data_LLT
# 
_chem_comp.id                                    LLT 
_chem_comp.name                                  L-deoxythymidine 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H14 N2 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;L-thymidine; beta-L-thymidine; L-dT; 2'-deoxy-L-thymidine; 1-(2-deoxy-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2009-06-04 
_chem_comp.pdbx_modified_date                    2020-05-27 
_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                        242.229 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LLT 
_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        3HP1 
_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 
LLT O4     O4   O 0 1 N N N 62.721 33.040 17.468 -4.578 0.297  0.359  O4   LLT 1  
LLT C4     C4   C 0 1 N N N 64.018 33.245 17.818 -3.392 0.117  0.145  C4   LLT 2  
LLT C5     C5   C 0 1 N N N 64.422 34.504 18.209 -2.495 1.212  0.134  C5   LLT 3  
LLT C7     C7   C 0 1 N N N 63.451 35.646 18.251 -2.994 2.612  0.384  C7   LLT 4  
LLT C6     C6   C 0 1 N N N 65.747 34.696 18.574 -1.185 0.985  -0.105 C6   LLT 5  
LLT N3     N3   N 0 1 N N N 64.906 32.230 17.790 -2.922 -1.127 -0.076 N3   LLT 6  
LLT C2     C2   C 0 1 N N N 66.194 32.463 18.123 -1.611 -1.324 -0.311 C2   LLT 7  
LLT O2     O2   O 0 1 N N N 67.061 31.422 18.085 -1.201 -2.452 -0.509 O2   LLT 8  
LLT N1     N1   N 0 1 N N N 66.615 33.673 18.518 -0.748 -0.292 -0.330 N1   LLT 9  
LLT "C1'"  C1*  C 0 1 N N S 67.995 33.920 18.912 0.672  -0.538 -0.589 C1*  LLT 10 
LLT "O4'"  O4*  O 0 1 N N N 68.307 35.327 18.883 1.427  0.686  -0.457 O4*  LLT 11 
LLT "C4'"  C4*  C 0 1 N N S 69.251 35.673 19.901 2.792  0.270  -0.235 C4*  LLT 12 
LLT "C5'"  C5*  C 0 1 N N N 68.779 36.917 20.640 3.593  1.399  0.417  C5*  LLT 13 
LLT "O5'"  O5*  O 0 1 N N N 69.221 38.106 19.941 3.716  2.487  -0.501 O5*  LLT 14 
LLT "C3'"  C3*  C 0 1 N N R 69.353 34.464 20.816 2.685  -0.937 0.724  C3*  LLT 15 
LLT "O3'"  O3*  O 0 1 N N N 70.629 33.857 20.568 3.663  -1.926 0.394  O3*  LLT 16 
LLT "C2'"  C2*  C 0 1 N N N 68.230 33.530 20.374 1.259  -1.481 0.485  C2*  LLT 17 
LLT H7     H7   H 0 1 N N N 63.213 35.888 19.297 -4.070 2.588  0.555  H7   LLT 18 
LLT H7A    H7A  H 0 1 N N N 63.898 36.525 17.764 -2.496 3.023  1.262  H7A  LLT 19 
LLT H7B    H7B  H 0 1 N N N 62.529 35.363 17.722 -2.777 3.236  -0.483 H7B  LLT 20 
LLT H6     H6   H 0 1 N N N 66.080 35.669 18.903 -0.486 1.808  -0.118 H6   LLT 21 
LLT HN3    HN3  H 0 1 N N N 64.613 31.312 17.525 -3.530 -1.882 -0.066 HN3  LLT 22 
LLT "H1'"  H1*  H 0 1 N N N 68.607 33.336 18.209 0.808  -0.964 -1.583 H1*  LLT 23 
LLT "H4'"  H4*  H 0 1 N N N 70.242 35.914 19.488 3.255  -0.030 -1.175 H4*  LLT 24 
LLT "H5'"  H5*  H 0 1 N N N 67.680 36.914 20.693 3.079  1.738  1.316  H5*  LLT 25 
LLT "H5'A" H5*A H 0 0 N N N 69.202 36.916 21.655 4.585  1.033  0.682  H5*A LLT 26 
LLT "HO5'" HO5* H 0 0 N N N 69.318 38.820 20.560 4.214  3.240  -0.154 HO5* LLT 27 
LLT "H3'"  H3*  H 0 1 N N N 69.266 34.705 21.886 2.803  -0.614 1.758  H3*  LLT 28 
LLT "HO3'" HO3* H 0 0 N N N 70.740 33.723 19.634 3.641  -2.706 0.965  HO3* LLT 29 
LLT "H2'"  H2*  H 0 1 N N N 67.324 33.674 20.980 0.672  -1.427 1.402  H2*  LLT 30 
LLT "H2'A" H2*A H 0 0 N N N 68.487 32.467 20.495 1.298  -2.505 0.115  H2*A LLT 31 
# 
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 
LLT O4    C4     DOUB N N 1  
LLT N3    C4     SING N N 2  
LLT C4    C5     SING N N 3  
LLT C5    C7     SING N N 4  
LLT C5    C6     DOUB N N 5  
LLT C7    H7     SING N N 6  
LLT C7    H7A    SING N N 7  
LLT C7    H7B    SING N N 8  
LLT N1    C6     SING N N 9  
LLT C6    H6     SING N N 10 
LLT N3    C2     SING N N 11 
LLT N3    HN3    SING N N 12 
LLT O2    C2     DOUB N N 13 
LLT C2    N1     SING N N 14 
LLT N1    "C1'"  SING N N 15 
LLT "O4'" "C1'"  SING N N 16 
LLT "C1'" "C2'"  SING N N 17 
LLT "C1'" "H1'"  SING N N 18 
LLT "O4'" "C4'"  SING N N 19 
LLT "C4'" "C5'"  SING N N 20 
LLT "C4'" "C3'"  SING N N 21 
LLT "C4'" "H4'"  SING N N 22 
LLT "O5'" "C5'"  SING N N 23 
LLT "C5'" "H5'"  SING N N 24 
LLT "C5'" "H5'A" SING N N 25 
LLT "O5'" "HO5'" SING N N 26 
LLT "C2'" "C3'"  SING N N 27 
LLT "O3'" "C3'"  SING N N 28 
LLT "C3'" "H3'"  SING N N 29 
LLT "O3'" "HO3'" SING N N 30 
LLT "C2'" "H2'"  SING N N 31 
LLT "C2'" "H2'A" SING N N 32 
# 
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 
LLT SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CO"                                                                                        
LLT SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@@H]2C[C@@H](O)[C@H](CO)O2)C(=O)NC1=O"                                                                          
LLT SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O"                                                                               
LLT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)CO)O"                                                                          
LLT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O"                                                                                        
LLT InChI            InChI                1.03  "InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m1/s1" 
LLT InChIKey         InChI                1.03  IQFYYKKMVGJFEH-CSMHCCOUSA-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 
LLT "SYSTEMATIC NAME" ACDLabs              10.04 "1-(2-deoxy-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione"       
LLT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
LLT "Create component"  2009-06-04 RCSB 
LLT "Modify descriptor" 2011-06-04 RCSB 
LLT "Modify synonyms"   2020-05-27 PDBE 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 LLT L-thymidine                                                                     ? ? 
2 LLT beta-L-thymidine                                                                ? ? 
3 LLT L-dT                                                                            ? ? 
4 LLT "2'-deoxy-L-thymidine"                                                          ? ? 
5 LLT "1-(2-deoxy-beta-L-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" ? ? 
# 
