data_NGD
#

_chem_comp.id                                   NGD
_chem_comp.name                                 
;3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD
ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-
YL]PYRIDINIUM
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C21 H28 N7 O15 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "NICOTINAMIDE GUANINE DINUCLEOTIDE"
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2006-12-12
_chem_comp.pdbx_modified_date                   2020-06-17
_chem_comp.pdbx_ambiguous_flag                  ?
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       680.432
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    NGD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       2O3U
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
NGD  O6A     O6A   O  0  1  N  N  N  11.546  -0.150   0.691   2.717  -6.099  -4.059  O6A     NGD   1  
NGD  C6A     C6A   C  0  1  N  N  N  10.760   0.237   1.589   2.635  -5.837  -2.866  C6A     NGD   2  
NGD  C5A     C5A   C  0  1  Y  N  N  10.076  -0.675   2.392   1.730  -4.862  -2.323  C5A     NGD   3  
NGD  N7A     N7A   N  0  1  Y  N  N  10.042  -2.015   2.452   0.831  -4.074  -2.980  N7A     NGD   4  
NGD  C8A     C8A   C  0  1  Y  N  N   9.195  -2.369   3.433   0.264  -3.371  -2.019  C8A     NGD   5  
NGD  N9A     N9A   N  0  1  Y  N  N   8.689  -1.254   3.999   0.766  -3.679  -0.777  N9A     NGD   6  
NGD  C4A     C4A   C  0  1  Y  N  N   9.222  -0.195   3.378   1.715  -4.642  -0.966  C4A     NGD   7  
NGD  N3A     N3A   N  0  1  N  N  N   9.068   1.144   3.545   2.457  -5.228  -0.001  N3A     NGD   8  
NGD  C2A     C2A   C  0  1  N  N  N   9.730   2.017   2.763   3.295  -6.126  -0.470  C2A     NGD   9  
NGD  N2A     N2A   N  0  1  N  N  N   9.558   3.354   2.956   4.138  -6.833   0.349  N2A     NGD  10  
NGD  N1A     N1A   N  0  1  N  N  N  10.566   1.562   1.793   3.394  -6.432  -1.848  N1A     NGD  11  
NGD  "C1'"   C1*   C  0  1  N  N  R   7.704  -1.244   5.121   0.353  -3.080   0.490  "C1'"   NGD  12  
NGD  "O4'"   O4*   O  0  1  N  N  N   6.386  -0.797   4.755  -1.048  -2.748   0.436  "O4'"   NGD  13  
NGD  "C2'"   C2*   C  0  1  N  N  R   8.083  -0.284   6.232   1.081  -1.790   0.833  "C2'"   NGD  14  
NGD  "O2'"   O2*   O  0  1  N  N  N   9.180  -0.785   7.003   2.324  -2.037   1.459  "O2'"   NGD  15  
NGD  "C3'"   C3*   C  0  1  N  N  S   6.788  -0.236   7.008   0.080  -1.112   1.748  "C3'"   NGD  16  
NGD  "O3'"   O3*   O  0  1  N  N  N   6.789  -1.326   7.920   0.141  -1.707   3.044  "O3'"   NGD  17  
NGD  "C4'"   C4*   C  0  1  N  N  R   5.691  -0.511   5.981  -1.252  -1.479   1.101  "C4'"   NGD  18  
NGD  "C5'"   C5*   C  0  1  N  N  N   4.571   0.573   5.943  -1.708  -0.462   0.064  "C5'"   NGD  19  
NGD  "O5'"   O5*   O  0  1  N  N  N   4.917   1.877   5.463  -1.870   0.797   0.693  "O5'"   NGD  20  
NGD  PA      PA    P  0  1  N  N  S   4.705   3.294   6.253  -2.352   2.077  -0.172  PA      NGD  21  
NGD  O1A     O1A   O  0  1  N  N  N   3.714   3.287   7.364  -3.717   1.589  -0.889  O1A     NGD  22  
NGD  O2A     O2A   O  0  1  N  N  N   6.104   3.830   6.471  -2.485   3.351   0.612  O2A     NGD  23  
NGD  O3      O3    O  0  1  N  N  N   3.985   4.189   5.110  -1.299   2.159  -1.396  O3      NGD  24  
NGD  PB      PB    P  0  1  N  N  S   4.495   4.302   3.572   0.285   2.478  -1.414  PB      NGD  25  
NGD  O1B     O1B   O  0  1  N  N  N   4.069   5.691   3.147   0.669   3.823  -0.868  O1B     NGD  26  
NGD  O2B     O2B   O  0  1  N  N  N   5.931   3.853   3.463   0.931   1.216  -0.636  O2B     NGD  27  
NGD  "O5'R"  RO5*  O  0  0  N  N  N   3.561   3.252   2.780   0.640   2.214  -2.970  "O5'R"  NGD  28  
NGD  "C5'R"  RC5*  C  0  0  N  N  N   2.134   3.370   2.876   0.300   0.961  -3.537  "C5'R"  NGD  29  
NGD  "C4'R"  RC4*  C  0  0  N  N  R   1.483   3.786   1.554   0.727   0.945  -4.998  "C4'R"  NGD  30  
NGD  "C3'R"  RC3*  C  0  0  N  N  S  -0.005   3.508   1.604   0.412  -0.374  -5.696  "C3'R"  NGD  31  
NGD  "O3'R"  RO3*  O  0  0  N  N  N  -0.752   4.359   0.694   0.271  -0.131  -7.096  "O3'R"  NGD  32  
NGD  "C2'R"  RC2*  C  0  0  N  N  R  -0.110   2.043   1.234   1.671  -1.180  -5.448  "C2'R"  NGD  33  
NGD  "O2'R"  RO2*  O  0  0  N  N  N  -1.233   1.908   0.378   1.856  -2.220  -6.385  "O2'R"  NGD  34  
NGD  "O4'R"  RO4*  O  0  0  N  N  N   1.941   2.932   0.505   2.163   1.104  -5.055  "O4'R"  NGD  35  
NGD  "C1'R"  RC1*  C  0  0  N  N  R   1.201   1.701   0.514   2.743  -0.111  -5.568  "C1'R"  NGD  36  
NGD  N1      N1    N  1  1  Y  N  N   2.034   0.696   1.215   3.963  -0.510  -4.822  N1      NGD  37  
NGD  C6      C6    C  0  1  Y  N  N   3.384   0.696   1.024   4.943  -1.167  -5.468  C6      NGD  38  
NGD  C5      C5    C  0  1  Y  N  N   4.245  -0.205   1.666   6.095  -1.551  -4.798  C5      NGD  39  
NGD  C4      C4    C  0  1  Y  N  N   3.652  -1.155   2.506   6.217  -1.244  -3.446  C4      NGD  40  
NGD  C2      C2    C  0  1  Y  N  N   1.459  -0.220   2.021   4.064  -0.205  -3.515  C2      NGD  41  
NGD  C3      C3    C  0  1  Y  N  N   2.253  -1.163   2.681   5.193  -0.565  -2.793  C3      NGD  42  
NGD  C7      C7    C  0  1  N  N  N   1.634  -2.172   3.591   5.302  -0.237  -1.382  C7      NGD  43  
NGD  N7      N7    N  0  1  N  N  N   0.389  -2.392   3.651   4.241   0.444  -0.790  N7      NGD  44  
NGD  O7      O7    O  0  1  N  N  N   2.439  -2.846   4.382   6.312  -0.537  -0.721  O7      NGD  45  
NGD  H8A     H8A   H  0  1  N  N  N   8.958  -3.382   3.722  -0.510  -2.628  -2.157  H8A     NGD  46  
NGD  H2A1    1H2A  H  0  0  N  N  N   8.914   3.510   3.705   4.035  -6.728   1.332  H2A1    NGD  47  
NGD  H2A2    2H2A  H  0  0  N  N  N  10.009   4.073   2.428   4.818  -7.422  -0.071  H2A2    NGD  48  
NGD  HN1A    HN1A  H  0  0  N  N  N  11.049   2.221   1.216   4.069  -7.139  -2.123  HN1A    NGD  49  
NGD  "H1'"   H1*   H  0  1  N  N  N   7.711  -2.300   5.429   0.504  -3.862   1.242  "H1'"   NGD  50  
NGD  "H2'"   H2*   H  0  1  N  N  N   8.437   0.703   5.900   1.250  -1.182  -0.064  "H2'"   NGD  51  
NGD  HO2     HO2   H  0  1  N  N  N   9.938  -0.896   6.441   2.709  -2.825   1.036  HO2     NGD  52  
NGD  "H3'"   H3*   H  0  1  N  N  N   6.652   0.718   7.539   0.246  -0.038   1.866  "H3'"   NGD  53  
NGD  HO3     HO3   H  0  1  N  N  N   6.789  -2.144   7.437   1.009  -1.477   3.410  HO3     NGD  54  
NGD  "H4'"   H4*   H  0  1  N  N  N   5.070  -1.380   6.244  -2.044  -1.619   1.844  "H4'"   NGD  55  
NGD  H51     1H5   H  0  1  N  N  N   4.217   0.699   6.977  -2.664  -0.763  -0.374  H51     NGD  56  
NGD  H52     2H5   H  0  1  N  N  N   3.836   0.193   5.218  -0.964  -0.365  -0.732  H52     NGD  57  
NGD  HO1A    HO1A  H  0  0  N  N  N   4.171   3.286   8.197  -4.551   1.593  -0.373  HO1A    NGD  58  
NGD  HO2B    HO2B  H  0  0  N  N  N   6.165   3.759   2.547   0.880   1.183   0.343  HO2B    NGD  59  
NGD  "H5'1"  1H5*  H  0  0  N  N  N   1.899   4.132   3.633   0.811   0.171  -2.979  "H5'1"  NGD  60  
NGD  "H5'2"  2H5*  H  0  0  N  N  N   1.735   2.381   3.147  -0.782   0.817  -3.452  "H5'2"  NGD  61  
NGD  "HC4'"  HC4*  H  0  0  N  N  N   1.721   4.847   1.391   0.279   1.800  -5.515  "HC4'"  NGD  62  
NGD  "HC3'"  HC3*  H  0  0  N  N  N  -0.441   3.724   2.591  -0.502  -0.863  -5.350  "HC3'"  NGD  63  
NGD  "HO3'"  HO3*  H  0  0  N  N  N  -0.915   5.199   1.107  -0.097   0.761  -7.184  "HO3'"  NGD  64  
NGD  "HC2'"  HC2*  H  0  0  N  N  N  -0.247   1.370   2.093   1.660  -1.608  -4.439  "HC2'"  NGD  65  
NGD  "HO2'"  HO2*  H  0  0  N  N  N  -2.027   1.878   0.899   1.159  -2.130  -7.059  "HO2'"  NGD  66  
NGD  "HC1'"  HC1*  H  0  0  N  N  N   0.966   1.277  -0.474   3.081   0.052  -6.597  "HC1'"  NGD  67  
NGD  H6      H6    H  0  1  N  N  N   3.809   1.423   0.348   4.780  -1.371  -6.520  H6      NGD  68  
NGD  H5      H5    H  0  1  N  N  N   5.314  -0.168   1.520   6.886  -2.080  -5.318  H5      NGD  69  
NGD  H4      H4    H  0  1  N  N  N   4.265  -1.881   3.019   7.115  -1.540  -2.909  H4      NGD  70  
NGD  H2      H2    H  0  1  N  N  N   0.388  -0.225   2.156   3.224   0.325  -3.081  H2      NGD  71  
NGD  HN71    1HN7  H  0  0  N  N  N   0.197  -3.105   4.325   3.434   0.689  -1.353  HN71    NGD  72  
NGD  HN72    2HN7  H  0  0  N  N  N  -0.303  -1.921   3.104   4.257   0.700   0.192  HN72    NGD  73  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
NGD  O6A     C6A     DOUB  N  N   1  
NGD  C6A     N1A     SING  N  N   2  
NGD  C6A     C5A     SING  N  N   3  
NGD  C5A     N7A     SING  Y  N   4  
NGD  C5A     C4A     DOUB  Y  N   5  
NGD  N7A     C8A     DOUB  Y  N   6  
NGD  C8A     N9A     SING  Y  N   7  
NGD  C8A     H8A     SING  N  N   8  
NGD  N9A     C4A     SING  Y  N   9  
NGD  N9A     "C1'"   SING  N  N  10  
NGD  C4A     N3A     SING  N  N  11  
NGD  N3A     C2A     DOUB  N  N  12  
NGD  C2A     N1A     SING  N  N  13  
NGD  C2A     N2A     SING  N  N  14  
NGD  N2A     H2A1    SING  N  N  15  
NGD  N2A     H2A2    SING  N  N  16  
NGD  N1A     HN1A    SING  N  N  17  
NGD  "C1'"   "O4'"   SING  N  N  18  
NGD  "C1'"   "C2'"   SING  N  N  19  
NGD  "C1'"   "H1'"   SING  N  N  20  
NGD  "O4'"   "C4'"   SING  N  N  21  
NGD  "C2'"   "O2'"   SING  N  N  22  
NGD  "C2'"   "C3'"   SING  N  N  23  
NGD  "C2'"   "H2'"   SING  N  N  24  
NGD  "O2'"   HO2     SING  N  N  25  
NGD  "C3'"   "C4'"   SING  N  N  26  
NGD  "C3'"   "O3'"   SING  N  N  27  
NGD  "C3'"   "H3'"   SING  N  N  28  
NGD  "O3'"   HO3     SING  N  N  29  
NGD  "C4'"   "C5'"   SING  N  N  30  
NGD  "C4'"   "H4'"   SING  N  N  31  
NGD  "C5'"   "O5'"   SING  N  N  32  
NGD  "C5'"   H51     SING  N  N  33  
NGD  "C5'"   H52     SING  N  N  34  
NGD  "O5'"   PA      SING  N  N  35  
NGD  PA      O3      SING  N  N  36  
NGD  PA      O2A     DOUB  N  N  37  
NGD  PA      O1A     SING  N  N  38  
NGD  O1A     HO1A    SING  N  N  39  
NGD  O3      PB      SING  N  N  40  
NGD  PB      "O5'R"  SING  N  N  41  
NGD  PB      O1B     DOUB  N  N  42  
NGD  PB      O2B     SING  N  N  43  
NGD  O2B     HO2B    SING  N  N  44  
NGD  "O5'R"  "C5'R"  SING  N  N  45  
NGD  "C5'R"  "C4'R"  SING  N  N  46  
NGD  "C5'R"  "H5'1"  SING  N  N  47  
NGD  "C5'R"  "H5'2"  SING  N  N  48  
NGD  "C4'R"  "O4'R"  SING  N  N  49  
NGD  "C4'R"  "C3'R"  SING  N  N  50  
NGD  "C4'R"  "HC4'"  SING  N  N  51  
NGD  "C3'R"  "O3'R"  SING  N  N  52  
NGD  "C3'R"  "C2'R"  SING  N  N  53  
NGD  "C3'R"  "HC3'"  SING  N  N  54  
NGD  "O3'R"  "HO3'"  SING  N  N  55  
NGD  "C2'R"  "O2'R"  SING  N  N  56  
NGD  "C2'R"  "C1'R"  SING  N  N  57  
NGD  "C2'R"  "HC2'"  SING  N  N  58  
NGD  "O2'R"  "HO2'"  SING  N  N  59  
NGD  "O4'R"  "C1'R"  SING  N  N  60  
NGD  "C1'R"  N1      SING  N  N  61  
NGD  "C1'R"  "HC1'"  SING  N  N  62  
NGD  N1      C6      DOUB  Y  N  63  
NGD  N1      C2      SING  Y  N  64  
NGD  C6      C5      SING  Y  N  65  
NGD  C6      H6      SING  N  N  66  
NGD  C5      C4      DOUB  Y  N  67  
NGD  C5      H5      SING  N  N  68  
NGD  C4      C3      SING  Y  N  69  
NGD  C4      H4      SING  N  N  70  
NGD  C2      C3      DOUB  Y  N  71  
NGD  C2      H2      SING  N  N  72  
NGD  C3      C7      SING  N  N  73  
NGD  C7      N7      SING  N  N  74  
NGD  C7      O7      DOUB  N  N  75  
NGD  N7      HN71    SING  N  N  76  
NGD  N7      HN72    SING  N  N  77  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
NGD  SMILES_CANONICAL  CACTVS                3.341  "NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)NC(=Nc45)N)[C@@H](O)[C@H]2O"  
NGD  SMILES            CACTVS                3.341  "NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)[CH](O)[CH]2O"  
NGD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4N=C(NC5=O)N)O)O)O)O)C(=O)N"  
NGD  SMILES            "OpenEye OEToolkits"  1.5.0  "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4N=C(NC5=O)N)O)O)O)O)C(=O)N"  
NGD  InChI             InChI                 1.03   "InChI=1S/C21H27N7O15P2/c22-16(33)8-2-1-3-27(4-8)19-14(31)12(29)9(41-19)5-39-44(35,36)43-45(37,38)40-6-10-13(30)15(32)20(42-10)28-7-24-11-17(28)25-21(23)26-18(11)34/h1-4,7,9-10,12-15,19-20,29-32H,5-6H2,(H6-,22,23,25,26,33,34,35,36,37,38)/p+1/t9-,10-,12-,13-,14-,15-,19-,20-/m1/s1"  
NGD  InChIKey          InChI                 1.03   NCFRZZVNRVEQJK-NAJQWHGHSA-O  
#
_pdbx_chem_comp_identifier.comp_id          NGD
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.5.0
_pdbx_chem_comp_identifier.identifier       "[[(2R,3S,4R,5R)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl hydrogen phosphate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NGD  "Create component"   2006-12-12  PDBJ  
NGD  "Modify descriptor"  2011-06-04  RCSB  
NGD  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     NGD
_pdbx_chem_comp_synonyms.name        "NICOTINAMIDE GUANINE DINUCLEOTIDE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
