Thank you Shveta for NOTICING!!!
Please - everyone - check your restraints - programs make mistakes - you
(or the chemist who made the ligand) - are the experts!!!!
Eleanor
On 01/09/2012 10:05 AM, krish wrote:
> Dear Shveta,
>
> I have seen similar trends with PRODRG. I recommend you to use
> other molecular modeling programs like Hyperchem or Maestro to get more
> consistent geometric parameters for small molecules. Once you know the
> bondlengths and bond angles from aforesaid molecular modeling programs, you
> can use sketcher (CCP4) to define them manually. Save it to the monomer
> library and you are all set to run them in Refmac .
>
> or
>
> You can use Phenix.elbow or phenix.reel to load the coordinates of the
> small moleucle and optimize with AM1 (semi-empirical), then you should get
> reasonable geometirc parameters suc as bond length, bond angles and etc.
>
> Hope this helps !
>
> Cheers,
> Krishna
>
> Krishna Chinthalapudi, PhD
> Hannover Medical School
>
>
>
>
> On Mon, Jan 9, 2012 at 7:13 AM, 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.
>>
>> --
>> Shveta Bisht
>> Ph.D. Student,
>> Prof. M R N Murthy's Group,
>> Molecular Biophysics Unit,
>> Indian Institute of Science
>> Bangalore-12
>> --
>> This message has been scanned for viruses and
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>>
>>
>
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