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 0c7c1a145c4..4191372ce2b 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
@@ -2135,12 +2135,19 @@ private void placePositionalVariation(IAtomContainer mol) {
                         newvisit.clear();
                         for (Integer idx : visited) {
                             IAtom visitedAtom = mol.getAtom(idx);
+                            if (e.getKey().contains(visitedAtom) || e.getValue().contains(visitedAtom))
+                                continue;
                             for (Map.Entry<Set<IAtom>, IAtom> e2 : mapping.entries()) {
                                 if (e2.getKey().contains(visitedAtom)) {
                                     int other = idxs.get(e2.getValue());
                                     if (!visited.contains(other) && newvisit.add(other)) {
                                         visit(newvisit, adjlist, other);
                                     }
+                                } else if (e2.getValue() == visitedAtom) {
+                                    int other = idxs.get(e2.getKey().iterator().next());
+                                    if (!visited.contains(other) && newvisit.add(other)) {
+                                        visit(newvisit, adjlist, other);
+                                    }
                                 }
                             }
                         }