Geometrical Descriptors Plugin

This manual gives you a walk-through on how to use the Geometrical Descriptors Plugin:

Introduction

The Geometrical Descriptors Plugin calculates 3D geometric descriptors for a molecule. The following window shows a calculation result.

images/download/attachments/1806679/IMG_12082014_121449.png

Fig.1 Geometrical Descriptors Plugin result window

Options

The following options can be set in the Geometrical Descriptors Options window:

  • Type

    • Dreiding energy: calculates the energy of the 3D structure (conformation) of the molecule using Dreiding force field.

    • MMFF94 energy: calculates the energy of the 3D structure (conformation) of the molecule using MMFF94 force field.

    • Steric hindrance: calculates steric hindrance of an atom calculated from the covalent radii values and geometrical distances.

    • Minimal projection area: calculates the minimum of projection areas of the conformer, based on the van der Waals radius (in Å2).

    • Maximal projection area: calculates the maximum of projection areas of the conformer, based on the van der Waals radius (in Å2).

    • Minimal projection radius: calculates the radius for the minimal projection area of the conformer (in Å).

    • Maximal projection radius: calculates the radius for the maximal projection area of the conformer (in Å).

    • Maximal distance perpendicular to the min projection: calculates the maximal extension of the conformer perpendicular to the minimal projection area (in Å).

    • Maximal distance perpendicular to the max projection: calculates the maximal extension of the conformer perpendicular to the maximal projection area (in Å).

    • van der Waals volume: calculates the van der Waals volume of the conformer (in Å3).

  • Energy unit: unit of the calculated energy (kcal/mol or kJ/mol).

  • Decimal places: setting the number of decimal places with which the result value is given.

  • Set MMFF94 optimalization: The structure is optimized before MMFF94 energy calculation.

  • Set projection optimalization The structure is optimized before projection area and projection radius calculation(s).

  • Calculate for lowest energy conformer:

    • If molecule is in 2D: the lowest energy conformer is generated if the input molecule is in 2D; 3D input molecules are considered in the given conformation.

    • Never: the input molecule is used for calculation.

    • Always: the lowest energy conformer is generated (for 3D and 2D molecules as well).

  • Optimization limit: sets the rigour of convergence for optimization. Stricter convergence means lower gradient limit to reach during optimization. The values can be:

    • Very loose

    • Normal

    • Strict

    • Very strict

images/download/attachments/1806679/IMG_12082014_120958.png

Fig. 2 Geometrical Descriptors Options window