# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu May 21 10:12:22 2020
#   Inital geometry file: a 142 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)-3,4-dihydroxytetrahydrofuran-2-yl]methyl 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)OC[C@H]4OC[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
 G2Q  G2Q  '[(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)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  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_G2Q
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
 G2Q  N1    N  N      0  -0.540  -6.3323  -2.8532   1.1297
 G2Q  C2    C  CR6    0   0.664  -6.7043  -2.0310   0.1858
 G2Q  N2    N  NH2    0  -0.827  -7.9891  -1.9876  -0.1957
 G2Q  N3    N  NR16   0  -0.737  -5.8603  -1.1613  -0.4457
 G2Q  C4    C  CR56   0   0.625  -4.5699  -1.1743  -0.0214
 G2Q  C5    C  CR56   0  -0.105  -4.1179  -1.9929   0.9775
 G2Q  C6    C  CR6    0   0.416  -5.0458  -2.9016   1.6142
 G2Q  O6    O  O      0  -0.495  -4.7374  -3.6719   2.5164
 G2Q  N7    N  N      0  -0.443  -2.7802  -1.7719   1.1760
 G2Q  C8    C  CR15   0   0.085  -2.4500  -0.8534   0.3187
 G2Q  N9    N  NR5    0  -0.538  -3.5156  -0.4498  -0.4538
 G2Q  PA    P  P      0   1.353   0.9891   2.3493   0.7186
 G2Q  PB    P  P      0   1.338   2.9899   0.4558   1.5967
 G2Q  C1'   C  CH1    0   0.216  -3.5331   0.5281  -1.5377
 G2Q  O1A   O  O      0  -0.800   0.4430   2.3936   2.1096
 G2Q  O1B   O  O      0  -0.789   2.3722  -0.6418   2.4035
 G2Q  C1X   C  CH2    0  -0.175   6.8833  -1.8572  -1.8191
 G2Q  C2'   C  CH1    0  -0.064  -4.2557   1.8220  -1.1388
 G2Q  O2'   O  OH1    0  -0.658  -5.5945   1.7516  -1.5463
 G2Q  O2A   O  OP    -1  -0.791   1.6603   3.5481   0.1259
 G2Q  O2B   O  OP    -1  -0.800   3.6888   1.5939   2.2716
 G2Q  C2X   C  CH1    0  -0.021   7.6943  -2.0954  -0.5478
 G2Q  O2X   O  OH1    0  -0.668   8.8381  -2.8883  -0.7032
 G2Q  C3'   C  CH1    0  -0.007  -3.4162   2.8846  -1.8574
 G2Q  O3'   O  OH1    0  -0.665  -3.7557   2.9621  -3.2151
 G2Q  O3A   O  O2     0  -0.733   1.9161   1.0177   0.4905
 G2Q  C3X   C  CH1    0  -0.036   6.6640  -2.8081   0.3273
 G2Q  O3X   O  OH1    0  -0.672   6.5158  -4.1569  -0.0437
 G2Q  C4'   C  CH1    0  -0.070  -2.0269   2.2779  -1.7408
 G2Q  O4'   O  O2     0  -0.484  -2.2332   0.8665  -1.8712
 G2Q  C4X   C  CH1    0  -0.016   5.3887  -2.0590  -0.0409
 G2Q  O4X   O  O2     0  -0.499   5.5683  -1.5855  -1.3737
 G2Q  C5'   C  CH2    0  -0.153  -1.3435   2.6139  -0.4283
 G2Q  O5'   O  O2     0  -0.614  -0.1804   1.8302  -0.3254
 G2Q  C5X   C  CH2    0  -0.152   5.1130  -0.9038   0.9024
 G2Q  O5X   O  O2     0  -0.617   3.9739  -0.2036   0.4518
 G2Q  HN2   H  HNH2   0   0.411  -8.6022  -2.7030   0.1552
 G2Q  HN2A  H  HNH2   0   0.413  -8.2672  -1.5319  -1.0483
 G2Q  HN3   H  HNR6   0   0.431  -6.2061  -0.4539  -1.0824
 G2Q  H8    H  HCR5   0   0.294  -1.4672  -0.4272   0.1942
 G2Q  H1'   H  HCH1   0   0.277  -4.0378   0.0532  -2.3880
 G2Q  H2'   H  HCH1   0   0.270  -4.1785   1.9678  -0.0559
 G2Q  HO2'  H  HOH1   0   0.477  -6.1200   2.3567  -1.0122
 G2Q  H2X   H  HCH1   0   0.223   7.9378  -1.1301  -0.0842
 G2Q  HO2X  H  HOH1   0   0.463   9.4638  -2.4301  -1.2723
 G2Q  H3'   H  HCH1   0   0.254  -3.4837   3.8602  -1.3586
 G2Q  HO3'  H  HOH1   0   0.452  -4.7165   3.0068  -3.2835
 G2Q  H3X   H  HCH1   0   0.240   6.9000  -2.7122   1.3958
 G2Q  HO3X  H  HOH1   0   0.450   7.3914  -4.5576  -0.0732
 G2Q  H4'   H  HCH1   0   0.272  -1.3836   2.5882  -2.5682
 G2Q  H4X   H  HCH1   0   0.242   4.5286  -2.7382  -0.0123
 G2Q  H5'   H  HCH2   0   0.233  -1.1207   3.6880  -0.4361
 G2Q  H5'A  H  HCH2   0   0.214  -2.0107   2.4324   0.4235
 G2Q  H5X   H  HCH2   0   0.213   4.9686  -1.3204   1.9060
 G2Q  H5XA  H  HCH2   0   0.210   5.9773  -0.2302   0.9531
 G2Q  H1X   H  HCH2   0   0.230   7.2469  -1.0081  -2.4024
 G2Q  H1XA  H  HCH2   0   0.204   6.9159  -2.7481  -2.4581

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
 G2Q  C6   N1    single    1.376  0.020  1.376
 G2Q  C2   N1    double    1.306  0.020  1.306
 G2Q  N3   C2    single    1.367  0.020  1.367
 G2Q  C2   N2    single    1.341  0.020  1.341
 G2Q  N2   HN2   single    0.890  0.020  1.040
 G2Q  N2   HN2A  single    0.890  0.020  1.040
 G2Q  C4   N3    single    1.358  0.020  1.358
 G2Q  N3   HN3   single    0.860  0.020  1.020
 G2Q  N9   C4    aromatic  1.350  0.020  1.350
 G2Q  C4   C5    aromatic  1.368  0.020  1.368
 G2Q  N7   C5    aromatic  1.370  0.020  1.370
 G2Q  C5   C6    single    1.446  0.020  1.446
 G2Q  C6   O6    double    1.226  0.020  1.226
 G2Q  C8   N7    aromatic  1.299  0.020  1.299
 G2Q  C8   N9    aromatic  1.377  0.020  1.377
 G2Q  C8   H8    single    0.930  0.020  1.080
 G2Q  C1'  N9    single    1.460  0.020  1.460
 G2Q  O1A  PA    deloc     1.495  0.020  1.495
 G2Q  O3A  PA    single    1.638  0.020  1.638
 G2Q  PA   O5'   single    1.651  0.020  1.651
 G2Q  PA   O2A   deloc     1.496  0.020  1.496
 G2Q  O1B  PB    deloc     1.496  0.020  1.496
 G2Q  O2B  PB    deloc     1.496  0.020  1.496
 G2Q  PB   O3A   single    1.641  0.020  1.641
 G2Q  PB   O5X   single    1.647  0.020  1.647
 G2Q  C2'  C1'   single    1.535  0.020  1.535
 G2Q  C1'  O4'   single    1.384  0.020  1.384
 G2Q  C1'  H1'   single    0.970  0.020  1.090
 G2Q  O4X  C1X   single    1.415  0.020  1.415
 G2Q  C1X  C2X   single    1.527  0.020  1.527
 G2Q  C1X  H1X   single    0.970  0.020  1.090
 G2Q  C1X  H1XA  single    0.970  0.020  1.090
 G2Q  C3'  C2'   single    1.533  0.020  1.533
 G2Q  O2'  C2'   single    1.401  0.020  1.401
 G2Q  C2'  H2'   single    0.970  0.020  1.090
 G2Q  O2'  HO2'  single    0.850  0.020  0.980
 G2Q  C3X  C2X   single    1.528  0.020  1.528
 G2Q  O2X  C2X   single    1.400  0.020  1.400
 G2Q  C2X  H2X   single    0.970  0.020  1.090
 G2Q  O2X  HO2X  single    0.850  0.020  0.980
 G2Q  O3'  C3'   single    1.402  0.020  1.402
 G2Q  C3'  C4'   single    1.520  0.020  1.520
 G2Q  C3'  H3'   single    0.970  0.020  1.090
 G2Q  O3'  HO3'  single    0.850  0.020  0.980
 G2Q  C4X  C3X   single    1.524  0.020  1.524
 G2Q  O3X  C3X   single    1.407  0.020  1.407
 G2Q  C3X  H3X   single    0.970  0.020  1.090
 G2Q  O3X  HO3X  single    0.850  0.020  0.980
 G2Q  C4'  C5'   single    1.517  0.020  1.517
 G2Q  C4'  O4'   single    1.432  0.020  1.432
 G2Q  C4'  H4'   single    0.970  0.020  1.090
 G2Q  O4X  C4X   single    1.426  0.020  1.426
 G2Q  C4X  C5X   single    1.517  0.020  1.517
 G2Q  C4X  H4X   single    0.970  0.020  1.090
 G2Q  O5'  C5'   single    1.406  0.020  1.406
 G2Q  C5'  H5'   single    0.970  0.020  1.090
 G2Q  C5'  H5'A  single    0.970  0.020  1.090
 G2Q  O5X  C5X   single    1.411  0.020  1.411
 G2Q  C5X  H5X   single    0.970  0.020  1.090
 G2Q  C5X  H5XA  single    0.970  0.020  1.090

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
 G2Q  C6    N1   C2   122.90  3.000
 G2Q  N3    C2   N2   116.08  3.000
 G2Q  N2    C2   N1   119.93  3.000
 G2Q  N3    C2   N1   123.97  3.000
 G2Q  HN2A  N2   HN2  116.72  3.000
 G2Q  HN2A  N2   C2   121.38  3.000
 G2Q  HN2   N2   C2   117.51  3.000
 G2Q  HN3   N3   C4   121.84  3.000
 G2Q  HN3   N3   C2   121.61  3.000
 G2Q  C4    N3   C2   115.86  3.000
 G2Q  N9    C4   C5   107.27  3.000
 G2Q  C5    C4   N3   123.20  3.000
 G2Q  N9    C4   N3   129.53  3.000
 G2Q  N7    C5   C6   131.59  3.000
 G2Q  C6    C5   C4   119.03  3.000
 G2Q  N7    C5   C4   109.38  3.000
 G2Q  O6    C6   C5   123.88  3.000
 G2Q  O6    C6   N1   121.11  3.000
 G2Q  C5    C6   N1   115.01  3.000
 G2Q  C8    N7   C5   105.46  3.000
 G2Q  H8    C8   N9   121.65  3.000
 G2Q  H8    C8   N7   125.97  3.000
 G2Q  N9    C8   N7   112.39  3.000
 G2Q  C1'   N9   C8   128.48  3.000
 G2Q  C1'   N9   C4   126.00  3.000
 G2Q  C8    N9   C4   105.51  3.000
 G2Q  O5'   PA   O3A   93.28  3.000
 G2Q  O5'   PA   O2A  108.60  3.000
 G2Q  O3A   PA   O2A  110.01  3.000
 G2Q  O2A   PA   O1A  120.58  3.000
 G2Q  O5'   PA   O1A  109.81  3.000
 G2Q  O3A   PA   O1A  111.12  3.000
 G2Q  O5X   PB   O3A   93.41  3.000
 G2Q  O5X   PB   O2B  109.81  3.000
 G2Q  O3A   PB   O2B  110.44  3.000
 G2Q  O5X   PB   O1B  109.14  3.000
 G2Q  O3A   PB   O1B  110.16  3.000
 G2Q  O2B   PB   O1B  120.51  3.000
 G2Q  H1'   C1'  O4'  110.55  3.000
 G2Q  H1'   C1'  C2'  110.48  3.000
 G2Q  O4'   C1'  C2'  107.38  3.000
 G2Q  H1'   C1'  N9   106.92  3.000
 G2Q  O4'   C1'  N9   109.35  3.000
 G2Q  C2'   C1'  N9   112.17  3.000
 G2Q  H1XA  C1X  H1X  108.08  3.000
 G2Q  H1XA  C1X  O4X  111.53  3.000
 G2Q  H1X   C1X  O4X  109.16  3.000
 G2Q  H1XA  C1X  C2X  110.04  3.000
 G2Q  H1X   C1X  C2X  112.90  3.000
 G2Q  O4X   C1X  C2X  105.16  3.000
 G2Q  H2'   C2'  C3'  109.43  3.000
 G2Q  H2'   C2'  O2'  111.20  3.000
 G2Q  C3'   C2'  O2'  114.94  3.000
 G2Q  H2'   C2'  C1'  109.63  3.000
 G2Q  O2'   C2'  C1'  109.38  3.000
 G2Q  C3'   C2'  C1'  101.81  3.000
 G2Q  HO2'  O2'  C2'  109.18  3.000
 G2Q  H2X   C2X  C3X  108.52  3.000
 G2Q  H2X   C2X  O2X  111.31  3.000
 G2Q  C3X   C2X  O2X  110.50  3.000
 G2Q  H2X   C2X  C1X  109.40  3.000
 G2Q  O2X   C2X  C1X  115.46  3.000
 G2Q  C3X   C2X  C1X  101.04  3.000
 G2Q  HO2X  O2X  C2X  109.10  3.000
 G2Q  H3'   C3'  C4'  112.08  3.000
 G2Q  H3'   C3'  O3'  112.09  3.000
 G2Q  C4'   C3'  O3'  108.52  3.000
 G2Q  H3'   C3'  C2'  111.67  3.000
 G2Q  C4'   C3'  C2'  100.83  3.000
 G2Q  O3'   C3'  C2'  111.08  3.000
 G2Q  HO3'  O3'  C3'  108.22  3.000
 G2Q  PB    O3A  PA   123.69  3.000
 G2Q  H3X   C3X  C4X  111.83  3.000
 G2Q  H3X   C3X  O3X  111.28  3.000
 G2Q  C4X   C3X  O3X  108.63  3.000
 G2Q  H3X   C3X  C2X  111.81  3.000
 G2Q  O3X   C3X  C2X  111.54  3.000
 G2Q  C4X   C3X  C2X  101.34  3.000
 G2Q  HO3X  O3X  C3X  108.12  3.000
 G2Q  H4'   C4'  C5'  109.08  3.000
 G2Q  H4'   C4'  O4'  107.19  3.000
 G2Q  C5'   C4'  O4'  111.21  3.000
 G2Q  H4'   C4'  C3'  111.50  3.000
 G2Q  O4'   C4'  C3'  104.75  3.000
 G2Q  C5'   C4'  C3'  112.92  3.000
 G2Q  C4'   O4'  C1'  110.75  3.000
 G2Q  H4X   C4X  C5X  108.24  3.000
 G2Q  H4X   C4X  O4X  109.20  3.000
 G2Q  C5X   C4X  O4X  110.57  3.000
 G2Q  H4X   C4X  C3X  110.22  3.000
 G2Q  C5X   C4X  C3X  112.10  3.000
 G2Q  O4X   C4X  C3X  106.48  3.000
 G2Q  C4X   O4X  C1X  110.34  3.000
 G2Q  H5'A  C5'  H5'  106.92  3.000
 G2Q  H5'A  C5'  O5'  110.73  3.000
 G2Q  H5'   C5'  O5'  112.22  3.000
 G2Q  H5'A  C5'  C4'  111.17  3.000
 G2Q  H5'   C5'  C4'  107.59  3.000
 G2Q  O5'   C5'  C4'  108.20  3.000
 G2Q  C5'   O5'  PA   117.18  3.000
 G2Q  H5XA  C5X  H5X  107.15  3.000
 G2Q  H5XA  C5X  O5X  110.25  3.000
 G2Q  H5X   C5X  O5X  112.00  3.000
 G2Q  H5XA  C5X  C4X  110.69  3.000
 G2Q  H5X   C5X  C4X  107.69  3.000
 G2Q  O5X   C5X  C4X  109.04  3.000
 G2Q  C5X   O5X  PB   117.32  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
 G2Q  CONST_01  N7    C8   N9   C4      0.00   0.0  0
 G2Q  CONST_02  C8    N7   C5   C4      0.00   0.0  0
 G2Q  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 G2Q  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 G2Q  CONST_05  N9    C4   C5   N7      0.00   0.0  0
 G2Q  CONST_06  C1'   N9   C4   N3      0.00   0.0  0
 G2Q  CONST_07  C1'   N9   C4   C5    180.00   0.0  0
 G2Q  CONST_08  C1'   N9   C8   N7    180.00   0.0  0
 G2Q  CONST_09  C4    N3   C2   N1      0.00   0.0  0
 G2Q  CONST_10  C6    N1   C2   N3      0.00   0.0  0
 G2Q  CONST_11  C6    N1   C2   N2    180.00   0.0  0
 G2Q  CONST_12  C4    N3   C2   N2    180.00   0.0  0
 G2Q  CONST_13  H8    C8   N9   C4    180.00   0.0  0
 G2Q  CONST_14  HN3   N3   C2   N1    180.00   0.0  0
 G2Q  CONST_15  HN2   N2   C2   N1      0.00   0.0  0
 G2Q  CONST_16  HN2A  N2   C2   N1    180.00   0.0  0
 G2Q  Var_01    H1X   C1X  O4X  C4X  -140.67  30.0  1
 G2Q  Var_02    C4'   C5'  O5'  PA    159.72  30.0  3
 G2Q  Var_03    C4X   C5X  O5X  PB    145.97  30.0  3
 G2Q  Var_04    O1B   PB   O3A  PA     97.09  30.0  1
 G2Q  Var_05    O1A   PA   O3A  PB    -41.88  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
 G2Q  chir_03  C1'  N9   C2'  O4'  negativ
 G2Q  chir_04  C2'  O2'  C3'  C1'  positiv
 G2Q  chir_05  C2X  C1X  C3X  O2X  negativ
 G2Q  chir_06  C3'  C2'  O3'  C4'  positiv
 G2Q  chir_07  C3X  O3X  C4X  C2X  positiv
 G2Q  chir_08  C4'  C3'  C5'  O4'  negativ
 G2Q  chir_09  C4X  C3X  O4X  C5X  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
 G2Q  plan-1  N1    0.020
 G2Q  plan-1  C2    0.020
 G2Q  plan-1  N2    0.020
 G2Q  plan-1  N3    0.020
 G2Q  plan-1  C4    0.020
 G2Q  plan-1  C5    0.020
 G2Q  plan-1  C6    0.020
 G2Q  plan-1  O6    0.020
 G2Q  plan-1  N7    0.020
 G2Q  plan-1  C8    0.020
 G2Q  plan-1  N9    0.020
 G2Q  plan-1  C1'   0.020
 G2Q  plan-1  HN2   0.020
 G2Q  plan-1  HN2A  0.020
 G2Q  plan-1  HN3   0.020
 G2Q  plan-1  H8    0.020

