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'd like to follow up Ian Tickle's answer. A survey we carried out recently suggested that up to 70% of ligand structures in the PDB had bond and bond angle errors that could have been removed by better choice of restraints (to be published). Although most of the errors found are small, some were very large (> 10 s.d. from mean). The Mogul program (http://www.ccdc.cam.ac.uk/products/csd_system/mogul/) can be used to analyse the geometry of any feature in a 3D ligand model against data in the Cambridge Structural Database and is available to anyone who has access to the Cambridge Structural Database System. The GRADE dictionary generation software from Global Phasing uses Mogul information behind the scenes to generate bond and bond angle restraints. In addition ligand validation and restraint correction using Mogul will become available via COOT before too long. Finally you might like to know we are working with the PDB so that the geometry of ligand models can be validated on submission. Regards John Dr John W. Liebeschuetz Research & Applications Manager Cambridge Crystallographic Data Centre 12 Union Rd., Cambridge CB2 1EZ, UK T: +44-(0)1223-762532 F: +44-(0)1223-336033 LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmas...@ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ.
