data_M5O
# 
_chem_comp.id                                    M5O 
_chem_comp.name                                  "(2~{S},3~{R})-2-[3,4-bis(oxidanyl)phenyl]-3,4-dihydro-2~{H}-chromene-3,5,7-triol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H14 O6" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "(-)-catechin" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-07-22 
_chem_comp.pdbx_modified_date                    2023-08-25 
_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                        290.268 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     M5O 
_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        8AGQ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
M5O OAB O1  O 0 1 N N N -8.985 12.082 11.386 4.898  -2.601 -0.307 OAB M5O 1  
M5O CAT C1  C 0 1 Y N N -7.947 11.202 11.255 4.079  -1.523 -0.188 CAT M5O 2  
M5O CAK C2  C 0 1 Y N N -7.441 10.943 9.993  4.618  -0.254 -0.038 CAK M5O 3  
M5O CAY C3  C 0 1 Y N N -6.419 10.056 9.864  3.780  0.842  0.081  CAY M5O 4  
M5O OAG O2  O 0 1 N N N -5.859 9.808  8.653  4.309  2.086  0.228  OAG M5O 5  
M5O CBD C4  C 0 1 Y N N -5.843 9.419  10.970 2.400  0.676  0.050  CBD M5O 6  
M5O CAP C5  C 0 1 N N N -4.764 8.387  10.799 1.521  1.895  0.172  CAP M5O 7  
M5O CAN C6  C 0 1 Y N N -7.424 10.585 12.371 2.704  -1.689 -0.220 CAN M5O 8  
M5O CBC C7  C 0 1 Y N N -6.367 9.701  12.216 1.862  -0.590 -0.095 CBC M5O 9  
M5O OAR O3  O 0 1 N N N -5.827 9.197  13.379 0.519  -0.798 -0.118 OAR M5O 10 
M5O CBF C8  C 0 1 N N S -4.454 8.669  13.253 -0.326 0.325  -0.372 CBF M5O 11 
M5O CBE C9  C 0 1 N N R -4.447 7.652  12.094 0.101  1.470  0.554  CBE M5O 12 
M5O OAQ O4  O 0 1 N N N -3.197 6.998  12.014 -0.791 2.576  0.396  OAQ M5O 13 
M5O CBA C10 C 0 1 Y N N -3.999 8.208  14.619 -1.760 -0.046 -0.094 CBA M5O 14 
M5O CAO C11 C 0 1 Y N N -4.744 7.286  15.326 -2.763 0.399  -0.935 CAO M5O 15 
M5O CAV C12 C 0 1 Y N N -4.360 6.918  16.602 -4.082 0.059  -0.680 CAV M5O 16 
M5O OAD O5  O 0 1 N N N -5.075 6.052  17.388 -5.070 0.495  -1.507 OAD M5O 17 
M5O CAU C13 C 0 1 Y N N -3.167 7.405  17.129 -4.393 -0.731 0.423  CAU M5O 18 
M5O OAC O6  O 0 1 N N N -2.740 7.048  18.386 -5.686 -1.068 0.676  OAC M5O 19 
M5O CAI C14 C 0 1 Y N N -2.417 8.296  16.405 -3.383 -1.174 1.261  CAI M5O 20 
M5O CAJ C15 C 0 1 Y N N -2.843 8.705  15.150 -2.069 -0.835 0.998  CAJ M5O 21 
M5O H1  H1  H 0 1 N N N -9.223 12.158 12.303 5.143  -2.809 -1.219 H1  M5O 22 
M5O H2  H2  H 0 1 N N N -7.851 11.438 9.125  5.690  -0.121 -0.014 H2  M5O 23 
M5O H3  H3  H 0 1 N N N -5.165 9.167  8.750  4.469  2.546  -0.607 H3  M5O 24 
M5O H4  H4  H 0 1 N N N -5.094 7.653  10.049 1.921  2.556  0.940  H4  M5O 25 
M5O H5  H5  H 0 1 N N N -3.851 8.887  10.445 1.497  2.421  -0.783 H5  M5O 26 
M5O H6  H6  H 0 1 N N N -7.831 10.787 13.351 2.285  -2.677 -0.341 H6  M5O 27 
M5O H7  H7  H 0 1 N N N -3.800 9.502  12.954 -0.222 0.635  -1.412 H7  M5O 28 
M5O H8  H8  H 0 1 N N N -5.243 6.916  12.279 0.085  1.131  1.590  H8  M5O 29 
M5O H9  H9  H 0 1 N N N -3.022 6.548  12.832 -0.568 3.342  0.941  H9  M5O 30 
M5O H10 H10 H 0 1 N N N -5.628 6.852  14.882 -2.519 1.012  -1.790 H10 M5O 31 
M5O H11 H11 H 0 1 N N N -4.632 5.941  18.221 -5.264 -0.105 -2.240 H11 M5O 32 
M5O H12 H12 H 0 1 N N N -3.353 6.430  18.765 -5.968 -1.892 0.255  H12 M5O 33 
M5O H13 H13 H 0 1 N N N -1.493 8.680  16.813 -3.622 -1.786 2.118  H13 M5O 34 
M5O H14 H14 H 0 1 N N N -2.258 9.420  14.590 -1.282 -1.184 1.651  H14 M5O 35 
# 
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 
M5O OAG CAY SING N N 1  
M5O CAY CAK DOUB Y N 2  
M5O CAY CBD SING Y N 3  
M5O CAK CAT SING Y N 4  
M5O CAP CBD SING N N 5  
M5O CAP CBE SING N N 6  
M5O CBD CBC DOUB Y N 7  
M5O CAT OAB SING N N 8  
M5O CAT CAN DOUB Y N 9  
M5O OAQ CBE SING N N 10 
M5O CBE CBF SING N N 11 
M5O CBC CAN SING Y N 12 
M5O CBC OAR SING N N 13 
M5O CBF OAR SING N N 14 
M5O CBF CBA SING N N 15 
M5O CBA CAJ DOUB Y N 16 
M5O CBA CAO SING Y N 17 
M5O CAJ CAI SING Y N 18 
M5O CAO CAV DOUB Y N 19 
M5O CAI CAU DOUB Y N 20 
M5O CAV CAU SING Y N 21 
M5O CAV OAD SING N N 22 
M5O CAU OAC SING N N 23 
M5O OAB H1  SING N N 24 
M5O CAK H2  SING N N 25 
M5O OAG H3  SING N N 26 
M5O CAP H4  SING N N 27 
M5O CAP H5  SING N N 28 
M5O CAN H6  SING N N 29 
M5O CBF H7  SING N N 30 
M5O CBE H8  SING N N 31 
M5O OAQ H9  SING N N 32 
M5O CAO H10 SING N N 33 
M5O OAD H11 SING N N 34 
M5O OAC H12 SING N N 35 
M5O CAI H13 SING N N 36 
M5O CAJ H14 SING N N 37 
# 
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 
M5O InChI            InChI                1.06  "InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15+/m1/s1" 
M5O InChIKey         InChI                1.06  PFTAWBLQPZVEMU-HIFRSBDPSA-N                                                                                        
M5O SMILES_CANONICAL CACTVS               3.385 "O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c3ccc(O)c(O)c3"                                                                     
M5O SMILES           CACTVS               3.385 "O[CH]1Cc2c(O)cc(O)cc2O[CH]1c3ccc(O)c(O)c3"                                                                        
M5O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1[C@H]2[C@@H](Cc3c(cc(cc3O2)O)O)O)O)O"                                                                   
M5O SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C2C(Cc3c(cc(cc3O2)O)O)O)O)O"                                                                            
# 
_pdbx_chem_comp_identifier.comp_id           M5O 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S},3~{R})-2-[3,4-bis(oxidanyl)phenyl]-3,4-dihydro-2~{H}-chromene-3,5,7-triol" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      M5O 
_pdbx_chem_comp_synonyms.name         "(-)-catechin" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
M5O "Create component"  2022-07-22 PDBE 
M5O "Modify descriptor" 2022-08-22 RCSB 
M5O "Initial release"   2023-08-30 RCSB 
# 
