data_T39
# 
_chem_comp.id                                    T39 
_chem_comp.name                                  
;2'-O-METHOXYETHYLENE THYMIDINE 5'-MONOPHOSPHATE
;
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H21 N2 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               T 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1998-07-29 
_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                        396.287 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     T39 
_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        411D 
_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 
T39 P      P    P 0 1 N N N -4.559 6.080 7.621  0.199  0.170  -4.983 P      T39 1  
T39 O1P    O1P  O 0 1 N N N -5.756 6.865 7.275  0.642  1.539  -4.633 O1P    T39 2  
T39 O2P    O2P  O 0 1 N N N -4.719 4.826 8.388  1.256  -0.491 -6.001 O2P    T39 3  
T39 O3P    O3P  O 0 1 N Y N -3.667 7.084 8.485  -1.249 0.237  -5.682 O3P    T39 4  
T39 "O5'"  O5*  O 0 1 N N N -3.686 5.796 6.315  0.109  -0.722 -3.646 "O5'"  T39 5  
T39 "C5'"  C5*  C 0 1 N N N -3.385 6.839 5.374  -0.838 -0.086 -2.788 "C5'"  T39 6  
T39 "C4'"  C4*  C 0 1 N N R -2.338 6.393 4.391  -0.972 -0.888 -1.492 "C4'"  T39 7  
T39 "O4'"  O4*  O 0 1 N N N -1.089 6.154 5.094  0.287  -0.917 -0.799 "O4'"  T39 8  
T39 "C3'"  C3*  C 0 1 N N R -2.591 5.077 3.659  -1.993 -0.210 -0.558 "C3'"  T39 9  
T39 "O3'"  O3*  O 0 1 N N N -3.489 5.187 2.560  -3.082 -1.092 -0.279 "O3'"  T39 10 
T39 "C2'"  C2*  C 0 1 N N R -1.195 4.716 3.194  -1.190 0.083  0.732  "C2'"  T39 11 
T39 "O2'"  O2*  O 0 1 N N N -0.823 5.499 2.077  -1.975 -0.191 1.894  "O2'"  T39 12 
T39 "C1'"  C1*  C 0 1 N N R -0.383 5.106 4.435  -0.008 -0.911 0.614  "C1'"  T39 13 
T39 N1     N1   N 0 1 N N N -0.202 3.962 5.361  1.147  -0.440 1.380  N1     T39 14 
T39 C2     C2   C 0 1 N N N 0.885  3.135 5.134  1.657  0.780  1.134  C2     T39 15 
T39 O2     O2   O 0 1 N N N 1.671  3.278 4.215  1.149  1.481  0.281  O2     T39 16 
T39 N3     N3   N 0 1 N N N 1.020  2.113 6.022  2.715  1.240  1.827  N3     T39 17 
T39 C4     C4   C 0 1 N N N 0.200  1.824 7.089  3.290  0.475  2.777  C4     T39 18 
T39 O4     O4   O 0 1 N N N 0.467  0.862 7.799  4.251  0.889  3.401  O4     T39 19 
T39 C5     C5   C 0 1 N N N -0.924 2.713 7.270  2.767  -0.812 3.043  C5     T39 20 
T39 C5M    C5M  C 0 1 N N N -1.876 2.466 8.406  3.391  -1.687 4.099  C5M    T39 21 
T39 C6     C6   C 0 1 N N N -1.069 3.733 6.415  1.701  -1.247 2.336  C6     T39 22 
T39 "CA'"  CA*  C 0 1 N N N 0.493  5.193 1.578  -2.582 1.041  2.284  "CA'"  T39 23 
T39 "CD'"  CD*  C 0 1 N N N 0.035  7.582 -0.306 -3.474 0.142  5.723  "CD'"  T39 24 
T39 "CB'"  CB*  C 0 1 N N N 1.293  6.397 1.442  -3.441 0.815  3.529  "CB'"  T39 25 
T39 "OC'"  OC*  O 0 1 N N N 0.497  7.548 1.068  -2.619 0.332  4.594  "OC'"  T39 26 
T39 H2P    H2P  H 0 1 N N N -3.946 4.319 8.611  1.279  0.072  -6.786 H2P    T39 27 
T39 H3P    H3P  H 0 1 N N N -2.894 6.577 8.708  -1.500 -0.671 -5.893 H3P    T39 28 
T39 "H5'1" 1H5* H 0 0 N N N -3.091 7.784 5.888  -1.806 -0.038 -3.287 "H5'1" T39 29 
T39 "H5'2" 2H5* H 0 0 N N N -4.303 7.205 4.859  -0.499 0.923  -2.556 "H5'2" T39 30 
T39 "H4'"  H4*  H 0 1 N N N -2.181 7.201 3.639  -1.294 -1.905 -1.717 "H4'"  T39 31 
T39 "H3'"  H3*  H 0 1 N N N -2.962 4.309 4.377  -2.357 0.716  -1.000 "H3'"  T39 32 
T39 HA     HA   H 0 1 N N N -3.646 4.368 2.105  -3.544 -1.239 -1.116 HA     T39 33 
T39 "H2'"  H2*  H 0 1 N N N -1.107 3.626 2.975  -0.832 1.113  0.741  "H2'"  T39 34 
T39 "H1'"  H1*  H 0 1 N N N 0.617  5.482 4.116  -0.309 -1.905 0.947  "H1'"  T39 35 
T39 H3     H3   H 0 1 N N N 1.817  1.492 5.881  3.068  2.124  1.640  H3     T39 36 
T39 H5M1   1H5M H 0 0 N N N -1.755 1.617 9.118  4.232  -1.164 4.554  H5M1   T39 37 
T39 H5M2   2H5M H 0 0 N N N -2.902 2.400 7.976  2.650  -1.918 4.864  H5M2   T39 38 
T39 H5M3   3H5M H 0 0 N N N -1.931 3.403 9.008  3.743  -2.613 3.643  H5M3   T39 39 
T39 H6     H6   H 0 1 N N N -1.918 4.422 6.557  1.288  -2.227 2.525  H6     T39 40 
T39 "HA'1" 1HA* H 0 0 N N N 0.447  4.620 0.622  -3.210 1.409  1.472  "HA'1" T39 41 
T39 "HA'2" 2HA* H 0 0 N N N 1.004  4.429 2.209  -1.807 1.774  2.505  "HA'2" T39 42 
T39 "HD'1" 1HD* H 0 0 N N N -0.578 8.468 -0.594 -2.888 -0.227 6.564  "HD'1" T39 43 
T39 "HD'2" 2HD* H 0 0 N N N -0.521 6.645 -0.541 -3.937 1.091  5.992  "HD'2" T39 44 
T39 "HD'3" 3HD* H 0 0 N N N 0.902  7.480 -0.999 -4.249 -0.582 5.473  "HD'3" T39 45 
T39 "HB'1" 1HB* H 0 0 N N N 2.136  6.242 0.729  -4.217 0.082  3.308  "HB'1" T39 46 
T39 "HB'2" 2HB* H 0 0 N N N 1.879  6.597 2.369  -3.905 1.756  3.827  "HB'2" T39 47 
# 
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 
T39 P     O1P    DOUB N N 1  
T39 P     O2P    SING N N 2  
T39 P     O3P    SING N N 3  
T39 P     "O5'"  SING N N 4  
T39 O2P   H2P    SING N N 5  
T39 O3P   H3P    SING N N 6  
T39 "O5'" "C5'"  SING N N 7  
T39 "C5'" "C4'"  SING N N 8  
T39 "C5'" "H5'1" SING N N 9  
T39 "C5'" "H5'2" SING N N 10 
T39 "C4'" "O4'"  SING N N 11 
T39 "C4'" "C3'"  SING N N 12 
T39 "C4'" "H4'"  SING N N 13 
T39 "O4'" "C1'"  SING N N 14 
T39 "C3'" "O3'"  SING N N 15 
T39 "C3'" "C2'"  SING N N 16 
T39 "C3'" "H3'"  SING N N 17 
T39 "O3'" HA     SING N N 18 
T39 "C2'" "O2'"  SING N N 19 
T39 "C2'" "C1'"  SING N N 20 
T39 "C2'" "H2'"  SING N N 21 
T39 "O2'" "CA'"  SING N N 22 
T39 "C1'" N1     SING N N 23 
T39 "C1'" "H1'"  SING N N 24 
T39 N1    C2     SING N N 25 
T39 N1    C6     SING N N 26 
T39 C2    O2     DOUB N N 27 
T39 C2    N3     SING N N 28 
T39 N3    C4     SING N N 29 
T39 N3    H3     SING N N 30 
T39 C4    O4     DOUB N N 31 
T39 C4    C5     SING N N 32 
T39 C5    C5M    SING N N 33 
T39 C5    C6     DOUB N N 34 
T39 C5M   H5M1   SING N N 35 
T39 C5M   H5M2   SING N N 36 
T39 C5M   H5M3   SING N N 37 
T39 C6    H6     SING N N 38 
T39 "CA'" "CB'"  SING N N 39 
T39 "CA'" "HA'1" SING N N 40 
T39 "CA'" "HA'2" SING N N 41 
T39 "CD'" "OC'"  SING N N 42 
T39 "CD'" "HD'1" SING N N 43 
T39 "CD'" "HD'2" SING N N 44 
T39 "CD'" "HD'3" SING N N 45 
T39 "CB'" "OC'"  SING N N 46 
T39 "CB'" "HB'1" SING N N 47 
T39 "CB'" "HB'2" SING N N 48 
# 
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 
T39 SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCOC)COP(=O)(O)O"                                                                                                                                           
T39 InChI            InChI                1.02b "InChI=1/C13H21N2O10P/c1-7-5-15(13(18)14-11(7)17)12-10(23-4-3-22-2)9(16)8(25-12)6-24-26(19,20)21/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1/f/h14,19-20H" 
T39 InChIKey         InChI                1.02b BLSQXXFKLSKRRX-IHXBBRRKDL                                                                                                                                                                  
T39 SMILES_CANONICAL CACTVS               3.341 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                                       
T39 SMILES           CACTVS               3.341 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                             
T39 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)OCCOC"                                                                                                                       
T39 SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOC"                                                                                                                                         
# 
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 
T39 "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-O-(2-methoxyethyl)-5-methyluridine 5'-(dihydrogen phosphate)
;
T39 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-4-(2-methoxyethoxy)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
