data_T41
# 
_chem_comp.id                                    T41 
_chem_comp.name                                  
;1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE 5'-MONOPHOSPHATE
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               T 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1995-10-15 
_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                         ? 
_chem_comp.formula_weight                        352.234 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     T41 
_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        214D 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
T41 N1     N1   N 0 1 N N N 3.304 -0.962 4.148  -0.016 0.557  2.137  N1     T41 1  
T41 C2     C2   C 0 1 N N N 1.999 -0.558 3.869  0.249  1.086  3.345  C2     T41 2  
T41 N3     N3   N 0 1 N N N 1.635 -0.550 2.531  -0.540 0.827  4.403  N3     T41 3  
T41 C4     C4   C 0 1 N N N 2.434 -0.904 1.457  -1.611 0.019  4.270  C4     T41 4  
T41 C5     C5   C 0 1 N N N 3.763 -1.335 1.835  -1.899 -0.548 3.006  C5     T41 5  
T41 C5M    C5M  C 0 1 N N N 4.743 -1.802 0.787  -3.090 -1.455 2.830  C5M    T41 6  
T41 C6     C6   C 0 1 N N N 4.141 -1.344 3.131  -1.093 -0.267 1.960  C6     T41 7  
T41 O2     O2   O 0 1 N N N 1.193 -0.223 4.733  1.212  1.817  3.480  O2     T41 8  
T41 O4     O4   O 0 1 N N N 1.998 -0.837 0.311  -2.323 -0.220 5.228  O4     T41 9  
T41 "C1'"  C1*  C 0 1 N N R 3.768 -0.931 5.560  0.858  0.862  1.002  "C1'"  T41 10 
T41 "C2'"  C2*  C 0 1 N N S 4.242 -2.213 6.170  2.003  -0.170 0.908  "C2'"  T41 11 
T41 "O2'"  O2*  O 0 1 N N N 5.108 -2.927 5.341  1.624  -1.396 1.537  "O2'"  T41 12 
T41 "C3'"  C3*  C 0 1 N N R 5.025 -1.741 7.386  2.200  -0.379 -0.609 "C3'"  T41 13 
T41 "C4'"  C4*  C 0 1 N N R 5.520 -0.359 6.930  1.150  0.551  -1.256 "C4'"  T41 14 
T41 "O3'"  O3*  O 0 1 N N N 4.217 -1.546 8.537  3.520  0.003  -1.000 "O3'"  T41 15 
T41 "O4'"  O4*  O 0 1 N N N 4.820 -0.007 5.743  0.135  0.721  -0.243 "O4'"  T41 16 
T41 "C5'"  C5*  C 0 1 N N N 7.021 -0.314 6.617  0.556  -0.103 -2.505 "C5'"  T41 17 
T41 "O5'"  O5*  O 0 1 N N N 7.382 -1.246 5.616  -0.411 0.772  -3.087 "O5'"  T41 18 
T41 "C6'"  C6*  C 0 1 N N N 4.707 -4.254 5.404  2.827  -2.012 2.000  "C6'"  T41 19 
T41 P      P    P 0 1 N N N 8.853 -1.233 4.945  -0.992 0.024  -4.389 P      T41 20 
T41 O1P    O1P  O 0 1 N N N 9.846 -1.426 6.024  -1.617 -1.254 -3.985 O1P    T41 21 
T41 O2P    O2P  O 0 1 N N N 8.836 -2.153 3.787  -2.094 0.960  -5.098 O2P    T41 22 
T41 O3P    O3P  O 0 1 N Y N 9.004 0.284  4.394  0.208  -0.266 -5.421 O3P    T41 23 
T41 H3     H3   H 0 1 N N N 0.691 -0.255 2.338  -0.335 1.220  5.266  H3     T41 24 
T41 H5M1   1H5M H 0 0 N N N 4.390 -2.749 0.386  -3.612 -1.559 3.782  H5M1   T41 25 
T41 H5M2   2H5M H 0 0 N N N 4.805 -1.054 -0.001 -3.766 -1.027 2.090  H5M2   T41 26 
T41 H5M3   3H5M H 0 0 N N N 5.732 -1.948 1.222  -2.754 -2.435 2.492  H5M3   T41 27 
T41 H6     H6   H 0 1 N N N 5.138 -1.667 3.353  -1.298 -0.691 0.988  H6     T41 28 
T41 "H1'"  H1*  H 0 1 N N N 2.954 -0.777 6.235  1.261  1.870  1.095  "H1'"  T41 29 
T41 "H2'1" 1H2* H 0 0 N N N 3.339 -2.769 6.411  2.912  0.224  1.361  "H2'1" T41 30 
T41 "H3'"  H3*  H 0 1 N N N 5.830 -2.453 7.580  2.009  -1.417 -0.880 "H3'"  T41 31 
T41 "H4'"  H4*  H 0 1 N N N 5.340 0.414  7.680  1.599  1.511  -1.509 "H4'"  T41 32 
T41 HA     HA   H 0 1 N N N 3.911 -2.400 8.819  3.585  -0.147 -1.953 HA     T41 33 
T41 "H5'1" 1H5* H 0 0 N N N 7.246 0.693  6.264  1.350  -0.297 -3.226 "H5'1" T41 34 
T41 "H5'2" 2H5* H 0 0 N N N 7.590 -0.510 7.527  0.076  -1.042 -2.230 "H5'2" T41 35 
T41 H11    1H1  H 0 1 N N N 5.434 -4.821 4.847  2.587  -2.956 2.490  H11    T41 36 
T41 H12    2H1  H 0 1 N N N 4.674 -4.539 6.457  3.489  -2.199 1.155  H12    T41 37 
T41 H13    3H1  H 0 1 N N N 3.714 -4.303 4.954  3.324  -1.350 2.710  H13    T41 38 
T41 H2P    H2P  H 0 1 N N N 9.700 -2.145 3.392  -2.416 0.476  -5.871 H2P    T41 39 
T41 H3P    H3P  H 0 1 N N N 9.868 0.291  3.999  0.587  0.590  -5.658 H3P    T41 40 
# 
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 
T41 N1    C2     SING N N 1  
T41 N1    C6     SING N N 2  
T41 N1    "C1'"  SING N N 3  
T41 C2    N3     SING N N 4  
T41 C2    O2     DOUB N N 5  
T41 N3    C4     SING N N 6  
T41 N3    H3     SING N N 7  
T41 C4    C5     SING N N 8  
T41 C4    O4     DOUB N N 9  
T41 C5    C5M    SING N N 10 
T41 C5    C6     DOUB N N 11 
T41 C5M   H5M1   SING N N 12 
T41 C5M   H5M2   SING N N 13 
T41 C5M   H5M3   SING N N 14 
T41 C6    H6     SING N N 15 
T41 "C1'" "C2'"  SING N N 16 
T41 "C1'" "O4'"  SING N N 17 
T41 "C1'" "H1'"  SING N N 18 
T41 "C2'" "O2'"  SING N N 19 
T41 "C2'" "C3'"  SING N N 20 
T41 "C2'" "H2'1" SING N N 21 
T41 "O2'" "C6'"  SING N N 22 
T41 "C3'" "C4'"  SING N N 23 
T41 "C3'" "O3'"  SING N N 24 
T41 "C3'" "H3'"  SING N N 25 
T41 "C4'" "O4'"  SING N N 26 
T41 "C4'" "C5'"  SING N N 27 
T41 "C4'" "H4'"  SING N N 28 
T41 "O3'" HA     SING N N 29 
T41 "C5'" "O5'"  SING N N 30 
T41 "C5'" "H5'1" SING N N 31 
T41 "C5'" "H5'2" SING N N 32 
T41 "O5'" P      SING N N 33 
T41 "C6'" H11    SING N N 34 
T41 "C6'" H12    SING N N 35 
T41 "C6'" H13    SING N N 36 
T41 P     O1P    DOUB N N 37 
T41 P     O2P    SING N N 38 
T41 P     O3P    SING N N 39 
T41 O2P   H2P    SING N N 40 
T41 O3P   H3P    SING N N 41 
# 
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 
T41 SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OC)COP(=O)(O)O"                                                                                                                              
T41 InChI            InChI                1.02b "InChI=1/C11H17N2O9P/c1-5-3-13(11(16)12-9(5)15)10-8(20-2)7(14)6(22-10)4-21-23(17,18)19/h3,6-8,10,14H,4H2,1-2H3,(H,12,15,16)(H2,17,18,19)/t6-,7-,8+,10-/m1/s1/f/h12,17-18H" 
T41 InChIKey         InChI                1.02b AMKCISYJIZUJJQ-AFERGCJVDY                                                                                                                                                  
T41 SMILES_CANONICAL CACTVS               3.341 "CO[C@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                           
T41 SMILES           CACTVS               3.341 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                
T41 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"                                                                                                           
T41 SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC"                                                                                                                            
# 
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 
T41 "SYSTEMATIC NAME" ACDLabs              10.04 "5-methyl-1-(2-O-methyl-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione"                        
T41 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4S,5R)-3-hydroxy-4-methoxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
