Appendix B: Atom Types
Schrödinger Software Release 2015-2
426
51
SM
S
–
(thiolate anion)
52
S0
Any Sulfur
S
53
P3
Phosphorus,
trivalent
25
P
54
B2
Boron - sp
2
26
55
B3
Boron - sp
3
27
56
F0
Fluorine
11
57
Cl
Chlorine
12
58
Br
Bromine
13
59
I0
Iodine
14
60
Si
Silicon
19
61
Du
Dummy atom for FEP
62
Z0
Special
atom to be defined
63
Lp
Lone electron pair
LP
64
00
Any atom
0
*
65
Li
Li
+
Li
66
Na
Na
+
SOD
Na
67
K0
K
+
POT
K0
68
Rb
Rb
+
Rb
69
Cs
Cs
+
CES
70
Ca
Ca
+2
CAL
71
Ba
Ba
+2
72
Mg
Mg
+2
MG
73
M2
Mn
+2
74
M3
Mn
+3
75
M4
Mn
+4
76
M5
Mn
+5
77
M6
Mn
+6
Table B.1. Atom types and equivalents. (Continued)
No.
Symbol
Description
Equivalencies
MM2/
MM3
Charmm
Amber
Appendix B: Atom Types
Maestro 10.2 User Manual
427
78
M7
Mn
+7
79
f2
Fe
+2
80
f3
Fe
+3
81
o2
Co
+2
82
o3
Co
+3
83
n2
Ni
+2
84
n3
Ni
+3
85
c1
Cu
+
86
c2
Cu
+2
87
Zn
Zn
+2
88
m3
Mo
+3
89
m4
Mo
+4
90
m5
Mo
+5
91
m6
Mo
+6
92
Sr
Sr
+2
93
L0
Lithium
neutral
94
M0
Magnesium neutral
95
As
Arsenic, pentavalent tetrahedral
(e.g. AsO
4
3–
)
...
100
SP
S
+
101
S2
Sulfur - sp
2
102
Cm
Cl
–
CLA
103
B0
Any boron
104
Fm
F
–
105
Bm
Br
–
106
Im
I
–
Table B.1. Atom types and equivalents. (Continued)
No.
Symbol
Description
Equivalencies
MM2/
MM3
Charmm
Amber