data_BRD
# 
_chem_comp.id                                    BRD 
_chem_comp.name                                  1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 N2 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-09-17 
_chem_comp.pdbx_modified_date                    2025-09-23 
_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                        244.244 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     BRD 
_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        1MQ0 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
BRD C4     C4     C 0 1 N N N N N N 29.798 93.986 102.670 3.847  -1.016 -0.256 C4     BRD 1  
BRD N3     N3     N 0 1 N N N N N N 29.184 94.137 103.992 2.626  -1.230 -1.031 N3     BRD 2  
BRD C2     C2     C 0 1 N N N N N N 29.748 94.067 105.222 1.418  -0.890 -0.575 C2     BRD 3  
BRD N1     N1     N 0 1 N N N N N N 30.860 93.361 105.592 1.148  -0.139 0.496  N1     BRD 4  
BRD C7     C7     C 0 1 N N N N N N 31.227 92.181 104.800 2.167  0.223  1.479  C7     BRD 5  
BRD C6     C6     C 0 1 N N N N N N 31.821 92.600 103.480 3.231  1.063  0.810  C6     BRD 6  
BRD O2     O2     O 0 1 N N N N N N 29.052 94.750 106.154 0.463  -1.307 -1.201 O2     BRD 7  
BRD "C1'"  "C1'"  C 0 1 N N R N N N 31.635 93.783 106.788 -0.223 0.339  0.693  "C1'"  BRD 8  
BRD "O4'"  "O4'"  O 0 1 N N N N N N 32.989 94.060 106.483 -1.152 -0.766 0.655  "O4'"  BRD 9  
BRD "C4'"  "C4'"  C 0 1 N N R N N N 33.820 93.681 107.572 -2.436 -0.174 0.359  "C4'"  BRD 10 
BRD "C3'"  "C3'"  C 0 1 N N S N N N 32.932 93.065 108.677 -2.136 0.907  -0.704 "C3'"  BRD 11 
BRD "C2'"  "C2'"  C 0 1 N N R N N N 31.660 92.715 107.902 -0.647 1.252  -0.479 "C2'"  BRD 12 
BRD "O2'"  "O2'"  O 0 1 N N N N N N 30.521 92.819 108.720 -0.501 2.628  -0.120 "O2'"  BRD 13 
BRD "O3'"  "O3'"  O 0 1 N N N N N N 32.658 94.040 109.662 -2.955 2.058  -0.491 "O3'"  BRD 14 
BRD "C5'"  "C5'"  C 0 1 N N N N N N 34.924 92.725 107.039 -3.390 -1.227 -0.207 "C5'"  BRD 15 
BRD "O5'"  "O5'"  O 0 1 N N N N N N 34.513 91.373 107.089 -3.687 -2.193 0.804  "O5'"  BRD 16 
BRD C5     C5     C 0 1 N N N N N N 31.183 93.356 102.551 4.041  0.465  -0.027 C5     BRD 17 
BRD HC4    HC4    H 0 1 N N N N N N 29.114 93.370 102.068 3.762  -1.525 0.704  HC4    BRD 18 
BRD HN3    HN3    H 0 1 N N N N N N 28.201 94.319 103.985 2.695  -1.634 -1.910 HN3    BRD 19 
BRD HC7    HC7    H 0 1 N N N N N N 31.965 91.585 105.357 1.707  0.794  2.286  HC7    BRD 20 
BRD HC6    HC6    H 0 1 N N N N N N 32.827 92.275 103.257 3.320  2.120  1.016  HC6    BRD 21 
BRD "H1'"  "H1'"  H 0 1 N N N N N N 31.165 94.686 107.204 -0.306 0.872  1.640  "H1'"  BRD 22 
BRD "H4'"  "H4'"  H 0 1 N N N N N N 34.314 94.571 107.988 -2.859 0.281  1.254  "H4'"  BRD 23 
BRD "H3'1" "1H3'" H 0 0 N N N N N N 33.400 92.160 109.093 -2.289 0.508  -1.707 "H3'1" BRD 24 
BRD "H2'"  "H2'"  H 0 1 N N N N N N 31.754 91.714 107.457 -0.064 1.025  -1.371 "H2'"  BRD 25 
BRD "H2'1" "1H2'" H 0 0 N N N N N N 30.556 92.154 109.398 -0.753 3.246  -0.820 "H2'1" BRD 26 
BRD "H3'"  "H3'"  H 0 1 N N N N N N 32.112 93.660 110.341 -3.904 1.885  -0.560 "H3'"  BRD 27 
BRD "H5'1" "1H5'" H 0 0 N N N N N N 35.152 92.990 105.996 -4.312 -0.745 -0.531 "H5'1" BRD 28 
BRD "H5'2" "2H5'" H 0 0 N N N N N N 35.828 92.846 107.654 -2.921 -1.724 -1.057 "H5'2" BRD 29 
BRD "H5'"  "H5'"  H 0 1 N N N N N N 35.209 90.818 106.757 -4.289 -2.892 0.515  "H5'"  BRD 30 
BRD HC5    HC5    H 0 1 N N N N N N 31.713 93.531 101.627 4.822  1.012  -0.535 HC5    BRD 31 
BRD H1     H1     H 0 1 N N N N N N 29.866 94.993 102.232 4.700  -1.414 -0.806 H1     BRD 32 
BRD H2     H2     H 0 1 N N N N N N 30.329 91.573 104.617 2.619  -0.682 1.885  H2     BRD 33 
# 
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 
BRD C4    N3     SING N N 1  
BRD C4    C5     SING N N 2  
BRD C4    HC4    SING N N 3  
BRD N3    C2     SING N N 4  
BRD N3    HN3    SING N N 5  
BRD C2    N1     SING N N 6  
BRD C2    O2     DOUB N N 7  
BRD N1    C7     SING N N 8  
BRD N1    "C1'"  SING N N 9  
BRD C7    C6     SING N N 10 
BRD C7    HC7    SING N N 11 
BRD C6    C5     DOUB N N 12 
BRD C6    HC6    SING N N 13 
BRD "C1'" "O4'"  SING N N 14 
BRD "C1'" "C2'"  SING N N 15 
BRD "C1'" "H1'"  SING N N 16 
BRD "O4'" "C4'"  SING N N 17 
BRD "C4'" "C3'"  SING N N 18 
BRD "C4'" "C5'"  SING N N 19 
BRD "C4'" "H4'"  SING N N 20 
BRD "C3'" "C2'"  SING N N 21 
BRD "C3'" "O3'"  SING N N 22 
BRD "C3'" "H3'1" SING N N 23 
BRD "C2'" "O2'"  SING N N 24 
BRD "C2'" "H2'"  SING N N 25 
BRD "O2'" "H2'1" SING N N 26 
BRD "O3'" "H3'"  SING N N 27 
BRD "C5'" "O5'"  SING N N 28 
BRD "C5'" "H5'1" SING N N 29 
BRD "C5'" "H5'2" SING N N 30 
BRD "O5'" "H5'"  SING N N 31 
BRD C5    HC5    SING N N 32 
BRD C4    H1     SING N N 33 
BRD C7    H2     SING N N 34 
# 
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 
BRD SMILES           ACDLabs              14.52   "O=C1NCC=CCN1C1OC(CO)C(O)C1O"                                                                                            
BRD InChI            InChI                1.06    "InChI=1S/C10H16N2O5/c13-5-6-7(14)8(15)9(17-6)12-4-2-1-3-11-10(12)16/h1-2,6-9,13-15H,3-5H2,(H,11,16)/t6-,7-,8-,9-/m1/s1" 
BRD InChIKey         InChI                1.06    HBBIVXDEBCKFIZ-FNCVBFRFSA-N                                                                                              
BRD SMILES_CANONICAL CACTVS               3.385   "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2CC=CCNC2=O"                                                                           
BRD SMILES           CACTVS               3.385   "OC[CH]1O[CH]([CH](O)[CH]1O)N2CC=CCNC2=O"                                                                                
BRD SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1C=CCN(C(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O"                                                                    
BRD SMILES           "OpenEye OEToolkits" 3.1.0.0 "C1C=CCN(C(=O)N1)C2C(C(C(O2)CO)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 
BRD "SYSTEMATIC NAME" ACDLabs              14.52   1-beta-D-ribofuranosyl-1,3,4,7-tetrahydro-2H-1,3-diazepin-2-one                                                     
BRD "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "3-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-4,7-dihydro-1~{H}-1,3-diazepin-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
BRD "Create component"  2002-09-17 RCSB 
BRD "Modify descriptor" 2011-06-04 RCSB 
BRD "Modify formula"    2025-09-23 RCSB 
# 
