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: 39Y8L

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 OptHSide
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 -3230649.208637
FMO2-HF: Nuclear repulsion 3131855.506549
FMO2-HF: Total energy -98793.702088
FMO2-MP2: Total energy -99083.164019


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.
-6.035-1.2580.288-1.853-3.2120.007
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 : -0.010 / q_NPA : -0.021
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].
3A13ARG10.9830.9913.118-6.995-3.0300.272-1.615-2.6220.008
4A14LEU00.0010.0114.224-0.383-0.1640.001-0.027-0.1930.000
5A15GLN00.0010.0056.3560.0130.0130.0000.0000.0000.000
6A16ASP-1-0.877-0.9448.0270.3250.3250.0000.0000.0000.000
7A17LYS10.8200.9289.780-0.585-0.5850.0000.0000.0000.000
8A18VAL0-0.0110.00112.717-0.022-0.0220.0000.0000.0000.000
9A19ALA00.003-0.00314.787-0.001-0.0010.0000.0000.0000.000
10A20ILE00.0180.01816.828-0.013-0.0130.0000.0000.0000.000
11A21ILE0-0.0210.00014.9810.0020.0020.0000.0000.0000.000
12A22THR00.0090.00719.622-0.006-0.0060.0000.0000.0000.000
13A23GLY00.0370.02522.027-0.003-0.0030.0000.0000.0000.000
14A24GLY0-0.033-0.03520.738-0.007-0.0070.0000.0000.0000.000
15A25ALA00.000-0.00321.092-0.010-0.0100.0000.0000.0000.000
16A26GLY00.0090.02023.347-0.004-0.0040.0000.0000.0000.000
17A27GLY00.0400.01420.941-0.005-0.0050.0000.0000.0000.000
18A28ILE00.0420.01417.684-0.014-0.0140.0000.0000.0000.000
19A29GLY00.0330.03717.153-0.006-0.0060.0000.0000.0000.000
20A30GLU-1-0.778-0.87617.223-0.088-0.0880.0000.0000.0000.000
21A31THR0-0.013-0.02914.525-0.017-0.0170.0000.0000.0000.000
22A32THR0-0.004-0.02512.913-0.046-0.0460.0000.0000.0000.000
23A33ALA00.0060.00712.420-0.012-0.0120.0000.0000.0000.000
24A34LYS10.8080.89712.3340.1160.1160.0000.0000.0000.000
25A35LEU0-0.086-0.0267.068-0.121-0.1210.0000.0000.0000.000
26A36PHE00.050-0.0027.810-0.146-0.1460.0000.0000.0000.000
27A37VAL00.0090.0229.2800.0300.0300.0000.0000.0000.000
28A38ARG10.9170.9675.3781.1101.1100.0000.0000.0000.000
29A39TYR0-0.074-0.0363.319-0.812-0.2190.015-0.211-0.397-0.001
30A40GLY00.1230.0495.8480.6170.6170.0000.0000.0000.000
31A41ALA0-0.0230.0018.4860.1060.1060.0000.0000.0000.000
32A42LYS10.8130.91311.472-0.336-0.3360.0000.0000.0000.000
33A43VAL0-0.005-0.01913.766-0.001-0.0010.0000.0000.0000.000
34A44VAL0-0.004-0.00516.620-0.005-0.0050.0000.0000.0000.000
35A45ILE0-0.0090.00518.264-0.001-0.0010.0000.0000.0000.000
36A46ALA00.016-0.00221.0970.0040.0040.0000.0000.0000.000
37A47ASP-1-0.842-0.94424.485-0.004-0.0040.0000.0000.0000.000
38A48ILE00.0320.02927.0140.0020.0020.0000.0000.0000.000
39A49ALA0-0.043-0.00828.6080.0000.0000.0000.0000.0000.000
40A50ASP-1-0.820-0.93428.5170.0110.0110.0000.0000.0000.000
41A51ASP-1-0.820-0.89329.007-0.006-0.0060.0000.0000.0000.000
42A52HIS0-0.010-0.02528.816-0.002-0.0020.0000.0000.0000.000
43A53GLY00.0670.02625.105-0.006-0.0060.0000.0000.0000.000
44A54GLN0-0.089-0.04223.921-0.002-0.0020.0000.0000.0000.000
45A55LYS10.8040.88624.9220.0120.0120.0000.0000.0000.000
46A56VAL00.0070.01520.550-0.004-0.0040.0000.0000.0000.000
47A57CYS0-0.014-0.01120.013-0.008-0.0080.0000.0000.0000.000
48A58ASN0-0.079-0.01220.0710.0050.0050.0000.0000.0000.000
49A59ASN0-0.009-0.02619.607-0.012-0.0120.0000.0000.0000.000
50A60ILE0-0.071-0.01214.424-0.018-0.0180.0000.0000.0000.000
51A61GLY00.0190.00315.271-0.021-0.0210.0000.0000.0000.000
52A62SER0-0.022-0.01616.751-0.002-0.0020.0000.0000.0000.000
53A63PRO00.027-0.02018.6230.0080.0080.0000.0000.0000.000
54A64ASP-1-0.895-0.91017.7080.1280.1280.0000.0000.0000.000
55A65VAL0-0.060-0.02614.0300.0250.0250.0000.0000.0000.000
56A66ILE0-0.017-0.00216.143-0.005-0.0050.0000.0000.0000.000
57A67SER0-0.021-0.01118.2320.0030.0030.0000.0000.0000.000
58A68PHE00.0260.02221.444-0.003-0.0030.0000.0000.0000.000
59A69VAL0-0.019-0.00724.0620.0030.0030.0000.0000.0000.000
60A70HIS00.0390.02626.907-0.004-0.0040.0000.0000.0000.000
61A71CYS0-0.094-0.05428.0180.0050.0050.0000.0000.0000.000
62A72ASP-1-0.827-0.89629.8480.0150.0150.0000.0000.0000.000
63A73VAL00.000-0.03127.7920.0020.0020.0000.0000.0000.000
64A74THR0-0.055-0.03231.0810.0020.0020.0000.0000.0000.000
65A75LYS10.8090.89434.170-0.023-0.0230.0000.0000.0000.000
66A76ASP-1-0.774-0.86634.0030.0410.0410.0000.0000.0000.000
67A77GLU-1-0.841-0.92734.2410.0300.0300.0000.0000.0000.000
68A78ASP-1-0.778-0.86631.9080.0280.0280.0000.0000.0000.000
69A79VAL00.0210.00828.4360.0030.0030.0000.0000.0000.000
70A80ARG10.8660.93129.472-0.038-0.0380.0000.0000.0000.000
71A81ASN0-0.018-0.01330.5450.0060.0060.0000.0000.0000.000
72A82LEU00.0170.02824.2070.0040.0040.0000.0000.0000.000
73A83VAL0-0.015-0.01125.4030.0060.0060.0000.0000.0000.000
74A84ASP-1-0.807-0.89726.1250.0680.0680.0000.0000.0000.000
75A85THR0-0.009-0.01126.4290.0040.0040.0000.0000.0000.000
76A86THR0-0.021-0.01421.2620.0050.0050.0000.0000.0000.000
77A87ILE0-0.0380.00822.8260.0120.0120.0000.0000.0000.000
78A88ALA0-0.035-0.01024.7110.0050.0050.0000.0000.0000.000
79A89LYS10.8410.91521.837-0.087-0.0870.0000.0000.0000.000
80A90HIS00.002-0.01119.1640.0050.0050.0000.0000.0000.000
81A91GLY00.0020.01920.3150.0180.0180.0000.0000.0000.000
82A92LYS10.7270.84914.342-0.296-0.2960.0000.0000.0000.000
83A93LEU00.025-0.00419.241-0.002-0.0020.0000.0000.0000.000
84A94ASP-1-0.820-0.90514.9530.2550.2550.0000.0000.0000.000
85A95ILE00.003-0.00212.441-0.002-0.0020.0000.0000.0000.000
86A96MET0-0.0170.01017.164-0.015-0.0150.0000.0000.0000.000
87A97PHE0-0.012-0.01117.3190.0020.0020.0000.0000.0000.000
88A98GLY00.0510.02219.538-0.010-0.0100.0000.0000.0000.000
89A99ASN0-0.036-0.00220.785-0.002-0.0020.0000.0000.0000.000
90A100VAL00.0330.00622.905-0.007-0.0070.0000.0000.0000.000
91A101GLY0-0.034-0.02126.5790.0040.0040.0000.0000.0000.000
92A102VAL0-0.038-0.01328.809-0.004-0.0040.0000.0000.0000.000
93A103LEU00.0700.02430.7410.0020.0020.0000.0000.0000.000
94A104SER0-0.065-0.06233.8760.0010.0010.0000.0000.0000.000
95A105THR0-0.058-0.03837.643-0.002-0.0020.0000.0000.0000.000
96A106THR0-0.027-0.02639.7740.0000.0000.0000.0000.0000.000
97A107PRO0-0.008-0.01041.5850.0000.0000.0000.0000.0000.000
98A108TYR00.0170.02040.4390.0010.0010.0000.0000.0000.000
99A109SER00.0290.01442.4140.0010.0010.0000.0000.0000.000
100A110ILE00.033-0.00145.1360.0000.0000.0000.0000.0000.000
101A111LEU0-0.047-0.02346.8390.0010.0010.0000.0000.0000.000
102A112GLU-1-0.923-0.96847.184-0.002-0.0020.0000.0000.0000.000
103A113ALA0-0.0080.02344.0650.0000.0000.0000.0000.0000.000
104A114GLY00.0360.02544.5690.0000.0000.0000.0000.0000.000
105A115ASN00.011-0.00444.6620.0000.0000.0000.0000.0000.000
106A116GLU-1-0.792-0.89245.0480.0090.0090.0000.0000.0000.000
107A117ASP-1-0.736-0.82340.1520.0040.0040.0000.0000.0000.000
108A118PHE00.0200.00140.3480.0010.0010.0000.0000.0000.000
109A119LYS10.8320.87840.211-0.008-0.0080.0000.0000.0000.000
110A120ARG10.9280.98335.759-0.002-0.0020.0000.0000.0000.000
111A121VAL00.0060.00334.6830.0010.0010.0000.0000.0000.000
112A122MET0-0.023-0.01335.0820.0020.0020.0000.0000.0000.000
113A123ASP-1-0.885-0.94335.8470.0210.0210.0000.0000.0000.000
114A124ILE00.015-0.00431.6290.0020.0020.0000.0000.0000.000
115A125ASN0-0.053-0.02930.9180.0020.0020.0000.0000.0000.000
116A126VAL0-0.006-0.00330.8030.0020.0020.0000.0000.0000.000
117A127TYR0-0.0210.00032.5960.0050.0050.0000.0000.0000.000
118A128GLY00.0740.03531.5470.0030.0030.0000.0000.0000.000
119A129ALA0-0.025-0.00928.2740.0040.0040.0000.0000.0000.000
120A130PHE00.018-0.01028.7740.0060.0060.0000.0000.0000.000
121A131LEU0-0.027-0.00131.0330.0050.0050.0000.0000.0000.000
122A132VAL00.016-0.00324.9970.0040.0040.0000.0000.0000.000
123A133ALA00.0250.01526.2950.0060.0060.0000.0000.0000.000
124A134LYS10.8700.94027.369-0.035-0.0350.0000.0000.0000.000
125A135HIS0-0.019-0.03128.8940.0060.0060.0000.0000.0000.000
126A136ALA00.0380.02423.5420.0040.0040.0000.0000.0000.000
127A137ALA00.0380.00925.1470.0070.0070.0000.0000.0000.000
128A138ARG10.7420.85026.917-0.058-0.0580.0000.0000.0000.000
129A139VAL0-0.012-0.00823.7510.0000.0000.0000.0000.0000.000
130A140MET0-0.0350.00719.7660.0040.0040.0000.0000.0000.000
131A141ILE00.0470.03323.9110.0060.0060.0000.0000.0000.000
132A142PRO0-0.069-0.03426.5300.0000.0000.0000.0000.0000.000
133A143ALA0-0.006-0.00521.7740.0000.0000.0000.0000.0000.000
134A144LYS10.8120.91622.499-0.080-0.0800.0000.0000.0000.000
135A145LYS10.9350.97115.964-0.218-0.2180.0000.0000.0000.000
136A146GLY00.0330.00418.467-0.008-0.0080.0000.0000.0000.000
137A147SER0-0.047-0.00616.277-0.012-0.0120.0000.0000.0000.000
138A148ILE00.009-0.00318.330-0.005-0.0050.0000.0000.0000.000
139A149VAL00.000-0.00216.842-0.001-0.0010.0000.0000.0000.000
140A150PHE00.0200.00520.199-0.009-0.0090.0000.0000.0000.000
141A151THR0-0.003-0.01921.5020.0040.0040.0000.0000.0000.000
142A152ALA0-0.0020.00322.908-0.002-0.0020.0000.0000.0000.000
143A153SER00.036-0.00825.695-0.007-0.0070.0000.0000.0000.000
144A154ILE00.0520.04426.2530.0040.0040.0000.0000.0000.000
145A155SER0-0.022-0.00828.2740.0000.0000.0000.0000.0000.000
146A156SER0-0.034-0.03127.9590.0020.0020.0000.0000.0000.000
147A157PHE0-0.031-0.01627.4180.0020.0020.0000.0000.0000.000
148A158THR0-0.050-0.01531.742-0.002-0.0020.0000.0000.0000.000
149A159ALA00.0280.00234.1640.0000.0000.0000.0000.0000.000
150A160GLY00.026-0.00635.855-0.001-0.0010.0000.0000.0000.000
151A161GLU-1-0.948-0.95836.846-0.007-0.0070.0000.0000.0000.000
152A162GLY00.0230.00637.973-0.001-0.0010.0000.0000.0000.000
153A163VAL0-0.057-0.01733.9490.0000.0000.0000.0000.0000.000
154A164SER0-0.005-0.00636.6220.0020.0020.0000.0000.0000.000
155A165HIS00.0810.02937.4950.0020.0020.0000.0000.0000.000
156A166VAL00.0190.02137.4880.0010.0010.0000.0000.0000.000
157A167TYR00.0100.00828.5980.0030.0030.0000.0000.0000.000
158A168THR0-0.001-0.00633.6750.0020.0020.0000.0000.0000.000
159A169ALA0-0.0070.00734.6570.0020.0020.0000.0000.0000.000
160A170THR0-0.022-0.01033.4430.0020.0020.0000.0000.0000.000
161A171LYS10.8830.94426.761-0.012-0.0120.0000.0000.0000.000
162A172HIS0-0.029-0.01630.5380.0030.0030.0000.0000.0000.000
163A173ALA0-0.0170.00032.6430.0030.0030.0000.0000.0000.000
164A174VAL00.0030.00626.9560.0030.0030.0000.0000.0000.000
165A175LEU00.0430.03627.5640.0050.0050.0000.0000.0000.000
166A176GLY00.0080.00829.3240.0040.0040.0000.0000.0000.000
167A177LEU00.0060.01029.5490.0020.0020.0000.0000.0000.000
168A178THR0-0.019-0.01524.8010.0050.0050.0000.0000.0000.000
169A179THR0-0.015-0.01227.4340.0050.0050.0000.0000.0000.000
170A180SER0-0.047-0.03429.6500.0020.0020.0000.0000.0000.000
171A181LEU00.016-0.00427.5400.0010.0010.0000.0000.0000.000
172A182CYS0-0.0030.04625.8380.0070.0070.0000.0000.0000.000
173A183THR0-0.076-0.03926.8870.0020.0020.0000.0000.0000.000
174A184GLU-1-0.944-0.97230.0350.0580.0580.0000.0000.0000.000
175A185LEU0-0.004-0.02525.8450.0020.0020.0000.0000.0000.000
176A186GLY00.0470.03325.0170.0070.0070.0000.0000.0000.000
177A187GLU-1-0.947-0.96025.9120.0680.0680.0000.0000.0000.000
178A188TYR0-0.111-0.05825.9680.0010.0010.0000.0000.0000.000
179A189GLY0-0.002-0.00322.6150.0070.0070.0000.0000.0000.000
180A190ILE0-0.083-0.02720.8750.0150.0150.0000.0000.0000.000
181A191ARG10.8450.93014.295-0.237-0.2370.0000.0000.0000.000
182A192VAL0-0.0020.00021.0760.0000.0000.0000.0000.0000.000
183A193ASN0-0.014-0.01719.197-0.011-0.0110.0000.0000.0000.000
184A194CYS0-0.0180.00621.857-0.004-0.0040.0000.0000.0000.000
185A195VAL00.0400.03717.6440.0040.0040.0000.0000.0000.000
186A196SER0-0.001-0.03921.087-0.008-0.0080.0000.0000.0000.000
187A197PRO0-0.028-0.01320.943-0.001-0.0010.0000.0000.0000.000
188A198TYR00.0010.00723.1990.0030.0030.0000.0000.0000.000
189A199ILE0-0.024-0.02425.1120.0000.0000.0000.0000.0000.000
190A200VAL0-0.051-0.02420.716-0.005-0.0050.0000.0000.0000.000
191A201ALA00.006-0.01621.6910.0000.0000.0000.0000.0000.000
192A202SER00.0050.00823.7390.0020.0020.0000.0000.0000.000
193A203PRO0-0.021-0.01926.6110.0020.0020.0000.0000.0000.000
194A204LEU0-0.022-0.01329.490-0.002-0.0020.0000.0000.0000.000
195A205LEU00.0220.02232.0070.0020.0020.0000.0000.0000.000
196A206THR00.0010.00535.5350.0000.0000.0000.0000.0000.000
197A207ASP-1-0.927-0.95636.311-0.016-0.0160.0000.0000.0000.000
198A208VAL0-0.0080.01038.4980.0020.0020.0000.0000.0000.000
199A209PHE0-0.045-0.04041.054-0.001-0.0010.0000.0000.0000.000
200A210GLY0-0.032-0.01140.628-0.001-0.0010.0000.0000.0000.000
201A211VAL0-0.006-0.00535.3020.0000.0000.0000.0000.0000.000
202A212ASP-1-0.759-0.88033.226-0.036-0.0360.0000.0000.0000.000
203A213SER00.0470.00627.9570.0000.0000.0000.0000.0000.000
204A214SER0-0.037-0.01329.265-0.001-0.0010.0000.0000.0000.000
205A215ARG10.8810.92530.2900.0320.0320.0000.0000.0000.000
206A216VAL00.0080.00929.9060.0020.0020.0000.0000.0000.000
207A217GLU-1-0.913-0.95325.455-0.067-0.0670.0000.0000.0000.000
208A218GLU-1-0.881-0.93728.623-0.041-0.0410.0000.0000.0000.000
209A219LEU0-0.041-0.02431.0850.0010.0010.0000.0000.0000.000
210A220ALA00.0220.02928.1950.0030.0030.0000.0000.0000.000
211A221HIS00.0740.04726.8480.0010.0010.0000.0000.0000.000
212A222GLN0-0.047-0.02028.9130.0030.0030.0000.0000.0000.000
213A223ALA0-0.003-0.00632.2160.0020.0020.0000.0000.0000.000
214A224ALA0-0.0080.01627.3180.0030.0030.0000.0000.0000.000
215A225ASN0-0.040-0.01527.2100.0000.0000.0000.0000.0000.000
216A226LEU0-0.024-0.00921.363-0.001-0.0010.0000.0000.0000.000
217A227LYS10.8030.88025.8790.0290.0290.0000.0000.0000.000
218A228GLY00.000-0.00325.028-0.002-0.0020.0000.0000.0000.000
219A229THR0-0.032-0.01819.513-0.015-0.0150.0000.0000.0000.000
220A230LEU0-0.0090.00721.4850.0090.0090.0000.0000.0000.000
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