Appendix B: Atom Types
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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
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)