# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 21 04:55:11 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-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: Nc1ncnc2n(cnc12)[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
#
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
 ADQ  ADQ  '[(2R,3S,4R,5R)-5-(6-amino-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  61  38  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ADQ
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
 ADQ  PB    P  P      0   1.352  -1.5083   1.1060  -3.2893
 ADQ  O1B   O  O      0  -0.795  -2.5003   1.3891  -4.3719
 ADQ  O2B   O  OP    -1  -0.778  -0.7244   2.1948  -2.6373
 ADQ  O3B   O  O2     0  -0.628  -0.4655  -0.0737  -3.8007
 ADQ  PA    P  P      0   1.358  -3.0065   0.6516  -0.8173
 ADQ  O1A   O  O      0  -0.788  -3.8475  -0.5021  -0.3629
 ADQ  O2A   O  OP    -1  -0.800  -3.6240   1.9975  -1.0298
 ADQ  O3A   O  O2     0  -0.732  -2.2044   0.1431  -2.1464
 ADQ  O5D   O  O2     0  -0.614  -1.6883   0.7891   0.1632
 ADQ  C5D   C  CH2    0  -0.184  -1.8446   1.3663   1.4366
 ADQ  C4D   C  CH1    0   0.003  -2.3349   0.3830   2.4784
 ADQ  O4D   O  O2     0  -0.496  -1.4369  -0.7247   2.5798
 ADQ  C3D   C  CH1    0  -0.038  -2.3833   0.9806   3.8813
 ADQ  O3D   O  OH1    0  -0.656  -3.6082   1.6239   4.0923
 ADQ  C2D   C  CH1    0  -0.039  -2.1732  -0.2577   4.7596
 ADQ  O2D   O  OH1    0  -0.664  -3.3479  -1.0140   4.8563
 ADQ  C1D   C  CH1    0   0.173  -1.1841  -1.0518   3.9094
 ADQ  N9    N  NR5    0  -0.535   0.1986  -0.7074   4.2328
 ADQ  C8    C  CR15   0   0.101   1.0929   0.0203   3.4978
 ADQ  N7    N  N      0  -0.451   2.2625   0.1218   4.0604
 ADQ  C5    C  CR56   0  -0.002   2.1400  -0.5815   5.2291
 ADQ  C6    C  CR6    0   0.455   3.0353  -0.8695   6.2760
 ADQ  N6    N  NH2    0  -0.816   4.2913  -0.4180   6.2956
 ADQ  N1    N  N      0  -0.474   2.5911  -1.6170   7.2922
 ADQ  C2    C  CR16   0   0.039   1.3344  -2.0549   7.2764
 ADQ  N3    N  N      0  -0.457   0.4056  -1.8530   6.3582
 ADQ  C4    C  CR56   0   0.486   0.8640  -1.1087   5.3530
 ADQ  C1'   C  CH1    0   0.249  -0.1802  -0.2402  -5.1519
 ADQ  C2'   C  CH1    0  -0.012   0.6218  -1.5332  -5.3145
 ADQ  C3'   C  CH1    0  -0.011   1.9778  -1.3842  -4.6404
 ADQ  C4'   C  CH1    0   0.030   2.6948  -0.1538  -5.1824
 ADQ  C5'   C  CH1    0  -0.003   1.8000   1.0836  -5.0817
 ADQ  C6'   C  CH2    0  -0.162   2.4199   2.2600  -5.8074
 ADQ  O2'   O  OH1    0  -0.669  -0.0275  -2.6452  -4.7530
 ADQ  O3'   O  OH1    0  -0.677   2.8137  -2.4934  -4.8894
 ADQ  O4'   O  OH1    0  -0.674   3.8793   0.1070  -4.4684
 ADQ  O5'   O  O2     0  -0.504   0.5438   0.8309  -5.6862
 ADQ  O6'   O  OH1    0  -0.666   1.6315   3.4059  -5.5933
 ADQ  H5'1  H  HCH2   0   0.226  -2.5387   2.2150   1.4188
 ADQ  H5'2  H  HCH2   0   0.223  -0.8698   1.7638   1.7375
 ADQ  H4D   H  HCH1   0   0.250  -3.3256   0.0104   2.1982
 ADQ  H3D   H  HCH1   0   0.241  -1.5393   1.6698   4.0250
 ADQ  HO3'  H  HOH1   0   0.469  -3.5195   2.2265   4.8377
 ADQ  H2D   H  HCH1   0   0.260  -1.7653  -0.0083   5.7464
 ADQ  HO2'  H  HOH1   0   0.452  -4.0875  -0.4008   4.9487
 ADQ  H1D   H  HCH1   0   0.283  -1.2926  -2.1282   4.0695
 ADQ  H8    H  HCR5   0   0.296   0.8339   0.4470   2.5422
 ADQ  HN61  H  HNH2   0   0.403   4.9264  -0.7292   7.0103
 ADQ  HN62  H  HNH2   0   0.410   4.6751   0.0650   5.5023
 ADQ  H2    H  HCR6   0   0.252   1.0407  -2.6560   8.1304
 ADQ  H1'   H  HCH1   0   0.232  -1.1005  -0.2837  -5.7449
 ADQ  H2'   H  HCH1   0   0.222   0.7852  -1.6747  -6.3926
 ADQ  H3'   H  HCH1   0   0.218   1.8278  -1.2501  -3.5594
 ADQ  H4'   H  HCH1   0   0.204   2.9110  -0.3349  -6.2484
 ADQ  H5'   H  HCH1   0   0.227   1.6673   1.3473  -4.0243
 ADQ  H6'1  H  HCH2   0   0.206   3.4402   2.3980  -5.4329
 ADQ  H6'2  H  HCH2   0   0.192   2.5002   2.0149  -6.8761
 ADQ  HO2A  H  HOH1   0   0.457  -0.7381  -2.9183  -5.3410
 ADQ  HO3A  H  HOH1   0   0.455   2.4657  -3.2503  -4.4083
 ADQ  HO4'  H  HOH1   0   0.452   4.4326  -0.6800  -4.5101
 ADQ  HO6'  H  HOH1   0   0.453   2.0320   4.1319  -6.0795

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
 ADQ  PB   O1B   deloc     1.495  0.020  1.495
 ADQ  PB   O2B   deloc     1.492  0.020  1.492
 ADQ  PB   O3B   single    1.655  0.020  1.655
 ADQ  PB   O3A   single    1.649  0.020  1.649
 ADQ  O3B  C1'   single    1.391  0.020  1.391
 ADQ  PA   O1A   deloc     1.498  0.020  1.498
 ADQ  PA   O2A   deloc     1.496  0.020  1.496
 ADQ  PA   O3A   single    1.634  0.020  1.634
 ADQ  PA   O5D   single    1.649  0.020  1.649
 ADQ  O5D  C5D   single    1.407  0.020  1.407
 ADQ  C5D  C4D   single    1.514  0.020  1.514
 ADQ  C5D  H5'1  single    0.970  0.020  1.090
 ADQ  C5D  H5'2  single    0.970  0.020  1.090
 ADQ  C4D  O4D   single    1.430  0.020  1.430
 ADQ  C4D  C3D   single    1.526  0.020  1.526
 ADQ  C4D  H4D   single    0.970  0.020  1.090
 ADQ  O4D  C1D   single    1.392  0.020  1.392
 ADQ  C3D  O3D   single    1.400  0.020  1.400
 ADQ  C3D  C2D   single    1.533  0.020  1.533
 ADQ  C3D  H3D   single    0.970  0.020  1.090
 ADQ  O3D  HO3'  single    0.850  0.020  0.980
 ADQ  C2D  O2D   single    1.401  0.020  1.401
 ADQ  C2D  C1D   single    1.527  0.020  1.527
 ADQ  C2D  H2D   single    0.970  0.020  1.090
 ADQ  O2D  HO2'  single    0.850  0.020  0.980
 ADQ  C1D  N9    single    1.461  0.020  1.461
 ADQ  C1D  H1D   single    0.970  0.020  1.090
 ADQ  N9   C8    aromatic  1.367  0.020  1.367
 ADQ  N9   C4    aromatic  1.363  0.020  1.363
 ADQ  C8   N7    aromatic  1.302  0.020  1.302
 ADQ  C8   H8    single    0.930  0.020  1.080
 ADQ  N7   C5    aromatic  1.369  0.020  1.369
 ADQ  C5   C6    aromatic  1.407  0.020  1.407
 ADQ  C5   C4    aromatic  1.386  0.020  1.386
 ADQ  C6   N6    single    1.335  0.020  1.335
 ADQ  C6   N1    aromatic  1.337  0.020  1.337
 ADQ  N6   HN61  single    0.860  0.020  1.020
 ADQ  N6   HN62  single    0.860  0.020  1.020
 ADQ  N1   C2    aromatic  1.331  0.020  1.331
 ADQ  C2   N3    aromatic  1.322  0.020  1.322
 ADQ  C2   H2    single    0.930  0.020  1.080
 ADQ  N3   C4    aromatic  1.332  0.020  1.332
 ADQ  C1'  C2'   single    1.530  0.020  1.530
 ADQ  C1'  O5'   single    1.399  0.020  1.399
 ADQ  C1'  H1'   single    0.970  0.020  1.090
 ADQ  C2'  C3'   single    1.522  0.020  1.522
 ADQ  C2'  O2'   single    1.405  0.020  1.405
 ADQ  C2'  H2'   single    0.970  0.020  1.090
 ADQ  C3'  C4'   single    1.524  0.020  1.524
 ADQ  C3'  O3'   single    1.411  0.020  1.411
 ADQ  C3'  H3'   single    0.970  0.020  1.090
 ADQ  C4'  C5'   single    1.530  0.020  1.530
 ADQ  C4'  O4'   single    1.407  0.020  1.407
 ADQ  C4'  H4'   single    0.970  0.020  1.090
 ADQ  C5'  C6'   single    1.515  0.020  1.515
 ADQ  C5'  O5'   single    1.417  0.020  1.417
 ADQ  C5'  H5'   single    0.970  0.020  1.090
 ADQ  C6'  O6'   single    1.407  0.020  1.407
 ADQ  C6'  H6'1  single    0.970  0.020  1.090
 ADQ  C6'  H6'2  single    0.970  0.020  1.090
 ADQ  O2'  HO2A  single    0.850  0.020  0.980
 ADQ  O3'  HO3A  single    0.850  0.020  0.980
 ADQ  O4'  HO4'  single    0.850  0.020  0.980
 ADQ  O6'  HO6'  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
 ADQ  O3A   PB   O3B    93.67  3.000
 ADQ  O3A   PB   O2B   110.19  3.000
 ADQ  O3B   PB   O2B   108.92  3.000
 ADQ  O3A   PB   O1B   109.41  3.000
 ADQ  O3B   PB   O1B   109.21  3.000
 ADQ  O2B   PB   O1B   121.79  3.000
 ADQ  C1'   O3B  PB    120.97  3.000
 ADQ  O5D   PA   O3A    96.73  3.000
 ADQ  O5D   PA   O2A   109.85  3.000
 ADQ  O3A   PA   O2A   111.54  3.000
 ADQ  O5D   PA   O1A   109.43  3.000
 ADQ  O3A   PA   O1A   106.42  3.000
 ADQ  O2A   PA   O1A   120.28  3.000
 ADQ  PA    O3A  PB    126.13  3.000
 ADQ  C5D   O5D  PA    118.93  3.000
 ADQ  H5'2  C5D  H5'1  106.68  3.000
 ADQ  H5'2  C5D  C4D   109.57  3.000
 ADQ  H5'1  C5D  C4D   107.99  3.000
 ADQ  H5'2  C5D  O5D   107.39  3.000
 ADQ  H5'1  C5D  O5D   111.91  3.000
 ADQ  C4D   C5D  O5D   113.10  3.000
 ADQ  H4D   C4D  C3D   109.87  3.000
 ADQ  H4D   C4D  O4D   108.84  3.000
 ADQ  C3D   C4D  O4D   104.96  3.000
 ADQ  H4D   C4D  C5D   109.75  3.000
 ADQ  C3D   C4D  C5D   112.86  3.000
 ADQ  O4D   C4D  C5D   110.40  3.000
 ADQ  C1D   O4D  C4D   111.34  3.000
 ADQ  H3D   C3D  C2D   109.05  3.000
 ADQ  H3D   C3D  O3D   111.36  3.000
 ADQ  C2D   C3D  O3D   113.89  3.000
 ADQ  H3D   C3D  C4D   109.97  3.000
 ADQ  C2D   C3D  C4D   101.89  3.000
 ADQ  O3D   C3D  C4D   110.27  3.000
 ADQ  HO3'  O3D  C3D   108.89  3.000
 ADQ  H2D   C2D  C1D   112.23  3.000
 ADQ  H2D   C2D  O2D   111.88  3.000
 ADQ  C1D   C2D  O2D   107.51  3.000
 ADQ  H2D   C2D  C3D   112.52  3.000
 ADQ  C1D   C2D  C3D   100.95  3.000
 ADQ  O2D   C2D  C3D   111.16  3.000
 ADQ  HO2'  O2D  C2D   107.83  3.000
 ADQ  H1D   C1D  N9    107.06  3.000
 ADQ  H1D   C1D  C2D   111.47  3.000
 ADQ  N9    C1D  C2D   111.54  3.000
 ADQ  H1D   C1D  O4D   110.67  3.000
 ADQ  N9    C1D  O4D   109.14  3.000
 ADQ  C2D   C1D  O4D   106.97  3.000
 ADQ  C4    N9   C8    106.20  3.000
 ADQ  C4    N9   C1D   125.06  3.000
 ADQ  C8    N9   C1D   128.71  3.000
 ADQ  H8    C8   N7    124.61  3.000
 ADQ  H8    C8   N9    122.00  3.000
 ADQ  N7    C8   N9    113.38  3.000
 ADQ  C5    N7   C8    104.38  3.000
 ADQ  C4    C5   C6    116.19  3.000
 ADQ  C4    C5   N7    110.73  3.000
 ADQ  C6    C5   N7    133.08  3.000
 ADQ  N1    C6   N6    119.37  3.000
 ADQ  N1    C6   C5    117.93  3.000
 ADQ  N6    C6   C5    122.70  3.000
 ADQ  HN62  N6   HN61  117.95  3.000
 ADQ  HN62  N6   C6    120.69  3.000
 ADQ  HN61  N6   C6    120.00  3.000
 ADQ  C2    N1   C6    119.24  3.000
 ADQ  H2    C2   N3    116.18  3.000
 ADQ  H2    C2   N1    115.38  3.000
 ADQ  N3    C2   N1    128.44  3.000
 ADQ  C4    N3   C2    111.57  3.000
 ADQ  N3    C4   C5    126.64  3.000
 ADQ  N3    C4   N9    128.06  3.000
 ADQ  C5    C4   N9    105.30  3.000
 ADQ  H1'   C1'  O5'   104.97  3.000
 ADQ  H1'   C1'  C2'   110.44  3.000
 ADQ  O5'   C1'  C2'   109.58  3.000
 ADQ  H1'   C1'  O3B   110.99  3.000
 ADQ  O5'   C1'  O3B   112.68  3.000
 ADQ  C2'   C1'  O3B   108.17  3.000
 ADQ  H2'   C2'  O2'   111.02  3.000
 ADQ  H2'   C2'  C3'   108.33  3.000
 ADQ  O2'   C2'  C3'   108.20  3.000
 ADQ  H2'   C2'  C1'   106.90  3.000
 ADQ  O2'   C2'  C1'   112.59  3.000
 ADQ  C3'   C2'  C1'   109.71  3.000
 ADQ  H3'   C3'  O3'   110.50  3.000
 ADQ  H3'   C3'  C4'   108.39  3.000
 ADQ  O3'   C3'  C4'   107.05  3.000
 ADQ  H3'   C3'  C2'   109.02  3.000
 ADQ  O3'   C3'  C2'   111.89  3.000
 ADQ  C4'   C3'  C2'   109.93  3.000
 ADQ  H4'   C4'  O4'   110.85  3.000
 ADQ  H4'   C4'  C5'   108.12  3.000
 ADQ  O4'   C4'  C5'   107.99  3.000
 ADQ  H4'   C4'  C3'   107.67  3.000
 ADQ  O4'   C4'  C3'   111.42  3.000
 ADQ  C5'   C4'  C3'   110.76  3.000
 ADQ  H5'   C5'  O5'   110.28  3.000
 ADQ  H5'   C5'  C6'   108.92  3.000
 ADQ  O5'   C5'  C6'   107.27  3.000
 ADQ  H5'   C5'  C4'   109.17  3.000
 ADQ  O5'   C5'  C4'   110.25  3.000
 ADQ  C6'   C5'  C4'   110.93  3.000
 ADQ  H6'2  C6'  H6'1  107.00  3.000
 ADQ  H6'2  C6'  O6'   111.74  3.000
 ADQ  H6'1  C6'  O6'   111.54  3.000
 ADQ  H6'2  C6'  C5'   108.81  3.000
 ADQ  H6'1  C6'  C5'   108.37  3.000
 ADQ  O6'   C6'  C5'   109.28  3.000
 ADQ  HO2A  O2'  C2'   108.77  3.000
 ADQ  HO3A  O3'  C3'   108.42  3.000
 ADQ  HO4'  O4'  C4'   108.07  3.000
 ADQ  C5'   O5'  C1'   115.62  3.000
 ADQ  HO6'  O6'  C6'   107.74  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
 ADQ  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 ADQ  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 ADQ  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 ADQ  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 ADQ  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 ADQ  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 ADQ  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 ADQ  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 ADQ  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 ADQ  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 ADQ  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 ADQ  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 ADQ  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 ADQ  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 ADQ  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 ADQ  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 ADQ  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 ADQ  CONST_18  N7    C8   N9   C1D  180.00   0.0  0
 ADQ  CONST_19  C5    C4   N9   C1D  180.00   0.0  0
 ADQ  CONST_20  N3    C4   N9   C1D    0.00   0.0  0
 ADQ  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 ADQ  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 ADQ  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 ADQ  CONST_24  H8    C8   N9   C1D    0.00   0.0  0
 ADQ  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 ADQ  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 ADQ  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 ADQ  Var_01    C4D   C5D  O5D  PA    83.32  30.0  3
 ADQ  Var_02    O1A   PA   O3A  PB   160.50  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
 ADQ  chir_03  C4D  C5D  O4D  C3D  negativ
 ADQ  chir_04  C3D  O3D  C4D  C2D  positiv
 ADQ  chir_05  C2D  O2D  C3D  C1D  positiv
 ADQ  chir_06  C1D  O4D  N9   C2D  negativ
 ADQ  chir_07  C1'  O3B  C2'  O5'  positiv
 ADQ  chir_08  C2'  O2'  C1'  C3'  negativ
 ADQ  chir_09  C3'  O3'  C2'  C4'  positiv
 ADQ  chir_10  C4'  O4'  C5'  C3'  positiv
 ADQ  chir_11  C5'  O5'  C4'  C6'  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
 ADQ  plan-1  C6    0.020
 ADQ  plan-1  N6    0.020
 ADQ  plan-1  HN61  0.020
 ADQ  plan-1  HN62  0.020
 ADQ  plan-2  C1D   0.020
 ADQ  plan-2  N9    0.020
 ADQ  plan-2  C8    0.020
 ADQ  plan-2  N7    0.020
 ADQ  plan-2  C5    0.020
 ADQ  plan-2  C6    0.020
 ADQ  plan-2  N6    0.020
 ADQ  plan-2  N1    0.020
 ADQ  plan-2  C2    0.020
 ADQ  plan-2  N3    0.020
 ADQ  plan-2  C4    0.020
 ADQ  plan-2  H8    0.020
 ADQ  plan-2  H2    0.020

