diff --git a/molexpress/datasets/encoders.py b/molexpress/datasets/encoders.py
index fa9cfa2..2850a5b 100644
--- a/molexpress/datasets/encoders.py
+++ b/molexpress/datasets/encoders.py
@@ -103,7 +103,10 @@ def __call__(self, molecule: types.Molecule) -> np.ndarray:
             return {"edge_src": edge_src, "edge_dst": edge_dst}
 
         if molecule.GetNumBonds() == 0:
-            edge_state = np.zeros(shape=(0, self.output_dim), dtype=self.output_dtype)
+            edge_state = np.zeros(
+                shape=(0, self.output_dim + int(self.self_loops)),
+                dtype=self.output_dtype
+            )
             return {
                 "edge_src": edge_src,
                 "edge_dst": edge_dst,