FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JM8L9

Calculation Name: 3IF8-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IF8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H900

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 272
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2996365.603606
FMO2-HF: Nuclear repulsion 2892180.117028
FMO2-HF: Total energy -104185.486578
FMO2-MP2: Total energy -104491.841843


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-4:GLY )


Summations of interaction energy for fragment #1(A:-4:GLY )
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-4.209-0.7140.527-1.819-2.204-0.007
Interaction energy analysis for fragmet #1(A:-4:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.010
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A-2LEU 00.000-0.0053.065-1.4090.3780.106-0.786-1.1070.005
4A-1GLY 0-0.031-0.0094.349-0.490-0.4530.000-0.024-0.0140.000
5A0SER 0-0.031-0.0086.300-0.312-0.3120.0000.0000.0000.000
6A1MET 00.0510.0098.0620.1630.1630.0000.0000.0000.000
7A2TRP 00.008-0.0107.4310.0780.0780.0000.0000.0000.000
8A3GLU -1-0.904-0.9176.8730.7720.7720.0000.0000.0000.000
9A4ARG 10.9610.9617.910-0.069-0.0690.0000.0000.0000.000
10A5LEU 00.0080.01210.8110.0190.0190.0000.0000.0000.000
11A6ASN 0-0.012-0.0177.1100.0890.0890.0000.0000.0000.000
12A7CYS 0-0.0210.0147.9730.1010.1010.0000.0000.0000.000
13A8ALA 00.0440.0225.8230.1140.1140.0000.0000.0000.000
14A9ALA 00.002-0.0097.0770.0210.0210.0000.0000.0000.000
15A10GLU -1-0.727-0.84810.4420.2070.2070.0000.0000.0000.000
16A11ASP -1-0.838-0.9237.9970.4660.4660.0000.0000.0000.000
17A12PHE 0-0.067-0.0249.167-0.020-0.0200.0000.0000.0000.000
18A13TYR 00.0390.01110.519-0.096-0.0960.0000.0000.0000.000
19A14SER 00.0310.01813.207-0.059-0.0590.0000.0000.0000.000
20A15ARG 10.8930.9419.466-0.512-0.5120.0000.0000.0000.000
21A16LEU 0-0.008-0.01013.624-0.054-0.0540.0000.0000.0000.000
22A17LEU 00.0130.01315.862-0.038-0.0380.0000.0000.0000.000
23A18GLN 0-0.013-0.00315.270-0.047-0.0470.0000.0000.0000.000
24A19LYS 10.9170.97016.000-0.260-0.2600.0000.0000.0000.000
25A20PHE 00.0620.04019.988-0.022-0.0220.0000.0000.0000.000
26A21ASN 0-0.002-0.01721.883-0.023-0.0230.0000.0000.0000.000
27A22GLU -1-0.981-0.97820.9930.1400.1400.0000.0000.0000.000
28A23GLU -1-0.788-0.93522.9720.1020.1020.0000.0000.0000.000
29A24LYS 10.7620.92725.317-0.118-0.1180.0000.0000.0000.000
30A25LYS 10.8790.91527.504-0.088-0.0880.0000.0000.0000.000
31A26GLY 00.0300.03726.903-0.005-0.0050.0000.0000.0000.000
32A27ILE 00.009-0.01125.7670.0050.0050.0000.0000.0000.000
33A28ARG 10.8540.90617.735-0.154-0.1540.0000.0000.0000.000
34A29LYS 10.9270.98522.084-0.069-0.0690.0000.0000.0000.000
35A30ASP -1-0.802-0.89817.8290.1270.1270.0000.0000.0000.000
36A31PRO 0-0.034-0.00216.9540.0150.0150.0000.0000.0000.000
37A32PHE 00.0110.00311.753-0.004-0.0040.0000.0000.0000.000
38A33LEU 00.0520.01210.6310.0270.0270.0000.0000.0000.000
39A34TYR 0-0.068-0.0295.607-0.078-0.0780.0000.0000.0000.000
40A35GLU -1-0.865-0.9602.677-1.3750.2960.421-1.009-1.083-0.012
41A36ALA 0-0.0070.0146.299-0.187-0.1870.0000.0000.0000.000
42A37ASP -1-0.856-0.9388.206-0.047-0.0470.0000.0000.0000.000
43A38VAL 00.0080.0118.3310.0510.0510.0000.0000.0000.000
44A39GLN 0-0.014-0.01010.2310.0410.0410.0000.0000.0000.000
45A40VAL 00.006-0.01012.2520.0110.0110.0000.0000.0000.000
46A41GLN 00.0150.01315.0460.0000.0000.0000.0000.0000.000
47A42LEU 0-0.034-0.01418.8140.0120.0120.0000.0000.0000.000
48A43ILE 0-0.0010.00621.339-0.013-0.0130.0000.0000.0000.000
49A44SER 00.014-0.01224.750-0.004-0.0040.0000.0000.0000.000
50A45LYS 10.8860.92827.751-0.088-0.0880.0000.0000.0000.000
51A46GLY 00.0920.05131.4240.0000.0000.0000.0000.0000.000
52A47GLN 0-0.0540.00226.2950.0020.0020.0000.0000.0000.000
53A48PRO 0-0.001-0.01828.8160.0010.0010.0000.0000.0000.000
54A49ASN 00.0930.05726.6280.0080.0080.0000.0000.0000.000
55A50PRO 0-0.035-0.02823.698-0.006-0.0060.0000.0000.0000.000
56A51LEU 00.0260.01723.500-0.004-0.0040.0000.0000.0000.000
57A52LYS 10.8920.95127.303-0.066-0.0660.0000.0000.0000.000
58A53ASN 0-0.067-0.02328.697-0.006-0.0060.0000.0000.0000.000
59A54ILE 0-0.041-0.01926.662-0.004-0.0040.0000.0000.0000.000
60A55LEU 00.0090.02527.3420.0000.0000.0000.0000.0000.000
61A56ASN 00.014-0.02131.745-0.003-0.0030.0000.0000.0000.000
62A57GLU -1-0.895-0.92830.8510.0720.0720.0000.0000.0000.000
63A58ASN 0-0.050-0.04130.7300.0070.0070.0000.0000.0000.000
64A59ASP -1-0.871-0.91928.0500.0890.0890.0000.0000.0000.000
65A60ILE 0-0.038-0.03425.3260.0010.0010.0000.0000.0000.000
66A61VAL 0-0.007-0.00322.2640.0070.0070.0000.0000.0000.000
67A62PHE 0-0.002-0.01117.6380.0030.0030.0000.0000.0000.000
68A63ILE 0-0.033-0.01318.959-0.005-0.0050.0000.0000.0000.000
69A64VAL 0-0.017-0.01112.5140.0120.0120.0000.0000.0000.000
70A65GLU -1-0.914-0.97414.6760.0930.0930.0000.0000.0000.000
71A66LYS 10.9200.96413.1680.0510.0510.0000.0000.0000.000
72A67VAL 0-0.048-0.02212.3610.0040.0040.0000.0000.0000.000
73A68PRO 0-0.022-0.01914.935-0.020-0.0200.0000.0000.0000.000
74A69NME 00.0170.02218.037-0.009-0.0090.0000.0000.0000.000
75A96ACE 00.016-0.00526.783-0.001-0.0010.0000.0000.0000.000
76A97GLY 0-0.030-0.01724.9340.0020.0020.0000.0000.0000.000
77A98PRO 00.0020.00121.161-0.003-0.0030.0000.0000.0000.000
78A99LEU 00.0010.01417.724-0.007-0.0070.0000.0000.0000.000
79A100ALA 0-0.008-0.00417.6320.0180.0180.0000.0000.0000.000
80A101LEU 0-0.013-0.00311.299-0.012-0.0120.0000.0000.0000.000
81A102PRO 00.0740.03212.6250.0030.0030.0000.0000.0000.000
82A103VAL 00.0140.01414.4090.0490.0490.0000.0000.0000.000
83A104GLY 0-0.002-0.00214.2610.0310.0310.0000.0000.0000.000
84A105LYS 10.9140.9605.601-0.785-0.7850.0000.0000.0000.000
85A106ALA 00.0520.02411.1070.1170.1170.0000.0000.0000.000
86A107ARG 10.9780.98513.632-0.116-0.1160.0000.0000.0000.000
87A108GLN 00.0370.0247.2170.1030.1030.0000.0000.0000.000
88A109LEU 0-0.0200.0048.0630.0720.0720.0000.0000.0000.000
89A110ILE 00.0080.00811.347-0.020-0.0200.0000.0000.0000.000
90A111GLY 00.0180.01713.737-0.037-0.0370.0000.0000.0000.000
91A112LEU 00.008-0.0097.522-0.064-0.0640.0000.0000.0000.000
92A113TYR 0-0.041-0.03012.112-0.058-0.0580.0000.0000.0000.000
93A114THR 0-0.003-0.00414.919-0.056-0.0560.0000.0000.0000.000
94A115MET 0-0.050-0.03912.816-0.039-0.0390.0000.0000.0000.000
95A116ALA 00.0010.00113.707-0.031-0.0310.0000.0000.0000.000
96A117HIS 10.8210.90215.505-0.276-0.2760.0000.0000.0000.000
97A118ASN 0-0.0030.01218.678-0.037-0.0370.0000.0000.0000.000
98A119PRO 00.0310.02020.2500.0040.0040.0000.0000.0000.000
99A120ASN 0-0.049-0.03922.440-0.004-0.0040.0000.0000.0000.000
100A121MET 0-0.059-0.01213.1230.0020.0020.0000.0000.0000.000
101A122THR 0-0.003-0.00417.895-0.001-0.0010.0000.0000.0000.000
102A123HIS 00.0190.02216.5780.0300.0300.0000.0000.0000.000
103A124LEU 0-0.056-0.05613.780-0.027-0.0270.0000.0000.0000.000
104A125LYS 10.8770.93211.341-0.255-0.2550.0000.0000.0000.000
105A126ILE 0-0.051-0.01815.053-0.013-0.0130.0000.0000.0000.000
106A127ASN 00.0230.01018.136-0.002-0.0020.0000.0000.0000.000
107A128LEU 0-0.013-0.00921.621-0.014-0.0140.0000.0000.0000.000
108A129PRO 00.0060.00322.2700.0120.0120.0000.0000.0000.000
109A130VAL 0-0.0080.00619.2340.0020.0020.0000.0000.0000.000
110A131THR 0-0.032-0.02321.825-0.014-0.0140.0000.0000.0000.000
111A132ALA 00.0360.00221.7630.0180.0180.0000.0000.0000.000
112A133LEU 0-0.071-0.03717.583-0.001-0.0010.0000.0000.0000.000
113A134PRO 00.0260.01321.614-0.006-0.0060.0000.0000.0000.000
114A135PRO 00.0890.06420.9420.0260.0260.0000.0000.0000.000
115A136LEU 0-0.031-0.00114.4400.0060.0060.0000.0000.0000.000
116A137TRP 00.0370.02018.980-0.006-0.0060.0000.0000.0000.000
117A138VAL 0-0.022-0.02114.0790.0120.0120.0000.0000.0000.000
118A139ARG 10.9570.99517.260-0.114-0.1140.0000.0000.0000.000
119A140CYS 0-0.070-0.03116.9360.0170.0170.0000.0000.0000.000
120A141ASP -1-0.814-0.91918.2220.0450.0450.0000.0000.0000.000
121A142SER 0-0.033-0.00820.203-0.014-0.0140.0000.0000.0000.000
122A143SER 0-0.056-0.03619.9960.0000.0000.0000.0000.0000.000
123A144ASP -1-0.840-0.90720.8670.0690.0690.0000.0000.0000.000
124A145PRO 00.0110.00422.691-0.002-0.0020.0000.0000.0000.000
125A146GLU -1-0.972-0.98925.3880.0560.0560.0000.0000.0000.000
126A147GLY 0-0.093-0.04524.9780.0020.0020.0000.0000.0000.000
127A148THR 0-0.004-0.01821.2700.0020.0020.0000.0000.0000.000
128A149CYS 0-0.037-0.02721.9280.0000.0000.0000.0000.0000.000
129A150TRP 00.005-0.00420.2690.0090.0090.0000.0000.0000.000
130A151LEU 0-0.010-0.00617.230-0.005-0.0050.0000.0000.0000.000
131A152GLY 00.0440.02119.3280.0160.0160.0000.0000.0000.000
132A153ALA 0-0.033-0.01719.194-0.003-0.0030.0000.0000.0000.000
133A154GLU -1-0.873-0.93821.0990.1200.1200.0000.0000.0000.000
134A155LEU 0-0.0290.00121.142-0.003-0.0030.0000.0000.0000.000
135A156ILE 00.0250.02124.818-0.009-0.0090.0000.0000.0000.000
136A157THR 0-0.024-0.02527.0520.0040.0040.0000.0000.0000.000
137A158THR 0-0.0090.01329.507-0.008-0.0080.0000.0000.0000.000
138A159ASN 0-0.021-0.02632.606-0.001-0.0010.0000.0000.0000.000
139A160ASN 0-0.016-0.01128.6960.0020.0020.0000.0000.0000.000
140A161SER 00.0040.01528.8150.0080.0080.0000.0000.0000.000
141A162ILE 00.0380.02023.099-0.002-0.0020.0000.0000.0000.000
142A163THR 00.009-0.02526.524-0.010-0.0100.0000.0000.0000.000
143A164GLY 00.0100.01625.607-0.003-0.0030.0000.0000.0000.000
144A165ILE 0-0.009-0.00721.0690.0080.0080.0000.0000.0000.000
145A166VAL 0-0.0160.00924.420-0.009-0.0090.0000.0000.0000.000
146A167LEU 0-0.014-0.01420.3950.0150.0150.0000.0000.0000.000
147A168TYR 0-0.056-0.02423.099-0.017-0.0170.0000.0000.0000.000
148A169VAL 00.021-0.00422.8160.0130.0130.0000.0000.0000.000
149A170VAL 00.0050.01224.156-0.009-0.0090.0000.0000.0000.000
150A171SER 00.0420.02825.0130.0020.0020.0000.0000.0000.000
151A172CYS 0-0.015-0.01827.476-0.004-0.0040.0000.0000.0000.000
152A173LYS 10.9410.97329.443-0.038-0.0380.0000.0000.0000.000
153A174ALA 00.0270.01432.3280.0010.0010.0000.0000.0000.000
154A175ASP -1-0.842-0.92134.7090.0160.0160.0000.0000.0000.000
155A176LYS 10.9210.97338.068-0.011-0.0110.0000.0000.0000.000
156A177ASN 0-0.078-0.04641.1510.0000.0000.0000.0000.0000.000
157A178TYR 00.0380.01339.9450.0010.0010.0000.0000.0000.000
158A179SER 0-0.007-0.00740.524-0.002-0.0020.0000.0000.0000.000
159A180VAL 00.0040.00939.6690.0020.0020.0000.0000.0000.000
160A181ASN 00.0400.00741.860-0.001-0.0010.0000.0000.0000.000
161A182LEU 00.0750.02942.8050.0020.0020.0000.0000.0000.000
162A183GLU -1-0.861-0.92643.6670.0310.0310.0000.0000.0000.000
163A184ASN 0-0.041-0.02441.2780.0010.0010.0000.0000.0000.000
164A185LEU 00.0030.00237.4240.0020.0020.0000.0000.0000.000
165A186LYS 10.9921.00839.206-0.032-0.0320.0000.0000.0000.000
166A187ASN 0-0.004-0.01041.0350.0020.0020.0000.0000.0000.000
167A188LEU 0-0.058-0.01334.4790.0010.0010.0000.0000.0000.000
168A189HIS 00.0140.00434.4930.0030.0030.0000.0000.0000.000
169A190LYS 10.9510.97137.194-0.033-0.0330.0000.0000.0000.000
170A191LYS 10.9210.94438.529-0.034-0.0340.0000.0000.0000.000
171A192ARG 10.9200.97528.489-0.070-0.0700.0000.0000.0000.000
172A193HIS 0-0.005-0.00830.8000.0040.0040.0000.0000.0000.000
173A194HIS 0-0.0120.01535.375-0.002-0.0020.0000.0000.0000.000
174A195LEU 00.0280.02137.4380.0000.0000.0000.0000.0000.000
175A196SER 0-0.007-0.00341.211-0.001-0.0010.0000.0000.0000.000
176A197THR 0-0.005-0.00944.450-0.001-0.0010.0000.0000.0000.000
177A198VAL 00.0140.00040.4490.0020.0020.0000.0000.0000.000
178A199THR 00.0020.00841.873-0.003-0.0030.0000.0000.0000.000
179A200SER 00.0150.01241.3440.0010.0010.0000.0000.0000.000
180A201LYS 10.9951.02838.442-0.049-0.0490.0000.0000.0000.000
181A202GLY 00.0150.01240.6060.0010.0010.0000.0000.0000.000
182A203PHE 0-0.026-0.02737.5630.0010.0010.0000.0000.0000.000
183A204ALA 0-0.0020.01140.814-0.001-0.0010.0000.0000.0000.000
184A205GLN 0-0.055-0.03836.6240.0000.0000.0000.0000.0000.000
185A206TYR 0-0.010-0.00441.172-0.001-0.0010.0000.0000.0000.000
186A207GLU -1-0.910-0.96240.3230.0290.0290.0000.0000.0000.000
187A208LEU 0-0.033-0.01542.969-0.002-0.0020.0000.0000.0000.000
188A209PHE 0-0.011-0.00644.266-0.002-0.0020.0000.0000.0000.000
189A210LYS 10.9750.99537.183-0.028-0.0280.0000.0000.0000.000
190A211SER 00.010-0.01141.5390.0000.0000.0000.0000.0000.000
191A212NME 0-0.0240.00638.678-0.001-0.0010.0000.0000.0000.000
192A221ACE 00.0310.00637.1060.0000.0000.0000.0000.0000.000
193A222GLN 00.002-0.02637.5730.0020.0020.0000.0000.0000.000
194A223THR 0-0.080-0.02438.944-0.001-0.0010.0000.0000.0000.000
195A224ALA 00.0100.00738.439-0.001-0.0010.0000.0000.0000.000
196A225ILE 00.0000.00640.3220.0020.0020.0000.0000.0000.000
197A226ALA 00.0170.01540.006-0.001-0.0010.0000.0000.0000.000
198A227LEU 0-0.0070.00042.0660.0010.0010.0000.0000.0000.000
199A228ASP -1-0.767-0.85838.2830.0450.0450.0000.0000.0000.000
200A229ILE 0-0.008-0.01341.779-0.001-0.0010.0000.0000.0000.000
201A230SER 0-0.033-0.02541.0700.0020.0020.0000.0000.0000.000
202A231TRP 00.0230.02143.1950.0000.0000.0000.0000.0000.000
203A232SER 0-0.107-0.07844.1220.0020.0020.0000.0000.0000.000
204A233PRO 0-0.0080.00245.632-0.001-0.0010.0000.0000.0000.000
205A234VAL 0-0.032-0.02842.825-0.001-0.0010.0000.0000.0000.000
206A235ASP -1-0.950-0.97446.0620.0270.0270.0000.0000.0000.000
207A236GLU -1-0.901-0.96147.6040.0220.0220.0000.0000.0000.000
208A237ILE 0-0.044-0.03243.5910.0020.0020.0000.0000.0000.000
209A238LEU 0-0.023-0.02643.763-0.001-0.0010.0000.0000.0000.000
210A239GLN 00.0820.05746.0610.0000.0000.0000.0000.0000.000
211A240ILE 0-0.011-0.00747.1520.0010.0010.0000.0000.0000.000
212A241PRO 0-0.023-0.00345.9370.0000.0000.0000.0000.0000.000
213A242PRO 00.0350.03448.493-0.001-0.0010.0000.0000.0000.000
214A243LEU 00.0370.01350.5970.0010.0010.0000.0000.0000.000
215A244SER 0-0.032-0.00451.2320.0000.0000.0000.0000.0000.000
216A245SER 0-0.071-0.05846.8010.0020.0020.0000.0000.0000.000
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