UPDATE
I found the original design wasn't quite accurate in it's measurements, especially as I changed print heads, so I created a new one (two new pictures) where everything is flush. I've included the source Sketchup file. Each bolt set is made of individual components so you can tune them to your printer. Once you have the dimensions right for you, you can copy the components into whatever project you're working on to use as subtraction objects.

Original
I bought this multi-piece bolt set from https://www.amazon.ca/gp/product/B0C38YFL3D/ and wanted to make a sizing reference for myself. It was also an opportunity to actually learn how to make aligned holes in two pieces and the hexagonal grooves for the nuts.

As the kit only included M2, M3, M4, and M5 sizing, that's all this reference shows. You don't have to screw in the bolts like I did but it keeps the two parts together, looks neat, and gives you a clear sense of the size of the nuts and bolt heads.

Keep turning it away from you and you'll get the reference for the hole sizes and the groove sizes.

The hole sizes are the radius of each in mm and the groove sizes are the length from the centre of the hole to the farthest vertex to the left or right,

Some provisos for this current version:

• All the grooves are the same depth (3mm) which doesn't work for each nut (M2 and M3 are less flush) but the difference is small
• The grooves themselves are not a perfect fit so the nuts do turn slightly when bolted in (I'd say somewhere in the order of 1-5 degrees). This doesn't seem to cause a problem for keeping a piece together but it means you may have to play with the the given values if you need more precision