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Marvinsketch v21

Manufactured by ChemAxon

Marvinsketch v21.11 is a chemical structure drawing and editing software tool developed by ChemAxon. It allows users to create, modify, and visualize chemical structures and reactions. The software provides a range of features for drawing, editing, and manipulating chemical diagrams.

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Lab products found in correlation

2 protocols using marvinsketch v21

1

Structural Optimization and Docking of Mn2+ Complex

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Firstly, the structure of the Mn 2+ -complex was drawn in Marvinsketch v21.11 (Chemaxon Ltd; https://chemaxon.com) enabling correct assignment of coordinate bonding. The resulting structure was 'cleaned' in 3D and saved in .gjf format for input into the Gaussian 16 revC.01 package (Gaussian Inc.
340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA). The molecular structure of the Mn 2+ -complex was subsequently optimized in water as a solvent via the hybrid B3LYP (Becke-3 Parameter-Lee-Yang-Parr) [35] (link) DFT (Density Functional Theory) method in GEN mode to enable assignment in the calculation of the 6-31G** and LANL2DZ basis sets, to atoms H, O, C, N and Mn respectively. Gaussview 6 (Gaussian Inc. 340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA) was next used to examine the structures of all converged structures and the nal optimized structure was exported in .pdb le format.
The Mn 2+ -complex was subsequently imported into MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/) and docked to PDB entry 1XQ8 with triangle matching placement and scoring with the London dG scoring function. Subsequent re nement of all docked poses using the GBVI/WSA dG scoring function with induced t was undertaken. Finally, the top docked pose was manipulated and visualized also using MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/).
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2

Structural Optimization and Docking of Mn2+ Complex

Check if the same lab product or an alternative is used in the 5 most similar protocols
Firstly, the structure of the Mn 2+ -complex was drawn in Marvinsketch v21.11 (Chemaxon Ltd; https://chemaxon.com) enabling correct assignment of coordinate bonding. The resulting structure was 'cleaned' in 3D and saved in .gjf format for input into the Gaussian 16 revC.01 package (Gaussian Inc.
340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA). The molecular structure of the Mn 2+ -complex was subsequently optimized in water as a solvent via the hybrid B3LYP (Becke-3 Parameter-Lee-Yang-Parr) [35] (link) DFT (Density Functional Theory) method in GEN mode to enable assignment in the calculation of the 6-31G** and LANL2DZ basis sets, to atoms H, O, C, N and Mn respectively. Gaussview 6 (Gaussian Inc. 340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA) was next used to examine the structures of all converged structures and the nal optimized structure was exported in .pdb le format.
The Mn 2+ -complex was subsequently imported into MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/) and docked to PDB entry 1XQ8 with triangle matching placement and scoring with the London dG scoring function. Subsequent re nement of all docked poses using the GBVI/WSA dG scoring function with induced t was undertaken. Finally, the top docked pose was manipulated and visualized also using MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/).
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