I'm sad to think that scientists may not 'bother' to use the CSD system 'just' to check the geometry of small molecule ligands, as they may, of course, be the main focus of the study, or the focus of subsequent researchers who use the structures. Moreover, comparison of small molecule and protein-bound ligand structures can be most revealing.
In answer to your question of access, the vast majority of research universities in the world (with a chemistry department) already have access to the CSD. In fact it is available in 72 counties, to scientists in around 1,500 institutions. The problem you highlight is that it's quite common for scientists not to realise that another department, or their institutions library, already provide access to the CSD system. I'll reply to any off-board emails should folks want to know who their local contact is. In terms of affordability, the CSD system is maintained by the Cambridge Crystallographic Data Centre, which is a non-profit, charitable organisation. It is available at below cost to academics. Anyone who genuinely cannot afford the modest charge, which is used for the ongoing funding of the CSD, is of course given free access. The CSD and other chemistry databases are also freely available to UK researchers through the excellent (EPSRC funded) Chemical Database Service operated from Daresbury. You're right that the CCDC:PDB collaboration to develop on-line tools check ligands and generate dictionaries 'is great'- and Gerard might let us know how he's getting on? Colin Dr Colin R Groom Email: gr...@ccdc.cam.ac.uk Executive Director Phone-direct: +44-(0)1223-336020 Cambridge Crystallographic Data Centre Phone-messages: +44-(0)1223-336408 12 Union Road FAX: +44-(0)1223-336033 Cambridge CB2 1EZ, UK Website: http://www.ccdc.cam.ac.uk -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen Graham Sent: 10 January 2012 10:23 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file "...available to anyone who has access to the Cambridge Structural Database System" How many academic labs will bother / can afford to buy a CCSD license just to check the geometry of small molecule ligands, especially when they need to do so them only once every blue moon? The ability for the PDB to check a ligand against the CCSD upon deposition would be great. The ability to generate the restraint definition for free via the web before deposition is better: that's why people use PRODRG! Stephen On 10 January 2012 09:50, John Liebeschuetz <j...@ccdc.cam.ac.uk> wrote: > 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. -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638 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.
