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               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1995-10-15 
_chem_comp.pdbx_modified_date                    2018-03-14 
_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        Corina 
_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 2.146  0.131  -0.498 N1     T41 1  
T41 C2     C2     C 0 1 N N N 1.999 -0.558 3.869 2.179  0.508  0.793  C2     T41 2  
T41 N3     N3     N 0 1 N N N 1.635 -0.550 2.531 3.214  1.217  1.281  N3     T41 3  
T41 C4     C4     C 0 1 N N N 2.434 -0.904 1.457 4.240  1.561  0.478  C4     T41 4  
T41 C5     C5     C 0 1 N N N 3.763 -1.335 1.835 4.219  1.171  -0.883 C5     T41 5  
T41 C5M    C5M    C 0 1 N N N 4.743 -1.802 0.787 5.354  1.543  -1.802 C5M    T41 6  
T41 C6     C6     C 0 1 N N N 4.141 -1.344 3.131 3.168  0.461  -1.346 C6     T41 7  
T41 O2     O2     O 0 1 N N N 1.193 -0.223 4.733 1.260  0.204  1.530  O2     T41 8  
T41 O4     O4     O 0 1 N N N 1.998 -0.837 0.311 5.177  2.203  0.919  O4     T41 9  
T41 "C1'"  "C1'"  C 0 1 N N R 3.768 -0.931 5.560 1.009  -0.644 -0.999 "C1'"  T41 10 
T41 "C2'"  "C2'"  C 0 1 N N S 4.242 -2.213 6.170 0.960  -2.030 -0.317 "C2'"  T41 11 
T41 "O2'"  "O2'"  O 0 1 N N N 5.108 -2.927 5.341 1.626  -1.989 0.947  "O2'"  T41 12 
T41 "C3'"  "C3'"  C 0 1 N N R 5.025 -1.741 7.386 -0.549 -2.301 -0.126 "C3'"  T41 13 
T41 "C4'"  "C4'"  C 0 1 N N R 5.520 -0.359 6.930 -1.233 -1.048 -0.715 "C4'"  T41 14 
T41 "O3'"  "O3'"  O 0 1 N N N 4.217 -1.546 8.537 -0.942 -3.471 -0.846 "O3'"  T41 15 
T41 "O4'"  "O4'"  O 0 1 N N N 4.820 -0.007 5.743 -0.235 -0.008 -0.631 "O4'"  T41 16 
T41 "C5'"  "C5'"  C 0 1 N N N 7.021 -0.314 6.617 -2.463 -0.674 0.115  "C5'"  T41 17 
T41 "O5'"  "O5'"  O 0 1 N N N 7.382 -1.246 5.616 -3.147 0.414  -0.511 "O5'"  T41 18 
T41 "C6'"  "C6'"  C 0 1 N N N 4.707 -4.254 5.404 2.223  -3.230 1.329  "C6'"  T41 19 
T41 P      P      P 0 1 N N N 8.853 -1.233 4.945 -4.489 1.069  0.091  P      T41 20 
T41 O1P    O1P    O 0 1 N N N 9.846 -1.426 6.024 -4.247 1.495  1.487  O1P    T41 21 
T41 O2P    O2P    O 0 1 N N N 8.836 -2.153 3.787 -4.907 2.346  -0.796 O2P    T41 22 
T41 O3P    O3P    O 0 1 N Y N 9.004 0.284  4.394 -5.676 -0.018 0.060  O3P    T41 23 
T41 H3     H3     H 0 1 N N N 0.702 -0.259 2.321 3.221  1.481  2.215  H3     T41 24 
T41 H5M1   H5M1   H 0 0 N N N 5.690 -2.085 1.270 6.100  2.111  -1.246 H5M1   T41 25 
T41 H5M2   H5M2   H 0 0 N N N 4.327 -2.672 0.258 5.809  0.637  -2.202 H5M2   T41 26 
T41 H5M3   H5M3   H 0 0 N N N 4.926 -0.989 0.069 4.972  2.151  -2.622 H5M3   T41 27 
T41 H6     H6     H 0 1 N N N 5.143 -1.665 3.377 3.134  0.155  -2.381 H6     T41 28 
T41 "H1'"  "H1'"  H 0 1 N N N 2.916 -0.590 6.166 1.074  -0.756 -2.081 "H1'"  T41 29 
T41 "H2'1" "H2'1" H 0 0 N N N 3.385 -2.824 6.489 1.409  -2.787 -0.960 "H2'1" T41 30 
T41 "H3'"  "H3'"  H 0 1 N N N 5.877 -2.409 7.583 -0.787 -2.405 0.933  "H3'"  T41 31 
T41 "H4'"  "H4'"  H 0 1 N N N 5.306 0.370  7.726 -1.514 -1.222 -1.754 "H4'"  T41 32 
T41 HA     HA     H 0 1 N N N 4.760 -1.253 9.260 -1.880 -3.689 -0.761 HA     T41 33 
T41 "H5'1" "H5'1" H 0 0 N N N 7.281 0.697  6.271 -3.131 -1.532 0.182  "H5'1" T41 34 
T41 "H5'2" "H5'2" H 0 0 N N N 7.582 -0.544 7.535 -2.149 -0.378 1.116  "H5'2" T41 35 
T41 H11    H11    H 0 1 N N N 5.360 -4.866 4.764 1.454  -3.999 1.395  H11    T41 36 
T41 H12    H12    H 0 1 N N N 4.775 -4.609 6.443 2.964  -3.521 0.584  H12    T41 37 
T41 H13    H13    H 0 1 N N N 3.667 -4.340 5.055 2.708  -3.116 2.299  H13    T41 38 
T41 H2P    H2P    H 0 1 N N N 9.520 -2.805 3.890 -5.710 2.791  -0.490 H2P    T41 39 
T41 H3P    H3P    H 0 1 N N N 9.692 0.729  4.874 -5.890 -0.343 -0.825 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              12.01 "N1(C(NC(C(C)=C1)=O)=O)C2C(OC)C(C(O2)COP(=O)(O)O)O"                                                                                                            
T41 InChI            InChI                1.03  "InChI=1S/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" 
T41 InChIKey         InChI                1.03  AMKCISYJIZUJJQ-BDNRQGISSA-N                                                                                                                                    
T41 SMILES_CANONICAL CACTVS               3.385 "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               3.385 "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" 1.7.6 "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" 1.7.6 "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              12.01 "5-methyl-1-(2-O-methyl-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione"                                      
T41 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4S,5R)-4-methoxy-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-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 
T41 "Create component"      1995-10-15 PDBJ 
T41 "Modify descriptor"     2011-06-04 RCSB 
T41 "Modify parent residue" 2018-03-14 RCSB 
# 
