data_XEC
# 
_chem_comp.id                                    XEC 
_chem_comp.name                                  "1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-11-14 
_chem_comp.pdbx_modified_date                    2023-04-07 
_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                        338.208 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     XEC 
_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        8F27 
_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 
XEC N1    N1  N 0 1 N N N 21.099 1.358  -7.711  2.199  -0.552 -0.338 N1    XEC 1  
XEC C2    C1  C 0 1 N N N 21.514 2.259  -6.796  3.501  -0.215 -0.374 C2    XEC 2  
XEC N3    N2  N 0 1 N N N 22.372 1.905  -5.809  4.457  -1.115 -0.076 N3    XEC 3  
XEC C4    C2  C 0 1 N N N 22.887 0.634  -5.689  4.121  -2.375 0.265  C4    XEC 4  
XEC C5    C3  C 0 1 N N N 22.492 -0.323 -6.670  2.755  -2.743 0.307  C5    XEC 5  
XEC C6    C4  C 0 1 N N N 21.614 0.040  -7.668  1.817  -1.821 0.004  C6    XEC 6  
XEC O2    O1  O 0 1 N N N 21.095 3.407  -6.840  3.819  0.917  -0.681 O2    XEC 7  
XEC O4    O2  O 0 1 N N N 23.704 0.384  -4.791  4.985  -3.190 0.535  O4    XEC 8  
XEC "C1'" C5  C 0 1 N N S 20.154 1.812  -8.801  1.181  0.450  -0.662 "C1'" XEC 9  
XEC "C2'" C6  C 0 1 N N S 18.739 1.857  -8.361  1.278  1.648  0.308  "C2'" XEC 10 
XEC "O2'" O3  O 0 1 N N N 17.883 2.698  -9.188  2.009  2.720  -0.291 "O2'" XEC 11 
XEC CM2   C7  C 0 1 N N N 18.007 4.133  -8.943  2.721  3.532  0.645  CM2   XEC 12 
XEC "C3'" C8  C 0 1 N N S 18.400 0.392  -8.602  -0.192 2.058  0.546  "C3'" XEC 13 
XEC "C4'" C9  C 0 1 N N S 18.919 0.261  -10.013 -1.004 1.060  -0.308 "C4'" XEC 14 
XEC "O3'" O4  O 0 1 N N N 17.001 0.233  -8.585  -0.417 3.397  0.100  "O3'" XEC 15 
XEC "O4'" O5  O 0 1 N N N 20.253 0.855  -9.881  -0.141 -0.090 -0.451 "O4'" XEC 16 
XEC "C5'" C10 C 0 1 N N N 19.032 -1.156 -10.542 -2.297 0.670  0.411  "C5'" XEC 17 
XEC "O5'" O6  O 0 1 N N N 19.888 -1.834 -9.641  -3.052 -0.219 -0.413 "O5'" XEC 18 
XEC P     P1  P 0 1 N N N 20.423 -3.335 -10.019 -4.473 -0.833 0.030  P     XEC 19 
XEC OP1   O7  O 0 1 N N N 21.015 -3.915 -8.799  -4.330 -1.517 1.334  OP1   XEC 20 
XEC OP2   O8  O 0 1 N N N 19.354 -4.065 -10.732 -5.552 0.355  0.162  OP2   XEC 21 
XEC H1    H1  H 0 1 N N N 22.643 2.596  -5.139  5.391  -0.855 -0.107 H1    XEC 22 
XEC H2    H2  H 0 1 N N N 22.880 -1.330 -6.631  2.467  -3.748 0.578  H2    XEC 23 
XEC H3    H3  H 0 1 N N N 21.319 -0.680 -8.417  0.769  -2.083 0.031  H3    XEC 24 
XEC H4    H4  H 0 1 N N N 20.461 2.808  -9.152  1.295  0.786  -1.693 H4    XEC 25 
XEC H5    H5  H 0 1 N N N 18.656 2.110  -7.294  1.746  1.344  1.245  H5    XEC 26 
XEC H6    H6  H 0 1 N N N 17.326 4.680  -9.611  3.250  4.323  0.111  H6    XEC 27 
XEC H7    H7  H 0 1 N N N 17.747 4.350  -7.897  2.017  3.977  1.349  H7    XEC 28 
XEC H8    H8  H 0 1 N N N 19.042 4.450  -9.136  3.439  2.918  1.188  H8    XEC 29 
XEC H9    H9  H 0 1 N N N 18.930 -0.272 -7.903  -0.450 1.960  1.601  H9    XEC 30 
XEC H10   H10 H 0 1 N N N 18.299 0.862  -10.694 -1.227 1.490  -1.285 H10   XEC 31 
XEC H11   H11 H 0 1 N N N 16.683 0.317  -7.694  -1.325 3.707  0.226  H11   XEC 32 
XEC H12   H12 H 0 1 N N N 18.043 -1.636 -10.566 -2.054 0.176  1.352  H12   XEC 33 
XEC H13   H13 H 0 1 N N N 19.464 -1.154 -11.554 -2.884 1.566  0.613  H13   XEC 34 
XEC H15   H15 H 0 1 N N N 19.169 -4.879 -10.279 -5.697 0.848  -0.657 H15   XEC 35 
XEC OP3   O9  O 0 1 N Y N 21.624 -3.046 -11.097 -4.970 -1.889 -1.079 OP3   XEC 36 
XEC H14   H14 H 0 1 N Y N 22.457 -3.309 -10.722 -5.823 -2.299 -0.877 H14   XEC 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 
XEC OP2   P     SING N N 1  
XEC "C5'" "C4'" SING N N 2  
XEC "C5'" "O5'" SING N N 3  
XEC P     "O5'" SING N N 4  
XEC P     OP1   DOUB N N 5  
XEC "C4'" "O4'" SING N N 6  
XEC "C4'" "C3'" SING N N 7  
XEC "O4'" "C1'" SING N N 8  
XEC "O2'" CM2   SING N N 9  
XEC "O2'" "C2'" SING N N 10 
XEC "C1'" "C2'" SING N N 11 
XEC "C1'" N1    SING N N 12 
XEC "C3'" "O3'" SING N N 13 
XEC "C3'" "C2'" SING N N 14 
XEC N1    C6    SING N N 15 
XEC N1    C2    SING N N 16 
XEC C6    C5    DOUB N N 17 
XEC O2    C2    DOUB N N 18 
XEC C2    N3    SING N N 19 
XEC C5    C4    SING N N 20 
XEC N3    C4    SING N N 21 
XEC C4    O4    DOUB N N 22 
XEC N3    H1    SING N N 23 
XEC C5    H2    SING N N 24 
XEC C6    H3    SING N N 25 
XEC "C1'" H4    SING N N 26 
XEC "C2'" H5    SING N N 27 
XEC CM2   H6    SING N N 28 
XEC CM2   H7    SING N N 29 
XEC CM2   H8    SING N N 30 
XEC "C3'" H9    SING N N 31 
XEC "C4'" H10   SING N N 32 
XEC "O3'" H11   SING N N 33 
XEC "C5'" H12   SING N N 34 
XEC "C5'" H13   SING N N 35 
XEC OP2   H15   SING N N 36 
XEC P     OP3   SING N N 37 
XEC OP3   H14   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 
XEC SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(N2C=CC(=O)NC2=O)C(OC)C1O"                                                                                                                
XEC InChI            InChI                1.06  "InChI=1S/C10H15N2O9P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m0/s1" 
XEC InChIKey         InChI                1.06  FHMMECZNEPGJSJ-ZITKLIBNSA-N                                                                                                                               
XEC SMILES_CANONICAL CACTVS               3.385 "CO[C@H]1[C@@H](O)[C@H](CO[P](O)(O)=O)O[C@@H]1N2C=CC(=O)NC2=O"                                                                                            
XEC SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"                                                                                                  
XEC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@H]1[C@H]([C@@H](O[C@@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O"                                                                                              
XEC SMILES           "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)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 
XEC "SYSTEMATIC NAME" ACDLabs              12.01 "1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione"                                                     
XEC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{S},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-methoxy-3-oxidanyl-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 
XEC "Create component" 2022-11-14 RCSB 
XEC "Initial release"  2023-04-12 RCSB 
# 
