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