The pick was Solomon Thomas, but the man who got the loudest cheers from 49ers fans was John Lynch.

Coming off like someone who’s been running drafts for decades, San Francisco’s neophyte general manager pulled off a master’s move in Round 1: picking up three extra draft picks and then taking the player — Thomas, the defensive lineman from Stanford — he was going to take with the second overall pick in the draft one spot later at pick No. 3.

Lynch got a big assist from team executive Paraag Marathe, who, as in previous years, handled the details of the trade. Their partner was the Chicago Bears, who grabbed North Carolina quarterback Mitch Trubisky at pick No. 2. In return, the 49ers added picks in the third (No. 67) and fourth (No. 111) rounds as well as Chicago’s third-round pick next year.

San Francisco now has three picks in the fourth round this year as well as three picks in Rounds 3, 5 and 6. This year’s draft is believed to be particularly deep in the middle rounds.

Thomas, who played football 15 miles up Highway 101 at Stanford, called his selection the “best surprise of my life.”

He said he had little interaction with the 49ers after the scouting combine in March but kept seeing his name linked to San Francisco in mock drafts. He said he resisted picturing himself in a 49ers uniform.

“In my head, I was like, ‘You know, I love that, but I’m not going to allow myself to ride the roller coaster, I can’t believe this stuff because I’m going to get my heart broken,'” he said.

His selection reunited him with a former classmate — Lynch.

The 49ers general manager, who played safety at Stanford in the 1990s, returned to the university in 2014 to finish his degree. Thomas, 21, was a freshman that year and they took a class together, Management Science and Engineering.

“I remember I was star struck the first day of class,” Thomas said. “I was like, ‘What? John Lynch is in out class?’ So I tried to cling on to him, learn from him. … It was a really cool experience to be in class with him.”

Thomas said the two spoke on the phone several times since, including before Stanford’s Sun Bowl game in December against North Carolina. Thomas was debating whether to enter the draft at the time and Lynch, 45, told him to block out the distractions and “just show them you’re unstoppable and un-blockable.”

Thomas took that advice to heart, dominating the Tar Heels offensive line and harassing Trubisky throughout the game, including a sack on North Carolina’s pivotal, final offensive snap.

Thomas overshadowed the more heralded Trubisky in Stanford’s win, which launched his rise up draft boards. He continued that ascent with an outstanding performance at the scouting combine.

The redshirt sophomore finished in the Top 5 among defensive linemen in five combine categories, including the 40-yard dash (4.69 seconds) and the bench press (30 repetitions of 225 pounds).

How he fits into a 49ers defense that used first-round picks on Arik Armstead and DeForest Buckner the last two years will be determined this spring.

Thomas played several positions along the Cardinal defensive line in 2016, particularly left defensive end and defensive tackle. It’s possible he could line up at left defensive end on base down in the 49ers’ defense and then slide inside to defensive tackle on passing downs. Tank Carradine, a former second-round pick, was San Francisco’s first-string left defensive end during this week’s minicamp.

The 49ers defense is modeled after the Seattle Seahawks’ aggressive unit, which features Michael Bennett at left defensive end. Thomas said he’s studied Bennett’s game.

“We’re both very versatile, we’re quick,” Thomas said. “Before I can be even compared to him I have to play my first down, earn the trust of my teammates and earn their respect. That’s what I’m trying to do right now.”

Armstead and Buckner — who are friends from their playing days at Oregon — plan to head to Hawaii this summer where they will meet up with Bennett. Does Thomas want to tag along?

“That would be awesome,” he said. “… Being able to train with some great NFL players and learn from them — that would be a blessing.”

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