You're assuming a linear relationship between civilian casualties and Japanese military leadership's willingness to surrender. Why would e.g. dropping the first bomb on a less-populated shipyard and the second on a city centre have been less effective?
That was Hiroshima. Although there was a high number of civilian casualties it was actually chosen on the basis of its importance to the Japanese imperial army, both as a base and an industrialized city.
>Hiroshima was a supply and logistics base for the Japanese military.[117] The city was a communications center, a key port for shipping, and an assembly area for troops.[78] It supported a large war industry, manufacturing parts for planes and boats, for bombs, rifles, and handguns.[118]
