Summary of information
PROJECT
2-(2'-Hydroxyphenyl)benzoxazole C-aryl-nucleotide fragment

Wiki Logo

Upload 14-01-2006 09:16 (Day-Month-Year, Paris time)



Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Francois-Yves

Lastname Dupradeau

Institute UFR de pharmacie, UPJV

City Amiens

Country FRANCE


General information about the Project

Molecule keywords

HBO Model base pair Enol-imine Deoxyribose Phosphate DNA major or minor groove Unusual nucleotide


Abstract

RESP atomic charges based on the Connolly surface algorithm and the HF/6-31G* theory level for 2 fragments of two 2-(2'-Hydroxyphenyl)benzoxazole (or HBO) C-aryl nucleotides (HBO enol-imine oriented in the DNA major or minor groove). 3 structures, i. e. Dimethylphosphate (conformation gauche, gauche; single mol. orientation), 2-(2'-Hydroxyphenyl)benzoxazole C5- and C3-aryl-nucleosides (both nucleosides: conformation C2'endo - the intra-molecular hydrogen bond within the HBO enol-imine being broken; single mol. orientation) are used in the charge derivation. Procedure automatically carried out using the R.E.D.-III program (mol. orientation generated by the QM program is conserved for each structure). Charges suitable for MD simulations using the Cornell et al. AMBER force field (and/or its different adaptations). Charge values to be compared with the project F-58, and to be used together with the project F-57 (see the corresponding publication).

Publication YES      

Author(s) F.-Y. Dupradeau, D. A. Case, C. Yu, R. Jimenez and F. E. Romesberg

Journal J. Am. Chem. Soc.

Year 2005

Volume 127

Page(s) 15612-15617


"Whole molecule" or "Molecule fragment" type projectMOLECULE FRAGMENT

Interface R.E.D. used ? YES


Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 2

Contain charge values & information about molecular topology

No Name Download Wikipedia 3D visualization
1 Fragment HBA Link Wiki Logo Jmol Logo
2 Fragment HBI Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 3

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 Dimethylphosphate 1 QM Reorient Algo GAUSSIAN 1 Link Wiki Logo
2 2-(2'-Hydroxyphenyl)benzoxazole C5-aryl-nucleoside 1 QM Reorient Algo GAUSSIAN 1 Link Wiki Logo
3 2-(2'-Hydroxyphenyl)benzoxazole C3-aryl-nucleoside 1 QM Reorient Algo GAUSSIAN 1 Link Wiki Logo



Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 1998

Theory level 1 HF

More information 1 Opt=Tight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 1998

Theory level 2 HF

More information 2 IOp(6/33=2)

Basis set 2 6-31G*

Algorithm CONNOLY SURFACE


Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1 Link

input of stage 2 Link



Files the author of the project wishes to provide...

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...Link
A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...Link
A file to provide new force field parameters compatible with the Tripos mol2 file(s)...Link
A file (choice made by the author) to provide more information about the project...Link
A file (choice made by the author) to provide more information about the project...Link

Download the whole project... Link



Valid XHTML 1.0 Strict CSS Valide !

Internet page © 2006-2012. All rights reserved.
Université de Picardie Jules Verne - Sanford|Burnham Medical Research Institute.
R.E.DD.B. projects free.