From the menubar go to the File pulldown and select the Read... command. Select the file "DHFR_MTX.mol2", which is an adaptation of "1rg7.pdb" where the enzyme and inhibitor have been separated into two molecular areas. Press the OK button. DHFR should be displayed in the SYBYL M1 molecular display area and MTX should be displayed in M2.

The charges attached to these molecules were calculated with the Sybyl Gasteiger-Hückel algorithm. The atomic potential calculated by Zap uses atomic charge as input, so the charge model used may make a difference.

Now, pulldown eslc to Zap; select Molecular Energies & Properties, and Electrostatic Binding Energy.... This invokes the Zap Electrostatic Binding Energy dialog box. First we must select the Target Atoms.... In the Atom Expression dialog box verify that M1 is the chosen molecular area and press the All push button to select all atoms of dihydrofolate reductase. (Press OK.) Next we must select the Ligand Atoms... (Choose All atoms in M2 and press OK. We will use Calc. Resolution of Medium. Use the suggested Dielectric Constants of 2.00 for Inside and 80.00 for Outside. Press the More Zap Details... button to active the Zap Details dialog and select kcal/mol for the display Units. Dielectric Model should be Gaussian. The default Convergence parameters are fine. Likewise leave for now the default Zap VDW radius for H and Zap Salt Concentration; we will explore one of these options in a moment. Press OK in the Details dialog and OK in the Electrostatic Binding Energy dialog. The calculation will take a minute or so to complete. When it is done, an information dialog reporting that the Electrostatic Binding Energy is -0.751598 kcal/mol will be presented.

Now repeat the calculation under a high salt condition, i.e., where Zap Salt Concentration is set to User Defined and Ionic Strength is 1.00 M. Under this condition the Electrostatic Binding Energy is kcal/mol.

The Zap Electrostatic Structure Report is a collection of two and three dimensional descriptors representing electrostatic and structural aspects of a molecule. Similar results can be obtained in a QSAR-like setting with the "ZAPDESCRIPTORS" column type as used with the Sybyl Molecular SpreadSheet.

We will use the DHFR molecule in Molecular Area M1 for this example. Pulldown eslc to Zap; select Molecular Energies & Properties, and Electrostatic Structure Report.... The Zap Electrostatic Structure Report dialog is presented. This has familiar options as well as some specific to this function.

Choose All of the Atoms... of M1. Then, the Surface Basis describes whether the analysis is to proceed based on the Molcular (Van der Waals) or (Solvent) Accessible surface of the molecule. Choose Accessible. The thresholds are ranges of potential on the surface that the structure will be parsed into. Choose the No. of Surface Thresholds (5), Minimum (-0.500) and Maximum (0.500) Thresholds. The actual thresholds will be chosen by evenly dividing the number of threholds between the minimum and maximum. Also, the number and size of charged surface "patches" will be reported. Here we select the Min and Max Patch Thresholds (-0.500 and 0.500).

Choose Calc. Resolution = Fine and select a name for the Report File such as DHFRZapStructure.rpt. This is a fairly rapid calculation so there normally is little need for Batch.

Zap Structure Report for Dihydrofolate Reductase

The Zap Structure Report is an ascii text file. In a different unix shell than the one in which Sybyl is running, cd to the zap1.0S_demo subdirectory.

The report first lists the molecule name, number of atoms, Solvation Energy, Sum of Absolute Value of Charges, Sum of Charges and Total Surface Area. Of particular note in the DHFR case is that the Sum of charges, -9, is fairly negative -- this will influence other structural parameters. The next block of data lists the threshold ranges and the percentage of surface area within those ranges. For the DHFR case, the largest fraction of the area has potential less than -0.500 (which is consistent with the very negative total charge). Smaller fractions of area are within the succeeding bands (-0.500 to -0.250, etc.) and with potential greater than 0.500. The third block of data is a report of patch counts and sizes. Basically, this descriptor represents the number and areas of charged (positive and negative) surface area regions. The fourth block of data is a collection of steric (shape) multipoles for the molecules 3D structure. Lastly, a list of input parameters is provided in the report.