data_TDY
# 
_chem_comp.id                                    TDY 
_chem_comp.name                                  
;5-(METHYLAMINO)THYMIDINE 5'-(DIHYDROGEN PHOSPHATE)
;
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H20 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-08-14 
_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                        353.266 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     TDY 
_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        2WQ6 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
TDY P     P     P 0 1 N N N -3.343 -25.687 23.393 -4.335 -1.275 -0.045 P     TDY 1  
TDY OP1   OP1   O 0 1 N N N -2.999 -27.045 23.787 -5.520 -0.444 -0.355 OP1   TDY 2  
TDY "O5'" "O5'" O 0 1 N N N -3.482 -25.655 21.840 -3.149 -0.335 0.503  "O5'" TDY 3  
TDY "C5'" "C5'" C 0 1 N N N -3.671 -24.395 21.182 -2.653 0.794  -0.219 "C5'" TDY 4  
TDY "C4'" "C4'" C 0 1 N N R -3.405 -24.532 19.694 -1.534 1.461  0.582  "C4'" TDY 5  
TDY "O4'" "O4'" O 0 1 N N N -4.523 -25.237 19.074 -0.387 0.589  0.677  "O4'" TDY 6  
TDY "C3'" "C3'" C 0 1 N N S -3.301 -23.237 18.932 -0.985 2.698  -0.173 "C3'" TDY 7  
TDY "O3'" "O3'" O 0 1 N N N -1.983 -22.735 19.041 -1.758 3.862  0.126  "O3'" TDY 8  
TDY "C2'" "C2'" C 0 1 N N N -3.665 -23.677 17.518 0.446  2.822  0.405  "C2'" TDY 9  
TDY "C1'" "C1'" C 0 1 N N R -4.634 -24.826 17.727 0.750  1.420  0.966  "C1'" TDY 10 
TDY N1    N1    N 0 1 N N N -6.096 -24.517 17.468 1.944  0.872  0.319  N1    TDY 11 
TDY C2    C2    C 0 1 N N N -6.711 -25.215 16.530 1.925  0.617  -1.000 C2    TDY 12 
TDY O2    O2    O 0 1 N N N -6.169 -26.082 15.828 0.952  0.942  -1.652 O2    TDY 13 
TDY N3    N3    N 0 1 N N N -8.046 -24.953 16.265 2.955  0.012  -1.615 N3    TDY 14 
TDY C4    C4    C 0 1 N N N -8.799 -24.011 16.968 3.937  -0.575 -0.906 C4    TDY 15 
TDY O4    O4    O 0 1 N N N -9.968 -23.833 16.664 4.898  -1.045 -1.476 O4    TDY 16 
TDY C5    C5    C 0 1 N N R -8.156 -23.374 18.202 3.841  -0.647 0.597  C5    TDY 17 
TDY C5M   C5M   C 0 1 N N N -8.418 -24.203 19.437 5.246  -0.737 1.195  C5M   TDY 18 
TDY C6    C6    C 0 1 N N N -6.619 -23.260 18.023 3.145  0.616  1.117  C6    TDY 19 
TDY N5    N5    N 0 1 N N N -8.583 -22.104 18.337 3.066  -1.835 0.983  N5    TDY 20 
TDY OP2   OP2   O 0 1 N N N -4.478 -24.971 24.026 -4.721 -2.362 1.079  OP2   TDY 21 
TDY CM5   CM5   C 0 1 N N N -8.870 -21.005 19.163 3.706  -3.063 0.493  CM5   TDY 22 
TDY OP3   OP3   O 0 1 N Y N -2.126 -24.745 23.663 -3.847 -2.033 -1.379 OP3   TDY 23 
TDY HA    HA    H 0 1 N N N -4.284 -24.818 24.943 -5.431 -2.964 0.816  HA    TDY 24 
TDY HP3   HP3   H 0 1 N N N -1.685 -24.554 22.844 -3.072 -2.597 -1.250 HP3   TDY 25 
TDY HA1   HA1   H 0 1 N N N -4.707 -24.059 21.335 -2.264 0.466  -1.183 HA1   TDY 26 
TDY HB2   HB2   H 0 1 N N N -2.969 -23.661 21.605 -3.462 1.507  -0.377 HB2   TDY 27 
TDY HB    HB    H 0 1 N N N -2.437 -25.051 19.639 -1.887 1.739  1.575  HB    TDY 28 
TDY HC    HC    H 0 1 N N N -3.945 -22.419 19.287 -0.957 2.518  -1.247 HC    TDY 29 
TDY HD    HD    H 0 1 N N N -4.352 -25.592 16.990 0.903  1.477  2.044  HD    TDY 30 
TDY "H3'" "H3'" H 0 1 N N N -1.614 -22.622 18.173 -1.454 4.663  -0.322 "H3'" TDY 31 
TDY HB1   HB1   H 0 1 N N N -4.132 -22.858 16.952 1.154  3.080  -0.383 HB1   TDY 32 
TDY HC2   HC2   H 0 1 N N N -2.784 -23.972 16.930 0.473  3.566  1.201  HC2   TDY 33 
TDY H61C  H61C  H 0 0 N N N -6.149 -23.067 18.999 3.822  1.467  1.037  H61C  TDY 34 
TDY H62C  H62C  H 0 0 N N N -6.390 -22.432 17.336 2.863  0.473  2.160  H62C  TDY 35 
TDY H3    H3    H 0 1 N N N -8.493 -25.466 15.532 2.991  -0.002 -2.584 H3    TDY 36 
TDY H5M1  H5M1  H 0 0 N N N -8.482 -25.265 19.159 5.819  0.145  0.910  H5M1  TDY 37 
TDY H5M2  H5M2  H 0 0 N N N -7.597 -24.060 20.155 5.176  -0.790 2.282  H5M2  TDY 38 
TDY H5M3  H5M3  H 0 0 N N N -9.366 -23.887 19.896 5.744  -1.631 0.820  H5M3  TDY 39 
TDY H51N  H51N  H 0 0 N N N -7.888 -21.666 17.767 2.933  -1.870 1.983  H51N  TDY 40 
TDY HM51  HM51  H 0 0 N N N -8.945 -21.341 20.208 4.707  -3.145 0.917  HM51  TDY 41 
TDY HM52  HM52  H 0 0 N N N -8.066 -20.260 19.074 3.112  -3.926 0.793  HM52  TDY 42 
TDY HM53  HM53  H 0 0 N N N -9.824 -20.554 18.854 3.774  -3.028 -0.594 HM53  TDY 43 
# 
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 
TDY P     OP1   DOUB N N 1  
TDY P     "O5'" SING N N 2  
TDY P     OP2   SING N N 3  
TDY P     OP3   SING N N 4  
TDY "O5'" "C5'" SING N N 5  
TDY "C5'" "C4'" SING N N 6  
TDY "C4'" "O4'" SING N N 7  
TDY "C4'" "C3'" SING N N 8  
TDY "O4'" "C1'" SING N N 9  
TDY "C3'" "O3'" SING N N 10 
TDY "C3'" "C2'" SING N N 11 
TDY "C2'" "C1'" SING N N 12 
TDY "C1'" N1    SING N N 13 
TDY N1    C2    SING N N 14 
TDY N1    C6    SING N N 15 
TDY C2    O2    DOUB N N 16 
TDY C2    N3    SING N N 17 
TDY N3    C4    SING N N 18 
TDY C4    O4    DOUB N N 19 
TDY C4    C5    SING N N 20 
TDY C5    C5M   SING N N 21 
TDY C5    C6    SING N N 22 
TDY C5    N5    SING N N 23 
TDY OP2   HA    SING N N 24 
TDY OP3   HP3   SING N N 25 
TDY "C5'" HA1   SING N N 26 
TDY "C5'" HB2   SING N N 27 
TDY "C4'" HB    SING N N 28 
TDY "C3'" HC    SING N N 29 
TDY "C1'" HD    SING N N 30 
TDY "O3'" "H3'" SING N N 31 
TDY "C2'" HB1   SING N N 32 
TDY "C2'" HC2   SING N N 33 
TDY C6    H61C  SING N N 34 
TDY C6    H62C  SING N N 35 
TDY N3    H3    SING N N 36 
TDY C5M   H5M1  SING N N 37 
TDY C5M   H5M2  SING N N 38 
TDY C5M   H5M3  SING N N 39 
TDY N5    H51N  SING N N 40 
TDY N5    CM5   SING N N 41 
TDY CM5   HM51  SING N N 42 
TDY CM5   HM52  SING N N 43 
TDY CM5   HM53  SING N N 44 
# 
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 
TDY SMILES           ACDLabs              10.04 "O=C1N(CC(C(=O)N1)(NC)C)C2OC(C(O)C2)COP(=O)(O)O"                                                                                                               
TDY SMILES_CANONICAL CACTVS               3.352 "CN[C@]1(C)CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                               
TDY SMILES           CACTVS               3.352 "CN[C]1(C)CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                    
TDY SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C[C@]1(CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)NC"                                                                                                 
TDY SMILES           "OpenEye OEToolkits" 1.6.1 "CC1(CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O)NC"                                                                                                                 
TDY InChI            InChI                1.03  "InChI=1S/C11H20N3O8P/c1-11(12-2)5-14(10(17)13-9(11)16)8-3-6(15)7(22-8)4-21-23(18,19)20/h6-8,12,15H,3-5H2,1-2H3,(H,13,16,17)(H2,18,19,20)/t6-,7+,8+,11+/m0/s1" 
TDY InChIKey         InChI                1.03  GANAXGZWNNBICE-PRKAOEEVSA-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 
TDY "SYSTEMATIC NAME" ACDLabs              10.04 
;5-(methylamino)thymidine 5'-(dihydrogen phosphate)
;
TDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-5-methylamino-2,4-dioxo-1,3-diazinan-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 
TDY "Create component"  2009-08-14 EBI  
TDY "Modify descriptor" 2011-06-04 RCSB 
# 
