It seems obvious that is has something to do with the bottles on the shelves behind the safe. I don't know if it's due to my brightness configuration (perhaps too dark), but I wasn't able to see anything over there, or to find any item in the bottles... So where is the combination ?
The first key code combination in LGS games, and since their demise companies who follow on in their spirit, is 451 or a variant thereof (e.g. 45100). This is a reference to Fahrenheit 451.
This means you can guess the combination quickly without even looking!
This tradition started in System Shock 1 and is followed by System Shock 2, Deus Ex, BioShock and now Dishonored :)
Thats all wrong. The code is 528. Look at the note it says 3 months. Month of wind, month of seeds, and month of ice. Thats the order. In the book you will see different months all saying the month of whatever. And each month starting with wind is 5, seeds is 2, and ice is 8. Therefore the code is 528. I put it in myself and it opened.