Summary of information
PROJECT
Nucleoside

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Upload 12-01-2006 15:03 (Day-Month-Year, Paris time)
Update 28-09-2011 16:01 (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

Glycosylamine Nucleobase Ribose RNA Ribonucleic acid


Abstract

ESP atomic charges for the four nucleosides of RNA, i. e. Adenosine, Cytidine, Guanosine and Uridine (conformation C3'endo; dihedral constraints were used in the geometry optimization step to avoid intra-molecular hydrogen bonds and transition state type structures: HO3'-O3'-C3'-C4' = 180 deg., HO2'-O2'-C2'-C3' = 290 deg.) based on the CHELPG algorithm and the HF/6-31G* theory level. Charges derived using 1 mol. conformation and 6 mol. orientations (Rigid-Body Reorientation Algorithm). Charge values to be compared with those reported in the projects W-74, W-75, W-76 and W-78 and compatible with the project W-72 (DNA nucleosides).

Publication YES      

Author(s) F.-Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak

Journal Phys. Chem. Chem. Phys.

Year 2010

Volume 12

Page(s) 7821-7839


"Whole molecule" or "Molecule fragment" type project WHOLE MOLECULE

Interface R.E.D. used ? YES


Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 4

Contain charge values & information about molecular topology

No Name Download Wikipedia 3D visualization
1 Adenosine Link Wiki Logo Jmol Logo
2 Cytidine Link Wiki Logo Jmol Logo
3 Guanosine Link Wiki Logo Jmol Logo
4 Uridine Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 4

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 Adenosine 1 Rigid Body Reorient Algo 6 Link Wiki Logo
2 Cytidine 1 Rigid Body Reorient Algo 6 Link Wiki Logo
3 Guanosine 1 Rigid Body Reorient Algo 6 Link Wiki Logo
4 Uridine 1 Rigid Body Reorient Algo 6 Link Wiki Logo



Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 1998

Theory level 1 HF

More information 1 Opt=VTight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 1998

Theory level 2 HF

More information 2 IOp(6/33=2) NoSymm

Basis set 2 6-31G*

Algorithm CHELPG


Information about the charge fit

Program RESP

Number of stage(s) 1

input of stage 1 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



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