diff --git a/packages/ketcher-core/src/application/editor/tools/Clear.ts b/packages/ketcher-core/src/application/editor/tools/Clear.ts
index ce2270da39..eef1a7b2bb 100644
--- a/packages/ketcher-core/src/application/editor/tools/Clear.ts
+++ b/packages/ketcher-core/src/application/editor/tools/Clear.ts
@@ -16,6 +16,7 @@
 import { CoreEditor, EditorHistory } from 'application/editor/internal';
 import { SequenceMode } from 'application/editor/modes';
 import { BaseTool } from 'application/editor/tools/Tool';
+import { ReinitializeSequenceModeCommand } from 'application/editor/operations/modes';
 
 class ClearTool implements BaseTool {
   private history: EditorHistory;
@@ -24,12 +25,13 @@ class ClearTool implements BaseTool {
     this.editor = editor;
     this.history = new EditorHistory(editor);
 
+    const modelChanges = this.editor.drawingEntitiesManager.deleteAllEntities();
+    this.editor.renderersContainer.update(modelChanges);
+
     if (editor.mode instanceof SequenceMode) {
-      return;
+      modelChanges.addOperation(new ReinitializeSequenceModeCommand());
     }
 
-    const modelChanges = this.editor.drawingEntitiesManager.deleteAllEntities();
-    this.editor.renderersContainer.update(modelChanges);
     this.history.update(modelChanges);
   }