| 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 |
Abstract | |
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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General view |
Detailed view
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References |
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No citations associated with these parameters. | |
These are experimental values or high-level quantum mechanics values, which will be used for comparison with computed values (found in individual versions).
All deposited versions are available and can be downloaded individually. Higher version numbers are more recent. Files that changed between versions can be identified by differing SHA1 hash checksums.
Score N/A
Computed validation values
| Type | Description | Hash (SHA1) |
|---|---|---|
| Topology | ZNM.itp | 7bfea7ad24132a54bd5b2fe0aa21b32434c32bf7 |
| Structure | ZNM.pdb | 3b17e87a7e53c06678e9a49c3d0cc471b602530d |
Compound details |
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| 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 | — |
| CAS RN | — |
| Other names | |
License |
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| Type | CC BY-SA – Creative Commons Attribution-Share Alike License | |
| Name | Oliver Beckstein | |
| (hidden) | ||
| Source | optimized using a genetic algorithm |
Jan Domański, Oliver Beckstein, Bogdan I. Iorga; Ligandbook: an online repository for small and drug-like molecule force field parameters, Bioinformatics, Volume 33, Issue 11, 1 June 2017, Pages 1747–1749, https://doi.org/10.1093/bioinformatics/btx037
"Throwing the Baby Away With the SPC" (S. Hayward)
