data_CMR # _chem_comp.id CMR _chem_comp.name "2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O6 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-10-09 _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 305.224 _chem_comp.one_letter_code C _chem_comp.three_letter_code CMR _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 ? _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 CMR P P P 0 1 N N S 1.831 -4.111 -9.307 -3.957 -1.699 3.179 P CMR 1 CMR CMP CMP C 0 1 N N N 0.915 -2.570 -9.146 -5.108 -0.340 3.138 CMP CMR 2 CMR OP1 O1P O 0 1 N N N 1.262 -5.135 -10.161 -4.267 -2.721 4.233 OP1 CMR 3 CMR "O5'" O5* O 0 1 N N N 2.079 -4.828 -7.884 -2.493 -1.028 3.315 "O5'" CMR 4 CMR "C5'" C5* C 0 1 N N N 2.720 -6.096 -7.842 -2.005 -0.136 2.327 "C5'" CMR 5 CMR "C4'" C4* C 0 1 N N R 2.738 -6.727 -6.446 -0.611 0.328 2.728 "C4'" CMR 6 CMR "O4'" O4* O 0 1 N N N 3.555 -5.962 -5.577 0.247 -0.829 2.764 "O4'" CMR 7 CMR "C1'" C1* C 0 1 N N R 2.919 -5.808 -4.323 1.157 -0.778 1.657 "C1'" CMR 8 CMR N1 N1 N 0 1 N N N 3.357 -4.491 -3.765 1.164 -2.047 0.989 N1 CMR 9 CMR C6 C6 C 0 1 N N N 3.271 -3.366 -4.550 -0.008 -2.785 0.956 C6 CMR 10 CMR C5 C5 C 0 1 N N N 3.853 -2.204 -4.167 -0.094 -3.972 0.359 C5 CMR 11 CMR C4 C4 C 0 1 N N N 4.512 -2.192 -2.905 1.147 -4.479 -0.282 C4 CMR 12 CMR N4 N4 N 0 1 N N N 5.121 -1.100 -2.510 1.101 -5.702 -0.910 N4 CMR 13 CMR N3 N3 N 0 1 N N N 4.567 -3.251 -2.102 2.260 -3.794 -0.259 N3 CMR 14 CMR C2 C2 C 0 1 N N N 4.007 -4.421 -2.518 2.328 -2.561 0.367 C2 CMR 15 CMR O2 O2 O 0 1 N N N 4.093 -5.393 -1.756 3.386 -1.929 0.379 O2 CMR 16 CMR "C3'" C3* C 0 1 N N S 1.338 -6.854 -5.828 0.008 1.286 1.720 "C3'" CMR 17 CMR "C2'" C2* C 0 1 N N N 1.422 -5.893 -4.640 0.710 0.360 0.754 "C2'" CMR 18 CMR "O3'" O3* O 0 1 N N N 1.138 -8.219 -5.484 0.965 2.121 2.368 "O3'" CMR 19 CMR OP3 O3P O 0 1 N Y N ? ? ? -3.994 -2.278 1.669 OP3 CMR 20 CMR HMP1 1HMP H 0 0 N N N -0.097 -2.783 -8.833 -5.310 0.012 4.153 HMP1 CMR 21 CMR HMP2 2HMP H 0 0 N N N 1.394 -1.941 -8.409 -4.692 0.486 2.554 HMP2 CMR 22 CMR HMP3 3HMP H 0 0 N N N 0.897 -2.060 -10.097 -6.048 -0.658 2.680 HMP3 CMR 23 CMR "H5'" 1H5* H 0 1 N N N 2.196 -6.777 -8.512 -1.971 -0.654 1.366 "H5'" CMR 24 CMR "H5''" 2H5* H 0 0 N N N 3.748 -5.992 -8.194 -2.683 0.718 2.254 "H5''" CMR 25 CMR "H4'" H4* H 0 1 N N N 3.180 -7.721 -6.539 -0.644 0.753 3.736 "H4'" CMR 26 CMR "H1'" H1* H 0 1 N N N 3.197 -6.639 -3.665 2.163 -0.604 2.054 "H1'" CMR 27 CMR H6 H6 H 0 1 N N N 2.765 -3.445 -5.504 -0.867 -2.341 1.449 H6 CMR 28 CMR H5 H5 H 0 1 N N N 3.785 -1.334 -4.803 -1.005 -4.554 0.330 H5 CMR 29 CMR H41 1H4 H 0 1 N N N 5.499 -1.088 -1.569 0.349 -6.310 -0.691 H41 CMR 30 CMR H42 2H4 H 0 1 N N N 5.155 -0.268 -3.092 1.822 -5.923 -1.553 H42 CMR 31 CMR "H3'" H3* H 0 1 N N N 0.571 -6.532 -6.534 -0.722 1.941 1.236 "H3'" CMR 32 CMR "H2'" 1H2* H 0 1 N N N 0.854 -6.255 -3.789 -0.003 -0.001 0.003 "H2'" CMR 33 CMR "H2''" 2H2* H 0 0 N N N 1.037 -4.923 -4.952 1.556 0.818 0.232 "H2''" CMR 34 CMR "HO3'" H3T H 0 0 N Y N 0.272 -8.298 -5.102 0.743 3.042 2.146 "HO3'" CMR 35 CMR HOP3 3HOP H 0 0 N N N 0.484 -0.813 -0.085 -3.480 -3.087 1.458 HOP3 CMR 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 CMR P CMP SING N N 1 CMR P OP1 DOUB N N 2 CMR P "O5'" SING N N 3 CMR P OP3 SING N N 4 CMR CMP HMP1 SING N N 5 CMR CMP HMP2 SING N N 6 CMR CMP HMP3 SING N N 7 CMR "O5'" "C5'" SING N N 8 CMR "C5'" "C4'" SING N N 9 CMR "C5'" "H5'" SING N N 10 CMR "C5'" "H5''" SING N N 11 CMR "C4'" "O4'" SING N N 12 CMR "C4'" "C3'" SING N N 13 CMR "C4'" "H4'" SING N N 14 CMR "O4'" "C1'" SING N N 15 CMR "C1'" N1 SING N N 16 CMR "C1'" "C2'" SING N N 17 CMR "C1'" "H1'" SING N N 18 CMR N1 C6 SING N N 19 CMR N1 C2 SING N N 20 CMR C6 C5 DOUB N N 21 CMR C6 H6 SING N N 22 CMR C5 C4 SING N N 23 CMR C5 H5 SING N N 24 CMR C4 N4 SING N N 25 CMR C4 N3 DOUB N N 26 CMR N4 H41 SING N N 27 CMR N4 H42 SING N N 28 CMR N3 C2 SING N N 29 CMR C2 O2 DOUB N N 30 CMR "C3'" "C2'" SING N N 31 CMR "C3'" "O3'" SING N N 32 CMR "C3'" "H3'" SING N N 33 CMR "C2'" "H2'" SING N N 34 CMR "C2'" "H2''" SING N N 35 CMR "O3'" "HO3'" SING N N 36 CMR 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 CMR SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)C" CMR SMILES_CANONICAL CACTVS 3.341 "C[P@@](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=NC2=O)N" CMR SMILES CACTVS 3.341 "C[P](O)(=O)OC[CH]1O[CH](C[CH]1O)N2C=CC(=NC2=O)N" CMR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[P@@](=O)(O)OC[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=NC2=O)N)O" CMR SMILES "OpenEye OEToolkits" 1.5.0 "CP(=O)(O)OCC1C(CC(O1)N2C=CC(=NC2=O)N)O" CMR InChI InChI 1.03 "InChI=1S/C10H16N3O6P/c1-20(16,17)18-5-7-6(14)4-9(19-7)13-3-2-8(11)12-10(13)15/h2-3,6-7,9,14H,4-5H2,1H3,(H,16,17)(H2,11,12,15)/t6-,7+,9+/m0/s1" CMR InChIKey InChI 1.03 HGVVWCDXVSXKJT-LKEWCRSYSA-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 CMR "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-[(S)-hydroxy(methyl)phosphoryl]cytidine" CMR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-methyl-phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site CMR "Create component" 2001-10-09 RCSB CMR "Modify descriptor" 2011-06-04 RCSB #