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<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.
--
Shveta Bisht
Ph.D. Student,
Prof. M R N Murthy's Group,
Molecular Biophysics Unit,
Indian Institute of Science
Bangalore-12
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