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: LZ899

Calculation Name: 2BGK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BGK

Chain ID: A

ChEMBL ID:

UniProt ID: Q94KL8

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptAll
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 267
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3236903.987548
FMO2-HF: Nuclear repulsion 3138109.762744
FMO2-HF: Total energy -98794.224805
FMO2-MP2: Total energy -99083.664619


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:11:THR)


Summations of interaction energy for fragment #1(A:11:THR)
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.
-3.6030.1180.119-1.405-2.4340
Interaction energy analysis for fragmet #1(A:11:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.008
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].
3A13ARG10.8910.9443.464-3.439-0.3880.114-1.248-1.9170.001
4A14LEU0-0.013-0.0034.105-0.0430.1690.002-0.023-0.1910.000
5A15GLN00.0360.0176.0890.1450.1450.0000.0000.0000.000
6A16ASP-1-0.892-0.9427.7590.0990.0990.0000.0000.0000.000
7A17LYS10.8020.9218.975-0.206-0.2060.0000.0000.0000.000
8A18VAL00.0010.00412.347-0.011-0.0110.0000.0000.0000.000
9A19ALA0-0.014-0.01214.735-0.009-0.0090.0000.0000.0000.000
10A20ILE00.0170.01316.7830.0020.0020.0000.0000.0000.000
11A21ILE0-0.032-0.01315.325-0.006-0.0060.0000.0000.0000.000
12A22THR00.007-0.00119.9280.0020.0020.0000.0000.0000.000
13A23GLY00.0300.02022.680-0.006-0.0060.0000.0000.0000.000
14A24GLY0-0.035-0.02421.438-0.007-0.0070.0000.0000.0000.000
15A25ALA00.0010.00021.701-0.006-0.0060.0000.0000.0000.000
16A26GLY00.0180.02323.591-0.001-0.0010.0000.0000.0000.000
17A27GLY00.0370.00920.829-0.007-0.0070.0000.0000.0000.000
18A28ILE00.0510.02518.191-0.017-0.0170.0000.0000.0000.000
19A29GLY00.0340.03717.334-0.014-0.0140.0000.0000.0000.000
20A30GLU-1-0.771-0.87517.312-0.104-0.1040.0000.0000.0000.000
21A31THR0-0.028-0.03714.575-0.022-0.0220.0000.0000.0000.000
22A32THR00.004-0.01713.071-0.060-0.0600.0000.0000.0000.000
23A33ALA00.0020.00712.704-0.033-0.0330.0000.0000.0000.000
24A34LYS10.8000.88612.5440.1180.1180.0000.0000.0000.000
25A35LEU0-0.092-0.0217.520-0.094-0.0940.0000.0000.0000.000
26A36PHE00.046-0.0048.095-0.188-0.1880.0000.0000.0000.000
27A37VAL0-0.0050.0109.470-0.003-0.0030.0000.0000.0000.000
28A38ARG10.9050.9645.6111.0271.0270.0000.0000.0000.000
29A39TYR0-0.079-0.0563.635-0.975-0.5170.003-0.134-0.326-0.001
30A40GLY00.1040.0415.9580.4460.4460.0000.0000.0000.000
31A41ALA0-0.0180.0078.2580.1160.1160.0000.0000.0000.000
32A42LYS10.8060.91211.220-0.219-0.2190.0000.0000.0000.000
33A43VAL00.000-0.00814.122-0.014-0.0140.0000.0000.0000.000
34A44VAL00.000-0.00217.0590.0070.0070.0000.0000.0000.000
35A45ILE0-0.0170.00618.726-0.007-0.0070.0000.0000.0000.000
36A46ALA00.0200.00221.5100.0080.0080.0000.0000.0000.000
37A47ASP-1-0.805-0.91624.937-0.035-0.0350.0000.0000.0000.000
38A48ILE00.0310.02727.4310.0040.0040.0000.0000.0000.000
39A49ALA0-0.034-0.00728.7710.0020.0020.0000.0000.0000.000
40A50ASP-1-0.835-0.94229.122-0.007-0.0070.0000.0000.0000.000
41A51ASP-1-0.805-0.88629.073-0.016-0.0160.0000.0000.0000.000
42A52HIS00.023-0.00428.789-0.001-0.0010.0000.0000.0000.000
43A53GLY00.0500.02325.112-0.006-0.0060.0000.0000.0000.000
44A54GLN0-0.085-0.03824.139-0.001-0.0010.0000.0000.0000.000
45A55LYS10.7930.88524.9440.0190.0190.0000.0000.0000.000
46A56VAL00.0090.01220.717-0.002-0.0020.0000.0000.0000.000
47A57CYS00.002-0.00120.440-0.007-0.0070.0000.0000.0000.000
48A58ASN0-0.081-0.03120.3850.0060.0060.0000.0000.0000.000
49A59ASN0-0.044-0.02820.1900.0020.0020.0000.0000.0000.000
50A60ILE0-0.071-0.02514.684-0.026-0.0260.0000.0000.0000.000
51A61GLY00.0270.00615.132-0.015-0.0150.0000.0000.0000.000
52A62SER0-0.028-0.02716.688-0.003-0.0030.0000.0000.0000.000
53A63PRO00.031-0.00818.5850.0030.0030.0000.0000.0000.000
54A64ASP-1-0.872-0.90517.4390.1260.1260.0000.0000.0000.000
55A65VAL0-0.045-0.02313.7220.0150.0150.0000.0000.0000.000
56A66ILE0-0.0020.00116.060-0.022-0.0220.0000.0000.0000.000
57A67SER0-0.043-0.01918.1530.0110.0110.0000.0000.0000.000
58A68PHE00.0160.00621.604-0.009-0.0090.0000.0000.0000.000
59A69VAL0-0.016-0.00224.3400.0060.0060.0000.0000.0000.000
60A70HIS00.0340.02627.424-0.005-0.0050.0000.0000.0000.000
61A71CYS0-0.083-0.05628.2210.0030.0030.0000.0000.0000.000
62A72ASP-1-0.834-0.90029.997-0.012-0.0120.0000.0000.0000.000
63A73VAL00.004-0.02228.1520.0020.0020.0000.0000.0000.000
64A74THR0-0.031-0.02931.3210.0020.0020.0000.0000.0000.000
65A75LYS10.7980.89034.4770.0010.0010.0000.0000.0000.000
66A76ASP-1-0.741-0.84334.2570.0070.0070.0000.0000.0000.000
67A77GLU-1-0.862-0.94134.1910.0040.0040.0000.0000.0000.000
68A78ASP-1-0.752-0.84932.3160.0010.0010.0000.0000.0000.000
69A79VAL00.0300.01428.5210.0010.0010.0000.0000.0000.000
70A80ARG10.8180.91329.147-0.009-0.0090.0000.0000.0000.000
71A81ASN0-0.031-0.02630.0320.0040.0040.0000.0000.0000.000
72A82LEU00.0280.03524.2240.0030.0030.0000.0000.0000.000
73A83VAL0-0.0040.00524.9310.0030.0030.0000.0000.0000.000
74A84ASP-1-0.801-0.88925.5760.0250.0250.0000.0000.0000.000
75A85THR0-0.020-0.02026.4300.0050.0050.0000.0000.0000.000
76A86THR0-0.031-0.02921.0070.0040.0040.0000.0000.0000.000
77A87ILE0-0.034-0.00422.6370.0090.0090.0000.0000.0000.000
78A88ALA0-0.038-0.01724.3840.0070.0070.0000.0000.0000.000
79A89LYS10.8550.93521.332-0.051-0.0510.0000.0000.0000.000
80A90HIS0-0.008-0.00418.9010.0130.0130.0000.0000.0000.000
81A91GLY0-0.0100.00420.0650.0110.0110.0000.0000.0000.000
82A92LYS10.7050.82114.400-0.145-0.1450.0000.0000.0000.000
83A93LEU00.028-0.00518.865-0.001-0.0010.0000.0000.0000.000
84A94ASP-1-0.806-0.87114.7320.0950.0950.0000.0000.0000.000
85A95ILE00.003-0.00412.114-0.007-0.0070.0000.0000.0000.000
86A96MET0-0.0110.00416.837-0.002-0.0020.0000.0000.0000.000
87A97PHE00.0040.00517.768-0.003-0.0030.0000.0000.0000.000
88A98GLY00.0580.02819.8780.0000.0000.0000.0000.0000.000
89A99ASN0-0.034-0.01821.049-0.003-0.0030.0000.0000.0000.000
90A100VAL00.0130.01823.168-0.003-0.0030.0000.0000.0000.000
91A101GLY0-0.022-0.01326.7130.0020.0020.0000.0000.0000.000
92A102VAL0-0.053-0.02129.003-0.003-0.0030.0000.0000.0000.000
93A103LEU00.0580.02230.7980.0010.0010.0000.0000.0000.000
94A104SER0-0.043-0.04433.9540.0010.0010.0000.0000.0000.000
95A105THR0-0.053-0.05237.676-0.001-0.0010.0000.0000.0000.000
96A106THR0-0.046-0.02640.1220.0000.0000.0000.0000.0000.000
97A107PRO00.0190.01041.873-0.001-0.0010.0000.0000.0000.000
98A108TYR0-0.011-0.00140.0440.0010.0010.0000.0000.0000.000
99A109SER00.0440.03842.9860.0000.0000.0000.0000.0000.000
100A110ILE00.019-0.00745.3800.0000.0000.0000.0000.0000.000
101A111LEU0-0.056-0.03147.1620.0010.0010.0000.0000.0000.000
102A112GLU-1-0.910-0.97047.171-0.012-0.0120.0000.0000.0000.000
103A113ALA00.0000.00643.9440.0000.0000.0000.0000.0000.000
104A114GLY00.0590.05044.3430.0000.0000.0000.0000.0000.000
105A115ASN0-0.008-0.01245.033-0.001-0.0010.0000.0000.0000.000
106A116GLU-1-0.775-0.88445.146-0.006-0.0060.0000.0000.0000.000
107A117ASP-1-0.713-0.79840.185-0.015-0.0150.0000.0000.0000.000
108A118PHE00.012-0.00440.442-0.001-0.0010.0000.0000.0000.000
109A119LYS10.8220.88440.4950.0060.0060.0000.0000.0000.000
110A120ARG10.8510.92835.8130.0170.0170.0000.0000.0000.000
111A121VAL0-0.009-0.00534.9920.0000.0000.0000.0000.0000.000
112A122MET0-0.014-0.01535.4220.0000.0000.0000.0000.0000.000
113A123ASP-1-0.896-0.95136.223-0.006-0.0060.0000.0000.0000.000
114A124ILE00.0250.00332.0040.0000.0000.0000.0000.0000.000
115A125ASN0-0.042-0.02131.207-0.001-0.0010.0000.0000.0000.000
116A126VAL0-0.020-0.01131.2490.0000.0000.0000.0000.0000.000
117A127TYR0-0.0030.01333.1860.0020.0020.0000.0000.0000.000
118A128GLY00.0700.02832.1000.0010.0010.0000.0000.0000.000
119A129ALA0-0.0090.00028.6960.0010.0010.0000.0000.0000.000
120A130PHE00.023-0.00229.0130.0020.0020.0000.0000.0000.000
121A131LEU0-0.038-0.00830.7490.0020.0020.0000.0000.0000.000
122A132VAL00.012-0.01025.3130.0020.0020.0000.0000.0000.000
123A133ALA00.0100.00826.0580.0020.0020.0000.0000.0000.000
124A134LYS10.8670.93227.141-0.002-0.0020.0000.0000.0000.000
125A135HIS0-0.006-0.01828.5260.0050.0050.0000.0000.0000.000
126A136ALA00.0430.02623.2370.0030.0030.0000.0000.0000.000
127A137ALA00.0470.02224.9230.0040.0040.0000.0000.0000.000
128A138ARG10.7380.84326.695-0.015-0.0150.0000.0000.0000.000
129A139VAL0-0.022-0.01023.3970.0020.0020.0000.0000.0000.000
130A140MET0-0.027-0.00119.4950.0030.0030.0000.0000.0000.000
131A141ILE00.0280.02423.5780.0030.0030.0000.0000.0000.000
132A142PRO0-0.053-0.02726.3130.0010.0010.0000.0000.0000.000
133A143ALA00.003-0.00521.5900.0010.0010.0000.0000.0000.000
134A144LYS10.8010.91421.938-0.025-0.0250.0000.0000.0000.000
135A145LYS10.9200.95815.584-0.085-0.0850.0000.0000.0000.000
136A146GLY00.0480.01218.076-0.001-0.0010.0000.0000.0000.000
137A147SER0-0.063-0.02816.052-0.002-0.0020.0000.0000.0000.000
138A148ILE00.0140.01018.006-0.005-0.0050.0000.0000.0000.000
139A149VAL0-0.006-0.00716.9980.0000.0000.0000.0000.0000.000
140A150PHE00.0270.00420.421-0.004-0.0040.0000.0000.0000.000
141A151THR0-0.012-0.02621.649-0.002-0.0020.0000.0000.0000.000
142A152ALA00.0170.02323.0850.0030.0030.0000.0000.0000.000
143A153SER00.029-0.01225.876-0.004-0.0040.0000.0000.0000.000
144A154ILE00.0520.03726.3840.0030.0030.0000.0000.0000.000
145A155SER0-0.035-0.00328.3760.0020.0020.0000.0000.0000.000
146A156SER0-0.018-0.02028.0360.0020.0020.0000.0000.0000.000
147A157PHE0-0.021-0.01227.3470.0020.0020.0000.0000.0000.000
148A158THR0-0.049-0.02431.6650.0000.0000.0000.0000.0000.000
149A159ALA00.0420.00334.0320.0000.0000.0000.0000.0000.000
150A160GLY00.0190.00136.353-0.001-0.0010.0000.0000.0000.000
151A161GLU-1-0.921-0.94637.367-0.018-0.0180.0000.0000.0000.000
152A162GLY00.0180.01337.833-0.001-0.0010.0000.0000.0000.000
153A163VAL0-0.042-0.03033.9300.0000.0000.0000.0000.0000.000
154A164SER00.0340.00936.5490.0010.0010.0000.0000.0000.000
155A165HIS00.0380.00037.6650.0000.0000.0000.0000.0000.000
156A166VAL00.0250.03137.7530.0000.0000.0000.0000.0000.000
157A167TYR00.0210.03328.8640.0000.0000.0000.0000.0000.000
158A168THR0-0.005-0.00633.759-0.001-0.0010.0000.0000.0000.000
159A169ALA00.0030.00934.6250.0000.0000.0000.0000.0000.000
160A170THR0-0.032-0.02533.9300.0000.0000.0000.0000.0000.000
161A171LYS10.8810.94826.8720.0290.0290.0000.0000.0000.000
162A172HIS0-0.055-0.02830.6410.0010.0010.0000.0000.0000.000
163A173ALA0-0.0100.00132.7880.0010.0010.0000.0000.0000.000
164A174VAL00.0100.01327.1470.0010.0010.0000.0000.0000.000
165A175LEU00.0320.03427.7710.0010.0010.0000.0000.0000.000
166A176GLY00.0130.01429.6470.0020.0020.0000.0000.0000.000
167A177LEU0-0.0040.00829.5220.0020.0020.0000.0000.0000.000
168A178THR0-0.022-0.02024.7960.0010.0010.0000.0000.0000.000
169A179THR0-0.017-0.01827.1940.0020.0020.0000.0000.0000.000
170A180SER0-0.047-0.03629.4550.0020.0020.0000.0000.0000.000
171A181LEU00.017-0.00227.3970.0010.0010.0000.0000.0000.000
172A182CYS00.0090.04125.7740.0030.0030.0000.0000.0000.000
173A183THR0-0.085-0.04626.7830.0010.0010.0000.0000.0000.000
174A184GLU-1-0.893-0.91629.9300.0100.0100.0000.0000.0000.000
175A185LEU0-0.016-0.02625.4560.0010.0010.0000.0000.0000.000
176A186GLY00.0500.03024.5040.0030.0030.0000.0000.0000.000
177A187GLU-1-0.944-0.95825.3640.0140.0140.0000.0000.0000.000
178A188TYR0-0.135-0.09025.5490.0020.0020.0000.0000.0000.000
179A189GLY00.0010.00022.1390.0030.0030.0000.0000.0000.000
180A190ILE0-0.100-0.03520.4700.0040.0040.0000.0000.0000.000
181A191ARG10.8480.92213.662-0.043-0.0430.0000.0000.0000.000
182A192VAL00.0050.00020.730-0.002-0.0020.0000.0000.0000.000
183A193ASN0-0.022-0.01818.9340.0000.0000.0000.0000.0000.000
184A194CYS0-0.0200.00621.898-0.002-0.0020.0000.0000.0000.000
185A195VAL00.0330.03217.6530.0010.0010.0000.0000.0000.000
186A196SER0-0.021-0.05321.065-0.001-0.0010.0000.0000.0000.000
187A197PRO0-0.0080.00221.0720.0010.0010.0000.0000.0000.000
188A198TYR0-0.025-0.01123.3170.0060.0060.0000.0000.0000.000
189A199ILE0-0.009-0.01525.042-0.003-0.0030.0000.0000.0000.000
190A200VAL0-0.009-0.00220.850-0.003-0.0030.0000.0000.0000.000
191A201ALA0-0.006-0.00522.615-0.001-0.0010.0000.0000.0000.000
192A202SER00.0150.01424.5210.0060.0060.0000.0000.0000.000
193A203PRO0-0.0080.01126.5400.0030.0030.0000.0000.0000.000
194A204LEU00.0270.01629.5650.0010.0010.0000.0000.0000.000
195A205LEU00.0240.01032.1950.0010.0010.0000.0000.0000.000
196A206THR0-0.005-0.00135.7180.0010.0010.0000.0000.0000.000
197A207ASP-1-0.937-0.95836.712-0.024-0.0240.0000.0000.0000.000
198A208VAL0-0.004-0.00238.9590.0020.0020.0000.0000.0000.000
199A209PHE0-0.040-0.02341.4460.0000.0000.0000.0000.0000.000
200A210GLY0-0.045-0.02040.6140.0000.0000.0000.0000.0000.000
201A211VAL0-0.023-0.02135.402-0.001-0.0010.0000.0000.0000.000
202A212ASP-1-0.753-0.86033.576-0.038-0.0380.0000.0000.0000.000
203A213SER0-0.023-0.04128.638-0.002-0.0020.0000.0000.0000.000
204A214SER0-0.019-0.01529.620-0.002-0.0020.0000.0000.0000.000
205A215ARG10.8880.92230.6620.0340.0340.0000.0000.0000.000
206A216VAL00.0030.00230.1960.0010.0010.0000.0000.0000.000
207A217GLU-1-0.910-0.94525.123-0.070-0.0700.0000.0000.0000.000
208A218GLU-1-0.884-0.94128.742-0.040-0.0400.0000.0000.0000.000
209A219LEU0-0.041-0.01831.0050.0020.0020.0000.0000.0000.000
210A220ALA00.0140.02128.0170.0020.0020.0000.0000.0000.000
211A221HIS00.0640.03826.9700.0000.0000.0000.0000.0000.000
212A222GLN0-0.039-0.01528.7670.0020.0020.0000.0000.0000.000
213A223ALA0-0.011-0.01532.1460.0020.0020.0000.0000.0000.000
214A224ALA00.0030.02427.1700.0020.0020.0000.0000.0000.000
215A225ASN0-0.050-0.02327.4400.0030.0030.0000.0000.0000.000
216A226LEU0-0.0180.00021.4040.0010.0010.0000.0000.0000.000
217A227LYS10.8060.88226.1060.0370.0370.0000.0000.0000.000
218A228GLY0-0.009-0.00925.041-0.002-0.0020.0000.0000.0000.000
219A229THR0-0.019-0.00619.651-0.009-0.0090.0000.0000.0000.000
220A230LEU0-0.0080.00521.6250.0070.0070.0000.0000.0000.000
221A231LEU0-0.0310.00419.424-0.007-0.0070.0000.0000.0000.000
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