The timing never worked out for that. The first bombs were not ready until the summer of 1945, at which point Germany was out of the game. Even as early as 1944 they could foresee that the bombs would not likely be ready for use on the European front and that Germany would almost certainly capitulate before they were ready.

Roosevelt had a glimmer of interest in using one against Germany in December 1944, but, again, they weren't ready. Much more discussion about this here.

The issue was briefly considered at the very start of the Manhattan Project, in 1943, but was dismissed at that time because they were worried that if the bomb was a dud, the Germans might be able to use it against the USA. I don't consider that a very serious discussion, though — it was tacked on at the end of a long meeting, and there were many pressing things to be worked out before they worried too much about targets.

Initially Germany was the intended target. The Manhattan Project was more or less a response to the German atomic project. Or I suppose I should say Germany was the intended target of a deterrence. The American bomb was initially intended to keep the Germans from using theirs. But that changed pretty early on.

The first official proposed target was at a large anchorage like Truk. In May of 1943 no one had any faith that it would go off. So the idea of dropping it on a deep water anchorage was ideal. They thought the waters of Truk would be hard to retrieve a gadget from, and the Japanese would be less likely to gain any significant engineering insight than the Germans. But it would be another two years before actual targets lists would be drawn up.

When the formal lists were made in the Spring of 1945, Germany was already on its last legs. German cities had been ravaged, Allied forces were already in Germany proper on both fronts. No one thought they were going to last until July, which was pretty clearly the likely first delivery date. So there wasn't a reason to bother drawing up a list of targets that the Allied planners believed would already be in their hands.

Interestingly though General Groves said that around the time of the Battle of the Bulge Roosevelt approached Groves to see if the bomb could be ready early. Groves replied that it wouldn't be available for some months. He then recited a list of reasons why bombing Germany would be bad: the war would likely be over before a bomb was ready, German air defense was still too good, the Americans didn't have an appropriate plane in Europe and would have to either use British forces to deliver the bomb or set up B-29s in England, and Japanese cities were thought to be more vulnerable to atomic weapons than German cities. This apparently satisfied Roosevelt. There certainly isn't any record I'm aware of that it was ever brought up again.

But it does show that both the President and the military weren't opposed to targeting Germany. And Groves had far too comprehensive an answer to have made it up off the cuff. The discussions were informal, but Groves had clearly looked at Germany as a target.

Followup question: how long would it have taken to make a third nuclear bomb if the first two did not result in Japan's surrender?