diff --git a/src/alphafold3/model/atom_layout/atom_layout.py b/src/alphafold3/model/atom_layout/atom_layout.py
index 541fe7f8..f74b23f6 100644
--- a/src/alphafold3/model/atom_layout/atom_layout.py
+++ b/src/alphafold3/model/atom_layout/atom_layout.py
@@ -677,7 +677,7 @@ def get_link_drop_atoms(
         *chemical_component_sets.GLYCAN_OTHER_LIGANDS,
         *chemical_component_sets.GLYCAN_LINKING_LIGANDS,
     }:
-      if 'O1' not in bonded_atoms:
+      if bonded_atoms and 'O1' not in bonded_atoms:
         drop_atoms.update({'O1'})
   return drop_atoms
 
diff --git a/src/alphafold3/model/pipeline/structure_cleaning.py b/src/alphafold3/model/pipeline/structure_cleaning.py
index 4043a3f8..91938a6d 100644
--- a/src/alphafold3/model/pipeline/structure_cleaning.py
+++ b/src/alphafold3/model/pipeline/structure_cleaning.py
@@ -166,9 +166,13 @@ def clean_structure(
         *chemical_component_sets.GLYCAN_OTHER_LIGANDS,
         *chemical_component_sets.GLYCAN_LINKING_LIGANDS,
     }
-    # If only glycan ligands and no O1 atoms, we can do parallel drop.
+    # If only glycan ligands and no O1 atoms, we can do parallel drop. If there are no glycan bonds at all, keep O1.
+    has_any_glycan_bond = bool(
+        ligand_ligand_bonds.atom_name.size or polymer_ligand_bonds.atom_name.size
+    )
     if (
         only_glycan_ligands_for_leaving_atoms
+        and has_any_glycan_bond
         and (not (ligand_ligand_bonds.atom_name == 'O1').any())
         and (not (polymer_ligand_bonds.atom_name == 'O1').any())
     ):