diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
index bf0e25c236b..71f6968dbbf 100644
--- a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
+++ b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
@@ -825,13 +825,21 @@ private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer
         List<double[]> limits = new ArrayList<>();
         final int numFragments = frags.size();
 
+        // avoid overwriting our state
+        Set<IAtom> afixbackup = new HashSet<>(afix);
+        Set<IBond> bfixbackup = new HashSet<>(bfix);
+
         // generate the sub-layouts
         for (IAtomContainer fragment : frags) {
-            setMolecule(fragment, false);
+            setMolecule(fragment, false, afix, bfix);
             generateCoordinates(DEFAULT_BOND_VECTOR, true, true);
             limits.add(GeometryUtil.getMinMax(fragment));
         }
 
+        // restore
+        afix = afixbackup;
+        bfix = bfixbackup;
+
         final int nRow = (int) Math.floor(Math.sqrt(numFragments));
         final int nCol = (int) Math.ceil(numFragments / (double) nRow);