# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 26 16:09:38 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([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)c2N1
#
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
 GZ0  GZ0  '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  66  41  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GZ0
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
 GZ0  O3B  O  OP    -1  -0.829   0.9506   0.2276  -0.0113
 GZ0  PB   P  P      0   1.358   1.8708   0.9730   0.8981
 GZ0  O2B  O  O      0  -0.828   2.2294   0.4462   2.2491
 GZ0  O1B  O  O2     0  -0.677   3.2729   1.3356   0.0758
 GZ0  C11  C  CH1    0   0.296   4.3335   0.4525   0.1517
 GZ0  C21  C  CH1    0   0.028   5.5448   1.0648  -0.5439
 GZ0  O21  O  OH1    0  -0.681   6.0107   2.2170   0.1163
 GZ0  C31  C  CH1    0  -0.102   6.6864   0.0489  -0.5575
 GZ0  O31  O  OH1    0  -0.652   7.1438  -0.2348   0.7439
 GZ0  C41  C  CH1    0   0.025   6.2161  -1.2805  -1.1588
 GZ0  O41  O  OH1    0  -0.604   5.9377  -1.1387  -2.5303
 GZ0  C51  C  CH1    0  -0.030   4.9458  -1.7327  -0.4479
 GZ0  C61  C  CH1    0  -0.064   4.3299  -3.0053  -1.0318
 GZ0  C71  C  CH2    0  -0.110   3.0738  -3.3980  -0.2656
 GZ0  O71  O  OH1    0  -0.600   2.5135  -4.5363  -0.8812
 GZ0  O6A  O  OH1    0  -0.668   5.2819  -4.0431  -1.0608
 GZ0  O51  O  O2     0  -0.467   3.9643  -0.7230  -0.5171
 GZ0  O3A  O  O2     0  -0.701   1.4313   2.5520   0.9969
 GZ0  PA   P  P      0   1.334  -0.0534   3.0995   1.4178
 GZ0  O1A  O  O      0  -0.838  -0.7649   2.1217   2.2983
 GZ0  O2A  O  OP    -1  -0.913   0.1110   4.5271   1.8340
 GZ0  O5'  O  O2     0  -0.639  -0.6964   3.0461  -0.1014
 GZ0  C5'  C  CH2    0  -0.190  -2.0727   3.3182  -0.2264
 GZ0  C4'  C  CH1    0   0.015  -2.5631   2.6910  -1.5141
 GZ0  C3'  C  CH1    0  -0.009  -4.0596   2.8560  -1.7178
 GZ0  O3'  O  OH1    0  -0.726  -4.3440   2.7232  -3.0825
 GZ0  C2'  C  CH1    0  -0.035  -4.5896   1.6636  -0.9189
 GZ0  O2'  O  OH1    0  -0.680  -5.8422   1.1927  -1.3384
 GZ0  O4'  O  O2     0  -0.500  -2.3448   1.2759  -1.4928
 GZ0  C1'  C  CH1    0   0.246  -3.5167   0.5994  -1.1869
 GZ0  N9   N  NR5    0  -0.557  -3.2851  -0.2581  -0.0316
 GZ0  C4   C  CR56   0   0.586  -4.1322  -1.2037   0.4362
 GZ0  N3   N  NR16   0  -0.594  -5.3795  -1.5438   0.0129
 GZ0  C2   C  CR6    0   0.590  -5.9850  -2.5590   0.6970
 GZ0  N2   N  NH2    0  -0.842  -7.2344  -2.8673   0.3149
 GZ0  C8   C  CR15   0   0.099  -2.1560  -0.3471   0.7533
 GZ0  N7   N  N      0  -0.393  -2.2682  -1.2617   1.6694
 GZ0  C5   C  CR56   0  -0.071  -3.5042  -1.8256   1.4805
 GZ0  C6   C  CR6    0   0.384  -4.1841  -2.8966   2.1750
 GZ0  O6   O  O      0  -0.630  -3.7097  -3.4966   3.1319
 GZ0  N1   N  N      0  -0.432  -5.4349  -3.1998   1.6912
 GZ0  H2   H  HCH1   0   0.195   4.5760   0.2209   1.2008
 GZ0  H3   H  HCH1   0   0.233   5.2623   1.2822  -1.5827
 GZ0  H4   H  HOH1   0   0.455   5.2827   2.8415   0.1978
 GZ0  H5   H  HCH1   0   0.227   7.5020   0.4464  -1.1814
 GZ0  H6   H  HOH1   0   0.455   7.2849   0.6010   1.2023
 GZ0  H7   H  HCH1   0   0.244   6.9987  -2.0297  -0.9812
 GZ0  H8   H  HOH1   0   0.468   6.7586  -0.9304  -2.9875
 GZ0  H9   H  HCH1   0   0.256   5.2153  -1.9211   0.6029
 GZ0  H10  H  HCH1   0   0.234   4.0567  -2.8205  -2.0750
 GZ0  H11  H  HCH2   0   0.120   3.3406  -3.5950   0.7824
 GZ0  H12  H  HCH2   0   0.192   2.3761  -2.5535  -0.2665
 GZ0  H13  H  HOH1   0   0.471   1.6678  -4.7120  -0.4611
 GZ0  H14  H  HOH1   0   0.438   5.4883  -4.2987  -0.1552
 GZ0  H16  H  HCH2   0   0.270  -2.6334   2.9164   0.6268
 GZ0  H17  H  HCH2   0   0.302  -2.2676   4.3998  -0.2441
 GZ0  H18  H  HCH1   0   0.268  -2.0045   3.1030  -2.3601
 GZ0  H19  H  HCH1   0   0.288  -4.4248   3.8076  -1.3066
 GZ0  H20  H  HOH1   0   0.463  -5.2830   2.5255  -3.1780
 GZ0  H21  H  HCH1   0   0.230  -4.5922   1.9238   0.1471
 GZ0  H22  H  HOH1   0   0.454  -6.5408   1.6695  -0.8749
 GZ0  H23  H  HCH1   0   0.263  -3.8170  -0.0507  -2.0177
 GZ0  H24  H  HNR6   0   0.454  -5.8770  -0.9813  -0.6665
 GZ0  H25  H  HNH2   0   0.415  -7.6541  -3.6884   0.7154
 GZ0  H26  H  HNH2   0   0.390  -7.6030  -2.5564  -0.5671
 GZ0  H27  H  HCR5   0   0.316  -1.2934   0.2820   0.5964

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
 GZ0  N2   C2   single    1.342  0.020  1.342
 GZ0  C2   N1   double    1.305  0.020  1.305
 GZ0  C2   N3   single    1.366  0.020  1.366
 GZ0  N1   C6   single    1.375  0.020  1.375
 GZ0  O2'  C2'  single    1.402  0.020  1.402
 GZ0  N3   C4   single    1.360  0.020  1.360
 GZ0  C6   O6   double    1.225  0.020  1.225
 GZ0  C6   C5   single    1.446  0.020  1.446
 GZ0  C4   C5   aromatic  1.368  0.020  1.368
 GZ0  C4   N9   aromatic  1.353  0.020  1.353
 GZ0  O3'  C3'  single    1.400  0.020  1.400
 GZ0  C5   N7   aromatic  1.372  0.020  1.372
 GZ0  C2'  C1'  single    1.535  0.020  1.535
 GZ0  C2'  C3'  single    1.530  0.020  1.530
 GZ0  N9   C1'  single    1.457  0.020  1.457
 GZ0  N9   C8   aromatic  1.378  0.020  1.378
 GZ0  C1'  O4'  single    1.387  0.020  1.387
 GZ0  C3'  C4'  single    1.519  0.020  1.519
 GZ0  N7   C8   aromatic  1.299  0.020  1.299
 GZ0  O2B  PB   deloc     1.494  0.020  1.494
 GZ0  O4'  C4'  single    1.432  0.020  1.432
 GZ0  C4'  C5'  single    1.514  0.020  1.514
 GZ0  O3A  PB   single    1.642  0.020  1.642
 GZ0  O3A  PA   single    1.637  0.020  1.637
 GZ0  PB   O3B  deloc     1.493  0.020  1.493
 GZ0  PB   O1B  single    1.665  0.020  1.665
 GZ0  C5'  O5'  single    1.409  0.020  1.409
 GZ0  O5'  PA   single    1.650  0.020  1.650
 GZ0  O31  C31  single    1.408  0.020  1.408
 GZ0  PA   O1A  deloc     1.496  0.020  1.496
 GZ0  PA   O2A  deloc     1.496  0.020  1.496
 GZ0  C11  O1B  single    1.382  0.020  1.382
 GZ0  C11  O51  single    1.402  0.020  1.402
 GZ0  C11  C21  single    1.525  0.020  1.525
 GZ0  O21  C21  single    1.407  0.020  1.407
 GZ0  O51  C51  single    1.410  0.020  1.410
 GZ0  C21  C31  single    1.528  0.020  1.528
 GZ0  C31  C41  single    1.533  0.020  1.533
 GZ0  C51  C41  single    1.524  0.020  1.524
 GZ0  C51  C61  single    1.530  0.020  1.530
 GZ0  C41  O41  single    1.407  0.020  1.407
 GZ0  C71  C61  single    1.523  0.020  1.523
 GZ0  C71  O71  single    1.410  0.020  1.410
 GZ0  C61  O6A  single    1.409  0.020  1.409
 GZ0  C11  H2   single    0.970  0.020  1.090
 GZ0  C21  H3   single    0.970  0.020  1.090
 GZ0  O21  H4   single    0.850  0.020  0.980
 GZ0  C31  H5   single    0.970  0.020  1.090
 GZ0  O31  H6   single    0.850  0.020  0.980
 GZ0  C41  H7   single    0.970  0.020  1.090
 GZ0  O41  H8   single    0.850  0.020  0.980
 GZ0  C51  H9   single    0.970  0.020  1.090
 GZ0  C61  H10  single    0.970  0.020  1.090
 GZ0  C71  H11  single    0.970  0.020  1.090
 GZ0  C71  H12  single    0.970  0.020  1.090
 GZ0  O71  H13  single    0.850  0.020  0.980
 GZ0  O6A  H14  single    0.850  0.020  0.980
 GZ0  C5'  H16  single    0.970  0.020  1.090
 GZ0  C5'  H17  single    0.970  0.020  1.090
 GZ0  C4'  H18  single    0.970  0.020  1.090
 GZ0  C3'  H19  single    0.970  0.020  1.090
 GZ0  O3'  H20  single    0.850  0.020  0.980
 GZ0  C2'  H21  single    0.970  0.020  1.090
 GZ0  O2'  H22  single    0.850  0.020  0.980
 GZ0  C1'  H23  single    0.970  0.020  1.090
 GZ0  N3   H24  single    0.860  0.020  1.020
 GZ0  N2   H25  single    0.890  0.020  1.040
 GZ0  N2   H26  single    0.890  0.020  1.040
 GZ0  C8   H27  single    0.930  0.020  1.080

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
 GZ0  O3A  PB   O1B   92.62  3.000
 GZ0  O1B  PB   O2B  108.74  3.000
 GZ0  O3A  PB   O2B  110.42  3.000
 GZ0  O1B  PB   O3B  109.08  3.000
 GZ0  O3A  PB   O3B  110.60  3.000
 GZ0  O2B  PB   O3B  121.51  3.000
 GZ0  C11  O1B  PB   118.67  3.000
 GZ0  H2   C11  O51  109.63  3.000
 GZ0  H2   C11  C21  110.12  3.000
 GZ0  O51  C11  C21  109.16  3.000
 GZ0  H2   C11  O1B  110.83  3.000
 GZ0  C21  C11  O1B  109.14  3.000
 GZ0  O51  C11  O1B  107.91  3.000
 GZ0  H3   C21  C31  108.38  3.000
 GZ0  H3   C21  O21  111.52  3.000
 GZ0  C31  C21  O21  107.52  3.000
 GZ0  H3   C21  C11  107.85  3.000
 GZ0  C31  C21  C11  109.30  3.000
 GZ0  O21  C21  C11  112.19  3.000
 GZ0  H4   O21  C21  108.69  3.000
 GZ0  H5   C31  C41  108.55  3.000
 GZ0  H5   C31  O31  110.84  3.000
 GZ0  C41  C31  O31  106.70  3.000
 GZ0  H5   C31  C21  108.56  3.000
 GZ0  C41  C31  C21  110.53  3.000
 GZ0  O31  C31  C21  111.61  3.000
 GZ0  H6   O31  C31  108.21  3.000
 GZ0  H7   C41  C51  108.43  3.000
 GZ0  H7   C41  O41  111.57  3.000
 GZ0  C51  C41  O41  108.64  3.000
 GZ0  H7   C41  C31  108.04  3.000
 GZ0  O41  C41  C31  110.84  3.000
 GZ0  C51  C41  C31  109.27  3.000
 GZ0  H8   O41  C41  108.43  3.000
 GZ0  H9   C51  O51  109.86  3.000
 GZ0  H9   C51  C61  108.69  3.000
 GZ0  O51  C51  C61  107.26  3.000
 GZ0  H9   C51  C41  106.97  3.000
 GZ0  C61  C51  C41  113.85  3.000
 GZ0  O51  C51  C41  110.18  3.000
 GZ0  H10  C61  O6A  105.88  3.000
 GZ0  H10  C61  C71  108.50  3.000
 GZ0  O6A  C61  C71  112.20  3.000
 GZ0  H10  C61  C51  108.91  3.000
 GZ0  O6A  C61  C51  110.41  3.000
 GZ0  C71  C61  C51  110.77  3.000
 GZ0  H12  C71  H11  107.07  3.000
 GZ0  H12  C71  O71  111.65  3.000
 GZ0  H11  C71  O71  111.59  3.000
 GZ0  H12  C71  C61  109.04  3.000
 GZ0  H11  C71  C61  109.01  3.000
 GZ0  O71  C71  C61  108.44  3.000
 GZ0  H13  O71  C71  107.85  3.000
 GZ0  H14  O6A  C61  108.72  3.000
 GZ0  C51  O51  C11  113.19  3.000
 GZ0  PA   O3A  PB   125.43  3.000
 GZ0  O5'  PA   O2A  109.25  3.000
 GZ0  O2A  PA   O1A  120.81  3.000
 GZ0  O5'  PA   O1A  109.60  3.000
 GZ0  O2A  PA   O3A  106.91  3.000
 GZ0  O1A  PA   O3A  111.35  3.000
 GZ0  O5'  PA   O3A   96.08  3.000
 GZ0  C5'  O5'  PA   117.14  3.000
 GZ0  H17  C5'  H16  106.40  3.000
 GZ0  H17  C5'  C4'  109.67  3.000
 GZ0  H16  C5'  C4'  110.13  3.000
 GZ0  H17  C5'  O5'  111.39  3.000
 GZ0  H16  C5'  O5'  111.07  3.000
 GZ0  C4'  C5'  O5'  108.18  3.000
 GZ0  H18  C4'  O4'  107.80  3.000
 GZ0  H18  C4'  C3'  110.99  3.000
 GZ0  O4'  C4'  C3'  105.04  3.000
 GZ0  H18  C4'  C5'  109.65  3.000
 GZ0  O4'  C4'  C5'  110.33  3.000
 GZ0  C3'  C4'  C5'  112.84  3.000
 GZ0  H19  C3'  C2'  111.36  3.000
 GZ0  H19  C3'  O3'  112.29  3.000
 GZ0  C2'  C3'  O3'  111.38  3.000
 GZ0  H19  C3'  C4'  111.79  3.000
 GZ0  C2'  C3'  C4'  100.76  3.000
 GZ0  O3'  C3'  C4'  108.69  3.000
 GZ0  H20  O3'  C3'  108.29  3.000
 GZ0  H21  C2'  C1'  109.62  3.000
 GZ0  H21  C2'  O2'  111.60  3.000
 GZ0  C1'  C2'  O2'  109.84  3.000
 GZ0  H21  C2'  C3'  108.86  3.000
 GZ0  C1'  C2'  C3'  101.94  3.000
 GZ0  O2'  C2'  C3'  114.51  3.000
 GZ0  H22  O2'  C2'  109.70  3.000
 GZ0  C1'  O4'  C4'  110.88  3.000
 GZ0  H23  C1'  N9   107.16  3.000
 GZ0  H23  C1'  O4'  110.69  3.000
 GZ0  N9   C1'  O4'  109.12  3.000
 GZ0  H23  C1'  C2'  110.60  3.000
 GZ0  O4'  C1'  C2'  106.92  3.000
 GZ0  N9   C1'  C2'  112.38  3.000
 GZ0  C8   N9   C4   105.72  3.000
 GZ0  C8   N9   C1'  128.30  3.000
 GZ0  C4   N9   C1'  125.86  3.000
 GZ0  C5   C4   N3   123.01  3.000
 GZ0  C5   C4   N9   107.11  3.000
 GZ0  N3   C4   N9   129.89  3.000
 GZ0  H24  N3   C2   122.08  3.000
 GZ0  H24  N3   C4   121.35  3.000
 GZ0  C2   N3   C4   115.88  3.000
 GZ0  N1   C2   N2   119.78  3.000
 GZ0  N1   C2   N3   124.05  3.000
 GZ0  N2   C2   N3   116.15  3.000
 GZ0  H26  N2   H25  116.68  3.000
 GZ0  H26  N2   C2   121.33  3.000
 GZ0  H25  N2   C2   117.56  3.000
 GZ0  H27  C8   N7   125.58  3.000
 GZ0  H27  C8   N9   122.31  3.000
 GZ0  N7   C8   N9   112.10  3.000
 GZ0  C5   N7   C8   105.67  3.000
 GZ0  C6   C5   N7   131.44  3.000
 GZ0  N7   C5   C4   109.39  3.000
 GZ0  C6   C5   C4   119.17  3.000
 GZ0  N1   C6   O6   121.27  3.000
 GZ0  O6   C6   C5   123.76  3.000
 GZ0  N1   C6   C5   114.96  3.000
 GZ0  C6   N1   C2   122.92  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
 GZ0  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 GZ0  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 GZ0  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 GZ0  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 GZ0  CONST_05  C5   C4   N9   C8      0.00   0.0  0
 GZ0  CONST_06  N3   C4   N9   C1'     0.00   0.0  0
 GZ0  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 GZ0  CONST_08  N7   C8   N9   C1'   180.00   0.0  0
 GZ0  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 GZ0  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 GZ0  CONST_11  N2   C2   N3   C4    180.00   0.0  0
 GZ0  CONST_12  C6   N1   C2   N2    180.00   0.0  0
 GZ0  CONST_13  H27  C8   N9   C1'     0.00   0.0  0
 GZ0  CONST_14  H24  N3   C2   N1    180.00   0.0  0
 GZ0  CONST_15  H25  N2   C2   N3    180.00   0.0  0
 GZ0  Var_01    O3A  PB   O1B  C11   155.03  30.0  2
 GZ0  Var_02    C4'  C5'  O5'  PA   -157.33  30.0  1
 GZ0  Var_03    O5'  PA   O3A  PB    -86.91  30.0  3

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
 GZ0  chir_02  C11  O1B  O51  C21  negativ
 GZ0  chir_03  C21  O21  C11  C31  positiv
 GZ0  chir_04  C31  O31  C21  C41  positiv
 GZ0  chir_05  C41  O41  C31  C51  negativ
 GZ0  chir_06  C51  O51  C61  C41  negativ
 GZ0  chir_07  C61  O6A  C51  C71  positiv
 GZ0  chir_09  C4'  C3'  O4'  C5'  positiv
 GZ0  chir_10  C3'  O3'  C2'  C4'  negativ
 GZ0  chir_11  C2'  O2'  C1'  C3'  negativ
 GZ0  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
 GZ0  plan-1  C1'  0.020
 GZ0  plan-1  N9   0.020
 GZ0  plan-1  C4   0.020
 GZ0  plan-1  N3   0.020
 GZ0  plan-1  C2   0.020
 GZ0  plan-1  N2   0.020
 GZ0  plan-1  C8   0.020
 GZ0  plan-1  N7   0.020
 GZ0  plan-1  C5   0.020
 GZ0  plan-1  C6   0.020
 GZ0  plan-1  O6   0.020
 GZ0  plan-1  N1   0.020
 GZ0  plan-1  H24  0.020
 GZ0  plan-1  H25  0.020
 GZ0  plan-1  H26  0.020
 GZ0  plan-1  H27  0.020

