data_ND7
#

_chem_comp.id                                   ND7
_chem_comp.name                                 "5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H15 N6 O6 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-05-10
_chem_comp.pdbx_modified_date                   2019-05-17
_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                       346.236
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ND7
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       6OM4
_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
ND7  O1A    O1   O  0  1  N  N  N  -15.742  -5.500  -14.762  -5.162   2.116  -1.302  O1A    ND7   1  
ND7  PA     P1   P  0  1  N  N  N  -15.046  -5.189  -16.056  -4.866   1.015  -0.165  PA     ND7   2  
ND7  O2A    O2   O  0  1  N  N  N  -15.561  -5.865  -17.319  -4.789   1.679   1.156  O2A    ND7   3  
ND7  N3A    N1   N  0  1  N  N  N  -15.203  -3.505  -16.211  -6.104  -0.124  -0.150  N3A    ND7   4  
ND7  "O5'"  O3   O  0  1  N  N  N  -13.491  -5.498  -16.022  -3.467   0.283  -0.479  "O5'"  ND7   5  
ND7  "C5'"  C1   C  0  1  N  N  N  -12.751  -4.927  -14.900  -2.822  -0.594   0.447  "C5'"  ND7   6  
ND7  "C4'"  C2   C  0  1  N  N  R  -11.496  -5.824  -14.747  -1.520  -1.114  -0.165  "C4'"  ND7   7  
ND7  "C3'"  C3   C  0  1  N  N  S  -11.932  -7.186  -14.108  -0.868  -2.161   0.766  "C3'"  ND7   8  
ND7  "O3'"  O4   O  0  1  N  N  N  -11.440  -8.273  -14.791  -1.180  -3.484   0.328  "O3'"  ND7   9  
ND7  "C2'"  C4   C  0  1  N  N  R  -11.457  -6.982  -12.607   0.647  -1.889   0.633  "C2'"  ND7  10  
ND7  "O2'"  O5   O  0  1  N  N  N  -10.993  -8.267  -12.037   1.317  -3.037   0.109  "O2'"  ND7  11  
ND7  "C1'"  C5   C  0  1  N  N  R  -10.410  -6.149  -12.679   0.731  -0.711  -0.362  "C1'"  ND7  12  
ND7  "O4'"  O6   O  0  1  N  N  N  -10.693  -5.188  -13.953  -0.549  -0.050  -0.261  "O4'"  ND7  13  
ND7  N9     N2   N  0  1  Y  N  N  -10.208  -5.247  -11.581   1.809   0.204   0.021  N9     ND7  14  
ND7  C4     C6   C  0  1  Y  N  N   -9.038  -5.055  -10.911   3.134   0.084  -0.315  C4     ND7  15  
ND7  C5     C7   C  0  1  Y  N  N   -9.261  -4.114   -9.970   3.784   1.183   0.271  C5     ND7  16  
ND7  N7     N3   N  0  1  Y  N  N  -10.551  -3.716  -10.063   2.840   1.904   0.922  N7     ND7  17  
ND7  C8     C8   C  0  1  Y  N  N  -11.100  -4.398  -11.049   1.679   1.334   0.771  C8     ND7  18  
ND7  N3     N4   N  0  1  Y  N  N   -7.826  -5.632  -11.051   3.848  -0.789  -1.020  N3     ND7  19  
ND7  C2     C9   C  0  1  Y  N  N   -6.855  -5.259  -10.273   5.146  -0.628  -1.168  C2     ND7  20  
ND7  N1     N5   N  0  1  Y  N  N   -7.050  -4.342   -9.319   5.800   0.389  -0.637  N1     ND7  21  
ND7  C6     C10  C  0  1  Y  N  N   -8.207  -3.758   -9.155   5.171   1.311   0.083  C6     ND7  22  
ND7  N6     N6   N  0  1  N  N  N   -8.392  -2.766   -8.111   5.865   2.374   0.636  N6     ND7  23  
ND7  H1     H1   H  0  1  N  N  N  -16.450  -6.113  -14.922  -5.991   2.598  -1.176  H1     ND7  24  
ND7  H2     H2   H  0  1  N  N  N  -14.865  -3.060  -15.382  -6.177  -0.591  -1.041  H2     ND7  25  
ND7  H3     H3   H  0  1  N  N  N  -14.671  -3.192  -16.998  -5.975  -0.789   0.598  H3     ND7  26  
ND7  H4     H4   H  0  1  N  N  N  -12.460  -3.889  -15.118  -2.600  -0.052   1.366  H4     ND7  27  
ND7  H5     H5   H  0  1  N  N  N  -13.358  -4.953  -13.983  -3.480  -1.434   0.671  H5     ND7  28  
ND7  H6     H6   H  0  1  N  N  N  -11.063  -6.015  -15.740  -1.710  -1.547  -1.148  H6     ND7  29  
ND7  H7     H7   H  0  1  N  N  N  -13.032  -7.211  -14.102  -1.195  -2.011   1.795  H7     ND7  30  
ND7  H8     H8   H  0  1  N  N  N  -11.730  -9.072  -14.367  -0.796  -4.181   0.877  H8     ND7  31  
ND7  H9     H9   H  0  1  N  N  N  -12.290  -6.574  -12.016   1.070  -1.608   1.598  H9     ND7  32  
ND7  H10    H10  H  0  1  N  N  N  -10.712  -8.133  -11.140   1.244  -3.824   0.667  H10    ND7  33  
ND7  H11    H11  H  0  1  N  N  N   -9.479  -6.698  -12.883   0.891  -1.081  -1.375  H11    ND7  34  
ND7  H12    H12  H  0  1  N  N  N  -12.122  -4.289  -11.381   0.751   1.702   1.183  H12    ND7  35  
ND7  H13    H13  H  0  1  N  N  N   -5.875  -5.696  -10.398   5.697  -1.355  -1.747  H13    ND7  36  
ND7  H14    H14  H  0  1  N  N  N   -7.536  -2.647   -7.608   5.394   3.040   1.160  H14    ND7  37  
ND7  H15    H15  H  0  1  N  N  N   -8.660  -1.895   -8.523   6.822   2.451   0.499  H15    ND7  38  
#   #
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
ND7  O2A    PA     DOUB  N  N   1  
ND7  N3A    PA     SING  N  N   2  
ND7  PA     "O5'"  SING  N  N   3  
ND7  PA     O1A    SING  N  N   4  
ND7  "O5'"  "C5'"  SING  N  N   5  
ND7  "C5'"  "C4'"  SING  N  N   6  
ND7  "O3'"  "C3'"  SING  N  N   7  
ND7  "C4'"  "C3'"  SING  N  N   8  
ND7  "C4'"  "O4'"  SING  N  N   9  
ND7  "C3'"  "C2'"  SING  N  N  10  
ND7  "O4'"  "C1'"  SING  N  N  11  
ND7  "C1'"  "C2'"  SING  N  N  12  
ND7  "C1'"  N9     SING  N  N  13  
ND7  "C2'"  "O2'"  SING  N  N  14  
ND7  N9     C8     SING  Y  N  15  
ND7  N9     C4     SING  Y  N  16  
ND7  N3     C4     DOUB  Y  N  17  
ND7  N3     C2     SING  Y  N  18  
ND7  C8     N7     DOUB  Y  N  19  
ND7  C4     C5     SING  Y  N  20  
ND7  C2     N1     DOUB  Y  N  21  
ND7  N7     C5     SING  Y  N  22  
ND7  C5     C6     DOUB  Y  N  23  
ND7  N1     C6     SING  Y  N  24  
ND7  C6     N6     SING  N  N  25  
ND7  O1A    H1     SING  N  N  26  
ND7  N3A    H2     SING  N  N  27  
ND7  N3A    H3     SING  N  N  28  
ND7  "C5'"  H4     SING  N  N  29  
ND7  "C5'"  H5     SING  N  N  30  
ND7  "C4'"  H6     SING  N  N  31  
ND7  "C3'"  H7     SING  N  N  32  
ND7  "O3'"  H8     SING  N  N  33  
ND7  "C2'"  H9     SING  N  N  34  
ND7  "O2'"  H10    SING  N  N  35  
ND7  "C1'"  H11    SING  N  N  36  
ND7  C8     H12    SING  N  N  37  
ND7  C2     H13    SING  N  N  38  
ND7  N6     H14    SING  N  N  39  
ND7  N6     H15    SING  N  N  40  
#   #
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
ND7  SMILES            ACDLabs               12.01  "OP(OCC3C(C(O)C(n1cnc2c1ncnc2N)O3)O)(=O)N"  
ND7  InChI             InChI                 1.03   "InChI=1S/C10H15N6O6P/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(22-10)1-21-23(12,19)20/h2-4,6-7,10,17-18H,1H2,(H2,11,13,14)(H3,12,19,20)/t4-,6-,7-,10-/m1/s1"  
ND7  InChIKey          InChI                 1.03   LDEMREUBLBGZBO-KQYNXXCUSA-N  
ND7  SMILES_CANONICAL  CACTVS                3.385  "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](N)(O)=O)[C@@H](O)[C@H]3O"  
ND7  SMILES            CACTVS                3.385  "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](N)(O)=O)[CH](O)[CH]3O"  
ND7  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N)O)O)O)N"  
ND7  SMILES            "OpenEye OEToolkits"  2.0.7  "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(N)O)O)O)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
ND7  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine"  
ND7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphonamidic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ND7  "Create component"  2019-05-10  RCSB  
ND7  "Initial release"   2019-05-22  RCSB  
##
