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                    2009-01-07 
_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 InChI            InChI                1.02b "InChI=1/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/f/h12,16-17H" 
NYM InChIKey         InChI                1.02b BQZMHQZNZNBJNF-KKSGRANYDR                                                                                                                                    
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"                                                                                                                  
# 
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" 
# 
