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: 2J35R

Calculation Name: 2WFM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WFM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SE93

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 255
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3537014.337983
FMO2-HF: Nuclear repulsion 3432772.343091
FMO2-HF: Total energy -104241.994892
FMO2-MP2: Total energy -104533.09212


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:9:GLN)


Summations of interaction energy for fragment #1(A:9:GLN)
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.
2.3234.6750.046-0.857-1.5420.003
Interaction energy analysis for fragmet #1(A:9:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.014
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].
3A11LYS10.9340.9732.8132.1874.3990.048-0.838-1.4220.003
4A12HIS00.0630.0446.0880.5270.5270.0000.0000.0000.000
5A13PHE00.0210.0028.375-0.169-0.1690.0000.0000.0000.000
6A14VAL00.0180.00812.1730.1350.1350.0000.0000.0000.000
7A15LEU0-0.029-0.01615.344-0.065-0.0650.0000.0000.0000.000
8A16VAL00.0310.00018.3160.0400.0400.0000.0000.0000.000
9A17HIS0-0.023-0.00721.599-0.015-0.0150.0000.0000.0000.000
10A18GLY00.0640.01924.896-0.009-0.0090.0000.0000.0000.000
11A19GLY00.0050.00927.8710.0140.0140.0000.0000.0000.000
12A20CYS0-0.0080.01131.451-0.003-0.0030.0000.0000.0000.000
13A21LEU00.0020.02128.3020.0070.0070.0000.0000.0000.000
14A22GLY00.047-0.00427.9010.0050.0050.0000.0000.0000.000
15A23ALA00.0270.00323.538-0.009-0.0090.0000.0000.0000.000
16A24TRP00.0410.01223.8420.0050.0050.0000.0000.0000.000
17A25ILE00.0270.00923.7670.0060.0060.0000.0000.0000.000
18A26TRP0-0.014-0.01919.887-0.021-0.0210.0000.0000.0000.000
19A27TYR0-0.058-0.04120.6450.0290.0290.0000.0000.0000.000
20A28LYS10.8920.95621.559-0.018-0.0180.0000.0000.0000.000
21A29LEU00.0150.00615.6920.0150.0150.0000.0000.0000.000
22A30LYS10.8720.92316.348-0.387-0.3870.0000.0000.0000.000
23A31PRO00.0730.02915.3340.0540.0540.0000.0000.0000.000
24A32LEU0-0.051-0.01615.1350.0600.0600.0000.0000.0000.000
25A33LEU0-0.008-0.01111.2740.0120.0120.0000.0000.0000.000
26A34GLU-1-0.828-0.90410.4410.6070.6070.0000.0000.0000.000
27A35SER0-0.045-0.01411.1420.2120.2120.0000.0000.0000.000
28A36ALA0-0.091-0.0358.5250.1040.1040.0000.0000.0000.000
29A37GLY00.0100.0136.8760.0940.0940.0000.0000.0000.000
30A38HIS00.0120.0154.5590.8820.990-0.001-0.017-0.0900.000
31A39LYS11.0031.0088.472-0.770-0.7700.0000.0000.0000.000
32A40VAL0-0.028-0.01510.903-0.237-0.2370.0000.0000.0000.000
33A41THR0-0.024-0.02714.0690.0900.0900.0000.0000.0000.000
34A42ALA0-0.033-0.02017.023-0.067-0.0670.0000.0000.0000.000
35A43VAL0-0.0020.00719.9990.0260.0260.0000.0000.0000.000
36A44ASP-1-0.842-0.91922.4440.0730.0730.0000.0000.0000.000
37A45LEU0-0.005-0.00524.6310.0040.0040.0000.0000.0000.000
38A46SER0-0.027-0.04027.5960.0150.0150.0000.0000.0000.000
39A47ALA0-0.066-0.03331.024-0.010-0.0100.0000.0000.0000.000
40A48ALA0-0.0080.01729.743-0.006-0.0060.0000.0000.0000.000
41A49GLY00.0520.01929.7250.0120.0120.0000.0000.0000.000
42A50ILE0-0.041-0.00829.065-0.004-0.0040.0000.0000.0000.000
43A51ASN00.0150.02529.1990.0030.0030.0000.0000.0000.000
44A52PRO00.015-0.00231.491-0.009-0.0090.0000.0000.0000.000
45A53ARG10.9310.99133.525-0.062-0.0620.0000.0000.0000.000
46A54ARG10.8660.91035.795-0.030-0.0300.0000.0000.0000.000
47A55LEU00.0520.01736.226-0.003-0.0030.0000.0000.0000.000
48A56ASP-1-0.869-0.92038.2130.0140.0140.0000.0000.0000.000
49A57GLU-1-0.870-0.93238.0080.0370.0370.0000.0000.0000.000
50A58ILE0-0.051-0.02434.0180.0000.0000.0000.0000.0000.000
51A59HIS00.0290.00537.187-0.008-0.0080.0000.0000.0000.000
52A60THR0-0.0110.00834.831-0.007-0.0070.0000.0000.0000.000
53A61PHE00.0380.00327.6610.0050.0050.0000.0000.0000.000
54A62ARG10.9380.95428.4890.0670.0670.0000.0000.0000.000
55A63ASP-1-0.856-0.92230.0600.0010.0010.0000.0000.0000.000
56A64TYR0-0.037-0.01729.2620.0130.0130.0000.0000.0000.000
57A65SER00.011-0.01026.0440.0010.0010.0000.0000.0000.000
58A66GLU-1-0.874-0.93225.7350.0130.0130.0000.0000.0000.000
59A67PRO00.0120.01925.5140.0080.0080.0000.0000.0000.000
60A68LEU0-0.046-0.01719.1940.0150.0150.0000.0000.0000.000
61A69MET0-0.051-0.03021.074-0.013-0.0130.0000.0000.0000.000
62A70GLU-1-0.891-0.94122.2400.0940.0940.0000.0000.0000.000
63A71VAL0-0.031-0.01417.3440.0300.0300.0000.0000.0000.000
64A72MET0-0.066-0.03415.8180.0250.0250.0000.0000.0000.000
65A73ALA0-0.017-0.00218.078-0.003-0.0030.0000.0000.0000.000
66A74SER0-0.086-0.03218.6330.0350.0350.0000.0000.0000.000
67A75ILE0-0.038-0.01112.7680.0750.0750.0000.0000.0000.000
68A76PRO00.0370.02612.780-0.079-0.0790.0000.0000.0000.000
69A77PRO0-0.007-0.02713.840-0.059-0.0590.0000.0000.0000.000
70A78ASP-1-0.890-0.93610.2630.3940.3940.0000.0000.0000.000
71A79GLU-1-0.996-0.9889.0300.8330.8330.0000.0000.0000.000
72A80LYS10.8720.9268.7250.6560.6560.0000.0000.0000.000
73A81VAL0-0.027-0.0028.8880.0930.0930.0000.0000.0000.000
74A82VAL0-0.032-0.0098.647-0.174-0.1740.0000.0000.0000.000
75A83LEU00.0020.00511.3800.1290.1290.0000.0000.0000.000
76A84LEU00.0160.01415.219-0.067-0.0670.0000.0000.0000.000
77A85GLY00.0160.01217.3550.0580.0580.0000.0000.0000.000
78A86HIS00.0020.01821.079-0.014-0.0140.0000.0000.0000.000
79A87SER00.0900.05423.8750.0210.0210.0000.0000.0000.000
80A88PHE00.019-0.02626.893-0.015-0.0150.0000.0000.0000.000
81A89GLY00.0370.02424.5730.0010.0010.0000.0000.0000.000
82A90GLY0-0.033-0.01323.380-0.012-0.0120.0000.0000.0000.000
83A91MET0-0.001-0.00324.337-0.022-0.0220.0000.0000.0000.000
84A92SER0-0.008-0.00324.1140.0000.0000.0000.0000.0000.000
85A93LEU00.0070.00718.9540.0030.0030.0000.0000.0000.000
86A94GLY00.0430.01321.414-0.017-0.0170.0000.0000.0000.000
87A95LEU00.000-0.00423.676-0.007-0.0070.0000.0000.0000.000
88A96ALA00.0390.02519.5140.0060.0060.0000.0000.0000.000
89A97MET0-0.062-0.02118.663-0.004-0.0040.0000.0000.0000.000
90A98GLU-1-0.753-0.87420.450-0.222-0.2220.0000.0000.0000.000
91A99THR0-0.094-0.05522.9440.0070.0070.0000.0000.0000.000
92A100TYR00.023-0.00218.2740.0210.0210.0000.0000.0000.000
93A101PRO00.0270.03517.596-0.028-0.0280.0000.0000.0000.000
94A102GLU-1-0.887-0.97315.781-0.304-0.3040.0000.0000.0000.000
95A103LYS10.8300.92213.7450.0040.0040.0000.0000.0000.000
96A104ILE00.0220.03012.8050.0230.0230.0000.0000.0000.000
97A105SER0-0.057-0.0288.208-0.014-0.0140.0000.0000.0000.000
98A106VAL0-0.042-0.02810.739-0.064-0.0640.0000.0000.0000.000
99A107ALA00.0320.02113.0750.0560.0560.0000.0000.0000.000
100A108VAL0-0.030-0.03214.170-0.022-0.0220.0000.0000.0000.000
101A109PHE00.016-0.00517.1550.0620.0620.0000.0000.0000.000
102A110MET00.0190.00520.223-0.020-0.0200.0000.0000.0000.000
103A111SER00.0510.00021.9650.0280.0280.0000.0000.0000.000
104A112ALA0-0.037-0.01024.1580.0220.0220.0000.0000.0000.000
105A113MET0-0.0190.01426.067-0.014-0.0140.0000.0000.0000.000
106A114MET00.0050.01122.038-0.012-0.0120.0000.0000.0000.000
107A115PRO0-0.013-0.00824.8530.0050.0050.0000.0000.0000.000
108A116ASP-1-0.737-0.87226.450-0.250-0.2500.0000.0000.0000.000
109A117PRO00.0040.00926.5270.0200.0200.0000.0000.0000.000
110A118ASN0-0.040-0.01529.2560.0210.0210.0000.0000.0000.000
111A119HIS10.8120.91332.1600.1850.1850.0000.0000.0000.000
112A120SER00.0310.01832.953-0.006-0.0060.0000.0000.0000.000
113A121LEU00.025-0.00130.060-0.008-0.0080.0000.0000.0000.000
114A122THR00.0460.02733.070-0.001-0.0010.0000.0000.0000.000
115A123TYR00.0110.02233.7310.0040.0040.0000.0000.0000.000
116A124PRO00.0180.00031.1300.0010.0010.0000.0000.0000.000
117A125PHE00.012-0.00331.5030.0020.0020.0000.0000.0000.000
118A126GLU-1-0.920-0.96435.987-0.095-0.0950.0000.0000.0000.000
119A127LYS10.9050.94735.6110.1330.1330.0000.0000.0000.000
120A128TYR0-0.072-0.11634.2260.0020.0020.0000.0000.0000.000
121A129ASN0-0.022-0.01537.0520.0040.0040.0000.0000.0000.000
122A130GLU-1-0.943-0.96640.375-0.111-0.1110.0000.0000.0000.000
123A131LYS10.8780.94336.7920.1360.1360.0000.0000.0000.000
124A132CYS0-0.058-0.00537.1820.0000.0000.0000.0000.0000.000
125A133PRO00.0380.02740.6390.0020.0020.0000.0000.0000.000
126A134ALA00.001-0.01342.8820.0000.0000.0000.0000.0000.000
127A135ASP-1-0.889-0.93944.947-0.049-0.0490.0000.0000.0000.000
128A136MET0-0.026-0.00438.7370.0020.0020.0000.0000.0000.000
129A137MET00.0130.00937.100-0.001-0.0010.0000.0000.0000.000
130A138LEU0-0.0260.00441.0090.0050.0050.0000.0000.0000.000
131A139ASP-1-0.776-0.89742.936-0.018-0.0180.0000.0000.0000.000
132A140SER0-0.026-0.01340.4390.0050.0050.0000.0000.0000.000
133A141GLN0-0.062-0.01642.5860.0010.0010.0000.0000.0000.000
134A142PHE00.024-0.01040.2210.0000.0000.0000.0000.0000.000
135A143SER0-0.023-0.01144.1760.0030.0030.0000.0000.0000.000
136A144THR00.005-0.01044.6190.0000.0000.0000.0000.0000.000
137A145TYR0-0.021-0.01538.7320.0020.0020.0000.0000.0000.000
138A146GLY00.0360.01944.406-0.004-0.0040.0000.0000.0000.000
139A147ASN0-0.044-0.00745.2240.0010.0010.0000.0000.0000.000
140A148PRO00.0280.00647.610-0.003-0.0030.0000.0000.0000.000
141A149GLU-1-0.891-0.96149.591-0.016-0.0160.0000.0000.0000.000
142A150ASN0-0.126-0.07144.241-0.006-0.0060.0000.0000.0000.000
143A151PRO00.0410.06644.8460.0010.0010.0000.0000.0000.000
144A152GLY00.0360.00341.955-0.005-0.0050.0000.0000.0000.000
145A153MET0-0.023-0.02341.0140.0030.0030.0000.0000.0000.000
146A154SER0-0.046-0.00539.829-0.002-0.0020.0000.0000.0000.000
147A155MET0-0.005-0.01536.822-0.005-0.0050.0000.0000.0000.000
148A156ILE00.0210.00539.0090.0040.0040.0000.0000.0000.000
149A157LEU00.0370.00833.991-0.005-0.0050.0000.0000.0000.000
150A158GLY00.0460.03438.7230.0060.0060.0000.0000.0000.000
151A159PRO00.021-0.00939.858-0.003-0.0030.0000.0000.0000.000
152A160GLN00.003-0.00240.1630.0010.0010.0000.0000.0000.000
153A161PHE00.0050.00435.662-0.005-0.0050.0000.0000.0000.000
154A162MET0-0.005-0.00334.620-0.004-0.0040.0000.0000.0000.000
155A163ALA00.003-0.00335.866-0.003-0.0030.0000.0000.0000.000
156A164LEU0-0.029-0.01637.288-0.003-0.0030.0000.0000.0000.000
157A165LYS10.8070.87536.4160.0530.0530.0000.0000.0000.000
158A166MET0-0.049-0.00331.581-0.006-0.0060.0000.0000.0000.000
159A167PHE00.026-0.01230.337-0.004-0.0040.0000.0000.0000.000
160A168GLN0-0.0030.02032.9360.0100.0100.0000.0000.0000.000
161A169ASN0-0.075-0.04030.2370.0090.0090.0000.0000.0000.000
162A170CYS0-0.115-0.04529.7210.0030.0030.0000.0000.0000.000
163A171SER0-0.0140.00530.8840.0040.0040.0000.0000.0000.000
164A172VAL00.0590.00533.021-0.003-0.0030.0000.0000.0000.000
165A173GLU-1-0.890-0.95032.7370.0460.0460.0000.0000.0000.000
166A174ASP-1-0.809-0.89629.0870.0430.0430.0000.0000.0000.000
167A175LEU0-0.0150.00431.902-0.001-0.0010.0000.0000.0000.000
168A176GLU-1-0.933-0.97634.7080.0320.0320.0000.0000.0000.000
169A177LEU00.0060.00429.4520.0040.0040.0000.0000.0000.000
170A178ALA0-0.014-0.02232.5600.0020.0020.0000.0000.0000.000
171A179LYS10.9050.94933.752-0.017-0.0170.0000.0000.0000.000
172A180MET0-0.058-0.01436.2060.0030.0030.0000.0000.0000.000
173A181LEU0-0.042-0.01731.1230.0060.0060.0000.0000.0000.000
174A182THR0-0.101-0.03234.095-0.002-0.0020.0000.0000.0000.000
175A183ARG10.8270.89933.809-0.044-0.0440.0000.0000.0000.000
176A184PRO00.000-0.01136.368-0.006-0.0060.0000.0000.0000.000
177A185GLY00.0350.02335.2510.0030.0030.0000.0000.0000.000
178A186SER0-0.016-0.02834.894-0.003-0.0030.0000.0000.0000.000
179A187LEU00.009-0.00133.311-0.002-0.0020.0000.0000.0000.000
180A188PHE0-0.015-0.00633.365-0.009-0.0090.0000.0000.0000.000
181A189PHE00.0280.02936.453-0.003-0.0030.0000.0000.0000.000
182A190GLN00.0990.03938.060-0.009-0.0090.0000.0000.0000.000
183A191ASP-1-0.860-0.93135.240-0.054-0.0540.0000.0000.0000.000
184A192LEU00.028-0.00131.964-0.005-0.0050.0000.0000.0000.000
185A193ALA0-0.042-0.02835.642-0.007-0.0070.0000.0000.0000.000
186A194LYS10.8450.92638.3830.0490.0490.0000.0000.0000.000
187A195ALA0-0.0170.02033.3400.0000.0000.0000.0000.0000.000
188A196LYS10.9370.96531.7130.1030.1030.0000.0000.0000.000
189A197LYS10.9090.95831.9430.1610.1610.0000.0000.0000.000
190A198PHE0-0.004-0.00926.6630.0020.0020.0000.0000.0000.000
191A199SER0-0.017-0.01227.180-0.001-0.0010.0000.0000.0000.000
192A200THR00.012-0.01926.125-0.013-0.0130.0000.0000.0000.000
193A201GLU-1-0.910-0.95024.774-0.249-0.2490.0000.0000.0000.000
194A202ARG10.8470.93122.8790.1740.1740.0000.0000.0000.000
195A203TYR00.009-0.00121.734-0.045-0.0450.0000.0000.0000.000
196A204GLY0-0.074-0.04421.590-0.030-0.0300.0000.0000.0000.000
197A205SER0-0.060-0.01920.130-0.035-0.0350.0000.0000.0000.000
198A206VAL0-0.034-0.00715.827-0.071-0.0710.0000.0000.0000.000
199A207LYS10.9320.97711.4271.2671.2670.0000.0000.0000.000
200A208ARG10.9140.96016.2430.4060.4060.0000.0000.0000.000
201A209ALA0-0.017-0.01615.827-0.049-0.0490.0000.0000.0000.000
202A210TYR0-0.015-0.01917.8590.0500.0500.0000.0000.0000.000
203A211ILE0-0.012-0.00816.664-0.035-0.0350.0000.0000.0000.000
204A212PHE0-0.004-0.03120.7830.0260.0260.0000.0000.0000.000
205A213CYS0-0.0070.03123.989-0.013-0.0130.0000.0000.0000.000
206A214ASN0-0.022-0.02826.1210.0030.0030.0000.0000.0000.000
207A215GLU-1-0.884-0.92829.017-0.090-0.0900.0000.0000.0000.000
208A216ASP-1-0.779-0.89329.115-0.097-0.0970.0000.0000.0000.000
209A217LYS10.9330.95631.1640.0630.0630.0000.0000.0000.000
210A218SER0-0.063-0.01632.2670.0060.0060.0000.0000.0000.000
211A219PHE0-0.0170.03628.448-0.002-0.0020.0000.0000.0000.000
212A220PRO00.1010.05831.208-0.011-0.0110.0000.0000.0000.000
213A221VAL00.0730.03728.981-0.012-0.0120.0000.0000.0000.000
214A222GLU-1-0.929-0.97630.963-0.145-0.1450.0000.0000.0000.000
215A223PHE0-0.0110.00831.918-0.006-0.0060.0000.0000.0000.000
216A224GLN0-0.023-0.01226.838-0.029-0.0290.0000.0000.0000.000
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