Package name:

Package ID: 2934
Force-field: CHARMM/CGENFF | Code: Gromacs
Created by Bogdan Iorga (biorga)
Created at 2020-12-10 11:18:01
Modified at 2020-12-10 11:18:01


The Zinc dummy model consisted of a central Zn atom surrounded by six dummy atoms forming an octahedral shell. The van der Waal parameters of the atoms were optimized using a genetic algorithm to reproduce the hydration energy of -1956 kJ/mol and an ion-oxygen distance of 2.08 Å in simulations with water. The optimization ran through six iterations at which point it reproduced these values within 1% and 0.3%, respectively. The model was then validated with 200 ns simulations using PDB models for beta-glucanase (1U0A), stromelysin-1 (2USN) and DNA polymerase (1A5T). These models were chosen for their high resolution, 1.6, 2,2 and 2,2 Å respectively, and for the diversity in their coordinating residues, which were HHDD, HHHD, and CCCC, respectively.

Chemical structure

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Reference validation values

These are experimental values or high-level quantum mechanics values, which will be used for comparison with computed values (found in individual versions).

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Version 1 created at 2020-12-10

Score N/A

Computed validation values

preprocessor output "grompp-compatible"
Created at 2020-12-10 11:18:01 | Modified at 2020-12-10 11:18:01 | [download zip]
Type Description Hash (SHA1)
Topology ZNM.itp 7bfea7ad24132a54bd5b2fe0aa21b32434c32bf7
Structure ZNM.pdb 3b17e87a7e53c06678e9a49c3d0cc471b602530d

Compound details

Ligand code UNL
Molecule identifier 826813478118D0A2
Displayed name
Canonical IUPAC name
Formula ?H6D6
Molecular weight 18.13
Charge 0
Number of atoms 7
SMILES [Znd].[2H].[2H].[2H].[2H].[2H].[2H]
PubChem CID
Other names


Type CC BY-SA – Creative Commons Attribution-Share Alike License
Name Oliver Beckstein
Email (hidden)
Source optimized using a genetic algorithm