It wasn't a ship, it was a plane and its name was The Bockscar
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"fat man" was the name of the atomic bomb dropped on Nagaski. "little boy" was dropped in Hiroshima.
The Enola Gay wasn't the atomic bomb. That honor goes to Little Boy and Fat Man. The Enola Gay was the plane specially created to drop the atomic bombs :)
See: Atomic bombings of Hiroshima and Nagasaki
Actually there is no secret to the atomic bomb. However Klaus Fuchs & Ted Hall provided the plans of Fat Man. This saved them considerable engineering effort.
Plutonium was and still is used for atomic bombs. The atomic bombs you are talking about would be fat man and little boy. They were the two used to bomb Hiroshima and Nagasaki Many people were killed when the b-29 bomber dropped fat man.