data_XE6
# 
_chem_comp.id                                    XE6 
_chem_comp.name                                  "4-amino-1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidin-2(1H)-one" 
_chem_comp.type                                  "RNA 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                     2022-11-14 
_chem_comp.pdbx_modified_date                    2023-09-15 
_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                     XE6 
_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        8F5C 
_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 
XE6 O2    O1  O 0 1 N N N 0.602  -14.312 6.427 3.847  -0.909 0.541  O2    XE6 1  
XE6 C2    C1  C 0 1 N N N 0.794  -13.232 6.980 3.460  0.230  0.337  C2    XE6 2  
XE6 N3    N1  N 0 1 N N N 1.882  -13.030 7.805 4.346  1.179  0.041  N3    XE6 3  
XE6 C4    C2  C 0 1 N N N 2.122  -11.861 8.396 3.953  2.426  -0.187 C4    XE6 4  
XE6 N4    N2  N 0 1 N N N 3.195  -11.749 9.130 4.877  3.398  -0.492 N4    XE6 5  
XE6 C5    C3  C 0 1 N N N 1.254  -10.793 8.202 2.582  2.748  -0.115 C5    XE6 6  
XE6 C6    C4  C 0 1 N N N 0.115  -11.005 7.449 1.694  1.772  0.187  C6    XE6 7  
XE6 N1    N3  N 0 1 N N N -0.084 -12.221 6.805 2.145  0.505  0.408  N1    XE6 8  
XE6 "C1'" C5  C 0 1 N N S -1.224 -12.501 5.922 1.194  -0.562 0.730  "C1'" XE6 9  
XE6 "O4'" O2  O 0 1 N N N -2.266 -11.528 6.194 -0.159 -0.057 0.721  "O4'" XE6 10 
XE6 "C4'" C6  C 0 1 N N S -2.468 -10.747 4.989 -1.027 -1.187 0.534  "C4'" XE6 11 
XE6 "C5'" C7  C 0 1 N N N -2.858 -9.301  5.330 -2.247 -0.774 -0.293 "C5'" XE6 12 
XE6 "O5'" O3  O 0 1 N N N -1.834 -8.707  6.089 -3.040 0.149  0.455  "O5'" XE6 13 
XE6 P     P1  P 0 1 N N N -2.092 -7.294  6.810 -4.403 0.793  -0.109 P     XE6 14 
XE6 OP1   O4  O 0 1 N N N -0.799 -6.849  7.312 -5.326 -0.288 -0.522 OP1   XE6 15 
XE6 OP2   O5  O 0 1 N N N -2.864 -6.334  5.913 -5.095 1.679  1.043  OP2   XE6 16 
XE6 "C3'" C8  C 0 1 N N S -1.118 -10.892 4.320 -0.222 -2.263 -0.220 "C3'" XE6 17 
XE6 "O3'" O6  O 0 1 N N N -1.230 -10.507 2.914 -0.151 -3.465 0.550  "O3'" XE6 18 
XE6 "C2'" C9  C 0 1 N N S -0.822 -12.332 4.485 1.185  -1.640 -0.384 "C2'" XE6 19 
XE6 "O2'" O7  O 0 1 N N N -1.748 -13.059 3.634 2.204  -2.615 -0.157 "O2'" XE6 20 
XE6 C22   C10 C 0 1 N N N -1.508 -14.464 3.510 2.631  -3.296 -1.339 C22   XE6 21 
XE6 H1    H1  H 0 1 N N N 3.812  -12.529 9.237 5.819  3.173  -0.541 H1    XE6 22 
XE6 H2    H2  H 0 1 N N N 3.401  -10.883 9.586 4.586  4.308  -0.658 H2    XE6 23 
XE6 H3    H3  H 0 1 N N N 1.464  -9.823  8.628 2.246  3.758  -0.297 H3    XE6 24 
XE6 H4    H4  H 0 1 N N N -0.624 -10.223 7.360 0.639  1.994  0.249  H4    XE6 25 
XE6 H5    H5  H 0 1 N N N -1.595 -13.523 6.089 1.431  -1.007 1.697  H5    XE6 26 
XE6 H6    H6  H 0 1 N N N -3.248 -11.199 4.358 -1.349 -1.571 1.502  H6    XE6 27 
XE6 H7    H7  H 0 1 N N N -3.003 -8.731  4.400 -1.915 -0.302 -1.218 H7    XE6 28 
XE6 H8    H8  H 0 1 N N N -3.792 -9.300  5.910 -2.841 -1.657 -0.528 H8    XE6 29 
XE6 H10   H10 H 0 1 N N N -2.364 -5.534  5.801 -5.923 2.099  0.772  H10   XE6 30 
XE6 H11   H11 H 0 1 N N N -0.367 -10.278 4.839 -0.668 -2.460 -1.195 H11   XE6 31 
XE6 H12   H12 H 0 1 N N N -1.420 -9.578  2.854 -1.005 -3.898 0.683  H12   XE6 32 
XE6 H13   H13 H 0 1 N N N 0.234  -12.582 4.304 1.297  -1.184 -1.367 H13   XE6 33 
XE6 H14   H14 H 0 1 N N N -2.265 -14.909 2.847 3.405  -4.019 -1.083 H14   XE6 34 
XE6 H15   H15 H 0 1 N N N -0.507 -14.629 3.086 1.783  -3.815 -1.786 H15   XE6 35 
XE6 H16   H16 H 0 1 N N N -1.568 -14.935 4.502 3.030  -2.573 -2.050 H16   XE6 36 
XE6 OP3   OP3 O 0 1 N Y N -3.077 -7.640  8.020 -4.070 1.727  -1.378 OP3   XE6 37 
XE6 H9    H9  H 0 1 N Y N -2.631 -7.489  8.845 -3.469 2.459  -1.181 H9    XE6 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 
XE6 "O3'" "C3'" SING N N 1  
XE6 C22   "O2'" SING N N 2  
XE6 "O2'" "C2'" SING N N 3  
XE6 "C3'" "C2'" SING N N 4  
XE6 "C3'" "C4'" SING N N 5  
XE6 "C2'" "C1'" SING N N 6  
XE6 "C4'" "C5'" SING N N 7  
XE6 "C4'" "O4'" SING N N 8  
XE6 "C5'" "O5'" SING N N 9  
XE6 OP2   P     SING N N 10 
XE6 "C1'" "O4'" SING N N 11 
XE6 "C1'" N1    SING N N 12 
XE6 "O5'" P     SING N N 13 
XE6 O2    C2    DOUB N N 14 
XE6 N1    C2    SING N N 15 
XE6 N1    C6    SING N N 16 
XE6 P     OP1   DOUB N N 17 
XE6 C2    N3    SING N N 18 
XE6 C6    C5    DOUB N N 19 
XE6 N3    C4    DOUB N N 20 
XE6 C5    C4    SING N N 21 
XE6 C4    N4    SING N N 22 
XE6 N4    H1    SING N N 23 
XE6 N4    H2    SING N N 24 
XE6 C5    H3    SING N N 25 
XE6 C6    H4    SING N N 26 
XE6 "C1'" H5    SING N N 27 
XE6 "C4'" H6    SING N N 28 
XE6 "C5'" H7    SING N N 29 
XE6 "C5'" H8    SING N N 30 
XE6 OP2   H10   SING N N 31 
XE6 "C3'" H11   SING N N 32 
XE6 "O3'" H12   SING N N 33 
XE6 "C2'" H13   SING N N 34 
XE6 C22   H14   SING N N 35 
XE6 C22   H15   SING N N 36 
XE6 C22   H16   SING N N 37 
XE6 P     OP3   SING N N 38 
XE6 OP3   H9    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 
XE6 SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(N2C=CC(N)=NC2=O)C(OC)C1O"                                                                                                                 
XE6 InChI            InChI                1.06  "InChI=1S/C10H16N3O8P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m0/s1" 
XE6 InChIKey         InChI                1.06  USRXKJOTSNCJMA-ZITKLIBNSA-N                                                                                                                                
XE6 SMILES_CANONICAL CACTVS               3.385 "CO[C@H]1[C@@H](O)[C@H](CO[P](O)(O)=O)O[C@@H]1N2C=CC(=NC2=O)N"                                                                                             
XE6 SMILES           CACTVS               3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N"                                                                                                   
XE6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@H]1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O"                                                                                               
XE6 SMILES           "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=NC2=O)N)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 
XE6 "SYSTEMATIC NAME" ACDLabs              12.01 "4-amino-1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidin-2(1H)-one"                                                        
XE6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{S},5~{S})-5-(4-azanyl-2-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 
XE6 "Create component" 2022-11-14 RCSB 
XE6 "Initial release"  2023-09-20 RCSB 
# 
