data_MDQ # _chem_comp.id MDQ _chem_comp.name ;2'-deoxy-3-(oxidomethyl)cytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-07-23 _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 337.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code MDQ _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 3O1S _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 MDQ P P P 0 1 N N N -0.141 0.294 0.199 4.528 1.153 0.070 P MDQ 1 MDQ N1 N1 N 0 1 N N N 3.101 -1.258 -3.505 -1.916 -0.482 0.002 N1 MDQ 2 MDQ C2 C2 C 0 1 N N N 3.453 -1.679 -4.770 -3.033 -0.215 0.704 C2 MDQ 3 MDQ O2 O2 O 0 1 N N N 4.582 -1.361 -5.225 -3.103 -0.558 1.873 O2 MDQ 4 MDQ N3 N3 N 1 1 N N N 2.599 -2.428 -5.552 -4.063 0.417 0.145 N3 MDQ 5 MDQ C4 C4 C 0 1 N N N 1.360 -2.757 -5.059 -4.014 0.801 -1.124 C4 MDQ 6 MDQ N4 N4 N 0 1 N N N 0.400 -3.451 -5.809 -5.083 1.454 -1.691 N4 MDQ 7 MDQ C5 C5 C 0 1 N N N 0.982 -2.379 -3.763 -2.858 0.536 -1.888 C5 MDQ 8 MDQ C6 C6 C 0 1 N N N 1.885 -1.631 -3.003 -1.817 -0.102 -1.303 C6 MDQ 9 MDQ "C1'" "C1'" C 0 1 N N R 3.985 -0.400 -2.727 -0.800 -1.179 0.645 "C1'" MDQ 10 MDQ O1P O1P O 0 1 N N N -0.797 1.493 0.758 5.654 0.253 -0.267 O1P MDQ 11 MDQ "C2'" "C2'" C 0 1 N N N 4.059 1.029 -3.319 -0.585 -2.551 -0.022 "C2'" MDQ 12 MDQ C20 C20 C 0 1 N N N 2.994 -2.827 -6.891 -5.263 0.691 0.938 C20 MDQ 13 MDQ O21 O21 O -1 1 N N N 2.773 -1.748 -7.790 -5.298 2.077 1.286 O21 MDQ 14 MDQ O2P O2P O 0 1 N N N -0.817 -0.109 -1.090 4.163 2.059 -1.209 O2P MDQ 15 MDQ "C3'" "C3'" C 0 1 N N S 4.163 1.931 -2.085 0.876 -2.501 -0.532 "C3'" MDQ 16 MDQ "O3'" "O3'" O 0 1 N N N 5.531 2.101 -1.705 1.539 -3.746 -0.304 "O3'" MDQ 17 MDQ "C4'" "C4'" C 0 1 N N R 3.403 1.117 -1.017 1.488 -1.380 0.346 "C4'" MDQ 18 MDQ "O4'" "O4'" O 0 1 N N N 3.657 -0.263 -1.328 0.411 -0.423 0.474 "O4'" MDQ 19 MDQ "C5'" "C5'" C 0 1 N N N 1.876 1.398 -0.953 2.693 -0.744 -0.351 "C5'" MDQ 20 MDQ "O5'" "O5'" O 0 1 N N N 1.332 0.565 -0.058 3.245 0.273 0.488 "O5'" MDQ 21 MDQ O8 O8 O 0 1 N N N -0.240 -0.851 1.183 4.950 2.103 1.299 O8 MDQ 22 MDQ H1N4 H1N4 H 0 0 N N N -0.496 -3.650 -5.412 -5.877 1.635 -1.163 H1N4 MDQ 23 MDQ H2N4 H2N4 H 0 0 N N N 0.611 -3.747 -6.740 -5.044 1.734 -2.619 H2N4 MDQ 24 MDQ H5 H5 H 0 1 N N N 0.019 -2.658 -3.363 -2.801 0.846 -2.921 H5 MDQ 25 MDQ H6 H6 H 0 1 N N N 1.617 -1.341 -1.998 -0.921 -0.316 -1.867 H6 MDQ 26 MDQ "H1'" "H1'" H 0 1 N N N 4.949 -0.926 -2.792 -1.008 -1.311 1.707 "H1'" MDQ 27 MDQ "H12'" "H12'" H 0 0 N N N 3.164 1.264 -3.914 -0.707 -3.353 0.707 "H12'" MDQ 28 MDQ "H22'" "H22'" H 0 0 N N N 4.933 1.146 -3.977 -1.276 -2.683 -0.855 "H22'" MDQ 29 MDQ H20 H20 H 0 1 N N N 4.061 -3.095 -6.894 -6.149 0.440 0.356 H20 MDQ 30 MDQ "H3'" "H3'" H 0 1 N N N 3.761 2.943 -2.240 0.910 -2.232 -1.588 "H3'" MDQ 31 MDQ "HO3'" "HO3'" H 0 0 N N N 5.580 2.662 -0.940 1.135 -4.496 -0.762 "HO3'" MDQ 32 MDQ "H4'" "H4'" H 0 1 N N N 3.764 1.407 -0.019 1.771 -1.773 1.322 "H4'" MDQ 33 MDQ "H15'" "H15'" H 0 0 N N N 1.700 2.440 -0.648 3.447 -1.508 -0.540 "H15'" MDQ 34 MDQ "H25'" "H25'" H 0 0 N N N 1.424 1.231 -1.942 2.376 -0.303 -1.296 "H25'" MDQ 35 MDQ H15 H15 H 0 1 N N N -1.527 0.493 -1.277 3.432 2.674 -1.060 H15 MDQ 36 MDQ H16 H16 H 0 1 N N N -0.705 -0.562 1.960 5.717 2.663 1.118 H16 MDQ 37 MDQ H161 H161 H 0 0 N N N 2.397 -3.696 -7.206 -5.243 0.089 1.847 H161 MDQ 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 MDQ P "O5'" SING N N 1 MDQ P O8 SING N N 2 MDQ N1 "C1'" SING N N 3 MDQ N1 C2 SING N N 4 MDQ C2 O2 DOUB N N 5 MDQ N3 C2 SING N N 6 MDQ N3 C20 SING N N 7 MDQ C4 N3 DOUB N N 8 MDQ N4 C4 SING N N 9 MDQ N4 H1N4 SING N N 10 MDQ N4 H2N4 SING N N 11 MDQ C5 C6 DOUB N N 12 MDQ C5 C4 SING N N 13 MDQ C5 H5 SING N N 14 MDQ C6 N1 SING N N 15 MDQ C6 H6 SING N N 16 MDQ "C1'" "H1'" SING N N 17 MDQ O1P P DOUB N N 18 MDQ "C2'" "C3'" SING N N 19 MDQ "C2'" "C1'" SING N N 20 MDQ "C2'" "H12'" SING N N 21 MDQ "C2'" "H22'" SING N N 22 MDQ C20 O21 SING N N 23 MDQ C20 H20 SING N N 24 MDQ O2P P SING N N 25 MDQ O2P H15 SING N N 26 MDQ "C3'" "O3'" SING N N 27 MDQ "C3'" "H3'" SING N N 28 MDQ "O3'" "HO3'" SING N N 29 MDQ "C4'" "O4'" SING N N 30 MDQ "C4'" "C3'" SING N N 31 MDQ "C4'" "H4'" SING N N 32 MDQ "O4'" "C1'" SING N N 33 MDQ "C5'" "C4'" SING N N 34 MDQ "C5'" "H15'" SING N N 35 MDQ "C5'" "H25'" SING N N 36 MDQ "O5'" "C5'" SING N N 37 MDQ O8 H16 SING N N 38 MDQ C20 H161 SING N N 39 # 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 MDQ SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)[N+](=C(N)C=C1)C[O-])CC2O" MDQ SMILES_CANONICAL CACTVS 3.370 "NC1=[N+](C[O-])C(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" MDQ SMILES CACTVS 3.370 "NC1=[N+](C[O-])C(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" MDQ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=[N+](C2=O)C[O-])N)COP(=O)(O)O)O" MDQ SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C=CC(=[N+](C2=O)C[O-])N)COP(=O)(O)O)O" MDQ InChI InChI 1.03 "InChI=1S/C10H15N3O8P/c11-8-1-2-12(10(16)13(8)5-14)9-3-6(15)7(21-9)4-20-22(17,18)19/h1-2,6-7,9,11,15H,3-5H2,(H2,17,18,19)/q-1/p+1/t6-,7+,9+/m0/s1" MDQ InChIKey InChI 1.03 BDBXEKDYKCTPAE-LKEWCRSYSA-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 MDQ "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-3-(oxidomethyl)cytidine 5'-(dihydrogen phosphate) ; MDQ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[6-azanyl-3-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2-oxo-pyrimidin-1-ium-1-yl]methanolate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site MDQ "Create component" 2010-07-23 RCSB MDQ "Modify descriptor" 2011-06-04 RCSB #