data_NYM
#

_chem_comp.id                                   NYM
_chem_comp.name                                 "3'-DEOXY-3'-AMINOTHYMIDINE MONOPHOSPHATE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "PHOSPHORIC ACID MONO-[3-AMINO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2003-01-15
_chem_comp.pdbx_modified_date                   2021-03-13
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        T37
_chem_comp.formula_weight                       321.224
_chem_comp.one_letter_code                      N
_chem_comp.three_letter_code                    NYM
_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       1NMZ
_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
NYM  N1      N1    N  0  1  N  N  N  13.411  77.709  24.069   2.302  -0.342  -0.391  N1      NYM   1  
NYM  C6      C6    C  0  1  N  N  N  12.696  76.830  23.319   3.408  -0.195  -1.184  C6      NYM   2  
NYM  C2      C2    C  0  1  N  N  N  13.808  79.004  23.630   2.249   0.232   0.825  C2      NYM   3  
NYM  O2      O2    O  0  1  N  N  N  14.484  79.727  24.367   1.257   0.087   1.513  O2      NYM   4  
NYM  N3      N3    N  0  1  N  N  N  13.336  79.377  22.417   3.279   0.964   1.290  N3      NYM   5  
NYM  C4      C4    C  0  1  N  N  N  12.575  78.536  21.592   4.388   1.129   0.541  C4      NYM   6  
NYM  O4      O4    O  0  1  N  N  N  12.240  79.043  20.399   5.320   1.791   0.961  O4      NYM   7  
NYM  C5      C5    C  0  1  N  N  N  12.241  77.175  22.107   4.455   0.535  -0.742  C5      NYM   8  
NYM  C7      C7    C  0  1  N  N  N  11.395  76.340  21.134   5.681   0.708  -1.601  C7      NYM   9  
NYM  "O4'"   O4*   O  0  1  N  N  N  14.642  76.069  25.048  -0.042  -0.359  -0.780  "O4'"   NYM  10  
NYM  "N3'"   N3*   N  0  1  N  N  N  14.220  76.133  28.361  -1.142  -3.544   0.572  "N3'"   NYM  11  
NYM  "C1'"   C1*   C  0  1  N  N  R  13.969  77.201  25.374   1.166  -1.133  -0.870  "C1'"   NYM  12  
NYM  "C2'"   C2*   C  0  1  N  N  N  12.916  76.698  26.381   0.983  -2.379   0.019  "C2'"   NYM  13  
NYM  "C3'"   C3*   C  0  1  N  N  S  13.594  75.540  27.101  -0.459  -2.244   0.568  "C3'"   NYM  14  
NYM  "C4'"   C4*   C  0  1  N  N  S  14.787  75.246  26.192  -1.108  -1.280  -0.457  "C4'"   NYM  15  
NYM  "O5'"   O5*   O  0  1  N  N  N  13.498  73.264  25.851  -2.942   0.250  -0.824  "O5'"   NYM  16  
NYM  "C5'"   C5*   C  0  1  N  N  N  14.888  73.703  25.935  -2.291  -0.542   0.172  "C5'"   NYM  17  
NYM  P1      P1    P  0  1  N  N  N  13.018  71.741  26.106  -4.170   0.995  -0.096  P1      NYM  18  
NYM  OP2     OP2   O  0  1  N  N  N  13.627  71.047  27.280  -4.871   2.010  -1.131  OP2     NYM  19  
NYM  OP1     OP1   O  0  1  N  N  N  11.587  71.814  25.809  -3.666   1.752   1.072  OP1     NYM  20  
NYM  OP3     OP3   O  0  1  N  N  N  14.039  71.077  24.986  -5.245  -0.098   0.395  OP3     NYM  21  
NYM  HC61    1HC6  H  0  0  N  N  N  12.481  75.817  23.701   3.442  -0.659  -2.158  HC61    NYM  22  
NYM  HN31    1HN3  H  0  0  N  N  N  13.561  80.324  22.114   3.224   1.371   2.169  HN31    NYM  23  
NYM  HC71    1HC7  H  0  0  N  N  N  11.016  76.627  20.125   5.565   1.594  -2.225  HC71    NYM  24  
NYM  HC72    2HC7  H  0  0  N  N  N  11.960  75.390  20.983   6.557   0.825  -0.963  HC72    NYM  25  
NYM  HC73    3HC7  H  0  0  N  N  N  10.496  76.023  21.713   5.807  -0.170  -2.235  HC73    NYM  26  
NYM  "H3'1"  1H3*  H  0  0  N  N  N  14.674  75.357  28.843  -0.613  -4.148   1.183  "H3'1"  NYM  27  
NYM  "H3'2"  2H3*  H  0  0  N  N  N  13.555  76.640  28.944  -2.038  -3.400   1.011  "H3'2"  NYM  28  
NYM  "H1'1"  1H1*  H  0  0  N  N  N  14.537  78.041  25.835   1.335  -1.437  -1.903  "H1'1"  NYM  29  
NYM  "H2'1"  1H2*  H  0  0  N  N  N  12.524  77.489  27.062   1.082  -3.288  -0.573  "H2'1"  NYM  30  
NYM  "H2'2"  2H2*  H  0  0  N  N  N  11.935  76.434  25.919   1.704  -2.374   0.836  "H2'2"  NYM  31  
NYM  HC31    1HC3  H  0  0  N  N  N  12.921  74.677  27.319  -0.455  -1.806   1.566  HC31    NYM  32  
NYM  "H4'1"  1H4*  H  0  0  N  N  N  15.773  75.500  26.645  -1.425  -1.823  -1.347  "H4'1"  NYM  33  
NYM  "H5'1"  1H5*  H  0  0  N  N  N  15.509  73.425  25.051  -2.997  -1.266   0.578  "H5'1"  NYM  34  
NYM  "H5'2"  2H5*  H  0  0  N  N  N  15.497  73.152  26.689  -1.932   0.104   0.973  "H5'2"  NYM  35  
NYM  HP31    1HP3  H  0  0  N  N  N  13.345  70.152  27.429  -5.600   2.434  -0.657  HP31    NYM  36  
NYM  HP21    1HP2  H  0  0  N  N  N  13.757  70.182  25.135  -5.548  -0.567  -0.394  HP21    NYM  37  
#   #
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
NYM  N1     C6      SING  N  N   1  
NYM  N1     C2      SING  N  N   2  
NYM  N1     "C1'"   SING  N  N   3  
NYM  C6     C5      DOUB  N  N   4  
NYM  C6     HC61    SING  N  N   5  
NYM  C2     O2      DOUB  N  N   6  
NYM  C2     N3      SING  N  N   7  
NYM  N3     C4      SING  N  N   8  
NYM  N3     HN31    SING  N  N   9  
NYM  C4     O4      DOUB  N  N  10  
NYM  C4     C5      SING  N  N  11  
NYM  C5     C7      SING  N  N  12  
NYM  C7     HC71    SING  N  N  13  
NYM  C7     HC72    SING  N  N  14  
NYM  C7     HC73    SING  N  N  15  
NYM  "O4'"  "C1'"   SING  N  N  16  
NYM  "O4'"  "C4'"   SING  N  N  17  
NYM  "N3'"  "C3'"   SING  N  N  18  
NYM  "N3'"  "H3'1"  SING  N  N  19  
NYM  "N3'"  "H3'2"  SING  N  N  20  
NYM  "C1'"  "C2'"   SING  N  N  21  
NYM  "C1'"  "H1'1"  SING  N  N  22  
NYM  "C2'"  "C3'"   SING  N  N  23  
NYM  "C2'"  "H2'1"  SING  N  N  24  
NYM  "C2'"  "H2'2"  SING  N  N  25  
NYM  "C3'"  "C4'"   SING  N  N  26  
NYM  "C3'"  HC31    SING  N  N  27  
NYM  "C4'"  "C5'"   SING  N  N  28  
NYM  "C4'"  "H4'1"  SING  N  N  29  
NYM  "O5'"  "C5'"   SING  N  N  30  
NYM  "O5'"  P1      SING  N  N  31  
NYM  "C5'"  "H5'1"  SING  N  N  32  
NYM  "C5'"  "H5'2"  SING  N  N  33  
NYM  P1     OP2     SING  N  N  34  
NYM  P1     OP1     DOUB  N  N  35  
NYM  P1     OP3     SING  N  N  36  
NYM  OP2    HP31    SING  N  N  37  
NYM  OP3    HP21    SING  N  N  38  
#   #
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
NYM  SMILES            ACDLabs               10.04  "O=C1NC(=O)N(C=C1C)C2OC(C(N)C2)COP(=O)(O)O"  
NYM  SMILES_CANONICAL  CACTVS                3.341  "CC1=CN([C@H]2C[C@H](N)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
NYM  SMILES            CACTVS                3.341  "CC1=CN([CH]2C[CH](N)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
NYM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)N"  
NYM  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)N"  
NYM  InChI             InChI                 1.03   "InChI=1S/C10H16N3O7P/c1-5-3-13(10(15)12-9(5)14)8-2-6(11)7(20-8)4-19-21(16,17)18/h3,6-8H,2,4,11H2,1H3,(H,12,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1"  
NYM  InChIKey          InChI                 1.03   BQZMHQZNZNBJNF-XLPZGREQSA-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
NYM  "SYSTEMATIC NAME"  ACDLabs               10.04  "3'-amino-3'-deoxythymidine 5'-(dihydrogen phosphate)"  
NYM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2S,3S,5R)-3-amino-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen 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
NYM  "Create component"   2003-01-15  RCSB  
NYM  "Modify descriptor"  2011-06-04  RCSB  
NYM  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     NYM
_pdbx_chem_comp_synonyms.name        "PHOSPHORIC ACID MONO-[3-AMINO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##