Phi / Psi / Omega Angle Converter

PPC

Torsion Angle Converter for Pyranoses

German Cancer Research Center
Central Spectroscopy
Im Neuenheimer Feld 280
69120 Heidelberg, Germany
Contact:  Andreas Bohne-L.

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NMR-Definition

Web-Converter
<----- [ Torsion Angle Values ] ----->

Crystal Definition

Work

Conversion Form

Monosaccharide 1 Link Monosaccharide 2

- - -( - )- - -

Type of conversion:

Phi: Psi: Omega:

If you want to convert something like this GalNAc-alfa-(1-3)-beta-L-Rha
you have to convert the input. In the example you need to enter a - D - Galp - ( 1 - 3 ) - b - L - Rhap.

Definitions

Table 1: Definitions of , angles for (1-1), (1-2), (1-3) and (1-4) linkage

NMR-definition

C-1 crystallography definition

(1-1)-connection is not defined

C+1 Crystallography definition

(1-1)-connection is defined

_H=H₁-C₁-O-C'_x

_H=C₁-O-C'_x-H'_x

_C-1= O₅-C₁-O-C'_x

_C-1= C₁-O-C'_x-C'_x-1

X is not 1

_C+1= O₅-C₁-O-C'_x

_C+1= C₁-O-C'_x-C'_x+1

For 1-x with x in {1,2,3,4}

Table 2: Definitions of , , angles for (1-6)-linkage

NMR-definition

Crystallography definition

_H=H₁-C₁-O-C'₆

_H =C₁-O-C'₆-C'₅

_H =O-C'₆-C'₅-H'₅

_C = O₍₅₎-C₁-O-C'₆

_C = C₁-O-C'₆-C'₅

_C = O-C'₆-C'₅-O'₅

Example from the web where this tool could be useful

Carbohydrate Chain of Soybean Agglutinin

a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+
The result page of the Sweet building and Tinker optimizing.

Create a simple saccharide with the Sweet web tool and look at the connection to the angle convertion tool.

Go to [Angle (Phi/Psi)] at the bottom of the result list.

NMR: Table 3 from A flexible model for the cell wall polysaccharide of Streptococcus mitis J22 determined by three-dimensional 13C edited NOESY spectra and 13C-1H long range coupling constants
Conformational studies on O-specific polysaccharides of Shigella dysenteriae
Comparison of NMR and Molecular Modeling Results for a Rigid and a Flexible Oligosaccharide combined with molecular modeling

Download the c-source of the program. The source is distributed by GPL.
To connect your output to our web tool you can use the URL encoding parameter submission:
a-D-Manp-(1-4)-a-D-Manp cry2nmr with angles phi=123 psi=23 and omega is not set

Table 1: Definitions of , angles for (1-1), (1-2), (1-3) and (1-4) linkage
NMR-definition	C-1 crystallography definition (1-1)-connection is not defined	C+1 Crystallography definition (1-1)-connection is defined
_H=H₁-C₁-O-C'_x _H=C₁-O-C'_x-H'_x	_C-1= O₅-C₁-O-C'_x _C-1= C₁-O-C'_x-C'_x-1 X is not 1	_C+1= O₅-C₁-O-C'_x _C+1= C₁-O-C'_x-C'_x+1
For 1-x with x in {1,2,3,4}