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 
# 
