FAQs
For questions not addressed by a support solution here, please Contact Us. Please do include a description of the problem as well as your operating system and version.
What can we help you with?
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What input file format do I need for a Hydrogen Bond Propensity calculation?
… The Hydrogen Bond Propensity tool (accessed from within Mercury) accepts molecular input in a wide variety of formats. If you simply want to assess …
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Why are my H-bond constraints not being taken into account?
… A ligand atom may be constrained to form a hydrogen bond to a particular protein atom. One atom should be a hydrogen atom on a H-bond donor and the other …
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Can I search on bonds, angles and torsions involving metals or hydrogen atoms?
… distances involving metals however it is not possible to search for angles and torsions involving metals. No bonds, angles or torsions involving hydrogen atoms …
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Is it possible to include any additional probe groups?
… useful probes to start exploring a binding site are usually: Alcohol Oxygen: the hydroxyl group can both donate and accept hydrogen bonds, so favorable spots …
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Why does Mercury not generate an ESD for a particular bond length, angle, torsion or other measurement in my structure?
… ’. In this example the non-hydrogen atomic coordinates would have ESDs, but the hydrogen positions would not. Mercury will tabulate the measured values of all bond lengths …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… being docked. Water mediated hydrogen bonding is important and all the waters have been removed during protein preparation. If so, identify and extract important …
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What is the difference between the ‘exact’ and ‘substructure’ settings in Structure Search?
… of molecules respectively. Exact match will only find hits for complete molecules. This will automatically add any additional hydrogens as a constraint necessary …
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How do I edit & re-run a Crystal Packing Feature search?
… Feature search set-up including change to element types, number of hydrogens, number of bonds, charge and cyclicity as well as the 3D query itself. …
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What is CSD-Materials?
… of CSD-Materials include everything in CSD-Core as well as: Polymorph risk assessment through hydrogen bond propensity, conformational and intermolecular …
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Why is GOLD unable to dock a particular ligand?
… and ligand must have all hydrogen atoms added. In addition, each ligand and protein atom must be assigned an atom type. GOLD atom typing is based on SYBYL atom …
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