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akiyamalab / restretto

REstretto (REuse of sub-STRuctures as an Effective Technique for protein-ligand docking TOol): An virtual screening-oriented protein-ligand docking tool with reuse of fragments
MIT License
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Amide bonds should be classified as non-rotatable bonds #6

Open keisuke-yanagisawa opened 1 year ago

keisuke-yanagisawa commented 1 year ago

Now below SDF file will be decomposed into two fragments. Decomposition was done for the amide bond, it is not expected.

     RDKit          3D
  5  4  0  0  0  0  0  0  0  0999 V2000
    1.9690    0.0107   -0.0063 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7354   -0.7242   -0.0633 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4781    0.0523    0.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4228    1.3047    0.1108 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8034   -0.6436   -0.0473 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
M  END
$$$$

OpenBabel has IsAmide() function, it must be useful.

BTW, perhaps other (sp2-hybridized) bonds are also considered as rotatable. We probably should check some of them....