R.E.DD.B.: code F-58

Upload 14-01-2006 08:54 (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 8 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 stabilized; 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-59, 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) 8

Contain charge values & information about molecular topology

No	Name	Download	Wikipedia	3D Display 1	3D Display 2
1	Fragment HBA3
2	Fragment HBA5
3	Fragment HBA
4	Fragment HBAN
5	Fragment HBI3
6	Fragment HBI5
7	Fragment HBI
8	Fragment HBIN

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
1	Dimethylphosphate	1	QM Reorient Algo GAUSSIAN	1
2	2-(2'-Hydroxyphenyl)benzoxazole C5-aryl-nucleoside	1	QM Reorient Algo GAUSSIAN	1
3	2-(2'-Hydroxyphenyl)benzoxazole C3-aryl-nucleoside	1	QM Reorient Algo GAUSSIAN	1

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 CONNOLLY SURFACE

Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1

input of stage 2

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

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...

A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...

A file to provide new force field parameters compatible with the Tripos mol2 file(s)...

A file (choice made by the author) to provide more information about the project...

Download the whole project...