Several Iranian nuclear sites are located in Isfahan province.
Questions have been raised whether cloud seeding could've caused the heavy rain.
Some countries, including the UAE, China and the US, have been trying to modify the weather.
"We know deeply what these 5000 lives, or potential lives, meant for the parents, either for the future or for the past."
A strike has also killed four people in Rafah, say Palestinian officials.
Almost all the ballistic missiles and drones Iran launched at Israel were intercepted.
US officials said Tehran did not warn Washington and that it was aiming to cause significant damage.
The threat of open warfare erupting between the arch Middle East foes and dragging in the United States has put the region on edge.
The attack could lead to a major escalation between the regional archenemies.