Re: [ccp4bb]: Comments on ligands

[<david.borhani@abbott.com>]

I agree w/ much of what Phil and Jim have said well.

RE: NADPH, I was amazed how difficult it was to address the geometry of the nicotinamide ring at 1.05 A resolution (entry 1KMS). We consulted HICCUP and the PDB (CSD was also very helpful), both of which helped some. But, ultimately, common chemical sense prevailed...if it's a C=C double bond, the bond length is so-and-so, if it's a C-C single bond, it's longer, etc. (I am sure that the French group which has aldose reductase w/ NADP(H) at 0.6 A will set us all straight!)

I find that the (Refmac, CNX, etc.) dictionaries can often be inadequate/questionable/wrong. GIGO. And be careful.

Also, remember that it is energetically very costly to distort bond lengths, somewhat less so bond angles, and torsion angles can be fiddled with almost with impunity (though staggered is preferred). So if you see in a PDB entry a ligand where the phenyl ring substituent comes off at 110 degrees, it is probably wrong. If that C-C bond is 1.65 A, it is probably wrong. If the Mg-O distance is 2.9 instead of 2.2 A, maybe it is a water, not Mg. (I could continue...but won't!)

And yes, Gerard is right...deposit theose SF's! 

Dave
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David Borhani
Group Leader, Biochemistry
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