data_ME6
# 
_chem_comp.id                                    ME6 
_chem_comp.name                                  "[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H17 N3 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DC 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2009-05-21 
_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                        322.232 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     ME6 
_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        3H8X 
_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 
ME6 O2     O2     O 0 1 N N N -8.930  9.508  -2.417 -3.272 -0.754 1.844  O2   ME6 1  
ME6 C2     C2     C 0 1 N N N -8.302  8.516  -1.984 -3.260 -0.138 0.792  C2   ME6 2  
ME6 N3     N3     N 1 1 N N N -9.020  7.416  -1.742 -4.297 0.636  0.474  N3   ME6 3  
ME6 C20    C20    C 0 1 N N N -10.467 7.450  -2.007 -5.434 0.737  1.391  C20  ME6 4  
ME6 C4     C4     C 0 1 N N N -8.433  6.295  -1.283 -4.310 1.317  -0.665 C4   ME6 5  
ME6 N4     N4     N 0 1 N N N -9.167  5.174  -1.051 -5.385 2.113  -0.983 N4   ME6 6  
ME6 C5     C5     C 0 1 N N N -7.061  6.271  -1.040 -3.214 1.219  -1.548 C5   ME6 7  
ME6 C6     C6     C 0 1 N N N -6.305  7.411  -1.275 -2.168 0.429  -1.210 C6   ME6 8  
ME6 N1     N1     N 0 1 N N N -6.888  8.525  -1.766 -2.198 -0.247 -0.027 N1   ME6 9  
ME6 "C1'"  "C1'"  C 0 1 N N R -5.993  9.700  -1.945 -1.070 -1.101 0.353  C1*  ME6 10 
ME6 "O4'"  "O4'"  O 0 1 N N N -6.319  10.788 -2.828 0.170  -0.365 0.265  O4*  ME6 11 
ME6 "C2'"  "C2'"  C 0 1 N N N -4.531  9.358  -2.213 -0.913 -2.264 -0.652 C2*  ME6 12 
ME6 "C3'"  "C3'"  C 0 1 N N S -4.029  10.778 -2.275 0.615  -2.446 -0.780 C3*  ME6 13 
ME6 "O3'"  "O3'"  O 0 1 N N N -4.180  11.325 -0.978 1.002  -3.753 -0.351 O3*  ME6 14 
ME6 "C4'"  "C4'"  C 0 1 N N R -5.066  11.392 -3.175 1.202  -1.370 0.164  C4*  ME6 15 
ME6 "C5'"  "C5'"  C 0 1 N N N -4.767  10.784 -4.517 2.474  -0.768 -0.436 C5*  ME6 16 
ME6 "O5'"  "O5'"  O 0 1 N N N -6.032  10.289 -4.852 3.022  0.191  0.471  O5*  ME6 17 
ME6 P      P      P 0 1 N N N -6.143  8.904  -5.616 4.366  1.022  0.163  P    ME6 18 
ME6 O3P    O3P    O 0 1 N Y N -5.452  7.861  -4.762 4.120  1.991  -1.099 O1P  ME6 19 
ME6 O2P    O2P    O 0 1 N N N -5.681  9.101  -7.047 4.757  1.906  1.450  O2P  ME6 20 
ME6 H20    H20    H 0 1 N N N -11.015 7.458  -1.053 -5.266 1.557  2.089  H20  ME6 21 
ME6 H20A   H20A   H 0 0 N N N -10.714 8.356  -2.579 -6.345 0.924  0.822  H20A ME6 22 
ME6 H20B   H20B   H 0 0 N N N -10.754 6.560  -2.587 -5.538 -0.196 1.946  H20B ME6 23 
ME6 HN4    HN4    H 0 1 N N N -8.577  4.440  -0.715 -6.137 2.178  -0.373 HN4  ME6 24 
ME6 H5     H5     H 0 1 N N N -6.589  5.372  -0.672 -3.210 1.767  -2.478 H5   ME6 25 
ME6 H6     H6     H 0 1 N N N -5.246  7.407  -1.064 -1.318 0.337  -1.870 H6   ME6 26 
ME6 "H1'"  "H1'"  H 0 1 N N N -6.190  10.089 -0.935 -1.211 -1.488 1.362  H1*  ME6 27 
ME6 "H2'"  "H2'"  H 0 1 N N N -4.062  8.751  -1.425 -1.375 -3.171 -0.261 H2*  ME6 28 
ME6 "H2'A" "H2'A" H 0 0 N N N -4.326  8.725  -3.089 -1.351 -1.999 -1.614 H2*A ME6 29 
ME6 "H3'"  "H3'"  H 0 1 N N N -2.989  10.914 -2.606 0.936  -2.272 -1.808 H3*  ME6 30 
ME6 "HO3'" "HO3'" H 0 0 N Y N -4.214  10.622 -0.339 0.613  -4.469 -0.872 HO3* ME6 31 
ME6 "H4'"  "H4'"  H 0 1 N N N -5.079  12.491 -3.128 1.411  -1.800 1.144  H4*  ME6 32 
ME6 "H5'"  "H5'"  H 0 1 N N N -4.394  11.521 -5.243 3.203  -1.559 -0.612 H5*  ME6 33 
ME6 "H5'A" "H5'A" H 0 0 N N N -3.967  10.029 -4.510 2.234  -0.279 -1.380 H5*A ME6 34 
ME6 HO3P   HO3P   H 0 0 N Y N -5.307  7.075  -5.276 3.410  2.634  -0.969 HO1P ME6 35 
ME6 HO2P   HO2P   H 0 0 N N N -6.437  9.142  -7.621 5.559  2.435  1.335  HO2P ME6 36 
ME6 O1P    O1P    O 0 1 N N N -6.695  7.229  -6.104 5.468  0.083  -0.144 O7   ME6 37 
ME6 H17    H17    H 0 1 N N N -10.153 5.095  -1.195 -5.392 2.610  -1.816 H17  ME6 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 
ME6 O2    C2     DOUB N N 1  
ME6 C2    N1     SING N N 2  
ME6 C2    N3     SING N N 3  
ME6 N3    C4     DOUB N N 4  
ME6 C20   N3     SING N N 5  
ME6 C20   H20    SING N N 6  
ME6 C20   H20A   SING N N 7  
ME6 C20   H20B   SING N N 8  
ME6 C4    N4     SING N N 9  
ME6 C4    C5     SING N N 10 
ME6 N4    HN4    SING N N 11 
ME6 C5    H5     SING N N 12 
ME6 C6    C5     DOUB N N 13 
ME6 C6    H6     SING N N 14 
ME6 N1    C6     SING N N 15 
ME6 "C1'" N1     SING N N 16 
ME6 "C1'" "H1'"  SING N N 17 
ME6 "O4'" "C1'"  SING N N 18 
ME6 "C2'" "C1'"  SING N N 19 
ME6 "C2'" "H2'"  SING N N 20 
ME6 "C2'" "H2'A" SING N N 21 
ME6 "C3'" "C2'"  SING N N 22 
ME6 "C3'" "O3'"  SING N N 23 
ME6 "C3'" "H3'"  SING N N 24 
ME6 "O3'" "HO3'" SING N N 25 
ME6 "C4'" "O4'"  SING N N 26 
ME6 "C4'" "C3'"  SING N N 27 
ME6 "C4'" "H4'"  SING N N 28 
ME6 "C5'" "C4'"  SING N N 29 
ME6 "C5'" "H5'"  SING N N 30 
ME6 "C5'" "H5'A" SING N N 31 
ME6 "O5'" "C5'"  SING N N 32 
ME6 P     "O5'"  SING N N 33 
ME6 P     O3P    SING N N 34 
ME6 P     O1P    DOUB N N 35 
ME6 O3P   HO3P   SING N N 36 
ME6 O2P   P      SING N N 37 
ME6 O2P   HO2P   SING N N 38 
ME6 N4    H17    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 
ME6 SMILES_CANONICAL CACTVS               3.352 "C[N+]1=C(N)C=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C1=O"                                                                                    
ME6 SMILES           CACTVS               3.352 "C[N+]1=C(N)C=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C1=O"                                                                                        
ME6 SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C[N+]1=C(C=CN(C1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)N"                                                                                      
ME6 SMILES           "OpenEye OEToolkits" 1.6.1 "C[N+]1=C(C=CN(C1=O)C2CC(C(O2)COP(=O)(O)O)O)N"                                                                                                   
ME6 InChI            InChI                1.03  "InChI=1S/C10H16N3O7P/c1-12-8(11)2-3-13(10(12)15)9-4-6(14)7(20-9)5-19-21(16,17)18/h2-3,6-7,9,11,14H,4-5H2,1H3,(H2,16,17,18)/p+1/t6-,7+,9+/m0/s1" 
ME6 InChIKey         InChI                1.03  SXDBYGVVLMSJDZ-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 
ME6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-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 
ME6 "Create component"  2009-05-21 RCSB 
ME6 "Modify descriptor" 2011-06-04 RCSB 
# 
