data_V9M
# 
_chem_comp.id                                    V9M 
_chem_comp.name                                  "(3R)-N-[(1S)-1-carboxy-2-methylpropyl]-N,3,5,5-tetramethylhexan-1-aminium" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C15 H32 N O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    1 
_chem_comp.pdbx_initial_date                     2020-07-21 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        258.420 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V9M 
_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        7JFR 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
V9M C    C    C 0 1 N N N Y N Y 2.912  41.442 16.580 2.695  1.354  -0.089 C    V9M 1  
V9M CA   CA   C 0 1 N N S Y N N 2.448  40.340 17.542 2.735  -0.081 0.371  CA   V9M 2  
V9M CB   CB   C 0 1 N N N N N N 2.666  40.739 18.992 3.995  -0.756 -0.173 CB   V9M 3  
V9M CG1  CG1  C 0 1 N N N N N N 4.142  41.128 19.336 5.232  -0.107 0.451  CG1  V9M 4  
V9M N    N    N 1 1 N N N Y Y N 3.009  39.062 17.160 1.547  -0.788 -0.126 N    V9M 5  
V9M C40  C40  C 0 1 N N N N N N 2.153  38.044 17.721 0.337  -0.089 0.327  C40  V9M 6  
V9M C42  C42  C 0 1 N N N N N N 2.796  37.243 18.720 -0.900 -0.888 -0.092 C42  V9M 7  
V9M C43  C43  C 0 1 N N R N N N 1.855  36.349 19.376 -2.160 -0.161 0.379  C43  V9M 8  
V9M C44  C44  C 0 1 N N N N N N 0.939  37.081 20.248 -3.397 -0.892 -0.145 C44  V9M 9  
V9M C45  C45  C 0 1 N N N N N N -0.515 37.095 20.105 -4.578 0.079  -0.203 C45  V9M 10 
V9M C46  C46  C 0 1 N N N N N N -1.137 35.819 20.347 -4.253 1.220  -1.170 C46  V9M 11 
V9M C47  C47  C 0 1 N N N N N N -1.033 37.666 18.893 -5.825 -0.662 -0.689 C47  V9M 12 
V9M C48  C48  C 0 1 N N N N N N -0.968 37.953 21.165 -4.836 0.652  1.192  C48  V9M 13 
V9M C49  C49  C 0 1 N N N N N N 1.201  35.432 18.482 -2.193 -0.136 1.909  C49  V9M 14 
V9M O    O    O 0 1 N N N Y N Y 4.068  41.756 16.420 1.868  1.706  -0.897 O    V9M 15 
V9M C54  C54  C 0 1 N N N N N N 3.024  38.934 15.694 1.574  -0.820 -1.594 C54  V9M 16 
V9M CG2  CG2  C 0 1 N N N N N N 1.835  41.865 19.313 3.968  -2.245 0.178  CG2  V9M 17 
V9M OXT  OXT  O 0 1 N Y N Y N Y 1.843  42.077 15.847 3.574  2.241  0.401  OXT  V9M 18 
V9M HA   HA   H 0 1 N N N Y N N 1.359  40.263 17.408 2.748  -0.112 1.461  HA   V9M 19 
V9M HB   HB   H 0 1 N N N N N N 2.387  39.887 19.629 4.031  -0.639 -1.256 HB   V9M 20 
V9M HG13 HG13 H 0 0 N N N N N N 4.211  41.402 20.399 5.196  -0.224 1.534  HG13 V9M 21 
V9M HG11 HG11 H 0 0 N N N N N N 4.803  40.272 19.134 6.130  -0.588 0.064  HG11 V9M 22 
V9M HG12 HG12 H 0 0 N N N N N N 4.450  41.983 18.716 5.251  0.954  0.201  HG12 V9M 23 
V9M H    HN   H 0 1 N N N Y Y N 3.938  38.971 17.519 1.544  -1.732 0.231  HN   V9M 24 
V9M H401 H401 H 0 0 N N N N N N 1.281  38.535 18.177 0.357  0.007  1.412  H401 V9M 25 
V9M H402 H402 H 0 0 N N N N N N 1.818  37.384 16.908 0.299  0.902  -0.125 H402 V9M 26 
V9M H422 H422 H 0 0 N N N N N N 3.585  36.643 18.243 -0.920 -0.984 -1.177 H422 V9M 27 
V9M H421 H421 H 0 0 N N N N N N 3.244  37.906 19.475 -0.862 -1.879 0.360  H421 V9M 28 
V9M H431 H431 H 0 0 N N N N N N 2.463  35.725 20.048 -2.154 0.861  -0.001 H431 V9M 29 
V9M H442 H442 H 0 0 N N N N N N 1.131  36.701 21.262 -3.195 -1.277 -1.145 H442 V9M 30 
V9M H441 H441 H 0 0 N N N N N N 1.251  38.134 20.185 -3.640 -1.720 0.521  H441 V9M 31 
V9M H463 H463 H 0 0 N N N N N N -0.737 35.386 21.276 -4.069 0.812  -2.164 H463 V9M 32 
V9M H462 H462 H 0 0 N N N N N N -2.224 35.954 20.444 -5.095 1.912  -1.211 H462 V9M 33 
V9M H461 H461 H 0 0 N N N N N N -0.925 35.142 19.506 -3.365 1.748  -0.824 H461 V9M 34 
V9M H472 H472 H 0 0 N N N N N N -2.132 37.618 18.905 -6.056 -1.474 -0.000 H472 V9M 35 
V9M H473 H473 H 0 0 N N N N N N -0.713 38.716 18.816 -6.666 0.030  -0.730 H473 V9M 36 
V9M H471 H471 H 0 0 N N N N N N -0.651 37.102 18.029 -5.641 -1.069 -1.683 H471 V9M 37 
V9M H482 H482 H 0 0 N N N N N N -0.603 37.569 22.129 -4.022 1.323  1.466  H482 V9M 38 
V9M H483 H483 H 0 0 N N N N N N -0.580 38.970 21.005 -5.777 1.203  1.190  H483 V9M 39 
V9M H481 H481 H 0 0 N N N N N N -2.068 37.977 21.173 -4.894 -0.163 1.914  H481 V9M 40 
V9M H493 H493 H 0 0 N N N N N N 0.509  34.794 19.052 -3.139 0.289  2.245  H493 V9M 41 
V9M H491 H491 H 0 0 N N N N N N 0.638  35.997 17.724 -2.095 -1.152 2.291  H491 V9M 42 
V9M H492 H492 H 0 0 N N N N N N 1.955  34.803 17.986 -1.369 0.474  2.280  H492 V9M 43 
V9M H542 H542 H 0 0 N N N N N N 3.452  37.960 15.415 0.654  -1.271 -1.965 H542 V9M 44 
V9M H543 H543 H 0 0 N N N N N N 1.996  39.007 15.309 1.661  0.197  -1.978 H543 V9M 45 
V9M H541 H541 H 0 0 N N N N N N 3.635  39.740 15.262 2.428  -1.408 -1.929 H541 V9M 46 
V9M HG21 HG21 H 0 0 N N N N N N 1.995  42.152 20.363 3.049  -2.691 -0.201 HG21 V9M 47 
V9M HG23 HG23 H 0 0 N N N N N N 2.094  42.710 18.659 4.826  -2.741 -0.276 HG23 V9M 48 
V9M HG22 HG22 H 0 0 N N N N N N 0.779  41.596 19.163 4.011  -2.364 1.261  HG22 V9M 49 
V9M HXT  HXT  H 0 1 N Y N Y N Y 2.205  42.735 15.265 3.510  3.149  0.076  HXT  V9M 50 
# 
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 
V9M C54 N    SING N N 1  
V9M O   C    DOUB N N 2  
V9M C   CA   SING N N 3  
V9M N   CA   SING N N 4  
V9M N   C40  SING N N 5  
V9M CA  CB   SING N N 6  
V9M C40 C42  SING N N 7  
V9M C49 C43  SING N N 8  
V9M C42 C43  SING N N 9  
V9M C47 C45  SING N N 10 
V9M CB  CG2  SING N N 11 
V9M CB  CG1  SING N N 12 
V9M C43 C44  SING N N 13 
V9M C45 C44  SING N N 14 
V9M C45 C46  SING N N 15 
V9M C45 C48  SING N N 16 
V9M C   OXT  SING N N 17 
V9M CA  HA   SING N N 18 
V9M CB  HB   SING N N 19 
V9M CG1 HG13 SING N N 20 
V9M CG1 HG11 SING N N 21 
V9M CG1 HG12 SING N N 22 
V9M N   H    SING N N 23 
V9M C40 H401 SING N N 24 
V9M C40 H402 SING N N 25 
V9M C42 H422 SING N N 26 
V9M C42 H421 SING N N 27 
V9M C43 H431 SING N N 28 
V9M C44 H442 SING N N 29 
V9M C44 H441 SING N N 30 
V9M C46 H463 SING N N 31 
V9M C46 H462 SING N N 32 
V9M C46 H461 SING N N 33 
V9M C47 H472 SING N N 34 
V9M C47 H473 SING N N 35 
V9M C47 H471 SING N N 36 
V9M C48 H482 SING N N 37 
V9M C48 H483 SING N N 38 
V9M C48 H481 SING N N 39 
V9M C49 H493 SING N N 40 
V9M C49 H491 SING N N 41 
V9M C49 H492 SING N N 42 
V9M C54 H542 SING N N 43 
V9M C54 H543 SING N N 44 
V9M C54 H541 SING N N 45 
V9M CG2 HG21 SING N N 46 
V9M CG2 HG23 SING N N 47 
V9M CG2 HG22 SING N N 48 
V9M OXT HXT  SING N N 49 
# 
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 
V9M SMILES           ACDLabs              12.01 "C(C(C(C)C)[NH+](CCC(CC(C)(C)C)C)C)(O)=O"                                                                            
V9M InChI            InChI                1.03  "InChI=1S/C15H31NO2/c1-11(2)13(14(17)18)16(7)9-8-12(3)10-15(4,5)6/h11-13H,8-10H2,1-7H3,(H,17,18)/p+1/t12-,13-/m0/s1" 
V9M InChIKey         InChI                1.03  OJDKVOGMPHTYGS-STQMWFEESA-O                                                                                          
V9M SMILES_CANONICAL CACTVS               3.385 "CC(C)[C@H]([NH+](C)CC[C@H](C)CC(C)(C)C)C(O)=O"                                                                      
V9M SMILES           CACTVS               3.385 "CC(C)[CH]([NH+](C)CC[CH](C)CC(C)(C)C)C(O)=O"                                                                        
V9M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](CC[NH+](C)[C@@H](C(C)C)C(=O)O)CC(C)(C)C"                                                                    
V9M SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(=O)O)[NH+](C)CCC(C)CC(C)(C)C"                                                                              
# 
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 
V9M "SYSTEMATIC NAME" ACDLabs              12.01 "(3R)-N-[(1S)-1-carboxy-2-methylpropyl]-N,3,5,5-tetramethylhexan-1-aminium"                             
V9M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "methyl-[(2~{S})-3-methyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]-[(3~{R})-3,5,5-trimethylhexyl]azanium" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
V9M "Create component" 2020-07-21 RCSB 
V9M "Initial release"  2020-09-16 RCSB 
V9M "Modify backbone"  2023-11-03 PDBE 
V9M "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            V9M 
_pdbx_chem_comp_pcm.modified_residue_id                VAL 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_pdbx_chem_comp_pcm.position                           "Amino-acid backbone" 
_pdbx_chem_comp_pcm.polypeptide_position               N-terminal 
_pdbx_chem_comp_pcm.comp_id_linking_atom               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
