Maestro User Manual

Chapter 5: Building and Adjusting Structures

Maestro 10.2 User Manual

83

These libraries are described briefly below. 

• Organic—This library contains the common organic functional groups, a selection of

simple ring structures, some common ions such as hydroxide, sulfate, nitrate, ammonium,

and a hydrogen molecule. 

• Rings—This library contains some more complex ring structures than those in the

organic fragments library, including some fused ring structures, a basic steroid structure,

porphyrin and phthalocyanine, buckminsterfullerene, and dodecaborane.

• Heterocycles—The four heterocycle fragment libraries provide a range of ring structures

that contain nitrogen, oxygen, and sulfur atoms.

• Furanose and pyranose structures—Sugars can assume cyclized forms that include

either five or six members. The five-membered ring form is called the furanose form, and

the six-membered version is called the pyranose form. The natural state of most sugars is

the pyranose form, but some derivatives assume a furanose form. Maestro provides both

options in both 

D

 and 

L

 forms.

• Metal centers and ligands—These libraries contain common ligands used in inorganic

chemistry and metal centers with various coordination numbers, but with the specific

metal undefined. To change the metal type, retype the center once it is placed in the

Workspace.

• Amino acids—The 

Amino acids

 library contains the 22 naturally-occurring amino acids.

The 

Nonstandard amino acids

 library includes the 

D

 forms of the 22 naturally-occurring

amino acids and various other residues. The 

Modified amino acids

 library includes the five

residues MSE (selenomethionine), ASQ (phosphoaspartate), TPO (phosphothreonine),

PTR (phosphotyrosine), and SEP (phosphoserine).

• Protein capping groups—This library contains some common molecules used to cap

peptides.

• Protein ions & solvents—This library contains common solvents and solvent ions found

in protein structures, and is primarily intended for placement of these species in PrimeX.

These fragments cannot be used for growing because they do not have designated grow

bonds.

• Nucleic acids—The 

Deoxyribonucleic acids

 library contains Adenosine, Cytosine, Gua-

nine, and Thymine, while the 

Ribonucleic acids

 library contains Adenosine, Cytosine,

Guanine, and Uracil. The double-stranded DNA libraries contain deoxyribonucleic and

ribonucleic acid base pairs in the A and B helix formations.

• Double-stranded DNA and RNA—These four libraries provide the fragments for build-

ing DNA and RNA in the A and B helix conformations. 

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Chapter 5: Building and Adjusting Structures

Schrödinger Software Release 2015-2 

84

• Diverse fragments—This is a collection of chemically diverse fragments with chains of

various lengths attached to the main functional group. It is useful for examining structure-

activity relationships. It is intended for use with MCPRO+ for free-energy perturbation

calculations of relative ligand binding energies.

To select a fragment library, choose the library from the 

Fragments

 option menu. The area

below this menu contains a grid of buttons that you use to select fragments. Each button

displays either the name of the fragment, an abbreviation for the fragment name, or the frag-

ment structure. If a structure is displayed, the name of the fragment is given in the Balloon help

for the button.

If the particular fragment you want to use is not in the supplied libraries, you can build it from

other fragments, or select a fragment with a geometry similar to the one you want to use, then

replace atoms with those of different elements from the 

Atom Properties

 tab.

The fragment libraries and grow rules are read and interpreted at run time. If you are interested

in creating your own fragments or fragment libraries, please write to 

[e-mail]

 to

obtain the appropriate instructions.

5.3.1

Building Structures Using Place Mode

You can use Place mode to create multiple molecular structures in the Workspace, to assemble

structures from multiple fragments, and to change a fragment into another fragment within a

structure. Place mode is the mode in force when you use the 

Fragments

 toolbar to build struc-

tures. To enter Place mode when using the 

Build

 panel, select 

Place

 in the 

Fragments

 tab.

To create multiple structures in the Workspace in Place mode, select a fragment from the build

toolbar or choose a library from the 

Fragments

 option menu in the 

Build

 panel and select a

fragment, then click in the Workspace. Repeat this process, clicking in a different place in the

Workspace for each new fragment you want to place. The fragments are placed in a predefined

orientation at the location you select, and are completed with hydrogen atoms to form mole-

cules. If you now want to join these structures to form a single molecule, you can use the tools

in the 

Connect/Fuse

 panel. See 

Section 5.8 on page 97

 for details.

When you build a structure from fragments, a new project entry is automatically created, with

the default title 

Structure

N. You can edit the title of the entry to change it. If the Workspace

contains a single entry when you start building, placing a fragment that is not connected to the

structure in the Workspace, adds the new fragment to the Workspace entry. This means that

placing multiple fragments will put all these fragments into a single project entry. If there are

two or more project entries in the Workspace, you are prompted to choose an entry to add the

fragment to, or to create a new entry. Each new fragment you place in these circumstances will

produce a prompt, so it is best to start placing fragments in an empty Workspace or one with

only one entry.

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