Preheat oven to 400°F. On a small rimmed baking sheet, combine panko, 2 tablespoons olive oil, 1/4 of the grated garlic, and a pinch of salt. Massage mixture together.
In a 9x13-inch baking dish, combine white wine, red pepper flakes, the remaining garlic, and 1 tablespoon olive oil. Add cleaned clams to the dish and stir gently to coat.
Transfer both pans to the oven. Bake the panko mixture, tossing once, until golden brown—8 to 10 minutes.
Remove panko from oven and increase oven temperature to 475°F. Continue roasting clams until they open, 8 to 10 minutes more. Discard any clams that remain closed.
Toss toasted panko with chopped parsley and lemon zest.
Drizzle lemon juice and remaining tablespoon of oil over the clams. Top with half the lemony panko and serve the rest on the side for extra crunch.