diff --git a/src/main/org/openscience/cdk/fragment/MurckoFragmenter.java b/src/main/org/openscience/cdk/fragment/MurckoFragmenter.java
index 86a5c86ce30..0606b3e97ee 100644
--- a/src/main/org/openscience/cdk/fragment/MurckoFragmenter.java
+++ b/src/main/org/openscience/cdk/fragment/MurckoFragmenter.java
@@ -149,14 +149,16 @@ private void run(IAtomContainer atomContainer) throws CDKException {
         // only add this in if there is actually a framework
         // in some cases we might just have rings and sidechains
         if (hasframework(currentFramework)) {
-            smiles = smilesGenerator.createSMILES(clone);
+            smiles = smilesGenerator.createSMILES(currentFramework);
 
             // if we only want the single framework according to Murcko, then
             // it was the first framework that is added, since subsequent recursive
             // calls will work on substructures of the original framework
             if (singleFrameworkOnly) {
-                if (frameMap.size() == 0) frameMap.put(smiles, clone);
-            } else frameMap.put(smiles, clone);
+                if (frameMap.size() == 0) {
+                    frameMap.put(smiles, currentFramework);
+                }
+            } else frameMap.put(smiles, currentFramework);
         }
 
         // extract ring systems - we also delete pseudo linker bonds as described by
diff --git a/src/test/org/openscience/cdk/fragment/MurckoFragmenterTest.java b/src/test/org/openscience/cdk/fragment/MurckoFragmenterTest.java
index 26c5bccd208..3efda833539 100644
--- a/src/test/org/openscience/cdk/fragment/MurckoFragmenterTest.java
+++ b/src/test/org/openscience/cdk/fragment/MurckoFragmenterTest.java
@@ -200,7 +200,7 @@ public void testCarbinoxamine_Bug3088164() throws Exception {
         fragmenter.generateFragments(mol);
 
         String[] f = fragmenter.getFrameworks();
-        IAtomContainer[] fc = fragmenter.getFragmentsAsContainers();
+        IAtomContainer[] fc = fragmenter.getFrameworksAsContainers();
         Assert.assertEquals(1, f.length);
         Assert.assertEquals(f.length, fc.length);
         Assert.assertEquals("c1ccc(cc1)Cc2ncccc2", f[0]);
@@ -219,17 +219,17 @@ public void testCarbinoxamine_Bug3088164() throws Exception {
     public void testPirenperone_Bug3088164() throws Exception {
         SmilesGenerator sg = new SmilesGenerator(true);
 
-        IAtomContainer mol = smilesParser.parseSmiles("Fc1ccc(cc1)C(=O)C4CCN(CCC\\3=C(\\N=C2\\C=C/C=C\\N2C/3=O");
+        IAtomContainer mol = smilesParser.parseSmiles("Fc1ccc(cc1)C(=O)C4CCN(CCC\\3=C(\\N=C2\\C=C/C=C\\N2C/3=O)C)CC4");
         CDKHueckelAromaticityDetector.detectAromaticity(mol);
         MurckoFragmenter fragmenter = new MurckoFragmenter(true, 6);
         fragmenter.generateFragments(mol);
 
         String[] f = fragmenter.getFrameworks();
-        IAtomContainer[] fc = fragmenter.getFragmentsAsContainers();
+        IAtomContainer[] fc = fragmenter.getFrameworksAsContainers();
 
         Assert.assertEquals(1, f.length);
         Assert.assertEquals(f.length, fc.length);
-        Assert.assertEquals("N=1C=C(CN2C=CC=CC=12)CCN4CCC(Cc3ccccc3)CC4", f[0]);
+        Assert.assertEquals("C=1N=C4C=CC=CN4(CC=1CCN3CCC(Cc2ccccc2)CC3)", f[0]);
 
         for (int i = 0; i < f.length; i++) {
             String newsmiles = sg.createSMILES(fc[i]);
@@ -250,7 +250,7 @@ public void testIsomoltane_Bug3088164() throws Exception {
         fragmenter.generateFragments(mol);
 
         String[] f = fragmenter.getFrameworks();
-        IAtomContainer[] fc = fragmenter.getFragmentsAsContainers();
+        IAtomContainer[] fc = fragmenter.getFrameworksAsContainers();
         Assert.assertEquals(1, f.length);
         Assert.assertEquals(f.length, fc.length);
         Assert.assertEquals("c1ccccc1n2cccc2", f[0]);