Small Molecule Properties with all its boxes checked.
Small Molecule Properties is one of two windows opened by the Ligand Properties tool or mode. Small Molecule Properties can show several numerical measures that are useful for assessing the design of a ligand in a in a Foldit small molecule design puzzle.
The values shown in the Small Molecule Properties panel may also determine the value of the objectives for a given puzzle. For example, a puzzle may have a cLogP objective, which starts to deduct points if cLogP exceeds a certain value. Objectives may also feature the number of hydrogen bond donors, the number of rotatable bonds, the polar surface area, and other values displayed in Small Molecule Properties.
The Small Molecules Property panel has several checkboxes. When a box is checked, the corresponding value appears in the area below the checkboxes.
Mcl weight
Many objectives in a small molecule design puzzle depend on values reported in the Small Molecule Properties panel.
The "Mcl weight" checkbox shows the molecular weight of the ligand. The units are daltons (Da), also known as unified atomic mass units (u). The abbreviations "Da" and "u" can be used interchangeably. Some sources use "Da", some sources use "u". The value shown is rounded to the nearest whole number.
Heavy atoms
The heavy atoms checkbox shows the number of heavy atoms in the ligand. Any atom which is not hydrogen is considered a heavy atom.
Hbond donors
The "Hbond donors" checkbox shows the number of atoms in the ligand which can act as hydrogen bond donors. The "show bondable atoms" checkbox in View Options shows hydrogen bond donors in blue, and atoms which can act as either donors or acceptors in purple. A puzzle objective may deduct points if too many hydrogen bond donors are present.
Hbond acceptors
The "Hbond acceptors" checkbox shows the number of atoms in the ligand which can act as hydrogen bond acceptors. The "show bondable atoms" checkbox in View Options shows hydrogen bond acceptors in red, and atoms which can act as either donors or acceptors in purple.
cLogP
The "cLogP" check box shows the cLogP or "calculated log(P)" of the ligand. CLogP is a measure of how hydrophobic or hydrophilic the ligand is. Lower values of cLogP indicate the ligand is more hydrophilic, higher values indicate the ligand is more hydrophobic. Successful drugs tend to be more hydrophilic. A puzzle objective may deduct points if cLogP exceeds a certain value.
rotatable bonds
The "rotatable bonds" checkbox shows how many bonds in the ligand can rotate. Rotatable bonds are generally single bonds between heavy atoms that are not in a ring. The objectives for some puzzles may deduct points if too many rotatable bonds are found.
aromatic rings
The "aromatic rings" checkbox shows the number of aromatic rings in the ligand. Aromatic rings are generally "unsaturated", with a limited number of hydrogens, and the ring atoms which tend to have double bonds. Benzene is the classic example of an aromatic ring.
aliphatic rings
The "aromatic rings" checkbox shows the number of aliphatic rings in the ligand. Aliphatic are generally "saturated", with ring atoms joined by single bonds, allowing bonding with more hydrogen atoms. Cyclohexane is an example of a saturated aliphatic ring, in contrast to benzene, an unsaturated aromatic ring. Both cyclohexane and benzene consist of six carbon atoms in a ring.
polar surface area
The "polar surface area" checkbox shows the polar surface area of the ligand. Polar surface area is also known as TPSA, or "topological polar surface area". The polar surface area is the area over the charged parts of the ligand. The value shown is in square Angstroms.
The idea "surface" is similar to what's seen in the isosurface view of a protein. (Foldit doesn't have an isosurface view that covers only a ligand.) The "polar" part presumably means the surface includes only the more charged portions of the surface, that would be shown in red or blue. The more neutral gray areas of the isosurface would not be included.
Polar surface area is considered a key indication of how likely a drug molecule is to permeate a cell membrane. The higher the polar surface area, the less likely a molecule is to make it into a cell. Puzzles objectives may deduct points if the polar surface area, or "Ligand TPSA" is too high.
See the wikipedia article polar surface area for more.