# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 02:19:01 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4-dihydroxy-5-sulfanyltetrahydrofuran-2-yl]methyl 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)OC[C@H]4O[C@H](S)[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
 KXG  KXG  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5R)-3,4-dihydroxy-5-sulfanyltetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KXG
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
 KXG  C1B   C  CH1    0   0.208  18.6272  -22.1336   -7.4346
 KXG  C1D   C  CR15   0  -0.116  24.3180  -29.7850   -6.1583
 KXG  C2A   C  CR16   0   0.044  15.4012  -19.7935   -9.1630
 KXG  C2B   C  CH1    0  -0.022  18.5269  -23.2740   -6.4225
 KXG  C2D   C  CR15   0  -0.033  23.8441  -31.0158   -6.9230
 KXG  C3B   C  CH1    0  -0.040  19.8849  -23.1787   -5.7291
 KXG  C3D   C  CR15   0   0.000  23.9318  -30.5008   -8.3568
 KXG  C4A   C  CR56   0   0.489  16.8046  -21.4767   -9.0261
 KXG  C4B   C  CH1    0  -0.033  20.7858  -22.8350   -6.9179
 KXG  C4D   C  CR15   0   0.019  25.2107  -29.6632   -8.2983
 KXG  C5A   C  CR56   0  -0.010  16.3057  -22.0627  -10.1788
 KXG  C5B   C  CH2    0  -0.180  21.3495  -24.0479   -7.6460
 KXG  C5D   C  CH2    0  -0.198  25.3641  -28.6189   -9.3846
 KXG  C6A   C  CR6    0   0.455  15.2505  -21.3859  -10.8162
 KXG  C8A   C  CR15   0   0.108  17.8461  -23.3389   -9.5065
 KXG  N1A   N  N      0  -0.471  14.8217  -20.2407  -10.2740
 KXG  N3A   N  N      0  -0.454  16.3883  -20.3394   -8.4744
 KXG  N6A   N  NH2    0  -0.815  14.6574  -21.8467  -11.9202
 KXG  N7A   N  N      0  -0.446  16.9745  -23.2258  -10.4632
 KXG  N9A   N  NR5    0  -0.540  17.7948  -22.3146   -8.5981
 KXG  O1A   O  O      0  -0.788  20.8935  -26.6613   -6.1923
 KXG  O1N   O  O      0  -0.795  25.0599  -25.8500   -8.2925
 KXG  O2A   O  OP    -1  -0.781  23.3700  -26.4003   -5.4052
 KXG  O2B   O  OH1    0  -0.652  17.3927  -23.0929   -5.6357
 KXG  O2N   O  OP    -1  -0.778  23.1144  -25.6563  -10.0215
 KXG  O3    O  O2     0  -0.751  22.7423  -26.9325   -7.8581
 KXG  O3B   O  OH1    0  -0.668  19.8217  -22.1392   -4.7865
 KXG  O4B   O  O2     0  -0.494  19.9706  -22.0779   -7.8191
 KXG  O4D   O  O      0  -0.478  25.1707  -29.0619   -7.0147
 KXG  O5B   O  O2     0  -0.624  22.3457  -24.6280   -6.8326
 KXG  O5D   O  O2     0  -0.609  24.1970  -27.8759   -9.6453
 KXG  PA    P  P      0   1.370  22.3054  -26.2258   -6.4394
 KXG  PN    P  P      0   1.349  23.8525  -26.4188   -8.9660
 KXG  S1D   S  S2     0  -0.223  25.1510  -30.2714   -4.6159
 KXG  H1B   H  HCH1   0   0.258  18.3016  -21.1940   -6.9754
 KXG  H1N   H  HCR5   0   0.280  23.4706  -29.1566   -5.8797
 KXG  H2A   H  HCR6   0   0.250  15.0085  -18.8590   -8.7761
 KXG  H2B   H  HCH1   0   0.245  18.4979  -24.2326   -6.9590
 KXG  H2D   H  HCR5   0   0.248  22.8197  -31.2792   -6.6350
 KXG  H3B   H  HCH1   0   0.251  20.1748  -24.1302   -5.2687
 KXG  H3D   H  HCR5   0   0.232  23.0758  -29.8366   -8.5263
 KXG  H4B   H  HCH1   0   0.250  21.6226  -22.2040   -6.5984
 KXG  H4D   H  HCR5   0   0.213  26.0818  -30.3307   -8.3785
 KXG  H52A  H  HCH2   0   0.208  20.5502  -24.7571   -7.8842
 KXG  H51A  H  HCH2   0   0.231  21.7928  -23.7321   -8.5931
 KXG  H51N  H  HCH2   0   0.227  26.2116  -27.9690   -9.1466
 KXG  H52N  H  HCH2   0   0.225  25.6214  -29.1479  -10.3076
 KXG  H8A   H  HCR5   0   0.301  18.5578  -24.1459   -9.4107
 KXG  H61A  H  HNH2   0   0.401  13.9676  -21.2847  -12.3889
 KXG  H62A  H  HNH2   0   0.409  15.0187  -22.6511  -12.4025
 KXG  HO2A  H  HOH1   0   0.461  17.2494  -23.8849   -5.1083
 KXG  H2    H  HOH1   0   0.457  24.4865  -32.8142   -7.2545
 KXG  HO3A  H  HOH1   0   0.453  20.6930  -22.0385   -4.3900
 KXG  H1S   H  HSH1   0   0.217  25.0298  -29.0811   -4.0157
 KXG  O2D   O  OH1    0  -0.660  24.7345  -32.0752   -6.6885
 KXG  O3D   O  OH1    0  -0.664  23.9644  -31.5550   -9.2751
 KXG  HO3N  H  HOH1   0   0.461  23.7418  -31.2168  -10.1472

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
 KXG  C1B  C2B   single    1.528  0.020  1.528
 KXG  C1B  N9A   single    1.442  0.020  1.442
 KXG  C1B  O4B   single    1.398  0.020  1.398
 KXG  C1D  C2D   single    1.524  0.020  1.524
 KXG  C1D  O4D   single    1.408  0.020  1.408
 KXG  C1D  S1D   single    1.819  0.020  1.819
 KXG  C2A  N1A   aromatic  1.330  0.020  1.330
 KXG  C2A  N3A   aromatic  1.322  0.020  1.322
 KXG  C2B  C3B   single    1.528  0.020  1.528
 KXG  C2B  O2B   single    1.392  0.020  1.392
 KXG  C2D  C3D   single    1.526  0.020  1.526
 KXG  C2D  O2D   single    1.404  0.020  1.404
 KXG  C3B  C4B   single    1.531  0.020  1.531
 KXG  C3B  O3B   single    1.405  0.020  1.405
 KXG  C3D  C4D   single    1.530  0.020  1.530
 KXG  C3D  O3D   single    1.398  0.020  1.398
 KXG  C4A  C5A   aromatic  1.386  0.020  1.386
 KXG  C4A  N3A   aromatic  1.331  0.020  1.331
 KXG  C4A  N9A   aromatic  1.366  0.020  1.366
 KXG  C4B  C5B   single    1.523  0.020  1.523
 KXG  C4B  O4B   single    1.432  0.020  1.432
 KXG  C4D  C5D   single    1.515  0.020  1.515
 KXG  C4D  O4D   single    1.418  0.020  1.418
 KXG  C5A  C6A   aromatic  1.406  0.020  1.406
 KXG  C5A  N7A   aromatic  1.371  0.020  1.371
 KXG  C5B  O5B   single    1.411  0.020  1.411
 KXG  C5D  O5D   single    1.408  0.020  1.408
 KXG  C6A  N1A   aromatic  1.338  0.020  1.338
 KXG  C6A  N6A   single    1.335  0.020  1.335
 KXG  C8A  N7A   aromatic  1.299  0.020  1.299
 KXG  C8A  N9A   aromatic  1.370  0.020  1.370
 KXG  O1A  PA    deloc     1.498  0.020  1.498
 KXG  O1N  PN    deloc     1.495  0.020  1.495
 KXG  O2A  PA    deloc     1.494  0.020  1.494
 KXG  O2N  PN    deloc     1.497  0.020  1.497
 KXG  O3   PA    single    1.644  0.020  1.644
 KXG  O3   PN    single    1.650  0.020  1.650
 KXG  O5B  PA    single    1.646  0.020  1.646
 KXG  O5D  PN    single    1.644  0.020  1.644
 KXG  C1B  H1B   single    0.970  0.020  1.090
 KXG  C1D  H1N   single    0.970  0.020  1.090
 KXG  C2A  H2A   single    0.930  0.020  1.080
 KXG  C2B  H2B   single    0.970  0.020  1.090
 KXG  C2D  H2D   single    0.970  0.020  1.090
 KXG  C3B  H3B   single    0.970  0.020  1.090
 KXG  C3D  H3D   single    0.970  0.020  1.090
 KXG  C4B  H4B   single    0.970  0.020  1.090
 KXG  C4D  H4D   single    0.970  0.020  1.090
 KXG  C5B  H52A  single    0.970  0.020  1.090
 KXG  C5B  H51A  single    0.970  0.020  1.090
 KXG  C5D  H51N  single    0.970  0.020  1.090
 KXG  C5D  H52N  single    0.970  0.020  1.090
 KXG  C8A  H8A   single    0.930  0.020  1.080
 KXG  N6A  H61A  single    0.860  0.020  1.020
 KXG  N6A  H62A  single    0.860  0.020  1.020
 KXG  O2B  HO2A  single    0.850  0.020  0.980
 KXG  O2D  H2    single    0.850  0.020  0.980
 KXG  O3B  HO3A  single    0.850  0.020  0.980
 KXG  O3D  HO3N  single    0.850  0.020  0.980
 KXG  S1D  H1S   single    1.200  0.020  1.300

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
 KXG  H1B   C1B  O4B   111.51  3.000
 KXG  H1B   C1B  N9A   105.92  3.000
 KXG  O4B   C1B  N9A   109.74  3.000
 KXG  H1B   C1B  C2B   110.06  3.000
 KXG  O4B   C1B  C2B   105.96  3.000
 KXG  N9A   C1B  C2B   113.76  3.000
 KXG  H1N   C1D  S1D   107.04  3.000
 KXG  H1N   C1D  O4D   109.26  3.000
 KXG  S1D   C1D  O4D   112.06  3.000
 KXG  H1N   C1D  C2D   110.59  3.000
 KXG  S1D   C1D  C2D   110.59  3.000
 KXG  O4D   C1D  C2D   107.32  3.000
 KXG  H2A   C2A  N3A   116.13  3.000
 KXG  H2A   C2A  N1A   115.44  3.000
 KXG  N3A   C2A  N1A   128.43  3.000
 KXG  H2B   C2B  O2B   111.58  3.000
 KXG  H2B   C2B  C3B   107.43  3.000
 KXG  O2B   C2B  C3B   117.36  3.000
 KXG  H2B   C2B  C1B   109.23  3.000
 KXG  O2B   C2B  C1B   109.31  3.000
 KXG  C3B   C2B  C1B   101.29  3.000
 KXG  H2D   C2D  O2D   111.56  3.000
 KXG  H2D   C2D  C3D   112.43  3.000
 KXG  O2D   C2D  C3D   112.04  3.000
 KXG  H2D   C2D  C1D   110.65  3.000
 KXG  O2D   C2D  C1D   109.17  3.000
 KXG  C3D   C2D  C1D   100.43  3.000
 KXG  H3B   C3B  O3B   111.87  3.000
 KXG  H3B   C3B  C4B   111.44  3.000
 KXG  O3B   C3B  C4B   112.42  3.000
 KXG  H3B   C3B  C2B   111.81  3.000
 KXG  O3B   C3B  C2B   108.10  3.000
 KXG  C4B   C3B  C2B   100.64  3.000
 KXG  H3D   C3D  O3D   111.92  3.000
 KXG  H3D   C3D  C4D   109.08  3.000
 KXG  O3D   C3D  C4D   114.73  3.000
 KXG  H3D   C3D  C2D   107.74  3.000
 KXG  O3D   C3D  C2D   111.34  3.000
 KXG  C4D   C3D  C2D   101.36  3.000
 KXG  N9A   C4A  N3A   128.40  3.000
 KXG  N9A   C4A  C5A   105.20  3.000
 KXG  N3A   C4A  C5A   126.40  3.000
 KXG  H4B   C4B  O4B   108.29  3.000
 KXG  H4B   C4B  C5B   108.38  3.000
 KXG  O4B   C4B  C5B   109.33  3.000
 KXG  H4B   C4B  C3B   110.63  3.000
 KXG  O4B   C4B  C3B   105.82  3.000
 KXG  C5B   C4B  C3B   114.23  3.000
 KXG  H4D   C4D  O4D   110.21  3.000
 KXG  H4D   C4D  C5D   106.61  3.000
 KXG  O4D   C4D  C5D   111.08  3.000
 KXG  H4D   C4D  C3D   109.08  3.000
 KXG  O4D   C4D  C3D   104.07  3.000
 KXG  C5D   C4D  C3D   115.77  3.000
 KXG  N7A   C5A  C6A   132.85  3.000
 KXG  N7A   C5A  C4A   110.82  3.000
 KXG  C6A   C5A  C4A   116.33  3.000
 KXG  H51A  C5B  H52A  107.15  3.000
 KXG  H51A  C5B  O5B   109.40  3.000
 KXG  H52A  C5B  O5B   112.00  3.000
 KXG  H51A  C5B  C4B   109.54  3.000
 KXG  H52A  C5B  C4B   110.47  3.000
 KXG  O5B   C5B  C4B   108.25  3.000
 KXG  H52N  C5D  H51N  106.76  3.000
 KXG  H52N  C5D  O5D   107.09  3.000
 KXG  H51N  C5D  O5D   111.65  3.000
 KXG  H52N  C5D  C4D   107.18  3.000
 KXG  H51N  C5D  C4D   109.39  3.000
 KXG  O5D   C5D  C4D   114.37  3.000
 KXG  N6A   C6A  N1A   119.23  3.000
 KXG  N6A   C6A  C5A   122.81  3.000
 KXG  N1A   C6A  C5A   117.96  3.000
 KXG  H8A   C8A  N9A   121.62  3.000
 KXG  H8A   C8A  N7A   124.91  3.000
 KXG  N9A   C8A  N7A   113.46  3.000
 KXG  C6A   N1A  C2A   119.12  3.000
 KXG  C4A   N3A  C2A   111.76  3.000
 KXG  H62A  N6A  H61A  118.05  3.000
 KXG  H62A  N6A  C6A   120.88  3.000
 KXG  H61A  N6A  C6A   119.81  3.000
 KXG  C8A   N7A  C5A   104.38  3.000
 KXG  C8A   N9A  C4A   106.14  3.000
 KXG  C8A   N9A  C1B   127.39  3.000
 KXG  C4A   N9A  C1B   126.46  3.000
 KXG  HO2A  O2B  C2B   108.90  3.000
 KXG  PN    O3   PA    128.63  3.000
 KXG  HO3A  O3B  C3B   108.25  3.000
 KXG  C4B   O4B  C1B   110.66  3.000
 KXG  C4D   O4D  C1D   110.47  3.000
 KXG  PA    O5B  C5B   121.30  3.000
 KXG  PN    O5D  C5D   124.39  3.000
 KXG  O5B   PA   O3    101.80  3.000
 KXG  O5B   PA   O2A   105.14  3.000
 KXG  O3    PA   O2A   110.96  3.000
 KXG  O5B   PA   O1A   110.16  3.000
 KXG  O3    PA   O1A   105.54  3.000
 KXG  O2A   PA   O1A   121.56  3.000
 KXG  O5D   PN   O3     98.19  3.000
 KXG  O5D   PN   O2N   105.27  3.000
 KXG  O3    PN   O2N   107.47  3.000
 KXG  O5D   PN   O1N   110.74  3.000
 KXG  O3    PN   O1N   111.06  3.000
 KXG  O2N   PN   O1N   121.48  3.000
 KXG  H1S   S1D  C1D    95.79  3.000
 KXG  H2    O2D  C2D   108.51  3.000
 KXG  HO3N  O3D  C3D   108.97  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
 KXG  CONST_01  C5A   C6A  N1A  C2A    0.00   0.0  0
 KXG  CONST_02  C5A   C4A  N3A  C2A    0.00   0.0  0
 KXG  CONST_03  N9A   C4A  N3A  C2A  180.00   0.0  0
 KXG  CONST_04  N1A   C6A  C5A  C4A    0.00   0.0  0
 KXG  CONST_05  C8A   N7A  C5A  C4A    0.00   0.0  0
 KXG  CONST_06  N1A   C2A  N3A  C4A    0.00   0.0  0
 KXG  CONST_07  N7A   C8A  N9A  C4A    0.00   0.0  0
 KXG  CONST_08  C8A   N9A  C4A  C5A    0.00   0.0  0
 KXG  CONST_09  N9A   C8A  N7A  C5A    0.00   0.0  0
 KXG  CONST_10  N3A   C4A  C5A  C6A    0.00   0.0  0
 KXG  CONST_11  N9A   C4A  C5A  C6A  180.00   0.0  0
 KXG  CONST_12  C8A   N7A  C5A  C6A  180.00   0.0  0
 KXG  CONST_13  N3A   C2A  N1A  C6A    0.00   0.0  0
 KXG  CONST_14  N3A   C4A  N9A  C8A  180.00   0.0  0
 KXG  CONST_15  N7A   C5A  C6A  N1A  180.00   0.0  0
 KXG  CONST_16  N7A   C5A  C4A  N3A  180.00   0.0  0
 KXG  CONST_17  N9A   C4A  C5A  N7A    0.00   0.0  0
 KXG  CONST_18  C5A   C4A  N9A  C1B  180.00   0.0  0
 KXG  CONST_19  N3A   C4A  N9A  C1B    0.00   0.0  0
 KXG  CONST_20  N7A   C8A  N9A  C1B  180.00   0.0  0
 KXG  CONST_21  N6A   C6A  N1A  C2A  180.00   0.0  0
 KXG  CONST_22  N6A   C6A  C5A  C4A  180.00   0.0  0
 KXG  CONST_23  N7A   C5A  C6A  N6A    0.00   0.0  0
 KXG  CONST_24  H8A   C8A  N9A  C1B    0.00   0.0  0
 KXG  CONST_25  H2A   C2A  N3A  C4A  180.00   0.0  0
 KXG  CONST_26  H61A  N6A  C6A  C5A  180.00   0.0  0
 KXG  CONST_27  H62A  N6A  C6A  C5A    0.00   0.0  0
 KXG  Var_01    O1A   PA   O5B  C5B  -38.24  30.0  3
 KXG  Var_02    O1N   PN   O5D  C5D   12.92  30.0  3
 KXG  Var_03    H52A  C5B  O5B  PA     4.87  30.0  1
 KXG  Var_04    H51N  C5D  O5D  PN   -30.28  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
 KXG  chir_01  C1B  C2B  N9A  O4B  positiv
 KXG  chir_02  C1D  C2D  O4D  S1D  positiv
 KXG  chir_03  C2B  C1B  C3B  O2B  negativ
 KXG  chir_04  C2D  C1D  C3D  O2D  negativ
 KXG  chir_05  C3B  C2B  C4B  O3B  negativ
 KXG  chir_06  C3D  C2D  C4D  O3D  negativ
 KXG  chir_07  C4B  C3B  C5B  O4B  negativ
 KXG  chir_08  C4D  C3D  C5D  O4D  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
 KXG  plan-1  C6A   0.020
 KXG  plan-1  N6A   0.020
 KXG  plan-1  H61A  0.020
 KXG  plan-1  H62A  0.020
 KXG  plan-2  C1B   0.020
 KXG  plan-2  C2A   0.020
 KXG  plan-2  C4A   0.020
 KXG  plan-2  C5A   0.020
 KXG  plan-2  C6A   0.020
 KXG  plan-2  C8A   0.020
 KXG  plan-2  N1A   0.020
 KXG  plan-2  N3A   0.020
 KXG  plan-2  N6A   0.020
 KXG  plan-2  N7A   0.020
 KXG  plan-2  N9A   0.020
 KXG  plan-2  H2A   0.020
 KXG  plan-2  H8A   0.020

