diff --git a/api/tests/integration/tests/formats/ref/rna_mod.ket b/api/tests/integration/tests/formats/ref/rna_mod.ket
index 07ca6d4d89..6d1970f1a0 100644
--- a/api/tests/integration/tests/formats/ref/rna_mod.ket
+++ b/api/tests/integration/tests/formats/ref/rna_mod.ket
@@ -2,10 +2,10 @@
     "root": {
         "nodes": [
             {
-                "$ref": "mol1"
+                "$ref": "mol0"
             },
             {
-                "$ref": "mol2"
+                "$ref": "mol1"
             },
             {
                 "$ref": "monomer0"
diff --git a/core/indigo-core/molecule/src/molecule_json_saver.cpp b/core/indigo-core/molecule/src/molecule_json_saver.cpp
index 6da54d01b1..808c9cf8e5 100644
--- a/core/indigo-core/molecule/src/molecule_json_saver.cpp
+++ b/core/indigo-core/molecule/src/molecule_json_saver.cpp
@@ -1366,7 +1366,7 @@ void MoleculeJsonSaver::saveRoot(BaseMolecule& mol, JsonWriter& writer)
             _no_template_molecules.emplace_back(std::move(component));
             writer.StartObject();
             writer.Key("$ref");
-            std::string mol_node = std::string("mol") + std::to_string(idx);
+            std::string mol_node = std::string("mol") + std::to_string(_no_template_molecules.size() - 1);
             writer.String(mol_node.c_str());
             writer.EndObject();
         }