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Related Pages
Related Symbols
MoleculeModify
MoleculeValue
MoleculeProperty
MoleculePlot3D
Related Categories
Chemistry
Find the Lowest-Energy Structure Among Randomly Generated Molecular Conformations
Example Notebook
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Get the molecule for adenosine:
I
n
[
1
]
:
=
m
=
M
o
l
e
c
u
l
e
[
"
a
d
e
n
o
s
i
n
e
"
]
O
u
t
[
1
]
=
M
o
l
e
c
u
l
e
F
o
r
m
u
l
a
:
C
1
0
H
1
3
N
5
O
4
A
t
o
m
s
:
3
2
B
o
n
d
s
:
3
4
Use
M
o
l
e
c
u
l
e
M
o
d
i
f
y
to generate a list of 100 molecules with different randomly generated coordinates:
I
n
[
2
]
:
=
(
c
o
n
f
o
r
m
e
r
s
=
M
o
l
e
c
u
l
e
M
o
d
i
f
y
[
m
,
{
"
G
e
n
e
r
a
t
e
C
o
n
f
o
r
m
e
r
s
"
,
1
0
0
}
]
)
/
/
S
h
o
r
t
[
#
,
.
5
]
&
O
u
t
[
2
]
/
/
S
h
o
r
t
=
M
o
l
e
c
u
l
e
F
o
r
m
u
l
a
:
C
1
0
H
1
3
N
5
O
4
A
t
o
m
s
:
3
2
B
o
n
d
s
:
3
4
,
M
o
l
e
c
u
l
e
F
o
r
m
u
l
a
:
C
1
0
H
1
3
N
5
O
4
A
t
o
m
s
:
3
2
B
o
n
d
s
:
3
4
,
9
7
,
M
o
l
e
c
u
l
e
F
o
r
m
u
l
a
:
C
1
0
H
1
3
N
5
O
4
A
t
o
m
s
:
3
2
B
o
n
d
s
:
3
4
Visualize the molecules as closely packed together as possible:
I
n
[
3
]
:
=
S
h
o
w
[
M
a
p
[
M
o
l
e
c
u
l
e
P
l
o
t
3
D
,
c
o
n
f
o
r
m
e
r
s
]
]
O
u
t
[
3
]
=
Use
M
o
l
e
c
u
l
e
V
a
l
u
e
to find and visualize the force-field energy for the different conformations:
I
n
[
4
]
:
=
H
i
s
t
o
g
r
a
m
M
o
l
e
c
u
l
e
V
a
l
u
e
[
c
o
n
f
o
r
m
e
r
s
,
"
M
M
F
F
E
n
e
r
g
y
"
]
,
.
.
.
O
u
t
[
4
]
=
Now optimize the energy conformations using the MMFF force field:
I
n
[
5
]
:
=
o
p
t
i
m
i
z
e
d
=
M
a
p
[
M
o
l
e
c
u
l
e
M
o
d
i
f
y
[
"
E
n
e
r
g
y
M
i
n
i
m
i
z
e
A
t
o
m
C
o
o
r
d
i
n
a
t
e
s
"
]
,
c
o
n
f
o
r
m
e
r
s
]
;
Visualize the result. Note that the energy spread is smaller and the overall energies have decreased:
O
u
t
[
5
]
=
Use
T
a
k
e
S
m
a
l
l
e
s
t
B
y
to find the molecule with the lowest-energy conformation:
I
n
[
6
]
:
=
M
o
l
e
c
u
l
e
P
l
o
t
3
D
[
F
i
r
s
t
[
T
a
k
e
S
m
a
l
l
e
s
t
B
y
[
o
p
t
i
m
i
z
e
d
,
M
o
l
e
c
u
l
e
P
r
o
p
e
r
t
y
[
"
M
M
F
F
E
n
e
r
g
y
"
]
,
1
]
]
]
O
u
t
[
6
]
=
See Also
Torsional Potential Energy Surface of Butane
RotateBonds3D
Related Symbols
MoleculeModify
MoleculeValue
MoleculeProperty
MoleculePlot3D
Publisher Information
Contributed by:
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