Rinse salmon under cold running water and pat dry with kitchen paper. Rub with salt and pepper. Lay the salmon in a greased ovenproof dish.
Mix honey, mustard, water, balsamic vinegar and pomegranate molasses in a small saucepan and bring to the boil. Add thyme, ginger, cayenne pepper, almonds and prunes and let simmer until thickened, stirring once in a while.
Pour the sauce over the salmon and cover with foil. Bake in the preheated oven until the fish breaks up easily with a fork, about 30 minutes, baste the fish a few times with some of the sauce so it doesn't dry out. During the last 10 minutes remove the foil, or turn on the grill to help slightly caramelise the top of the salmon.
Sprinkle with pomegranate seeds and serve with rice.