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Hi Harry The results you get are obviously going to be highly sample-dependent, so it's important when choosing your sample a) to have a fully representative sample, b) not to limit the sample unnecessarily and end up with a sample which is too small to give statistically significant results, and c) most importantly to choose only the most accurately determined structures (R < .05, & exclude disordered, structures with errors, polymers, powders & organometallics) to be in your sample (though necessarily this conflicts with the 2nd requirement). Including inaccurate structures in the sample will inevitably increase the dispersion of values, and torsion angles are particularly sensitive to co-ordinate errors. For info, I'm using the latest CSD release (5.27 with Jan & May '06 updates). So using the same O-methyl ester search pattern as you did & using the above quality criteria I get: N = 317 (0 outliers excluded) Range = 170.2 - 189.0 Mean = 180.0 SE of mean = 0.2 Sample SD = 3.4 For the N-methyl amides I only got 15 observations so I didn't bother to do the stats. The methyl esters and amides you have chosen are not really representative, for one thing the -O-Me group is often disordered, or at least has a high B factor and is often difficult to locate accurately, which would tend to undermine precise determination of the torsion angle. Hence I chose the search pattern XC(H)(R)C(=O)OC(H)(R)R and the corresponding secondary amide (X=any, R=C or H), and also specified that the ester/amide group is acyclic to avoid any bias due to ring constraints. This includes the previous pattern as a subset, as well as the large set of peptides so we shouldn't be short of samples for the amide group! So now for esters & still using the same exclusion criteria I get: N = 5124 (1 outlier excluded) Range = 160.8 - 200.2 Mean = 180.0 SE of mean = 0.1 Sample SD = 4.7 and for amides: N = 860 (0 outliers excluded) Range = 157.4 - 200.5 Mean = 179.2 SE of mean = 0.2 Sample SD = 6.0 The ranges for ester & amide are about the same, however using the range as a measure of dispersion is not reliable due to sensitivity to outliers. The dispersion as measured by the sample SD, whose values I reported previously, is clearly lower for esters than for amides - admittedly this does seem to run contrary to chemical intuition but the evidence of the data seems to be incontrovertible. As I said the key here is to use as big a sample as possible of the highest quality data while still being representative. Regards -- Ian > -----Original Message----- > From: Harry M. Greenblatt [mailto:[EMAIL PROTECTED] > Sent: Sunday, July 16, 2006 12:56 PM > To: Ian Tickle > Subject: ester vs peptide planarity > > BS"D > > Dear Ian, > > > > Hi, sorry but this theory doesn't accord with observation: for > non-conjugated acyclic esters in the CSD the RMSD of > the C-O torsion > about the mean (= 0) is ~ 4.7 deg; for non-conjugated > acyclic primary > amides it's well known that the RMSD of the C-N torsion > is ~ 6.0 deg > (mean = -1.0), so on average the ester is actually > slightly more planar > than the amide. I know this because this is how we > obtain torsion > weights for ligand dictionaries (not perfect I know but > better than > nothing!). > > > > > Pursuant to my earlier e-mail to the BB, I did a search in > the CSD on two related structures: > > R-CH2-CO-O-CH3 and R-CH2-CO-NH-CH3 > > The results are in keeping with an ester having less double > bond character, although the "study" is somewhat flawed by > the imbalance in sample sizes. > > **Ester case** > -------------------- > > 839 observations, > > Min. 152.6 > Max. -100.55 > Range 106.8 > Mean 179.9 > > Taking out the 2 most obvious outliers (from the same > structure, as a matter of fact) > > 837 observations, > > Min. 168. > Max. -163.6 > Range 28.4 > Mean -179.9 > > ////////////////////////////////////////////////////////////// > //////////////////////////////////// > **Amide case** > ---------------------- > > 78 observations > > Min. 169.7 > Max. -173.9 > Range 16.3 > Mean 178.8 > > Thus, the range of values in the case of the esters is much > larger than that of the amides for the above case, consistent > with less double bond character. > > Harry > > -------------------------------------------------------------- > ----------- > > Harry M. Greenblatt > > Staff Scientist > > Dept of Structural Biology [EMAIL PROTECTED] > > Weizmann Institute of Science Phone: 972-8-934-3625 > > Rehovot, 76100 Facsimile: 972-8-934-4159 > > Israel > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. 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