Directory UMM :wiley:Public:journals:jcc:suppmat:21:
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CHARMM27 All-Hydrogen Nucleic Acid Topology File
Foloppe, N. and MacKerell, A.D., Jr.
All-atom emiprical force field for nucleic acids:
1) Parameter optimization based on small molecule and
condensed phase macromolecular target data.
J. Computational Chemistry, Submitted
and
MacKerell, A.D., Jr. and Banavali, N.
All-atom emiprical force field for nucleic acids:
2) Application to molecular dynamics simulations of DNA
and RNA in solution
J. Computational Chemistry, Submitted
MASS 1
MASS 2
MASS 3
MASS 4
MASS 5
MASS 6
MASS 7
MASS 8
MASS 9
MASS 10
MASS 11
MASS 12
MASS 13
MASS 20
MASS 21
MASS 22
MASS 23
MASS 24
MASS 25
MASS 26
MASS 27
MASS 28
MASS 29
MASS 30
MASS 31
MASS 32
MASS 33
MASS 34
MASS 35
MASS 36
MASS 37
MASS 38
MASS 39
MASS 50
MASS 51
MASS 52
MASS 53
MASS 54
Sasha)
MASS 55
MASS 56
MASS 57
HT
HN1
HN2
HN3
HN3B
HN3C
HNP
HN4
HN5
HN6
HN7
HN8
HN9
CN1
CN1A
CN1T
CN2
CN3
CN3A
CN3B
CN3C
CN3D
CN3T
CN4
CN5
CN5G
CN7
CN7B
CN7C
CN7D
CN8
CN8B
CN9
NN1
NN1C
NN2
NN2B
NN2C
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
14.007000
14.007000
14.007000
14.007000
14.007000
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
N
N
N
N
N
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
TIPS3P WATER HYDROGEN
Nucleic acid amine proton
Nucleic acid ring nitrogen proton
Nucleic acid aromatic carbon proton
NAD+ aromatic hydrogen
Standard aromatic hydrogen (as in benzene)
pure aromatic H
Nucleic acid phosphate hydroxyl proton
Nucleic acid ribose hydroxyl proton
Nucleic acid ribose aliphatic proton
Nucleic acid proton (equivalent to protein HA)
Bound to CN8 in nucleic acids/model compounds
Bound to CN9 in nucleic acids/model compounds
Nucleic acid carbonyl carbon
NAD+/NADH amide carbonyl carbon
Nucleic acid carbonyl carbon (T/U C2)
Nucleic acid aromatic carbon to amide
Nucleic acid aromatic carbon
NAD+ aromatic carbon
NAD+ aromatic carbon
NADH aromatic carbon
Nucleic acid aromatic carbon for 5MC
Nucleic acid aromatic carbon, Thy C5
Nucleic acid purine C8 and ADE C2
Nucleic acid purine C4 and C5
Nucleic acid guanine C5
Nucleic acid carbon (equivalent to protein CT1)
Nucleic acid aliphatic carbon for C1'
C2' in arabinose
C2' in nucleic acids fluorine derivatives
Nucleic acid carbon (equivalent to protein CT2)
Nucleic acid carbon (equivalent to protein CT2)
Nucleic acid carbon (equivalent to protein CT3)
Nucleic acid amide nitrogen
Nucleic acid imino nitrogen (cyt taut Sasha)
Nucleic acid protonated ring nitrogen
From NN2, for N9 in GUA different from ADE
Nucleic acid protonated ring nitrogen (cyt taut
NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen
MASS
N3
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
58
NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and
59
60
61
62
70
71
72
73
74
75
76
77
78
82
83
90
102
103
104
105
106
107
NN3I
NN3G
NN4
NN5
OT
ON1
ON1C
ON2
ON3
ON4
ON5
ON6
ON6B
P
P2
SOD
CPH1
CPH2
HR3
HR1
NR1
NR2
14.007000
14.007000
14.007000
14.007000
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
30.974000
30.974000
22.989770
12.011000
12.011000
1.008000
1.008000
14.007000
14.007000
N ! Nucleic acid unprotonated ring nitrogen, inosine N3
N ! Nucleic acid unprotonated ring nitrogen, gua N3
N ! Nucleic acid purine N7
N ! Nucleic acid sp2 amine nitrogen
O ! TIPS3P WATER OXYGEN
O ! Nucleic acid carbonyl oxygen
O ! Nucleic acid carbonyl oxygen, cyt O2
O ! Nucleic acid phosphate ester oxygen
O ! Nucleic acid =O in phosphate
O ! Nucleic acid phosphate hydroxyl oxygen
O ! Nucleic acid ribose hydroxyl oxygen
O ! Nucleic acid deoxyribose ring oxygen
O ! Nucleic acid ribose ring oxygen
P ! phosphorus
P ! pyrophosphate phosphorus
NA ! Sodium Ion
C ! For imidazole model compound (NF)
C ! For imidazole model compound (NF)
H ! For imidazole model compound (NF)
H ! For imidazole model compound (NF)
H ! For nitrogen in imidazol (NF)
H ! For nitrogen in imidazol (NF)
! oligonucleotide connectivity information
DECL +P
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFA FIRS none LAST none
AUTOGENERATE ANGLES DIHEDRALS
!Note that the default nucleotides are RNA. The
!patches DEO1 and DEO2 must be applied to create
!the corresponding DNA nucleotides.
RESI GUA
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N9
ATOM C4
ATOM N3
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2B
CN5
NN3G
-0.02
0.26
-0.74
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
O6
||
C6
/ \
H1-N1
C5--N7\\
|
||
C8-H8
C2
C4--N9/
/ \\ /
\
H21-N2
N3
\
|
\
H22
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
ATOM C2
CN2
0.75 !
ATOM N1
NN2G
-0.34 !
ATOM H1
HN2
0.26 !
ATOM N2
NN1
-0.68 !
ATOM H21 HN1
0.32
ATOM H22 HN1
0.35
ATOM C6
CN1
0.54
ATOM O6
ON1
-0.51
ATOM C5
CN5G
0.00
ATOM N7
NN4
-0.60
ATOM C8
CN4
0.25
ATOM H8
HN3
0.16
GROUP
ATOM C2' CN7B
0.14
ATOM H2'' HN7
0.09
ATOM O2' ON5
-0.66
ATOM H2' HN5
0.43
GROUP
ATOM C3' CN7
0.01
ATOM H3' HN7
0.09
ATOM O3' ON2
-0.57
BOND P
O1P
P
O2P
BOND O5' C5'
C5' C4'
BOND C1' N9
C1' C2'
BOND C2
N2
C2
N1
BOND N2
H22
N1
H1
BOND C5
N7
C2' C3'
BOND C2' O2'
O2' H2'
BOND C1' H1'
C2' H2''
BOND C5' H5''
C8
H8
BOND C2 N3
C4
C5
IMPH N2
N3
N1
C2
O6
DONO H21 N2
DONO H22 N2
DONO H1
N1
DONO H2' O2'
ACCE O6
C6
ACCE N3
ACCE N7
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! Chi and sugar-phosphate backbone
BILD -O3' P
O5' C5'
1.6001
BILD -O3' O5' *P
O1P
1.6001
BILD -O3' O5' *P
O2P
1.6001
BILD P
O5' C5' C4'
1.5996
BILD O5' C5' C4' C3'
1.4401
BILD C5' C4' C3' O3'
1.5160
BILD C4' C3' O3' +P
1.5284
BILD C3' O3' +P
+O5'
1.4212
BILD O4' C3' *C4' C5'
1.4572
BILD C2' C4' *C3' O3'
1.5284
BILD C4' C3' C2' C1'
1.5284
O3' H3' O2' H2''
|
|
H2'
P
C4'
N9
N2
N1
C3'
O5'
O4'
C4
H21
C6
O3'
C3'
H3'
N7
N1
C8
C5
C6
C4'
N9
C3'
C8
C6
O3'
C5
+P
C4'
H4'
C6
O6
H22
H21
O4'
C4
C1'
N3
C5'
H5'
C2
N2
in B-DNA like conformation
101.45 -46.90 119.00
1.4401
101.45 -115.82 109.74
1.4802
101.45 115.90 109.80
1.4801
119.00 -146.00 110.04
1.5160
108.83
60.00 116.10
1.5284
116.10 140.00 115.12
1.4212
111.92 155.00 119.05
1.6001
119.05 -95.20 101.45
1.5996
104.06 -120.04 116.10
1.5160
100.16 -124.08 115.12
1.4212
100.16 -30.00 102.04
1.5251
!alpha
!beta
!gamma
!delta
!epsilon
!zeta
!puck
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
C3'
O4'
C1'
C4
C8
N9
C5
C4
N1
N3
H21
N3
C6
C5
N9
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
RESI ADE
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM C6
ATOM N6
ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
C2'
C1'
C4
N9
N9
C5
C4
N3
N3
C2
C2
C2
C2
N1
N7
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
C1'
N9
*N9
C8
C4
*C4
N3
C2
*C2
N2
*N2
N1
*N1
*C6
*C8
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
N9
C4
C8
N7
C5
N3
C2
N1
N2
H21
H22
C6
H1
O6
H8
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
CN5
NN4
CN4
HN3
NN2
NN3A
CN4
HN3
NN3A
CN5
CN2
NN1
HN1
HN1
0.28
-0.71
0.34
0.12
-0.05
-0.74
0.50
0.13
-0.75
0.43
0.46
-0.77
0.38
0.38
CN7B
HN7
ON5
0.14
0.09
-0.66
1.5284
1.5251
1.4896
1.377
1.374
1.377
1.377
1.355
1.375
1.327
1.01
1.327
1.393
1.415
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
101.97
113.71
125.59
106.0
106.0
105.6
128.4
111.8
124.0
119.7
127.0
124.0
124.9
111.7
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0
147.80
-97.2
-179.99
0.0
0.0
180.0
0.0
0.0
180.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
H61
\
113.71
125.59
106.0
113.5
105.6
128.4
111.8
124.0
119.7
127.0
116.5
124.9
117.4
120.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
H62!
/
N6
|
C6
// \
N1
C5--N7\\
|
||
C8-H8
C2
C4--N9/
/ \\ /
\
H2
N3
\
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
1.4896
1.3783 !chi
1.374
1.304
1.377
1.355
1.327
1.375
1.341
1.01
1.01
1.393
1.03
1.239
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
BOND C2
BOND N6
BOND C2'
BOND C1'
BOND C5'
BOND N1
IMPH H62
DONO H61
DONO H62
DONO H2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1P
ACCE O2P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3'
BILD -O3'
BILD -O3'
BILD P
BILD O5'
BILD C5'
BILD C4'
BILD C3'
BILD O4'
BILD C2'
BILD C4'
BILD C3'
BILD O4'
BILD C1'
BILD C4
BILD C8
BILD C8
BILD N7
BILD C5
BILD N9
BILD C5
BILD N1
BILD H61
BILD C5
BILD N1
BILD H61
BILD N9
BILD N1
BILD C1'
BILD H2'
HN5
0.43
CN7
0.01
HN7
0.09
ON2
-0.57
O1P
P
C5'
C5'
N9
C1'
N1
C6
H61
N6
C3'
C2'
H1'
C2'
H5''
C8
C6
C2
C6
H61 N6
N6
N6
O2'
O2P
C4'
C2'
N6
H62
O2'
H2''
H8
N3
N6
P
C4'
N9
O5'
O4'
C4
C6
O2'
C3'
C2
C4
N1
C5
H2'
H3'
H2
C5
C5
C4'
N9
C3'
C8
O4'
C4
C1'
N3
C5
C3'
C4'
N7
O3'
H4'
O3'
C5'
+P
H5'
N7
C8
C6
P
P
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C4
N9
N9
N7
C5
C6
C5
N1
C6
C6
N1
C6
C6
N7
N3
C3'
O2'
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N9
*N9
C8
C4
C5
C6
N1
*C4
*C6
N6
*N6
*C6
N6
*N6
*C8
*C2
*C2'
C2'
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N9
C4
C8
N7
C5
C6
N1
C2
N3
N6
H61
H62
N6
H61
H62
H8
H2
O2'
C3'
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.376
1.367
0.0
0.0
0.0
1.376
1.409
1.337
1.01
1.409
1.337
1.01
0.0
0.0
1.5284
0.9600
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0
0.0
0.0
102.04
114.97
-46.90
-115.82
115.90
-146.00
60.00
140.00
155.00
-95.20
-120.04
-124.08
-30.00
147.80
-97.2
-179.94
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
125.59
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00
0.0
0.0
110.81
111.92
1.4401
1.4802
1.4801
1.5160
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3783
1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284
!alpha
!beta
!gamma
!delta
!epsilon
!zeta
!puck
!chi
BILD
BILD
BILD
BILD
BILD
BILD
O4'
C1'
C2'
C3'
C4'
C4'
RESI CYT
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM C4
ATOM N4
ATOM H41
ATOM H42
ATOM C5
ATOM H5
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
BOND C2
BOND C4
BOND C2'
BOND C1'
BOND C5'
BOND C2
IMPH O2
IMPH H42
DONO H42
DONO H2'
DONO H41
C2'
C3'
C4'
O4'
O5'
O5'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2
CN3
HN3
CN1
ON1C
NN3
CN2
NN1
HN1
HN1
CN3
HN3
-0.13
0.05
0.17
0.52
-0.49
-0.66
0.65
-0.75
0.37
0.33
-0.13
0.07
CN7B
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
CN7
0.01
HN7
0.09
ON2
-0.57
O1P
P
C5'
C5'
N1
C1'
N3
C4
C5
C2'
O2'
O2'
H1'
C2'
H5''
C5
O2
C5
N1
N3
C2
C4
H41 N4
N4
O2'
N4
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
-115.0
115.0
115.0
-115.0
-115.0
115.0
0.0
0.0
0.0
0.0
0.0
0.0
H42
\
0.0
0.0
0.0
0.0
0.0
0.0
H41
/
N4
|
C4
/
H5-C5
||
H6-C6
\
\\
N3
|
C2
/ \\
N1
O2
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
O2P
C4'
C2'
N4
C3'
H2'
H2''
H5
C6
N4
P
C4'
N1
N4
C3'
O5'
O4'
C2
H41
O3'
C3'
C6
N3
N3
H3'
H6
C4
C5
C4
C4'
N1
N4
O3'
C3'
C6
H42
+P
O4'
C1'
C4'
H4'
C5'
H5'
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
O2
N3
O1P
O2P
O2'
O3'
O4'
O5'
-O3'
-O3'
-O3'
P
O5'
C5'
C4'
C3'
O4'
C2'
C4'
C3'
O4'
C1'
C2
C6
N1
N1
C5
N3
H41
C6
N1
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
RESI THY
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N1
ATOM C6
C2
P
P
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C2
N1
N1
N3
C2
N3
C4
C4
C4
C5
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N1
*N1
C6
C2
*C2
N3
*C4
N4
*N4
*C5
*C6
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N1
C2
C6
C5
N3
O2
C4
N4
H41
H42
H5
H6
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2B
CN3
-0.34
0.17
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.399
1.364
1.399
1.399
1.426
1.337
1.01
0.0
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
117.79
120.6
120.6
118.9
118.9
121.8
117.9
118.9
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0
-46.90
-115.82
115.90
-146.00
60.00
140.00
155.00
-95.20
-120.04
-124.08
-30.00
147.89
-97.2
-180.00
0.0
0.0
180.0
0.0
180.00
0.00
180.00
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
125.59
120.6
121.0
118.9
121.9
120.0
118.9
118.9
120.7
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
H51
O4
|
||
H52-C5M
C4
H3
| \ / \ /
H53 C5
N3
||
|
H6-C6
C2
\ / \\
N1
O2
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
1.4401
1.4802
1.4801
1.5160
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3783
1.364
1.337
1.356
1.237
1.334
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
!alpha
!beta
!gamma
!delta
!epsilon
!zeta
!chi
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM C5M
ATOM H51
ATOM H52
ATOM H53
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
BOND C2
BOND C5
BOND C2'
BOND C1'
BOND C5'
BOND C2
IMPH O2
DONO H3
DONO H2'
ACCE O2
ACCE O4
ACCE O1P
ACCE O2P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3T
CN9
HN9
HN9
HN9
0.17
0.51
-0.41
-0.46
0.36
0.50
-0.45
-0.15
-0.11
0.07
0.07
0.07
CN7B
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C2
N1
-O3'
-O3'
-O3'
P
O5'
C5'
C4'
C3'
O4'
C2'
C4'
C3'
O4'
C1'
C2
CN7
0.01
HN7
0.09
ON2
-0.57
O1P
P
C5'
C5'
N1
C1'
N3
N3
C5M
C2'
O2'
O2'
H1'
C2'
H5''
C6
O2
C4
N1
N3
C2
N3
O2'
C2
C4
P
P
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N1
*N1
C6
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N1
C2
C6
C5
!
!
!
!
!
!
!
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
O2P
C4'
C2'
H3
C3'
H2'
H2''
H6
O4
O4
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.3746
P
C4'
N1
N3
C3'
O5'
O4'
C2
C4
O3'
C3'
C5M
C5
N3
H3'
H51
C6
C5
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
117.06
122.08
C4' C3'
N1
C6
C4
C5
O3' +P
C4'
C5M
C4
-46.90
-115.82
115.90
-146.00
60.00
140.00
155.00
-95.20
-120.04
-124.08
-30.00
147.89
-97.2
-179.96
-0.02
H4'
H52
C5M
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
125.59
122.08
121.23
C4
O4'
C1'
C5'
C5M
H5'
H53
C6
C5
1.4401 !alpha
1.4802
1.4801
1.5160 !beta
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3783 !chi
1.3704
1.3432
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
C6
N1
N1
C5
C2
C4
N1
C6
C5
H51
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
RESI URA
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM H5
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
N1
N3
C2
N3
C4
C6
C5
C5
H51
H52
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
C2
*C2
N3
*C4
*N3
*C5
*C6
C5M
*C5M
*C5M
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
N3
O2
C4
O4
H3
C5M
H6
H51
H52
H53
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2B
CN3
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3
HN3
-0.34
0.20
0.14
0.55
-0.45
-0.46
0.36
0.53
-0.48
-0.15
0.10
CN7B
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
CN7
HN7
ON2
O1P
C5'
N1
0.01
0.09
-0.57
P
C5'
C1'
1.3704
1.3746
1.3746
1.4439
1.3813
1.4439
0.0
0.0
0.0
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
122.08
115.38
115.38
114.07
126.46
120.78
0.0
0.0
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.
0.06
-179.95
-0.07
179.98
180.00
-179.94
180.0
0.0
115.0
-115.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
115.38
121.70
126.46
120.59
116.77
121.63
0.0
0.0
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
O4
||
C4
/
H5-C5
||
H6-C6
\
1.3813
1.2191
1.3795
1.2327
1.0900
1.5000
0.0
0.0
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
H3
\
/
N3
|
C2
/ \\
N1
O2
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
O2P
C4'
C2'
P
C4'
N1
O5'
O4'
C2
C4'
N1
C3'
C6
O4'
C1'
BOND
BOND
BOND
BOND
BOND
BOND
IMPH
DONO
DONO
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
C2
C2'
C2'
C1'
C5'
C2
O2
H3
H2'
O2
O4
O1P
O2P
O2'
O3'
O4'
O5'
-O3'
-O3'
-O3'
P
O5'
C5'
C4'
C3'
O4'
C2'
C4'
C3'
O4'
C1'
C2
C6
N1
N1
C5
C2
C6
N1
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
N3
C3'
O2'
H1'
H5''
O2
N1
N3
N3
O2'
C2
C4
P
P
N3
C3'
O2'
C2'
C5
C4
C2
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C2
N1
N1
N3
C2
N3
C4
C4
C5
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N1
C2
C6
C5
N3
O2
C4
O4
H3
H5
H6
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N1
*N1
C6
C2
*C2
N3
*C4
*N3
*C5
*C6
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
H3
O3'
H2'
H2''
H5
O4
O4
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.379
1.380
1.379
1.379
1.440
1.373
0.0
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
N3
O3'
C4
+P
C4
C5
C3'
C6
C5
N3
H3'
H6
C6
C5
C4'
H4'
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
117.06
121.3
121.3
114.8
114.8
114.7
127.0
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0
C5'
C4
-39.25
-115.82
115.90
-151.39
-179.85
76.70
159.13
-98.86
-120.04
-124.08
39.58
144.39
-96.0
-180.0
0.0
0.0
-180.0
0.0
180.0
180.0
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
117.06
121.3
122.8
114.8
122.0
127.0
119.8
116.5
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
1.4401
1.4802
1.4801
1.5160
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3746
1.379
1.338
1.373
1.218
1.383
1.227
1.03
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
! Selected patches to create DNA, and individual bases included
! methylated analogs
!
!
!
!
!
!
NOTE the option to regenerate all angles and dihedrals allows
the explicit inclusion of the THET and DIHE terms to be omitted
even if the PRES is used in a PATCH statement. It is important to
inspect the patches prior to use to determine if they should be used
in a GENErate or PATCh statement and/or if the AUTOgeneration of
angles and dihedrals is required.
H5'
! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
! documentation
PRES DEO1
DELETE ATOM O2'
GROUP !
ATOM C4' CN7
ATOM H4' HN7
ATOM O4' ON6
ATOM C1' CN7B
ATOM H1' HN7
GROUP
ATOM C2' CN8
ATOM H2' HN8
ATOM H2'' HN8
BOND
THET
DIHE
DIHE
BILD
C2'
C1'
H2'
H2'
C1'
H2'
C2'
C2'
C2'
C3'
PRES DEO2
DELETE ATOM O2'
GROUP !
ATOM C4' CN7
ATOM H4' HN7
ATOM O4' ON6
ATOM C1' CN7B
ATOM H1' HN7
GROUP
ATOM C2' CN8
ATOM H2' HN8
ATOM H2'' HN8
BOND
THET
DIHE
DIHE
BILD
C2'
C1'
H2'
H2'
C1'
PRES PYRC
H2'
C2'
C2'
C2'
C3'
0.000 ! Patch to make DEOXYribose in PYRIMIDINES
! necessary due to auto-generate dihedrals
0.16
0.09
-0.50
0.16
0.09
!
!
!
!
!
-0.18
0.09
0.09
H2'
C3' C2' H2'
H2' C2' H2''
C1' O4'
H2' C2' C1' N1
H2' C2'
C3' C4'
H2' C2' C3' O3'
H2' C2'
*C2' H2' 0.0 0.0 -115.0 0.0 0.0
C1'
C3'
H1'
H3'
0.000 ! Patch to make DEOXYribose in PURINES
! necessary due to auto-generate dihedrals
0.16
0.09
-0.50
0.16
0.09
!
!
!
!
!
-0.18
0.09
0.09
H2'
C3' C2' H2'
H2' C2' H2''
C1' O4'
H2' C2' C1' N9
H2' C2'
C3' C4'
H2' C2' C3' O3'
H2' C2'
*C2' H2' 0.0 0.0 -115.0 0.0 0.0
0.00 ! Patch to generate CYTOSINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
C1'
C3'
H1'
H3'
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM H1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM C4
ATOM N4
ATOM H41
ATOM H42
ATOM C5
ATOM H5
BOND N1
IMPH H1
BILD C5
H2''
O2'
H2'
C3'
O3'
H3'
NN2
-0.50
HN2
0.37
CN3
0.05
HN3
0.17
CN1
0.52
ON1C
-0.49
NN3
-0.66
CN2
0.65
NN1
-0.75
HN1
0.37
HN1
0.33
CN3
-0.13
HN3
0.07
H1
C6
C2
N1
C6
N1
H1
PRES PYRU
0.00
PRES PYRT
0.00
0.0 0.0 180.0 0.0 0.0
! Patch to generate URACIL base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM N1
NN2B
-0.82 !
ATOM H1
HN2
0.48 !
ATOM C6
CN3
0.20 !
ATOM H6
HN3
0.14 !
BOND N1
H1
BILD C5
C6
N1
H1
0.0 0.0 180.0 0.0 0.0
! Patch to generate THYMINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM H1
ATOM C6
ATOM H6
BOND N1
BILD C5
PRES PURG
P
O1P
O2P
O5'
C5'
H5'
H5''
C4'
H4'
O4'
C1'
H1'
C2'
H2''
O2'
H2'
C3'
O3'
H3'
NN2B
-0.80
HN2
0.46
CN3
0.17
HN3
0.17
H1
C6
N1
H1
!
!
!
!
0.0 0.0 180.0 0.0 0.0
0.00 ! Patch to generate GUANINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM N9
NN2B
-0.38 !
ATOM C4
CN5
0.26 !
ATOM H9
HN2
0.36 !
ATOM N3
NN3G
-0.74 !
ATOM C2
CN2
0.75 !
ATOM N1
NN2G
-0.34 !
ATOM H1
HN2
0.26 !
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
BOND
IMPH
BILD
N2
H21
H22
C6
O6
C5
N7
C8
H8
N9
H9
C5
NN1
-0.68 !
HN1
0.32 !
HN1
0.35 !
CN1
0.54 !
ON1
-0.51 !
CN5G
0.00 !
NN4
-0.60 !
CN4
0.25 !
HN3
0.16 !
H9
C8 C4 N9
C4 N9 H9 0.0
0.0
180.0 0.0 0.0
PRES PURA
0.00 ! Patch to generate ADENINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM C5
CN5
0.28
ATOM N7
NN4
-0.71
ATOM C8
CN4
0.34
ATOM H8
HN3
0.12
ATOM N9
NN2
-0.37
ATOM H9
HN2
0.32
ATOM N1
NN3A
-0.74
ATOM C2
CN4
0.50
ATOM H2
HN3
0.13
ATOM N3
NN3A
-0.75
ATOM C4
CN5
0.43
ATOM C6
CN2
0.46
ATOM N6
NN1
-0.77
ATOM H61 HN1
0.38
ATOM H62 HN1
0.38
BOND N9
H9
BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0
PRES 5TER
GROUP
0.00
! 5'-terminal HYDROXYL patch
! use in generate statement
ATOM H5T HN5
0.43
ATOM O5' ON5
-0.66
ATOM C5' CN8B
0.05
ATOM H5' HN8
0.09
ATOM H5'' HN8
0.09
!
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
!
BOND H5T
O5'
DONO H5T
O5'
BILD H5T O5'
C5' C4'
PRES 5PHO
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM O5T
ATOM H5T
BOND O5T
DONO H5T
BILD C4'
BILD C5'
BILD O5T
BILD O5T
BILD H5T
-1.00
CN8B
HN8
HN8
P
ON3
ON3
ON2
ON4
HN4
P
O5T
C5'
O5'
O5'
O5'
O5T
PRES 5POM
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM O5T
ATOM C5T
ATOM H5T1
ATOM H5T2
ATOM H5T3
BOND
BOND
BILD
BILD
BILD
BILD
BILD
O5T
C5T
C4'
C5'
O5T
O5T
C5T
P
0.00
180.00
0.00
0.0000
! 5'terminal PHOSPHATE patch
! use in generate statement
-0.08
0.09
0.09
1.50
-0.82
-0.82
-0.62
-0.68
0.34
H5T O5T
O5'
P
*P
*P
P
P
O5T
O1P
O2P
O5'
-1.00
CN8B
HN8
HN8
P
ON3
ON3
ON2
ON2
CN9
HN9
HN9
HN9
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
000.00 -146.00
000.00 -46.90
000.00 -115.82
000.00 115.90
000.00 -95.20
000.00
000.00
000.00
000.00
000.00
0.0000
0.0000
0.0000
0.0000
0.0000
! 5'terminal Methyl-Phosphate patch
! use in generate statement
-0.08
0.09
0.09
1.50
-0.78
-0.78
-0.57
-0.57
-0.17
0.09
0.09
0.09
O5T
H5T3
C5' O5'
O5' P
O5' *P
O5' *P
O5T P
C5T
P
O5T
O1P
O2P
O5'
C5T
0.0000
0.0000
0.0000
0.0000
0.0000
H5T1
C5T
000.00 -146.00
000.00 -46.90
000.00 -115.82
000.00 115.90
000.00 -95.20
H5T2
000.00
000.00
000.00
000.00
000.00
0.0000
0.0000
0.0000
0.0000
0.0000
BILD H5T1
BILD H5T2
BILD H5T3
C5T
C5T
C5T
PRES 3TER
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
ATOM H3T
BOND O3'
DONO H3T
BILD H3T
PRES 3PHO
O5T
O5T
O5T
P
P
P
0.00
CN7
HN7
ON5
HN5
H3T
O3'
O3'
0.0000
0.0000
0.0000
000.00
000.00
000.00
180.20
60.00
-60.00
0.0000
0.0000
0.0000
! 3'terminal HYDROXYL patch
! use in generate statement
0.14
0.09
-0.66
0.43
C3'
C4'
-1.00
0.9600
114.97
148.63
0.000
111.92
1.5284
! 3'terminal PHOSPHATE patch
! use in generate statement
GROUP
ATOM C3' CN7
0.01
ATOM H3' HN7
0.09
ATOM P3
P
1.50
ATOM O1P3 ON3
-0.82
ATOM O2P3 ON3
-0.82
ATOM O3' ON2
-0.62
ATOM O3T ON4
-0.68
ATOM H3T HN4
0.34
BOND O3' P3
P3 O1P3
P3 O2P3
P3 O3T O3T
DONO H3T O3T
ACCE O3T
ACCE O1P2
ACCE O1P3
! Build in B-DNA-like conformation (NF)
BILD C4'
C3' O3' P3
0.0000 000.00 155.00
BILD C3'
O3' P3 O3T
0.0000 000.00 -95.20
BILD O3T
O3' *P3 O1P3
0.0000 000.00 -115.82
BILD O3T
O3' *P3 O2P3
0.0000 000.00 115.90
BILD H3T
O3T P3 O3'
0.0000 000.00 -46.90
PRES 9MG
000.00
000.00
000.00
! 9-Methyl guanine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
H3T
000.00
000.00
000.00
000.00
000.00
0.0000
0.0000
0.0000
0.0000
0.0000
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N9
ATOM C4
ATOM C9
ATOM N3
ATOM C2
ATOM N1
ATOM H1
ATOM N2
ATOM H21
ATOM H22
ATOM C6
ATOM O6
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM H91
ATOM H92
ATOM H93
BOND N9
BILD C8
BILD C8
BILD N9
BILD H91
PRES 9EG
C3'
O3'
H3'
NN2B
CN5
CN9
NN3G
CN2
NN2G
HN2
NN1
HN1
HN1
CN1
ON1
CN5G
NN4
CN4
HN3
HN9
HN9
HN9
C9
C4
N9
H91
H92
-0.02
0.26
-0.27
-0.74
0.75
-0.34
0.26
-0.68
0.32
0.35
0.54
-0.51
0.00
-0.60
0.25
0.16
0.09
0.09
0.09
C9
H91
*N9 C9
C9
H91
*C9 H92
*C9 H93
0.000
C9 H92
0.0
0.0
0.0
0.0
C9
0.0
0.0
0.0
0.0
H93
180.0
180.0
-115.0
115.0
! 9-Ethyl guanine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM C9
CN8 -0.18
ATOM H91 HN8
0.09
ATOM H92 HN8
0.09
GROUP
ATOM C9B CN9 -0.27
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
ATOM
ATOM
ATOM
BOND
BOND
BILD
BILD
BILD
BILD
BILD
BILD
BILD
H9B1
H9B2
H9B3
N9
C9
C8
C8
N9
C9B
N9
C9
H9B1
PRES 9MA
HN9
HN9
HN9
C9
C9B
C4
N9
C9B
H91
C9
H9B1
H9B2
0.09
0.09
0.09
C9
H91
C9B H9B1
*N9 C9
C9
C9B
*C9 H91
*C9 H92
C9B H9B1
*C9B H9B2
*C9B H9B3
0.00
C9 H92
C9B H9B2
0.0
0.0
0.0
0.0
0.0
0.0
0.0
C9
C9B
0.0
0.0
0.0
0.0
0.0
0.0
0.0
H93
H9B3
180.0
0.0
-115.0
115.0
180.0
-115.0
115.0
! 9-Methyl adenine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
! all atoms included in patch to get correct atom
! order to simplify analysis
GROUP
ATOM C5
CN5
0.28
ATOM N7
NN4 -0.71
ATOM C8
CN4
0.34
ATOM H8
HN3
0.12
ATOM N9
NN2 -0.05
ATOM C9
CN9 -0.27
ATOM N1
NN3A -0.74
ATOM C2
CN4
0.50
ATOM H2
HN3
0.13
ATOM N3
NN3A -0.75
ATOM C4
CN5
0.43
ATOM C6
CN2
0.46
ATOM N6
NN1 -0.77
ATOM H61 HN1
0.38
ATOM H62 HN1
0.38
ATOM H91 HN9
0.09
ATOM H92 HN9
0.09
ATOM H93 HN9
0.09
BOND N9
C9
C9
H91
C9 H92
C9
H93
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
BILD
BILD
BILD
BILD
C8
C4
N9
H91
PRES 1MC
C4
N9
H91
H92
*N9
C9
*C9
*C9
C9
H91
H92
H93
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
180.0
180.0
-115.0
115.0
! 1-Methyl Cytosine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM N1
NN2
-0.13
ATOM C1
CN9
-0.27
ATOM C6
CN3
0.05
ATOM H6
HN3
0.17
ATOM C2
CN1
0.52
ATOM O2
ON1C
-0.49
ATOM N3
NN3
-0.66
ATOM C4
CN2
0.65
ATOM N4
NN1
-0.75
ATOM H41 HN1
0.37
ATOM H42 HN1
0.33
ATOM C5
CN3
-0.13
ATOM H5
HN3
0.07
ATOM H11 HN9
0.09
ATOM H12 HN9
0.09
ATOM H13 HN9
0.09
BOND N1
C1
C1
H11
C1 H12
C1
H13
BILD C6
C2
*N1 C1
0.0
0.0
180.0
BILD C2
N1
C1
H11
0.0
0.0
180.0
BILD N1
H11 *C1 H12
0.0
0.0 -115.0
BILD H11 H12 *C1 H13
0.0
0.0
115.0
PRES 1MT
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.000
0.00
! 1-Methyl Thymine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM C1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM C5M
ATOM H51
ATOM H52
ATOM H53
ATOM H11
ATOM H12
ATOM H13
BOND N1
BILD C6
BILD C2
BILD N1
BILD H11
PRES 1MU
C5'
H5'
H5''
C4'
H4'
O4'
C1'
H1'
C2'
H2''
O2'
H2'
C3'
O3'
H3'
NN2B
CN9
CN3
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3T
CN9
HN9
HN9
HN9
HN9
HN9
HN9
C1
C2
N1
H11
H12
-0.34
-0.27
0.17
0.17
0.51
-0.41
-0.46
0.36
0.50
-0.45
-0.15
-0.11
0.07
0.07
0.07
0.09
0.09
0.09
C1
H11
*N1 C1
C1
H11
*C1 H12
*C1 H13
0.00
C1 H12
0.0
0.0
0.0
0.0
C1
0.0
0.0
0.0
0.0
H13
180.0
180.0
-115.0
115.0
! 1-Methyl Uracil patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM C1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM H5
ATOM H11
ATOM H12
ATOM H13
BOND N1
BILD C6
BILD C2
BILD N1
BILD H11
O2'
H2'
C3'
O3'
H3'
NN2B
CN9
CN3
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3
HN3
HN9
HN9
HN9
C1
C2
N1
H11
H12
-0.34
-0.27
0.20
0.14
0.55
-0.45
-0.46
0.36
0.53
-0.48
-0.15
0.10
0.09
0.09
0.09
C1
H11
*N1 C1
C1
H11
*C1 H12
*C1 H13
C1 H12
0.0
0.0
0.0
0.0
C1
0.0
0.0
0.0
0.0
H13
180.0
180.0
-115.0
115.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
! Model compounds used for parameter optimization
RESI THF
0.00 ! tetrahydrofuran
!
! Figure 3A, interaction with water
!
GROUP
ATOM O4' ON6
-0.50 !
H41' O4' H11'
ATOM C4' CN8
0.07 !
\ / \ /
ATOM C3' CN8
-0.18 !
H42'--C4' C1'--H12'
ATOM C2' CN8
-0.18 !
|
|
ATOM C1' CN8
0.07 !
H31'--C3'--C2'--H21'
ATOM H11' HN8
0.09 !
/
\
ATOM H12' HN8
0.09 !
H32'
H22'
ATOM H21' HN8
0.09 !
ATOM H22' HN8
0.09 !
ATOM H31' HN8
0.09 !
ATOM H32' HN8
0.09 !
ATOM H41' HN8
0.09 !
ATOM H42' HN8
0.09 !
BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C1' H11'
C1' H12' C2' H21' C2' H22' C3' H31' C3'
BOND C4' H41' C4' H42'
PATC FIRS NONE LAST NONE
RESI THFO
0.00 ! 3'-hydroxyl-tetrahydrofuran
!
! Figure 3B, interaction with water
!
H32'
GROUP
ATOM O4'
ATOM C1'
ATOM C2'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H21'
ATOM H22'
ATOM H41'
ATOM H42'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM H32'
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
ON6
CN7B
CN8
CN7
HN7
HN7
HN8
HN8
HN7
HN7
-0.50
0.07
-0.18
0.07
0.09
0.09
0.09
0.09
0.09
0.09
CN7
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
!
!
!
!
!
!
!
!
!
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
H32'
C1' O4' C1' C2' C2'
C1' H11' C1' H12' C2'
C4' H42' O3' H32'
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
H22'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
H32'
O3'
C3'
FIRS NONE LAST NONE
RESI DMPA
!
! Model compound
!
GROUP
ATOM P1
P
ATOM O3
ON3
ATOM O4
ON3
ATOM O1
ON2
ATOM O2
ON2
ATOM C1
CN9
ATOM H11 HN9
ATOM H12 HN9
ATOM H13 HN9
ATOM C2
CN9
ATOM H21 HN9
ATOM H22 HN9
ATOM H23 HN9
-1.00
BOND P1
BOND C1
P1
C1
O1
H11
C3' C3'
H21' C2'
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
C1'
O4'
C4'
C4' C4'
H22' C3'
1.4055
1.4127
1.5457
1.5346
1.5211
1.0856
1.0818
1.0846
1.0822
1.0806
1.0891
1.0808
1.4028
0.9492
O4' C3'
H31' C4'
108.09
23.45
106.18
3.96
103.11 -26.93
100.86
41.73
103.15 -41.62
111.62 123.53
113.32 -114.11
110.65
91.68
110.88 -148.45
113.53 162.89
110.89
77.76
108.72 -162.12
110.98 -77.39
108.72
44.80
O3'
H41'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
110.98
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
1.5211
! Dimethylphosphate
A
1.500
-0.780
-0.780
-0.570
-0.570
-0.170
0.090
0.090
0.090
-0.170
0.090
0.090
0.090
O2
H12
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H11!
|
H13- C1-H12
\
O3
O1
\\ /
(-)
P1
// \
O4
O2
/
H23-C2-H22
|
H21
P1
C1
O3
H13
P1
C2
O4
H21
O1
C2
C1
H22
O2
C2
C2
H23
! IC FOR THE
IC O3
P1
IC O4
P1
IC O1
P1
IC O2
P1
IC H11 C1
IC H12 C1
IC H13 C1
IC H21 C2
IC H22 C2
IC H23 C2
g,g conformation (3-21G* opt.
O1
C1
1.4723
107.31
O2
C2
1.4722
000.0
O2
C2
1.6343
000.0
O1
C1
1.6344
000.0
O1
P1
1.0827
107.8
O1
P1
1.0800
110.4
O1
P1
1.0848
110.7
O2
P1
1.0827
107.9
O2
P1
1.0800
110.4
O2
P1
1.0848
110.7
RESI T5PH
!
! Model compound
!
GROUP
ATOM C5' CN8B
ATOM H5' HN8
ATOM H5'' HN8
ATOM O5' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3P ON4
ATOM H5T HN4
GROUP
ATOM O4' ON6
ATOM C1' CN7B
ATOM H1' HN7
ATOM H1'' HN7
ATOM C4' CN7
ATOM H4'' HN7
GROUP
ATOM C2' CN8
ATOM H2' HN8
ATOM H2'' HN8
GROUP
ATOM C3' CN7
ATOM H3' HN7
ATOM H3'' HN7
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
C1'
C1'
C4'
P
C4'
O4'
C1'
C2'
C3'
H1'
H1''
H2'
H2''
H3'
H3''
structure)
000.0
117.79
000.0
117.79
73.8
117.79
73.7
117.79
174.8
117.79
54.1
117.79
294.3
117.79
174.7
117.79
54.1
117.79
294.2
117.79
1.4356
1.4357
1.4357
1.4356
1.6343
1.6343
1.6343
1.6344
1.6344
1.6344
-1.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -1)
B
-0.08
0.09
0.09
-0.62
1.50
-0.82
-0.82
-0.68
0.34
-0.50
0.07
0.09
0.09
0.16
0.09
!
!
O1P
H5T
!
||
/
! O2P==P==O3P
!
|
!
O5'
!
|
! H5'' |
!
\ |
! H5'--C5'
O4' H1'
!
\ / \ /
!
H4'--C4' C1'--H1''
!
|
|
!
H3'--C3'--C2'--H2'
!
/
\
!
H3''
H2''
!
-0.18
0.09
0.09
-0.18
0.09
0.09
O4' C1'
H1' C1'
H4'' C5'
O2P P
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
C2'
C3'
C3'
C2'
H1''
H5'
O3P
C1'
C2'
C3'
C4'
O4'
C2'
C2'
C3'
C3'
C4'
C4'
C2'
C2'
C5'
O3P
C3' C3' C4' C4' O4' C4'
H2' C2' H2'' C3' H3' C3'
H5'' C5' O5' O5' P
P
H5T
C2'
1.4416 109.61
0.45
C3'
1.4471 106.74 -21.92
C4'
1.5328 103.38
33.49
O4'
1.5200 102.18 -34.11
C1'
1.5321 105.43
21.23
C3'
1.1099 113.03 -141.96
C3'
1.1111 111.16
93.50
C4'
1.1135 109.13 -81.76
C4'
1.1076 113.49 155.97
O4'
1.1127 108.68
81.68
O4'
1.1069 112.41 -156.66
C5'
H3''
O1P
106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
105.43
105.43
1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
1.4416
1.4416
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
H4''
C4'
C5'
C4'
H51'
C5'
H52'
C5'
O4'
C4'
O4'
C4'
O4'
C4'
C4'
C5'
C5'
O5'
C5'
O5'
C5'
O5'
O5'
P
FIRS NONE LAST
O4'
O4'
C4'
C4'
C5'
C5'
C5'
O5'
P
P
P
O3P
NONE
C1'
C1'
O4'
O4'
O5'
H5'
H5''
P
O1P
O2P
O3P
H5T
1.1127
1.5325
1.1092
1.1104
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
106.71
108.43
110.48
110.01
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
-95.75
144.82
180.00
-60.00
60.0
180.0
-60.0
180.0
-60.0
180.0
60.0
180.0
109.61
109.61
108.43
108.43
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
1.4471
1.4471
1.4416
1.4416
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
RESI TH5P
-2.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -2)
!
! Model compound B with dianionic phosphate, vibrational analysis
!
GROUP
!
O1P (-2)
ATOM O4' ON6
-0.50 !
||
ATOM C1' CN7B
0.07 ! O2P==P==O2P
ATOM H1' HN7
0.09 !
|
ATOM H1'' HN7
0.09 ! H5'' |
ATOM C4' CN7
0.16 !
\ |
ATOM H4'' HN7
0.09 ! H5'--C5'
O4' H1'
GROUP
!
\ / \ /
ATOM C2' CN8
-0.18 !
H4'--C4' C1'--H1''
ATOM H2' HN8
0.09 !
|
|
ATOM H2'' HN8
0.09 !
H3'--C3'--C2'--H2'
GROUP
!
/
\
ATOM C3' CN7
-0.18 !
H3''
H2''
ATOM H3' HN7
0.09 !
ATOM H3'' HN7
0.09
GROUP
ATOM C5' CN8B
-0.18
ATOM H5' HN8
0.09
ATOM H5'' HN8
0.09
GROUP
ATOM O5' ON2
-0.40
ATOM P
P
1.10
ATOM O1P ON3
-0.90
ATOM O2P ON3
-0.90
ATOM O3P ON3
-0.90
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
C1'
C1'
C4'
P
C4'
O4'
C1'
C2'
C3'
H1'
H1''
H2'
H2''
O4' C1'
H1' C1'
H4'' C5'
O2P P
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
C2'
C2' C2' C3' C3' C4' C4' O4' C4'
H1'' C2' H2' C2' H2'' C3' H3' C3'
H5' C5' H5'' C5' O5' O5' P
P
O3P
C1'
C2'
1.4416 109.61
0.45
C2'
C3'
1.4471 106.74 -21.92
C3'
C4'
1.5328 103.38
33.49
C4'
O4'
1.5200 102.18 -34.11
O4'
C1'
1.5321 105.43
21.23
C2'
C3'
1.1099 113.03 -141.96
C2'
C3'
1.1111 111.16
93.50
C3'
C4'
1.1135 109.13 -81.76
C3'
C4'
1.1076 113.49 155.97
C5'
H3''
O1P
106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
H3'
C3'
H3''
C3'
H4''
C4'
C5'
C4'
H51'
C5'
H52'
C5'
O4'
C4'
C4'
C5'
C5'
O5'
C5'
O5'
C5'
O5'
FIRS NONE LAST
RESI T3PH
!
! Model compound
!
GROUP
ATOM O4' ON6
ATOM C1' CN7B
ATOM H11' HN7
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN8
ATOM H21' HN8
ATOM H22' HN8
GROUP
ATOM C3' CN7
ATOM H31' HN7
ATOM O3' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3T ON4
ATOM H3T HN4
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
C4'
C4'
O4'
O4'
C4'
C4'
C5'
O5'
P
P
P
NONE
O4'
O4'
C1'
C1'
O4'
O4'
O5'
P
O1P
O2P
O3P
1.1127
1.1069
1.1127
1.5325
1.1092
1.1104
0.0
0.0
0.0
0.0
0.0
108.68
81.68
112.41 -156.66
106.71 -95.75
108.43 144.82
110.48 180.00
110.01 -60.00
0.0
60.00
0.0
180.0
0.0
-60.0
0.0
180.0
0.0
60.0
105.43
105.43
109.61
109.61
108.43
108.43
0.0
0.0
0.0
0.0
0.0
1.4416
1.4416
1.4471
1.4471
1.4416
1.4416
0.0
0.0
0.0
0.0
0.0
-1.00 ! monoanionic 3'phosphate-tetrahydrofuran
C
-0.50
0.07
0.09
0.09
0.07
0.09
0.09
-0.18
0.09
0.09
0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.68
0.34
C1' O4' C1'
C1' H11' C1'
C4' H42' O3'
C4'
O4'
O4'
C1'
C1'
C2'
C2'
C3'
C3'
C4'
H11'
C1'
H12'
C1'
H21'
C2'
H22'
C2'
H31'
C3'
H41'
C4'
H42'
C4'
O3'
C3'
P
O3'
O1P
P
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
O1P==P==O2P
|
O3T (-1)
\
H3T
C2' C2' C3' C3' C4' C4' O4' C3'
H12' C2' H21' C2' H22' C3' H31' C4'
P
P
O1P P
O2P P
O3T O3T
C1'
C2'
1.4055 108.09
23.45
C2'
C3'
1.4127 106.18
3.96
C3'
C4'
1.5457 103.11 -26.93
C4'
O4'
1.5346 100.86
41.73
O4'
C1'
1.5211 103.15 -41.62
C2'
C3'
1.0856 111.62 123.53
C2'
C3'
1.0818 113.32 -114.11
C3'
C4'
1.0846 110.65
91.68
C3'
C4'
1.0822 110.88 -148.45
C4'
O4'
1.0806 113.53 162.89
O4'
C1'
1.0891 110.89
77.76
O4'
C1'
1.0808 108.72 -162.12
C4'
O4'
1.4028 110.98 -77.39
C3'
C4'
0.0
0.0
180.00
O3'
C3'
0.0
0.0
-60.0
O3'
H41'
H3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
IC
O2P
P
IC
O3T
P
IC
H3T
O3T
PATC FIRS NONE LAST
RESI R3PH
!
! Model compound
!
GROUP
ATOM O4' ON6B
ATOM C1' CN7B
ATOM H11' HN7
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN7B
ATOM H21' HN7
ATOM O2' ON5
ATOM H22' HN5
GROUP
ATOM C3' CN7
ATOM H31' HN7
ATOM O3' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3T ON4
ATOM H3T HN4
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
O3'
O3'
P
NONE
C3'
C3'
O3'
0.0
0.0
0.0
60.0
180.0
180.0
0.0
0.0
0.0
0.0
0.0
0.0
-1.00 ! monoanionic 3'phosphate-tetrahydrofuran
C, monoanionic with 2'hydroxyl
-0.50
0.07
0.09
0.09
0.07
0.09
0.09
0.14
0.09
-0.66
0.43
0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.68
0.34
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
O2'
|
|
O1P==P==O2P
H22'
|
O3T (-1)
\
H3T
C1' O4' C1' C2' C2'
C1' H11' C1' H12' C2'
C4' H42' O3' P
P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
O2'
C2'
C3'
H22'
O2'
C2'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3T
P
O3'
H3T
O3T
P
FIRS NONE LAST NONE
RESI T3PM
0.0
0.0
0.0
C3' C3' C4'
H21' C2' O2'
O1P P
O2P
C2'
1.4055
C3'
1.4127
C4'
1.5457
O4'
1.5346
C1'
1.5211
C3'
1.0856
C3'
1.0818
C4'
1.0846
C4'
1.0822
C3'
1.0822
O4'
1.0806
C1'
1.0891
C1'
1.0808
O4'
1.4028
C4'
0.0
C3'
0.0
C3'
0.0
C3'
0.0
O3'
0.0
C4' O4' C3'
O2' H22' C3'
P
O3T O3T
108.09
23.45
106.18
3.96
103.11 -26.93
100.86
41.73
103.15 -41.62
111.62 123.53
113.32 -114.11
110.65
91.68
110.88 283.41
110.88
0.00
113.53 162.89
110.89
77.76
108.72 -162.12
110.98 -77.39
0.0
180.00
0.0
-60.0
0.0
60.0
0.0
180.0
0.0
180.0
O3'
H31' C4'
H3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0
0.0
H41'
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0
-1.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1)
!
! Model compound
!
GROUP
ATOM O4' ON6
ATOM C1' CN7B
ATOM H11' HN7
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN8
ATOM H21' HN8
ATOM H22' HN8
GROUP
ATOM C3' CN7
ATOM H31' HN7
GROUP
ATOM O3' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3T ON2
ATOM C3T CN8B
ATOM H3T1 HN8
ATOM H3T2 HN8
ATOM H3T3 HN8
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
D
-0.50
0.07
0.09
0.09
0.07
0.09
0.09
-0.18
0.09
0.09
0.01
0.09
-0.57
1.50
-0.78
-0.78
-0.57
-0.17
0.09
0.09
0.09
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H41'
O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
O1P==P==O2P
|
O3T (-1)
\
C3T--H3T3
/ \
H3T1 H3T2
C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3'
C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4'
C4' H42' O3' P
P
O1P P
O2P P
O3T O3T
C3T H3T1
C3T H3T2 C3T H3T3
C4'
O4'
C1'
C2'
1.4055 108.09
23.45
O4'
C1'
C2'
C3'
1.4127 106.18
3.96
C1'
C2'
C3'
C4'
1.5457 103.11 -26.93
C2'
C3'
C4'
O4'
1.5346 100.86
41.73
C3'
C4'
O4'
C1'
1.5211 103.15 -41.62
H11'
C1'
C2'
C3'
1.0856 111.62 123.53
H12'
C1'
C2'
C3'
1.0818 113.32 -114.11
H21'
C2'
C3'
C4'
1.0846 110.65
91.68
H22'
C2'
C3'
C4'
1.0822 110.88 -148.45
H31'
C3'
C4'
O4'
1.0806 113.53 162.89
H41'
C4'
O4'
C1'
1.0891 110.89
77.76
H42'
C4'
O4'
C1'
1.0808 108.72 -162.12
O3'
C3'
C4'
O4'
1.4028 110.98 -77.39
P
O3'
C3'
C4'
0.0000 000.00 180.00
C3'
O3'
P
O3T
0.0000 000.00 -95.22
O3T
O3'
*P
O1P
0.0000 000.00 -115.82
O3T
O3'
*P
O2P
0.0000 000.00 115.90
C3T
O3T
P
O3'
0.0000 000.00 -46.90
H3T1
C3T
O3T
P
0.0000 000.00 180.00
H3T2
C3T
O3T
P
0.0000 000.00
60.00
H3T3
C3T
O3T
P
0.0000 000.00 -60.00
FIRS NONE LAST NONE
RESI THFI
0.00
! imidazole analog with THF ring
O3'
H41'
C3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
!
! Model compound E, with imidazole
!
GROUP
ATOM O4' ON6
-0.50 !
H41' O4' Imidazole
ATOM C1' CN7B
0.16 !
\ / \ /
ATOM H12' HN7
0.09 !
H42'--C4' C1'--H12'
ATOM C4' CN7
0.07 !
|
|
ATOM H41' HN7
0.09 !
H31'--C3'--C2'--H21'
ATOM H42' HN7
0.09 !
/
\
GROUP
!
H32'
H22'
ATOM C2' CN8
-0.18 !
ATOM H21' HN8
0.09 !
ATOM H22' HN8
0.09 !
GROUP
!
ATOM C3' CN7
-0.18 !
ATOM H31' HN7
0.09 !
ATOM H32' HN7
0.09 !
GROUP ! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG
CPH1 -0.05 !
C1'
HE1
ATOM HG
HR3
0.09 !
\
/
ATOM CD2 CPH1
0.22 !
ND1---CE1
ATOM HD2 HR3
0.10 !
/
|
ATOM ND1 NR1
-0.04 ! HG-CG
|
ATOM CE1 CPH2
0.25 !
\
|
ATOM HE1 HR1
0.13 !
CD2---NE2
ATOM NE2 NR2
-0.70 !
|
!
HD2
BOND
BOND
BOND
BOND
BOND
IMPH
IMPH
IMPH
IMPH
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1'
C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
C4' H41' C4' H42'
ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1
CE1 HE1 CD2 HD2 CG HG
ND1 CG
CE1 C1'
ND1 CE1 CG
C1'
CD2 CG
NE2 HD2
CD2 NE2 CG
HD2
CE1 ND1 NE2 HE1
CE1 NE2 ND1 HE1
CG
CD2 ND1 HG
CG
ND1 CD2 HG
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
H12' C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
H21' C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
H22' C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
H31' C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
H32' C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
H41' C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
H42' C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
C4'
O4'
C1'
ND1
0.0 0.0 256.98 0.0 0.0
O4'
C1'
ND1
CE1
0.0 0.0 180.00 0.0 0.0
C1'
ND1
CE1
NE2
0.0 0.0 181.56 0.0 0.0
ND1
CE1
NE2
CD2
0.0 0.0
0.34 0.0 0.0
CE1
NE2
CD2
CG
0.0 0.0
0.00 0.0 0.0
HE1
CE1
NE2
CD2
0.0 0.0 180.40 0.0 0.0
CE1
NE2
CD2
HD2
0.0 0.0 179.83 0.0 0.0
NE2
CD2
CG
HG
0.0 0.0 178.45 0.0 0.0
FIRS NONE LAST NONE
ND1
RESI THMI
0.00
! thf-ch3-imidazole
!
! Model compound E with imidazole base and 5'methyl, vibrational analysis
!
GROUP
! Sugar: transferred from thf
ATOM O4' ON6
-0.50 !
H52' H53'
ATOM C1' CN7B
0.16 !
\ /
ATOM H12' HN7
0.09 ! H51'-C5' O4' Imidazole
ATOM C4' CN7
0.16 !
\ / \ /
ATOM H42' HN7
0.09 !
H42'--C4' C1'--H12'
GROUP
!
|
|
ATOM C2' CN8
-0.18 !
H31'--C3'--C2'--H21'
ATOM H21' HN8
0.09 !
/
\
ATOM H22' HN8
0.09 !
H32'
H22'
GROUP
ATOM C3' CN7
-0.18
ATOM H31' HN7
0.09
ATOM H32' HN7
0.09
GROUP
ATOM C5' CN8B
-0.27
ATOM H51' HN8
0.09
ATOM H52' HN8
0.09
ATOM H53' HN8
0.09
GROUP ! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG
CPH1
-0.05 !
C1'
HE1
ATOM HG
HR3
0.09 !
\
/
ATOM CD2 CPH1
0.22 !
ND1---CE1
ATOM HD2 HR3
0.10 !
/
||
ATOM ND1 NR1
-0.04 ! HG-CG
||
ATOM CE1 CPH2
0.25 !
\\
||
ATOM HE1 HR1
0.13 !
CD2---NE2
ATOM NE2 NR2
-0.70 !
|
!
HD2
BOND
BOND
BOND
BOND
BOND
BOND
IMPH
IMPH
IMPH
IMPH
! ic
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1'
C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
C4' H42' C4' C5' C5' H51' C5' H52' C5' H53'
ND1 CE1 NE2 CD2 CG ND1
CE1 HE1 CD2 HD2 CG HG
CG CD2
CE1 NE2
ND1 CG CE1 C1'
ND1 CE1 CG
C1'
CD2 CG NE2 HD2
CD2 NE2 CG
HD2
CE1 ND1 NE2 HE1
CE1 NE2 ND1 HE1
CG CD2 ND1 HG
CG
ND1 CD2 HG
table for thfim, from Nicolas:
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
H12' C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
H21' C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
H22' C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
H31' C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
H32' C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
C5'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0
H52'
C5'
C4'
O4'
0.0 0.0 -59.66 0.0
H53'
C5'
C4'
O4'
0.0 0.0
59.68 0.0
H42' C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
ND1
0.0
0.0
0.0
IC
IC
IC
IC
IC
IC
IC
IC
PATC
C4'
O4'
C1'
ND1
O4'
C1'
ND1
CE1
C1'
ND1
CE1
NE2
ND1
CE1
NE2
CD2
CE1
NE2
CD2
CG
HE1
CE1
NE2
CD2
CE1
NE2
CD2
HD2
NE2
CD2
CG
HG
FIRS NONE LAST NONE
RESI TADE
!
! Model compound
!
GROUP
ATOM C5
CN5
ATOM N7
NN4
ATOM C8
CN4
ATOM H8
HN3
ATOM N9
NN2
ATOM C1' CN7B
ATOM N1
NN3A
ATOM C2
CN4
ATOM H2
HN3
ATOM N3
NN3A
ATOM C4
CN5
ATOM C6
CN2
ATOM N6
NN1
ATOM H61 HN1
ATOM H62 HN1
ATOM O4' ON6
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN8
ATOM H21' HN8
ATOM H22' HN8
GROUP
ATOM C3' CN7
ATOM H31' HN7
ATOM H32' HN7
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IMPH
! ic
IC
IC
IC
IC
0.0 0.0 256.98 0.0 0.0
0.0 0.0 180.00 0.0 0.0
0.0 0.0 181.56 0.0 0.0
0.0 0.0
0.34 0.0 0.0
0.0 0.0
0.00 0.0 0.0
0.0 0.0 180.40 0.0 0.0
0.0 0.0 179.83 0.0 0.0
0.0 0.0 178.45 0.0 0.0
0.00 ! thf with adenine
E with adenine
0.28
-0.71
0.34
0.12
-0.05
0.16
-0.74
0.50
0.13
-0.75
0.43
0.46
-0.77
0.38
0.38
-0.50
0.09
0.07
0.09
0.09
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
-0.18 !
0.09
0.09
H61
\
H62!
/
N6
|
C6
// \
N1
C5--N7\\
|
||
C8-H8
C2
C4--N9/
/ \\ /
\
H2
N3
\
\
\
\
H42' O4' \
\ /
\ \
H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32'
H21' H22'
-0.1
*
*
*
*
*
*
*
*
*
*
*
*
CHARMM27 All-Hydrogen Nucleic Acid Topology File
Foloppe, N. and MacKerell, A.D., Jr.
All-atom emiprical force field for nucleic acids:
1) Parameter optimization based on small molecule and
condensed phase macromolecular target data.
J. Computational Chemistry, Submitted
and
MacKerell, A.D., Jr. and Banavali, N.
All-atom emiprical force field for nucleic acids:
2) Application to molecular dynamics simulations of DNA
and RNA in solution
J. Computational Chemistry, Submitted
MASS 1
MASS 2
MASS 3
MASS 4
MASS 5
MASS 6
MASS 7
MASS 8
MASS 9
MASS 10
MASS 11
MASS 12
MASS 13
MASS 20
MASS 21
MASS 22
MASS 23
MASS 24
MASS 25
MASS 26
MASS 27
MASS 28
MASS 29
MASS 30
MASS 31
MASS 32
MASS 33
MASS 34
MASS 35
MASS 36
MASS 37
MASS 38
MASS 39
MASS 50
MASS 51
MASS 52
MASS 53
MASS 54
Sasha)
MASS 55
MASS 56
MASS 57
HT
HN1
HN2
HN3
HN3B
HN3C
HNP
HN4
HN5
HN6
HN7
HN8
HN9
CN1
CN1A
CN1T
CN2
CN3
CN3A
CN3B
CN3C
CN3D
CN3T
CN4
CN5
CN5G
CN7
CN7B
CN7C
CN7D
CN8
CN8B
CN9
NN1
NN1C
NN2
NN2B
NN2C
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
1.008000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
12.011000
14.007000
14.007000
14.007000
14.007000
14.007000
H
H
H
H
H
H
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
N
N
N
N
N
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
TIPS3P WATER HYDROGEN
Nucleic acid amine proton
Nucleic acid ring nitrogen proton
Nucleic acid aromatic carbon proton
NAD+ aromatic hydrogen
Standard aromatic hydrogen (as in benzene)
pure aromatic H
Nucleic acid phosphate hydroxyl proton
Nucleic acid ribose hydroxyl proton
Nucleic acid ribose aliphatic proton
Nucleic acid proton (equivalent to protein HA)
Bound to CN8 in nucleic acids/model compounds
Bound to CN9 in nucleic acids/model compounds
Nucleic acid carbonyl carbon
NAD+/NADH amide carbonyl carbon
Nucleic acid carbonyl carbon (T/U C2)
Nucleic acid aromatic carbon to amide
Nucleic acid aromatic carbon
NAD+ aromatic carbon
NAD+ aromatic carbon
NADH aromatic carbon
Nucleic acid aromatic carbon for 5MC
Nucleic acid aromatic carbon, Thy C5
Nucleic acid purine C8 and ADE C2
Nucleic acid purine C4 and C5
Nucleic acid guanine C5
Nucleic acid carbon (equivalent to protein CT1)
Nucleic acid aliphatic carbon for C1'
C2' in arabinose
C2' in nucleic acids fluorine derivatives
Nucleic acid carbon (equivalent to protein CT2)
Nucleic acid carbon (equivalent to protein CT2)
Nucleic acid carbon (equivalent to protein CT3)
Nucleic acid amide nitrogen
Nucleic acid imino nitrogen (cyt taut Sasha)
Nucleic acid protonated ring nitrogen
From NN2, for N9 in GUA different from ADE
Nucleic acid protonated ring nitrogen (cyt taut
NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen
MASS
N3
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
MASS
58
NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and
59
60
61
62
70
71
72
73
74
75
76
77
78
82
83
90
102
103
104
105
106
107
NN3I
NN3G
NN4
NN5
OT
ON1
ON1C
ON2
ON3
ON4
ON5
ON6
ON6B
P
P2
SOD
CPH1
CPH2
HR3
HR1
NR1
NR2
14.007000
14.007000
14.007000
14.007000
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
15.999400
30.974000
30.974000
22.989770
12.011000
12.011000
1.008000
1.008000
14.007000
14.007000
N ! Nucleic acid unprotonated ring nitrogen, inosine N3
N ! Nucleic acid unprotonated ring nitrogen, gua N3
N ! Nucleic acid purine N7
N ! Nucleic acid sp2 amine nitrogen
O ! TIPS3P WATER OXYGEN
O ! Nucleic acid carbonyl oxygen
O ! Nucleic acid carbonyl oxygen, cyt O2
O ! Nucleic acid phosphate ester oxygen
O ! Nucleic acid =O in phosphate
O ! Nucleic acid phosphate hydroxyl oxygen
O ! Nucleic acid ribose hydroxyl oxygen
O ! Nucleic acid deoxyribose ring oxygen
O ! Nucleic acid ribose ring oxygen
P ! phosphorus
P ! pyrophosphate phosphorus
NA ! Sodium Ion
C ! For imidazole model compound (NF)
C ! For imidazole model compound (NF)
H ! For imidazole model compound (NF)
H ! For imidazole model compound (NF)
H ! For nitrogen in imidazol (NF)
H ! For nitrogen in imidazol (NF)
! oligonucleotide connectivity information
DECL +P
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFA FIRS none LAST none
AUTOGENERATE ANGLES DIHEDRALS
!Note that the default nucleotides are RNA. The
!patches DEO1 and DEO2 must be applied to create
!the corresponding DNA nucleotides.
RESI GUA
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N9
ATOM C4
ATOM N3
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2B
CN5
NN3G
-0.02
0.26
-0.74
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
O6
||
C6
/ \
H1-N1
C5--N7\\
|
||
C8-H8
C2
C4--N9/
/ \\ /
\
H21-N2
N3
\
|
\
H22
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
ATOM C2
CN2
0.75 !
ATOM N1
NN2G
-0.34 !
ATOM H1
HN2
0.26 !
ATOM N2
NN1
-0.68 !
ATOM H21 HN1
0.32
ATOM H22 HN1
0.35
ATOM C6
CN1
0.54
ATOM O6
ON1
-0.51
ATOM C5
CN5G
0.00
ATOM N7
NN4
-0.60
ATOM C8
CN4
0.25
ATOM H8
HN3
0.16
GROUP
ATOM C2' CN7B
0.14
ATOM H2'' HN7
0.09
ATOM O2' ON5
-0.66
ATOM H2' HN5
0.43
GROUP
ATOM C3' CN7
0.01
ATOM H3' HN7
0.09
ATOM O3' ON2
-0.57
BOND P
O1P
P
O2P
BOND O5' C5'
C5' C4'
BOND C1' N9
C1' C2'
BOND C2
N2
C2
N1
BOND N2
H22
N1
H1
BOND C5
N7
C2' C3'
BOND C2' O2'
O2' H2'
BOND C1' H1'
C2' H2''
BOND C5' H5''
C8
H8
BOND C2 N3
C4
C5
IMPH N2
N3
N1
C2
O6
DONO H21 N2
DONO H22 N2
DONO H1
N1
DONO H2' O2'
ACCE O6
C6
ACCE N3
ACCE N7
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! Chi and sugar-phosphate backbone
BILD -O3' P
O5' C5'
1.6001
BILD -O3' O5' *P
O1P
1.6001
BILD -O3' O5' *P
O2P
1.6001
BILD P
O5' C5' C4'
1.5996
BILD O5' C5' C4' C3'
1.4401
BILD C5' C4' C3' O3'
1.5160
BILD C4' C3' O3' +P
1.5284
BILD C3' O3' +P
+O5'
1.4212
BILD O4' C3' *C4' C5'
1.4572
BILD C2' C4' *C3' O3'
1.5284
BILD C4' C3' C2' C1'
1.5284
O3' H3' O2' H2''
|
|
H2'
P
C4'
N9
N2
N1
C3'
O5'
O4'
C4
H21
C6
O3'
C3'
H3'
N7
N1
C8
C5
C6
C4'
N9
C3'
C8
C6
O3'
C5
+P
C4'
H4'
C6
O6
H22
H21
O4'
C4
C1'
N3
C5'
H5'
C2
N2
in B-DNA like conformation
101.45 -46.90 119.00
1.4401
101.45 -115.82 109.74
1.4802
101.45 115.90 109.80
1.4801
119.00 -146.00 110.04
1.5160
108.83
60.00 116.10
1.5284
116.10 140.00 115.12
1.4212
111.92 155.00 119.05
1.6001
119.05 -95.20 101.45
1.5996
104.06 -120.04 116.10
1.5160
100.16 -124.08 115.12
1.4212
100.16 -30.00 102.04
1.5251
!alpha
!beta
!gamma
!delta
!epsilon
!zeta
!puck
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
C3'
O4'
C1'
C4
C8
N9
C5
C4
N1
N3
H21
N3
C6
C5
N9
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
RESI ADE
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM N9
ATOM N1
ATOM C2
ATOM H2
ATOM N3
ATOM C4
ATOM C6
ATOM N6
ATOM H61
ATOM H62
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
C2'
C1'
C4
N9
N9
C5
C4
N3
N3
C2
C2
C2
C2
N1
N7
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
C1'
N9
*N9
C8
C4
*C4
N3
C2
*C2
N2
*N2
N1
*N1
*C6
*C8
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
N9
C4
C8
N7
C5
N3
C2
N1
N2
H21
H22
C6
H1
O6
H8
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
CN5
NN4
CN4
HN3
NN2
NN3A
CN4
HN3
NN3A
CN5
CN2
NN1
HN1
HN1
0.28
-0.71
0.34
0.12
-0.05
-0.74
0.50
0.13
-0.75
0.43
0.46
-0.77
0.38
0.38
CN7B
HN7
ON5
0.14
0.09
-0.66
1.5284
1.5251
1.4896
1.377
1.374
1.377
1.377
1.355
1.375
1.327
1.01
1.327
1.393
1.415
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
101.97
113.71
125.59
106.0
106.0
105.6
128.4
111.8
124.0
119.7
127.0
124.0
124.9
111.7
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0
147.80
-97.2
-179.99
0.0
0.0
180.0
0.0
0.0
180.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
H61
\
113.71
125.59
106.0
113.5
105.6
128.4
111.8
124.0
119.7
127.0
116.5
124.9
117.4
120.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
H62!
/
N6
|
C6
// \
N1
C5--N7\\
|
||
C8-H8
C2
C4--N9/
/ \\ /
\
H2
N3
\
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
1.4896
1.3783 !chi
1.374
1.304
1.377
1.355
1.327
1.375
1.341
1.01
1.01
1.393
1.03
1.239
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
BOND C2
BOND N6
BOND C2'
BOND C1'
BOND C5'
BOND N1
IMPH H62
DONO H61
DONO H62
DONO H2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1P
ACCE O2P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
BILD -O3'
BILD -O3'
BILD -O3'
BILD P
BILD O5'
BILD C5'
BILD C4'
BILD C3'
BILD O4'
BILD C2'
BILD C4'
BILD C3'
BILD O4'
BILD C1'
BILD C4
BILD C8
BILD C8
BILD N7
BILD C5
BILD N9
BILD C5
BILD N1
BILD H61
BILD C5
BILD N1
BILD H61
BILD N9
BILD N1
BILD C1'
BILD H2'
HN5
0.43
CN7
0.01
HN7
0.09
ON2
-0.57
O1P
P
C5'
C5'
N9
C1'
N1
C6
H61
N6
C3'
C2'
H1'
C2'
H5''
C8
C6
C2
C6
H61 N6
N6
N6
O2'
O2P
C4'
C2'
N6
H62
O2'
H2''
H8
N3
N6
P
C4'
N9
O5'
O4'
C4
C6
O2'
C3'
C2
C4
N1
C5
H2'
H3'
H2
C5
C5
C4'
N9
C3'
C8
O4'
C4
C1'
N3
C5
C3'
C4'
N7
O3'
H4'
O3'
C5'
+P
H5'
N7
C8
C6
P
P
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C4
N9
N9
N7
C5
C6
C5
N1
C6
C6
N1
C6
C6
N7
N3
C3'
O2'
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N9
*N9
C8
C4
C5
C6
N1
*C4
*C6
N6
*N6
*C6
N6
*N6
*C8
*C2
*C2'
C2'
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N9
C4
C8
N7
C5
C6
N1
C2
N3
N6
H61
H62
N6
H61
H62
H8
H2
O2'
C3'
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.376
1.367
0.0
0.0
0.0
1.376
1.409
1.337
1.01
1.409
1.337
1.01
0.0
0.0
1.5284
0.9600
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
125.97
106.0
106.0
0.0
0.0
0.0
105.6
117.6
121.2
119.0
117.6
119.0
119.0
0.0
0.0
102.04
114.97
-46.90
-115.82
115.90
-146.00
60.00
140.00
155.00
-95.20
-120.04
-124.08
-30.00
147.80
-97.2
-179.94
0.0
0.0
180.0
180.0
0.0
-180.0
-180.0
0.0
180.0
-180.0
0.0
180.0
180.0
180.0
-114.67
148.63
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
125.59
106.0
113.6
105.6
0.0
0.0
0.0
126.9
121.2
119.0
119.00
119.0
119.0
121.00
0.0
0.0
110.81
111.92
1.4401
1.4802
1.4801
1.5160
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3783
1.367
1.312
1.382
0.0
0.0
0.0
1.342
1.337
1.01
1.01
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284
!alpha
!beta
!gamma
!delta
!epsilon
!zeta
!puck
!chi
BILD
BILD
BILD
BILD
BILD
BILD
O4'
C1'
C2'
C3'
C4'
C4'
RESI CYT
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM C4
ATOM N4
ATOM H41
ATOM H42
ATOM C5
ATOM H5
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
BOND C2
BOND C4
BOND C2'
BOND C1'
BOND C5'
BOND C2
IMPH O2
IMPH H42
DONO H42
DONO H2'
DONO H41
C2'
C3'
C4'
O4'
O5'
O5'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2
CN3
HN3
CN1
ON1C
NN3
CN2
NN1
HN1
HN1
CN3
HN3
-0.13
0.05
0.17
0.52
-0.49
-0.66
0.65
-0.75
0.37
0.33
-0.13
0.07
CN7B
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
CN7
0.01
HN7
0.09
ON2
-0.57
O1P
P
C5'
C5'
N1
C1'
N3
C4
C5
C2'
O2'
O2'
H1'
C2'
H5''
C5
O2
C5
N1
N3
C2
C4
H41 N4
N4
O2'
N4
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
-115.0
115.0
115.0
-115.0
-115.0
115.0
0.0
0.0
0.0
0.0
0.0
0.0
H42
\
0.0
0.0
0.0
0.0
0.0
0.0
H41
/
N4
|
C4
/
H5-C5
||
H6-C6
\
\\
N3
|
C2
/ \\
N1
O2
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
O2P
C4'
C2'
N4
C3'
H2'
H2''
H5
C6
N4
P
C4'
N1
N4
C3'
O5'
O4'
C2
H41
O3'
C3'
C6
N3
N3
H3'
H6
C4
C5
C4
C4'
N1
N4
O3'
C3'
C6
H42
+P
O4'
C1'
C4'
H4'
C5'
H5'
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
O2
N3
O1P
O2P
O2'
O3'
O4'
O5'
-O3'
-O3'
-O3'
P
O5'
C5'
C4'
C3'
O4'
C2'
C4'
C3'
O4'
C1'
C2
C6
N1
N1
C5
N3
H41
C6
N1
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
RESI THY
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N1
ATOM C6
C2
P
P
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C2
N1
N1
N3
C2
N3
C4
C4
C4
C5
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N1
*N1
C6
C2
*C2
N3
*C4
N4
*N4
*C5
*C6
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N1
C2
C6
C5
N3
O2
C4
N4
H41
H42
H5
H6
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2B
CN3
-0.34
0.17
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.399
1.364
1.399
1.399
1.426
1.337
1.01
0.0
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
117.79
120.6
120.6
118.9
118.9
121.8
117.9
118.9
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0
-46.90
-115.82
115.90
-146.00
60.00
140.00
155.00
-95.20
-120.04
-124.08
-30.00
147.89
-97.2
-180.00
0.0
0.0
180.0
0.0
180.00
0.00
180.00
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
125.59
120.6
121.0
118.9
121.9
120.0
118.9
118.9
120.7
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
H51
O4
|
||
H52-C5M
C4
H3
| \ / \ /
H53 C5
N3
||
|
H6-C6
C2
\ / \\
N1
O2
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
1.4401
1.4802
1.4801
1.5160
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3783
1.364
1.337
1.356
1.237
1.334
1.337
1.01
1.01
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
!alpha
!beta
!gamma
!delta
!epsilon
!zeta
!chi
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM C5M
ATOM H51
ATOM H52
ATOM H53
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
BOND C2
BOND C5
BOND C2'
BOND C1'
BOND C5'
BOND C2
IMPH O2
DONO H3
DONO H2'
ACCE O2
ACCE O4
ACCE O1P
ACCE O2P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3T
CN9
HN9
HN9
HN9
0.17
0.51
-0.41
-0.46
0.36
0.50
-0.45
-0.15
-0.11
0.07
0.07
0.07
CN7B
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C2
N1
-O3'
-O3'
-O3'
P
O5'
C5'
C4'
C3'
O4'
C2'
C4'
C3'
O4'
C1'
C2
CN7
0.01
HN7
0.09
ON2
-0.57
O1P
P
C5'
C5'
N1
C1'
N3
N3
C5M
C2'
O2'
O2'
H1'
C2'
H5''
C6
O2
C4
N1
N3
C2
N3
O2'
C2
C4
P
P
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N1
*N1
C6
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N1
C2
C6
C5
!
!
!
!
!
!
!
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
O2P
C4'
C2'
H3
C3'
H2'
H2''
H6
O4
O4
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.3746
P
C4'
N1
N3
C3'
O5'
O4'
C2
C4
O3'
C3'
C5M
C5
N3
H3'
H51
C6
C5
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
117.06
122.08
C4' C3'
N1
C6
C4
C5
O3' +P
C4'
C5M
C4
-46.90
-115.82
115.90
-146.00
60.00
140.00
155.00
-95.20
-120.04
-124.08
-30.00
147.89
-97.2
-179.96
-0.02
H4'
H52
C5M
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
125.59
122.08
121.23
C4
O4'
C1'
C5'
C5M
H5'
H53
C6
C5
1.4401 !alpha
1.4802
1.4801
1.5160 !beta
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3783 !chi
1.3704
1.3432
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
C6
N1
N1
C5
C2
C4
N1
C6
C5
H51
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
RESI URA
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM C5'
ATOM H5'
ATOM H5''
GROUP
ATOM C4'
ATOM H4'
ATOM O4'
ATOM C1'
ATOM H1'
GROUP
ATOM N1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM H5
GROUP
ATOM C2'
ATOM H2''
ATOM O2'
ATOM H2'
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
BOND P
BOND O5'
BOND C1'
N1
N3
C2
N3
C4
C6
C5
C5
H51
H52
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
C2
*C2
N3
*C4
*N3
*C5
*C6
C5M
*C5M
*C5M
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
N3
O2
C4
O4
H3
C5M
H6
H51
H52
H53
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
P
ON3
ON3
ON2
CN8B
HN8
HN8
-1.00
1.50
-0.78
-0.78
-0.57
-0.08
0.09
0.09
CN7
HN7
ON6B
CN7B
HN7
0.16
0.09
-0.50
0.16
0.09
NN2B
CN3
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3
HN3
-0.34
0.20
0.14
0.55
-0.45
-0.46
0.36
0.53
-0.48
-0.15
0.10
CN7B
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
CN7
HN7
ON2
O1P
C5'
N1
0.01
0.09
-0.57
P
C5'
C1'
1.3704
1.3746
1.3746
1.4439
1.3813
1.4439
0.0
0.0
0.0
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
122.08
115.38
115.38
114.07
126.46
120.78
0.0
0.0
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.
0.06
-179.95
-0.07
179.98
180.00
-179.94
180.0
0.0
115.0
-115.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
115.38
121.70
126.46
120.59
116.77
121.63
0.0
0.0
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
O4
||
C4
/
H5-C5
||
H6-C6
\
1.3813
1.2191
1.3795
1.2327
1.0900
1.5000
0.0
0.0
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
H3
\
/
N3
|
C2
/ \\
N1
O2
\
\
\
O1P
H5' H4' O4' \
|
|
\ /
\ \
-P-O5'-C5'---C4'
C1'
|
|
\
/ \
O2P
H5''
C3'--C2' H1'
/ \
/ \
O3' H3' O2' H2''
|
|
H2'
O2P
C4'
C2'
P
C4'
N1
O5'
O4'
C2
C4'
N1
C3'
C6
O4'
C1'
BOND
BOND
BOND
BOND
BOND
BOND
IMPH
DONO
DONO
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
ACCE
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
BILD
C2
C2'
C2'
C1'
C5'
C2
O2
H3
H2'
O2
O4
O1P
O2P
O2'
O3'
O4'
O5'
-O3'
-O3'
-O3'
P
O5'
C5'
C4'
C3'
O4'
C2'
C4'
C3'
O4'
C1'
C2
C6
N1
N1
C5
C2
C6
N1
C1'
H2'
O4'
C1'
C2'
C3'
C4'
C4'
N3
C3'
O2'
H1'
H5''
O2
N1
N3
N3
O2'
C2
C4
P
P
N3
C3'
O2'
C2'
C5
C4
C2
P
O5'
O5'
O5'
C5'
C4'
C3'
O3'
C3'
C4'
C3'
C2'
C1'
C2
N1
N1
N3
C2
N3
C4
C4
C5
C3'
O2'
C2'
C3'
C4'
O4'
O5'
O5'
C5'
O1P
O2P
C4'
C3'
O3'
+P
+O5'
C5'
O3'
C1'
N1
C2
C6
C5
N3
O2
C4
O4
H3
H5
H6
O2'
C3'
H1'
H2''
H3'
H4'
H5'
H5''
O5'
*P
*P
C5'
C4'
C3'
O3'
+P
*C4'
*C3'
C2'
C1'
N1
*N1
C6
C2
*C2
N3
*C4
*N3
*C5
*C6
*C2'
C2'
*C1'
*C2'
*C3'
*C4'
*C5'
*C5'
H3
O3'
H2'
H2''
H5
O4
O4
1.6001
1.6001
1.6001
1.5996
1.4401
1.5160
1.5284
1.4212
1.4572
1.5284
1.5284
1.5284
1.5251
1.4896
1.379
1.380
1.379
1.379
1.440
1.373
0.0
0.0
1.5284
0.9600
0.0
0.0
0.0
0.0
0.0
0.0
N3
O3'
C4
+P
C4
C5
C3'
C6
C5
N3
H3'
H6
C6
C5
C4'
H4'
101.45
101.45
101.45
119.00
108.83
116.10
111.92
119.05
104.06
100.16
100.16
101.97
113.71
117.06
121.3
121.3
114.8
114.8
114.7
127.0
0.0
0.0
102.04
114.97
0.0
0.0
0.0
0.0
0.0
0.0
C5'
C4
-39.25
-115.82
115.90
-151.39
-179.85
76.70
159.13
-98.86
-120.04
-124.08
39.58
144.39
-96.0
-180.0
0.0
0.0
-180.0
0.0
180.0
180.0
180.0
180.0
-114.67
148.63
-115.0
115.0
115.0
-115.0
-115.0
115.0
119.00
109.74
109.80
110.04
116.10
115.12
119.05
101.45
116.10
115.12
102.04
113.71
117.06
121.3
122.8
114.8
122.0
127.0
119.8
116.5
0.0
0.0
110.81
111.92
0.0
0.0
0.0
0.0
0.0
0.0
1.4401
1.4802
1.4801
1.5160
1.5284
1.4212
1.6001
1.5996
1.5160
1.4212
1.5251
1.4896
1.3746
1.379
1.338
1.373
1.218
1.383
1.227
1.03
0.0
0.0
1.4212
1.5284
0.0
0.0
0.0
0.0
0.0
0.0
! Selected patches to create DNA, and individual bases included
! methylated analogs
!
!
!
!
!
!
NOTE the option to regenerate all angles and dihedrals allows
the explicit inclusion of the THET and DIHE terms to be omitted
even if the PRES is used in a PATCH statement. It is important to
inspect the patches prior to use to determine if they should be used
in a GENErate or PATCh statement and/or if the AUTOgeneration of
angles and dihedrals is required.
H5'
! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
! documentation
PRES DEO1
DELETE ATOM O2'
GROUP !
ATOM C4' CN7
ATOM H4' HN7
ATOM O4' ON6
ATOM C1' CN7B
ATOM H1' HN7
GROUP
ATOM C2' CN8
ATOM H2' HN8
ATOM H2'' HN8
BOND
THET
DIHE
DIHE
BILD
C2'
C1'
H2'
H2'
C1'
H2'
C2'
C2'
C2'
C3'
PRES DEO2
DELETE ATOM O2'
GROUP !
ATOM C4' CN7
ATOM H4' HN7
ATOM O4' ON6
ATOM C1' CN7B
ATOM H1' HN7
GROUP
ATOM C2' CN8
ATOM H2' HN8
ATOM H2'' HN8
BOND
THET
DIHE
DIHE
BILD
C2'
C1'
H2'
H2'
C1'
PRES PYRC
H2'
C2'
C2'
C2'
C3'
0.000 ! Patch to make DEOXYribose in PYRIMIDINES
! necessary due to auto-generate dihedrals
0.16
0.09
-0.50
0.16
0.09
!
!
!
!
!
-0.18
0.09
0.09
H2'
C3' C2' H2'
H2' C2' H2''
C1' O4'
H2' C2' C1' N1
H2' C2'
C3' C4'
H2' C2' C3' O3'
H2' C2'
*C2' H2' 0.0 0.0 -115.0 0.0 0.0
C1'
C3'
H1'
H3'
0.000 ! Patch to make DEOXYribose in PURINES
! necessary due to auto-generate dihedrals
0.16
0.09
-0.50
0.16
0.09
!
!
!
!
!
-0.18
0.09
0.09
H2'
C3' C2' H2'
H2' C2' H2''
C1' O4'
H2' C2' C1' N9
H2' C2'
C3' C4'
H2' C2' C3' O3'
H2' C2'
*C2' H2' 0.0 0.0 -115.0 0.0 0.0
0.00 ! Patch to generate CYTOSINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
C1'
C3'
H1'
H3'
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM H1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM C4
ATOM N4
ATOM H41
ATOM H42
ATOM C5
ATOM H5
BOND N1
IMPH H1
BILD C5
H2''
O2'
H2'
C3'
O3'
H3'
NN2
-0.50
HN2
0.37
CN3
0.05
HN3
0.17
CN1
0.52
ON1C
-0.49
NN3
-0.66
CN2
0.65
NN1
-0.75
HN1
0.37
HN1
0.33
CN3
-0.13
HN3
0.07
H1
C6
C2
N1
C6
N1
H1
PRES PYRU
0.00
PRES PYRT
0.00
0.0 0.0 180.0 0.0 0.0
! Patch to generate URACIL base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM N1
NN2B
-0.82 !
ATOM H1
HN2
0.48 !
ATOM C6
CN3
0.20 !
ATOM H6
HN3
0.14 !
BOND N1
H1
BILD C5
C6
N1
H1
0.0 0.0 180.0 0.0 0.0
! Patch to generate THYMINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM H1
ATOM C6
ATOM H6
BOND N1
BILD C5
PRES PURG
P
O1P
O2P
O5'
C5'
H5'
H5''
C4'
H4'
O4'
C1'
H1'
C2'
H2''
O2'
H2'
C3'
O3'
H3'
NN2B
-0.80
HN2
0.46
CN3
0.17
HN3
0.17
H1
C6
N1
H1
!
!
!
!
0.0 0.0 180.0 0.0 0.0
0.00 ! Patch to generate GUANINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM N9
NN2B
-0.38 !
ATOM C4
CN5
0.26 !
ATOM H9
HN2
0.36 !
ATOM N3
NN3G
-0.74 !
ATOM C2
CN2
0.75 !
ATOM N1
NN2G
-0.34 !
ATOM H1
HN2
0.26 !
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
BOND
IMPH
BILD
N2
H21
H22
C6
O6
C5
N7
C8
H8
N9
H9
C5
NN1
-0.68 !
HN1
0.32 !
HN1
0.35 !
CN1
0.54 !
ON1
-0.51 !
CN5G
0.00 !
NN4
-0.60 !
CN4
0.25 !
HN3
0.16 !
H9
C8 C4 N9
C4 N9 H9 0.0
0.0
180.0 0.0 0.0
PRES PURA
0.00 ! Patch to generate ADENINE base
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM C5
CN5
0.28
ATOM N7
NN4
-0.71
ATOM C8
CN4
0.34
ATOM H8
HN3
0.12
ATOM N9
NN2
-0.37
ATOM H9
HN2
0.32
ATOM N1
NN3A
-0.74
ATOM C2
CN4
0.50
ATOM H2
HN3
0.13
ATOM N3
NN3A
-0.75
ATOM C4
CN5
0.43
ATOM C6
CN2
0.46
ATOM N6
NN1
-0.77
ATOM H61 HN1
0.38
ATOM H62 HN1
0.38
BOND N9
H9
BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0
PRES 5TER
GROUP
0.00
! 5'-terminal HYDROXYL patch
! use in generate statement
ATOM H5T HN5
0.43
ATOM O5' ON5
-0.66
ATOM C5' CN8B
0.05
ATOM H5' HN8
0.09
ATOM H5'' HN8
0.09
!
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
!
BOND H5T
O5'
DONO H5T
O5'
BILD H5T O5'
C5' C4'
PRES 5PHO
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM O5T
ATOM H5T
BOND O5T
DONO H5T
BILD C4'
BILD C5'
BILD O5T
BILD O5T
BILD H5T
-1.00
CN8B
HN8
HN8
P
ON3
ON3
ON2
ON4
HN4
P
O5T
C5'
O5'
O5'
O5'
O5T
PRES 5POM
GROUP
ATOM C5'
ATOM H5'
ATOM H5''
ATOM P
ATOM O1P
ATOM O2P
ATOM O5'
ATOM O5T
ATOM C5T
ATOM H5T1
ATOM H5T2
ATOM H5T3
BOND
BOND
BILD
BILD
BILD
BILD
BILD
O5T
C5T
C4'
C5'
O5T
O5T
C5T
P
0.00
180.00
0.00
0.0000
! 5'terminal PHOSPHATE patch
! use in generate statement
-0.08
0.09
0.09
1.50
-0.82
-0.82
-0.62
-0.68
0.34
H5T O5T
O5'
P
*P
*P
P
P
O5T
O1P
O2P
O5'
-1.00
CN8B
HN8
HN8
P
ON3
ON3
ON2
ON2
CN9
HN9
HN9
HN9
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
000.00 -146.00
000.00 -46.90
000.00 -115.82
000.00 115.90
000.00 -95.20
000.00
000.00
000.00
000.00
000.00
0.0000
0.0000
0.0000
0.0000
0.0000
! 5'terminal Methyl-Phosphate patch
! use in generate statement
-0.08
0.09
0.09
1.50
-0.78
-0.78
-0.57
-0.57
-0.17
0.09
0.09
0.09
O5T
H5T3
C5' O5'
O5' P
O5' *P
O5' *P
O5T P
C5T
P
O5T
O1P
O2P
O5'
C5T
0.0000
0.0000
0.0000
0.0000
0.0000
H5T1
C5T
000.00 -146.00
000.00 -46.90
000.00 -115.82
000.00 115.90
000.00 -95.20
H5T2
000.00
000.00
000.00
000.00
000.00
0.0000
0.0000
0.0000
0.0000
0.0000
BILD H5T1
BILD H5T2
BILD H5T3
C5T
C5T
C5T
PRES 3TER
GROUP
ATOM C3'
ATOM H3'
ATOM O3'
ATOM H3T
BOND O3'
DONO H3T
BILD H3T
PRES 3PHO
O5T
O5T
O5T
P
P
P
0.00
CN7
HN7
ON5
HN5
H3T
O3'
O3'
0.0000
0.0000
0.0000
000.00
000.00
000.00
180.20
60.00
-60.00
0.0000
0.0000
0.0000
! 3'terminal HYDROXYL patch
! use in generate statement
0.14
0.09
-0.66
0.43
C3'
C4'
-1.00
0.9600
114.97
148.63
0.000
111.92
1.5284
! 3'terminal PHOSPHATE patch
! use in generate statement
GROUP
ATOM C3' CN7
0.01
ATOM H3' HN7
0.09
ATOM P3
P
1.50
ATOM O1P3 ON3
-0.82
ATOM O2P3 ON3
-0.82
ATOM O3' ON2
-0.62
ATOM O3T ON4
-0.68
ATOM H3T HN4
0.34
BOND O3' P3
P3 O1P3
P3 O2P3
P3 O3T O3T
DONO H3T O3T
ACCE O3T
ACCE O1P2
ACCE O1P3
! Build in B-DNA-like conformation (NF)
BILD C4'
C3' O3' P3
0.0000 000.00 155.00
BILD C3'
O3' P3 O3T
0.0000 000.00 -95.20
BILD O3T
O3' *P3 O1P3
0.0000 000.00 -115.82
BILD O3T
O3' *P3 O2P3
0.0000 000.00 115.90
BILD H3T
O3T P3 O3'
0.0000 000.00 -46.90
PRES 9MG
000.00
000.00
000.00
! 9-Methyl guanine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
H3T
000.00
000.00
000.00
000.00
000.00
0.0000
0.0000
0.0000
0.0000
0.0000
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N9
ATOM C4
ATOM C9
ATOM N3
ATOM C2
ATOM N1
ATOM H1
ATOM N2
ATOM H21
ATOM H22
ATOM C6
ATOM O6
ATOM C5
ATOM N7
ATOM C8
ATOM H8
ATOM H91
ATOM H92
ATOM H93
BOND N9
BILD C8
BILD C8
BILD N9
BILD H91
PRES 9EG
C3'
O3'
H3'
NN2B
CN5
CN9
NN3G
CN2
NN2G
HN2
NN1
HN1
HN1
CN1
ON1
CN5G
NN4
CN4
HN3
HN9
HN9
HN9
C9
C4
N9
H91
H92
-0.02
0.26
-0.27
-0.74
0.75
-0.34
0.26
-0.68
0.32
0.35
0.54
-0.51
0.00
-0.60
0.25
0.16
0.09
0.09
0.09
C9
H91
*N9 C9
C9
H91
*C9 H92
*C9 H93
0.000
C9 H92
0.0
0.0
0.0
0.0
C9
0.0
0.0
0.0
0.0
H93
180.0
180.0
-115.0
115.0
! 9-Ethyl guanine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM C9
CN8 -0.18
ATOM H91 HN8
0.09
ATOM H92 HN8
0.09
GROUP
ATOM C9B CN9 -0.27
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
ATOM
ATOM
ATOM
BOND
BOND
BILD
BILD
BILD
BILD
BILD
BILD
BILD
H9B1
H9B2
H9B3
N9
C9
C8
C8
N9
C9B
N9
C9
H9B1
PRES 9MA
HN9
HN9
HN9
C9
C9B
C4
N9
C9B
H91
C9
H9B1
H9B2
0.09
0.09
0.09
C9
H91
C9B H9B1
*N9 C9
C9
C9B
*C9 H91
*C9 H92
C9B H9B1
*C9B H9B2
*C9B H9B3
0.00
C9 H92
C9B H9B2
0.0
0.0
0.0
0.0
0.0
0.0
0.0
C9
C9B
0.0
0.0
0.0
0.0
0.0
0.0
0.0
H93
H9B3
180.0
0.0
-115.0
115.0
180.0
-115.0
115.0
! 9-Methyl adenine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
! all atoms included in patch to get correct atom
! order to simplify analysis
GROUP
ATOM C5
CN5
0.28
ATOM N7
NN4 -0.71
ATOM C8
CN4
0.34
ATOM H8
HN3
0.12
ATOM N9
NN2 -0.05
ATOM C9
CN9 -0.27
ATOM N1
NN3A -0.74
ATOM C2
CN4
0.50
ATOM H2
HN3
0.13
ATOM N3
NN3A -0.75
ATOM C4
CN5
0.43
ATOM C6
CN2
0.46
ATOM N6
NN1 -0.77
ATOM H61 HN1
0.38
ATOM H62 HN1
0.38
ATOM H91 HN9
0.09
ATOM H92 HN9
0.09
ATOM H93 HN9
0.09
BOND N9
C9
C9
H91
C9 H92
C9
H93
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
BILD
BILD
BILD
BILD
C8
C4
N9
H91
PRES 1MC
C4
N9
H91
H92
*N9
C9
*C9
*C9
C9
H91
H92
H93
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
180.0
180.0
-115.0
115.0
! 1-Methyl Cytosine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
DELE ATOM O2'
DELE ATOM H2'
DELE ATOM C3'
DELE ATOM O3'
DELE ATOM H3'
GROUP
ATOM N1
NN2
-0.13
ATOM C1
CN9
-0.27
ATOM C6
CN3
0.05
ATOM H6
HN3
0.17
ATOM C2
CN1
0.52
ATOM O2
ON1C
-0.49
ATOM N3
NN3
-0.66
ATOM C4
CN2
0.65
ATOM N4
NN1
-0.75
ATOM H41 HN1
0.37
ATOM H42 HN1
0.33
ATOM C5
CN3
-0.13
ATOM H5
HN3
0.07
ATOM H11 HN9
0.09
ATOM H12 HN9
0.09
ATOM H13 HN9
0.09
BOND N1
C1
C1
H11
C1 H12
C1
H13
BILD C6
C2
*N1 C1
0.0
0.0
180.0
BILD C2
N1
C1
H11
0.0
0.0
180.0
BILD N1
H11 *C1 H12
0.0
0.0 -115.0
BILD H11 H12 *C1 H13
0.0
0.0
115.0
PRES 1MT
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.000
0.00
! 1-Methyl Thymine patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM C1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM C5M
ATOM H51
ATOM H52
ATOM H53
ATOM H11
ATOM H12
ATOM H13
BOND N1
BILD C6
BILD C2
BILD N1
BILD H11
PRES 1MU
C5'
H5'
H5''
C4'
H4'
O4'
C1'
H1'
C2'
H2''
O2'
H2'
C3'
O3'
H3'
NN2B
CN9
CN3
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3T
CN9
HN9
HN9
HN9
HN9
HN9
HN9
C1
C2
N1
H11
H12
-0.34
-0.27
0.17
0.17
0.51
-0.41
-0.46
0.36
0.50
-0.45
-0.15
-0.11
0.07
0.07
0.07
0.09
0.09
0.09
C1
H11
*N1 C1
C1
H11
*C1 H12
*C1 H13
0.00
C1 H12
0.0
0.0
0.0
0.0
C1
0.0
0.0
0.0
0.0
H13
180.0
180.0
-115.0
115.0
! 1-Methyl Uracil patch
! use in generate statement
! DELETE PHOSPHATE AND RIBOSE ATOMS
DELE ATOM P
DELE ATOM O1P
DELE ATOM O2P
DELE ATOM O5'
DELE ATOM C5'
DELE ATOM H5'
DELE ATOM H5''
DELE ATOM C4'
DELE ATOM H4'
DELE ATOM O4'
DELE ATOM C1'
DELE ATOM H1'
DELE ATOM C2'
DELE ATOM H2''
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
DELE ATOM
GROUP
ATOM N1
ATOM C1
ATOM C6
ATOM H6
ATOM C2
ATOM O2
ATOM N3
ATOM H3
ATOM C4
ATOM O4
ATOM C5
ATOM H5
ATOM H11
ATOM H12
ATOM H13
BOND N1
BILD C6
BILD C2
BILD N1
BILD H11
O2'
H2'
C3'
O3'
H3'
NN2B
CN9
CN3
HN3
CN1T
ON1
NN2U
HN2
CN1
ON1
CN3
HN3
HN9
HN9
HN9
C1
C2
N1
H11
H12
-0.34
-0.27
0.20
0.14
0.55
-0.45
-0.46
0.36
0.53
-0.48
-0.15
0.10
0.09
0.09
0.09
C1
H11
*N1 C1
C1
H11
*C1 H12
*C1 H13
C1 H12
0.0
0.0
0.0
0.0
C1
0.0
0.0
0.0
0.0
H13
180.0
180.0
-115.0
115.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
! Model compounds used for parameter optimization
RESI THF
0.00 ! tetrahydrofuran
!
! Figure 3A, interaction with water
!
GROUP
ATOM O4' ON6
-0.50 !
H41' O4' H11'
ATOM C4' CN8
0.07 !
\ / \ /
ATOM C3' CN8
-0.18 !
H42'--C4' C1'--H12'
ATOM C2' CN8
-0.18 !
|
|
ATOM C1' CN8
0.07 !
H31'--C3'--C2'--H21'
ATOM H11' HN8
0.09 !
/
\
ATOM H12' HN8
0.09 !
H32'
H22'
ATOM H21' HN8
0.09 !
ATOM H22' HN8
0.09 !
ATOM H31' HN8
0.09 !
ATOM H32' HN8
0.09 !
ATOM H41' HN8
0.09 !
ATOM H42' HN8
0.09 !
BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'
BOND C1' H11'
C1' H12' C2' H21' C2' H22' C3' H31' C3'
BOND C4' H41' C4' H42'
PATC FIRS NONE LAST NONE
RESI THFO
0.00 ! 3'-hydroxyl-tetrahydrofuran
!
! Figure 3B, interaction with water
!
H32'
GROUP
ATOM O4'
ATOM C1'
ATOM C2'
ATOM C4'
ATOM H11'
ATOM H12'
ATOM H21'
ATOM H22'
ATOM H41'
ATOM H42'
GROUP
ATOM C3'
ATOM H31'
ATOM O3'
ATOM H32'
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
ON6
CN7B
CN8
CN7
HN7
HN7
HN8
HN8
HN7
HN7
-0.50
0.07
-0.18
0.07
0.09
0.09
0.09
0.09
0.09
0.09
CN7
HN7
ON5
HN5
0.14
0.09
-0.66
0.43
!
!
!
!
!
!
!
!
!
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
H32'
C1' O4' C1' C2' C2'
C1' H11' C1' H12' C2'
C4' H42' O3' H32'
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
H22'
C2'
C3'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
H32'
O3'
C3'
FIRS NONE LAST NONE
RESI DMPA
!
! Model compound
!
GROUP
ATOM P1
P
ATOM O3
ON3
ATOM O4
ON3
ATOM O1
ON2
ATOM O2
ON2
ATOM C1
CN9
ATOM H11 HN9
ATOM H12 HN9
ATOM H13 HN9
ATOM C2
CN9
ATOM H21 HN9
ATOM H22 HN9
ATOM H23 HN9
-1.00
BOND P1
BOND C1
P1
C1
O1
H11
C3' C3'
H21' C2'
C2'
C3'
C4'
O4'
C1'
C3'
C3'
C4'
C4'
O4'
C1'
C1'
O4'
C4'
C4' C4'
H22' C3'
1.4055
1.4127
1.5457
1.5346
1.5211
1.0856
1.0818
1.0846
1.0822
1.0806
1.0891
1.0808
1.4028
0.9492
O4' C3'
H31' C4'
108.09
23.45
106.18
3.96
103.11 -26.93
100.86
41.73
103.15 -41.62
111.62 123.53
113.32 -114.11
110.65
91.68
110.88 -148.45
113.53 162.89
110.89
77.76
108.72 -162.12
110.98 -77.39
108.72
44.80
O3'
H41'
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
110.98
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
1.5211
! Dimethylphosphate
A
1.500
-0.780
-0.780
-0.570
-0.570
-0.170
0.090
0.090
0.090
-0.170
0.090
0.090
0.090
O2
H12
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H11!
|
H13- C1-H12
\
O3
O1
\\ /
(-)
P1
// \
O4
O2
/
H23-C2-H22
|
H21
P1
C1
O3
H13
P1
C2
O4
H21
O1
C2
C1
H22
O2
C2
C2
H23
! IC FOR THE
IC O3
P1
IC O4
P1
IC O1
P1
IC O2
P1
IC H11 C1
IC H12 C1
IC H13 C1
IC H21 C2
IC H22 C2
IC H23 C2
g,g conformation (3-21G* opt.
O1
C1
1.4723
107.31
O2
C2
1.4722
000.0
O2
C2
1.6343
000.0
O1
C1
1.6344
000.0
O1
P1
1.0827
107.8
O1
P1
1.0800
110.4
O1
P1
1.0848
110.7
O2
P1
1.0827
107.9
O2
P1
1.0800
110.4
O2
P1
1.0848
110.7
RESI T5PH
!
! Model compound
!
GROUP
ATOM C5' CN8B
ATOM H5' HN8
ATOM H5'' HN8
ATOM O5' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3P ON4
ATOM H5T HN4
GROUP
ATOM O4' ON6
ATOM C1' CN7B
ATOM H1' HN7
ATOM H1'' HN7
ATOM C4' CN7
ATOM H4'' HN7
GROUP
ATOM C2' CN8
ATOM H2' HN8
ATOM H2'' HN8
GROUP
ATOM C3' CN7
ATOM H3' HN7
ATOM H3'' HN7
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
C1'
C1'
C4'
P
C4'
O4'
C1'
C2'
C3'
H1'
H1''
H2'
H2''
H3'
H3''
structure)
000.0
117.79
000.0
117.79
73.8
117.79
73.7
117.79
174.8
117.79
54.1
117.79
294.3
117.79
174.7
117.79
54.1
117.79
294.2
117.79
1.4356
1.4357
1.4357
1.4356
1.6343
1.6343
1.6343
1.6344
1.6344
1.6344
-1.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -1)
B
-0.08
0.09
0.09
-0.62
1.50
-0.82
-0.82
-0.68
0.34
-0.50
0.07
0.09
0.09
0.16
0.09
!
!
O1P
H5T
!
||
/
! O2P==P==O3P
!
|
!
O5'
!
|
! H5'' |
!
\ |
! H5'--C5'
O4' H1'
!
\ / \ /
!
H4'--C4' C1'--H1''
!
|
|
!
H3'--C3'--C2'--H2'
!
/
\
!
H3''
H2''
!
-0.18
0.09
0.09
-0.18
0.09
0.09
O4' C1'
H1' C1'
H4'' C5'
O2P P
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
C2'
C3'
C3'
C2'
H1''
H5'
O3P
C1'
C2'
C3'
C4'
O4'
C2'
C2'
C3'
C3'
C4'
C4'
C2'
C2'
C5'
O3P
C3' C3' C4' C4' O4' C4'
H2' C2' H2'' C3' H3' C3'
H5'' C5' O5' O5' P
P
H5T
C2'
1.4416 109.61
0.45
C3'
1.4471 106.74 -21.92
C4'
1.5328 103.38
33.49
O4'
1.5200 102.18 -34.11
C1'
1.5321 105.43
21.23
C3'
1.1099 113.03 -141.96
C3'
1.1111 111.16
93.50
C4'
1.1135 109.13 -81.76
C4'
1.1076 113.49 155.97
O4'
1.1127 108.68
81.68
O4'
1.1069 112.41 -156.66
C5'
H3''
O1P
106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
105.43
105.43
1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
1.4416
1.4416
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
H4''
C4'
C5'
C4'
H51'
C5'
H52'
C5'
O4'
C4'
O4'
C4'
O4'
C4'
C4'
C5'
C5'
O5'
C5'
O5'
C5'
O5'
O5'
P
FIRS NONE LAST
O4'
O4'
C4'
C4'
C5'
C5'
C5'
O5'
P
P
P
O3P
NONE
C1'
C1'
O4'
O4'
O5'
H5'
H5''
P
O1P
O2P
O3P
H5T
1.1127
1.5325
1.1092
1.1104
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
106.71
108.43
110.48
110.01
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
-95.75
144.82
180.00
-60.00
60.0
180.0
-60.0
180.0
-60.0
180.0
60.0
180.0
109.61
109.61
108.43
108.43
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
1.4471
1.4471
1.4416
1.4416
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
RESI TH5P
-2.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -2)
!
! Model compound B with dianionic phosphate, vibrational analysis
!
GROUP
!
O1P (-2)
ATOM O4' ON6
-0.50 !
||
ATOM C1' CN7B
0.07 ! O2P==P==O2P
ATOM H1' HN7
0.09 !
|
ATOM H1'' HN7
0.09 ! H5'' |
ATOM C4' CN7
0.16 !
\ |
ATOM H4'' HN7
0.09 ! H5'--C5'
O4' H1'
GROUP
!
\ / \ /
ATOM C2' CN8
-0.18 !
H4'--C4' C1'--H1''
ATOM H2' HN8
0.09 !
|
|
ATOM H2'' HN8
0.09 !
H3'--C3'--C2'--H2'
GROUP
!
/
\
ATOM C3' CN7
-0.18 !
H3''
H2''
ATOM H3' HN7
0.09 !
ATOM H3'' HN7
0.09
GROUP
ATOM C5' CN8B
-0.18
ATOM H5' HN8
0.09
ATOM H5'' HN8
0.09
GROUP
ATOM O5' ON2
-0.40
ATOM P
P
1.10
ATOM O1P ON3
-0.90
ATOM O2P ON3
-0.90
ATOM O3P ON3
-0.90
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
C1'
C1'
C4'
P
C4'
O4'
C1'
C2'
C3'
H1'
H1''
H2'
H2''
O4' C1'
H1' C1'
H4'' C5'
O2P P
O4'
C1'
C2'
C3'
C4'
C1'
C1'
C2'
C2'
C2' C2' C3' C3' C4' C4' O4' C4'
H1'' C2' H2' C2' H2'' C3' H3' C3'
H5' C5' H5'' C5' O5' O5' P
P
O3P
C1'
C2'
1.4416 109.61
0.45
C2'
C3'
1.4471 106.74 -21.92
C3'
C4'
1.5328 103.38
33.49
C4'
O4'
1.5200 102.18 -34.11
O4'
C1'
1.5321 105.43
21.23
C2'
C3'
1.1099 113.03 -141.96
C2'
C3'
1.1111 111.16
93.50
C3'
C4'
1.1135 109.13 -81.76
C3'
C4'
1.1076 113.49 155.97
C5'
H3''
O1P
106.74
103.38
102.18
105.43
109.61
103.38
103.38
102.18
102.18
1.5328
1.5200
1.5321
1.4416
1.4471
1.5200
1.5200
1.5321
1.5321
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
H3'
C3'
H3''
C3'
H4''
C4'
C5'
C4'
H51'
C5'
H52'
C5'
O4'
C4'
C4'
C5'
C5'
O5'
C5'
O5'
C5'
O5'
FIRS NONE LAST
RESI T3PH
!
! Model compound
!
GROUP
ATOM O4' ON6
ATOM C1' CN7B
ATOM H11' HN7
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN8
ATOM H21' HN8
ATOM H22' HN8
GROUP
ATOM C3' CN7
ATOM H31' HN7
ATOM O3' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3T ON4
ATOM H3T HN4
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
C4'
C4'
O4'
O4'
C4'
C4'
C5'
O5'
P
P
P
NONE
O4'
O4'
C1'
C1'
O4'
O4'
O5'
P
O1P
O2P
O3P
1.1127
1.1069
1.1127
1.5325
1.1092
1.1104
0.0
0.0
0.0
0.0
0.0
108.68
81.68
112.41 -156.66
106.71 -95.75
108.43 144.82
110.48 180.00
110.01 -60.00
0.0
60.00
0.0
180.0
0.0
-60.0
0.0
180.0
0.0
60.0
105.43
105.43
109.61
109.61
108.43
108.43
0.0
0.0
0.0
0.0
0.0
1.4416
1.4416
1.4471
1.4471
1.4416
1.4416
0.0
0.0
0.0
0.0
0.0
-1.00 ! monoanionic 3'phosphate-tetrahydrofuran
C
-0.50
0.07
0.09
0.09
0.07
0.09
0.09
-0.18
0.09
0.09
0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.68
0.34
C1' O4' C1'
C1' H11' C1'
C4' H42' O3'
C4'
O4'
O4'
C1'
C1'
C2'
C2'
C3'
C3'
C4'
H11'
C1'
H12'
C1'
H21'
C2'
H22'
C2'
H31'
C3'
H41'
C4'
H42'
C4'
O3'
C3'
P
O3'
O1P
P
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
O1P==P==O2P
|
O3T (-1)
\
H3T
C2' C2' C3' C3' C4' C4' O4' C3'
H12' C2' H21' C2' H22' C3' H31' C4'
P
P
O1P P
O2P P
O3T O3T
C1'
C2'
1.4055 108.09
23.45
C2'
C3'
1.4127 106.18
3.96
C3'
C4'
1.5457 103.11 -26.93
C4'
O4'
1.5346 100.86
41.73
O4'
C1'
1.5211 103.15 -41.62
C2'
C3'
1.0856 111.62 123.53
C2'
C3'
1.0818 113.32 -114.11
C3'
C4'
1.0846 110.65
91.68
C3'
C4'
1.0822 110.88 -148.45
C4'
O4'
1.0806 113.53 162.89
O4'
C1'
1.0891 110.89
77.76
O4'
C1'
1.0808 108.72 -162.12
C4'
O4'
1.4028 110.98 -77.39
C3'
C4'
0.0
0.0
180.00
O3'
C3'
0.0
0.0
-60.0
O3'
H41'
H3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
IC
O2P
P
IC
O3T
P
IC
H3T
O3T
PATC FIRS NONE LAST
RESI R3PH
!
! Model compound
!
GROUP
ATOM O4' ON6B
ATOM C1' CN7B
ATOM H11' HN7
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN7B
ATOM H21' HN7
ATOM O2' ON5
ATOM H22' HN5
GROUP
ATOM C3' CN7
ATOM H31' HN7
ATOM O3' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3T ON4
ATOM H3T HN4
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
O3'
O3'
P
NONE
C3'
C3'
O3'
0.0
0.0
0.0
60.0
180.0
180.0
0.0
0.0
0.0
0.0
0.0
0.0
-1.00 ! monoanionic 3'phosphate-tetrahydrofuran
C, monoanionic with 2'hydroxyl
-0.50
0.07
0.09
0.09
0.07
0.09
0.09
0.14
0.09
-0.66
0.43
0.01
0.09
-0.62
1.50
-0.82
-0.82
-0.68
0.34
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H41' O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
O2'
|
|
O1P==P==O2P
H22'
|
O3T (-1)
\
H3T
C1' O4' C1' C2' C2'
C1' H11' C1' H12' C2'
C4' H42' O3' P
P
C4'
O4'
C1'
O4'
C1'
C2'
C1'
C2'
C3'
C2'
C3'
C4'
C3'
C4'
O4'
H11'
C1'
C2'
H12'
C1'
C2'
H21'
C2'
C3'
O2'
C2'
C3'
H22'
O2'
C2'
H31'
C3'
C4'
H41'
C4'
O4'
H42'
C4'
O4'
O3'
C3'
C4'
P
O3'
C3'
O1P
P
O3'
O2P
P
O3'
O3T
P
O3'
H3T
O3T
P
FIRS NONE LAST NONE
RESI T3PM
0.0
0.0
0.0
C3' C3' C4'
H21' C2' O2'
O1P P
O2P
C2'
1.4055
C3'
1.4127
C4'
1.5457
O4'
1.5346
C1'
1.5211
C3'
1.0856
C3'
1.0818
C4'
1.0846
C4'
1.0822
C3'
1.0822
O4'
1.0806
C1'
1.0891
C1'
1.0808
O4'
1.4028
C4'
0.0
C3'
0.0
C3'
0.0
C3'
0.0
O3'
0.0
C4' O4' C3'
O2' H22' C3'
P
O3T O3T
108.09
23.45
106.18
3.96
103.11 -26.93
100.86
41.73
103.15 -41.62
111.62 123.53
113.32 -114.11
110.65
91.68
110.88 283.41
110.88
0.00
113.53 162.89
110.89
77.76
108.72 -162.12
110.98 -77.39
0.0
180.00
0.0
-60.0
0.0
60.0
0.0
180.0
0.0
180.0
O3'
H31' C4'
H3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
100.86
103.15
108.09
108.09
103.15
0.0
0.0
0.0
0.0
0.0
H41'
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0
0.0
0.0
0.0
0.0
-1.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1)
!
! Model compound
!
GROUP
ATOM O4' ON6
ATOM C1' CN7B
ATOM H11' HN7
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN8
ATOM H21' HN8
ATOM H22' HN8
GROUP
ATOM C3' CN7
ATOM H31' HN7
GROUP
ATOM O3' ON2
ATOM P
P
ATOM O1P ON3
ATOM O2P ON3
ATOM O3T ON2
ATOM C3T CN8B
ATOM H3T1 HN8
ATOM H3T2 HN8
ATOM H3T3 HN8
BOND
BOND
BOND
BOND
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
D
-0.50
0.07
0.09
0.09
0.07
0.09
0.09
-0.18
0.09
0.09
0.01
0.09
-0.57
1.50
-0.78
-0.78
-0.57
-0.17
0.09
0.09
0.09
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
H41'
O4' H11'
\ / \ /
H42'--C4' C1'--H12'
|
|
H31'--C3'--C2'--H21'
/
\
O3'
H22'
|
O1P==P==O2P
|
O3T (-1)
\
C3T--H3T3
/ \
H3T1 H3T2
C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3'
C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4'
C4' H42' O3' P
P
O1P P
O2P P
O3T O3T
C3T H3T1
C3T H3T2 C3T H3T3
C4'
O4'
C1'
C2'
1.4055 108.09
23.45
O4'
C1'
C2'
C3'
1.4127 106.18
3.96
C1'
C2'
C3'
C4'
1.5457 103.11 -26.93
C2'
C3'
C4'
O4'
1.5346 100.86
41.73
C3'
C4'
O4'
C1'
1.5211 103.15 -41.62
H11'
C1'
C2'
C3'
1.0856 111.62 123.53
H12'
C1'
C2'
C3'
1.0818 113.32 -114.11
H21'
C2'
C3'
C4'
1.0846 110.65
91.68
H22'
C2'
C3'
C4'
1.0822 110.88 -148.45
H31'
C3'
C4'
O4'
1.0806 113.53 162.89
H41'
C4'
O4'
C1'
1.0891 110.89
77.76
H42'
C4'
O4'
C1'
1.0808 108.72 -162.12
O3'
C3'
C4'
O4'
1.4028 110.98 -77.39
P
O3'
C3'
C4'
0.0000 000.00 180.00
C3'
O3'
P
O3T
0.0000 000.00 -95.22
O3T
O3'
*P
O1P
0.0000 000.00 -115.82
O3T
O3'
*P
O2P
0.0000 000.00 115.90
C3T
O3T
P
O3'
0.0000 000.00 -46.90
H3T1
C3T
O3T
P
0.0000 000.00 180.00
H3T2
C3T
O3T
P
0.0000 000.00
60.00
H3T3
C3T
O3T
P
0.0000 000.00 -60.00
FIRS NONE LAST NONE
RESI THFI
0.00
! imidazole analog with THF ring
O3'
H41'
C3T
106.18
103.11
100.86
103.15
108.09
103.11
103.11
100.86
100.86
103.15
108.09
108.09
103.15
000.00
000.00
000.00
000.00
000.00
000.00
000.00
000.00
1.5457
1.5346
1.5211
1.4055
1.4127
1.5346
1.5346
1.5211
1.5211
1.4055
1.4127
1.4127
1.4055
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
!
! Model compound E, with imidazole
!
GROUP
ATOM O4' ON6
-0.50 !
H41' O4' Imidazole
ATOM C1' CN7B
0.16 !
\ / \ /
ATOM H12' HN7
0.09 !
H42'--C4' C1'--H12'
ATOM C4' CN7
0.07 !
|
|
ATOM H41' HN7
0.09 !
H31'--C3'--C2'--H21'
ATOM H42' HN7
0.09 !
/
\
GROUP
!
H32'
H22'
ATOM C2' CN8
-0.18 !
ATOM H21' HN8
0.09 !
ATOM H22' HN8
0.09 !
GROUP
!
ATOM C3' CN7
-0.18 !
ATOM H31' HN7
0.09 !
ATOM H32' HN7
0.09 !
GROUP ! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG
CPH1 -0.05 !
C1'
HE1
ATOM HG
HR3
0.09 !
\
/
ATOM CD2 CPH1
0.22 !
ND1---CE1
ATOM HD2 HR3
0.10 !
/
|
ATOM ND1 NR1
-0.04 ! HG-CG
|
ATOM CE1 CPH2
0.25 !
\
|
ATOM HE1 HR1
0.13 !
CD2---NE2
ATOM NE2 NR2
-0.70 !
|
!
HD2
BOND
BOND
BOND
BOND
BOND
IMPH
IMPH
IMPH
IMPH
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
PATC
C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1'
C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
C4' H41' C4' H42'
ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1
CE1 HE1 CD2 HD2 CG HG
ND1 CG
CE1 C1'
ND1 CE1 CG
C1'
CD2 CG
NE2 HD2
CD2 NE2 CG
HD2
CE1 ND1 NE2 HE1
CE1 NE2 ND1 HE1
CG
CD2 ND1 HG
CG
ND1 CD2 HG
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
H12' C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
H21' C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
H22' C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
H31' C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
H32' C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
H41' C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
H42' C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
C4'
O4'
C1'
ND1
0.0 0.0 256.98 0.0 0.0
O4'
C1'
ND1
CE1
0.0 0.0 180.00 0.0 0.0
C1'
ND1
CE1
NE2
0.0 0.0 181.56 0.0 0.0
ND1
CE1
NE2
CD2
0.0 0.0
0.34 0.0 0.0
CE1
NE2
CD2
CG
0.0 0.0
0.00 0.0 0.0
HE1
CE1
NE2
CD2
0.0 0.0 180.40 0.0 0.0
CE1
NE2
CD2
HD2
0.0 0.0 179.83 0.0 0.0
NE2
CD2
CG
HG
0.0 0.0 178.45 0.0 0.0
FIRS NONE LAST NONE
ND1
RESI THMI
0.00
! thf-ch3-imidazole
!
! Model compound E with imidazole base and 5'methyl, vibrational analysis
!
GROUP
! Sugar: transferred from thf
ATOM O4' ON6
-0.50 !
H52' H53'
ATOM C1' CN7B
0.16 !
\ /
ATOM H12' HN7
0.09 ! H51'-C5' O4' Imidazole
ATOM C4' CN7
0.16 !
\ / \ /
ATOM H42' HN7
0.09 !
H42'--C4' C1'--H12'
GROUP
!
|
|
ATOM C2' CN8
-0.18 !
H31'--C3'--C2'--H21'
ATOM H21' HN8
0.09 !
/
\
ATOM H22' HN8
0.09 !
H32'
H22'
GROUP
ATOM C3' CN7
-0.18
ATOM H31' HN7
0.09
ATOM H32' HN7
0.09
GROUP
ATOM C5' CN8B
-0.27
ATOM H51' HN8
0.09
ATOM H52' HN8
0.09
ATOM H53' HN8
0.09
GROUP ! Imidazole: transferred from isolated imidazole (IMIA)
ATOM CG
CPH1
-0.05 !
C1'
HE1
ATOM HG
HR3
0.09 !
\
/
ATOM CD2 CPH1
0.22 !
ND1---CE1
ATOM HD2 HR3
0.10 !
/
||
ATOM ND1 NR1
-0.04 ! HG-CG
||
ATOM CE1 CPH2
0.25 !
\\
||
ATOM HE1 HR1
0.13 !
CD2---NE2
ATOM NE2 NR2
-0.70 !
|
!
HD2
BOND
BOND
BOND
BOND
BOND
BOND
IMPH
IMPH
IMPH
IMPH
! ic
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
IC
C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1'
C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'
C4' H42' C4' C5' C5' H51' C5' H52' C5' H53'
ND1 CE1 NE2 CD2 CG ND1
CE1 HE1 CD2 HD2 CG HG
CG CD2
CE1 NE2
ND1 CG CE1 C1'
ND1 CE1 CG
C1'
CD2 CG NE2 HD2
CD2 NE2 CG
HD2
CE1 ND1 NE2 HE1
CE1 NE2 ND1 HE1
CG CD2 ND1 HG
CG
ND1 CD2 HG
table for thfim, from Nicolas:
C1'
C2'
C3'
C4'
0.0 0.0 324.92 0.0 0.0
C2'
C3'
C4'
O4'
0.0 0.0 33.390 0.0 0.0
H12' C1'
C2'
C3'
0.0 0.0 268.35 0.0 0.0
H21' C2'
C3'
C4'
0.0 0.0 82.530 0.0 0.0
H22' C2'
C3'
C4'
0.0 0.0 204.06 0.0 0.0
H31' C3'
C4'
O4'
0.0 0.0 155.99 0.0 0.0
H32' C3'
C4'
O4'
0.0 0.0 276.70 0.0 0.0
C5'
C4'
O4'
C1'
0.0 0.0 132.30 0.0 0.0
H51'
C5'
C4'
O4'
0.0 0.0 -179.98 0.0
H52'
C5'
C4'
O4'
0.0 0.0 -59.66 0.0
H53'
C5'
C4'
O4'
0.0 0.0
59.68 0.0
H42' C4'
O4'
C1'
0.0 0.0 220.70 0.0 0.0
ND1
0.0
0.0
0.0
IC
IC
IC
IC
IC
IC
IC
IC
PATC
C4'
O4'
C1'
ND1
O4'
C1'
ND1
CE1
C1'
ND1
CE1
NE2
ND1
CE1
NE2
CD2
CE1
NE2
CD2
CG
HE1
CE1
NE2
CD2
CE1
NE2
CD2
HD2
NE2
CD2
CG
HG
FIRS NONE LAST NONE
RESI TADE
!
! Model compound
!
GROUP
ATOM C5
CN5
ATOM N7
NN4
ATOM C8
CN4
ATOM H8
HN3
ATOM N9
NN2
ATOM C1' CN7B
ATOM N1
NN3A
ATOM C2
CN4
ATOM H2
HN3
ATOM N3
NN3A
ATOM C4
CN5
ATOM C6
CN2
ATOM N6
NN1
ATOM H61 HN1
ATOM H62 HN1
ATOM O4' ON6
ATOM H12' HN7
ATOM C4' CN7
ATOM H41' HN7
ATOM H42' HN7
GROUP
ATOM C2' CN8
ATOM H21' HN8
ATOM H22' HN8
GROUP
ATOM C3' CN7
ATOM H31' HN7
ATOM H32' HN7
BOND
BOND
BOND
BOND
BOND
BOND
BOND
IMPH
! ic
IC
IC
IC
IC
0.0 0.0 256.98 0.0 0.0
0.0 0.0 180.00 0.0 0.0
0.0 0.0 181.56 0.0 0.0
0.0 0.0
0.34 0.0 0.0
0.0 0.0
0.00 0.0 0.0
0.0 0.0 180.40 0.0 0.0
0.0 0.0 179.83 0.0 0.0
0.0 0.0 178.45 0.0 0.0
0.00 ! thf with adenine
E with adenine
0.28
-0.71
0.34
0.12
-0.05
0.16
-0.74
0.50
0.13
-0.75
0.43
0.46
-0.77
0.38
0.38
-0.50
0.09
0.07
0.09
0.09
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
!
-0.18 !
0.09
0.09
H61
\
H62!
/
N6
|
C6
// \
N1
C5--N7\\
|
||
C8-H8
C2
C4--N9/
/ \\ /
\
H2
N3
\
\
\
\
H42' O4' \
\ /
\ \
H41'-C4'
C1'
\
/ \
H31'--C3'--C2' H12'
/
/ \
H32'
H21' H22'
-0.1