Re: [ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge?

[Boaz Shaanan]

Hi Nadir, Which "One" do you use? I may have missed it in the thread.   Thanks,             Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Nadir Mrabet [nadir.mra...@univ-lorraine.fr] Sent: Tuesday, June 10, 2014 1:02 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge? Hi Jacob, Hbo energy is an empirical function for most biological molecules. The one I use takes into account Coulomb's law for charges and van der Waals (both attractive and repulsive) interactions. The equation's parameters are adjusted to implicitly take into account contributions from "charge transfer" and polarization. There is also a cosinusoidal parameter to account for directionality as the Hbo interaction is by essence non isotropic. This parameter is 1 for both N -H °°° O and H°°°O=C equal to 180 ° and 0 if either N -H °°° O or H°°°O=C is 90 ° Other electron-donor atoms may be involved but the strategy used is similar. Parameter values in between are calculated by means of a cosinusoidal equation. As you may see, explicit H atoms are required to calculate this energy and therefore they need to be built "adequately" prior to doing that and that is a real challenge far from being trivial. Best, Nadir Mrabet Pr. Nadir T. Mrabet Structural & Molecular Biochemistry N-gere - INSERM U-964 University of Lorraine, Nancy School of Science and Technology and School of Medicine 9, Avenue de la Foret de Haye 54500 Vandoeuvre-les-Nancy, France Tel. (direct) : +33 (0)3.83.68.32.73 Tel. (secretary) : +33 (0)3.83.68.32.92 Fax. : +33 (0)3.83.68.32.79 Email : Nadir.Mrabet <at> univ-lorraine.fr Hi Jacob, Modeling programs need to take hydrogen bonding into account in their force fields so they typically have good measures for hydrogen bonds. I personally use YASARA to get the numbers you want. This is also what PDB_REDO uses to give you the hydrogen bond energy and the the number of hydrogen bonds for each ligand. Cheers, Robbie Sent from my Windows Phone Van: Keller, Jacob Verzonden: 10-6-2014 4:45 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge? Dear Crystallographers, Is anyone aware of a relationship between H-bond distance and energy thereof, maybe with a little geometry and +/- charge thrown in? I am looking at a structure with many H-bonds to a ligand, and wondered about the relative importance of each. JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************