Chapter 5: Building and Adjusting Structures
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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.
Chapter 5: Building and Adjusting Structures
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• 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
help@schrodinger.com
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.