data_NMT
# 
_chem_comp.id                                    NMT 
_chem_comp.name                                  "1-(O2-(METHYLCARBAMOYL)-O5-HYDROXYPHOSPHINYL-BETA-D-RIBOFURANOSYL)THYMINE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H20 N3 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2004-11-22 
_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                        397.275 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     NMT 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1XUW 
_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 
NMT P      P      P 0 1 N N N 16.777 16.674 7.656  2.787  0.324  -4.407 P      NMT 1  
NMT OP3    O3P    O 0 1 N Y N 17.984 15.953 7.255  1.198  0.588  -4.548 OP3    NMT 2  
NMT OP2    O2P    O 0 1 N N N 16.842 18.013 8.292  2.921  -1.270 -4.647 OP2    NMT 3  
NMT "O5'"  O5*    O 0 1 N N N 15.767 16.902 6.424  3.063  0.476  -2.819 "O5'"  NMT 4  
NMT N1     N1     N 0 1 N N N 12.293 18.488 5.568  0.452  2.524  0.177  N1     NMT 5  
NMT C6     C6     C 0 1 N N N 13.107 18.762 6.629  0.309  2.663  -1.199 C6     NMT 6  
NMT C2     C2     C 0 1 N N N 11.195 19.263 5.312  -0.300 3.336  1.055  C2     NMT 7  
NMT O2     O2     O 0 1 N N N 10.432 19.056 4.366  -0.225 3.269  2.283  O2     NMT 8  
NMT N3     N3     N 0 1 N N N 11.004 20.296 6.211  -1.159 4.248  0.431  N3     NMT 9  
NMT C4     C4     C 0 1 N N N 11.797 20.620 7.311  -1.338 4.427  -0.932 C4     NMT 10 
NMT O4     O4     O 0 1 N N N 11.476 21.575 7.987  -2.112 5.251  -1.413 O4     NMT 11 
NMT C5     C5     C 0 1 N N N 12.939 19.749 7.500  -0.514 3.537  -1.792 C5     NMT 12 
NMT C5M    C5M    C 0 1 N N N 13.833 20.047 8.675  -0.651 3.669  -3.275 C5M    NMT 13 
NMT "C2'"  C2*    C 0 1 N N R 13.218 17.774 3.392  0.748  0.163  0.786  "C2'"  NMT 14 
NMT "C5'"  C5*    C 0 1 N N N 15.566 15.836 5.507  2.282  -0.292 -1.921 "C5'"  NMT 15 
NMT "C4'"  C4*    C 0 1 N N R 14.503 16.172 4.557  2.725  0.023  -0.498 "C4'"  NMT 16 
NMT "O4'"  O4*    O 0 1 N N N 13.236 16.317 5.281  2.470  1.422  -0.246 "O4'"  NMT 17 
NMT "C1'"  C1*    C 0 1 N N R 12.500 17.339 4.577  1.373  1.543  0.675  "C1'"  NMT 18 
NMT "C3'"  C3*    C 0 1 N N R 14.630 17.513 3.861  1.940  -0.742 0.560  "C3'"  NMT 19 
NMT "O3'"  O3*    O 0 1 N N N 15.594 17.409 2.830  2.742  -0.809 1.739  "O3'"  NMT 20 
NMT "O6'"  "O6'"  O 0 1 N N N 13.015 16.912 2.326  0.137  -0.058 2.041  "O6'"  NMT 21 
NMT "C7'"  "C7'"  C 0 1 N N S 11.845 16.829 1.692  -0.929 -1.020 1.984  "C7'"  NMT 22 
NMT "N8'"  "N8'"  N 0 1 N N N 11.743 15.985 0.607  -1.544 -1.171 3.305  "N8'"  NMT 23 
NMT "C9'"  "C9'"  C 0 1 N N N 10.417 15.832 -0.001 -2.057 0.089  3.824  "C9'"  NMT 24 
NMT "O7'"  "O7'"  O 0 1 N N N 10.868 17.409 2.086  -0.453 -2.263 1.469  "O7'"  NMT 25 
NMT OP1    O1P    O 0 1 N N N ?      ?      ?      3.659  1.172  -5.286 OP1    NMT 26 
NMT HOP3   3HOP   H 0 0 N N N 17.942 15.096 6.848  0.799  0.616  -5.443 HOP3   NMT 27 
NMT HOP2   2HOP   H 0 0 N N N 16.058 18.482 8.553  2.886  -1.617 -5.563 HOP2   NMT 28 
NMT H6     H6     H 0 1 N N N 13.989 18.122 6.800  0.928  1.995  -1.790 H6     NMT 29 
NMT HN3    HN3    H 0 1 N N N 10.188 20.884 6.044  -1.709 4.843  1.045  HN3    NMT 30 
NMT H71    1H5M   H 0 1 N N N 14.865 20.157 8.267  -1.057 2.748  -3.690 H71    NMT 31 
NMT H72    2H5M   H 0 1 N N N 13.692 20.876 9.407  0.324  3.866  -3.719 H72    NMT 32 
NMT H73    3H5M   H 0 1 N N N 13.896 19.107 9.271  -1.320 4.497  -3.510 H73    NMT 33 
NMT "H2'"  H2*    H 0 1 N N N 12.942 18.801 3.057  -0.000 0.004  -0.000 "H2'"  NMT 34 
NMT "H5'"  1H5*   H 0 1 N N N 15.366 14.871 6.029  1.229  -0.035 -2.051 "H5'"  NMT 35 
NMT "H5''" 2H5*   H 0 0 N N N 16.511 15.551 4.989  2.428  -1.352 -2.133 "H5''" NMT 36 
NMT "H4'"  H4*    H 0 1 N N N 14.563 15.347 3.809  3.804  -0.139 -0.410 "H4'"  NMT 37 
NMT "H1'"  H1*    H 0 1 N N N 11.518 16.953 4.217  1.754  1.910  1.633  "H1'"  NMT 38 
NMT "H3'"  H3*    H 0 1 N N N 14.994 18.361 4.487  1.675  -1.764 0.277  "H3'"  NMT 39 
NMT "HO3'" H3T    H 0 0 N Y N 16.482 17.245 3.125  3.447  -0.153 1.628  "HO3'" NMT 40 
NMT "H7'"  "H7'"  H 0 1 N N N 11.987 17.905 1.438  -1.686 -0.639 1.288  "H7'"  NMT 41 
NMT "H8'"  "H8'"  H 0 1 N N N 12.110 15.066 0.856  -2.300 -1.852 3.246  "H8'"  NMT 42 
NMT "H9'1" "1H9'" H 0 0 N N N 10.016 16.836 -0.274 -1.263 0.632  4.343  "H9'1" NMT 43 
NMT "H9'2" "2H9'" H 0 0 N N N 10.335 15.149 -0.879 -2.874 -0.096 4.527  "H9'2" NMT 44 
NMT "H9'3" "3H9'" H 0 0 N N N 9.685  15.521 0.780  -2.431 0.710  3.006  "H9'3" NMT 45 
NMT H1     H1     H 0 1 N N N 10.034 17.350 1.634  -0.157 -2.788 2.232  H1     NMT 46 
# 
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 
NMT P     OP3    SING N N 1  
NMT P     OP2    SING N N 2  
NMT P     "O5'"  SING N N 3  
NMT P     OP1    DOUB N N 4  
NMT OP3   HOP3   SING N N 5  
NMT OP2   HOP2   SING N N 6  
NMT "O5'" "C5'"  SING N N 7  
NMT N1    C6     SING N N 8  
NMT N1    C2     SING N N 9  
NMT N1    "C1'"  SING N N 10 
NMT C6    C5     DOUB N N 11 
NMT C6    H6     SING N N 12 
NMT C2    O2     DOUB N N 13 
NMT C2    N3     SING N N 14 
NMT N3    C4     SING N N 15 
NMT N3    HN3    SING N N 16 
NMT C4    O4     DOUB N N 17 
NMT C4    C5     SING N N 18 
NMT C5    C5M    SING N N 19 
NMT C5M   H71    SING N N 20 
NMT C5M   H72    SING N N 21 
NMT C5M   H73    SING N N 22 
NMT "C2'" "C1'"  SING N N 23 
NMT "C2'" "C3'"  SING N N 24 
NMT "C2'" "O6'"  SING N N 25 
NMT "C2'" "H2'"  SING N N 26 
NMT "C5'" "C4'"  SING N N 27 
NMT "C5'" "H5'"  SING N N 28 
NMT "C5'" "H5''" SING N N 29 
NMT "C4'" "O4'"  SING N N 30 
NMT "C4'" "C3'"  SING N N 31 
NMT "C4'" "H4'"  SING N N 32 
NMT "O4'" "C1'"  SING N N 33 
NMT "C1'" "H1'"  SING N N 34 
NMT "C3'" "O3'"  SING N N 35 
NMT "C3'" "H3'"  SING N N 36 
NMT "O3'" "HO3'" SING N N 37 
NMT "O6'" "C7'"  SING N N 38 
NMT "C7'" "N8'"  SING N N 39 
NMT "C7'" "O7'"  SING N N 40 
NMT "C7'" "H7'"  SING N N 41 
NMT "N8'" "C9'"  SING N N 42 
NMT "N8'" "H8'"  SING N N 43 
NMT "C9'" "H9'1" SING N N 44 
NMT "C9'" "H9'2" SING N N 45 
NMT "C9'" "H9'3" SING N N 46 
NMT "O7'" H1     SING N N 47 
# 
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 
NMT SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OC(O)NC)COP(=O)(O)O"                                                                                                                                    
NMT SMILES_CANONICAL CACTVS               3.341 "CN[C@@H](O)O[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                           
NMT SMILES           CACTVS               3.341 "CN[CH](O)O[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                   
NMT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC(NC)O"                                                                                                                
NMT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC(NC)O"                                                                                                                                  
NMT InChI            InChI                1.03  "InChI=1S/C12H20N3O10P/c1-5-3-15(11(18)14-9(5)17)10-8(25-12(19)13-2)7(16)6(24-10)4-23-26(20,21)22/h3,6-8,10,12-13,16,19H,4H2,1-2H3,(H,14,17,18)(H2,20,21,22)/t6-,7-,8-,10-,12+/m1/s1" 
NMT InChIKey         InChI                1.03  NBDRJSHPMIOFTH-REKNECKOSA-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 
NMT "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-O-[(S)-hydroxy(methylamino)methyl]-5-methyluridine 5'-(dihydrogen phosphate)
;
NMT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-4-(hydroxy-methylamino-methoxy)-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 
NMT "Create component"  2004-11-22 RCSB 
NMT "Modify descriptor" 2011-06-04 RCSB 
# 
