There was only one center scheduled to become a free agent the 49ers would have wanted over Daniel Kilgore, general manager John Lynch said Thursday.

But because the 49ers did not know a month ago if they would be able to get that player, they went ahead and re-signed Kilgore to keep him off the free-agent market.

Lynch said the 49ers’ top two targets in free agency were center Weston Richburg and running back Jerick McKinnon. They negotiated against a handful of teams for the services of both players and finalized the deals on Wednesday at the opening of the free-agent signing period.

After the 49ers signed Richburg, the club worked a trade with the Miami Dolphins to send Kilgore to a team that needs a starting center.

“We thought about, do we play Weston at guard?” Lynch said. “Ultimately, once we decided to invest in someone, you put him at his best position. That happens to be his best position and center is Dan’s best position, too.”

Just one month ago, Kilgore signed a three-year, $11.75 million with the 49ers with the expectation he would remain with the club that selected him in the fifth round of the 2011 draft. Because of the way the deal was structured, the Dolphins will pick up every penny of the contract. The first payment from the Dolphins is a $2.3 million guaranteed roster bonus.

“I’ve been here for seven years,” Kilgore said on a conference call in mid-February. “I consider the Bay Area my second home. And to be able to extend my career wearing the 49ers jersey was special to me. This team heading in the right direction, I wanted to be a part of it.”


The availability of Richburg changed the 49ers’ plan, Lynch said.

Richburg was the only interior offensive linemen the 49ers pursued in free agency, Lynch said.. The team did not even place a call of interest to the agent of free-agent guard Andrew Norwell, who was not considered a fit for Kyle Shanahan’s blocking scheme.

Lynch was asked if there was anything he would have done differently in his handling of the center position this offseason.

“As we looked at this situation, we asked ourselves that question,” Lynch said. “But I really don’t think we could’ve. We are happy we were able to find a nice landing spot. He’s a starting center for an exciting team.”

Lynch, who played 15 NFL seasons, has made it a point to treat players as he would have wanted to be treated. He said the 49ers tried to do what was right for both sides.

They got little from the Dolphins in compensation for Kilgore. The 49ers sent Kilgore and the ninth pick of the seventh round (No. 227 overall) to the Dolphins in exchange for the fifth pick of the seventh round (No. 223 overall).

“I think our players know we genuinely care of them,” Lynch said. “I think they really get that. That’s one of our strengths, as far as the vibe we have going here. Yes, actions have to reflect that. I will tell you, we left this in a really good place with Danny. We’ve had really good conversations with him all the way through it.”

In other 49ers free-agent news . . .

Former 49ers defensive end/outside linebacker Aaron Lynch is signing a one-year contract with the Chicago Bears, the NFL Network reported. Lynch’s defensive coordinator will be Vic Fangio, who coached him as a rookie with the 49ers. Lynch had 12.5 sacks in his first two seasons, 2.5 in his last two years. The 49ers made no effort to re-sign him.