# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 04:52:11 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: [(2R,3R,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl 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)OC[C@H]4OC[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
 G2R  G2R  '[(2R,3R,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_G2R
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
 G2R  O6    O  OC     0  -0.476   2.1495   5.6083   0.0709
 G2R  C6    C  CR6    0   0.500   1.8566   4.6697  -0.6514
 G2R  N1    N  NR16   0  -0.726   1.1372   4.8823  -1.8355
 G2R  C2    C  CR6    0   0.682   0.7458   3.9250  -2.7268
 G2R  N2    N  NH2    0  -0.832   0.0901   4.3444  -3.8204
 G2R  N3    N  N      0  -0.515   1.0152   2.6530  -2.5702
 G2R  C4    C  CR56   0   0.498   1.7044   2.3977  -1.4477
 G2R  C5    C  CR56   0  -0.088   2.1440   3.2857  -0.4837
 G2R  N7    N  N      0  -0.453   2.8032   2.6198   0.5173
 G2R  C8    C  CR15   0   0.106   2.7658   1.3706   0.1642
 G2R  N9    N  NR5    0  -0.526   2.1081   1.1734  -1.0228
 G2R  C1'   C  CH1    0   0.177   1.8611  -0.0688  -1.7407
 G2R  O4'   O  O2     0  -0.510   1.9951  -1.1410  -0.8627
 G2R  C2'   C  CH1    0  -0.045   2.8658  -0.3018  -2.8861
 G2R  O2'   O  OH1    0  -0.666   2.2901  -1.0915  -3.8934
 G2R  C3'   C  CH1    0  -0.030   3.9383  -1.1376  -2.1841
 G2R  O3'   O  OH1    0  -0.689   4.7810  -0.3034  -1.4366
 G2R  C4'   C  CH1    0   0.002   3.0686  -1.9975  -1.2707
 G2R  C5'   C  CH2    0  -0.167   3.7411  -2.5609  -0.0355
 G2R  O5'   O  O2     0  -0.615   4.7427  -3.4445  -0.4871
 G2R  PA    P  P      0   1.396   5.7062  -4.2244   0.5896
 G2R  O1A   O  O      0  -0.777   6.6460  -5.0366  -0.2429
 G2R  O2A   O  OP    -1  -0.799   4.8718  -4.8498   1.6628
 G2R  O3A   O  O2     0  -0.759   6.4443  -2.8951   1.2156
 G2R  PB    P  P      0   1.356   7.7848  -2.7911   2.1571
 G2R  O2B   O  O      0  -0.786   7.4991  -1.7842   3.2233
 G2R  O1B   O  OP    -1  -0.802   8.2855  -4.1636   2.4751
 G2R  O5X   O  O2     0  -0.621   8.8060  -2.0296   1.1229
 G2R  C5X   C  CH2    0  -0.197   9.3403  -2.7053   0.0012
 G2R  C4X   C  CH1    0  -0.008   9.2219  -1.7965  -1.2166
 G2R  O4X   O  O2     0  -0.506   9.9935  -2.3578  -2.2741
 G2R  C1X   C  CH2    0  -0.177   9.1674  -2.6856  -3.3713
 G2R  C2X   C  CH1    0  -0.024   7.7444  -2.7438  -2.8164
 G2R  O2X   O  OH1    0  -0.659   6.7483  -2.5869  -3.7870
 G2R  C3X   C  CH1    0  -0.066   7.7894  -1.6700  -1.7270
 G2R  O3X   O  OH1    0  -0.694   7.5295  -0.4224  -2.3598
 G2R  HN1   H  HNR6   0   0.424   0.9008   5.8458  -2.0343
 G2R  HN21  H  HNH2   0   0.411  -0.3317   3.6401  -4.4018
 G2R  HN22  H  HNH2   0   0.414  -0.3404   5.2537  -3.8442
 G2R  H8    H  HCR5   0   0.285   3.1865   0.5558   0.7288
 G2R  H1'   H  HCH1   0   0.270   0.8365  -0.0087  -2.1230
 G2R  H2'   H  HCH1   0   0.259   3.2651   0.6411  -3.2765
 G2R  HO2'  H  HOH1   0   0.459   1.6066  -0.5807  -4.3389
 G2R  H3'   H  HCH1   0   0.262   4.4929  -1.7592  -2.8910
 G2R  HO3'  H  HOH1   0   0.464   5.6421  -0.2467  -1.8776
 G2R  H4'   H  HCH1   0   0.240   2.6568  -2.8281  -1.8561
 G2R  H5'1  H  HCH2   0   0.223   2.9986  -3.0848   0.5768
 G2R  H5'2  H  HCH2   0   0.213   4.1610  -1.7534   0.5703
 G2R  H5X1  H  HCH2   0   0.226  10.3979  -2.9259   0.1779
 G2R  H5X2  H  HCH2   0   0.226   8.8369  -3.6580  -0.1885
 G2R  H4X   H  HCH1   0   0.238   9.6311  -0.8117  -0.9536
 G2R  H1X1  H  HCH2   0   0.233   9.4924  -3.6385  -3.7939
 G2R  H1X2  H  HCH2   0   0.203   9.2398  -1.9258  -4.1620
 G2R  H2X   H  HCH1   0   0.263   7.5587  -3.7071  -2.3364
 G2R  HO2X  H  HOH1   0   0.445   6.8424  -1.7129  -4.1821
 G2R  H3X   H  HCH1   0   0.274   7.0578  -1.8478  -0.9366
 G2R  HO3X  H  HOH1   0   0.467   7.8677   0.2891  -1.8053

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
 G2R  O6   C6    double    1.220  0.020  1.220
 G2R  C6   C5    aromatic  1.423  0.020  1.423
 G2R  C6   N1    aromatic  1.402  0.020  1.402
 G2R  N1   C2    aromatic  1.365  0.020  1.365
 G2R  N1   HN1   single    0.860  0.020  1.020
 G2R  C2   N3    aromatic  1.310  0.020  1.310
 G2R  C2   N2    single    1.342  0.020  1.342
 G2R  N2   HN21  single    0.890  0.020  1.040
 G2R  N2   HN22  single    0.890  0.020  1.040
 G2R  N3   C4    aromatic  1.342  0.020  1.342
 G2R  C4   N9    aromatic  1.357  0.020  1.357
 G2R  C4   C5    aromatic  1.382  0.020  1.382
 G2R  C5   N7    aromatic  1.371  0.020  1.371
 G2R  N7   C8    aromatic  1.299  0.020  1.299
 G2R  C8   N9    aromatic  1.371  0.020  1.371
 G2R  C8   H8    single    0.930  0.020  1.080
 G2R  N9   C1'   single    1.456  0.020  1.456
 G2R  C1'  O4'   single    1.392  0.020  1.392
 G2R  C1'  C2'   single    1.541  0.020  1.541
 G2R  C1'  H1'   single    0.970  0.020  1.090
 G2R  O4'  C4'   single    1.433  0.020  1.433
 G2R  C2'  C3'   single    1.530  0.020  1.530
 G2R  C2'  O2'   single    1.403  0.020  1.403
 G2R  C2'  H2'   single    0.970  0.020  1.090
 G2R  O2'  HO2'  single    0.850  0.020  0.980
 G2R  C3'  O3'   single    1.402  0.020  1.402
 G2R  C3'  C4'   single    1.526  0.020  1.526
 G2R  C3'  H3'   single    0.970  0.020  1.090
 G2R  O3'  HO3'  single    0.850  0.020  0.980
 G2R  C4'  C5'   single    1.515  0.020  1.515
 G2R  C4'  H4'   single    0.970  0.020  1.090
 G2R  C5'  O5'   single    1.410  0.020  1.410
 G2R  C5'  H5'1  single    0.970  0.020  1.090
 G2R  C5'  H5'2  single    0.970  0.020  1.090
 G2R  O5'  PA    single    1.642  0.020  1.642
 G2R  PA   O3A   single    1.644  0.020  1.644
 G2R  PA   O1A   deloc     1.495  0.020  1.495
 G2R  PA   O2A   deloc     1.496  0.020  1.496
 G2R  O3A  PB    single    1.641  0.020  1.641
 G2R  PB   O2B   deloc     1.494  0.020  1.494
 G2R  PB   O5X   single    1.641  0.020  1.641
 G2R  PB   O1B   deloc     1.495  0.020  1.495
 G2R  O5X  C5X   single    1.414  0.020  1.414
 G2R  C5X  C4X   single    1.524  0.020  1.524
 G2R  C5X  H5X1  single    0.970  0.020  1.090
 G2R  C5X  H5X2  single    0.970  0.020  1.090
 G2R  C4X  C3X   single    1.526  0.020  1.526
 G2R  C4X  O4X   single    1.424  0.020  1.424
 G2R  C4X  H4X   single    0.970  0.020  1.090
 G2R  O4X  C1X   single    1.412  0.020  1.412
 G2R  C1X  C2X   single    1.528  0.020  1.528
 G2R  C1X  H1X1  single    0.970  0.020  1.090
 G2R  C1X  H1X2  single    0.970  0.020  1.090
 G2R  C2X  O2X   single    1.400  0.020  1.400
 G2R  C2X  C3X   single    1.530  0.020  1.530
 G2R  C2X  H2X   single    0.970  0.020  1.090
 G2R  O2X  HO2X  single    0.850  0.020  0.980
 G2R  C3X  O3X   single    1.423  0.020  1.423
 G2R  C3X  H3X   single    0.970  0.020  1.090
 G2R  O3X  HO3X  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
 G2R  C5    C6   N1    110.52  3.000
 G2R  N1    C6   O6    120.44  3.000
 G2R  C5    C6   O6    129.03  3.000
 G2R  HN1   N1   C2    118.19  3.000
 G2R  HN1   N1   C6    115.49  3.000
 G2R  C2    N1   C6    126.32  3.000
 G2R  N3    C2   N2    120.09  3.000
 G2R  N2    C2   N1    116.93  3.000
 G2R  N3    C2   N1    122.96  3.000
 G2R  HN22  N2   HN21  116.08  3.000
 G2R  HN22  N2   C2    120.70  3.000
 G2R  HN21  N2   C2    117.19  3.000
 G2R  C4    N3   C2    112.99  3.000
 G2R  N9    C4   C5    105.46  3.000
 G2R  C5    C4   N3    128.65  3.000
 G2R  N9    C4   N3    125.89  3.000
 G2R  N7    C5   C4    110.49  3.000
 G2R  N7    C5   C6    130.94  3.000
 G2R  C4    C5   C6    118.57  3.000
 G2R  C8    N7   C5    104.76  3.000
 G2R  H8    C8   N9    122.17  3.000
 G2R  H8    C8   N7    125.03  3.000
 G2R  N9    C8   N7    112.80  3.000
 G2R  C1'   N9   C8    129.12  3.000
 G2R  C1'   N9   C4    124.39  3.000
 G2R  C8    N9   C4    106.49  3.000
 G2R  H1'   C1'  C2'   111.02  3.000
 G2R  H1'   C1'  O4'   110.63  3.000
 G2R  C2'   C1'  O4'   106.82  3.000
 G2R  H1'   C1'  N9    106.50  3.000
 G2R  C2'   C1'  N9    112.63  3.000
 G2R  O4'   C1'  N9    109.26  3.000
 G2R  C4'   O4'  C1'   110.67  3.000
 G2R  H2'   C2'  C3'   112.21  3.000
 G2R  H2'   C2'  O2'   112.20  3.000
 G2R  C3'   C2'  O2'   108.02  3.000
 G2R  H2'   C2'  C1'   111.85  3.000
 G2R  O2'   C2'  C1'   110.55  3.000
 G2R  C3'   C2'  C1'   101.45  3.000
 G2R  HO2'  O2'  C2'   108.95  3.000
 G2R  H3'   C3'  C4'   110.85  3.000
 G2R  H3'   C3'  O3'   112.23  3.000
 G2R  C4'   C3'  O3'   111.02  3.000
 G2R  H3'   C3'  C2'   111.70  3.000
 G2R  C4'   C3'  C2'   100.54  3.000
 G2R  O3'   C3'  C2'   109.94  3.000
 G2R  HO3'  O3'  C3'   109.05  3.000
 G2R  H4'   C4'  C5'   108.68  3.000
 G2R  H4'   C4'  C3'   108.74  3.000
 G2R  C5'   C4'  C3'   116.39  3.000
 G2R  H4'   C4'  O4'   108.88  3.000
 G2R  C5'   C4'  O4'   108.83  3.000
 G2R  C3'   C4'  O4'   105.10  3.000
 G2R  H5'2  C5'  H5'1  107.69  3.000
 G2R  H5'2  C5'  O5'   111.56  3.000
 G2R  H5'1  C5'  O5'   111.15  3.000
 G2R  H5'2  C5'  C4'   110.34  3.000
 G2R  H5'1  C5'  C4'   109.43  3.000
 G2R  O5'   C5'  C4'   106.70  3.000
 G2R  PA    O5'  C5'   120.30  3.000
 G2R  O3A   PA   O2A   108.37  3.000
 G2R  O2A   PA   O1A   121.51  3.000
 G2R  O3A   PA   O1A   111.65  3.000
 G2R  O2A   PA   O5'   109.98  3.000
 G2R  O1A   PA   O5'   105.17  3.000
 G2R  O3A   PA   O5'    97.42  3.000
 G2R  PB    O3A  PA    129.51  3.000
 G2R  O5X   PB   O1B   110.59  3.000
 G2R  O1B   PB   O2B   122.06  3.000
 G2R  O5X   PB   O2B   104.84  3.000
 G2R  O1B   PB   O3A   109.71  3.000
 G2R  O5X   PB   O3A   100.15  3.000
 G2R  O2B   PB   O3A   107.21  3.000
 G2R  C5X   O5X  PB    120.89  3.000
 G2R  H5X2  C5X  H5X1  107.28  3.000
 G2R  H5X2  C5X  C4X   110.17  3.000
 G2R  H5X1  C5X  C4X   108.91  3.000
 G2R  H5X2  C5X  O5X   112.32  3.000
 G2R  H5X1  C5X  O5X   109.46  3.000
 G2R  C4X   C5X  O5X   108.63  3.000
 G2R  H4X   C4X  C3X   110.82  3.000
 G2R  H4X   C4X  O4X   109.22  3.000
 G2R  C3X   C4X  O4X   107.03  3.000
 G2R  H4X   C4X  C5X   108.33  3.000
 G2R  O4X   C4X  C5X   108.43  3.000
 G2R  C3X   C4X  C5X   112.93  3.000
 G2R  C1X   O4X  C4X   110.58  3.000
 G2R  H1X2  C1X  H1X1  107.78  3.000
 G2R  H1X2  C1X  C2X   110.41  3.000
 G2R  H1X1  C1X  C2X   112.60  3.000
 G2R  H1X2  C1X  O4X   111.10  3.000
 G2R  H1X1  C1X  O4X   109.22  3.000
 G2R  C2X   C1X  O4X   105.75  3.000
 G2R  H2X   C2X  C3X   108.12  3.000
 G2R  H2X   C2X  O2X   106.41  3.000
 G2R  C3X   C2X  O2X   115.84  3.000
 G2R  H2X   C2X  C1X   110.58  3.000
 G2R  C3X   C2X  C1X   101.79  3.000
 G2R  O2X   C2X  C1X   113.99  3.000
 G2R  HO2X  O2X  C2X   108.44  3.000
 G2R  H3X   C3X  O3X   110.02  3.000
 G2R  H3X   C3X  C2X   112.43  3.000
 G2R  O3X   C3X  C2X   107.06  3.000
 G2R  H3X   C3X  C4X   111.93  3.000
 G2R  O3X   C3X  C4X   113.14  3.000
 G2R  C2X   C3X  C4X   101.98  3.000
 G2R  HO3X  O3X  C3X   109.11  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
 G2R  CONST_01  N3    C4   C5   C6      0.00   0.0  0
 G2R  CONST_02  N9    C4   C5   C6    180.00   0.0  0
 G2R  CONST_03  C8    N7   C5   C6    180.00   0.0  0
 G2R  CONST_04  N3    C2   N1   C6      0.00   0.0  0
 G2R  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 G2R  CONST_06  N7    C5   C6   N1    180.00   0.0  0
 G2R  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 G2R  CONST_08  C5    C6   N1   C2      0.00   0.0  0
 G2R  CONST_09  N9    C4   N3   C2    180.00   0.0  0
 G2R  CONST_10  C5    C4   N3   C2      0.00   0.0  0
 G2R  CONST_11  C8    N9   C4   N3    180.00   0.0  0
 G2R  CONST_12  N7    C5   C4   N3    180.00   0.0  0
 G2R  CONST_13  N7    C8   N9   C4      0.00   0.0  0
 G2R  CONST_14  C8    N7   C5   C4      0.00   0.0  0
 G2R  CONST_15  C8    N9   C4   C5      0.00   0.0  0
 G2R  CONST_16  N9    C8   N7   C5      0.00   0.0  0
 G2R  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 G2R  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 G2R  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 G2R  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 G2R  CONST_21  C4    C5   C6   O6    180.00   0.0  0
 G2R  CONST_22  N7    C5   C6   O6      0.00   0.0  0
 G2R  CONST_23  C2    N1   C6   O6    180.00   0.0  0
 G2R  CONST_24  N2    C2   N1   C6    180.00   0.0  0
 G2R  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 G2R  CONST_26  HN1   N1   C2   N3    180.00   0.0  0
 G2R  CONST_27  H8    C8   N9   C4    180.00   0.0  0
 G2R  CONST_28  HN21  N2   C2   N1    180.00   0.0  0
 G2R  Var_01    C2X   C1X  O4X  C4X   -18.54  30.0  1
 G2R  Var_02    C4X   C5X  O5X  PB    134.30  30.0  3
 G2R  Var_03    O3A   PA   O5'  C5'   -64.04  30.0  3
 G2R  Var_04    O2B   PB   O3A  PA   -137.39  30.0  3
 G2R  Var_05    H5'1  C5'  O5'  PA    -62.01  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
 G2R  chir_01  C1'  N9   O4'  C2'  positiv
 G2R  chir_02  C2'  O2'  C1'  C3'  negativ
 G2R  chir_03  C3'  O3'  C4'  C2'  negativ
 G2R  chir_04  C4'  O4'  C3'  C5'  negativ
 G2R  chir_07  C4X  C5X  C3X  O4X  positiv
 G2R  chir_08  C2X  O2X  C3X  C1X  positiv
 G2R  chir_09  C3X  O3X  C4X  C2X  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
 G2R  plan-1  O6    0.020
 G2R  plan-1  C6    0.020
 G2R  plan-1  N1    0.020
 G2R  plan-1  C2    0.020
 G2R  plan-1  N2    0.020
 G2R  plan-1  N3    0.020
 G2R  plan-1  C4    0.020
 G2R  plan-1  C5    0.020
 G2R  plan-1  N7    0.020
 G2R  plan-1  C8    0.020
 G2R  plan-1  N9    0.020
 G2R  plan-1  C1'   0.020
 G2R  plan-1  HN1   0.020
 G2R  plan-1  H8    0.020
 G2R  plan-2  C2    0.020
 G2R  plan-2  N2    0.020
 G2R  plan-2  HN21  0.020
 G2R  plan-2  HN22  0.020

