data_IMC # _chem_comp.id IMC _chem_comp.name "N1-[2-DEOXY-RIBOFURANOSYL]-[2-AMINO-5-METHYL-4-OXO-4H-PYRIMIDINE]-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 321.224 _chem_comp.one_letter_code C _chem_comp.three_letter_code IMC _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 1BE5 _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 IMC P P P 0 1 N N N -10.252 -2.198 2.057 0.893 -0.196 -4.153 P IMC 1 IMC OP1 O1P O 0 1 N N N -11.004 -3.462 1.887 1.904 0.768 -3.666 OP1 IMC 2 IMC OP2 O2P O 0 1 N N N -10.966 -0.972 2.479 1.631 -1.409 -4.912 OP2 IMC 3 IMC OP3 O3P O 0 1 N Y N -9.475 -1.878 0.656 -0.106 0.545 -5.174 OP3 IMC 4 IMC "O5'" O5* O 0 1 N N N -9.039 -2.454 3.113 0.056 -0.773 -2.905 "O5'" IMC 5 IMC "C5'" C5* C 0 1 N N N -8.267 -3.653 2.963 -0.571 0.345 -2.277 "C5'" IMC 6 IMC "C4'" C4* C 0 1 N N R -6.822 -3.653 3.472 -1.388 -0.135 -1.076 "C4'" IMC 7 IMC "O4'" O4* O 0 1 N N N -6.073 -2.509 3.073 -0.523 -0.676 -0.051 "O4'" IMC 8 IMC "C1'" C1* C 0 1 N N R -4.859 -2.463 3.851 -1.256 -0.625 1.183 "C1'" IMC 9 IMC N1 N1 N 0 1 N N N -4.560 -1.021 4.052 -0.341 -0.357 2.295 N1 IMC 10 IMC C6 C6 C 0 1 N N N -5.607 -0.185 4.327 0.853 0.258 2.057 C6 IMC 11 IMC C4 C4 C 0 1 N N N -4.114 1.691 4.215 1.301 0.101 4.394 C4 IMC 12 IMC O4 O4 O 0 1 N N N -3.866 2.894 4.198 2.039 0.308 5.345 O4 IMC 13 IMC N3 N3 N 0 1 N N N -3.112 0.776 4.049 0.115 -0.495 4.577 N3 IMC 14 IMC C2 C2 C 0 1 N N N -3.302 -0.550 3.946 -0.687 -0.723 3.557 C2 IMC 15 IMC N2 N2 N 0 1 N N N -2.244 -1.333 3.738 -1.890 -1.340 3.773 N2 IMC 16 IMC C5 C5 C 0 1 N N N -5.448 1.150 4.377 1.689 0.500 3.089 C5 IMC 17 IMC C5M C5M C 0 1 N N N -6.643 2.102 4.583 3.015 1.178 2.858 C5M IMC 18 IMC "C2'" C2* C 0 1 N N N -5.241 -3.116 5.189 -2.283 0.517 1.062 "C2'" IMC 19 IMC "C3'" C3* C 0 1 N N S -6.645 -3.758 4.983 -2.082 1.058 -0.373 "C3'" IMC 20 IMC "O3'" O3* O 0 1 N N N -6.830 -5.137 5.356 -3.338 1.353 -0.988 "O3'" IMC 21 IMC HOP2 2HOP H 0 0 N N N -10.483 -0.161 2.588 2.120 -1.021 -5.651 HOP2 IMC 22 IMC HOP3 3HOP H 0 0 N N N -8.992 -1.067 0.765 -0.747 -0.116 -5.467 HOP3 IMC 23 IMC "H5'" 1H5* H 0 1 N N N -8.209 -3.860 1.903 -1.231 0.840 -2.990 "H5'" IMC 24 IMC "H5''" 2H5* H 0 0 N N N -8.798 -4.460 3.465 0.190 1.048 -1.940 "H5''" IMC 25 IMC "H4'" H4* H 0 1 N N N -6.347 -4.473 2.960 -2.123 -0.878 -1.386 "H4'" IMC 26 IMC "H1'" H1* H 0 1 N N N -4.036 -2.995 3.351 -1.772 -1.571 1.347 "H1'" IMC 27 IMC H6 H6 H 0 1 N N N -6.538 -0.688 4.497 1.126 0.549 1.053 H6 IMC 28 IMC HN21 1HN2 H 0 0 N N N -2.362 -2.321 3.592 -2.176 -1.543 4.678 HN21 IMC 29 IMC HN22 2HN2 H 0 0 N N N -1.298 -0.969 3.736 -2.457 -1.573 3.022 HN22 IMC 30 IMC H71 1H5M H 0 1 N N N -6.295 3.137 4.540 3.539 1.283 3.808 H71 IMC 31 IMC H72 2H5M H 0 1 N N N -7.379 1.965 3.789 3.616 0.578 2.175 H72 IMC 32 IMC H73 3H5M H 0 1 N N N -7.112 1.944 5.553 2.848 2.164 2.425 H73 IMC 33 IMC "H2'" 1H2* H 0 1 N N N -4.416 -3.753 5.518 -3.296 0.134 1.188 "H2'" IMC 34 IMC "H2''" 2H2* H 0 0 N N N -5.330 -2.322 5.941 -2.075 1.296 1.796 "H2''" IMC 35 IMC "H3'" H3* H 0 1 N N N -7.410 -3.166 5.476 -1.437 1.937 -0.371 "H3'" IMC 36 IMC "HO3'" *HO3 H 0 0 N Y N -6.719 -5.202 6.297 -3.758 2.038 -0.450 "HO3'" IMC 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 IMC P OP1 DOUB N N 1 IMC P OP2 SING N N 2 IMC P OP3 SING N N 3 IMC P "O5'" SING N N 4 IMC OP2 HOP2 SING N N 5 IMC OP3 HOP3 SING N N 6 IMC "O5'" "C5'" SING N N 7 IMC "C5'" "C4'" SING N N 8 IMC "C5'" "H5'" SING N N 9 IMC "C5'" "H5''" SING N N 10 IMC "C4'" "O4'" SING N N 11 IMC "C4'" "C3'" SING N N 12 IMC "C4'" "H4'" SING N N 13 IMC "O4'" "C1'" SING N N 14 IMC "C1'" N1 SING N N 15 IMC "C1'" "C2'" SING N N 16 IMC "C1'" "H1'" SING N N 17 IMC N1 C6 SING N N 18 IMC N1 C2 SING N N 19 IMC C6 C5 DOUB N N 20 IMC C6 H6 SING N N 21 IMC C4 O4 DOUB N N 22 IMC C4 N3 SING N N 23 IMC C4 C5 SING N N 24 IMC N3 C2 DOUB N N 25 IMC C2 N2 SING N N 26 IMC N2 HN21 SING N N 27 IMC N2 HN22 SING N N 28 IMC C5 C5M SING N N 29 IMC C5M H71 SING N N 30 IMC C5M H72 SING N N 31 IMC C5M H73 SING N N 32 IMC "C2'" "C3'" SING N N 33 IMC "C2'" "H2'" SING N N 34 IMC "C2'" "H2''" SING N N 35 IMC "C3'" "O3'" SING N N 36 IMC "C3'" "H3'" SING N N 37 IMC "O3'" "HO3'" 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 IMC SMILES ACDLabs 10.04 "O=C1N=C(N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O)N" IMC SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=NC1=O)N" IMC SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=NC1=O)N" IMC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=NC1=O)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" IMC SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=NC1=O)N)C2CC(C(O2)COP(=O)(O)O)O" IMC InChI InChI 1.03 "InChI=1S/C10H16N3O7P/c1-5-3-13(10(11)12-9(5)15)8-2-6(14)7(20-8)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" IMC InChIKey InChI 1.03 LBQNUQWNLDITAW-XLPZGREQSA-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 IMC "SYSTEMATIC NAME" ACDLabs 10.04 "2-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methylpyrimidin-4(1H)-one" IMC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2-amino-5-methyl-4-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 IMC "Create component" 1999-07-08 RCSB IMC "Modify descriptor" 2011-06-04 RCSB #