Biofuel company Amyris Inc. went public on Monday night, raising nearly $85 million. It closed its first day of trading up 3% to $16.50 per share, but that’s still well below its plans to price between $18 and $20 per share.

It’s also a far cry from the price at which Amyris sold most of  its shares to venture capitalists over the past few years. For example, the company raised $66.1 million in 2008, by selling Series B-1 preferred stock at $25.26 per share. Overall, it raised just over $363 million in private funding between April 2007 and this past June.

My initial thought was that Amyris must represent a giant crater for its VC backers. It’s one thing to whiff on a small deal, but not when the company raised around $363 million. Truth is, however,the firm’s early VC investors are actually in the black. Here’s is how it breaks down, based on the $16.50 per share price:

• Kleiner Perkins: $16.48 million investment, now worth $69 million
• Khosla Ventures: $15.59 million investment, now worth $65.36 million
• TPG Biotech: $15.95 million investment, now worth $53.83 million

Each of those firms participated in the dirt-cheap Series A round, the over-priced Series B round and the Series C down-round. More importantly, they missed the two priciest — and largest — rounds: Series B-1 and Series D.

Here’s a look at firms that didn’t invest in the Series A:

• DAG Ventures: $22.69 million investment, now worth $18.47 million
• Advanced Equities: $35.05 million investment, now worth $29.7 million (including possible warrant conversion at $16.50 per share)
• Total Gas & Power USA: $133.2 million investment, now worth $159 million.

Total Gas did alright thanks to a generous conversion plan, plus the fact that the Series D stock in bought was valued lower than either the Series B, Series B-1 or Series C shares.

It certainly is possible that Amyris shares could double in price, thus putting all VC backers in the black (they’re up another 16 cents as of this writing). It also is worth noting that the approximately 4x cash-on-cash returns for the early investors must be put in the context of annualized IRRs (net of management fees and carried interest).

But, those caveats aside, it was DAG Ventures and Advanced Equities that got taken. Both firms are known as Series C and Series D investors for companies originally backed by firms like Kleiner Perkins. That means that they’re often paying sky-high valuations, and hoping that they never fall. So far with Amyris, they’re still left hoping.