Mr. Dubowitz’s main concerns about the deal were its lack of any limits on the regime’s ballistic missile program and its “sunset provisions” that would allow Iran to increase its capacity to enrich uranium beginning seven years from now. Mr. Dubowitz said the deal gave Iran tens of billions in economic relief that it had used to fund terrorism and foreign adventurism.

Now that Mr. Trump has decided to withdraw from an agreement he called “one of the worst and most one-sided transactions the United States has ever entered into,” Mr. Dubowitz’s campaign to draw attention to what he saw as its flaws has taken its place among the most consequential ever undertaken by a Washington think tank leader.

But in written responses to questions, Mr. Dubowitz said he felt “ambivalent” about the withdrawal: happy that Mr. Trump saw the agreement as flawed but disappointed in the rejection of the proposed fix, which he said “seemed closer than anyone would have expected.”

“I was very invested in the process of trying to help the E3 bridge the gap with us,” he added, referring to negotiations with British, French and German diplomats.

The Joint Comprehensive Plan of Action, as the Iran deal is formally known, is 109 pages, and Mr. Dubowitz was often able to cite its provisions by heart. He is widely seen as understanding the multifarious mechanics of sanctions, a rare feat.

But he is far from the usual tweedy think-tanker. Raised in Canada, trained as a lawyer and having worked in venture capital, Mr. Dubowitz wears tailored French suits and keeps his curly hair just so. In 2016, he received $560,221 in compensation as the foundation’s chief executive.

Top officials in the Obama administration often dismissed Washington’s foreign policy think tanks as paid agents of Israel, Saudi Arabia and the United Arab Emirates, countries that annually invest tens of millions in the Washington influence game. Those nations were implacably opposed to the Iran deal in part because they feared that it would achieve exactly what Mr. Obama and his European counterparts intended, which was to normalize Iran’s clerical government.