data_VIB
# 
_chem_comp.id                                    VIB 
_chem_comp.name                                  "3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C12 H17 N4 O S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "THIAMIN; VITAMIN B1" 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2001-04-17 
_chem_comp.pdbx_modified_date                    2020-01-26 
_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                        265.355 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VIB 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1IG3 
_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 
VIB CM2  CM2  C 0 1 N N N 7.184 69.654 25.180 5.038  1.578  1.354  CM2  VIB 1  
VIB N4A  N4A  N 0 1 N N N 4.578 71.418 21.377 2.558  -2.230 -0.166 N4A  VIB 2  
VIB CM4  CM4  C 0 1 N N N 6.456 72.345 16.851 -1.096 1.522  -1.063 CM4  VIB 3  
VIB O1   O1   O 0 1 N N N 5.885 69.796 12.826 -5.653 1.650  0.322  O1   VIB 4  
VIB C7   C7   C 0 1 N N N 6.138 69.427 14.175 -4.614 0.769  -0.110 C7   VIB 5  
VIB C6   C6   C 0 1 N N N 5.176 70.216 15.068 -3.432 0.861  0.857  C6   VIB 6  
VIB C2   C2   C 0 1 Y N N 5.981 69.324 18.758 -0.615 -2.005 -0.142 C2   VIB 7  
VIB S1   S1   S 0 1 Y N N 5.267 68.452 17.383 -2.048 -1.783 0.814  S1   VIB 8  
VIB C5   C5   C 0 1 Y N N 5.545 70.005 16.519 -2.337 -0.068 0.401  C5   VIB 9  
VIB C4   C4   C 0 1 Y N N 6.111 70.939 17.325 -1.292 0.167  -0.433 C4   VIB 10 
VIB N3   N3   N 1 1 Y N N 6.319 70.514 18.520 -0.458 -0.820 -0.686 N3   VIB 11 
VIB C7A  C7A  C 0 1 N N N 6.917 71.344 19.588 0.673  -0.590 -1.588 C7A  VIB 12 
VIB C4A  C4A  C 0 1 Y N N 5.814 70.960 21.877 2.720  -0.854 -0.132 C4A  VIB 13 
VIB N3A  N3A  N 0 1 Y N N 5.898 70.553 23.219 3.730  -0.309 0.539  N3A  VIB 14 
VIB C2A  C2A  C 0 1 Y N N 7.105 70.091 23.750 3.884  0.999  0.577  C2A  VIB 15 
VIB N1A  N1A  N 0 1 Y N N 8.245 70.041 22.931 3.061  1.814  -0.050 N1A  VIB 16 
VIB C6A  C6A  C 0 1 Y N N 8.176 70.447 21.584 2.034  1.346  -0.745 C6A  VIB 17 
VIB C5A  C5A  C 0 1 Y N N 6.968 70.911 21.045 1.829  -0.018 -0.808 C5A  VIB 18 
VIB HM21 1HM2 H 0 0 N N N 8.147 69.285 25.603 4.726  1.767  2.381  HM21 VIB 19 
VIB HM22 2HM2 H 0 0 N N N 6.814 70.487 25.822 5.869  0.873  1.351  HM22 VIB 20 
VIB HM23 3HM2 H 0 0 N N N 6.404 68.875 25.352 5.354  2.513  0.892  HM23 VIB 21 
VIB H4A1 1H4A H 0 0 N N N 4.517 71.713 20.402 1.820  -2.619 -0.661 H4A1 VIB 22 
VIB H4A2 2H4A H 0 0 N N N 4.244 72.176 21.971 3.181  -2.803 0.307  H4A2 VIB 23 
VIB HM41 1HM4 H 0 0 N N N 6.920 73.112 17.513 -0.396 2.104  -0.464 HM41 VIB 24 
VIB HM42 2HM4 H 0 0 N N N 7.106 72.243 15.950 -0.699 1.400  -2.071 HM42 VIB 25 
VIB HM43 3HM4 H 0 0 N N N 5.526 72.790 16.425 -2.053 2.042  -1.111 HM43 VIB 26 
VIB HO1  HO1  H 0 1 N N N 6.481 69.306 12.272 -6.377 1.562  -0.313 HO1  VIB 27 
VIB HC71 1HC7 H 0 0 N N N 6.075 68.326 14.340 -4.288 1.055  -1.110 HC71 VIB 28 
VIB HC72 2HC7 H 0 0 N N N 7.205 69.561 14.466 -4.990 -0.254 -0.129 HC72 VIB 29 
VIB HC61 1HC6 H 0 0 N N N 5.139 71.296 14.795 -3.758 0.575  1.857  HC61 VIB 30 
VIB HC62 2HC6 H 0 0 N N N 4.109 69.963 14.863 -3.057 1.884  0.876  HC62 VIB 31 
VIB HC2  HC2  H 0 1 N N N 6.226 69.116 19.812 -0.009 -2.892 -0.260 HC2  VIB 32 
VIB H7A1 1H7A H 0 0 N N N 7.959 71.587 19.276 0.378  0.111  -2.368 H7A1 VIB 33 
VIB H7A2 2H7A H 0 0 N N N 6.418 72.340 19.554 0.973  -1.534 -2.042 H7A2 VIB 34 
VIB H6AC CH6A H 0 0 N N N 9.074 70.401 20.946 1.365  2.024  -1.255 H6AC VIB 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 
VIB CM2 C2A  SING N N 1  
VIB CM2 HM21 SING N N 2  
VIB CM2 HM22 SING N N 3  
VIB CM2 HM23 SING N N 4  
VIB N4A C4A  SING N N 5  
VIB N4A H4A1 SING N N 6  
VIB N4A H4A2 SING N N 7  
VIB CM4 C4   SING N N 8  
VIB CM4 HM41 SING N N 9  
VIB CM4 HM42 SING N N 10 
VIB CM4 HM43 SING N N 11 
VIB O1  C7   SING N N 12 
VIB O1  HO1  SING N N 13 
VIB C7  C6   SING N N 14 
VIB C7  HC71 SING N N 15 
VIB C7  HC72 SING N N 16 
VIB C6  C5   SING N N 17 
VIB C6  HC61 SING N N 18 
VIB C6  HC62 SING N N 19 
VIB C2  S1   SING Y N 20 
VIB C2  N3   DOUB Y N 21 
VIB C2  HC2  SING N N 22 
VIB S1  C5   SING Y N 23 
VIB C5  C4   DOUB Y N 24 
VIB C4  N3   SING Y N 25 
VIB N3  C7A  SING N N 26 
VIB C7A C5A  SING N N 27 
VIB C7A H7A1 SING N N 28 
VIB C7A H7A2 SING N N 29 
VIB C4A N3A  SING Y N 30 
VIB C4A C5A  DOUB Y N 31 
VIB N3A C2A  DOUB Y N 32 
VIB C2A N1A  SING Y N 33 
VIB N1A C6A  DOUB Y N 34 
VIB C6A C5A  SING Y N 35 
VIB C6A H6AC SING N N 36 
# 
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 
VIB SMILES           ACDLabs              10.04 "n1c(c(cnc1C)C[n+]2c(c(sc2)CCO)C)N"                                                                               
VIB SMILES_CANONICAL CACTVS               3.341 "Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1"                                                                                 
VIB SMILES           CACTVS               3.341 "Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1"                                                                                 
VIB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO"                                                                                   
VIB SMILES           "OpenEye OEToolkits" 1.5.0 "Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO"                                                                                   
VIB InChI            InChI                1.03  "InChI=1S/C12H17N4OS/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15)/q+1" 
VIB InChIKey         InChI                1.03  JZRWCGZRTZMZEH-UHFFFAOYSA-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 
VIB "SYSTEMATIC NAME" ACDLabs              10.04 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-hydroxyethyl)-4-methyl-1,3-thiazol-3-ium" 
VIB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethanol"   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VIB "Create component"  2001-04-17 EBI  
VIB "Modify descriptor" 2011-06-04 RCSB 
VIB "Modify synonyms"   2019-12-17 PDBE 
VIB "Modify synonyms"   2020-01-26 RCSB 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 VIB THIAMIN      ? ? 
2 VIB "VITAMIN B1" ? ? 
# 
