data_ATL # _chem_comp.id ATL _chem_comp.name "[(1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-02-06 _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 350.219 _chem_comp.one_letter_code T _chem_comp.three_letter_code ATL _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 1GV6 _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 ATL OP1 O1P O 0 1 N N N 6.896 -11.308 -15.933 0.268 0.986 -4.881 OP1 ATL 1 ATL P P P 0 1 N N N 5.436 -11.135 -15.771 0.952 -0.123 -4.181 P ATL 2 ATL OP2 O2P O 0 1 N N N 4.587 -12.315 -15.490 2.535 -0.041 -4.465 OP2 ATL 3 ATL "O5'" O5* O 0 1 N N N 5.179 -10.046 -14.608 0.684 -0.005 -2.598 "O5'" ATL 4 ATL "C5'" C5* C 0 1 N N N 6.050 -8.948 -14.391 -0.729 -0.084 -2.411 "C5'" ATL 5 ATL "C4'" C4* C 0 1 N N S 5.274 -7.834 -13.682 -1.054 0.022 -0.920 "C4'" ATL 6 ATL "O4'" O4* O 0 1 N N N 4.358 -7.216 -14.579 -0.498 -1.015 -0.063 "O4'" ATL 7 ATL "C3'" C3* C 0 1 N N R 6.074 -6.647 -13.163 -2.570 -0.019 -0.505 "C3'" ATL 8 ATL "O3'" O3* O 0 1 N N N 6.993 -6.935 -12.122 -3.321 1.058 -1.066 "O3'" ATL 9 ATL "C2'" C2* C 0 1 N N S 4.772 -6.031 -12.660 -2.250 0.196 1.019 "C2'" ATL 10 ATL "O2'" O2* O 0 1 N N N 4.200 -7.017 -11.806 -1.465 1.423 0.969 "O2'" ATL 11 ATL "C1'" C1* C 0 1 N N R 3.988 -5.982 -13.979 -1.178 -0.923 1.204 "C1'" ATL 12 ATL "C6'" C6* C 0 1 N N N 4.521 -8.262 -12.411 -0.642 1.350 -0.212 "C6'" ATL 13 ATL N1 N1 N 0 1 N N N 2.514 -5.831 -13.803 -0.233 -0.551 2.260 N1 ATL 14 ATL C2 C2 C 0 1 N N N 1.995 -4.545 -13.623 -0.597 -0.666 3.550 C2 ATL 15 ATL O2 O2 O 0 1 N N N 2.697 -3.541 -13.519 -1.707 -1.079 3.826 O2 ATL 16 ATL N3 N3 N 0 1 N N N 0.611 -4.443 -13.573 0.250 -0.332 4.541 N3 ATL 17 ATL C4 C4 C 0 1 N N N -0.296 -5.489 -13.689 1.486 0.121 4.253 C4 ATL 18 ATL O4 O4 O 0 1 N N N -1.503 -5.258 -13.617 2.254 0.424 5.148 O4 ATL 19 ATL C5 C5 C 0 1 N N N 0.324 -6.794 -13.891 1.880 0.253 2.899 C5 ATL 20 ATL C5M C5M C 0 1 N N N -0.520 -8.039 -14.098 3.254 0.763 2.550 C5M ATL 21 ATL C6 C6 C 0 1 N N N 1.674 -6.918 -13.919 1.010 -0.089 1.926 C6 ATL 22 ATL OXT OXT O 0 1 N Y N 4.870 -10.407 -17.107 0.383 -1.529 -4.718 OXT ATL 23 ATL HO2P HO2P H 0 0 N N N 3.649 -12.203 -15.386 2.652 -0.115 -5.422 HO2P ATL 24 ATL "H5'" 1H5* H 0 1 N N N 6.893 -9.269 -13.776 -1.213 0.732 -2.948 "H5'" ATL 25 ATL "H5''" 2H5* H 0 0 N N N 6.423 -8.567 -15.343 -1.094 -1.036 -2.796 "H5''" ATL 26 ATL "H3'" H3* H 0 1 N N N 6.533 -6.082 -13.978 -3.031 -0.987 -0.703 "H3'" ATL 27 ATL HA HA H 0 1 N N N 7.492 -6.194 -11.798 -4.159 1.095 -0.584 HA ATL 28 ATL "H2'" 1H2* H 0 1 N N N 4.884 -5.057 -12.186 -3.098 0.192 1.703 "H2'" ATL 29 ATL "H1'" H1* H 0 1 N N N 4.366 -5.172 -14.603 -1.659 -1.870 1.445 "H1'" ATL 30 ATL "H9'1" 1H9* H 0 0 N N N 3.625 -8.832 -12.655 0.411 1.321 0.062 "H9'1" ATL 31 ATL "H9'2" 2H9* H 0 0 N N N 5.175 -8.838 -11.755 -0.840 2.202 -0.863 "H9'2" ATL 32 ATL H3 H3 H 0 1 N N N 0.225 -3.521 -13.427 -0.027 -0.422 5.466 H3 ATL 33 ATL H71 1H5M H 0 1 N N N -1.369 -7.810 -14.740 3.803 0.984 3.465 H71 ATL 34 ATL H72 2H5M H 0 1 N N N 0.071 -8.820 -14.583 3.790 0.004 1.980 H72 ATL 35 ATL H73 3H5M H 0 1 N N N -0.872 -8.408 -13.136 3.164 1.670 1.952 H73 ATL 36 ATL H6 H6 H 0 1 N N N 2.095 -7.899 -14.059 1.294 0.000 0.888 H6 ATL 37 ATL HXT HXT H 0 1 N N N 3.932 -10.295 -17.003 0.854 -2.224 -4.238 HXT ATL 38 # 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 ATL OP1 P DOUB N N 1 ATL P OP2 SING N N 2 ATL P "O5'" SING N N 3 ATL P OXT SING N N 4 ATL OP2 HO2P SING N N 5 ATL "O5'" "C5'" SING N N 6 ATL "C5'" "C4'" SING N N 7 ATL "C5'" "H5'" SING N N 8 ATL "C5'" "H5''" SING N N 9 ATL "C4'" "O4'" SING N N 10 ATL "C4'" "C3'" SING N N 11 ATL "C4'" "C6'" SING N N 12 ATL "O4'" "C1'" SING N N 13 ATL "C3'" "O3'" SING N N 14 ATL "C3'" "C2'" SING N N 15 ATL "C3'" "H3'" SING N N 16 ATL "O3'" HA SING N N 17 ATL "C2'" "O2'" SING N N 18 ATL "C2'" "C1'" SING N N 19 ATL "C2'" "H2'" SING N N 20 ATL "O2'" "C6'" SING N N 21 ATL "C1'" N1 SING N N 22 ATL "C1'" "H1'" SING N N 23 ATL "C6'" "H9'1" SING N N 24 ATL "C6'" "H9'2" SING N N 25 ATL N1 C2 SING N N 26 ATL N1 C6 SING N N 27 ATL C2 O2 DOUB N N 28 ATL C2 N3 SING N N 29 ATL N3 C4 SING N N 30 ATL N3 H3 SING N N 31 ATL C4 O4 DOUB N N 32 ATL C4 C5 SING N N 33 ATL C5 C5M SING N N 34 ATL C5 C6 DOUB N N 35 ATL C5M H71 SING N N 36 ATL C5M H72 SING N N 37 ATL C5M H73 SING N N 38 ATL C6 H6 SING N N 39 ATL OXT HXT SING N N 40 # 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 ATL SMILES ACDLabs 10.04 "O=C1C(=CN(C(=O)N1)C3OC2(C(O)C3OC2)COP(=O)(O)O)C" ATL SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@@H]2O[C@@]3(CO[C@H]2[C@H]3O)CO[P](O)(O)=O)C(=O)NC1=O" ATL SMILES CACTVS 3.341 "CC1=CN([CH]2O[C]3(CO[CH]2[CH]3O)CO[P](O)(O)=O)C(=O)NC1=O" ATL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]3[C@H]([C@](O2)(CO3)COP(=O)(O)O)O" ATL SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CO3)COP(=O)(O)O)O" ATL InChI InChI 1.03 "InChI=1S/C11H15N2O9P/c1-5-2-13(10(16)12-8(5)15)9-6-7(14)11(22-9,3-20-6)4-21-23(17,18)19/h2,6-7,9,14H,3-4H2,1H3,(H,12,15,16)(H2,17,18,19)/t6-,7+,9+,11-/m0/s1" ATL InChIKey InChI 1.03 BXKGBLDLIZEIJX-QJSROADHSA-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 ATL "SYSTEMATIC NAME" ACDLabs 10.04 "1-{2,5-anhydro-4-[(phosphonooxy)methyl]-beta-D-lyxofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione" ATL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1S,4S,5R,7R)-7-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-3,6-dioxabicyclo[2.2.1]heptan-1-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 ATL "Create component" 2002-02-06 EBI ATL "Modify linking type" 2011-06-04 RCSB ATL "Modify descriptor" 2011-06-04 RCSB #