MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro2.6 Adjusting Bond Orders, Atom Types, and FormalChargesMost PDB structures derived from X-ray crystallography data do not have hydrogen atoms,formal charges, or bond orders. When the structure is imported into Maestro, the conversionutility uses templates for assigning multiple bonds in standard residues, but cannot do so forligands. Thus you need to explicitly add multiple bonds and formal charges to the ligands ifnecessary. In this exercise you will learn how to perform these structural corrections manually,however the Protein Preparation Wizard (see the Protein Preparation Guide) is designed toautomate many of these routine tasks. The tools for these tasks are found in the Build panel oron the Build toolbar. The 1err ligand Raloxifene needs multiple bonds assigned, and the piperidinenitrogen adjusted to be a four-coordinate, positively charged ammonium group. In thisexercise you will convert single bonds to double bonds and adjust the formal charges. In thenext exercise, the hydrogen atoms will be added.1. Choose Molecules from the Display only selected atoms button menu and select an atomin the ligand.You can choose Molecule Number from the Color all atoms by scheme button menu, tohelp distinguish the ligand.2. If the molecule is not displayed in wire representation, choose Molecule from the Drawbonds in wire button menu and pick an atom in the ligand.3. Choose Element from the Color all atoms by scheme button menu.4. Click Show/Hide the build toolbar toolbar button.5. Click the Increment bond order button on the Build toolbar.MacroModel 9.7 Quick Start Guide 13