data_B8Q
# 
_chem_comp.id                                    B8Q 
_chem_comp.name                                  
;3-methyl, cytidine-5'-monophosphate
;
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H18 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               C 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-09-25 
_chem_comp.pdbx_modified_date                    2019-04-29 
_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                        339.239 
_chem_comp.one_letter_code                       C 
_chem_comp.three_letter_code                     B8Q 
_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        6EK0 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
B8Q N1    N1  N 0 1 N N N 226.264 348.521 210.046 -2.066 -0.108 -0.091 N1    B8Q 1  
B8Q C2    C1  C 0 1 N N N 225.534 347.355 210.346 -3.192 -0.093 -0.817 C2    B8Q 2  
B8Q C5    C2  C 0 1 N N N 227.937 347.194 209.016 -2.713 -1.949 1.235  C5    B8Q 3  
B8Q "C1'" C3  C 0 1 N N R 225.718 349.834 210.464 -1.040 0.896  -0.379 "C1'" B8Q 4  
B8Q "C2'" C4  C 0 1 N N R 225.969 350.127 211.940 -0.856 1.850  0.829  "C2'" B8Q 5  
B8Q "C3'" C5  C 0 1 N N S 227.219 350.985 211.851 0.592  2.359  0.623  "C3'" B8Q 6  
B8Q C4    C6  C 0 1 N N S 227.246 346.031 209.288 -4.004 -1.995 0.445  C4    B8Q 7  
B8Q "C4'" C7  C 0 1 N N R 226.922 351.825 210.631 1.239  1.297  -0.287 "C4'" B8Q 8  
B8Q "C5'" C8  C 0 1 N N N 228.106 352.491 209.990 2.466  0.698  0.404  "C5'" B8Q 9  
B8Q C6    C9  C 0 1 N N N 227.426 348.421 209.399 -1.826 -1.022 0.923  C6    B8Q 10 
B8Q C31   C10 C 0 1 N N N 225.266 344.889 210.265 -5.401 -0.955 -1.424 C31   B8Q 11 
B8Q N3    N2  N 0 1 N N N 226.027 346.102 209.966 -4.182 -0.985 -0.611 N3    B8Q 12 
B8Q N4    N3  N 0 1 N N N 227.745 344.838 208.908 -5.118 -1.843 1.391  N4    B8Q 13 
B8Q O2    O1  O 0 1 N N N 224.442 347.416 210.941 -3.324 0.747  -1.686 O2    B8Q 14 
B8Q "O2'" O2  O 0 1 N N N 224.874 350.887 212.419 -1.789 2.931  0.772  "O2'" B8Q 15 
B8Q "O3'" O3  O 0 1 N N N 227.506 351.738 213.012 0.587  3.634  -0.022 "O3'" B8Q 16 
B8Q "O4'" O4  O 0 1 N N N 226.336 350.865 209.721 0.256  0.274  -0.516 "O4'" B8Q 17 
B8Q "O5'" O5  O 0 1 N N N 229.263 351.687 210.124 3.126  -0.199 -0.491 "O5'" B8Q 18 
B8Q OP1   O6  O 0 1 N N N 230.746 350.180 208.832 4.216  -1.783 1.144  OP1   B8Q 19 
B8Q OP2   O7  O 0 1 N N N 231.401 352.667 209.257 4.850  -2.017 -1.288 OP2   B8Q 20 
B8Q P     P1  P 0 1 N N N 230.358 351.624 208.978 4.459  -1.010 -0.095 P     B8Q 21 
B8Q H1    H1  H 0 1 N N N 228.884 347.146 208.500 -2.519 -2.661 2.024  H1    B8Q 22 
B8Q H2    H2  H 0 1 N N N 224.632 349.843 210.287 -1.296 1.459  -1.276 H2    B8Q 23 
B8Q H3    H3  H 0 1 N N N 226.146 349.205 212.513 -0.948 1.309  1.770  H3    B8Q 24 
B8Q H4    H4  H 0 1 N N N 228.070 350.328 211.618 1.115  2.417  1.577  H4    B8Q 25 
B8Q H5    H5  H 0 1 N N N 226.718 346.118 208.327 -4.086 -2.983 -0.007 H5    B8Q 26 
B8Q H6    H6  H 0 1 N N N 226.178 352.591 210.896 1.532  1.750  -1.234 H6    B8Q 27 
B8Q H7    H7  H 0 1 N N N 228.282 353.462 210.477 3.150  1.498  0.687  H7    B8Q 28 
B8Q H8    H8  H 0 1 N N N 227.897 352.649 208.922 2.152  0.156  1.296  H8    B8Q 29 
B8Q H9    H9  H 0 1 N N N 227.981 349.319 209.169 -0.895 -0.975 1.469  H9    B8Q 30 
B8Q H10   H10 H 0 1 N N N 224.343 345.157 210.800 -6.141 -0.313 -0.945 H10   B8Q 31 
B8Q H11   H11 H 0 1 N N N 225.010 344.376 209.326 -5.167 -0.564 -2.414 H11   B8Q 32 
B8Q H12   H12 H 0 1 N N N 225.873 344.221 210.894 -5.801 -1.965 -1.516 H12   B8Q 33 
B8Q H13   H13 H 0 1 N N N 227.117 344.110 209.185 -5.115 -2.585 2.075  H13   B8Q 34 
B8Q H14   H14 H 0 1 N N N 227.854 344.824 207.914 -5.092 -0.939 1.838  H14   B8Q 35 
B8Q H16   H16 H 0 1 N N N 225.004 351.085 213.339 -1.714 3.556  1.506  H16   B8Q 36 
B8Q H17   H17 H 0 1 N N N 227.682 351.149 213.736 0.139  4.328  0.482  H17   B8Q 37 
B8Q H19   H19 H 0 1 N N N 232.255 352.255 209.313 5.645  -2.540 -1.118 H19   B8Q 38 
B8Q OP3   OP3 O 0 1 N N N 229.558 352.050 207.656 5.666  0.027  0.149  OP3   B8Q 39 
B8Q H15   H15 H 0 1 N N N 229.500 351.307 207.067 5.881  0.569  -0.623 H15   B8Q 40 
# 
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 
B8Q OP1   P     DOUB N N 1  
B8Q N4    C4    SING N N 2  
B8Q P     OP2   SING N N 3  
B8Q P     "O5'" SING N N 4  
B8Q C5    C4    SING N N 5  
B8Q C5    C6    DOUB N N 6  
B8Q C4    N3    SING N N 7  
B8Q C6    N1    SING N N 8  
B8Q "O4'" "C1'" SING N N 9  
B8Q "O4'" "C4'" SING N N 10 
B8Q N3    C31   SING N N 11 
B8Q N3    C2    SING N N 12 
B8Q "C5'" "O5'" SING N N 13 
B8Q "C5'" "C4'" SING N N 14 
B8Q N1    C2    SING N N 15 
B8Q N1    "C1'" SING N N 16 
B8Q C2    O2    DOUB N N 17 
B8Q "C1'" "C2'" SING N N 18 
B8Q "C4'" "C3'" SING N N 19 
B8Q "C3'" "C2'" SING N N 20 
B8Q "C3'" "O3'" SING N N 21 
B8Q "C2'" "O2'" SING N N 22 
B8Q C5    H1    SING N N 23 
B8Q "C1'" H2    SING N N 24 
B8Q "C2'" H3    SING N N 25 
B8Q "C3'" H4    SING N N 26 
B8Q C4    H5    SING N N 27 
B8Q "C4'" H6    SING N N 28 
B8Q "C5'" H7    SING N N 29 
B8Q "C5'" H8    SING N N 30 
B8Q C6    H9    SING N N 31 
B8Q C31   H10   SING N N 32 
B8Q C31   H11   SING N N 33 
B8Q C31   H12   SING N N 34 
B8Q N4    H13   SING N N 35 
B8Q N4    H14   SING N N 36 
B8Q "O2'" H16   SING N N 37 
B8Q "O3'" H17   SING N N 38 
B8Q OP2   H19   SING N N 39 
B8Q P     OP3   SING N N 40 
B8Q OP3   H15   SING N N 41 
# 
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 
B8Q InChI            InChI                1.03  "InChI=1S/C10H18N3O8P/c1-12-6(11)2-3-13(10(12)16)9-8(15)7(14)5(21-9)4-20-22(17,18)19/h2-3,5-9,14-15H,4,11H2,1H3,(H2,17,18,19)/t5-,6+,7-,8-,9-/m1/s1" 
B8Q InChIKey         InChI                1.03  HUUPYGHSEPUDJF-ANZWQOBJSA-N                                                                                                                          
B8Q SMILES_CANONICAL CACTVS               3.385 "CN1[C@H](N)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O"                                                                                  
B8Q SMILES           CACTVS               3.385 "CN1[CH](N)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O"                                                                                         
B8Q SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N"                                                                                      
B8Q SMILES           "OpenEye OEToolkits" 2.0.6 "CN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)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 
B8Q "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-3,4-bis(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 
B8Q "Create component"       2017-09-25 EBI 
B8Q "Modify linking type"    2017-09-25 EBI 
B8Q "Modify one letter code" 2019-04-29 EBI 
# 
