"...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 <[log in to unmask]> wrote:
> On 9 January 2012 06:13, Shveta Bisht <[log in to unmask]> 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
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>
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