0.020
 YO7  plan-1  N2   0.020
 YO7  plan-1  C8   0.020
 YO7  plan-1  N7   0.020
 YO7  plan-1  C5   0.020
 YO7  plan-1  C6   0.020
 YO7  plan-1  O6   0.020
 YO7  plan-1  N1   0.020
 YO7  plan-1  H24  0.020
 YO7  plan-1  H25  0.020
 YO7  plan-1  H26  0.020
 YO7  plan-1  H27  0.020

