Re: [ccp4bb] Van der Waals Interaction Distances

[Pius Padayatti]

Here is the original article.
Distinction between the weak hydrogen bond and the van der Waals
interaction
Thomas Steiner*a and Gautam R. Desiraju*
Chem. Commun., 1998 891-892

On Thu, Feb 19, 2009 at 11:27 PM, Pius Padayatti  wrote:
> Table 1 Numerical data for X–H···Y contacts with H···Y < 3.0 Å (2.7 Å for
> H···H contacts). Data for normalised H-atom positions
>MeanMeanMean
> Contact typeNumber  H···Y (Å)   X···Y (Å)   X–H···Y (°)
> C(sp3)–O–H···ONC33301.974(6)2.837(4)154.0(4)
> CáC–H···ONC 44  2.36(4) 3.31(2) 152(2)
> CNCH2···ONC 124 2.67(1) 3.56(2) 143(1)
> CH2–CH3···ONC   767 2.761(6)3.590(7)137.1(7)
> CH2–CH3···H–C   39752.500(2)3.246(4)128.6(3)
>
> ref:Chem. Commun., 1998 891
>
> On Thu, Feb 19, 2009 at 7:48 PM, Jim Fairman  wrote:
>> Fellow CCP4 Board Members,
>>
>> What is the general consensus of the structural biology community for a
>> range of distances that would be considered a Van der Waals
>> contact/interaction (eg: hydrogen bonds are usually considered to be 2.5-3.5
>> angstroms not including the hydrogen atoms)?
>>
>> Cheers, Jim
>>
>> --
>> Jim Fairman
>> Graduate Research Assistant
>> Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
>> University of Tennessee -- Knoxville
>> 216-368-3337 jfair...@utk.edu james.fair...@case.edu
>>
>
>
>
> --
> Pius S Padayatti
> Scientist,
> Polgenix, Inc.
> 11000 Cedar Ave, Suite 260
> Cleveland, OH 44106
> Phone: 216-658-4528
> Fax: 216-658-4529
>



-- 
Pius S Padayatti
Scientist,
Polgenix, Inc.
11000 Cedar Ave, Suite 260
Cleveland, OH 44106
Phone: 216-658-4528
Fax: 216-658-4529

Re: [ccp4bb] Van der Waals Interaction Distances

[Nadir T. Mrabet]

Hi,

This is one table (below) I use to convince my students that Evdw is 
still negative when R/Rm = 2, where Rm = Ri + Rj.
To take into account water screening effect, however, one should 
consider vdw attraction only while R < Rm + 2 x Rw,

where Rw is the radius of water.

hth,

Nadir

**

**



**



**



**

*1.00*



*1.000*



*1.000*



*-0.130*

*1.05*



*0.936*



*1.069*



*-0.122*

*1.10*



*0.810*



*1.234*



*-0.105*

*1.15*



*0.678*



*1.475*



*-0.088*

*1.20*



*0.558*



*1.793*



*-0.072*

*1.25*



*0.456*



*2.195*



*-0.059*

*1.30*



*0.371*



*2.692*



*-0.048*

*1.35*



*0.303*



*3.299*



*-0.039*

*1.40*



*0.248*



*4.033*



*-0.032*

*1.45*



*0.204*



*4.911*



*-0.026*

*1.50*



*0.168*



*5.957*



*-0.022*

*1.55*



*0.139*



*7.193*



*-0.018*

*1.60*



*0.116*



*8.646*



*-0.015*

*1.65*



*0.097*



*10.346*



*-0.013*

*1.70*



*0.081*



*12.324*



*-0.011*

*1.75*



*0.068*



*14.616*



*-0.009*

*1.80*



*0.058*



*17.260*



*-0.008*

*1.85*



*0.049*



*20.298*



*-0.006*

*1.90*



*0.042*



*23.776*



*-0.005*

*1.95*



*0.036*



*27.742*



*-0.005*

*2.00*



*0.031*



*32.252*



*-0.004*



--

Pr. Nadir T. Mrabet
   Cellular & Molecular Biochemistry
   INSERM U-724
   Nancy University, School of Medicine
   9, Avenue de la Foret de Haye, BP 184
   54505 Vandoeuvre-les-Nancy Cedex
   France
   Phone: +33 (0)3.83.68.32.73
   Fax:   +33 (0)3.83.68.32.79
   E-mail: nadir.mra...@medecine.uhp-nancy.fr
   




Jim Fairman wrote:

Fellow CCP4 Board Members,

What is the general consensus of the structural biology community for 
a range of distances that would be considered a Van der Waals 
contact/interaction (eg: hydrogen bonds are usually considered to be 
2.5-3.5 angstroms not including the hydrogen atoms)?


Cheers, Jim 


--
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu  
james.fair...@case.edu 

Re: [ccp4bb] Van der Waals Interaction Distances

[Pius Padayatti]

Table 1 Numerical data for X–H···Y contacts with H···Y < 3.0 Å (2.7 Å for  
H···H contacts). Data for normalised H-atom positions   
MeanMeanMean
Contact typeNumber  H···Y (Å)   X···Y (Å)   X–H···Y (°) 
C(sp3)–O–H···ONC33301.974(6)2.837(4)154.0(4)
CáC–H···ONC 44  2.36(4) 3.31(2) 152(2)  
CNCH2···ONC 124 2.67(1) 3.56(2) 143(1)  
CH2–CH3···ONC   767 2.761(6)3.590(7)137.1(7)
CH2–CH3···H–C   39752.500(2)3.246(4)128.6(3)

ref:Chem. Commun., 1998 891

On Thu, Feb 19, 2009 at 7:48 PM, Jim Fairman  wrote:
> Fellow CCP4 Board Members,
>
> What is the general consensus of the structural biology community for a
> range of distances that would be considered a Van der Waals
> contact/interaction (eg: hydrogen bonds are usually considered to be 2.5-3.5
> angstroms not including the hydrogen atoms)?
>
> Cheers, Jim
>
> --
> Jim Fairman
> Graduate Research Assistant
> Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
> University of Tennessee -- Knoxville
> 216-368-3337 jfair...@utk.edu james.fair...@case.edu
>



-- 
Pius S Padayatti
Scientist,
Polgenix, Inc.
11000 Cedar Ave, Suite 260
Cleveland, OH 44106
Phone: 216-658-4528
Fax: 216-658-4529

[ccp4bb] Van der Waals Interaction Distances

[Jim Fairman]

Fellow CCP4 Board Members,

What is the general consensus of the structural biology community for a
range of distances that would be considered a Van der Waals
contact/interaction (eg: hydrogen bonds are usually considered to be 2.5-3.5
angstroms not including the hydrogen atoms)?

Cheers, Jim

-- 
Jim Fairman
Graduate Research Assistant
Department of Biochemistry, Cellular, and Molecular Biology (BCMB)
University of Tennessee -- Knoxville
216-368-3337 jfair...@utk.edu james.fair...@case.edu