Last Modified
1 January 2024
Algorithm
Initial hydrogen atom coordinate prediction of a water molecule in the biomacromolecule crystal structure
Figure 1. Prediction algorithm of an initial hydrogen atom coordinate of water molecule.
Figure 2. Definition of potential hydrogen donor and acceptor regions (image).
First Hydrogen Atom Coordinate
As shown in Figure 1, the first hydrogen atom in a water molecule is positioned at the distance of 1.0 Å from its oxygen atom toward a hydrogen acceptor hetero atom, which fulfills the conditions of the hydrogen acceptor region (defined in Figure 2) with the minimum distance from the oxygen atom in the water molecule.
Second Hydrogen Atom Coordinate
When a hydrogen acceptor hetero atom with the second minimum distance is apart more than 90º from that with the first minimum distance, the second hydrogen atom in the water molecule is positioned at the distance of 1.0 Å from its oxygen atom toward the second hetero atom. Otherwise, the position of the second hydrogen atom is predicted on the basis of the lone pair information on the oxygen atom of the water molecule using the conditions of the hydrogen donor regions defined in Figure 2.
In the chemical calculations, an initial structure is the most important for obtaining a reliable structure, since the optimized structure strongly depends on the initial structure. The structure given from the molecular dynamics calculations also depends on the initial structure, if the structure is not subjected to very long-time samplings at a high temperature. Unfortunately, this can not be realized for a biomacromolecular system due to a large number of atoms.
Thus, our algorithm is useful for preparing a reliable final structure.
The Estimation of Hydrogen Atoms in Water program in the Homology Modeling Professional for HyperChem package carry this algorithm.
May 2005