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: 16J7Z

Calculation Name: 1E5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1E5R

Chain ID: A

ChEMBL ID:

UniProt ID: O09345

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 264
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3735885.326153
FMO2-HF: Nuclear repulsion 3629098.804058
FMO2-HF: Total energy -106786.522095
FMO2-MP2: Total energy -107102.780949


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-22.839-20.10124.875-10.879-16.733-0.073
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.004
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].
3A3SER00.0440.0132.356-3.464-1.1892.173-1.907-2.540-0.013
4A4HIS10.7650.8642.714-5.711-5.7903.587-1.335-2.1730.016
5A5ILE00.0100.0146.7140.1540.1540.0000.0000.0000.000
6A6LEU00.000-0.0015.7830.0280.091-0.001-0.002-0.0600.000
7A7GLY00.0310.0269.640-0.079-0.0790.0000.0000.0000.000
8A8LYS10.9060.95913.3670.0190.0190.0000.0000.0000.000
9A9ILE0-0.0030.03316.591-0.005-0.0050.0000.0000.0000.000
10A10GLU-1-0.937-0.97819.603-0.017-0.0170.0000.0000.0000.000
11A11LEU0-0.021-0.02921.289-0.003-0.0030.0000.0000.0000.000
12A12ASP-1-0.847-0.93224.584-0.027-0.0270.0000.0000.0000.000
13A13GLN00.0480.00527.868-0.003-0.0030.0000.0000.0000.000
14A14THR0-0.027-0.01729.514-0.002-0.0020.0000.0000.0000.000
15A15ARG10.8190.86828.7400.0360.0360.0000.0000.0000.000
16A16LEU00.0190.01224.923-0.002-0.0020.0000.0000.0000.000
17A17ALA0-0.042-0.02428.760-0.002-0.0020.0000.0000.0000.000
18A18PRO0-0.040-0.01531.232-0.001-0.0010.0000.0000.0000.000
19A19ASP-1-0.721-0.91028.058-0.047-0.0470.0000.0000.0000.000
20A20LEU0-0.046-0.01425.541-0.004-0.0040.0000.0000.0000.000
21A21ALA0-0.015-0.00729.029-0.001-0.0010.0000.0000.0000.000
22A22TYR00.017-0.06629.8810.0010.0010.0000.0000.0000.000
23A23LEU0-0.038-0.02025.185-0.001-0.0010.0000.0000.0000.000
24A24ALA0-0.061-0.03129.176-0.003-0.0030.0000.0000.0000.000
25A25ALA0-0.044-0.02830.8950.0020.0020.0000.0000.0000.000
26A26VAL0-0.0370.00229.7770.0010.0010.0000.0000.0000.000
27A27PRO00.010-0.01931.755-0.003-0.0030.0000.0000.0000.000
28A28THR0-0.074-0.01828.094-0.003-0.0030.0000.0000.0000.000
29A29VAL0-0.003-0.01128.9510.0050.0050.0000.0000.0000.000
30A30GLU-1-0.928-0.96230.104-0.044-0.0440.0000.0000.0000.000
31A31GLU-1-1.005-1.00523.980-0.104-0.1040.0000.0000.0000.000
32A32GLU-1-0.906-0.93926.555-0.077-0.0770.0000.0000.0000.000
33A33TYR0-0.053-0.04726.741-0.002-0.0020.0000.0000.0000.000
34A34ASP-1-0.935-0.95728.013-0.033-0.0330.0000.0000.0000.000
35A35GLU-1-0.880-0.91322.913-0.094-0.0940.0000.0000.0000.000
36A36PHE0-0.065-0.06021.6990.0140.0140.0000.0000.0000.000
37A37SER0-0.013-0.01522.473-0.002-0.0020.0000.0000.0000.000
38A38ASN0-0.076-0.03723.659-0.003-0.0030.0000.0000.0000.000
39A39GLY00.0320.00125.492-0.006-0.0060.0000.0000.0000.000
40A40PHE00.0330.02826.845-0.004-0.0040.0000.0000.0000.000
41A41TRP00.0280.01622.821-0.004-0.0040.0000.0000.0000.000
42A42LYS10.8760.94724.2330.0620.0620.0000.0000.0000.000
43A43HIS00.0230.00719.230-0.016-0.0160.0000.0000.0000.000
44A44VAL00.0410.02523.5510.0070.0070.0000.0000.0000.000
45A45PRO0-0.048-0.01622.786-0.005-0.0050.0000.0000.0000.000
46A46LEU00.029-0.03022.3560.0090.0090.0000.0000.0000.000
47A47TRP00.0220.01220.9810.0080.0080.0000.0000.0000.000
48A48ASN00.0080.04620.888-0.025-0.0250.0000.0000.0000.000
49A67GLN0-0.008-0.00923.763-0.002-0.0020.0000.0000.0000.000
50A68PRO00.0210.00125.098-0.004-0.0040.0000.0000.0000.000
51A69THR00.0100.02126.2140.0010.0010.0000.0000.0000.000
52A70ALA00.012-0.01728.2100.0020.0020.0000.0000.0000.000
53A71HIS00.0310.07527.9490.0050.0050.0000.0000.0000.000
54A72VAL0-0.0170.00726.2350.0020.0020.0000.0000.0000.000
55A73GLU-1-0.832-0.89928.461-0.050-0.0500.0000.0000.0000.000
56A74HIS0-0.076-0.01731.6020.0040.0040.0000.0000.0000.000
57A75VAL0-0.059-0.01230.957-0.001-0.0010.0000.0000.0000.000
58A76PRO00.0570.03928.793-0.003-0.0030.0000.0000.0000.000
59A77TYR00.0880.08325.959-0.001-0.0010.0000.0000.0000.000
60A78LEU00.039-0.00922.7570.0000.0000.0000.0000.0000.000
61A79LYS10.9170.94622.9960.0520.0520.0000.0000.0000.000
62A80GLU-1-0.813-0.78524.303-0.042-0.0420.0000.0000.0000.000
63A81ILE0-0.0200.01219.681-0.002-0.0020.0000.0000.0000.000
64A82VAL0-0.056-0.03718.9790.0010.0010.0000.0000.0000.000
65A83THR0-0.111-0.13719.853-0.001-0.0010.0000.0000.0000.000
66A84THR0-0.067-0.03521.584-0.001-0.0010.0000.0000.0000.000
67A85VAL00.0110.00515.620-0.002-0.0020.0000.0000.0000.000
68A86PHE0-0.026-0.03112.422-0.001-0.0010.0000.0000.0000.000
69A87ASP-1-0.805-0.88915.525-0.114-0.1140.0000.0000.0000.000
70A88GLY0-0.006-0.03716.132-0.003-0.0030.0000.0000.0000.000
71A89THR0-0.116-0.04916.678-0.007-0.0070.0000.0000.0000.000
72A90HIS00.0510.02512.076-0.009-0.0090.0000.0000.0000.000
73A91LEU0-0.0180.03014.475-0.021-0.0210.0000.0000.0000.000
74A92GLN0-0.026-0.01914.758-0.015-0.0150.0000.0000.0000.000
75A93MET0-0.020-0.03516.446-0.014-0.0140.0000.0000.0000.000
76A94ALA00.0240.02116.915-0.002-0.0020.0000.0000.0000.000
77A95ARG10.9070.95118.0960.1590.1590.0000.0000.0000.000
78A96SER00.0650.05719.613-0.003-0.0030.0000.0000.0000.000
79A97ARG10.9050.93016.1450.2040.2040.0000.0000.0000.000
80A98ASN00.0190.02220.9150.0000.0000.0000.0000.0000.000
81A99LEU0-0.018-0.00419.756-0.008-0.0080.0000.0000.0000.000
82A100LYS10.8790.95023.3960.0490.0490.0000.0000.0000.000
83A101ASN0-0.006-0.00226.3380.0000.0000.0000.0000.0000.000
84A102ALA00.0250.00324.0230.0020.0020.0000.0000.0000.000
85A103ILE0-0.055-0.02119.6920.0010.0010.0000.0000.0000.000
86A104VAL00.0160.03816.555-0.002-0.0020.0000.0000.0000.000
87A105ILE00.0230.00317.9700.0000.0000.0000.0000.0000.000
88A106PRO00.0160.02714.631-0.036-0.0360.0000.0000.0000.000
89A107HIS10.8490.92713.2110.2510.2510.0000.0000.0000.000
90A108ARG10.9320.9879.066-0.134-0.1340.0000.0000.0000.000
91A109ASP-1-0.921-0.9679.737-0.386-0.3860.0000.0000.0000.000
92A110PHE0-0.017-0.0049.5260.0540.0540.0000.0000.0000.000
93A119ARG10.8370.9096.7980.3830.3830.0000.0000.0000.000
94A120TYR0-0.012-0.0137.7590.2260.2260.0000.0000.0000.000
95A121PHE00.018-0.0043.449-1.194-0.5880.187-0.144-0.6490.000
96A122ARG10.9220.9657.3760.2190.2190.0000.0000.0000.000
97A123THR0-0.072-0.0518.5550.0360.0360.0000.0000.0000.000
98A124PHE0-0.021-0.03710.611-0.068-0.0680.0000.0000.0000.000
99A125MET00.0280.03012.9520.0330.0330.0000.0000.0000.000
100A126VAL0-0.0420.00515.818-0.013-0.0130.0000.0000.0000.000
101A127LEU0-0.005-0.02518.3810.0090.0090.0000.0000.0000.000
102A128GLU-1-0.786-0.85521.716-0.044-0.0440.0000.0000.0000.000
103A129ASP-1-0.918-0.96022.211-0.026-0.0260.0000.0000.0000.000
104A130SER0-0.024-0.00822.5830.0020.0020.0000.0000.0000.000
105A131PRO00.030-0.00322.557-0.004-0.0040.0000.0000.0000.000
106A132LEU0-0.048-0.01623.2790.0030.0030.0000.0000.0000.000
107A133ALA0-0.0030.01020.391-0.003-0.0030.0000.0000.0000.000
108A134PHE0-0.044-0.02317.2610.0080.0080.0000.0000.0000.000
109A135HIS0-0.005-0.00712.6210.0030.0030.0000.0000.0000.000
110A136SER0-0.006-0.02512.8750.0230.0230.0000.0000.0000.000
111A137ASN00.0060.0006.4240.2000.2000.0000.0000.0000.000
112A138GLU-1-0.771-0.8506.6640.7280.7280.0000.0000.0000.000
113A139ASP-1-0.896-0.9559.5120.4450.4450.0000.0000.0000.000
114A140THR0-0.095-0.0438.908-0.035-0.0350.0000.0000.0000.000
115A141VAL00.0440.01811.880-0.045-0.0450.0000.0000.0000.000
116A142ILE0-0.026-0.01410.5220.0130.0130.0000.0000.0000.000
117A143HIS10.9130.95713.9720.0210.0210.0000.0000.0000.000
118A144MET0-0.041-0.00411.3290.0150.0150.0000.0000.0000.000
119A145ARG10.8290.90615.6850.0020.0020.0000.0000.0000.000
120A146PRO00.008-0.01717.715-0.001-0.0010.0000.0000.0000.000
121A147GLY00.0610.04418.9650.0040.0040.0000.0000.0000.000
122A148GLU-1-0.842-0.91714.0080.0020.0020.0000.0000.0000.000
123A149ILE00.0180.02111.124-0.021-0.0210.0000.0000.0000.000
124A150TRP0-0.009-0.0218.2430.0820.0820.0000.0000.0000.000
125A151PHE00.0530.0331.8870.219-1.2609.991-2.356-6.156-0.021
126A152LEU0-0.105-0.0745.910-0.218-0.2180.0000.0000.0000.000
127A153ASP-1-0.798-0.8921.980-15.696-15.5008.902-4.813-4.285-0.054
128A154ALA00.0370.0264.6120.8160.907-0.001-0.017-0.0730.000
129A155ALA0-0.041-0.0284.5440.5340.595-0.001-0.001-0.0590.000
130A156THR0-0.064-0.0423.4660.1460.4140.011-0.071-0.2080.000
131A157VAL0-0.020-0.0186.306-0.176-0.1760.0000.0000.0000.000
132A158HIS10.8510.9408.9130.5790.5790.0000.0000.0000.000
133A159SER0-0.0140.02810.8730.0540.0540.0000.0000.0000.000
134A160ALA0-0.0020.00314.224-0.034-0.0340.0000.0000.0000.000
135A161VAL0-0.001-0.01216.7490.0150.0150.0000.0000.0000.000
136A162ASN00.0290.00720.2760.0030.0030.0000.0000.0000.000
137A163PHE0-0.042-0.03422.0730.0030.0030.0000.0000.0000.000
138A164SER0-0.051-0.00625.8230.0060.0060.0000.0000.0000.000
139A165GLU-1-0.869-0.93427.417-0.027-0.0270.0000.0000.0000.000
140A166ILE0-0.018-0.01127.062-0.002-0.0020.0000.0000.0000.000
141A167SER0-0.073-0.06726.290-0.006-0.0060.0000.0000.0000.000
142A168ARG10.9360.93718.2180.1130.1130.0000.0000.0000.000
143A169GLN00.0190.03321.579-0.020-0.0200.0000.0000.0000.000
144A170SER00.001-0.01517.6610.0010.0010.0000.0000.0000.000
145A171LEU00.0100.01017.998-0.005-0.0050.0000.0000.0000.000
146A172CYS0-0.073-0.03314.667-0.006-0.0060.0000.0000.0000.000
147A173VAL00.0610.03814.0440.0000.0000.0000.0000.0000.000
148A174ASP-1-0.743-0.83711.716-0.314-0.3140.0000.0000.0000.000
149A175PHE0-0.043-0.04510.0650.0510.0510.0000.0000.0000.000
150A176ALA00.0050.01310.881-0.077-0.0770.0000.0000.0000.000
151A177PHE00.0320.0008.9650.0350.0350.0000.0000.0000.000
152A178ASP-1-0.896-0.93611.126-0.304-0.3040.0000.0000.0000.000
153A179GLY0-0.054-0.06112.1350.0230.0230.0000.0000.0000.000
154A180PRO0-0.126-0.0658.5140.0120.0120.0000.0000.0000.000
155A181PHE00.0380.0495.607-0.0630.021-0.001-0.005-0.0780.000
156A182ASP-1-0.870-0.9316.073-0.952-0.9520.0000.0000.0000.000
157A183GLU-1-0.755-0.8213.7180.7881.4400.028-0.228-0.452-0.001
158A184LYS10.9300.9486.0810.4200.4200.0000.0000.0000.000
159A185GLU-1-0.896-0.9349.347-0.251-0.2510.0000.0000.0000.000
160A186ILE00.0020.0158.8760.0220.0220.0000.0000.0000.000
161A187PHE0-0.053-0.04410.3710.0090.0090.0000.0000.0000.000
162A188ALA00.0250.04214.037-0.016-0.0160.0000.0000.0000.000
163A189ASP-1-0.767-0.81017.521-0.060-0.0600.0000.0000.0000.000
164A190ALA00.008-0.00815.0650.0060.0060.0000.0000.0000.000
165A191THR0-0.207-0.19015.393-0.001-0.0010.0000.0000.0000.000
166A192LEU0-0.013-0.01515.9580.0060.0060.0000.0000.0000.000
167A193TYR0-0.141-0.0966.286-0.045-0.0450.0000.0000.0000.000
168A194ALA00.021-0.01712.513-0.025-0.0250.0000.0000.0000.000
169A195PRO0-0.015-0.0098.5740.0200.0200.0000.0000.0000.000
170A196GLY0-0.018-0.00710.1080.0060.0060.0000.0000.0000.000
171A197SER0-0.030-0.00712.654-0.007-0.0070.0000.0000.0000.000
172A198THR0-0.0100.00113.4220.0090.0090.0000.0000.0000.000
173A199PRO00.0140.00011.774-0.005-0.0050.0000.0000.0000.000
174A200ASP-1-0.923-0.95514.0200.0030.0030.0000.0000.0000.000
175A201LEU0-0.056-0.04112.041-0.013-0.0130.0000.0000.0000.000
176A202PRO00.0230.01716.0360.0080.0080.0000.0000.0000.000
177A203GLU-1-0.934-0.95718.5970.0560.0560.0000.0000.0000.000
178A204ARG10.8630.93615.146-0.113-0.1130.0000.0000.0000.000
179A205ARG10.8770.94121.734-0.033-0.0330.0000.0000.0000.000
180A206PRO00.1130.04923.5740.0050.0050.0000.0000.0000.000
181A207PHE00.0270.02622.774-0.014-0.0140.0000.0000.0000.000
182A208THR00.006-0.00124.7580.0080.0080.0000.0000.0000.000
183A209ALA00.0780.02627.908-0.001-0.0010.0000.0000.0000.000
184A210GLU-1-0.893-0.94829.4720.0500.0500.0000.0000.0000.000
185A211HIS00.0090.00226.850-0.004-0.0040.0000.0000.0000.000
186A212ARG10.8900.89524.298-0.110-0.1100.0000.0000.0000.000
187A213ARG10.9170.95128.302-0.058-0.0580.0000.0000.0000.000
188A214ARG10.8680.91931.274-0.051-0.0510.0000.0000.0000.000
189A215ILE00.0090.03525.675-0.005-0.0050.0000.0000.0000.000
190A216LEU00.0190.00228.108-0.004-0.0040.0000.0000.0000.000
191A217SER0-0.058-0.01831.235-0.005-0.0050.0000.0000.0000.000
192A218LEU00.0360.00729.579-0.003-0.0030.0000.0000.0000.000
193A219GLY0-0.022-0.01233.155-0.003-0.0030.0000.0000.0000.000
194A220GLN0-0.090-0.05634.184-0.004-0.0040.0000.0000.0000.000
195A221VAL0-0.027-0.00834.804-0.002-0.0020.0000.0000.0000.000
196A222ILE0-0.056-0.01630.529-0.002-0.0020.0000.0000.0000.000
197A223GLU-1-0.878-0.93334.5490.0120.0120.0000.0000.0000.000
198A224ARG10.8220.87634.176-0.013-0.0130.0000.0000.0000.000
199A225GLU-1-0.914-0.96334.0120.0020.0020.0000.0000.0000.000
200A226ASN0-0.0130.00733.632-0.001-0.0010.0000.0000.0000.000
201A227PHE00.0370.00526.9960.0000.0000.0000.0000.0000.000
202A228ARG10.9720.98227.4470.0290.0290.0000.0000.0000.000
203A229ASP-1-0.887-0.94027.508-0.008-0.0080.0000.0000.0000.000
204A230ILE0-0.008-0.01228.0460.0000.0000.0000.0000.0000.000
205A231LEU00.0350.03722.0300.0040.0040.0000.0000.0000.000
206A232PHE00.012-0.00623.425-0.001-0.0010.0000.0000.0000.000
207A233LEU0-0.047-0.00724.449-0.002-0.0020.0000.0000.0000.000
208A234LEU0-0.013-0.02123.6830.0030.0030.0000.0000.0000.000
209A235SER00.014-0.00820.0930.0050.0050.0000.0000.0000.000
210A236LYS10.9280.97319.9150.0080.0080.0000.0000.0000.000
211A237VAL0-0.043-0.01122.1490.0000.0000.0000.0000.0000.000
212A238HIS00.0240.05215.861-0.015-0.0150.0000.0000.0000.000
213A239TYR00.044-0.01216.7750.0050.0050.0000.0000.0000.000
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