data_N5M # _chem_comp.id N5M _chem_comp.name ;5-nitrocytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N4 O10 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-12-28 _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 368.194 _chem_comp.one_letter_code C _chem_comp.three_letter_code N5M _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 3BSN _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 N5M O4 O4 O 0 1 N N N 26.022 -17.636 -19.740 5.171 -0.195 2.237 O4 N5M 1 N5M N5 N5 N 1 1 N N N 24.940 -17.927 -19.251 5.088 -0.765 1.164 N5 N5M 2 N5M O3 O3 O -1 1 N N N 23.949 -17.289 -19.573 5.992 -1.492 0.790 O3 N5M 3 N5M C5 C5 C 0 1 N N N 24.860 -19.022 -18.309 3.888 -0.581 0.318 C5 N5M 4 N5M C4 C4 C 0 1 N N N 23.815 -19.171 -17.400 3.829 -1.143 -0.973 C4 N5M 5 N5M N4 N4 N 0 1 N N N 22.788 -18.287 -17.339 4.890 -1.871 -1.460 N4 N5M 6 N5M N3 N3 N 0 1 N N N 23.824 -20.227 -16.553 2.744 -0.967 -1.716 N3 N5M 7 N5M C2 C2 C 0 1 N N N 24.830 -21.135 -16.575 1.711 -0.264 -1.255 C2 N5M 8 N5M O2 O2 O 0 1 N N N 24.784 -22.091 -15.766 0.725 -0.116 -1.958 O2 N5M 9 N5M C6 C6 C 0 1 N N N 25.877 -19.970 -18.308 2.827 0.126 0.775 C6 N5M 10 N5M N1 N1 N 0 1 N N N 25.856 -21.006 -17.452 1.737 0.284 -0.027 N1 N5M 11 N5M "C1'" "C1'" C 0 1 N N R 26.958 -21.981 -17.499 0.585 1.051 0.453 "C1'" N5M 12 N5M "O4'" "O4'" O 0 1 N N N 28.123 -21.427 -18.133 -0.624 0.269 0.338 "O4'" N5M 13 N5M "C2'" "C2'" C 0 1 N N R 26.541 -23.195 -18.322 0.345 2.283 -0.448 "C2'" N5M 14 N5M "O2'" "O2'" O 0 1 N N N 26.764 -24.376 -17.547 0.912 3.454 0.142 "O2'" N5M 15 N5M "C3'" "C3'" C 0 1 N N S 27.429 -23.171 -19.552 -1.194 2.402 -0.519 "C3'" N5M 16 N5M "O3'" "O3'" O 0 1 N N N 27.840 -24.488 -19.935 -1.624 3.651 0.026 "O3'" N5M 17 N5M "C4'" "C4'" C 0 1 N N R 28.621 -22.336 -19.122 -1.702 1.229 0.348 "C4'" N5M 18 N5M "C5'" "C5'" C 0 1 N N N 29.301 -21.624 -20.289 -2.964 0.621 -0.266 "C5'" N5M 19 N5M "O5'" "O5'" O 0 1 N N N 28.508 -20.553 -20.804 -3.441 -0.433 0.573 "O5'" N5M 20 N5M P P P 0 1 N N N 29.160 -19.714 -22.022 -4.756 -1.298 0.232 P N5M 21 N5M OP2 OP2 O 0 1 N N N 27.801 -19.061 -22.131 -4.623 -1.888 -1.119 OP2 N5M 22 N5M OP1 OP1 O 0 1 N N N 29.921 -20.524 -23.048 -4.920 -2.475 1.318 OP1 N5M 23 N5M OP3 OP3 O 0 1 N Y N 30.199 -18.704 -21.344 -6.052 -0.343 0.276 OP3 N5M 24 N5M HN4 HN4 H 0 1 N N N 22.143 -18.566 -16.627 5.648 -2.066 -0.887 HN4 N5M 25 N5M HN4A HN4A H 0 0 N N N 22.690 -17.478 -17.919 4.880 -2.190 -2.376 HN4A N5M 26 N5M H6 H6 H 0 1 N N N 26.696 -19.873 -19.005 2.846 0.562 1.763 H6 N5M 27 N5M "H1'" "H1'" H 0 1 N N N 27.190 -22.257 -16.460 0.739 1.360 1.487 "H1'" N5M 28 N5M "H2'" "H2'" H 0 1 N N N 25.478 -23.181 -18.606 0.763 2.116 -1.441 "H2'" N5M 29 N5M "HO2'" "HO2'" H 0 0 N N N 26.813 -25.129 -18.124 0.790 4.257 -0.382 "HO2'" N5M 30 N5M "H3'" "H3'" H 0 1 N N N 26.911 -22.761 -20.431 -1.538 2.297 -1.548 "H3'" N5M 31 N5M "HO3'" "HO3'" H 0 0 N Y N 27.931 -24.530 -20.880 -1.284 4.424 -0.445 "HO3'" N5M 32 N5M "H4'" "H4'" H 0 1 N N N 29.417 -22.973 -18.709 -1.899 1.567 1.366 "H4'" N5M 33 N5M "H5'" "H5'" H 0 1 N N N 30.259 -21.213 -19.938 -3.732 1.389 -0.356 "H5'" N5M 34 N5M "H5'A" "H5'A" H 0 0 N N N 29.445 -22.357 -21.096 -2.732 0.222 -1.254 "H5'A" N5M 35 N5M HOP1 HOP1 H 0 0 N N N 30.081 -19.991 -23.818 -5.694 -3.038 1.174 HOP1 N5M 36 N5M HOP3 HOP3 H 0 0 N N N 30.894 -18.504 -21.960 -6.202 0.078 1.133 HOP3 N5M 37 # 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 N5M O4 N5 DOUB N N 1 N5M N5 O3 SING N N 2 N5M N5 C5 SING N N 3 N5M C5 C4 SING N N 4 N5M C5 C6 DOUB N N 5 N5M C4 N4 SING N N 6 N5M C4 N3 DOUB N N 7 N5M N3 C2 SING N N 8 N5M C2 O2 DOUB N N 9 N5M C2 N1 SING N N 10 N5M C6 N1 SING N N 11 N5M N1 "C1'" SING N N 12 N5M "C1'" "O4'" SING N N 13 N5M "C1'" "C2'" SING N N 14 N5M "O4'" "C4'" SING N N 15 N5M "C2'" "O2'" SING N N 16 N5M "C2'" "C3'" SING N N 17 N5M "C3'" "O3'" SING N N 18 N5M "C3'" "C4'" SING N N 19 N5M "C4'" "C5'" SING N N 20 N5M "C5'" "O5'" SING N N 21 N5M "O5'" P SING N N 22 N5M P OP2 DOUB N N 23 N5M P OP1 SING N N 24 N5M P OP3 SING N N 25 N5M N4 HN4 SING N N 26 N5M N4 HN4A SING N N 27 N5M C6 H6 SING N N 28 N5M "C1'" "H1'" SING N N 29 N5M "C2'" "H2'" SING N N 30 N5M "O2'" "HO2'" SING N N 31 N5M "C3'" "H3'" SING N N 32 N5M "O3'" "HO3'" SING N N 33 N5M "C4'" "H4'" SING N N 34 N5M "C5'" "H5'" SING N N 35 N5M "C5'" "H5'A" SING N N 36 N5M OP1 HOP1 SING N N 37 N5M OP3 HOP3 SING N N 38 # 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 N5M SMILES ACDLabs 10.04 "[O-][N+](=O)C=1C(=NC(=O)N(C=1)C2OC(C(O)C2O)COP(=O)(O)O)N" N5M SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1[N+]([O-])=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" N5M SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1[N+]([O-])=O)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" N5M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)[N+](=O)[O-]" N5M SMILES "OpenEye OEToolkits" 1.5.0 "C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)[N+](=O)[O-]" N5M InChI InChI 1.03 "InChI=1S/C9H13N4O10P/c10-7-3(13(17)18)1-12(9(16)11-7)8-6(15)5(14)4(23-8)2-22-24(19,20)21/h1,4-6,8,14-15H,2H2,(H2,10,11,16)(H2,19,20,21)/t4-,5-,6-,8-/m1/s1" N5M InChIKey InChI 1.03 QPCLJXMRTPOKPG-UAKXSSHOSA-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 N5M "SYSTEMATIC NAME" ACDLabs 10.04 ;5-nitrocytidine 5'-(dihydrogen phosphate) ; N5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-5-nitro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-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 N5M "Create component" 2007-12-28 RCSB N5M "Modify descriptor" 2011-06-04 RCSB #