data_NDA
# 
_chem_comp.id                                    NDA 
_chem_comp.name                                  3-AMINOMETHYL-PYRIDINIUM-ADENINE-DINUCLEOTIDE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H29 N7 O13 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-02-03 
_chem_comp.pdbx_modified_date                    2011-06-04 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        649.442 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     NDA 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1EBU 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
NDA PA   AP   P 0  1 N N S 41.067 21.183 70.797 -0.660  -0.887 -0.574 PA   NDA 1  
NDA O1A  AO1  O 0  1 N N N 40.609 22.504 71.369 -0.998  -0.022 -1.727 O1A  NDA 2  
NDA O2A  AO2  O 0  1 N N N 39.961 20.259 70.335 -0.031  -2.270 -1.106 O2A  NDA 3  
NDA O5B  AO5* O 0  1 N N N 41.992 20.376 71.890 -1.993  -1.194 0.275  O5B  NDA 4  
NDA C5B  AC5* C 0  1 N N N 42.964 21.111 72.687 -2.943  -1.750 -0.636 C5B  NDA 5  
NDA C4B  AC4* C 0  1 N N R 43.527 20.243 73.820 -4.241  -2.068 0.110  C4B  NDA 6  
NDA O4B  AO4* O 0  1 N N N 44.485 21.110 74.488 -4.862  -0.848 0.550  O4B  NDA 7  
NDA C3B  AC3* C 0  1 N N S 42.520 19.817 74.920 -5.230  -2.775 -0.836 C3B  NDA 8  
NDA O3B  AO3* O 0  1 N N N 42.617 18.404 75.172 -5.568  -4.071 -0.338 O3B  NDA 9  
NDA C2B  AC2* C 0  1 N N R 42.902 20.730 76.092 -6.477  -1.852 -0.835 C2B  NDA 10 
NDA O2B  AO2* O 0  1 N N N 42.567 20.130 77.374 -7.680  -2.621 -0.799 O2B  NDA 11 
NDA C1B  AC1* C 0  1 N N R 44.395 20.911 75.873 -6.290  -1.054 0.481  C1B  NDA 12 
NDA N9A  AN9  N 0  1 Y N N 44.987 22.100 76.529 -6.993  0.229  0.415  N9A  NDA 13 
NDA C8A  AC8  C 0  1 Y N N 44.794 23.422 76.186 -6.476  1.411  -0.026 C8A  NDA 14 
NDA N7A  AN7  N 0  1 Y N N 45.502 24.275 76.934 -7.377  2.347  0.051  N7A  NDA 15 
NDA C5A  AC5  C 0  1 Y N N 46.195 23.453 77.821 -8.526  1.827  0.545  C5A  NDA 16 
NDA C6A  AC6  C 0  1 Y N N 47.123 23.763 78.856 -9.799  2.345  0.840  C6A  NDA 17 
NDA N6A  AN6  N 0  1 N N N 47.511 24.994 79.204 -10.087 3.681  0.625  N6A  NDA 18 
NDA N1A  AN1  N 0  1 Y N N 47.579 22.709 79.641 -10.720 1.521  1.330  N1A  NDA 19 
NDA C2A  AC2  C 0  1 Y N N 47.229 21.434 79.239 -10.454 0.244  1.538  C2A  NDA 20 
NDA N3A  AN3  N 0  1 Y N N 46.408 21.032 78.279 -9.277  -0.284 1.276  N3A  NDA 21 
NDA C4A  AC4  C 0  1 Y N N 45.912 22.104 77.587 -8.296  0.460  0.779  C4A  NDA 22 
NDA O3   O3   O 0  1 N N N 42.084 21.489 69.612 0.412   -0.135 0.364  O3   NDA 23 
NDA PN   NP   P 0  1 N N N 42.766 20.508 68.440 1.453   0.603  -0.618 PN   NDA 24 
NDA O1N  NO1  O 0  1 N N N 41.641 20.074 67.544 0.833   1.923  -1.127 O1N  NDA 25 
NDA O2N  NO2  O -1 1 N N N 43.457 19.357 69.170 1.767   -0.316 -1.819 O2N  NDA 26 
NDA O5D  NO5* O 0  1 N N N 43.701 21.595 67.683 2.812   0.922  0.184  O5D  NDA 27 
NDA C5D  NC5* C 0  1 N N N 45.112 21.529 67.925 3.733   1.465  -0.764 C5D  NDA 28 
NDA C4D  NC4* C 0  1 N N R 45.824 22.609 67.134 5.053   1.792  -0.064 C4D  NDA 29 
NDA O4D  NO4* O 0  1 N N N 45.812 22.231 65.710 5.698   0.580  0.385  O4D  NDA 30 
NDA C3D  NC3* C 0  1 N N S 45.247 24.036 67.166 6.050   2.425  -1.059 C3D  NDA 31 
NDA O3D  NO3* O 0  1 N N N 46.325 25.009 67.152 6.046   3.849  -0.935 O3D  NDA 32 
NDA C2D  NC2* C 0  1 N N R 44.409 24.075 65.869 7.422   1.848  -0.636 C2D  NDA 33 
NDA O2D  NO2* O 0  1 N N N 44.175 25.455 65.470 8.307   2.898  -0.241 O2D  NDA 34 
NDA C1D  NC1* C 0  1 N N R 45.332 23.322 64.940 7.087   0.932  0.562  C1D  NDA 35 
NDA N1N  NN1  N 1  1 Y N N 44.731 22.832 63.673 7.925   -0.269 0.535  N1N  NDA 36 
NDA C2N  NC2  C 0  1 Y N N 43.546 22.069 63.607 8.966   -0.344 1.342  C2N  NDA 37 
NDA C3N  NC3  C 0  1 Y N N 43.026 21.552 62.283 9.783   -1.459 1.339  C3N  NDA 38 
NDA C7N  NC7  C 0  1 N N N 41.796 20.732 62.299 10.974  -1.534 2.259  C7N  NDA 39 
NDA N7N  NN7  N 0  1 N N N 41.110 20.439 63.425 12.154  -0.983 1.578  N7N  NDA 40 
NDA C4N  NC4  C 0  1 Y N N 43.762 21.918 61.007 9.489   -2.510 0.484  C4N  NDA 41 
NDA C5N  NC5  C 0  1 Y N N 44.975 22.748 61.254 8.383   -2.398 -0.344 C5N  NDA 42 
NDA C6N  NC6  C 0  1 Y N N 45.409 23.148 62.443 7.616   -1.249 -0.290 C6N  NDA 43 
NDA HOA2 2HOA H 0  0 N N N 40.249 19.428 69.975 0.174   -2.802 -0.325 HOA2 NDA 44 
NDA H51A AH51 H 0  0 N N N 43.777 21.533 72.052 -3.148  -1.033 -1.431 H51A NDA 45 
NDA H52A AH52 H 0  0 N N N 42.536 22.064 73.075 -2.540  -2.666 -1.068 H52A NDA 46 
NDA H4B  AH4* H 0  1 N N N 43.907 19.299 73.362 -4.028  -2.705 0.968  H4B  NDA 47 
NDA H3B  AH3* H 0  1 N N N 41.442 19.942 74.663 -4.811  -2.850 -1.839 H3B  NDA 48 
NDA HO3A AHO3 H 0  0 N N N 42.000 18.143 75.845 -6.233  -4.437 -0.938 HO3A NDA 49 
NDA H2B  AH2* H 0  1 N N N 42.352 21.700 76.121 -6.469  -1.186 -1.698 H2B  NDA 50 
NDA HO2A AHO2 H 0  0 N N N 42.803 20.695 78.099 -7.737  -3.091 -1.642 HO2A NDA 51 
NDA H1B  AH1* H 0  1 N N N 44.943 20.037 76.297 -6.635  -1.637 1.335  H1B  NDA 52 
NDA H8A  AH8  H 0  1 N N N 44.127 23.769 75.378 -5.468  1.550  -0.387 H8A  NDA 53 
NDA H61A AH61 H 0  0 N N N 48.175 25.216 79.945 -9.406  4.272  0.267  H61A NDA 54 
NDA H62A AH62 H 0  0 N N N 46.661 25.521 79.406 -10.969 4.027  0.833  H62A NDA 55 
NDA H2A  AH2  H 0  1 N N N 47.685 20.587 79.779 -11.232 -0.390 1.937  H2A  NDA 56 
NDA H51N NH51 H 0  0 N N N 45.352 21.579 69.012 3.315   2.375  -1.196 H51N NDA 57 
NDA H52N NH52 H 0  0 N N N 45.525 20.515 67.714 3.912   0.736  -1.555 H52N NDA 58 
NDA H4D  NH4* H 0  1 N N N 46.821 22.658 67.630 4.879   2.463  0.778  H4D  NDA 59 
NDA H3D  NH3* H 0  1 N N N 44.647 24.277 68.074 5.809   2.131  -2.081 H3D  NDA 60 
NDA HO3N NHO3 H 0  0 N N N 45.969 25.889 67.171 6.684   4.187  -1.578 HO3N NDA 61 
NDA H2D  NH2* H 0  1 N N N 43.384 23.637 65.920 7.859   1.267  -1.449 H2D  NDA 62 
NDA HO2N NHO2 H 0  0 N N N 43.659 25.479 64.672 8.428   3.467  -1.013 HO2N NDA 63 
NDA H1D  NH1* H 0  1 N N N 46.122 24.022 64.584 7.226   1.469  1.501  H1D  NDA 64 
NDA H2N  NH2  H 0  1 N N N 43.038 21.881 64.567 9.189   0.479  2.005  H2N  NDA 65 
NDA HC71 1HC7 H 0  0 N N N 41.077 21.200 61.586 11.162  -2.574 2.527  HC71 NDA 66 
NDA HC72 2HC7 H 0  0 N N N 42.036 19.765 61.797 10.773  -0.957 3.162  HC72 NDA 67 
NDA H71N NH71 H 0  0 N N N 40.261 19.873 63.436 11.977  0.001  1.443  H71N NDA 68 
NDA H72N NH72 H 0  0 N N N 40.889 21.323 63.883 12.923  -1.053 2.228  H72N NDA 69 
NDA H4N  NH4  H 0  1 N N N 43.445 21.610 59.996 10.107  -3.396 0.464  H4N  NDA 70 
NDA H5N  NH5  H 0  1 N N N 45.638 23.114 60.452 8.125   -3.197 -1.023 H5N  NDA 71 
NDA H6N  NH6  H 0  1 N N N 46.335 23.744 62.408 6.753   -1.154 -0.933 H6N  NDA 72 
# 
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 
NDA PA  O1A  DOUB N N 1  
NDA PA  O2A  SING N N 2  
NDA PA  O5B  SING N N 3  
NDA PA  O3   SING N N 4  
NDA O2A HOA2 SING N N 5  
NDA O5B C5B  SING N N 6  
NDA C5B C4B  SING N N 7  
NDA C5B H51A SING N N 8  
NDA C5B H52A SING N N 9  
NDA C4B O4B  SING N N 10 
NDA C4B C3B  SING N N 11 
NDA C4B H4B  SING N N 12 
NDA O4B C1B  SING N N 13 
NDA C3B O3B  SING N N 14 
NDA C3B C2B  SING N N 15 
NDA C3B H3B  SING N N 16 
NDA O3B HO3A SING N N 17 
NDA C2B O2B  SING N N 18 
NDA C2B C1B  SING N N 19 
NDA C2B H2B  SING N N 20 
NDA O2B HO2A SING N N 21 
NDA C1B N9A  SING N N 22 
NDA C1B H1B  SING N N 23 
NDA N9A C8A  SING Y N 24 
NDA N9A C4A  SING Y N 25 
NDA C8A N7A  DOUB Y N 26 
NDA C8A H8A  SING N N 27 
NDA N7A C5A  SING Y N 28 
NDA C5A C6A  SING Y N 29 
NDA C5A C4A  DOUB Y N 30 
NDA C6A N6A  SING N N 31 
NDA C6A N1A  DOUB Y N 32 
NDA N6A H61A SING N N 33 
NDA N6A H62A SING N N 34 
NDA N1A C2A  SING Y N 35 
NDA C2A N3A  DOUB Y N 36 
NDA C2A H2A  SING N N 37 
NDA N3A C4A  SING Y N 38 
NDA O3  PN   SING N N 39 
NDA PN  O1N  DOUB N N 40 
NDA PN  O2N  SING N N 41 
NDA PN  O5D  SING N N 42 
NDA O5D C5D  SING N N 43 
NDA C5D C4D  SING N N 44 
NDA C5D H51N SING N N 45 
NDA C5D H52N SING N N 46 
NDA C4D O4D  SING N N 47 
NDA C4D C3D  SING N N 48 
NDA C4D H4D  SING N N 49 
NDA O4D C1D  SING N N 50 
NDA C3D O3D  SING N N 51 
NDA C3D C2D  SING N N 52 
NDA C3D H3D  SING N N 53 
NDA O3D HO3N SING N N 54 
NDA C2D O2D  SING N N 55 
NDA C2D C1D  SING N N 56 
NDA C2D H2D  SING N N 57 
NDA O2D HO2N SING N N 58 
NDA C1D N1N  SING N N 59 
NDA C1D H1D  SING N N 60 
NDA N1N C2N  SING Y N 61 
NDA N1N C6N  DOUB Y N 62 
NDA C2N C3N  DOUB Y N 63 
NDA C2N H2N  SING N N 64 
NDA C3N C7N  SING N N 65 
NDA C3N C4N  SING Y N 66 
NDA C7N N7N  SING N N 67 
NDA C7N HC71 SING N N 68 
NDA C7N HC72 SING N N 69 
NDA N7N H71N SING N N 70 
NDA N7N H72N SING N N 71 
NDA C4N C5N  DOUB Y N 72 
NDA C4N H4N  SING N N 73 
NDA C5N C6N  SING Y N 74 
NDA C5N H5N  SING N N 75 
NDA C6N H6N  SING N N 76 
# 
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 
NDA SMILES_CANONICAL CACTVS               3.341 "NCc1ccc[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(N)ncnc45)[C@@H](O)[C@H]2O" 
NDA SMILES           CACTVS               3.341 "NCc1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O" 
NDA 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)n4cnc5c4ncnc5N)O)O)O)O)CN" 
NDA SMILES           "OpenEye OEToolkits" 1.5.0 "c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)CN" 
NDA InChI            InChI                1.03  
;InChI=1S/C21H29N7O13P2/c22-4-10-2-1-3-27(5-10)20-16(31)14(29)11(39-20)6-37-42(33,34)41-43(35,36)38-7-12-15(30)17(32)21(40-12)28-9-26-13-18(23)24-8-25-19(13)28/h1-3,5,8-9,11-12,14-17,20-21,29-32H,4,6-7,22H2,(H3-,23,24,25,33,34,35,36)/t11-,12-,14-,15-,16-,17-,20-,21-/m1/s1
;
NDA InChIKey         InChI                1.03  HMCRLFVYYFBZEZ-PLEFRAQWSA-N 
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
NDA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-[3-(aminomethyl)pyridin-1-ium-1-yl]-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 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 
NDA "Create component"  2000-02-03 RCSB 
NDA "Modify descriptor" 2011-06-04 RCSB 
# 
