Panera Bread Co. didn’t pay bonuses to its top executives last year because the company missed its earnings targets. The company also missed most goals in a three-year long-term incentive plan, which paid out at just 27 percent of its target value.

The misses are disclosed in Panera’s proxy statement, filed today with the Securities and Exchange Commission. It tallies Chief Executive Ronald Shaich’s total pay last year at $1.2 million, which includes a salary of $530,450 and a payout of $205,425 from the three-year incentive. The only goal that was met under the 2005-2007  plan was for systemwide average sales.

Shaich’s tally also includes $457,965 worth of stock and options, but those are accounting figures based on awards he received over several years. During 2007, Shaich received stock valued at $397,802 and options valued at $560,112. Using those figures instead of the accounting values would bring his 2007 compensation to $1.7 million.

The company also paid $13,405 in car expenses for Shaich.

If Shaich leaves the company after a change in control, his only compensation is $443,000 worth of stock that will receive accelerated vesting.

Panera’s earnings per share fell 2.7 percent last year, and its stock price fell by 36 percent.