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: YNQ22

Calculation Name: 2IF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IF4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LDC0

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 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 258
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3319320.232374
FMO2-HF: Nuclear repulsion 3214848.40647
FMO2-HF: Total energy -104471.825904
FMO2-MP2: Total energy -104771.159708


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:35:ASN)


Summations of interaction energy for fragment #1(A:35:ASN)
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.
-11.056-7.5465.854-3.57-5.7930.015
Interaction energy analysis for fragmet #1(A:35:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.006
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].
3A37PRO00.0070.0153.414-2.799-0.8050.022-1.016-1.000-0.001
4A38PRO00.0130.0014.7050.0820.177-0.001-0.002-0.0920.000
5A39LYS10.8540.9316.9592.8962.8960.0000.0000.0000.000
6A40VAL00.0110.00110.256-0.114-0.1140.0000.0000.0000.000
7A41ASP-1-0.899-0.94913.014-0.960-0.9600.0000.0000.0000.000
8A42SER0-0.071-0.03716.2930.0940.0940.0000.0000.0000.000
9A43GLU-1-0.845-0.91218.125-0.449-0.4490.0000.0000.0000.000
10A44ALA0-0.058-0.04418.944-0.037-0.0370.0000.0000.0000.000
11A45GLU-1-0.835-0.91620.073-0.278-0.2780.0000.0000.0000.000
12A46VAL00.010-0.01021.222-0.010-0.0100.0000.0000.0000.000
13A47LEU0-0.091-0.03520.2140.0150.0150.0000.0000.0000.000
14A48ASP-1-0.819-0.93024.010-0.068-0.0680.0000.0000.0000.000
15A49GLU-1-0.956-0.96024.618-0.140-0.1400.0000.0000.0000.000
16A50LYS10.7630.86922.7710.0670.0670.0000.0000.0000.000
17A51VAL0-0.034-0.00719.3120.0010.0010.0000.0000.0000.000
18A52SER00.0380.02418.838-0.027-0.0270.0000.0000.0000.000
19A53LYS10.7390.86416.2600.3540.3540.0000.0000.0000.000
20A54GLN0-0.0110.00514.4700.0080.0080.0000.0000.0000.000
21A55ILE00.0240.01414.433-0.097-0.0970.0000.0000.0000.000
22A56ILE0-0.030-0.0199.091-0.068-0.0680.0000.0000.0000.000
23A57LYS10.8160.90612.9800.5720.5720.0000.0000.0000.000
24A58GLU-1-0.754-0.85714.828-0.336-0.3360.0000.0000.0000.000
25A59GLY0-0.018-0.00817.581-0.033-0.0330.0000.0000.0000.000
26A60HIS0-0.059-0.02319.797-0.003-0.0030.0000.0000.0000.000
27A61GLY00.0330.01223.3290.0210.0210.0000.0000.0000.000
28A62SER0-0.002-0.00425.751-0.021-0.0210.0000.0000.0000.000
29A63LYS10.8420.91923.3670.2310.2310.0000.0000.0000.000
30A64PRO00.0180.01423.1250.0110.0110.0000.0000.0000.000
31A65SER0-0.032-0.03226.177-0.001-0.0010.0000.0000.0000.000
32A66LYS10.8330.89228.1970.0540.0540.0000.0000.0000.000
33A67TYR0-0.011-0.02828.6350.0010.0010.0000.0000.0000.000
34A68SER0-0.029-0.01126.1690.0130.0130.0000.0000.0000.000
35A69THR00.0010.00123.9850.0080.0080.0000.0000.0000.000
36A70CYS0-0.034-0.01020.270-0.027-0.0270.0000.0000.0000.000
37A71PHE00.0280.01419.2670.0390.0390.0000.0000.0000.000
38A72LEU0-0.050-0.03013.821-0.077-0.0770.0000.0000.0000.000
39A73HIS00.0840.06510.4340.2330.2330.0000.0000.0000.000
40A74TYR0-0.072-0.0849.348-0.268-0.2680.0000.0000.0000.000
41A75ARG10.7780.9022.755-2.440-1.2950.357-0.269-1.233-0.001
42A76ALA00.0160.0186.866-0.638-0.6380.0000.0000.0000.000
43A77TRP0-0.028-0.0352.699-0.4380.6270.329-0.479-0.915-0.002
44A78THR00.0650.0339.004-0.198-0.1980.0000.0000.0000.000
45A79LYS10.8730.92411.8740.3640.3640.0000.0000.0000.000
46A80ASN0-0.011-0.01713.470-0.198-0.1980.0000.0000.0000.000
47A81SER00.0170.00412.754-0.013-0.0130.0000.0000.0000.000
48A82GLN0-0.070-0.0377.791-0.308-0.3080.0000.0000.0000.000
49A83HIS00.0150.0207.243-0.020-0.0200.0000.0000.0000.000
50A84LYS10.8470.9002.274-15.194-16.1225.148-1.793-2.4260.019
51A85PHE0-0.024-0.0146.9070.2580.2580.0000.0000.0000.000
52A86GLU-1-0.741-0.8268.7800.7260.7260.0000.0000.0000.000
53A87ASP-1-0.760-0.9034.5248.4588.597-0.001-0.011-0.1270.000
54A88THR00.0660.0357.5310.1400.1400.0000.0000.0000.000
55A89TRP0-0.052-0.0246.562-0.320-0.3200.0000.0000.0000.000
56A90HIS0-0.067-0.0246.2930.6330.6330.0000.0000.0000.000
57A91GLU-1-0.929-0.9718.0131.4271.4270.0000.0000.0000.000
58A92GLN0-0.099-0.04310.795-0.377-0.3770.0000.0000.0000.000
59A93GLN0-0.021-0.01012.529-0.261-0.2610.0000.0000.0000.000
60A94PRO0-0.035-0.00913.8130.0810.0810.0000.0000.0000.000
61A95ILE00.0050.00414.5970.0030.0030.0000.0000.0000.000
62A96GLU-1-0.900-0.95516.8850.2000.2000.0000.0000.0000.000
63A97LEU0-0.048-0.03517.6790.0210.0210.0000.0000.0000.000
64A98VAL00.0090.01121.010-0.035-0.0350.0000.0000.0000.000
65A99LEU00.0360.01921.7080.0050.0050.0000.0000.0000.000
66A100GLY00.053-0.00125.118-0.018-0.0180.0000.0000.0000.000
67A101LYS10.7810.90026.617-0.106-0.1060.0000.0000.0000.000
68A102GLU-1-0.749-0.86222.2770.1060.1060.0000.0000.0000.000
69A103LYS10.8940.94820.797-0.224-0.2240.0000.0000.0000.000
70A104LYS10.9120.94922.057-0.151-0.1510.0000.0000.0000.000
71A105GLU-1-0.868-0.95019.1430.2750.2750.0000.0000.0000.000
72A106LEU0-0.013-0.00915.631-0.001-0.0010.0000.0000.0000.000
73A107ALA0-0.0040.00818.806-0.033-0.0330.0000.0000.0000.000
74A108GLY00.0540.00919.489-0.027-0.0270.0000.0000.0000.000
75A109LEU0-0.013-0.00313.802-0.053-0.0530.0000.0000.0000.000
76A110ALA00.0060.00417.137-0.035-0.0350.0000.0000.0000.000
77A111ILE00.0130.00620.282-0.023-0.0230.0000.0000.0000.000
78A112GLY00.0230.00417.689-0.033-0.0330.0000.0000.0000.000
79A113VAL0-0.015-0.02216.829-0.040-0.0400.0000.0000.0000.000
80A114ALA0-0.003-0.00118.935-0.016-0.0160.0000.0000.0000.000
81A115SER0-0.0150.00721.0540.0020.0020.0000.0000.0000.000
82A116MET0-0.089-0.02914.639-0.042-0.0420.0000.0000.0000.000
83A117LYS10.8130.88320.3270.3770.3770.0000.0000.0000.000
84A118SER0-0.004-0.01019.524-0.016-0.0160.0000.0000.0000.000
85A119GLY00.0340.01517.200-0.026-0.0260.0000.0000.0000.000
86A120GLU-1-0.791-0.86616.341-0.475-0.4750.0000.0000.0000.000
87A121ARG10.7560.8496.1901.7981.7980.0000.0000.0000.000
88A122ALA00.016-0.00212.602-0.059-0.0590.0000.0000.0000.000
89A123LEU0-0.0070.0038.853-0.074-0.0740.0000.0000.0000.000
90A124VAL00.0120.00611.9600.0750.0750.0000.0000.0000.000
91A125HIS10.8300.89513.5140.6330.6330.0000.0000.0000.000
92A126VAL0-0.010-0.00415.4800.0280.0280.0000.0000.0000.000
93A127GLY00.0570.03817.5610.0120.0120.0000.0000.0000.000
94A128TRP00.017-0.00319.6900.0330.0330.0000.0000.0000.000
95A129GLU-1-0.852-0.90520.655-0.019-0.0190.0000.0000.0000.000
96A130LEU0-0.0330.00121.4840.0150.0150.0000.0000.0000.000
97A131ALA00.0380.01417.8340.0110.0110.0000.0000.0000.000
98A132TYR0-0.044-0.05815.331-0.042-0.0420.0000.0000.0000.000
99A133GLY00.0060.00019.9320.0080.0080.0000.0000.0000.000
100A134LYN0-0.002-0.00122.089-0.023-0.0230.0000.0000.0000.000
101A135GLU-1-0.883-0.94424.7740.1220.1220.0000.0000.0000.000
102A136GLY0-0.0100.00720.8080.0060.0060.0000.0000.0000.000
103A137ASN0-0.055-0.03818.5480.0100.0100.0000.0000.0000.000
104A138PHE00.0470.02418.6990.0390.0390.0000.0000.0000.000
105A139SER0-0.046-0.03019.030-0.002-0.0020.0000.0000.0000.000
106A140PHE00.0050.00216.9020.0460.0460.0000.0000.0000.000
107A141PRO00.0210.04114.1430.1490.1490.0000.0000.0000.000
108A142ASN0-0.048-0.02014.185-0.148-0.1480.0000.0000.0000.000
109A143VAL00.0140.00713.8880.0600.0600.0000.0000.0000.000
110A144PRO00.0150.00615.496-0.040-0.0400.0000.0000.0000.000
111A145PRO00.0230.00418.489-0.012-0.0120.0000.0000.0000.000
112A146MET0-0.062-0.03221.363-0.027-0.0270.0000.0000.0000.000
113A147ALA00.0090.02616.633-0.041-0.0410.0000.0000.0000.000
114A148ASP-1-0.841-0.91917.477-0.102-0.1020.0000.0000.0000.000
115A149LEU0-0.049-0.02313.4280.0140.0140.0000.0000.0000.000
116A150LEU0-0.038-0.0279.734-0.115-0.1150.0000.0000.0000.000
117A151TYR00.0560.0269.5620.0950.0950.0000.0000.0000.000
118A152GLU-1-0.792-0.8525.298-3.473-3.4730.0000.0000.0000.000
119A153VAL00.001-0.0088.6490.3780.3780.0000.0000.0000.000
120A154GLU-1-0.798-0.91111.250-0.874-0.8740.0000.0000.0000.000
121A155VAL00.0190.02312.9900.1580.1580.0000.0000.0000.000
122A156ILE00.0080.00815.623-0.050-0.0500.0000.0000.0000.000
123A157GLY00.016-0.00117.976-0.042-0.0420.0000.0000.0000.000
124A158PHE0-0.024-0.00421.1450.0260.0260.0000.0000.0000.000
125A159ASP-1-0.840-0.90023.9040.0550.0550.0000.0000.0000.000
126A160GLU-1-0.792-0.86927.389-0.019-0.0190.0000.0000.0000.000
127A161THR00.0070.01329.8190.0060.0060.0000.0000.0000.000
128A162LYS10.8380.90931.501-0.063-0.0630.0000.0000.0000.000
129A163GLU-1-0.723-0.85235.826-0.005-0.0050.0000.0000.0000.000
130A164GLY00.0360.01839.3700.0020.0020.0000.0000.0000.000
131A165LYS10.9450.96143.119-0.015-0.0150.0000.0000.0000.000
132A166ALA00.0280.01344.4900.0030.0030.0000.0000.0000.000
133A167ARG10.7910.85444.933-0.009-0.0090.0000.0000.0000.000
134A168SER0-0.062-0.02746.5290.0020.0020.0000.0000.0000.000
135A169ASP-1-0.877-0.91443.7720.0410.0410.0000.0000.0000.000
136A170MET0-0.084-0.03139.2700.0040.0040.0000.0000.0000.000
137A171THR00.028-0.01537.352-0.003-0.0030.0000.0000.0000.000
138A172VAL00.0200.00536.548-0.007-0.0070.0000.0000.0000.000
139A173GLU-1-0.749-0.85132.8260.0700.0700.0000.0000.0000.000
140A174GLU-1-0.841-0.90034.5120.0520.0520.0000.0000.0000.000
141A175ARG10.8700.95836.534-0.032-0.0320.0000.0000.0000.000
142A176ILE00.001-0.00533.514-0.008-0.0080.0000.0000.0000.000
143A177GLY00.0330.02733.039-0.009-0.0090.0000.0000.0000.000
144A178ALA0-0.004-0.00533.881-0.010-0.0100.0000.0000.0000.000
145A179ALA0-0.021-0.00537.028-0.008-0.0080.0000.0000.0000.000
146A180ASP-1-0.778-0.88931.054-0.054-0.0540.0000.0000.0000.000
147A181ARG10.8510.92532.676-0.014-0.0140.0000.0000.0000.000
148A182ARG10.8520.91534.6320.0070.0070.0000.0000.0000.000
149A183LYS10.8570.92835.1620.0650.0650.0000.0000.0000.000
150A184MET0-0.090-0.04728.678-0.012-0.0120.0000.0000.0000.000
151A185ASP-1-0.866-0.92234.430-0.065-0.0650.0000.0000.0000.000
152A186GLY00.0810.02637.277-0.005-0.0050.0000.0000.0000.000
153A187ASN0-0.032-0.01933.6350.0000.0000.0000.0000.0000.000
154A188SER0-0.0190.00035.484-0.014-0.0140.0000.0000.0000.000
155A189LEU00.0000.01736.721-0.006-0.0060.0000.0000.0000.000
156A190PHE00.0090.01739.2930.0020.0020.0000.0000.0000.000
157A191LYS10.8250.89735.0940.1140.1140.0000.0000.0000.000
158A192GLU-1-0.852-0.91639.360-0.109-0.1090.0000.0000.0000.000
159A193GLU-1-0.914-0.95541.996-0.082-0.0820.0000.0000.0000.000
160A194LYS10.7460.84642.9560.0930.0930.0000.0000.0000.000
161A195LEU00.0390.04144.2680.0050.0050.0000.0000.0000.000
162A196GLU-1-0.860-0.94345.848-0.042-0.0420.0000.0000.0000.000
163A197GLU-1-0.840-0.92545.749-0.053-0.0530.0000.0000.0000.000
164A198ALA0-0.014-0.00542.0120.0010.0010.0000.0000.0000.000
165A199MET0-0.078-0.03143.3260.0020.0020.0000.0000.0000.000
166A200GLN00.0120.00645.6950.0050.0050.0000.0000.0000.000
167A201GLN0-0.013-0.01241.0340.0090.0090.0000.0000.0000.000
168A202TYR0-0.054-0.06338.2560.0020.0020.0000.0000.0000.000
169A203GLU-1-0.883-0.95942.534-0.029-0.0290.0000.0000.0000.000
170A204MET0-0.025-0.01943.6750.0060.0060.0000.0000.0000.000
171A205ALA0-0.027-0.00939.5240.0050.0050.0000.0000.0000.000
172A206ILE0-0.027-0.02941.3220.0050.0050.0000.0000.0000.000
173A207ALA00.0010.01543.6420.0050.0050.0000.0000.0000.000
174A208TYR0-0.069-0.04041.3030.0060.0060.0000.0000.0000.000
175A209MET0-0.087-0.03437.3810.0040.0040.0000.0000.0000.000
176A210GLY00.0560.03342.824-0.003-0.0030.0000.0000.0000.000
177A211ASP-1-0.893-0.95645.8270.0030.0030.0000.0000.0000.000
178A212ASP-1-0.806-0.87747.8000.0140.0140.0000.0000.0000.000
179A213PHE0-0.019-0.01639.1090.0040.0040.0000.0000.0000.000
180A214MET0-0.023-0.02740.3950.0030.0030.0000.0000.0000.000
181A215PHE0-0.0220.00944.0120.0020.0020.0000.0000.0000.000
182A216GLN0-0.077-0.02844.5450.0010.0010.0000.0000.0000.000
183A217LEU00.0150.01038.9060.0060.0060.0000.0000.0000.000
184A218TYR00.0080.00137.848-0.004-0.0040.0000.0000.0000.000
185A219GLY00.0170.00236.3520.0050.0050.0000.0000.0000.000
186A220LYS10.8570.91627.524-0.067-0.0670.0000.0000.0000.000
187A221TYR0-0.049-0.04333.407-0.003-0.0030.0000.0000.0000.000
188A222GLN0-0.010-0.00735.540-0.009-0.0090.0000.0000.0000.000
189A223ASP-1-0.874-0.93733.1260.0130.0130.0000.0000.0000.000
190A224MET0-0.069-0.02428.933-0.013-0.0130.0000.0000.0000.000
191A225ALA00.0460.02233.277-0.008-0.0080.0000.0000.0000.000
192A226LEU00.0070.01136.754-0.009-0.0090.0000.0000.0000.000
193A227ALA0-0.025-0.01932.131-0.009-0.0090.0000.0000.0000.000
194A228VAL0-0.065-0.02333.928-0.010-0.0100.0000.0000.0000.000
195A229LYS10.9100.93036.0530.0100.0100.0000.0000.0000.000
196A230ASN00.0200.00938.814-0.001-0.0010.0000.0000.0000.000
197A231PRO0-0.020-0.02935.118-0.006-0.0060.0000.0000.0000.000
198A232CYS0-0.0280.00838.046-0.007-0.0070.0000.0000.0000.000
199A233HIS00.0480.02840.0620.0000.0000.0000.0000.0000.000
200A234LEU0-0.018-0.01539.791-0.003-0.0030.0000.0000.0000.000
201A235ASN0-0.038-0.00638.269-0.006-0.0060.0000.0000.0000.000
202A236ILE00.0780.04841.629-0.003-0.0030.0000.0000.0000.000
203A237ALA00.005-0.00245.069-0.001-0.0010.0000.0000.0000.000
204A238ALA0-0.065-0.04443.122-0.001-0.0010.0000.0000.0000.000
205A239CYS0-0.0490.00044.560-0.003-0.0030.0000.0000.0000.000
206A240LEU00.0480.02846.2820.0030.0030.0000.0000.0000.000
207A241ILE0-0.039-0.03147.1040.0000.0000.0000.0000.0000.000
208A242LYS10.7690.86447.8110.0700.0700.0000.0000.0000.000
209A243LEU00.0560.04449.942-0.001-0.0010.0000.0000.0000.000
210A244LYS10.8580.93752.0580.0610.0610.0000.0000.0000.000
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