To elaborate further on software packages available that do a reasonable job of fitting small molecules and outputting reasonable dictionaries, one could consider Afitt from OpenEye Scientific Software. They have academic as well as commercial licenses to their software.
Cheers, tom -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Monday, 9 January 2012 11:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] unusual bond lengths in PRODRG cif file On 9 January 2012 06:13, Shveta Bisht <shv...@mbu.iisc.ernet.in> wrote: > Dear all > > I have generated a refmac cif file for a molecule using PRODRG. I used > JME editor to draw the molecule and ran PRODRG online with the > options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the > attachments for the molecule drawing and the expected bond lengths as > listed in the PRODRG generated cif file. There are some unusual > values. I have listed them below along with the likely explanations > (just guesses). > > DRG CAR CAK single 1.390 0.025 > DRG CAQ CAB single 1.390 0.025 > DRG CAT CAI single 1.390 0.020 > All three are C-C single bonds where one of the carbons belong to > aromatic ring. This might lead to a short bond, although 1.39 seems to > be too short for this. > > DRG CAI NAL double 1.340 0.022 > DRG CAP NAL single 1.340 0.022 > Here N and both the carbons are sp2 hybridization, so there can be > delocalization of electrons. Thus both bonds (single and double) are > of similar length. > > DRG CAP CAA double 1.530 0.025 > As mentioned above, if pi (unhybridized) electrons of CAP are involved > in CAP NAL bonding, then CAP CAA double bond essentially becomes a > single bond with 1.53 bond length. > > I need advise on the way I have run prodrg and the explanations for the > results. > Is it common to observe such values? Or it is due to the alternating single > and > double bonds in this structure. Dear Shveta I agree completely with your assessment, there are certainly some "unusual" values, but I think this goes beyond "mistakes". I have run your structure through our own dictionary auto-generation software which essentially takes suitable fragments from the CSD and stitches them together (similar to CCDC-MOGUL but it doesn't use MOGUL and the pieces are smaller). Here are the values I get for comparison: > DRG CAR CAK single 1.390 0.025 1.512(10) > DRG CAQ CAB single 1.390 0.025 1.498(7) > DRG CAT CAI single 1.390 0.020 1.449(24) > DRG CAI NAL double 1.340 0.022 1.273(13) > DRG CAP NAL single 1.340 0.022 1.350(28) > DRG CAP CAA double 1.530 0.025 1.329(21) so essentially backing up what you said. My suspicion is that it's not generally recognised the central role played by bond length & angle restraints in MX refinement (after all if they weren't important then we wouldn't need to use them!), and as a consequence some people seem to think that their exact values are unimportant and "anything will do". Their importance soon becomes obvious (particularly of course at medium-low resolution) if you try to do unrestrained refinement: then you can easily get deviations 10 times greater than you get with restraints. So personally I believe in using the most accurate restraints possible and "anything will NOT do". My main concern would be that grossly inaccurate values such as these find their way into the PDB and then people base their restraints on these structures (though it's not a great idea to use the PDB co-ordinates as a source of restraints!). Before you ask, unfortunately our software is not available for distribution but I can recommend GRADE from Global Phasing which gives very high quality restraints; there's also of course JLigand from CCP4, though I haven't used it personally and so cannot attest for the quality. Cheers -- Ian
