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107

P5

Phosphorus, pentavalent tetra-

hedral (e.g. PO

4

3–

)

108

P0

Any phosphorus

109

S4

Sulfur, tetravalent

110

S6

Sulfur, hexavalent octahedral 

(e.g. SF

6

)

111

P4

P

+

, tetravalent

112

Se

Selenium

113

ST

Sulfur, hexavalent tetrahedral 

(e.g. SO

4

2–

)

114

Sm

Sulfide anion, S

2–

115

Om

Oxide anion, O

2–

...

150

PI

Ligand dummy atom

Table B.1. Atom types and equivalents.  (Continued)

No.

Symbol

Description

Equivalencies

MM2/

MM3

Charmm

Amber

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Table B.2. Generalized atom types.

No.

Symbol

Description

151

GA

Isolated atom

152

GB

Linear-single coordinate

153

GC

Linear-two coordinate

154

GD

Trigonal-two coordinate

155

GE

Trigonal-three coordinate

156

GF

Tetrahedral-three coordinate

157

GG

Tetrahedral-four coordinate

158

GH

Trigonal bipyramid-three coordinate

159

GI

Trigonal bipyramid-four coordinate

160

GJ

Trigonal bipyramid-five coordinate

161

GK

Octahedral-four coordinate

162

GL

Octahedral-five coordinate

163

GM

Octahedral-six coordinate

164

GN

Pentagonal bipyramid-seven coordinate

165

GO

Twisted cube-eight coordinate

166

GP

Nine coordinate

167

GQ

Ten coordinate

168

GR

Eleven coordinate

169

GS

Icosahedron-twelve coordinate

170

GT

Thirteen coordinate

171

GU

Fourteen coordinate

172

GV

Fifteen coordinate

173

GW

Sixteen coordinate

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Appendix C

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Maestro User Manual

Appendix C:

Substructure Notation

This appendix describes a linear substructure notation proprietary to Schrödinger, referred to

as mmsubs. The mmsubs notation is based on the linear substructure notation used in Macro-

Model. The implementation is independent of the MacroModel implementation, and has some

extensions over the MacroModel notation, along with a few differences. 

Both mmsubs and MacroModel notations resemble the better-known SMILES and SMARTS

notations. They all involve atom type symbols, bond symbols, and other connectivity indica-

tions, such that an arbitrary topology (including branches and rings) can always be expressed

in a linear pattern string.

An mmsubs pattern expresses a molecular substructure as a list of atoms connected by bonds.

An atom can be specified either exactly, using a symbol for a specific atom type, or loosely,

using a symbol encompassing multiple atom types. Similarly, a bond can be specified either

exactly, using a symbol for a specific bond order, or loosely, using the wildcard bond order

symbol (which covers all bond orders).

Patterns can be limited to the required atoms and bonds. In mmsubs pattern matching, only the

atoms and bonds explicitly specified are searched for. No assumption is made about anything

else that may be attached: unspecified attachments cannot disqualify a match on the explicit

pattern. Pattern matching does not include checking of valency against the specified bond

orders. This is not usually a problem, because illegal valencies will generally not be matched.

The syntax to represent connectivity differs somewhat from that used in SMILES and

SMARTS. The support for expressing structural alternatives is also different between nota-

tions. The mmsubs notation is somewhat less flexible than SMILES and SMARTS, but the

reduced flexibility rarely presents a serious problem.

C.1

Atom and Bond Types

Structures expressed in mmsubs (or MacroModel) notation use MacroModel atom type

symbols. The MacroModel atom types are listed in 

Appendix B

. 

Every MacroModel atom type symbol is two characters long, and is case-sensitive. It can

consist of letters and numbers, so you must be careful to distinguish between O and 0 (upper-

case letter O and zero), and between l and 1 (lower-case letter L and one).

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If there are multiple atom types for an element, a wildcard symbol encompassing all of the

element’s atom types is provided. Our convention is to spell it with the usual first letter

followed by 0 (zero). For example, the wildcards to specify any carbon and any oxygen are C0

and O0, respectively. The atom type symbol 00 (two zeroes), which matches any atom type of

any element. You can use 00 in mmsubs patterns where an atom specification is needed to

define connectivity, but the specific type or element is irrelevant. 

The bond order symbols recognized in mmsubs patterns are given in 

Table C.1

.

Zero-order bonds are used in patterns when a bond needs to be expressed, but it is not possible

to define its precise nature. Some uses of zero-order bonds are:

• When the bond is in the process of being formed or broken. One example would be in the

(physically non-realistic) situation of a FEP simulation. Another, more physically realis-

tic, example is a transition state, where the bond is actually forming or breaking.

• Representation of certain metal-ligand interactions. Bonds that are significantly ionic in

nature can’t really be considered to have a bond order in the conventional sense.

As an example, the following mmsubs pattern specifies the essential atoms of ethyl vinyl ether:

C2=C2-O3-C3-C3

C2, O3, and C3 are the MacroModel atom type symbols for sp

2

 carbon, non-carbonyl oxygen,

and sp

3

 carbon, respectively. 

Observe the use of the bond symbol = to represent a double bond, and - for single bonds. 

Thus, ethyl vinyl ether can also be specified using wildcard atom types, like this:

C0=C0-O0-C0-C0

Table C.1. Bond order symbols in mmsubs notation

Symbol

Description

.

   

Zero-order bond (see Comment below)

-

   

Single bond

=

   

Double bond

%

   

Triple bond

*

   

Any bond order (wildcard)

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