If you did multiple Partition calculations in Lesson 1, there are probably several molecule objects currently defined and displayed by SYBYL. This lesson is specific to the COCAINE molecule which is probably displayed in M1, but any of the molecules suggested in Lesson 1 are applicable. To delete a molecule, pulldown Build/Edit to the Zap (Delete) Molecule command; select the Molecular area associated with for each molecule that you wish to Zap.
From the eslc pulldown on the SYBYL menubar, select MolconnZ followed by EState Map and Molecule.... This command sets up and executes calculation of a molecular electrotopological state density map with the aid of the Map Molecule dialog box. First choose the Atoms..., for one of the displayed molecule (select All in the Atoms Selection Dialog).
Next, define the three dimensional extents of the map region by pressing the Region Definition... button to call the Region Definition dialog box. For this type of calculation, pick the Molecule Extents radio button from the Region menu. Choose Molecule... to be M1 (COCAINE). Margin represents a border space to be placed around the region box defined by the molecule to allow adequate field decay. A value of 5.00 is normally used. Grid Resolution is the spacing between grid points in Angstroms; use a value of 1.00. Press OK to initiate the Region Definition calculation.
From Grid Types select EState to request a map where the electrotopological state for the heavy (non-hydrogen) atoms will be mapped. The other options in Grid Types, HEState (Heavy) and HEState (Protons), requesting maps where the Hydrogen EState is either centered on the heavy atoms, or on the attached hydrogens, respectively.
Next, set the Molconn-Z Distance Function.... The EState Distance Function dialog box allows the selection of the Functional Form of the distance response for EState density. For this exercise use 1/r**n as the Functional Form and n = 2; i.e., an inverse r-squared function.
The Cut Off Radius serves to reduce calculation time by not considering atoms farther away than this value from the grid points during the map construction. Enter a value of 6.0 for this parameter. Volume Averaging produces a smoother map by calculating eight density values for each grid point, and then averaging them. The main disadvantage is loss of calculation speed. Set this parameter to off. The Inside Mol Cut Off allows you to set a constant value for any grid point that is within the molecular van der Waals surface. Set this parameter to off. Lastly, choose the Map File name for the SYBYL contour file to contain the map field values. Use cocaine.cnt. Now that everything is set for this map calculation, press OK to initiate it. (This calculation is quite fast; there is no advantage to running it in batch.)
The last step is to contour the EState Maps for display. The Map Contour dialog box is automatically called at the completion of a EState Map calculation that is run interactively. This dialog box allows you to select the desired contour levels, their colors, and styles. The Contour File text field should be filled with cocaine.cnt, the Map File name chosen in the Map Molecule dialog box. First choose the Display Area as D1 and Style as Transparent.
The EState map typically has only positive map values. Enter a value of 10 for the Contour Value. From the Contour Color option menu pick Blue. Now press the Accept button to define the contour set. The Number of Defined Levels should be 1. Select the Done button to contour the EState Map. The contouring calculation should take only a few seconds; a blue contour surrounding the portion of the cocaine molecule with highest electron accessibility should appear.
Repeat the above procedure (steps 2 and 3) and calculate a Hydrogen EState map by selecting HEState (Protons) as the Grid Type and H_cocaine.cnt as the Map File name. Contour this as follows: +3 green-blue; -3 orange.
Electrotopological State map of cocaine
The contour levels suggested are only guidelines for representation of the Electrotopological State Maps. Choosing a different Distance Function or a different Grid Spacing would have profound influence on the map display. The EState is a unique, non-empirical vehicle for atom electronegativity, electronic structure and topology information. The 3D maps constructed by Molconn-Z allow the spatial component of the EState paradigm to be easily visualized. In general more electronegative and labile atoms will have larger positive EState values and field density.