data_A5M # _chem_comp.id A5M _chem_comp.name "2'-AMINE-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N4 O7 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-03-10 _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 322.212 _chem_comp.one_letter_code C _chem_comp.three_letter_code A5M _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1YRM _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 A5M P P P 0 1 N N N -9.460 29.698 52.637 0.446 -1.873 4.859 P A5M 1 A5M OP1 O1P O 0 1 N N N -10.659 30.137 53.398 -0.107 -2.073 6.241 OP1 A5M 2 A5M OP2 O2P O 0 1 N N N -8.106 30.004 53.165 1.980 -1.366 4.795 OP2 A5M 3 A5M "O5'" O5* O 0 1 N N N -9.589 28.125 52.453 -0.353 -0.795 3.953 "O5'" A5M 4 A5M "C5'" C5* C 0 1 N N N -10.740 27.578 51.827 0.105 -0.548 2.636 "C5'" A5M 5 A5M "C4'" C4* C 0 1 N N R -10.457 26.178 51.370 -0.801 0.494 1.992 "C4'" A5M 6 A5M "O4'" O4* O 0 1 N N N -9.420 26.202 50.352 -0.692 1.715 2.752 "O4'" A5M 7 A5M "C1'" C1* C 0 1 N N R -8.634 25.027 50.446 0.057 2.684 1.996 "C1'" A5M 8 A5M N1 N1 N 0 1 N N N -7.231 25.429 50.636 1.073 3.249 2.838 N1 A5M 9 A5M C6 C6 C 0 1 N N N -6.917 26.645 51.173 1.662 2.445 3.803 C6 A5M 10 A5M C2 C2 C 0 1 N N N -6.212 24.537 50.257 1.490 4.598 2.712 C2 A5M 11 A5M O2 O2 O 0 1 N N N -6.529 23.446 49.753 0.988 5.340 1.866 O2 A5M 12 A5M N3 N3 N 0 1 N N N -4.915 24.890 50.444 2.476 5.076 3.559 N3 A5M 13 A5M C4 C4 C 0 1 N N N -4.620 26.081 50.974 3.021 4.304 4.463 C4 A5M 14 A5M N4 N4 N 0 1 N N N -3.328 26.394 51.139 3.999 4.798 5.294 N4 A5M 15 A5M C5 C5 C 0 1 N N N -5.639 27.010 51.358 2.612 2.885 4.626 C5 A5M 16 A5M "C2'" C2* C 0 1 N N R -9.212 24.196 51.597 0.629 1.952 0.788 "C2'" A5M 17 A5M "N2'" N2* N 0 1 N N N -10.205 23.259 51.046 0.826 2.817 -0.363 "N2'" A5M 18 A5M "C3'" C3* C 0 1 N N S -9.870 25.282 52.440 -0.394 0.849 0.567 "C3'" A5M 19 A5M "O3'" O3* O 0 1 N N N ? ? ? -1.541 1.334 -0.132 "O3'" A5M 20 A5M OP3 O3P O 0 1 N Y N ? ? ? 0.451 -3.195 3.928 OP3 A5M 21 A5M HOP2 2HOP H 0 0 N N N -7.339 29.723 52.678 2.656 -1.831 5.333 HOP2 A5M 22 A5M "H5'" 1H5* H 0 1 N N N -11.638 27.629 52.485 1.131 -0.178 2.676 "H5'" A5M 23 A5M "H5''" 2H5* H 0 0 N N N -11.110 28.222 50.995 0.072 -1.477 2.064 "H5''" A5M 24 A5M "H4'" H4* H 0 1 N N N -11.446 25.789 51.032 -1.841 0.157 2.052 "H4'" A5M 25 A5M "H1'" H1* H 0 1 N N N -8.658 24.394 49.527 -0.632 3.489 1.718 "H1'" A5M 26 A5M H6 H6 H 0 1 N N N -7.714 27.349 51.464 1.304 1.422 3.854 H6 A5M 27 A5M H41 1H4 H 0 1 N N N -3.102 27.302 51.543 4.342 5.712 5.119 H41 A5M 28 A5M H42 2H4 H 0 1 N N N -2.843 26.296 50.246 4.319 4.219 6.032 H42 A5M 29 A5M H5 H5 H 0 1 N N N -5.440 28.003 51.794 3.075 2.263 5.380 H5 A5M 30 A5M "H2'" H2* H 0 1 N N N -8.482 23.577 52.169 1.591 1.494 1.051 "H2'" A5M 31 A5M "H'1N" 1NH* H 0 0 N N N -10.589 22.706 51.811 1.265 3.705 -0.221 "H'1N" A5M 32 A5M "H'2N" 2NH* H 0 0 N N N -9.823 22.679 50.298 0.344 2.598 -1.212 "H'2N" A5M 33 A5M "H3'" H3* H 0 1 N N N -9.975 25.556 53.515 -0.000 -0.001 0.002 "H3'" A5M 34 A5M "HO3'" H3T H 0 0 N Y N 0.368 -0.562 0.671 -1.289 1.389 -1.066 "HO3'" A5M 35 A5M HOP3 3HOP H 0 0 N N N 0.766 -0.280 -0.486 0.804 -4.033 4.296 HOP3 A5M 36 # 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 A5M P OP1 DOUB N N 1 A5M P OP2 SING N N 2 A5M P "O5'" SING N N 3 A5M P OP3 SING N N 4 A5M OP2 HOP2 SING N N 5 A5M "O5'" "C5'" SING N N 6 A5M "C5'" "C4'" SING N N 7 A5M "C5'" "H5'" SING N N 8 A5M "C5'" "H5''" SING N N 9 A5M "C4'" "O4'" SING N N 10 A5M "C4'" "C3'" SING N N 11 A5M "C4'" "H4'" SING N N 12 A5M "O4'" "C1'" SING N N 13 A5M "C1'" N1 SING N N 14 A5M "C1'" "C2'" SING N N 15 A5M "C1'" "H1'" SING N N 16 A5M N1 C6 SING N N 17 A5M N1 C2 SING N N 18 A5M C6 C5 DOUB N N 19 A5M C6 H6 SING N N 20 A5M C2 O2 DOUB N N 21 A5M C2 N3 SING N N 22 A5M N3 C4 DOUB N N 23 A5M C4 N4 SING N N 24 A5M C4 C5 SING N N 25 A5M N4 H41 SING N N 26 A5M N4 H42 SING N N 27 A5M C5 H5 SING N N 28 A5M "C2'" "N2'" SING N N 29 A5M "C2'" "C3'" SING N N 30 A5M "C2'" "H2'" SING N N 31 A5M "N2'" "H'1N" SING N N 32 A5M "N2'" "H'2N" SING N N 33 A5M "C3'" "O3'" SING N N 34 A5M "C3'" "H3'" SING N N 35 A5M "O3'" "HO3'" SING N N 36 A5M OP3 HOP3 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 A5M SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2N)COP(=O)(O)O" A5M SMILES_CANONICAL CACTVS 3.341 "N[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N" A5M SMILES CACTVS 3.341 "N[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N" A5M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)N" A5M SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)N" A5M InChI InChI 1.03 "InChI=1S/C9H15N4O7P/c10-5-1-2-13(9(15)12-5)8-6(11)7(14)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,14H,3,11H2,(H2,10,12,15)(H2,16,17,18)/t4-,6-,7?,8-/m1/s1" A5M InChIKey InChI 1.03 HGDDYYFPFZSUMP-WDGWZIQESA-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 A5M "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-amino-2'-deoxycytidine 5'-(dihydrogen phosphate) ; A5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-4-amino-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 A5M "Create component" 2005-03-10 RCSB A5M "Modify descriptor" 2011-06-04 RCSB #