diff --git a/openff/nagl/lookups.py b/openff/nagl/lookups.py
index 229a35e..9c7412b 100644
--- a/openff/nagl/lookups.py
+++ b/openff/nagl/lookups.py
@@ -137,8 +137,12 @@ def lookup(self, molecule: "Molecule") -> torch.Tensor:
             If the property value cannot be found for this molecule
         """
         from openff.toolkit.topology import Molecule
+        from openff.toolkit.utils.exceptions import EmptyInChiError
 
-        inchi_key = molecule.to_inchi(fixed_hydrogens=True)
+        try:
+            inchi_key = molecule.to_inchi(fixed_hydrogens=True)
+        except EmptyInChiError as e:
+            raise KeyError(e.msg)
         try:
             entry = self.properties[inchi_key]
         except KeyError:
diff --git a/openff/nagl/tests/nn/test_model.py b/openff/nagl/tests/nn/test_model.py
index 5486b27..f6f4b83 100644
--- a/openff/nagl/tests/nn/test_model.py
+++ b/openff/nagl/tests/nn/test_model.py
@@ -419,6 +419,11 @@ def test_outside_lookup_table(self, am1bcc_model):
             [-0.738375,  0.246125,  0.246125,  0.246125],
             atol=1e-5
         )
+    
+    def test_compute_long_molecule(self, am1bcc_model):
+        mol = Molecule.from_smiles(341 * "C")
+        charges = am1bcc_model.compute_property(mol, as_numpy=True)
+        assert charges.shape == (mol.n_atoms,)
 
 class TestChargeGNNModelRC3(BaseTestChargeGNNModel):
     model_name = "openff-gnn-am1bcc-0.1.0-rc.3"
diff --git a/openff/nagl/tests/test_lookups.py b/openff/nagl/tests/test_lookups.py
index 676699f..35fe030 100644
--- a/openff/nagl/tests/test_lookups.py
+++ b/openff/nagl/tests/test_lookups.py
@@ -97,3 +97,8 @@ def test_lookup_with_different_connectivity(self, lookup_table):
         mol = Molecule.from_mapped_smiles("[H:5][C:1]([H:6])([H:7])[N+2:2](-[O-:3])[O-:4]")
         properties = lookup_table.lookup(mol)
         assert_allclose(properties.numpy(), np.array([-0.103, 0.234, -0.209, -0.209, 0.096, 0.096, 0.096]))
+
+    def test_lookup_long(self, lookup_table):
+        mol = Molecule.from_smiles(341 * "C")
+        with pytest.raises(KeyError, match="failed to generate an InChI"):
+            lookup_table.lookup(mol)