diff --git a/packages/ketcher-react/src/script/editor/tool/atom.ts b/packages/ketcher-react/src/script/editor/tool/atom.ts
index dde9c6c4df..a630b3e4c3 100644
--- a/packages/ketcher-react/src/script/editor/tool/atom.ts
+++ b/packages/ketcher-react/src/script/editor/tool/atom.ts
@@ -57,9 +57,13 @@ class AtomTool implements Tool {
           editorSelection &&
           getGroupIdsFromItemArrays(struct.molecule, editorSelection);
         const sgroups = struct.molecule.functionalGroups;
-        const atomsInFunctionalGroup = editorSelection.atoms.map((atom) => {
-          return FunctionalGroup.atomsInFunctionalGroup(sgroups, atom);
-        });
+        const atomsInFunctionalGroup = editorSelection.atoms
+          .filter((atomId) => {
+            return !Atom.isSuperatomLeavingGroupAtom(struct.molecule, atomId);
+          })
+          .map((atom) => {
+            return FunctionalGroup.atomsInFunctionalGroup(sgroups, atom);
+          });
         if (atomsInFunctionalGroup.some((atom) => atom !== null)) {
           editor.event.removeFG.dispatch({ fgIds: [...selectedSGroupsId] });
           this.editor.hoverIcon.hide();
diff --git a/packages/ketcher-react/src/script/editor/tool/helper/getGroupIdsFromItems.ts b/packages/ketcher-react/src/script/editor/tool/helper/getGroupIdsFromItems.ts
index 88e58754bb..44ae15f46a 100644
--- a/packages/ketcher-react/src/script/editor/tool/helper/getGroupIdsFromItems.ts
+++ b/packages/ketcher-react/src/script/editor/tool/helper/getGroupIdsFromItems.ts
@@ -1,4 +1,4 @@
-import { mergeMapOfItemsToSet, Struct } from 'ketcher-core';
+import { Atom, mergeMapOfItemsToSet, Struct } from 'ketcher-core';
 
 type Items = {
   atoms?: number[];
@@ -9,12 +9,16 @@ function getGroupIdsFromItemArrays(struct: Struct, items?: Items): number[] {
   if (!struct.sgroups.size) return [];
 
   const groupsIds = new Set<number>();
-
-  items?.atoms?.forEach((atomId) => {
-    const groupId = struct.getGroupIdFromAtomId(atomId);
-    if (groupId !== null) groupsIds.add(groupId);
-  });
-
+  if (items?.atoms) {
+    items.atoms
+      .filter((atomId) => {
+        return !Atom.isSuperatomLeavingGroupAtom(struct, atomId);
+      })
+      .forEach((atomId) => {
+        const groupId = struct.getGroupIdFromAtomId(atomId);
+        if (groupId !== null) groupsIds.add(groupId);
+      });
+  }
   items?.bonds?.forEach((bondId) => {
     const groupId = struct.getGroupIdFromBondId(bondId);
     if (groupId !== null) groupsIds.add(groupId);