data_2OT
# 
_chem_comp.id                                    2OT 
_chem_comp.name                                  
;2'-O-[2-(N,N-DIMETHYLAMINOOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H24 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                     2004-12-21 
_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                        425.328 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     2OT 
_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        1YB9 
_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 
2OT P      P      P 0 1 N N N -4.388 6.442  6.972 2.787  0.324  -4.407 P      2OT 1  
2OT OP1    O1P    O 0 1 N N N -5.566 7.224  6.495 3.659  1.172  -5.286 OP1    2OT 2  
2OT OP2    O2P    O 0 1 N N N -4.598 5.174  7.651 1.198  0.588  -4.548 OP2    2OT 3  
2OT "O5'"  O5*    O 0 1 N N N -3.394 6.194  5.760 3.063  0.476  -2.819 "O5'"  2OT 4  
2OT "C5'"  C5*    C 0 1 N N N -3.050 7.257  4.865 2.282  -0.292 -1.921 "C5'"  2OT 5  
2OT "C4'"  C4*    C 0 1 N N R -2.007 6.788  3.892 2.725  0.023  -0.498 "C4'"  2OT 6  
2OT "O4'"  O4*    O 0 1 N N N -0.779 6.493  4.610 2.470  1.422  -0.246 "O4'"  2OT 7  
2OT "C1'"  C1*    C 0 1 N N R -0.101 5.410  3.970 1.373  1.543  0.675  "C1'"  2OT 8  
2OT N1     N1     N 0 1 N N N 0.045  4.298  4.948 0.452  2.524  0.177  N1     2OT 9  
2OT C6     C6     C 0 1 N N N -0.834 4.136  6.000 0.309  2.663  -1.199 C6     2OT 10 
2OT C2     C2     C 0 1 N N N 1.097  3.420  4.761 -0.300 3.336  1.055  C2     2OT 11 
2OT O2     O2     O 0 1 N N N 1.857  3.502  3.828 -0.225 3.269  2.283  O2     2OT 12 
2OT N3     N3     N 0 1 N N N 1.200  2.431  5.702 -1.159 4.248  0.431  N3     2OT 13 
2OT C4     C4     C 0 1 N N N 0.365  2.210  6.766 -1.338 4.427  -0.932 C4     2OT 14 
2OT O4     O4     O 0 1 N N N 0.581  1.274  7.528 -2.112 5.251  -1.413 O4     2OT 15 
2OT C5     C5     C 0 1 N N N -0.736 3.135  6.892 -0.514 3.537  -1.792 C5     2OT 16 
2OT C5M    C5M    C 0 1 N N N -1.713 2.924  8.002 -0.651 3.669  -3.275 C5M    2OT 17 
2OT "C2'"  C2*    C 0 1 N N R -0.938 5.011  2.754 0.748  0.163  0.786  "C2'"  2OT 18 
2OT "O2'"  O2*    O 0 1 N N N -0.434 5.818  1.665 0.137  -0.058 2.041  "O2'"  2OT 19 
2OT "CB'"  "CB'"  C 0 1 N N N 0.850  5.431  1.139 -0.332 -1.396 2.174  "CB'"  2OT 20 
2OT "CC'"  "CC'"  C 0 1 N N N 1.754  6.664  1.060 -0.951 -1.569 3.547  "CC'"  2OT 21 
2OT "OD'"  "OD'"  O 0 1 N N N 2.360  6.880  2.339 0.039  -1.320 4.537  "OD'"  2OT 22 
2OT "NE'"  "NE'"  N 0 1 N N N 3.001  8.048  2.553 -0.585 -1.494 5.845  "NE'"  2OT 23 
2OT "CF'"  "CF'"  C 0 1 N N N 4.116  7.889  3.481 -1.049 -2.878 5.852  "CF'"  2OT 24 
2OT "CG'"  "CG'"  C 0 1 N N N 2.051  9.035  3.047 0.502  -1.303 6.800  "CG'"  2OT 25 
2OT "C3'"  C3*    C 0 1 N N R -2.320 5.481  3.197 1.940  -0.742 0.560  "C3'"  2OT 26 
2OT "O3'"  O3*    O 0 1 N N N -3.277 5.608  2.155 2.742  -0.809 1.739  "O3'"  2OT 27 
2OT OP3    O3P    O 0 1 N Y N ?      ?      ?     2.921  -1.270 -4.647 OP3    2OT 28 
2OT HOP2   2HOP   H 0 0 N N N -3.848 4.676  7.955 0.799  0.616  -5.443 HOP2   2OT 29 
2OT "H5'"  1H5*   H 0 1 N N N -2.731 8.176  5.410 1.229  -0.035 -2.051 "H5'"  2OT 30 
2OT "H5''" 2H5*   H 0 0 N N N -3.945 7.676  4.349 2.428  -1.352 -2.133 "H5''" 2OT 31 
2OT "H4'"  H4*    H 0 1 N N N -1.945 7.613  3.145 3.804  -0.139 -0.410 "H4'"  2OT 32 
2OT "H1'"  H1*    H 0 1 N N N 0.923  5.688  3.627 1.754  1.910  1.633  "H1'"  2OT 33 
2OT H6     H6     H 0 1 N N N -1.664 4.849  6.136 0.928  1.995  -1.790 H6     2OT 34 
2OT HN3    HN3    H 0 1 N N N 1.985  1.788  5.599 -1.709 4.843  1.045  HN3    2OT 35 
2OT H71    1H5M   H 0 1 N N N -2.727 2.860  7.543 -1.057 2.748  -3.690 H71    2OT 36 
2OT H72    2H5M   H 0 1 N N N -1.632 2.094  8.742 0.324  3.866  -3.719 H72    2OT 37 
2OT H73    3H5M   H 0 1 N N N -1.770 3.877  8.579 -1.320 4.497  -3.510 H73    2OT 38 
2OT "H2'"  H2*    H 0 1 N N N -0.928 3.942  2.439 -0.000 0.004  -0.000 "H2'"  2OT 39 
2OT "HB'1" "1HB'" H 0 0 N N N 0.765  4.905  0.160 -1.066 -1.580 1.383  "HB'1" 2OT 40 
2OT "HB'2" "2HB'" H 0 0 N N N 1.314  4.602  1.723 0.520  -2.071 2.050  "HB'2" 2OT 41 
2OT "HC'1" "1HC'" H 0 0 N N N 1.212  7.565  0.689 -1.324 -2.588 3.686  "HC'1" 2OT 42 
2OT "HC'2" "2HC'" H 0 0 N N N 2.507  6.587  0.241 -1.768 -0.855 3.691  "HC'2" 2OT 43 
2OT "HF'1" "1HF'" H 0 0 N N N 4.820  7.095  3.138 -2.051 -2.941 5.420  "HF'1" 2OT 44 
2OT "HF'2" "2HF'" H 0 0 N N N 4.646  8.854  3.658 -1.082 -3.261 6.875  "HF'2" 2OT 45 
2OT "HF'3" "3HF'" H 0 0 N N N 3.785  7.425  4.439 -0.373 -3.506 5.264  "HF'3" 2OT 46 
2OT "HG'1" "1HG'" H 0 0 N N N 1.506  8.680  3.953 0.329  -0.399 7.390  "HG'1" 2OT 47 
2OT "HG'2" "2HG'" H 0 0 N N N 2.581  10.000 3.224 1.455  -1.204 6.274  "HG'2" 2OT 48 
2OT "HG'3" "3HG'" H 0 0 N N N 1.173  9.153  2.370 0.563  -2.159 7.478  "HG'3" 2OT 49 
2OT "H3'"  H3*    H 0 1 N N N -2.828 4.734  3.851 1.675  -1.764 0.277  "H3'"  2OT 50 
2OT "HO3'" H3T    H 0 0 N Y N -3.473 4.787  1.719 3.447  -0.153 1.628  "HO3'" 2OT 51 
2OT HOP3   3HOP   H 0 0 N N N 0.750  -0.498 0.304 2.886  -1.617 -5.563 HOP3   2OT 52 
# 
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 
2OT P     OP1    DOUB N N 1  
2OT P     OP2    SING N N 2  
2OT P     "O5'"  SING N N 3  
2OT P     OP3    SING N N 4  
2OT OP2   HOP2   SING N N 5  
2OT "O5'" "C5'"  SING N N 6  
2OT "C5'" "C4'"  SING N N 7  
2OT "C5'" "H5'"  SING N N 8  
2OT "C5'" "H5''" SING N N 9  
2OT "C4'" "O4'"  SING N N 10 
2OT "C4'" "C3'"  SING N N 11 
2OT "C4'" "H4'"  SING N N 12 
2OT "O4'" "C1'"  SING N N 13 
2OT "C1'" N1     SING N N 14 
2OT "C1'" "C2'"  SING N N 15 
2OT "C1'" "H1'"  SING N N 16 
2OT N1    C6     SING N N 17 
2OT N1    C2     SING N N 18 
2OT C6    C5     DOUB N N 19 
2OT C6    H6     SING N N 20 
2OT C2    O2     DOUB N N 21 
2OT C2    N3     SING N N 22 
2OT N3    C4     SING N N 23 
2OT N3    HN3    SING N N 24 
2OT C4    O4     DOUB N N 25 
2OT C4    C5     SING N N 26 
2OT C5    C5M    SING N N 27 
2OT C5M   H71    SING N N 28 
2OT C5M   H72    SING N N 29 
2OT C5M   H73    SING N N 30 
2OT "C2'" "O2'"  SING N N 31 
2OT "C2'" "C3'"  SING N N 32 
2OT "C2'" "H2'"  SING N N 33 
2OT "O2'" "CB'"  SING N N 34 
2OT "CB'" "CC'"  SING N N 35 
2OT "CB'" "HB'1" SING N N 36 
2OT "CB'" "HB'2" SING N N 37 
2OT "CC'" "OD'"  SING N N 38 
2OT "CC'" "HC'1" SING N N 39 
2OT "CC'" "HC'2" SING N N 40 
2OT "OD'" "NE'"  SING N N 41 
2OT "NE'" "CF'"  SING N N 42 
2OT "NE'" "CG'"  SING N N 43 
2OT "CF'" "HF'1" SING N N 44 
2OT "CF'" "HF'2" SING N N 45 
2OT "CF'" "HF'3" SING N N 46 
2OT "CG'" "HG'1" SING N N 47 
2OT "CG'" "HG'2" SING N N 48 
2OT "CG'" "HG'3" SING N N 49 
2OT "C3'" "O3'"  SING N N 50 
2OT "C3'" "H3'"  SING N N 51 
2OT "O3'" "HO3'" SING N N 52 
2OT OP3   HOP3   SING N N 53 
# 
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 
2OT SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCON(C)C)COP(=O)(O)O"                                                                                                                                              
2OT InChI            InChI                1.02b "InChI=1/C14H24N3O10P/c1-8-6-17(14(20)15-12(8)19)13-11(24-4-5-25-16(2)3)10(18)9(27-13)7-26-28(21,22)23/h6,9-11,13,18H,4-5,7H2,1-3H3,(H,15,19,20)(H2,21,22,23)/t9-,10-,11-,13-/m1/s1/f/h15,21-22H" 
2OT InChIKey         InChI                1.02b OPZZJWKFPFNZJV-MMYTUOPGDD                                                                                                                                                                         
2OT SMILES_CANONICAL CACTVS               3.341 "CN(C)OCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                                          
2OT SMILES           CACTVS               3.341 "CN(C)OCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                                
2OT 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)OCCON(C)C"                                                                                                                          
2OT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCON(C)C"                                                                                                                                            
# 
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 
2OT "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-O-{2-[(dimethylamino)oxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate)
;
2OT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-4-(2-dimethylaminooxyethoxy)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
