data_8RO # _chem_comp.id 8RO _chem_comp.name "[(2~{R},3~{S},5~{R})-5-(5-methyl-2-oxidanylidene-7-thia-1,3-diazabicyclo[4.1.0]hept-5-en-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O6 P S" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-09-01 _chem_comp.pdbx_modified_date 2017-09-15 _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 322.275 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8RO _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 5XUV _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 8RO P P1 P 0 1 N N N 3.030 9.324 -14.360 4.670 -1.049 0.064 P 8RO 1 8RO OP1 O1 O 0 1 N N N 2.259 10.435 -14.973 3.943 -2.448 0.390 OP1 8RO 2 8RO OP2 O2 O 0 1 N N N 3.996 9.543 -13.263 5.368 -1.357 -1.353 OP2 8RO 3 8RO "O5'" O3 O 0 1 N N N 1.967 8.264 -13.841 3.428 -0.120 -0.369 "O5'" 8RO 4 8RO "C5'" C1 C 0 1 N N N 1.024 7.722 -14.745 2.682 0.666 0.563 "C5'" 8RO 5 8RO "C4'" C2 C 0 1 N N R 0.259 6.650 -14.017 1.578 1.423 -0.178 "C4'" 8RO 6 8RO "O4'" O4 O 0 1 N N N 1.158 5.579 -13.669 0.599 0.505 -0.709 "O4'" 8RO 7 8RO "C3'" C3 C 0 1 N N S -0.340 7.140 -12.701 0.759 2.296 0.807 "C3'" 8RO 8 8RO "O3'" O5 O 0 1 N N N -1.760 7.115 -12.853 1.375 3.572 0.991 "O3'" 8RO 9 8RO "C2'" C4 C 0 1 N N N 0.237 6.196 -11.608 -0.593 2.437 0.067 "C2'" 8RO 10 8RO "C1'" C5 C 0 1 N N R 0.848 5.034 -12.408 -0.608 1.256 -0.922 "C1'" 8RO 11 8RO N1 N1 N 0 1 N N N 2.144 4.389 -11.883 -1.774 0.407 -0.666 N1 8RO 12 8RO C2 C6 C 0 1 N N N 2.154 3.043 -11.607 -1.816 -0.219 0.528 C2 8RO 13 8RO O2 O6 O 0 1 N N N 1.146 2.389 -11.753 -1.152 0.176 1.468 O2 8RO 14 8RO N3 N2 N 0 1 N N N 3.366 2.508 -11.141 -2.615 -1.291 0.646 N3 8RO 15 8RO C4 C7 C 0 1 N N N 4.582 3.188 -10.911 -3.833 -1.010 -0.090 C4 8RO 16 8RO S4 S1 S 0 1 N N N 5.671 2.617 -10.483 -3.934 -1.555 1.561 S4 8RO 17 8RO C5 C8 C 0 1 N N N 4.475 4.623 -11.236 -4.023 -0.385 -1.245 C5 8RO 18 8RO C7 C9 C 0 1 N N N 5.647 5.545 -11.078 -5.332 -0.379 -1.992 C7 8RO 19 8RO C6 C10 C 0 1 N N N 3.294 5.134 -11.690 -2.770 0.330 -1.725 C6 8RO 20 8RO H1 H1 H 0 1 N N N 1.696 10.091 -15.657 3.458 -2.454 1.227 H1 8RO 21 8RO H2 H2 H 0 1 N N N 4.383 8.713 -13.011 6.154 -1.917 -1.291 H2 8RO 22 8RO H3 H3 H 0 1 N N N 0.335 8.509 -15.085 2.234 0.013 1.312 H3 8RO 23 8RO H4 H4 H 0 1 N N N 1.543 7.289 -15.613 3.346 1.378 1.052 H4 8RO 24 8RO H5 H5 H 0 1 N N N -0.549 6.275 -14.663 2.003 2.035 -0.975 H5 8RO 25 8RO H6 H6 H 0 1 N N N 0.009 8.165 -12.505 0.630 1.787 1.762 H6 8RO 26 8RO H7 H7 H 0 1 N N N -2.170 7.415 -12.050 0.900 4.154 1.599 H7 8RO 27 8RO H8 H8 H 0 1 N N N 1.007 6.710 -11.014 -1.423 2.357 0.770 H8 8RO 28 8RO H9 H9 H 0 1 N N N -0.560 5.836 -10.941 -0.637 3.385 -0.470 H9 8RO 29 8RO H10 H10 H 0 1 N N N 0.087 4.247 -12.512 -0.637 1.629 -1.946 H10 8RO 30 8RO H11 H11 H 0 1 N N N 5.355 6.564 -11.373 -6.069 -0.958 -1.437 H11 8RO 31 8RO H12 H12 H 0 1 N N N 5.973 5.546 -10.027 -5.683 0.647 -2.101 H12 8RO 32 8RO H13 H13 H 0 1 N N N 6.473 5.201 -11.718 -5.189 -0.821 -2.978 H13 8RO 33 8RO H14 H14 H 0 1 N N N 3.522 5.585 -12.667 -3.031 1.339 -2.045 H14 8RO 34 8RO H15 H15 H 0 1 N N N 3.019 5.924 -10.976 -2.353 -0.216 -2.570 H15 8RO 35 # 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 8RO P OP1 SING N N 1 8RO P OP2 SING N N 2 8RO P "O5'" SING N N 3 8RO "O5'" "C5'" SING N N 4 8RO "C5'" "C4'" SING N N 5 8RO "C4'" "O4'" SING N N 6 8RO "C4'" "C3'" SING N N 7 8RO "O4'" "C1'" SING N N 8 8RO "C3'" "O3'" SING N N 9 8RO "C3'" "C2'" SING N N 10 8RO "C2'" "C1'" SING N N 11 8RO "C1'" N1 SING N N 12 8RO N1 C2 SING N N 13 8RO N1 C6 SING N N 14 8RO C2 O2 DOUB N N 15 8RO C2 N3 SING N N 16 8RO N3 C4 SING N N 17 8RO N3 S4 SING N N 18 8RO C4 S4 SING N N 19 8RO C4 C5 DOUB N N 20 8RO C5 C7 SING N N 21 8RO C5 C6 SING N N 22 8RO OP1 H1 SING N N 23 8RO OP2 H2 SING N N 24 8RO "C5'" H3 SING N N 25 8RO "C5'" H4 SING N N 26 8RO "C4'" H5 SING N N 27 8RO "C3'" H6 SING N N 28 8RO "O3'" H7 SING N N 29 8RO "C2'" H8 SING N N 30 8RO "C2'" H9 SING N N 31 8RO "C1'" H10 SING N N 32 8RO C7 H11 SING N N 33 8RO C7 H12 SING N N 34 8RO C7 H13 SING N N 35 8RO C6 H14 SING N N 36 8RO C6 H15 SING N N 37 # 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 8RO InChI InChI 1.03 "InChI=1S/C10H15N2O6PS/c1-5-3-11(10(14)12-9(5)20-12)8-2-6(13)7(18-8)4-17-19(15)16/h6-8,13,15-16H,2-4H2,1H3/t6-,7+,8+,12?/m0/s1" 8RO InChIKey InChI 1.03 GSELOCGYYRGWPL-AARIFPKGSA-N 8RO SMILES_CANONICAL CACTVS 3.385 "CC1=C2SN2C(=O)N(C1)[C@H]3C[C@H](O)[C@@H](COP(O)O)O3" 8RO SMILES CACTVS 3.385 "CC1=C2SN2C(=O)N(C1)[CH]3C[CH](O)[CH](COP(O)O)O3" 8RO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=C2N(S2)C(=O)N(C1)[C@H]3C[C@@H]([C@H](O3)COP(O)O)O" 8RO SMILES "OpenEye OEToolkits" 2.0.6 "CC1=C2N(S2)C(=O)N(C1)C3CC(C(O3)COP(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 8RO "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-(5-methyl-2-oxidanylidene-7-thia-1,3-diazabicyclo[4.1.0]hept-5-en-3-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 8RO "Create component" 2017-09-01 RCSB 8RO "Other modification" 2017-09-05 PDBJ 8RO "Initial release" 2017-09-20 RCSB #