diff --git a/prolif/molecule.py b/prolif/molecule.py
index 258248b..3138bff 100644
--- a/prolif/molecule.py
+++ b/prolif/molecule.py
@@ -369,7 +369,12 @@ def _adjust_hydrogens(template: Chem.Mol, pdbqt_mol: Chem.Mol) -> Chem.Mol:
         mol = rwmol.GetMol()
         # sanitize
         mol.UpdatePropertyCache()
-        Chem.SanitizeMol(mol)
+        Chem.SanitizeMol(
+            mol,
+            sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL
+            ^ Chem.SanitizeFlags.SANITIZE_KEKULIZE
+        )
+
         return mol
 
     def __len__(self) -> int: