data_LST
# 
_chem_comp.id                                    LST 
_chem_comp.name                                  "[(1R,5R,7R,8S)-2-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H18 N3 O10 P S" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-08-07 
_chem_comp.pdbx_modified_date                    2016-07-15 
_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                        427.324 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ? 
_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        5AXF 
_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 
LST C2    C1  C 0 1 N N N 1.265  41.718 18.077 3.502  -0.450 0.590  C2    LST 1  
LST C4    C2  C 0 1 N N N 0.683  43.018 16.109 3.908  -2.688 0.058  C4    LST 2  
LST C5    C3  C 0 1 N N N -0.438 42.146 15.883 2.535  -2.854 -0.244 C5    LST 3  
LST C6    C4  C 0 1 N N N -0.640 41.112 16.721 1.702  -1.798 -0.118 C6    LST 4  
LST "C1'" C5  C 0 1 N N R 0.054  39.733 18.714 1.292  0.553  0.437  "C1'" LST 5  
LST "C2'" C6  C 0 1 N N R -0.722 40.101 19.972 1.314  1.395  -0.861 "C2'" LST 6  
LST "C3'" C7  C 0 1 N N S -2.173 39.928 19.435 0.060  0.866  -1.610 "C3'" LST 7  
LST "O3'" O1  O 0 1 N N N -3.170 39.857 20.468 -0.486 1.870  -2.468 "O3'" LST 8  
LST "C4'" C8  C 0 1 N N R -2.020 38.567 18.742 -0.894 0.563  -0.430 "C4'" LST 9  
LST "C5'" C9  C 0 1 N N N -3.118 38.187 17.803 -1.953 -0.470 -0.820 "C5'" LST 10 
LST "O5'" O2  O 0 1 N N N -3.245 39.299 16.898 -2.879 -0.633 0.257  "O5'" LST 11 
LST "C6'" C10 C 0 1 N N N -1.900 37.473 19.791 -1.539 1.891  -0.001 "C6'" LST 12 
LST P     P1  P 0 1 N N N -4.328 39.123 15.693 -4.129 -1.645 0.193  P     LST 13 
LST OP1   O3  O 0 1 N N N -5.549 38.467 16.146 -4.949 -1.341 -1.001 OP1   LST 14 
LST OP2   O4  O 0 1 N N N -4.392 40.500 15.036 -3.589 -3.159 0.102  OP2   LST 15 
LST "N2'" N1  N 0 1 N N N -0.392 39.244 21.152 1.000  2.787  -0.461 "N2'" LST 16 
LST "C7'" C11 C 0 1 N N N 0.772  39.654 21.944 1.734  3.931  -1.008 "C7'" LST 17 
LST S     S1  S 0 1 N N N -0.507 37.634 20.870 -0.233 2.983  0.643  S     LST 18 
LST "O7'" O5  O 0 1 N N N -0.831 37.038 22.158 -0.610 4.347  0.518  "O7'" LST 19 
LST "O8'" O6  O 0 1 N N N 0.654  37.179 20.182 0.295  2.472  1.860  "O8'" LST 20 
LST "O4'" O7  O 0 1 N N N -0.747 38.740 18.054 -0.050 0.095  0.632  "O4'" LST 21 
LST N1    N2  N 0 1 N N N 0.196  40.874 17.796 2.195  -0.593 0.301  N1    LST 22 
LST C7    C12 C 0 1 N N N -1.329 42.441 14.729 2.010  -4.190 -0.705 C7    LST 23 
LST N3    N3  N 0 1 N N N 1.451  42.721 17.204 4.354  -1.484 0.468  N3    LST 24 
LST O2    O8  O 0 1 N N N 1.989  41.537 19.055 3.918  0.631  0.961  O2    LST 25 
LST O4    O9  O 0 1 N N N 0.959  43.985 15.404 4.679  -3.625 -0.052 O4    LST 26 
LST H1    H1  H 0 1 N N N -1.477 40.451 16.549 0.652  -1.906 -0.344 H1    LST 27 
LST H2    H2  H 0 1 N N N 1.040  39.330 18.987 1.600  1.168  1.282  H2    LST 28 
LST H3    H3  H 0 1 N N N -0.550 41.160 20.216 2.244  1.306  -1.422 H3    LST 29 
LST H4    H4  H 0 1 N N N -2.401 40.712 18.698 0.292  -0.040 -2.170 H4    LST 30 
LST H5    H5  H 0 1 N N N -3.253 40.705 20.887 0.118  2.165  -3.163 H5    LST 31 
LST H6    H6  H 0 1 N N N -4.057 38.028 18.353 -2.485 -0.128 -1.708 H6    LST 32 
LST H7    H7  H 0 1 N N N -2.855 37.271 17.254 -1.470 -1.424 -1.031 H7    LST 33 
LST H8    H8  H 0 1 N N N -2.813 37.485 20.405 -2.020 2.361  -0.859 H8    LST 34 
LST H9    H9  H 0 1 N N N -1.821 36.507 19.271 -2.279 1.705  0.778  H9    LST 35 
LST H11   H11 H 0 1 N N N -5.295 40.791 14.997 -3.043 -3.428 0.853  H11   LST 36 
LST H12   H12 H 0 1 N N N 1.368  38.768 22.207 1.238  4.283  -1.912 H12   LST 37 
LST H13   H13 H 0 1 N N N 1.389  40.349 21.356 1.757  4.734  -0.271 H13   LST 38 
LST H14   H14 H 0 1 N N N 0.432  40.153 22.863 2.753  3.628  -1.247 H14   LST 39 
LST H15   H15 H 0 1 N N N -2.134 41.693 14.686 2.830  -4.907 -0.746 H15   LST 40 
LST H16   H16 H 0 1 N N N -1.766 43.443 14.850 1.253  -4.543 -0.005 H16   LST 41 
LST H17   H17 H 0 1 N N N -0.746 42.405 13.797 1.569  -4.084 -1.696 H17   LST 42 
LST H18   H18 H 0 1 N N N 2.236  43.317 17.371 5.294  -1.362 0.677  H18   LST 43 
LST OP3   OP3 O 0 1 N N N -3.630 38.056 14.712 -5.027 -1.474 1.518  OP3   LST 44 
LST H10   H10 H 0 1 N N N -4.166 37.273 14.663 -5.799 -2.054 1.548  H10   LST 45 
# 
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 
LST C7    C5    SING N N 1  
LST OP2   P     SING N N 2  
LST O4    C4    DOUB N N 3  
LST P     OP1   DOUB N N 4  
LST P     "O5'" SING N N 5  
LST C5    C4    SING N N 6  
LST C5    C6    DOUB N N 7  
LST C4    N3    SING N N 8  
LST C6    N1    SING N N 9  
LST "O5'" "C5'" SING N N 10 
LST N3    C2    SING N N 11 
LST N1    C2    SING N N 12 
LST N1    "C1'" SING N N 13 
LST "C5'" "C4'" SING N N 14 
LST "O4'" "C1'" SING N N 15 
LST "O4'" "C4'" SING N N 16 
LST C2    O2    DOUB N N 17 
LST "C1'" "C2'" SING N N 18 
LST "C4'" "C3'" SING N N 19 
LST "C4'" "C6'" SING N N 20 
LST "C3'" "C2'" SING N N 21 
LST "C3'" "O3'" SING N N 22 
LST "C6'" S     SING N N 23 
LST "C2'" "N2'" SING N N 24 
LST "O8'" S     DOUB N N 25 
LST S     "N2'" SING N N 26 
LST S     "O7'" DOUB N N 27 
LST "N2'" "C7'" SING N N 28 
LST C6    H1    SING N N 29 
LST "C1'" H2    SING N N 30 
LST "C2'" H3    SING N N 31 
LST "C3'" H4    SING N N 32 
LST "O3'" H5    SING N N 33 
LST "C5'" H6    SING N N 34 
LST "C5'" H7    SING N N 35 
LST "C6'" H8    SING N N 36 
LST "C6'" H9    SING N N 37 
LST OP2   H11   SING N N 38 
LST "C7'" H12   SING N N 39 
LST "C7'" H13   SING N N 40 
LST "C7'" H14   SING N N 41 
LST C7    H15   SING N N 42 
LST C7    H16   SING N N 43 
LST C7    H17   SING N N 44 
LST N3    H18   SING N N 45 
LST P     OP3   SING N N 46 
LST OP3   H10   SING N N 47 
# 
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 
LST InChI            InChI                1.03  "InChI=1S/C12H18N3O10PS/c1-6-3-15(11(18)13-9(6)17)10-7-8(16)12(25-10,4-24-26(19,20)21)5-27(22,23)14(7)2/h3,7-8,10,16H,4-5H2,1-2H3,(H,13,17,18)(H2,19,20,21)/t7-,8+,10-,12+/m1/s1" 
LST InChIKey         InChI                1.03  GLEXYOQXMPFGCY-CCCLYZFWSA-N                                                                                                                                                       
LST SMILES_CANONICAL CACTVS               3.385 "CN1[C@@H]2[C@H](O)[C@](CO[P](O)(O)=O)(C[S]1(=O)=O)O[C@H]2N3C=C(C)C(=O)NC3=O"                                                                                                     
LST SMILES           CACTVS               3.385 "CN1[CH]2[CH](O)[C](CO[P](O)(O)=O)(C[S]1(=O)=O)O[CH]2N3C=C(C)C(=O)NC3=O"                                                                                                          
LST SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CS(=O)(=O)N3C)COP(=O)(O)O)O"                                                                                                      
LST SMILES           "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CS(=O)(=O)N3C)COP(=O)(O)O)O"                                                                                                                       
# 
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 
LST "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(1R,5R,7R,8S)-2-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-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 
LST "Create component" 2015-08-07 PDBJ 
LST "Initial release"  2016-07-20 RCSB 
# 
