diff --git a/flowermd/base/system.py b/flowermd/base/system.py
index 7f156ece..cccfb8ef 100644
--- a/flowermd/base/system.py
+++ b/flowermd/base/system.py
@@ -769,7 +769,9 @@ def _build_system(self):
                 try:
                     comp1 = self.all_molecules[next_idx]
                     comp2 = self.all_molecules[next_idx + 1]
-                    comp2.translate(self.basis_vector)
+                    comp2.translate(
+                        self.basis_vector * np.array([self.x, self.y, 0])
+                    )
                     # TODO: what if comp1 and comp2 have different names?
                     unit_cell = mb.Compound(
                         subcompounds=[comp1, comp2], name=comp1.name