# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 11:35:05 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: a 2 line input string
#   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)O[C@H]4O[C@@H]([C@@H](O)[C@H](O)[C@@H]4O)C(O)=O)[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
 GDX  GDX  '(2S,3S,4S,5S,6R)-6-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  60  40  .  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_GDX
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
 GDX  N2    N  NH2    0  -0.832  119.1228  139.5953  179.0155
 GDX  C2    C  CR6    0   0.689  119.4806  139.7272  180.3015
 GDX  N1    N  NR16   0  -0.727  118.6551  139.1737  181.2382
 GDX  N3    N  N      0  -0.512  120.5976  140.3387  180.6086
 GDX  C4    C  CR56   0   0.504  120.8506  140.3499  181.9246
 GDX  C5    C  CR56   0  -0.098  120.0942  139.8106  182.9473
 GDX  C6    C  CR6    0   0.498  118.8686  139.1603  182.6242
 GDX  O6    O  O      0  -0.465  118.0561  138.6425  183.3707
 GDX  N7    N  N      0  -0.445  120.6962  140.0264  184.1610
 GDX  C8    C  CR15   0   0.068  121.7813  140.6804  183.8835
 GDX  N9    N  NR5    0  -0.542  121.9305  140.9130  182.5352
 GDX  C1D   C  CH1    0   0.208  123.0034  141.6109  181.8791
 GDX  C2D   C  CH1    0  -0.014  123.2392  143.0227  182.4094
 GDX  O2D   O  OH1    0  -0.654  122.2842  143.8865  181.8759
 GDX  C3D   C  CH1    0  -0.050  124.6901  143.2510  181.9873
 GDX  O3D   O  OH1    0  -0.666  124.6856  143.6470  180.6383
 GDX  C4D   C  CH1    0  -0.013  125.2948  141.8501  182.1812
 GDX  O4D   O  O2     0  -0.493  124.2073  140.9262  182.0727
 GDX  C5D   C  CH2    0  -0.176  126.0288  141.6449  183.4887
 GDX  O5D   O  O2     0  -0.621  125.1801  141.9621  184.5653
 GDX  PA    P  P      0   1.379  125.2005  141.1724  186.0066
 GDX  O1A   O  O      0  -0.780  125.8195  139.8198  185.8426
 GDX  O2A   O  OP    -1  -0.771  123.8233  141.3488  186.5665
 GDX  O3A   O  O2     0  -0.739  126.1681  142.1581  186.8949
 GDX  PB    P  P      0   1.354  127.7949  142.1113  187.1426
 GDX  O2B   O  OP    -1  -0.771  128.1017  143.3228  187.9589
 GDX  O3B   O  O      0  -0.791  128.5180  141.8101  185.8683
 GDX  O1B   O  O2     0  -0.643  127.8939  140.8207  188.1672
 GDX  C1'   C  CH1    0   0.261  128.4403  139.5912  187.7807
 GDX  O5'   O  O2     0  -0.503  129.8033  139.5289  188.0711
 GDX  C5'   C  CH1    0  -0.078  130.1312  139.5992  189.4524
 GDX  C6'   C  C      0   0.363  131.6739  139.5384  189.5690
 GDX  O6A   O  O      0  -0.599  132.2158  138.5316  189.0754
 GDX  O6B   O  OC    -1  -0.595  132.2268  140.4881  190.1535
 GDX  C2'   C  CH1    0  -0.018  127.6542  138.4911  188.4908
 GDX  O2'   O  OH1    0  -0.674  128.0224  137.2698  187.8911
 GDX  C3'   C  CH1    0   0.005  127.9654  138.4934  189.9831
 GDX  O3'   O  OH1    0  -0.675  127.3012  137.3885  190.5566
 GDX  C4'   C  CH1    0  -0.002  129.4699  138.4390  190.1953
 GDX  O4'   O  OH1    0  -0.677  129.7053  138.5118  191.5870
 GDX  HN21  H  HNH2   0   0.411  119.6432  140.1167  178.3305
 GDX  HN22  H  HNH2   0   0.414  118.1913  139.3166  178.7572
 GDX  HN1   H  HNR6   0   0.423  117.8065  138.7187  180.9253
 GDX  H8    H  HCR5   0   0.303  122.5082  141.0133  184.6118
 GDX  H1'   H  HCH1   0   0.250  122.7295  141.6557  180.8186
 GDX  H2'   H  HCH1   0   0.251  123.2073  143.0095  183.5042
 GDX  HO2A  H  HOH1   0   0.459  122.2967  144.7080  182.3764
 GDX  H3'   H  HCH1   0   0.246  125.1933  143.9931  182.6197
 GDX  HO3A  H  HOH1   0   0.452  125.5982  143.7330  180.3454
 GDX  H4'   H  HCH1   0   0.247  126.0153  141.6489  181.3787
 GDX  H5'2  H  HCH2   0   0.225  126.3837  140.6125  183.5470
 GDX  H5'1  H  HCH2   0   0.212  126.9135  142.2903  183.4891
 GDX  HC1'  H  HCH1   0   0.228  128.3621  139.4484  186.7016
 GDX  HC5'  H  HCH1   0   0.192  129.7760  140.5433  189.8852
 GDX  HC2'  H  HCH1   0   0.223  126.5854  138.6905  188.3384
 GDX  HO2'  H  HOH1   0   0.446  127.6657  136.5604  188.4363
 GDX  HC3'  H  HCH1   0   0.207  127.5912  139.4344  190.4133
 GDX  HO3'  H  HOH1   0   0.448  127.6479  137.2631  191.4466
 GDX  HC4'  H  HCH1   0   0.206  129.8544  137.4983  189.7818
 GDX  HO4'  H  HOH1   0   0.455  130.5691  138.1344  191.7763

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
 GDX  N2   C2    single    1.341  0.020  1.341
 GDX  N2   HN21  single    0.890  0.020  1.040
 GDX  N2   HN22  single    0.890  0.020  1.040
 GDX  C2   N1    single    1.366  0.020  1.366
 GDX  C2   N3    double    1.310  0.020  1.310
 GDX  N1   C6    single    1.402  0.020  1.402
 GDX  N1   HN1   single    0.860  0.020  1.020
 GDX  N3   C4    single    1.340  0.020  1.340
 GDX  C4   C5    aromatic  1.382  0.020  1.382
 GDX  C4   N9    aromatic  1.362  0.020  1.362
 GDX  C5   C6    single    1.425  0.020  1.425
 GDX  C5   N7    aromatic  1.372  0.020  1.372
 GDX  C6   O6    double    1.219  0.020  1.219
 GDX  N7   C8    aromatic  1.297  0.020  1.297
 GDX  C8   N9    aromatic  1.376  0.020  1.376
 GDX  C8   H8    single    0.930  0.020  1.080
 GDX  N9   C1D   single    1.438  0.020  1.438
 GDX  C1D  C2D   single    1.526  0.020  1.526
 GDX  C1D  O4D   single    1.398  0.020  1.398
 GDX  C1D  H1'   single    0.970  0.020  1.090
 GDX  C2D  O2D   single    1.394  0.020  1.394
 GDX  C2D  C3D   single    1.528  0.020  1.528
 GDX  C2D  H2'   single    0.970  0.020  1.090
 GDX  O2D  HO2A  single    0.850  0.020  0.980
 GDX  C3D  O3D   single    1.406  0.020  1.406
 GDX  C3D  C4D   single    1.538  0.020  1.538
 GDX  C3D  H3'   single    0.970  0.020  1.090
 GDX  O3D  HO3A  single    0.850  0.020  0.980
 GDX  C4D  O4D   single    1.431  0.020  1.431
 GDX  C4D  C5D   single    1.513  0.020  1.513
 GDX  C4D  H4'   single    0.970  0.020  1.090
 GDX  C5D  O5D   single    1.407  0.020  1.407
 GDX  C5D  H5'2  single    0.970  0.020  1.090
 GDX  C5D  H5'1  single    0.970  0.020  1.090
 GDX  O5D  PA    single    1.644  0.020  1.644
 GDX  PA   O1A   deloc     1.497  0.020  1.497
 GDX  PA   O2A   deloc     1.497  0.020  1.497
 GDX  PA   O3A   single    1.642  0.020  1.642
 GDX  O3A  PB    single    1.646  0.020  1.646
 GDX  PB   O2B   deloc     1.493  0.020  1.493
 GDX  PB   O3B   deloc     1.496  0.020  1.496
 GDX  PB   O1B   single    1.651  0.020  1.651
 GDX  O1B  C1'   single    1.400  0.020  1.400
 GDX  C1'  O5'   single    1.395  0.020  1.395
 GDX  C1'  C2'   single    1.527  0.020  1.527
 GDX  C1'  HC1'  single    0.970  0.020  1.090
 GDX  O5'  C5'   single    1.421  0.020  1.421
 GDX  C5'  C6'   single    1.548  0.020  1.548
 GDX  C5'  C4'   single    1.528  0.020  1.528
 GDX  C5'  HC5'  single    0.970  0.020  1.090
 GDX  C6'  O6A   deloc     1.245  0.020  1.245
 GDX  C6'  O6B   deloc     1.245  0.020  1.245
 GDX  C2'  O2'   single    1.409  0.020  1.409
 GDX  C2'  C3'   single    1.524  0.020  1.524
 GDX  C2'  HC2'  single    0.970  0.020  1.090
 GDX  O2'  HO2'  single    0.850  0.020  0.980
 GDX  C3'  O3'   single    1.411  0.020  1.411
 GDX  C3'  C4'   single    1.520  0.020  1.520
 GDX  C3'  HC3'  single    0.970  0.020  1.090
 GDX  O3'  HO3'  single    0.850  0.020  0.980
 GDX  C4'  O4'   single    1.413  0.020  1.413
 GDX  C4'  HC4'  single    0.970  0.020  1.090
 GDX  O4'  HO4'  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
 GDX  HN22  N2   HN21  116.59  3.000
 GDX  HN22  N2   C2    121.36  3.000
 GDX  HN21  N2   C2    117.64  3.000
 GDX  N3    C2   N1    122.94  3.000
 GDX  N3    C2   N2    119.88  3.000
 GDX  N1    C2   N2    117.16  3.000
 GDX  HN1   N1   C6    115.39  3.000
 GDX  HN1   N1   C2    118.47  3.000
 GDX  C6    N1   C2    126.14  3.000
 GDX  C4    N3   C2    113.27  3.000
 GDX  N9    C4   C5    105.28  3.000
 GDX  N9    C4   N3    126.39  3.000
 GDX  C5    C4   N3    128.33  3.000
 GDX  N7    C5   C6    130.54  3.000
 GDX  N7    C5   C4    110.68  3.000
 GDX  C6    C5   C4    118.77  3.000
 GDX  O6    C6   C5    128.94  3.000
 GDX  O6    C6   N1    120.52  3.000
 GDX  C5    C6   N1    110.53  3.000
 GDX  C8    N7   C5    104.90  3.000
 GDX  H8    C8   N9    122.33  3.000
 GDX  H8    C8   N7    124.99  3.000
 GDX  N9    C8   N7    112.67  3.000
 GDX  C1D   N9   C8    127.57  3.000
 GDX  C1D   N9   C4    125.97  3.000
 GDX  C8    N9   C4    106.46  3.000
 GDX  H1'   C1D  O4D   111.65  3.000
 GDX  H1'   C1D  C2D   109.69  3.000
 GDX  O4D   C1D  C2D   105.77  3.000
 GDX  H1'   C1D  N9    105.95  3.000
 GDX  O4D   C1D  N9    109.96  3.000
 GDX  C2D   C1D  N9    113.93  3.000
 GDX  H2'   C2D  C3D   107.79  3.000
 GDX  H2'   C2D  O2D   111.72  3.000
 GDX  C3D   C2D  O2D   116.89  3.000
 GDX  H2'   C2D  C1D   109.36  3.000
 GDX  C3D   C2D  C1D   100.89  3.000
 GDX  O2D   C2D  C1D   109.53  3.000
 GDX  HO2A  O2D  C2D   108.73  3.000
 GDX  H3'   C3D  C4D   111.29  3.000
 GDX  H3'   C3D  O3D   111.34  3.000
 GDX  C4D   C3D  O3D   112.26  3.000
 GDX  H3'   C3D  C2D   112.16  3.000
 GDX  C4D   C3D  C2D   101.68  3.000
 GDX  O3D   C3D  C2D   107.70  3.000
 GDX  HO3A  O3D  C3D   108.31  3.000
 GDX  H4'   C4D  C5D   106.78  3.000
 GDX  H4'   C4D  O4D   108.98  3.000
 GDX  C5D   C4D  O4D   110.28  3.000
 GDX  H4'   C4D  C3D   109.45  3.000
 GDX  C5D   C4D  C3D   115.02  3.000
 GDX  O4D   C4D  C3D   106.24  3.000
 GDX  C4D   O4D  C1D   110.40  3.000
 GDX  H5'1  C5D  H5'2  107.11  3.000
 GDX  H5'1  C5D  O5D   110.74  3.000
 GDX  H5'2  C5D  O5D   111.58  3.000
 GDX  H5'1  C5D  C4D   108.19  3.000
 GDX  H5'2  C5D  C4D   109.36  3.000
 GDX  O5D   C5D  C4D   109.76  3.000
 GDX  PA    O5D  C5D   123.73  3.000
 GDX  O3A   PA   O2A   105.60  3.000
 GDX  O3A   PA   O1A   110.98  3.000
 GDX  O2A   PA   O1A   121.87  3.000
 GDX  O3A   PA   O5D   101.14  3.000
 GDX  O2A   PA   O5D   105.07  3.000
 GDX  O1A   PA   O5D   110.08  3.000
 GDX  PB    O3A  PA    130.28  3.000
 GDX  O1B   PB   O3B   110.02  3.000
 GDX  O1B   PB   O2B   106.42  3.000
 GDX  O3B   PB   O2B   122.00  3.000
 GDX  O1B   PB   O3A   100.07  3.000
 GDX  O3B   PB   O3A   110.81  3.000
 GDX  O2B   PB   O3A   105.21  3.000
 GDX  C1'   O1B  PB    122.60  3.000
 GDX  HC1'  C1'  C2'   109.18  3.000
 GDX  HC1'  C1'  O5'   105.66  3.000
 GDX  C2'   C1'  O5'   111.96  3.000
 GDX  HC1'  C1'  O1B   111.10  3.000
 GDX  C2'   C1'  O1B   107.66  3.000
 GDX  O5'   C1'  O1B   111.29  3.000
 GDX  C5'   O5'  C1'   115.18  3.000
 GDX  HC5'  C5'  C4'   108.74  3.000
 GDX  HC5'  C5'  C6'   109.06  3.000
 GDX  C4'   C5'  C6'   111.40  3.000
 GDX  HC5'  C5'  O5'   110.54  3.000
 GDX  C4'   C5'  O5'   109.58  3.000
 GDX  C6'   C5'  O5'   107.52  3.000
 GDX  O6B   C6'  O6A   127.57  3.000
 GDX  O6B   C6'  C5'   116.62  3.000
 GDX  O6A   C6'  C5'   115.81  3.000
 GDX  HC2'  C2'  C3'   109.53  3.000
 GDX  HC2'  C2'  O2'   110.65  3.000
 GDX  C3'   C2'  O2'   111.37  3.000
 GDX  HC2'  C2'  C1'   107.80  3.000
 GDX  C3'   C2'  C1'   110.43  3.000
 GDX  O2'   C2'  C1'   106.97  3.000
 GDX  HO2'  O2'  C2'   107.49  3.000
 GDX  HC3'  C3'  C4'   108.22  3.000
 GDX  HC3'  C3'  O3'   110.53  3.000
 GDX  C4'   C3'  O3'   112.41  3.000
 GDX  HC3'  C3'  C2'   108.33  3.000
 GDX  C4'   C3'  C2'   109.79  3.000
 GDX  O3'   C3'  C2'   107.49  3.000
 GDX  HO3'  O3'  C3'   107.94  3.000
 GDX  HC4'  C4'  O4'   110.91  3.000
 GDX  HC4'  C4'  C3'   108.96  3.000
 GDX  O4'   C4'  C3'   107.48  3.000
 GDX  HC4'  C4'  C5'   108.42  3.000
 GDX  O4'   C4'  C5'   111.56  3.000
 GDX  C3'   C4'  C5'   109.47  3.000
 GDX  HO4'  O4'  C4'   108.86  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
 GDX  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 GDX  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 GDX  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 GDX  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 GDX  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 GDX  CONST_06  C1D   N9   C4   N3     0.00   0.0  0
 GDX  CONST_07  C1D   N9   C4   C5   180.00   0.0  0
 GDX  CONST_08  C1D   N9   C8   N7   180.00   0.0  0
 GDX  CONST_09  C5    C6   N1   C2     0.00   0.0  0
 GDX  CONST_10  C4    N3   C2   N1     0.00   0.0  0
 GDX  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 GDX  CONST_12  C6    N1   C2   N2   180.00   0.0  0
 GDX  CONST_13  C4    N3   C2   N2   180.00   0.0  0
 GDX  CONST_14  O6    C6   N1   C2   180.00   0.0  0
 GDX  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 GDX  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 GDX  CONST_17  HN21  N2   C2   N1   180.00   0.0  0
 GDX  Var_01    O1A   PA   O5D  C5D  -21.34  30.0  3
 GDX  Var_02    O2B   PB   O3A  PA   176.10  30.0  3
 GDX  Var_03    H5'2  C5D  O5D  PA    23.60  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
 GDX  chir_01  C1D  N9   C2D  O4D  negativ
 GDX  chir_02  C2D  O2D  C3D  C1D  positiv
 GDX  chir_03  C3D  O3D  C4D  C2D  positiv
 GDX  chir_04  C4D  O4D  C3D  C5D  negativ
 GDX  chir_07  C1'  O1B  O5'  C2'  negativ
 GDX  chir_08  C5'  O5'  C6'  C4'  positiv
 GDX  chir_09  C2'  O2'  C1'  C3'  positiv
 GDX  chir_10  C3'  O3'  C2'  C4'  positiv
 GDX  chir_11  C4'  O4'  C3'  C5'  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
 GDX  plan-1  N2    0.020
 GDX  plan-1  C2    0.020
 GDX  plan-1  N1    0.020
 GDX  plan-1  N3    0.020
 GDX  plan-1  C4    0.020
 GDX  plan-1  C5    0.020
 GDX  plan-1  C6    0.020
 GDX  plan-1  O6    0.020
 GDX  plan-1  N7    0.020
 GDX  plan-1  C8    0.020
 GDX  plan-1  N9    0.020
 GDX  plan-1  C1D   0.020
 GDX  plan-1  HN21  0.020
 GDX  plan-1  HN22  0.020
 GDX  plan-1  HN1   0.020
 GDX  plan-1  H8    0.020
 GDX  plan-2  C5'   0.020
 GDX  plan-2  C6'   0.020
 GDX  plan-2  O6A   0.020
 GDX  plan-2  O6B   0.020

