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1996
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.
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, Close.
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6. ,
.
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53
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.
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54
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55
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, 3, 6
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.
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Brookhaven PDB .
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57
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, , .
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.
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:
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.
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:
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.
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.
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58
3. .
.
, .
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.
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-:
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4. 47 Residue/namber OK.
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.
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47 55 .
6. L-drag 47 55.
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59
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. ,
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. , Select Sphere - Display
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.
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60
, .
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.
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, .
:
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2. , Name+Seq.
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4. ,
:
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ALA58 VAL.
6. Select, GLY57.
PHE.
7. 56 ALA 55 VAL.
61
,
Z .
:
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3. , .
4. C C-C VAL,
:
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. ,
. Show Selection Only Display R-
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:
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62
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.
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65
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:
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66
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.
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67
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, .
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68
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.
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.
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.
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69
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70
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.
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J.B. Hendrickson, J.. Chem. Soc. 83, 4537 (1961)
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, Notepad, Write,
Microsoft Windows, WordPad Windows 95.
:
71
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.
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73
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, PDB ,
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74
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.
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.
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3-D .
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75
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.
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.
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; . 8
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OCCN 60 120 ,
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.
:
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:
76
= 74.59
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.
:
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2. , ,
.
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= 18.10
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NCCO :
OCO = 123.9 0
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NCCO 60 120 .
, NCCO ,
HyperChem,
.
, , Name Selection Select.
Other, ncco, .
4. R- , .
, ,
.
:
1. Save File, [Ctrl] + [S]
.
2. , HIN .
77
3. ala-gas.hin.
4. L- Comments. ,
:
- BER
5. .
2:
HyperChem
, ,
. , - ,
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, , :
1. ,
Labels.
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.
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,
. HyperChem
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.
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. ,
Smollest Box Enclossing Solute,
.
, , ,
. -
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18.70136 ,
78
56.10408A.
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.
2. .
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, , . ,
,
. , ,
.
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3. Molecules.
4. , ,
:
,
.
:
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2. Options, .
3. Custoffs .
Periodic Box HyperChem
Inner Other ,
.
Inner , Other
4 , ,
.
79
4. Dielectric,
.
.
5. Constant Distance dependent.
: ,
chem.ini .
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.
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.
.
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: 40
, .
80
. , ,
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.
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.
5. ala-liq.hin.
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3. Compliment Selection.
.
4. Clear Edit.
5. , ,
.
6. Show Periodic Box ,
.
7. ala-sol.hin.
- . ,
, ,
.
81
:
1. .
2. Name Selection Select, solvated.
.
3. , Marge File ala-gas.hin.
.
.
. .
4. ,
.
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5.
.
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.
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.
7.
.
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. ,
. ,
. ,
.
:
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Multiple Selections.
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.
3. Overlay Display.
82
4. R- , .
5. ,
.
:
6. , Save As File
ala-
sup.hin.
4:
, ,
.
- .
:
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.
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.
2. Heat time 0.1 .
3. Temperature step 30.
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100K 300,
30.
4. Run time 0.5 .
83
,
.
, -
. (
),
.
5. , Periodic boundary conditions .
HyperChem
, In vacio.
6. Step Size 0.0005 .
7. Data Collection period 4.
, , 0.5
,
. ,
.
, 4.
8. Constant Temperature.
9. :
, ,
.
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.
, , ,
, .
, , .
:
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.
2. ala-ran .
HyperChem ala-ran.
84
, ala-run.hin, HIN ,
. , ala-run.snp,
.
3. Snapshot 1 .
4. -
.
,
.
, ,
.
: Averaging, HyperChem
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, ,
, N-C-C-O
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.
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, Proceed .
85
-
.
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.
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86
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,
.
5: Langevin -
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Langevin ,
,
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.
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, HyperChem
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.
4. Set Time 0.001 .
5. Averages Snapshots .
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-
87
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2:
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4. , Max Delta, 0.05 .
.
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, .
.
5. Simulation Temperature 300 .
6. , Periodic boundary conditions ().
7. Data Collection period 4 .
-
8. .
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,
.
.
88
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ACCR , .
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89
7,
HyperChem 5 Windows.
11
-
,
,
.
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:
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.
4. , .
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.
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3.
:
91
- (RHF)
0.0001, ,
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Iteration limit, 50 - ,
. Total charge - 0,
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.
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92
3. Electrostatic Potential
2-D Contours.
HyperChem
.
4. Contour Grid,
.
5. Horizontal grid points 60.
6. Vertical grid points 60.
7. Contour levels 30.
8. Plane Offset 0.5.
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.
11. Plot Molecular Properties Options
3-D Isosurfase 2-D Contours.
3-D .
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3-D Mapped Isosurfase.
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93
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:
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2. , Total Charge Density , 2D Contours, L- , .
, .
3-D ,
3-D .
. , (
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, , .
.
94
-
- .
(HOMO)
(LUMO).
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. , CNDO
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.
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3.
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, .
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HyperChem
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95
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12. X Axis, 90, , Apply to Viewer,
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. ,
. [F3]
.
96
13. Orbitals
0 OMO-.
14. , Flat surfase.
0.05, .
, ,
1b1:
15. , Rotate Edit, -90, .
16. L- LUMO+ 0 1,
.
17. ,
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.
1,510 A (CC ) 1,089 (H ).
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.
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97
- , HyperChem
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7, ,
HyperChem 5 Windows.
12
N-
,
,
HyperChem,
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, - N-
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. ,
.
NMA
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3. Default Element, Explicit Hydrogens,
.
4. , 2-D :
5. , :
C-O .
6. ,
3-D .
- -NMA
98
, ,
trans-NMA, -NMA.
.
O-C-N-C C-N-C-O,
(O
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C) , -NMA:
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4. .
99
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7. amber3, .
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11, ,
. ,
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, 0.00.
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HyperChem .
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100
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101
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102
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103
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105
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106
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, , ,
- , ab initio .
ab initio ,
107
.
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ab initio .
.
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30
50
30
14
,
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,
ab initio .
H3O :
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2. , Allow Ions Build.
, Allow Ions,
, ,
.
. Allow Ions
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108
3. Labels Display, .
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O (),
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4. L- OK,
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+1 -
, .
.
:
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2. Other .
109
H3O +:
1. Ab Initio Setup.
2.
Options, Total charge = 1, Spin multiplicity = 1,
Spin pairing = RHF, Convergence limit = 0.01, Iteration limit = 50, Accelerate convergence =
Yes. Single Point only
.
3. L- , Ab Initio
L- , Ab Initio.
4. Geometry Optimization Compute.
110
STO-3G H2O+H +:
1. R-
H3O +, H2O.
H + - , H2O
H3O+
H2O.
2. Ab Initio Setup Options,
Total charge 1 0. .
3. Geometry Optimization Compute H2O,
H3O +.
STO-3G 100.0
0.99.
4. Single Point Compute.
H2O STO-3G -47041.82
/ SCF -47066.21/ MP2 ,
-24.45 / .
228.75 / SCF 234.77 / MP2.
.
111
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-
HyperChem REACT.SCR.
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- , HyperChem ,
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112
:
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113
6
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114
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116
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117
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118
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119
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120
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.
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121
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.
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.
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.
.
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122
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123
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124
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125
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129
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