I was able to locate and capture Moltres on Route 5 just south of Verdanturd Town. I had a Gengar at lv. 55 and made him hold leftovers, know the move mean look, and made sure he was the first Pokémon in my party. When I found Moltres I immediately used mean look to prevent it from running away, and used a lot of Poké balls, when I got attacked the leftovers helped heal my Gengar so I was able to keep working on capturing the Moltres. Hope this helps.