FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3N2QL

Calculation Name: 3GS3-A-Xray312

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3GS3

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8MSU4

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 250
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -3080710.575448
FMO2-HF: Nuclear repulsion 2982105.113747
FMO2-HF: Total energy -98605.461701
FMO2-MP2: Total energy -98886.322084


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:21:ACE )


Summations of interaction energy for fragment #1(A:21:ACE )
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.
-0.5020.4760.006-0.471-0.514-0.001
Interaction energy analysis for fragmet #1(A:21:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / 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].
3A23THR 00.1320.0613.8690.7191.478-0.005-0.349-0.4060.000
4A24ALA 00.0110.0107.2000.2910.2910.0000.0000.0000.000
5A25THR 00.001-0.0123.680-0.493-0.2740.011-0.122-0.108-0.001
6A26ALA 0-0.0120.0065.6320.3400.3400.0000.0000.0000.000
7A27ARG 11.0231.0066.9540.2670.2670.0000.0000.0000.000
8A28ALA 0-0.022-0.0119.1090.0520.0520.0000.0000.0000.000
9A29LYS 10.9840.9896.240-1.038-1.0380.0000.0000.0000.000
10A30VAL 00.0390.03510.8400.0010.0010.0000.0000.0000.000
11A31VAL 00.0000.00513.195-0.005-0.0050.0000.0000.0000.000
12A32ASP -1-0.924-0.95713.6130.1230.1230.0000.0000.0000.000
13A33TRP 0-0.036-0.02910.8880.0140.0140.0000.0000.0000.000
14A34CYS 0-0.030-0.02716.546-0.013-0.0130.0000.0000.0000.000
15A35ASN 00.005-0.00718.690-0.011-0.0110.0000.0000.0000.000
16A36GLU -1-0.930-0.95519.1150.1310.1310.0000.0000.0000.000
17A37LEU 0-0.031-0.01220.363-0.003-0.0030.0000.0000.0000.000
18A38VAL 0-0.054-0.02022.902-0.004-0.0040.0000.0000.0000.000
19A39ILE 0-0.031-0.02223.778-0.004-0.0040.0000.0000.0000.000
20A40ALA 0-0.0110.02123.6090.0020.0020.0000.0000.0000.000
21A41SER 00.0130.00225.744-0.008-0.0080.0000.0000.0000.000
22A42PRO 00.033-0.00926.9030.0030.0030.0000.0000.0000.000
23A43SER 00.0480.00826.3670.0000.0000.0000.0000.0000.000
24A44THR 00.0330.03022.0950.0020.0020.0000.0000.0000.000
25A45LYS 10.8890.94922.380-0.037-0.0370.0000.0000.0000.000
26A46CYS 0-0.054-0.02222.718-0.002-0.0020.0000.0000.0000.000
27A47GLU -1-0.921-0.96520.2320.1360.1360.0000.0000.0000.000
28A48LEU 0-0.042-0.02217.8910.0190.0190.0000.0000.0000.000
29A49LEU 0-0.0020.00417.8490.0010.0010.0000.0000.0000.000
30A50ALA 00.0160.01818.548-0.006-0.0060.0000.0000.0000.000
31A51LYS 10.9760.99214.125-0.217-0.2170.0000.0000.0000.000
32A52VAL 00.0200.00213.7310.0090.0090.0000.0000.0000.000
33A53GLN 0-0.021-0.01014.730-0.026-0.0260.0000.0000.0000.000
34A54GLU -1-0.937-0.97212.6420.2170.2170.0000.0000.0000.000
35A55THR 0-0.057-0.0249.1940.0250.0250.0000.0000.0000.000
36A56VAL 0-0.005-0.00611.450-0.061-0.0610.0000.0000.0000.000
37A57LEU 0-0.024-0.00613.839-0.028-0.0280.0000.0000.0000.000
38A58GLY 00.0290.01013.2820.0080.0080.0000.0000.0000.000
39A59SER 0-0.085-0.0357.602-0.018-0.0180.0000.0000.0000.000
40A60CYS 0-0.067-0.0348.300-0.198-0.1980.0000.0000.0000.000
41A61ALA 00.0680.03210.0030.0230.0230.0000.0000.0000.000
42A62GLU -1-0.962-0.98611.560-0.469-0.4690.0000.0000.0000.000
43A63LEU 0-0.024-0.01610.2710.0090.0090.0000.0000.0000.000
44A64ALA 0-0.044-0.01614.3050.0300.0300.0000.0000.0000.000
45A65GLU -1-0.918-0.97117.234-0.079-0.0790.0000.0000.0000.000
46A66GLU -1-0.908-0.95715.441-0.182-0.1820.0000.0000.0000.000
47A67PHE 0-0.029-0.03114.5710.0190.0190.0000.0000.0000.000
48A68LEU 00.0330.02319.2060.0170.0170.0000.0000.0000.000
49A69GLU -1-0.936-0.95522.000-0.021-0.0210.0000.0000.0000.000
50A70SER 0-0.002-0.02321.0150.0060.0060.0000.0000.0000.000
51A71VAL 0-0.0100.00720.0280.0100.0100.0000.0000.0000.000
52A72LEU 0-0.012-0.01123.0320.0060.0060.0000.0000.0000.000
53A73SER 0-0.0030.01526.1630.0030.0030.0000.0000.0000.000
54A74LEU 00.0310.00224.1630.0030.0030.0000.0000.0000.000
55A75ALA 0-0.054-0.01427.8230.0030.0030.0000.0000.0000.000
56A76HIS 00.006-0.01530.1520.0010.0010.0000.0000.0000.000
57A77ASP -1-0.830-0.89429.7480.0390.0390.0000.0000.0000.000
58A78SER 00.0370.01031.857-0.001-0.0010.0000.0000.0000.000
59A79ASN 0-0.022-0.01431.4290.0020.0020.0000.0000.0000.000
60A80MET 00.0210.00132.059-0.002-0.0020.0000.0000.0000.000
61A81GLU -1-0.883-0.94629.7050.0460.0460.0000.0000.0000.000
62A82VAL 00.007-0.00226.8760.0020.0020.0000.0000.0000.000
63A83ARG 10.8380.92127.630-0.024-0.0240.0000.0000.0000.000
64A84LYS 10.8620.93929.373-0.042-0.0420.0000.0000.0000.000
65A85GLN 0-0.033-0.00522.8470.0000.0000.0000.0000.0000.000
66A86VAL 00.0330.01724.6430.0000.0000.0000.0000.0000.000
67A87VAL 0-0.021-0.00226.005-0.005-0.0050.0000.0000.0000.000
68A88ALA 0-0.023-0.02124.299-0.004-0.0040.0000.0000.0000.000
69A89PHE 00.0170.01218.367-0.002-0.0020.0000.0000.0000.000
70A90VAL 00.0350.00422.868-0.008-0.0080.0000.0000.0000.000
71A91GLU -1-0.820-0.90525.4530.0120.0120.0000.0000.0000.000
72A92GLN 00.0040.00819.306-0.001-0.0010.0000.0000.0000.000
73A93VAL 0-0.002-0.00321.460-0.009-0.0090.0000.0000.0000.000
74A94CYS 0-0.052-0.02222.602-0.010-0.0100.0000.0000.0000.000
75A95LYS 10.9030.97123.181-0.012-0.0120.0000.0000.0000.000
76A96VAL 0-0.065-0.04418.559-0.004-0.0040.0000.0000.0000.000
77A97LYS 10.9080.97217.7030.1140.1140.0000.0000.0000.000
78A98VAL 00.0320.03321.8510.0020.0020.0000.0000.0000.000
79A99GLU -1-0.863-0.94222.222-0.081-0.0810.0000.0000.0000.000
80A100LEU 0-0.014-0.02420.7690.0020.0020.0000.0000.0000.000
81A101LEU 0-0.0100.02225.3380.0060.0060.0000.0000.0000.000
82A102PRO 0-0.001-0.02528.1330.0060.0060.0000.0000.0000.000
83A103HIS 00.0180.00926.3710.0060.0060.0000.0000.0000.000
84A104VAL 0-0.0010.00425.0660.0040.0040.0000.0000.0000.000
85A105ILE 0-0.011-0.00328.4050.0060.0060.0000.0000.0000.000
86A106ASN 00.026-0.00231.6720.0040.0040.0000.0000.0000.000
87A107VAL 0-0.0030.00529.2260.0030.0030.0000.0000.0000.000
88A108VAL 00.0000.00330.7820.0040.0040.0000.0000.0000.000
89A109SER 00.007-0.03332.9850.0020.0020.0000.0000.0000.000
90A110MET 0-0.001-0.02934.3690.0010.0010.0000.0000.0000.000
91A111LEU 0-0.0100.01131.0530.0020.0020.0000.0000.0000.000
92A112LEU 0-0.039-0.00835.5010.0030.0030.0000.0000.0000.000
93A113ARG 10.8820.95038.1920.0010.0010.0000.0000.0000.000
94A114ASP -1-0.776-0.87636.1050.0190.0190.0000.0000.0000.000
95A115ASN 00.0420.01038.878-0.001-0.0010.0000.0000.0000.000
96A116SER 0-0.080-0.03937.3060.0010.0010.0000.0000.0000.000
97A117ALA 00.1080.03638.911-0.001-0.0010.0000.0000.0000.000
98A118GLN 0-0.070-0.04736.1060.0020.0020.0000.0000.0000.000
99A119VAL 0-0.0080.00833.5920.0020.0020.0000.0000.0000.000
100A120ILE 00.0750.04634.9450.0000.0000.0000.0000.0000.000
101A121LYS 10.9120.95736.966-0.024-0.0240.0000.0000.0000.000
102A122ARG 10.8710.96527.207-0.029-0.0290.0000.0000.0000.000
103A123VAL 00.0300.00932.773-0.001-0.0010.0000.0000.0000.000
104A124ILE 00.0200.01133.823-0.002-0.0020.0000.0000.0000.000
105A125GLN 0-0.100-0.05033.1990.0010.0010.0000.0000.0000.000
106A126ALA 0-0.0100.00329.927-0.001-0.0010.0000.0000.0000.000
107A127CYS 0-0.036-0.02231.222-0.004-0.0040.0000.0000.0000.000
108A128GLY 00.0200.02733.736-0.003-0.0030.0000.0000.0000.000
109A129SER 0-0.096-0.07129.282-0.003-0.0030.0000.0000.0000.000
110A130ILE 00.0580.04028.956-0.004-0.0040.0000.0000.0000.000
111A131TYR 00.0140.00130.929-0.005-0.0050.0000.0000.0000.000
112A132LYS 10.8840.94732.8530.0050.0050.0000.0000.0000.000
113A133ASN 0-0.011-0.02428.1850.0010.0010.0000.0000.0000.000
114A134GLY 00.0530.00630.651-0.005-0.0050.0000.0000.0000.000
115A135LEU 0-0.032-0.00932.153-0.003-0.0030.0000.0000.0000.000
116A136GLN 0-0.038-0.02931.721-0.002-0.0020.0000.0000.0000.000
117A137TYR 00.0470.05928.556-0.002-0.0020.0000.0000.0000.000
118A138LEU 00.0190.00331.584-0.003-0.0030.0000.0000.0000.000
119A139CYS 0-0.080-0.03534.342-0.001-0.0010.0000.0000.0000.000
120A140SER 0-0.012-0.05432.8370.0010.0010.0000.0000.0000.000
121A141LEU 0-0.092-0.03230.953-0.003-0.0030.0000.0000.0000.000
122A142MET 0-0.027-0.01534.7290.0030.0030.0000.0000.0000.000
123A143GLU -1-0.969-0.97736.874-0.042-0.0420.0000.0000.0000.000
124A144PRO 0-0.039-0.01335.807-0.002-0.0020.0000.0000.0000.000
125A145GLY 00.0700.02835.2280.0010.0010.0000.0000.0000.000
126A146ASP -1-0.807-0.91936.476-0.032-0.0320.0000.0000.0000.000
127A147SER 0-0.059-0.03431.5770.0040.0040.0000.0000.0000.000
128A148ALA 0-0.0080.00033.8170.0020.0020.0000.0000.0000.000
129A149GLU -1-0.917-0.95734.685-0.023-0.0230.0000.0000.0000.000
130A150GLN 00.0280.00936.1230.0030.0030.0000.0000.0000.000
131A151ALA 0-0.020-0.01733.3130.0030.0030.0000.0000.0000.000
132A152TRP 00.032-0.00335.2000.0030.0030.0000.0000.0000.000
133A153ASN 00.0210.01937.5990.0030.0030.0000.0000.0000.000
134A154ILE 0-0.027-0.00935.6160.0030.0030.0000.0000.0000.000
135A155LEU 0-0.007-0.00333.7280.0030.0030.0000.0000.0000.000
136A156SER 0-0.033-0.01837.6160.0020.0020.0000.0000.0000.000
137A157LEU 0-0.011-0.00240.0000.0020.0020.0000.0000.0000.000
138A158ILE 0-0.015-0.00935.2340.0020.0020.0000.0000.0000.000
139A159LYS 10.8070.90039.5280.0120.0120.0000.0000.0000.000
140A160ALA 00.0310.02541.5680.0010.0010.0000.0000.0000.000
141A161GLN 0-0.0020.02839.840-0.001-0.0010.0000.0000.0000.000
142A162ILE 0-0.021-0.02737.9240.0020.0020.0000.0000.0000.000
143A163LEU 0-0.0060.00642.5270.0010.0010.0000.0000.0000.000
144A164ASP -1-0.859-0.92845.8150.0010.0010.0000.0000.0000.000
145A165MET 0-0.129-0.06040.8080.0020.0020.0000.0000.0000.000
146A166ILE 0-0.021-0.01345.9140.0020.0020.0000.0000.0000.000
147A167ASP -1-0.894-0.94947.8530.0060.0060.0000.0000.0000.000
148A168ASN 0-0.0390.00745.2260.0010.0010.0000.0000.0000.000
149A169GLU -1-0.858-0.92848.3480.0110.0110.0000.0000.0000.000
150A170ASN 0-0.074-0.04443.6880.0020.0020.0000.0000.0000.000
151A171ASP -1-0.744-0.86446.2100.0140.0140.0000.0000.0000.000
152A172GLY 0-0.019-0.01742.7850.0000.0000.0000.0000.0000.000
153A173ILE 0-0.020-0.01541.2160.0010.0010.0000.0000.0000.000
154A174ARG 10.8630.93342.764-0.012-0.0120.0000.0000.0000.000
155A175THR 0-0.034-0.01942.1580.0000.0000.0000.0000.0000.000
156A176ASN 0-0.054-0.05137.7420.0010.0010.0000.0000.0000.000
157A177ALA 00.0700.03640.596-0.001-0.0010.0000.0000.0000.000
158A178ILE 00.0320.02842.426-0.001-0.0010.0000.0000.0000.000
159A179LYS 10.9420.97537.134-0.012-0.0120.0000.0000.0000.000
160A180PHE 0-0.036-0.03136.769-0.001-0.0010.0000.0000.0000.000
161A181LEU 00.0330.00539.814-0.002-0.0020.0000.0000.0000.000
162A182GLU -1-0.903-0.93441.9400.0060.0060.0000.0000.0000.000
163A183GLY 0-0.010-0.01039.391-0.001-0.0010.0000.0000.0000.000
164A184VAL 00.0030.01440.048-0.002-0.0020.0000.0000.0000.000
165A185VAL 00.0130.02741.646-0.002-0.0020.0000.0000.0000.000
166A186VAL 0-0.018-0.01041.514-0.001-0.0010.0000.0000.0000.000
167A187LEU 0-0.050-0.01937.076-0.002-0.0020.0000.0000.0000.000
168A188GLN 0-0.042-0.03741.241-0.002-0.0020.0000.0000.0000.000
169A189SER 00.016-0.01244.1340.0010.0010.0000.0000.0000.000
170A190PHE 0-0.012-0.02545.112-0.001-0.0010.0000.0000.0000.000
171A191ALA 00.0260.03344.2300.0010.0010.0000.0000.0000.000
172A192ASP -1-0.813-0.90546.327-0.006-0.0060.0000.0000.0000.000
173A193GLU -1-1.031-1.02647.952-0.008-0.0080.0000.0000.0000.000
174A194ASP -1-0.948-0.97349.969-0.003-0.0030.0000.0000.0000.000
175A195SER 0-0.098-0.04145.8060.0010.0010.0000.0000.0000.000
176A196LEU 0-0.049-0.02343.8580.0000.0000.0000.0000.0000.000
177A197LYS 10.9660.97041.9230.0050.0050.0000.0000.0000.000
178A198ARG 10.9470.96834.868-0.005-0.0050.0000.0000.0000.000
179A199ASP -1-0.906-0.95733.4100.0010.0010.0000.0000.0000.000
180A200GLY 0-0.004-0.00334.086-0.002-0.0020.0000.0000.0000.000
181A201ASP -1-0.919-0.94834.786-0.007-0.0070.0000.0000.0000.000
182A202PHE 00.0410.01536.045-0.002-0.0020.0000.0000.0000.000
183A203SER 0-0.007-0.00938.5250.0020.0020.0000.0000.0000.000
184A204LEU 0-0.030-0.01041.306-0.002-0.0020.0000.0000.0000.000
185A205ALA 0-0.042-0.02843.610-0.001-0.0010.0000.0000.0000.000
186A206ASP -1-0.845-0.90938.473-0.017-0.0170.0000.0000.0000.000
187A207VAL 0-0.092-0.02939.155-0.002-0.0020.0000.0000.0000.000
188A208PRO 00.0260.01037.6590.0010.0010.0000.0000.0000.000
189A209ASP -1-0.905-0.95540.780-0.022-0.0220.0000.0000.0000.000
190A210HIS 0-0.048-0.03137.8200.0020.0020.0000.0000.0000.000
191A211CYS 00.0010.04440.1410.0000.0000.0000.0000.0000.000
192A212THR 0-0.029-0.03641.6690.0020.0020.0000.0000.0000.000
193A213LEU 00.0110.02637.6940.0000.0000.0000.0000.0000.000
194A214PHE 00.005-0.00139.3750.0020.0020.0000.0000.0000.000
195A215ARG 10.8990.92644.1390.0210.0210.0000.0000.0000.000
196A216ARG 10.9400.96744.0000.0190.0190.0000.0000.0000.000
197A217GLU -1-0.848-0.92446.957-0.011-0.0110.0000.0000.0000.000
198A218LYS 10.9880.99947.7400.0150.0150.0000.0000.0000.000
199A219LEU 00.0080.01842.2810.0010.0010.0000.0000.0000.000
200A220GLN 00.0510.02446.4240.0010.0010.0000.0000.0000.000
201A221GLU -1-0.987-0.98048.804-0.007-0.0070.0000.0000.0000.000
202A222GLU -1-0.806-0.90244.886-0.007-0.0070.0000.0000.0000.000
203A223GLY 0-0.017-0.01847.0300.0010.0010.0000.0000.0000.000
204A224ASN 0-0.025-0.03447.7850.0020.0020.0000.0000.0000.000
205A225ASN 00.0200.02050.9370.0010.0010.0000.0000.0000.000
206A226ILE 0-0.010-0.00344.9310.0010.0010.0000.0000.0000.000
207A227LEU 0-0.014-0.00949.1070.0010.0010.0000.0000.0000.000
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