data_LB9
# 
_chem_comp.id                                    LB9 
_chem_comp.name                                  5-azaniumylpentylazanium 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C5 H16 N2" 
_chem_comp.mon_nstd_parent_comp_id               N2P 
_chem_comp.pdbx_synonyms                         "cadaverine (protonated)" 
_chem_comp.pdbx_formal_charge                    2 
_chem_comp.pdbx_initial_date                     2022-06-29 
_chem_comp.pdbx_modified_date                    2023-02-17 
_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                        104.194 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LB9 
_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        8A71 
_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 
LB9 C1   C1  C 0 1 N N N 5.149 11.481 13.994 2.499  -0.514 0.002  C1   LB9 1  
LB9 C2   C2  C 0 1 N N N 5.684 10.615 15.084 1.249  0.369  -0.001 C2   LB9 2  
LB9 C3   C3  C 0 1 N N N 4.878 10.709 16.350 0.000  -0.514 0.002  C3   LB9 3  
LB9 C4   C4  C 0 1 N N N 5.468 9.991  17.516 -1.249 0.369  -0.001 C4   LB9 4  
LB9 NE2  N1  N 1 1 N N N 5.992 11.616 12.823 3.698  0.334  -0.001 NE2  LB9 5  
LB9 C5   C5  C 0 1 N N N 4.742 10.269 18.801 -2.499 -0.514 0.002  C5   LB9 6  
LB9 N1   N2  N 1 1 N N N 5.270 9.447  19.915 -3.698 0.334  -0.001 N1   LB9 7  
LB9 H1C1 H1  H 0 0 N N N 4.987 12.486 14.411 2.499  -1.141 0.894  H1C1 LB9 8  
LB9 H1C2 H2  H 0 0 N N N 4.186 11.059 13.670 2.499  -1.146 -0.886 H1C2 LB9 9  
LB9 H2C1 H3  H 0 0 N N N 5.676 9.571  14.739 1.249  1.001  0.887  H2C1 LB9 10 
LB9 H2C2 H4  H 0 0 N N N 6.718 10.922 15.302 1.249  0.996  -0.893 H2C2 LB9 11 
LB9 H3C1 H5  H 0 0 N N N 4.779 11.772 16.616 0.000  -1.146 -0.886 H3C1 LB9 12 
LB9 H3C2 H6  H 0 0 N N N 3.882 10.286 16.155 0.000  -1.141 0.894  H3C2 LB9 13 
LB9 H4C1 H7  H 0 0 N N N 5.430 8.910  17.318 -1.249 1.001  0.887  H4C1 LB9 14 
LB9 H4C2 H8  H 0 0 N N N 6.516 10.307 17.629 -1.249 0.996  -0.893 H4C2 LB9 15 
LB9 HE21 H9  H 0 0 N N N 5.545 12.213 12.157 4.522  -0.249 0.001  HE21 LB9 16 
LB9 HE22 H10 H 0 0 N N N 6.871 12.013 13.089 3.698  0.914  -0.827 HE22 LB9 17 
LB9 H11  H11 H 0 1 N N N 6.143 10.715 12.415 3.698  0.919  0.821  H11  LB9 18 
LB9 H5C1 H12 H 0 0 N N N 4.861 11.333 19.055 -2.499 -1.146 -0.886 H5C1 LB9 19 
LB9 H5C2 H13 H 0 0 N N N 3.675 10.041 18.664 -2.499 -1.141 0.894  H5C2 LB9 20 
LB9 H1N1 H14 H 0 0 N N N 4.766 9.657  20.753 -3.698 0.914  -0.827 H1N1 LB9 21 
LB9 H1N2 H15 H 0 0 N N N 5.161 8.478  19.694 -4.522 -0.249 0.001  H1N2 LB9 22 
LB9 H16  H16 H 0 1 N N N 6.240 9.652  20.050 -3.698 0.919  0.821  H16  LB9 23 
# 
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 
LB9 NE2 C1   SING N N 1  
LB9 C1  C2   SING N N 2  
LB9 C2  C3   SING N N 3  
LB9 C3  C4   SING N N 4  
LB9 C4  C5   SING N N 5  
LB9 C5  N1   SING N N 6  
LB9 C1  H1C1 SING N N 7  
LB9 C1  H1C2 SING N N 8  
LB9 C2  H2C1 SING N N 9  
LB9 C2  H2C2 SING N N 10 
LB9 C3  H3C1 SING N N 11 
LB9 C3  H3C2 SING N N 12 
LB9 C4  H4C1 SING N N 13 
LB9 C4  H4C2 SING N N 14 
LB9 NE2 HE21 SING N N 15 
LB9 NE2 HE22 SING N N 16 
LB9 NE2 H11  SING N N 17 
LB9 C5  H5C1 SING N N 18 
LB9 C5  H5C2 SING N N 19 
LB9 N1  H1N1 SING N N 20 
LB9 N1  H1N2 SING N N 21 
LB9 N1  H16  SING N N 22 
# 
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 
LB9 InChI            InChI                1.06  InChI=1S/C5H14N2/c6-4-2-1-3-5-7/h1-7H2/p+2 
LB9 InChIKey         InChI                1.06  VHRGRCVQAFMJIZ-UHFFFAOYSA-P                
LB9 SMILES_CANONICAL CACTVS               3.385 "[NH3+]CCCCC[NH3+]"                        
LB9 SMILES           CACTVS               3.385 "[NH3+]CCCCC[NH3+]"                        
LB9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CC[NH3+])CC[NH3+]"                      
LB9 SMILES           "OpenEye OEToolkits" 2.0.7 "C(CC[NH3+])CC[NH3+]"                      
# 
_pdbx_chem_comp_identifier.comp_id           LB9 
_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        5-azaniumylpentylazanium 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      LB9 
_pdbx_chem_comp_synonyms.name         "cadaverine (protonated)" 
_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 
LB9 "Create component"  2022-06-29 PDBE 
LB9 "Modify descriptor" 2022-08-22 RCSB 
LB9 "Initial release"   2023-02-22 RCSB 
# 
