# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 05:27:19 2022
#   Inital geometry file: a 140 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,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: NC1=Nc2n(cnc2C(=O)N1)[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
 G1R  G1R  '[(2R,3R,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-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  58  37  .  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_G1R
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
 G1R  O6    O  OC     0  -0.464  18.4108   7.5481  -27.9031
 G1R  C6    C  CR6    0   0.500  19.1151   7.8022  -26.9417
 G1R  N1    N  NR16   0  -0.728  19.9968   8.8926  -26.9733
 G1R  C2    C  CR6    0   0.689  20.8431   9.2732  -25.9715
 G1R  N2    N  NH2    0  -0.830  21.5897  10.3677  -26.1788
 G1R  N3    N  N      0  -0.513  20.9245   8.6379  -24.8286
 G1R  C4    C  CR56   0   0.508  20.0933   7.5914  -24.7446
 G1R  C5    C  CR56   0  -0.095  19.2047   7.1230  -25.6923
 G1R  N7    N  N      0  -0.440  18.5405   6.0153  -25.2288
 G1R  C8    C  CR15   0   0.088  19.0129   5.8207  -24.0374
 G1R  N9    N  NR5    0  -0.543  19.9580   6.7541  -23.6774
 G1R  C1'   C  CH1    0   0.196  20.7411   6.8101  -22.4716
 G1R  O4'   O  O2     0  -0.490  21.7221   5.8054  -22.5088
 G1R  C2'   C  CH1    0  -0.060  19.9414   6.6192  -21.1587
 G1R  O2'   O  OH1    0  -0.662  20.3237   7.6650  -20.3043
 G1R  C3'   C  CH1    0   0.001  20.4284   5.2516  -20.6693
 G1R  O3'   O  OH1    0  -0.684  19.6109   4.2694  -21.2567
 G1R  C4'   C  CH1    0  -0.013  21.8612   5.2758  -21.1955
 G1R  C5'   C  CH2    0  -0.189  22.6603   3.9942  -21.2017
 G1R  O5'   O  O2     0  -0.649  21.9587   2.9413  -21.8395
 G1R  PA    P  P      0   1.365  21.8788   1.4088  -21.2111
 G1R  O1A   O  O      0  -0.767  20.5957   0.8482  -21.7234
 G1R  O2A   O  OP    -1  -0.772  22.2244   1.4315  -19.7601
 G1R  O3A   O  O2     0  -0.725  23.0618   0.6541  -22.0728
 G1R  PB    P  P      0   1.381  24.6198   1.0431  -22.3329
 G1R  O2B   O  O      0  -0.785  24.7317   1.6316  -23.7244
 G1R  O1B   O  OP    -1  -0.765  25.2412   1.7698  -21.1884
 G1R  O5X   O  O2     0  -0.601  25.1255  -0.5133  -22.3933
 G1R  C5X   C  CH2    0  -0.197  26.4972  -0.8219  -22.5249
 G1R  C4X   C  CH1    0  -0.043  27.0666  -0.4869  -23.9012
 G1R  O4X   O  O2     0  -0.511  28.2811  -1.2007  -24.0159
 G1R  C1X   C  CH1    0   0.281  28.6156  -1.3971  -25.3728
 G1R  O1X   O  OH1    0  -0.668  29.5899  -0.5169  -25.8023
 G1R  C2X   C  CH1    0  -0.095  27.2958  -1.2313  -26.1701
 G1R  O2X   O  OH1    0  -0.679  27.3864  -0.1176  -27.0183
 G1R  C3X   C  CH1    0   0.012  26.2247  -0.9822  -25.0844
 G1R  O3X   O  OH1    0  -0.715  25.2764  -0.0829  -25.5764
 G1R  HN1   H  HNR6   0   0.424  19.9860   9.4338  -27.8292
 G1R  HN21  H  HNH2   0   0.411  22.3149  10.5667  -25.5105
 G1R  HN22  H  HNH2   0   0.414  21.7105  10.7517  -27.1007
 G1R  H8    H  HCR5   0   0.291  18.7204   5.0314  -23.3629
 G1R  H1'   H  HCH1   0   0.261  21.2015   7.8029  -22.4592
 G1R  H2'   H  HCH1   0   0.259  18.8591   6.6152  -21.3339
 G1R  HO2'  H  HOH1   0   0.459  19.8450   7.5715  -19.4740
 G1R  H3'   H  HCH1   0   0.242  20.4087   5.1789  -19.5744
 G1R  HO3'  H  HOH1   0   0.461  20.1678   3.5550  -21.5938
 G1R  H4'   H  HCH1   0   0.239  22.4289   5.9759  -20.5658
 G1R  H5'1  H  HCH2   0   0.231  22.8899   3.7455  -20.1640
 G1R  H5'2  H  HCH2   0   0.236  23.6120   4.1679  -21.7118
 G1R  H5X1  H  HCH2   0   0.231  26.5826  -1.9013  -22.3803
 G1R  H5X2  H  HCH2   0   0.232  27.0897  -0.3352  -21.7426
 G1R  H4X   H  HCH1   0   0.226  27.2393   0.5951  -23.9954
 G1R  H1X   H  HCH1   0   0.220  29.0192  -2.4101  -25.4445
 G1R  HO1X  H  HOH1   0   0.447  29.1373   0.1962  -26.2786
 G1R  H2X   H  HCH1   0   0.238  27.0811  -2.1355  -26.7491
 G1R  HO2X  H  HOH1   0   0.452  26.5756   0.3938  -26.8454
 G1R  H3X   H  HCH1   0   0.222  25.7639  -1.9423  -24.8124
 G1R  HO3X  H  HOH1   0   0.467  25.0424   0.5951  -24.8796

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
 G1R  O6   C6    double    1.219  0.020  1.219
 G1R  C6   N1    aromatic  1.403  0.020  1.403
 G1R  C6   C5    aromatic  1.425  0.020  1.425
 G1R  N1   C2    aromatic  1.366  0.020  1.366
 G1R  N1   HN1   single    0.860  0.020  1.020
 G1R  C2   N2    single    1.341  0.020  1.341
 G1R  C2   N3    aromatic  1.310  0.020  1.310
 G1R  N2   HN21  single    0.890  0.020  1.040
 G1R  N2   HN22  single    0.890  0.020  1.040
 G1R  N3   C4    aromatic  1.339  0.020  1.339
 G1R  C4   C5    aromatic  1.381  0.020  1.381
 G1R  C4   N9    aromatic  1.363  0.020  1.363
 G1R  C5   N7    aromatic  1.372  0.020  1.372
 G1R  N7   C8    aromatic  1.296  0.020  1.296
 G1R  C8   N9    aromatic  1.376  0.020  1.376
 G1R  C8   H8    single    0.930  0.020  1.080
 G1R  N9   C1'   single    1.439  0.020  1.439
 G1R  C1'  O4'   single    1.405  0.020  1.405
 G1R  C1'  C2'   single    1.549  0.020  1.549
 G1R  C1'  H1'   single    0.970  0.020  1.090
 G1R  O4'  C4'   single    1.423  0.020  1.423
 G1R  C2'  C3'   single    1.532  0.020  1.532
 G1R  C2'  O2'   single    1.404  0.020  1.404
 G1R  C2'  H2'   single    0.970  0.020  1.090
 G1R  O2'  HO2'  single    0.850  0.020  0.980
 G1R  C3'  C4'   single    1.527  0.020  1.527
 G1R  C3'  O3'   single    1.406  0.020  1.406
 G1R  C3'  H3'   single    0.970  0.020  1.090
 G1R  O3'  HO3'  single    0.850  0.020  0.980
 G1R  C4'  C5'   single    1.510  0.020  1.510
 G1R  C4'  H4'   single    0.970  0.020  1.090
 G1R  C5'  O5'   single    1.417  0.020  1.417
 G1R  C5'  H5'1  single    0.970  0.020  1.090
 G1R  C5'  H5'2  single    0.970  0.020  1.090
 G1R  O5'  PA    single    1.658  0.020  1.658
 G1R  PA   O3A   single    1.647  0.020  1.647
 G1R  PA   O1A   deloc     1.491  0.020  1.491
 G1R  PA   O2A   deloc     1.492  0.020  1.492
 G1R  O3A  PB    single    1.627  0.020  1.627
 G1R  PB   O2B   deloc     1.515  0.020  1.515
 G1R  PB   O5X   single    1.638  0.020  1.638
 G1R  PB   O1B   deloc     1.491  0.020  1.491
 G1R  O5X  C5X   single    1.412  0.020  1.412
 G1R  C5X  C4X   single    1.527  0.020  1.527
 G1R  C5X  H5X1  single    0.970  0.020  1.090
 G1R  C5X  H5X2  single    0.970  0.020  1.090
 G1R  C4X  C3X   single    1.534  0.020  1.534
 G1R  C4X  O4X   single    1.413  0.020  1.413
 G1R  C4X  H4X   single    0.970  0.020  1.090
 G1R  O4X  C1X   single    1.411  0.020  1.411
 G1R  C1X  C2X   single    1.551  0.020  1.551
 G1R  C1X  O1X   single    1.382  0.020  1.382
 G1R  C1X  H1X   single    0.970  0.020  1.090
 G1R  O1X  HO1X  single    0.850  0.020  0.980
 G1R  C2X  O2X   single    1.403  0.020  1.403
 G1R  C2X  C3X   single    1.545  0.020  1.545
 G1R  C2X  H2X   single    0.970  0.020  1.090
 G1R  O2X  HO2X  single    0.850  0.020  0.980
 G1R  C3X  O3X   single    1.396  0.020  1.396
 G1R  C3X  H3X   single    0.970  0.020  1.090
 G1R  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
 G1R  C5    C6   N1    110.54  3.000
 G1R  C5    C6   O6    128.96  3.000
 G1R  N1    C6   O6    120.51  3.000
 G1R  HN1   N1   C2    118.53  3.000
 G1R  HN1   N1   C6    115.33  3.000
 G1R  C2    N1   C6    126.14  3.000
 G1R  N3    C2   N2    119.74  3.000
 G1R  N3    C2   N1    122.91  3.000
 G1R  N2    C2   N1    117.33  3.000
 G1R  HN22  N2   HN21  116.53  3.000
 G1R  HN22  N2   C2    121.34  3.000
 G1R  HN21  N2   C2    117.39  3.000
 G1R  C4    N3   C2    113.27  3.000
 G1R  N9    C4   C5    105.37  3.000
 G1R  N9    C4   N3    126.21  3.000
 G1R  C5    C4   N3    128.43  3.000
 G1R  N7    C5   C4    110.70  3.000
 G1R  N7    C5   C6    130.58  3.000
 G1R  C4    C5   C6    118.71  3.000
 G1R  C8    N7   C5    104.79  3.000
 G1R  H8    C8   N9    121.26  3.000
 G1R  H8    C8   N7    125.85  3.000
 G1R  N9    C8   N7    112.89  3.000
 G1R  C1'   N9   C8    128.27  3.000
 G1R  C1'   N9   C4    125.32  3.000
 G1R  C8    N9   C4    106.26  3.000
 G1R  H1'   C1'  C2'   108.62  3.000
 G1R  H1'   C1'  O4'   110.81  3.000
 G1R  C2'   C1'  O4'   107.14  3.000
 G1R  H1'   C1'  N9    105.89  3.000
 G1R  C2'   C1'  N9    115.12  3.000
 G1R  O4'   C1'  N9    109.27  3.000
 G1R  C4'   O4'  C1'   108.06  3.000
 G1R  H2'   C2'  C3'   111.20  3.000
 G1R  H2'   C2'  O2'   111.64  3.000
 G1R  C3'   C2'  O2'   112.59  3.000
 G1R  H2'   C2'  C1'   112.00  3.000
 G1R  O2'   C2'  C1'   106.47  3.000
 G1R  C3'   C2'  C1'   102.51  3.000
 G1R  HO2'  O2'  C2'   108.49  3.000
 G1R  H3'   C3'  C4'   111.21  3.000
 G1R  H3'   C3'  O3'   111.10  3.000
 G1R  C4'   C3'  O3'   114.37  3.000
 G1R  H3'   C3'  C2'   111.85  3.000
 G1R  O3'   C3'  C2'   107.77  3.000
 G1R  C4'   C3'  C2'   100.03  3.000
 G1R  HO3'  O3'  C3'   109.08  3.000
 G1R  H4'   C4'  C5'   105.63  3.000
 G1R  H4'   C4'  C3'   107.29  3.000
 G1R  C5'   C4'  C3'   118.99  3.000
 G1R  H4'   C4'  O4'   110.00  3.000
 G1R  C5'   C4'  O4'   111.33  3.000
 G1R  C3'   C4'  O4'   103.43  3.000
 G1R  H5'2  C5'  H5'1  107.25  3.000
 G1R  H5'2  C5'  O5'   109.82  3.000
 G1R  H5'1  C5'  O5'   111.27  3.000
 G1R  H5'2  C5'  C4'   109.12  3.000
 G1R  H5'1  C5'  C4'   107.51  3.000
 G1R  O5'   C5'  C4'   111.74  3.000
 G1R  PA    O5'  C5'   122.69  3.000
 G1R  O3A   PA   O2A   110.46  3.000
 G1R  O2A   PA   O1A   122.64  3.000
 G1R  O3A   PA   O1A   105.44  3.000
 G1R  O2A   PA   O5'   110.08  3.000
 G1R  O1A   PA   O5'   104.99  3.000
 G1R  O3A   PA   O5'   100.99  3.000
 G1R  PB    O3A  PA    131.46  3.000
 G1R  O5X   PB   O1B   111.27  3.000
 G1R  O1B   PB   O2B   119.00  3.000
 G1R  O5X   PB   O2B   108.21  3.000
 G1R  O1B   PB   O3A   113.14  3.000
 G1R  O5X   PB   O3A    94.27  3.000
 G1R  O2B   PB   O3A   108.09  3.000
 G1R  C5X   O5X  PB    120.73  3.000
 G1R  H5X2  C5X  H5X1  107.59  3.000
 G1R  H5X2  C5X  C4X   110.16  3.000
 G1R  H5X1  C5X  C4X   107.88  3.000
 G1R  H5X2  C5X  O5X   111.21  3.000
 G1R  H5X1  C5X  O5X   106.23  3.000
 G1R  C4X   C5X  O5X   113.48  3.000
 G1R  H4X   C4X  C3X   109.74  3.000
 G1R  H4X   C4X  O4X   110.80  3.000
 G1R  C3X   C4X  O4X   104.23  3.000
 G1R  H4X   C4X  C5X   110.59  3.000
 G1R  O4X   C4X  C5X   106.43  3.000
 G1R  C3X   C4X  C5X   114.82  3.000
 G1R  C1X   O4X  C4X   110.61  3.000
 G1R  H1X   C1X  C2X   112.32  3.000
 G1R  H1X   C1X  O1X   108.04  3.000
 G1R  C2X   C1X  O1X   111.85  3.000
 G1R  H1X   C1X  O4X   106.24  3.000
 G1R  O1X   C1X  O4X   112.17  3.000
 G1R  C2X   C1X  O4X   106.13  3.000
 G1R  HO1X  O1X  C1X   106.98  3.000
 G1R  H2X   C2X  C3X   111.63  3.000
 G1R  H2X   C2X  O2X   110.40  3.000
 G1R  C3X   C2X  O2X   109.97  3.000
 G1R  H2X   C2X  C1X   110.52  3.000
 G1R  C3X   C2X  C1X   104.24  3.000
 G1R  O2X   C2X  C1X   109.93  3.000
 G1R  HO2X  O2X  C2X   104.82  3.000
 G1R  H3X   C3X  O3X   111.42  3.000
 G1R  H3X   C3X  C2X   108.89  3.000
 G1R  O3X   C3X  C2X   109.09  3.000
 G1R  H3X   C3X  C4X   108.73  3.000
 G1R  O3X   C3X  C4X   115.87  3.000
 G1R  C2X   C3X  C4X   102.32  3.000
 G1R  HO3X  O3X  C3X   110.49  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
 G1R  CONST_01  N3    C2   N1   C6      0.00   0.0  0
 G1R  CONST_02  N3    C4   C5   C6      0.00   0.0  0
 G1R  CONST_03  N9    C4   C5   C6    180.00   0.0  0
 G1R  CONST_04  C8    N7   C5   C6    180.00   0.0  0
 G1R  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 G1R  CONST_06  N7    C5   C6   N1    180.00   0.0  0
 G1R  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 G1R  CONST_08  C5    C6   N1   C2      0.00   0.0  0
 G1R  CONST_09  C5    C4   N3   C2      0.00   0.0  0
 G1R  CONST_10  N9    C4   N3   C2    180.00   0.0  0
 G1R  CONST_11  N7    C5   C4   N3    180.00   0.0  0
 G1R  CONST_12  C8    N9   C4   N3    180.00   0.0  0
 G1R  CONST_13  C8    N7   C5   C4      0.00   0.0  0
 G1R  CONST_14  N7    C8   N9   C4      0.00   0.0  0
 G1R  CONST_15  C8    N9   C4   C5      0.00   0.0  0
 G1R  CONST_16  N9    C8   N7   C5      0.00   0.0  0
 G1R  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 G1R  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 G1R  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 G1R  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 G1R  CONST_21  C2    N1   C6   O6    180.00   0.0  0
 G1R  CONST_22  C4    C5   C6   O6    180.00   0.0  0
 G1R  CONST_23  N7    C5   C6   O6      0.00   0.0  0
 G1R  CONST_24  N2    C2   N1   C6    180.00   0.0  0
 G1R  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 G1R  CONST_26  HN1   N1   C2   N3    180.00   0.0  0
 G1R  CONST_27  H8    C8   N9   C4    180.00   0.0  0
 G1R  CONST_28  HN21  N2   C2   N1    180.00   0.0  0
 G1R  Var_01    C4X   C5X  O5X  PB    -70.46  30.0  3
 G1R  Var_02    O3A   PA   O5'  C5'   -98.17  30.0  3
 G1R  Var_03    O2B   PB   O3A  PA   -102.17  30.0  3
 G1R  Var_04    H5'1  C5'  O5'  PA    -15.27  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
 G1R  chir_01  C1'  N9   O4'  C2'  positiv
 G1R  chir_02  C2'  O2'  C1'  C3'  negativ
 G1R  chir_03  C3'  O3'  C4'  C2'  negativ
 G1R  chir_04  C4'  O4'  C3'  C5'  negativ
 G1R  chir_07  C4X  C5X  C3X  O4X  positiv
 G1R  chir_08  C1X  O1X  O4X  C2X  negativ
 G1R  chir_09  C2X  O2X  C1X  C3X  negativ
 G1R  chir_10  C3X  O3X  C2X  C4X  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
 G1R  plan-1  O6    0.020
 G1R  plan-1  C6    0.020
 G1R  plan-1  N1    0.020
 G1R  plan-1  C2    0.020
 G1R  plan-1  N2    0.020
 G1R  plan-1  N3    0.020
 G1R  plan-1  C4    0.020
 G1R  plan-1  C5    0.020
 G1R  plan-1  N7    0.020
 G1R  plan-1  C8    0.020
 G1R  plan-1  N9    0.020
 G1R  plan-1  C1'   0.020
 G1R  plan-1  HN1   0.020
 G1R  plan-1  H8    0.020
 G1R  plan-2  C2    0.020
 G1R  plan-2  N2    0.020
 G1R  plan-2  HN21  0.020
 G1R  plan-2  HN22  0.020

