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: 85KZY

Calculation Name: 3ZXX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZXX

Chain ID: A

ChEMBL ID:

UniProt ID: Q52QI9

Base Structure: X-ray

Registration Date: 2023-06-26

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 269
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3441369.76577
FMO2-HF: Nuclear repulsion 3341595.283988
FMO2-HF: Total energy -99774.481782
FMO2-MP2: Total energy -100063.822794


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:LEU)


Summations of interaction energy for fragment #1(A:11:LEU)
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.
-2.6691.079-0.02-1.464-2.265-0.002
Interaction energy analysis for fragmet #1(A:11:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.023
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].
3A13GLY00.0540.0303.578-2.904-0.209-0.028-1.324-1.343-0.002
4A14ASP-1-0.823-0.9105.6462.7952.7950.0000.0000.0000.000
5A15HIS00.0190.0018.301-0.242-0.2420.0000.0000.0000.000
6A16ASN0-0.141-0.08511.583-0.290-0.2900.0000.0000.0000.000
7A17ILE0-0.053-0.0279.674-0.118-0.1180.0000.0000.0000.000
8A18ARG10.8820.94412.258-0.242-0.2420.0000.0000.0000.000
9A19VAL00.0270.01412.300-0.044-0.0440.0000.0000.0000.000
10A20ALA00.006-0.00215.4230.0090.0090.0000.0000.0000.000
11A21ILE0-0.017-0.00617.093-0.023-0.0230.0000.0000.0000.000
12A22LEU0-0.013-0.00320.5340.0100.0100.0000.0000.0000.000
13A23ASP-1-0.758-0.84824.135-0.032-0.0320.0000.0000.0000.000
14A24GLY00.021-0.01526.1670.0070.0070.0000.0000.0000.000
15A25PRO0-0.049-0.03226.9840.0050.0050.0000.0000.0000.000
16A26VAL00.0060.01221.948-0.007-0.0070.0000.0000.0000.000
17A27ASP-1-0.842-0.92925.1900.0260.0260.0000.0000.0000.000
18A28ILE0-0.006-0.02521.868-0.003-0.0030.0000.0000.0000.000
19A29ALA0-0.0060.01122.8630.0110.0110.0000.0000.0000.000
20A30HIS0-0.0230.00921.7130.0020.0020.0000.0000.0000.000
21A31PRO00.021-0.01021.5680.0100.0100.0000.0000.0000.000
22A32CYS0-0.059-0.02317.2300.0110.0110.0000.0000.0000.000
23A33PHE00.0290.01316.4840.0040.0040.0000.0000.0000.000
24A34GLN00.0000.01618.1260.0390.0390.0000.0000.0000.000
25A35GLY0-0.008-0.00915.572-0.005-0.0050.0000.0000.0000.000
26A36ALA0-0.025-0.00614.1920.0640.0640.0000.0000.0000.000
27A37ASP-1-0.869-0.91514.2100.4010.4010.0000.0000.0000.000
28A38LEU00.0020.00616.029-0.012-0.0120.0000.0000.0000.000
29A39THR0-0.040-0.01618.846-0.007-0.0070.0000.0000.0000.000
30A40VAL00.0120.00821.871-0.008-0.0080.0000.0000.0000.000
31A41LEU0-0.025-0.01123.8570.0010.0010.0000.0000.0000.000
32A42PRO00.0040.00426.961-0.008-0.0080.0000.0000.0000.000
33A43THR00.0460.02530.6180.0010.0010.0000.0000.0000.000
34A44LEU0-0.031-0.00632.5680.0010.0010.0000.0000.0000.000
35A45ALA00.0170.00035.196-0.004-0.0040.0000.0000.0000.000
36A46PRO00.0400.02837.8790.0010.0010.0000.0000.0000.000
37A47THR0-0.086-0.04939.0270.0000.0000.0000.0000.0000.000
38A48ALA00.028-0.00139.4620.0000.0000.0000.0000.0000.000
39A49ALA0-0.010-0.01039.8540.0000.0000.0000.0000.0000.000
40A50ARG10.8420.90337.1330.0090.0090.0000.0000.0000.000
41A51SER0-0.036-0.04237.533-0.002-0.0020.0000.0000.0000.000
42A52ASP-1-0.801-0.84535.403-0.011-0.0110.0000.0000.0000.000
43A53GLY00.0890.03832.353-0.003-0.0030.0000.0000.0000.000
44A54PHE0-0.040-0.02330.120-0.003-0.0030.0000.0000.0000.000
45A55MET0-0.0560.00328.5300.0030.0030.0000.0000.0000.000
46A56SER00.008-0.03625.258-0.005-0.0050.0000.0000.0000.000
47A57ALA0-0.031-0.01927.624-0.003-0.0030.0000.0000.0000.000
48A58HIS00.0060.01024.594-0.002-0.0020.0000.0000.0000.000
49A59GLY00.0490.02623.693-0.006-0.0060.0000.0000.0000.000
50A60THR00.024-0.00622.1750.0050.0050.0000.0000.0000.000
51A61HIS00.0070.03520.7010.0020.0020.0000.0000.0000.000
52A62VAL00.0490.02619.348-0.017-0.0170.0000.0000.0000.000
53A63ALA00.0150.01017.807-0.012-0.0120.0000.0000.0000.000
54A64SER0-0.028-0.03116.316-0.001-0.0010.0000.0000.0000.000
55A65ILE00.0330.02814.296-0.020-0.0200.0000.0000.0000.000
56A66ILE0-0.042-0.00611.708-0.079-0.0790.0000.0000.0000.000
57A67PHE0-0.007-0.01511.348-0.032-0.0320.0000.0000.0000.000
58A68GLY00.0330.03213.4260.0540.0540.0000.0000.0000.000
59A69GLN0-0.038-0.03111.8320.0100.0100.0000.0000.0000.000
60A70PRO0-0.007-0.0088.785-0.076-0.0760.0000.0000.0000.000
61A71GLU-1-0.937-0.96911.483-0.119-0.1190.0000.0000.0000.000
62A72THR0-0.032-0.00514.6640.0190.0190.0000.0000.0000.000
63A73SER0-0.020-0.03016.567-0.021-0.0210.0000.0000.0000.000
64A74VAL0-0.048-0.03315.717-0.011-0.0110.0000.0000.0000.000
65A75PRO0-0.0080.01011.4710.0190.0190.0000.0000.0000.000
66A76GLY00.0380.04111.724-0.041-0.0410.0000.0000.0000.000
67A77ILE0-0.080-0.0547.776-0.155-0.1550.0000.0000.0000.000
68A78ALA0-0.047-0.0346.893-0.449-0.4490.0000.0000.0000.000
69A79PRO0-0.019-0.0016.9160.2090.2090.0000.0000.0000.000
70A80GLN0-0.019-0.0084.976-0.300-0.198-0.001-0.004-0.0970.000
71A81CYS0-0.0660.0018.8760.0910.0910.0000.0000.0000.000
72A82ARG10.9751.00810.549-0.391-0.3910.0000.0000.0000.000
73A83GLY00.015-0.00914.268-0.045-0.0450.0000.0000.0000.000
74A84LEU0-0.053-0.03416.4190.0030.0030.0000.0000.0000.000
75A85ILE00.0300.00819.777-0.020-0.0200.0000.0000.0000.000
76A86VAL0-0.022-0.01922.3650.0060.0060.0000.0000.0000.000
77A87PRO0-0.0090.01725.142-0.010-0.0100.0000.0000.0000.000
78A88ILE0-0.004-0.01427.2610.0030.0030.0000.0000.0000.000
79A89PHE00.0150.00929.201-0.004-0.0040.0000.0000.0000.000
80A90SER00.0040.00333.0770.0040.0040.0000.0000.0000.000
81A91ASP-1-0.817-0.89935.8470.0120.0120.0000.0000.0000.000
82A92ASP-1-0.867-0.94433.6110.0080.0080.0000.0000.0000.000
83A93ARG10.8500.90335.188-0.012-0.0120.0000.0000.0000.000
84A94ARG10.8040.91637.916-0.014-0.0140.0000.0000.0000.000
85A95ARG10.8240.89437.0110.0100.0100.0000.0000.0000.000
86A96ILE00.0310.01931.8670.0030.0030.0000.0000.0000.000
87A97THR0-0.016-0.02335.296-0.003-0.0030.0000.0000.0000.000
88A98GLN0-0.020-0.04534.322-0.001-0.0010.0000.0000.0000.000
89A99LEU0-0.020-0.00434.0060.0020.0020.0000.0000.0000.000
90A100ASP-1-0.837-0.89133.8440.0180.0180.0000.0000.0000.000
91A101LEU00.0170.00927.6100.0040.0040.0000.0000.0000.000
92A102ALA0-0.002-0.00429.6050.0040.0040.0000.0000.0000.000
93A103ARG10.9760.99630.531-0.023-0.0230.0000.0000.0000.000
94A104GLY00.0100.00928.5650.0070.0070.0000.0000.0000.000
95A105ILE00.014-0.00525.6330.0080.0080.0000.0000.0000.000
96A106GLU-1-0.911-0.95626.0760.0460.0460.0000.0000.0000.000
97A107ARG10.8340.91527.725-0.051-0.0510.0000.0000.0000.000
98A108ALA00.0210.01222.4500.0120.0120.0000.0000.0000.000
99A109VAL00.014-0.00122.8830.0150.0150.0000.0000.0000.000
100A110ASN0-0.071-0.04824.1810.0140.0140.0000.0000.0000.000
101A111ALA0-0.0410.00023.1850.0080.0080.0000.0000.0000.000
102A112GLY0-0.023-0.01221.1160.0240.0240.0000.0000.0000.000
103A113ALA0-0.036-0.01318.4190.0260.0260.0000.0000.0000.000
104A114HIS00.0340.02814.8290.0050.0050.0000.0000.0000.000
105A115ILE0-0.010-0.00712.760-0.029-0.0290.0000.0000.0000.000
106A116ILE0-0.006-0.00316.8510.0180.0180.0000.0000.0000.000
107A117ASN00.0280.03217.763-0.035-0.0350.0000.0000.0000.000
108A118ILE00.001-0.01219.7820.0110.0110.0000.0000.0000.000
109A119SER00.023-0.00321.427-0.008-0.0080.0000.0000.0000.000
110A120GLY00.0100.01823.679-0.006-0.0060.0000.0000.0000.000
111A121GLY0-0.020-0.02027.162-0.002-0.0020.0000.0000.0000.000
112A122GLU-1-0.811-0.89229.861-0.011-0.0110.0000.0000.0000.000
113A123LEU0-0.044-0.02233.464-0.001-0.0010.0000.0000.0000.000
114A124THR0-0.084-0.03834.8630.0030.0030.0000.0000.0000.000
115A125ASP-1-0.963-0.97837.128-0.025-0.0250.0000.0000.0000.000
116A126PHE0-0.070-0.06035.728-0.004-0.0040.0000.0000.0000.000
117A127GLY0-0.0030.00434.0360.0000.0000.0000.0000.0000.000
118A128GLU-1-0.790-0.88534.428-0.017-0.0170.0000.0000.0000.000
119A129ALA00.022-0.00734.246-0.001-0.0010.0000.0000.0000.000
120A130ASP-1-0.875-0.92536.337-0.001-0.0010.0000.0000.0000.000
121A131GLY00.010-0.00836.5700.0010.0010.0000.0000.0000.000
122A132TRP0-0.010-0.00935.9630.0020.0020.0000.0000.0000.000
123A133LEU00.0280.00830.1040.0030.0030.0000.0000.0000.000
124A134GLU-1-0.858-0.92831.744-0.003-0.0030.0000.0000.0000.000
125A135ASN0-0.035-0.02232.2040.0000.0000.0000.0000.0000.000
126A136ALA00.0170.01229.7480.0040.0040.0000.0000.0000.000
127A137VAL00.0170.00326.8610.0050.0050.0000.0000.0000.000
128A138SER0-0.022-0.02227.4780.0000.0000.0000.0000.0000.000
129A139LEU0-0.0040.00928.0310.0040.0040.0000.0000.0000.000
130A140CYS00.0010.00823.5620.0090.0090.0000.0000.0000.000
131A141ARG10.9580.99024.1200.0020.0020.0000.0000.0000.000
132A142GLN0-0.056-0.03025.5670.0000.0000.0000.0000.0000.000
133A143ASN0-0.073-0.04524.5920.0090.0090.0000.0000.0000.000
134A144ASN0-0.051-0.02019.7680.0040.0040.0000.0000.0000.000
135A145VAL00.0340.02219.6550.0140.0140.0000.0000.0000.000
136A146LEU0-0.065-0.02715.763-0.015-0.0150.0000.0000.0000.000
137A147LEU00.0160.01218.9470.0040.0040.0000.0000.0000.000
138A148VAL00.0250.00716.646-0.010-0.0100.0000.0000.0000.000
139A149ALA00.006-0.01220.1190.0080.0080.0000.0000.0000.000
140A150ALA00.0210.02623.064-0.011-0.0110.0000.0000.0000.000
141A151ALA0-0.0060.00024.2020.0090.0090.0000.0000.0000.000
142A152GLY00.0710.04626.4370.0080.0080.0000.0000.0000.000
143A153ASN0-0.013-0.01327.458-0.013-0.0130.0000.0000.0000.000
144A154ASN00.0630.02230.1820.0010.0010.0000.0000.0000.000
145A155GLY00.0530.04032.0720.0020.0020.0000.0000.0000.000
146A156CYS0-0.075-0.02933.2820.0060.0060.0000.0000.0000.000
147A157ASP-1-0.800-0.87033.405-0.053-0.0530.0000.0000.0000.000
148A159LEU00.0480.03030.940-0.005-0.0050.0000.0000.0000.000
149A160HIS0-0.009-0.01229.5330.0040.0040.0000.0000.0000.000
150A161VAL0-0.0060.03630.451-0.001-0.0010.0000.0000.0000.000
151A162PRO00.050-0.02226.5130.0000.0000.0000.0000.0000.000
152A163ALA0-0.009-0.00225.9210.0010.0010.0000.0000.0000.000
153A164ALA00.005-0.00226.780-0.004-0.0040.0000.0000.0000.000
154A165LEU00.0150.02828.8230.0020.0020.0000.0000.0000.000
155A166PRO00.0410.00827.837-0.004-0.0040.0000.0000.0000.000
156A167ALA0-0.073-0.04024.5300.0060.0060.0000.0000.0000.000
157A168VAL00.0090.02323.2340.0030.0030.0000.0000.0000.000
158A169LEU0-0.043-0.01717.083-0.005-0.0050.0000.0000.0000.000
159A170ALA00.0050.01121.5060.0000.0000.0000.0000.0000.000
160A171VAL0-0.029-0.01518.616-0.015-0.0150.0000.0000.0000.000
161A172GLY00.0560.01921.5130.0130.0130.0000.0000.0000.000
162A173ALA0-0.035-0.02421.241-0.017-0.0170.0000.0000.0000.000
163A174MET0-0.030-0.01117.5640.0160.0160.0000.0000.0000.000
164A175ASP-1-0.770-0.90521.438-0.153-0.1530.0000.0000.0000.000
165A176ASP-1-0.900-0.95019.600-0.221-0.2210.0000.0000.0000.000
166A177HIS0-0.137-0.05520.133-0.018-0.0180.0000.0000.0000.000
167A178GLY0-0.065-0.02620.8010.0010.0010.0000.0000.0000.000
168A179HIS0-0.024-0.02721.5080.0090.0090.0000.0000.0000.000
169A180PRO0-0.030-0.01324.708-0.004-0.0040.0000.0000.0000.000
170A181LEU00.0280.01623.8820.0080.0080.0000.0000.0000.000
171A182ASP-1-0.845-0.93127.322-0.071-0.0710.0000.0000.0000.000
172A183PHE0-0.020-0.00925.5590.0060.0060.0000.0000.0000.000
173A184SER00.0080.01526.1150.0020.0020.0000.0000.0000.000
174A185ASN0-0.088-0.03728.2670.0010.0010.0000.0000.0000.000
175A186TRP0-0.016-0.02528.520-0.005-0.0050.0000.0000.0000.000
176A187GLY00.0590.03830.4590.0010.0010.0000.0000.0000.000
177A188SER00.0520.00430.894-0.003-0.0030.0000.0000.0000.000
178A189THR00.0180.01729.472-0.004-0.0040.0000.0000.0000.000
179A190TYR0-0.003-0.02726.7040.0000.0000.0000.0000.0000.000
180A191GLU-1-0.893-0.94225.980-0.074-0.0740.0000.0000.0000.000
181A192GLN0-0.061-0.02826.372-0.003-0.0030.0000.0000.0000.000
182A193GLN0-0.096-0.06323.6280.0010.0010.0000.0000.0000.000
183A194GLY00.0330.02022.8910.0010.0010.0000.0000.0000.000
184A195ILE0-0.013-0.00216.582-0.005-0.0050.0000.0000.0000.000
185A196LEU0-0.0220.00120.6900.0050.0050.0000.0000.0000.000
186A197ALA00.013-0.00516.238-0.028-0.0280.0000.0000.0000.000
187A198PRO00.0090.00314.9610.0230.0230.0000.0000.0000.000
188A199GLY00.038-0.00418.0770.0000.0000.0000.0000.0000.000
189A200GLU-1-0.859-0.92820.963-0.119-0.1190.0000.0000.0000.000
190A201ASP-1-0.883-0.94821.223-0.129-0.1290.0000.0000.0000.000
191A202ILE0-0.0070.00117.013-0.020-0.0200.0000.0000.0000.000
192A203LEU0-0.066-0.03816.8680.0220.0220.0000.0000.0000.000
193A204GLY00.0600.01217.944-0.016-0.0160.0000.0000.0000.000
194A205ALA0-0.012-0.01519.9290.0060.0060.0000.0000.0000.000
195A206LYS10.8210.90422.0540.0500.0500.0000.0000.0000.000
196A207PRO0-0.006-0.01725.8420.0060.0060.0000.0000.0000.000
197A208GLY0-0.0120.00027.524-0.003-0.0030.0000.0000.0000.000
198A209GLY0-0.014-0.00326.2220.0020.0020.0000.0000.0000.000
199A210GLY0-0.016-0.00325.469-0.004-0.0040.0000.0000.0000.000
200A211THR0-0.033-0.02520.6690.0050.0050.0000.0000.0000.000
201A212GLU-1-0.827-0.90823.106-0.053-0.0530.0000.0000.0000.000
202A213ARG10.8880.95017.8780.1800.1800.0000.0000.0000.000
203A214LEU00.0110.02422.6510.0100.0100.0000.0000.0000.000
204A215SER00.0660.04822.849-0.018-0.0180.0000.0000.0000.000
205A216GLY0-0.017-0.01623.8670.0130.0130.0000.0000.0000.000
206A217THR0-0.015-0.02722.857-0.010-0.0100.0000.0000.0000.000
207A218SER0-0.0200.00122.175-0.005-0.0050.0000.0000.0000.000
208A219PHE00.0060.00220.0090.0040.0040.0000.0000.0000.000
209A220ALA00.0490.03018.052-0.019-0.0190.0000.0000.0000.000
210A221THR0-0.017-0.03017.149-0.022-0.0220.0000.0000.0000.000
211A222PRO00.0210.01216.073-0.007-0.0070.0000.0000.0000.000
212A223ILE00.0080.01212.327-0.035-0.0350.0000.0000.0000.000
213A224VAL0-0.0020.00512.212-0.069-0.0690.0000.0000.0000.000
214A225SER0-0.018-0.02413.209-0.008-0.0080.0000.0000.0000.000
215A226GLY00.0260.01510.8690.0460.0460.0000.0000.0000.000
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