# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 24 02:50:22 2020
#   Inital geometry file: a 152 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,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-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](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
 GDG  GDG  '[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  62  39  .  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_GDG
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
 GDG  C21  C  CH1    0   0.209   4.3745  -0.5273  -0.1894
 GDG  C22  C  CH1    0   0.013   3.7899  -1.1679  -1.4583
 GDG  C24  C  CH1    0   0.023   2.6078  -2.7762   0.0237
 GDG  C01  C  CR15   0   0.140  -1.1009  -0.0549  -1.7716
 GDG  N02  N  N      0  -0.513  -0.6757  -1.2830  -1.8093
 GDG  C03  C  CR56   0  -0.041  -1.7070  -2.0517  -1.3418
 GDG  C04  C  CR56   0   0.621  -2.7649  -1.2421  -1.0377
 GDG  N05  N  NR5    0  -0.550  -2.3862   0.0303  -1.2994
 GDG  C06  C  CH1    0   0.238  -3.2096   1.2322  -1.1615
 GDG  C07  C  CH1    0  -0.073  -3.7014   1.4303   0.2790
 GDG  C08  C  CH1    0  -0.014  -3.6829   2.9557   0.3993
 GDG  C09  C  CH1    0  -0.071  -2.4397   3.2894  -0.4101
 GDG  O10  O  O2     0  -0.489  -2.4437   2.3403  -1.4863
 GDG  C11  C  CH2    0  -0.136  -1.1633   3.2138   0.4037
 GDG  O12  O  O2     0  -0.613  -0.0871   3.5797  -0.4300
 GDG  P13  P  P      0   1.361   1.3977   3.8641   0.2122
 GDG  O14  O  O      0  -0.786   2.1007   4.7814  -0.7328
 GDG  O15  O  OP    -1  -0.789   1.2630   4.1629   1.6701
 GDG  O16  O  O2     0  -0.732   2.0163   2.3385   0.0350
 GDG  O18  O  O      0  -0.774   4.4086   2.8649   0.8194
 GDG  O19  O  OP    -1  -0.793   3.9852   2.0868  -1.6156
 GDG  O20  O  O2     0  -0.629   3.5395   0.4914   0.3239
 GDG  C23  C  CH1    0  -0.020   2.4297  -1.7594  -1.1035
 GDG  C25  C  CH1    0  -0.009   3.3292  -2.1438   1.2157
 GDG  O26  O  O2     0  -0.496   4.5223  -1.4908   0.8005
 GDG  C27  C  CH2    0  -0.158   3.7311  -3.1854   2.2386
 GDG  O28  O  OH1    0  -0.672   4.2951  -2.5419   3.3576
 GDG  O29  O  OH1    0  -0.697   1.3766  -3.2732   0.4871
 GDG  O30  O  OH1    0  -0.712   1.8446  -2.3787  -2.2194
 GDG  O31  O  OH1    0  -0.715   3.7411  -0.3223  -2.5688
 GDG  O32  O  OH1    0  -0.663  -4.7904   3.5290  -0.2406
 GDG  O33  O  OH1    0  -0.661  -4.9653   0.8403   0.4336
 GDG  N34  N  NR16   0  -0.745  -3.9439  -1.7205  -0.5666
 GDG  C35  C  CR6    0   0.679  -4.0230  -3.0759  -0.4131
 GDG  N36  N  N      0  -0.535  -3.0354  -3.8990  -0.6651
 GDG  C37  C  CR6    0   0.446  -1.8129  -3.4717  -1.1049
 GDG  O38  O  O      0  -0.509  -0.8810  -4.2596  -1.2692
 GDG  N39  N  NH2    0  -0.826  -5.1934  -3.5573   0.0118
 GDG  H1   H  HCH1   0   0.248   5.3821  -0.1428  -0.3883
 GDG  H2   H  HCH1   0   0.201   4.4684  -1.9990  -1.7043
 GDG  H3   H  HCH1   0   0.187   3.2383  -3.5945  -0.3665
 GDG  H5   H  HCH1   0   0.282  -4.0554   1.1310  -1.8518
 GDG  H6   H  HCH1   0   0.274  -2.9745   1.0040   0.9809
 GDG  H7   H  HCH1   0   0.260  -3.5959   3.2782   1.4445
 GDG  H8   H  HCH1   0   0.274  -2.5166   4.2859  -0.8531
 GDG  H9   H  HCH2   0   0.230  -1.2601   3.9000   1.2500
 GDG  H10  H  HCH2   0   0.209  -1.0215   2.2076   0.8182
 GDG  H13  H  HCH1   0   0.207   1.7782  -0.9524  -0.7401
 GDG  H14  H  HCH1   0   0.221   2.6471  -1.4261   1.6923
 GDG  H15  H  HCH2   0   0.209   2.8387  -3.7594   2.5107
 GDG  H16  H  HCH2   0   0.192   4.4372  -3.8878   1.7735
 GDG  H17  H  HOH1   0   0.455   4.4942  -3.2137   4.0156
 GDG  H18  H  HOH1   0   0.448   0.8515  -3.5733  -0.2696
 GDG  H19  H  HOH1   0   0.463   0.9241  -2.0527  -2.2502
 GDG  H20  H  HOH1   0   0.448   3.7801   0.6229  -2.2809
 GDG  H21  H  HOH1   0   0.453  -5.5885   3.0971   0.0840
 GDG  H22  H  HOH1   0   0.481  -5.1530   0.7429   1.3743
 GDG  H23  H  HNR6   0   0.434  -4.6822  -1.0933  -0.2606
 GDG  H24  H  HNH2   0   0.416  -5.2695  -4.5397   0.2080
 GDG  H25  H  HNH2   0   0.416  -5.9607  -2.9640   0.2752
 GDG  P17  P  P      0   1.375   3.6119   2.0610  -0.1526
 GDG  H4   H  HCR5   0   0.304  -0.5387   0.8181  -2.0587

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
 GDG  N39  C35  single    1.335  0.020  1.335
 GDG  C35  N36  double    1.310  0.020  1.310
 GDG  C35  N34  single    1.366  0.020  1.366
 GDG  N36  C37  single    1.368  0.020  1.368
 GDG  N34  C04  single    1.357  0.020  1.357
 GDG  O33  C07  single    1.403  0.020  1.403
 GDG  C37  O38  double    1.231  0.020  1.231
 GDG  C37  C03  single    1.444  0.020  1.444
 GDG  C04  C03  aromatic  1.366  0.020  1.366
 GDG  C04  N05  aromatic  1.353  0.020  1.353
 GDG  C03  N02  aromatic  1.369  0.020  1.369
 GDG  C07  C06  single    1.535  0.020  1.535
 GDG  C07  C08  single    1.530  0.020  1.530
 GDG  O32  C08  single    1.402  0.020  1.402
 GDG  N05  C06  single    1.463  0.020  1.463
 GDG  N05  C01  aromatic  1.372  0.020  1.372
 GDG  C06  O10  single    1.386  0.020  1.386
 GDG  N02  C01  aromatic  1.300  0.020  1.300
 GDG  C08  C09  single    1.521  0.020  1.521
 GDG  O10  C09  single    1.435  0.020  1.435
 GDG  C09  C11  single    1.516  0.020  1.516
 GDG  C11  O12  single    1.410  0.020  1.410
 GDG  O12  P13  single    1.643  0.020  1.643
 GDG  O14  P13  deloc     1.493  0.020  1.493
 GDG  P13  O15  deloc     1.494  0.020  1.494
 GDG  P13  O16  single    1.656  0.020  1.656
 GDG  O29  C24  single    1.406  0.020  1.406
 GDG  O16  P17  single    1.630  0.020  1.630
 GDG  C27  C25  single    1.514  0.020  1.514
 GDG  C27  O28  single    1.409  0.020  1.409
 GDG  C25  C24  single    1.530  0.020  1.530
 GDG  C25  O26  single    1.422  0.020  1.422
 GDG  O18  P17  deloc     1.492  0.020  1.492
 GDG  C24  C23  single    1.529  0.020  1.529
 GDG  P17  O19  deloc     1.510  0.020  1.510
 GDG  P17  O20  single    1.642  0.020  1.642
 GDG  O26  C21  single    1.389  0.020  1.389
 GDG  C23  O30  single    1.404  0.020  1.404
 GDG  C23  C22  single    1.525  0.020  1.525
 GDG  O20  C21  single    1.414  0.020  1.414
 GDG  C21  C22  single    1.537  0.020  1.537
 GDG  C22  O31  single    1.397  0.020  1.397
 GDG  C21  H1   single    0.970  0.020  1.090
 GDG  C22  H2   single    0.970  0.020  1.090
 GDG  C24  H3   single    0.970  0.020  1.090
 GDG  C01  H4   single    0.930  0.020  1.080
 GDG  C06  H5   single    0.970  0.020  1.090
 GDG  C07  H6   single    0.970  0.020  1.090
 GDG  C08  H7   single    0.970  0.020  1.090
 GDG  C09  H8   single    0.970  0.020  1.090
 GDG  C11  H9   single    0.970  0.020  1.090
 GDG  C11  H10  single    0.970  0.020  1.090
 GDG  C23  H13  single    0.970  0.020  1.090
 GDG  C25  H14  single    0.970  0.020  1.090
 GDG  C27  H15  single    0.970  0.020  1.090
 GDG  C27  H16  single    0.970  0.020  1.090
 GDG  O28  H17  single    0.850  0.020  0.980
 GDG  O29  H18  single    0.850  0.020  0.980
 GDG  O30  H19  single    0.850  0.020  0.980
 GDG  O31  H20  single    0.850  0.020  0.980
 GDG  O32  H21  single    0.850  0.020  0.980
 GDG  O33  H22  single    0.850  0.020  0.980
 GDG  N34  H23  single    0.860  0.020  1.020
 GDG  N39  H24  single    0.860  0.020  1.020
 GDG  N39  H25  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
 GDG  H1   C21  O26  105.94  3.000
 GDG  H1   C21  O20  110.85  3.000
 GDG  O26  C21  O20  107.69  3.000
 GDG  H1   C21  C22  110.23  3.000
 GDG  O20  C21  C22  112.05  3.000
 GDG  O26  C21  C22  109.86  3.000
 GDG  H2   C22  O31  107.52  3.000
 GDG  H2   C22  C23  108.00  3.000
 GDG  O31  C22  C23  112.87  3.000
 GDG  H2   C22  C21  105.35  3.000
 GDG  O31  C22  C21  114.67  3.000
 GDG  C23  C22  C21  107.99  3.000
 GDG  H3   C24  O29  110.76  3.000
 GDG  H3   C24  C25  108.21  3.000
 GDG  O29  C24  C25  107.59  3.000
 GDG  H3   C24  C23  107.39  3.000
 GDG  C25  C24  C23  110.76  3.000
 GDG  O29  C24  C23  112.09  3.000
 GDG  H4   C01  N05  122.03  3.000
 GDG  H4   C01  N02  125.94  3.000
 GDG  N05  C01  N02  112.03  3.000
 GDG  C03  N02  C01  105.91  3.000
 GDG  C37  C03  C04  119.31  3.000
 GDG  C04  C03  N02  109.07  3.000
 GDG  C37  C03  N02  131.59  3.000
 GDG  N34  C04  N05  129.94  3.000
 GDG  N05  C04  C03  107.30  3.000
 GDG  N34  C04  C03  122.76  3.000
 GDG  C06  N05  C04  126.63  3.000
 GDG  C06  N05  C01  127.63  3.000
 GDG  C04  N05  C01  105.69  3.000
 GDG  H5   C06  O10  110.65  3.000
 GDG  H5   C06  C07  110.83  3.000
 GDG  O10  C06  C07  107.09  3.000
 GDG  H5   C06  N05  107.39  3.000
 GDG  O10  C06  N05  108.89  3.000
 GDG  C07  C06  N05  112.00  3.000
 GDG  H6   C07  O33  111.29  3.000
 GDG  H6   C07  C08  109.22  3.000
 GDG  O33  C07  C08  114.92  3.000
 GDG  H6   C07  C06  109.76  3.000
 GDG  C08  C07  C06  101.45  3.000
 GDG  O33  C07  C06  109.74  3.000
 GDG  H7   C08  O32  112.17  3.000
 GDG  H7   C08  C09  112.19  3.000
 GDG  O32  C08  C09  108.25  3.000
 GDG  H7   C08  C07  111.64  3.000
 GDG  C09  C08  C07  100.77  3.000
 GDG  O32  C08  C07  111.24  3.000
 GDG  H8   C09  C11  108.80  3.000
 GDG  H8   C09  O10  107.38  3.000
 GDG  C11  C09  O10  111.84  3.000
 GDG  H8   C09  C08  110.99  3.000
 GDG  C11  C09  C08  113.07  3.000
 GDG  O10  C09  C08  104.58  3.000
 GDG  C09  O10  C06  110.77  3.000
 GDG  H10  C11  H9   107.12  3.000
 GDG  H10  C11  O12  111.27  3.000
 GDG  H9   C11  O12  111.24  3.000
 GDG  H10  C11  C09  110.93  3.000
 GDG  H9   C11  C09  108.03  3.000
 GDG  O12  C11  C09  108.21  3.000
 GDG  P13  O12  C11  120.26  3.000
 GDG  O16  P13  O15  108.81  3.000
 GDG  O16  P13  O14  108.81  3.000
 GDG  O15  P13  O14  122.49  3.000
 GDG  O16  P13  O12   97.84  3.000
 GDG  O15  P13  O12  109.54  3.000
 GDG  O14  P13  O12  106.54  3.000
 GDG  P17  O16  P13  122.33  3.000
 GDG  P17  O20  C21  123.88  3.000
 GDG  H13  C23  O30  109.86  3.000
 GDG  H13  C23  C24  108.28  3.000
 GDG  O30  C23  C24  109.95  3.000
 GDG  H13  C23  C22  108.72  3.000
 GDG  O30  C23  C22  110.97  3.000
 GDG  C24  C23  C22  109.00  3.000
 GDG  H14  C25  C27  108.73  3.000
 GDG  H14  C25  O26  110.34  3.000
 GDG  C27  C25  O26  106.88  3.000
 GDG  H14  C25  C24  108.37  3.000
 GDG  O26  C25  C24  110.97  3.000
 GDG  C27  C25  C24  111.53  3.000
 GDG  C25  O26  C21  115.92  3.000
 GDG  H16  C27  H15  107.08  3.000
 GDG  H16  C27  O28  111.77  3.000
 GDG  H15  C27  O28  111.60  3.000
 GDG  H16  C27  C25  108.92  3.000
 GDG  H15  C27  C25  108.18  3.000
 GDG  O28  C27  C25  109.19  3.000
 GDG  H17  O28  C27  107.90  3.000
 GDG  H18  O29  C24  109.07  3.000
 GDG  H19  O30  C23  105.69  3.000
 GDG  H20  O31  C22  110.23  3.000
 GDG  H21  O32  C08  108.49  3.000
 GDG  H22  O33  C07  108.98  3.000
 GDG  H23  N34  C35  122.45  3.000
 GDG  H23  N34  C04  121.22  3.000
 GDG  C35  N34  C04  116.05  3.000
 GDG  N39  C35  N36  119.71  3.000
 GDG  N36  C35  N34  123.92  3.000
 GDG  N39  C35  N34  116.37  3.000
 GDG  C37  N36  C35  122.64  3.000
 GDG  O38  C37  N36  121.30  3.000
 GDG  O38  C37  C03  123.50  3.000
 GDG  N36  C37  C03  115.19  3.000
 GDG  H25  N39  H24  117.91  3.000
 GDG  H25  N39  C35  122.68  3.000
 GDG  H24  N39  C35  118.76  3.000
 GDG  O20  P17  O19  107.96  3.000
 GDG  O20  P17  O18  110.46  3.000
 GDG  O19  P17  O18  119.34  3.000
 GDG  O20  P17  O16   94.94  3.000
 GDG  O19  P17  O16  110.52  3.000
 GDG  O18  P17  O16  110.85  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
 GDG  CONST_01  C03  C04  N05  C01     0.00   0.0  0
 GDG  CONST_02  C04  C03  N02  C01     0.00   0.0  0
 GDG  CONST_03  N05  C04  C03  N02     0.00   0.0  0
 GDG  CONST_04  C04  N05  C01  N02     0.00   0.0  0
 GDG  CONST_05  N05  C01  N02  C03     0.00   0.0  0
 GDG  CONST_06  C06  N05  C01  N02   180.00   0.0  0
 GDG  CONST_07  C06  N05  C04  C03   180.00   0.0  0
 GDG  CONST_08  N34  C04  N05  C06     0.00   0.0  0
 GDG  CONST_09  N36  C35  N34  C04     0.00   0.0  0
 GDG  CONST_10  C37  N36  C35  N34     0.00   0.0  0
 GDG  CONST_11  N39  C35  N34  C04   180.00   0.0  0
 GDG  CONST_12  N39  C35  N36  C37   180.00   0.0  0
 GDG  CONST_13  H4   C01  N02  C03   180.00   0.0  0
 GDG  CONST_14  H23  N34  C35  N36   180.00   0.0  0
 GDG  CONST_15  H24  N39  C35  N34   180.00   0.0  0
 GDG  CONST_16  H25  N39  C35  N34     0.00   0.0  0
 GDG  Var_01    O16  P17  O20  C21   147.10  30.0  2
 GDG  Var_02    O14  P13  O12  C11  -154.91  30.0  3
 GDG  Var_03    H9   C11  O12  P13    50.36  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
 GDG  chir_01  C21  O26  O20  C22  positiv
 GDG  chir_02  C22  O31  C21  C23  negativ
 GDG  chir_03  C24  O29  C23  C25  negativ
 GDG  chir_04  C06  C07  N05  O10  positiv
 GDG  chir_05  C07  O33  C08  C06  positiv
 GDG  chir_06  C08  O32  C09  C07  positiv
 GDG  chir_07  C09  O10  C08  C11  negativ
 GDG  chir_10  C23  C24  O30  C22  positiv
 GDG  chir_11  C25  O26  C27  C24  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
 GDG  plan-1  C01  0.020
 GDG  plan-1  N02  0.020
 GDG  plan-1  C03  0.020
 GDG  plan-1  C04  0.020
 GDG  plan-1  N05  0.020
 GDG  plan-1  C06  0.020
 GDG  plan-1  N34  0.020
 GDG  plan-1  C35  0.020
 GDG  plan-1  N36  0.020
 GDG  plan-1  C37  0.020
 GDG  plan-1  O38  0.020
 GDG  plan-1  N39  0.020
 GDG  plan-1  H23  0.020
 GDG  plan-1  H24  0.020
 GDG  plan-1  H25  0.020
 GDG  plan-1  H4   0.020

