Setup of the starting 3D structure

Structure creation

Case 1. The structure is downloaded by a X-Ray database (CSD or PDB)

Run Maestro

Select  a convenient working directory: File - Change Working Directory and select the directory

Import starting structures: File - Import Structures

Carefully check if the structure is correct and eventually use edit tools to correct the structure and delete not useful atoms (e.g. solvent)

Case 2. The structure is build through the SMILES code

The SMILES can be obtained in two ways:

• it can be downloaded from various sources, e.g. ChemSpider
• the molecule is drawn in MarvinSketch and then is copied as SMILES using the option Edit - Copy as SMILES.

Conversion of SMILES in a 3D structure

The SMILES conversion depends on the project and it very IMPORTANT to establish is the project is under a disclosure agreement with a company or not.

Before starting with the following steps, ask to your director.

The molecule is not involved in a disclosure agreement

The code is converted in a 3D structure using CORINA (https://www.mn-am.com/online_demos/corina_demo)

• So far, CORINA represents the most robust SMILES converter
• In particular, it is able to efficiently handle chiral symbols

In Corina, save the structure as mol file to maintain information about bond order.

The molecule is involved in a disclosure agreement

The molecule cannot be prepared using online tools because they do not guarantee disclosure agreement conditions.

• Open the drawn molecule in MarvinSketch
• Click on Structure - Clean in 3D
• File - Save As - select mol2 option
• Use the same name of Marvin file
• Check the structure (see below)

Check of the structure

The check of the structure is mandatory and fundamental before submitting the structure to the next steps.

Use Maestro (educational or registered version) to load, edit and check the structure.

In particular, these properties must be checked:

• Bond order
• Atoms valency
• Formal atom charge (and molecule charge)
• Ionization

Furthermore, it is better to check the name of the molecule and the name of the residue loading the structure in an editing software

Two fields should be carefully checked and modified if it is required:

• @<TRIPOS>MOLECULE: the name should be checked and modified deleting extensions, directory tree and other not useful names. In principle, the name of the molecule should be identical to the name of the file.
• @<TRIPOS>ATOM: after the the subs_id, the ID number of the substructure containing the atom, the subs_name should be chosen accordingly to the file name and preferably with three letters. The name should be changed using the "replace" tool in every editor software (e.g. Notepad+). Pay attention to the last field in the file (@<TRIPOS>SUBSTRUCTURE) where the name should be defined and thus it also has to be replaced.
• atom_id atom_name x y z atom_type [subst_id [subst_name [charge [status_bit]]]

Instructions:

• File - Change Working Directory
• Select the directory where there is the structure of interest
• File - Import Structures
• Select the file with the 3D structure (e.g. the mol2 file prepared with MarvinSketch)
• Generally, click to import with default options
• If the file contains unnecessary atoms (e.g. solvent molecules in files retrieved from CSD or PDB)
• Use the Workspace Navigator to select the parts of molecule that you wants to delete or select the molecule and then invert selection to delete all it is not necessary
• Select - All

• Edit - Assign - Bond orders
• Bond orders are automatically assigned
• Check that the assignment is correct

• Then, use Build - Draw tool to eventually correct the molecule using the 2D representation as reference

• Finally, Select - All and Add Hydrogens
• Any missing hydrogen atoms are added

• When the structure is edited, export the file as mol2 format: File - Export Structures
• If the name of input and output files are the same you can overwrite the input file that is not useful
• Exit from Maestro
• Generally, it is not necessary to save the project

• Finally, the checked structure is saved in a file mol.mol2, where mol is the name of the molecule.
• The name mol will be kept for all steps thus a short name should be chosen.

To be edit. Furthermore, the mol name should be also abbreviated with a 3 letters short name that will be saved in the Tripos MOLECULE field and will be used in the subs_name field in the ATOM lines (the field where the name of the amino acids are reported) into the mol2 file.