FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: N9RJQ

Calculation Name: 5G5C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5G5C

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZJ1

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:

Apendix: None


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 270
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3977128.414595
FMO2-HF: Nuclear repulsion 3869504.735859
FMO2-HF: Total energy -107623.678735
FMO2-MP2: Total energy -107942.033151


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:19:HIS)


Summations of interaction energy for fragment #1(A:19:HIS)
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.
-26.139-23.30114.475-7.137-10.1770.024
Interaction energy analysis for fragmet #1(A:19:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.017
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].
3A21GLY00.0120.0241.945-14.746-15.96212.352-5.697-5.4400.041
4A22TYR0-0.013-0.0262.680-12.888-9.2672.125-1.354-4.392-0.018
5A23LYS10.9670.9924.7620.6140.642-0.001-0.004-0.0230.000
6A24MET0-0.057-0.0467.7630.1150.1150.0000.0000.0000.000
7A25VAL00.0260.0247.159-0.343-0.3430.0000.0000.0000.000
8A26ASN00.0100.0069.8360.2440.2440.0000.0000.0000.000
9A27PRO0-0.0010.01313.208-0.140-0.1400.0000.0000.0000.000
10A28PRO00.0170.01114.7680.0060.0060.0000.0000.0000.000
11A29ARG10.8230.90316.8160.4590.4590.0000.0000.0000.000
12A30VAL00.0270.01620.3680.0000.0000.0000.0000.0000.000
13A31VAL0-0.0030.00222.8380.0240.0240.0000.0000.0000.000
14A32GLY0-0.0030.00026.454-0.005-0.0050.0000.0000.0000.000
15A33ASN0-0.024-0.01929.0540.0020.0020.0000.0000.0000.000
16A34TRP0-0.033-0.00931.6400.0140.0140.0000.0000.0000.000
17A35THR0-0.020-0.02034.044-0.006-0.0060.0000.0000.0000.000
18A36PRO00.0620.01536.5270.0040.0040.0000.0000.0000.000
19A37LYS11.0191.02039.3750.1130.1130.0000.0000.0000.000
20A38ASP-1-0.868-0.92938.478-0.128-0.1280.0000.0000.0000.000
21A39LEU0-0.089-0.04238.1900.0020.0020.0000.0000.0000.000
22A40SER0-0.051-0.01642.2190.0060.0060.0000.0000.0000.000
23A41PHE00.0120.00542.6790.0040.0040.0000.0000.0000.000
24A42GLU-1-0.857-0.90343.034-0.093-0.0930.0000.0000.0000.000
25A43TYR0-0.019-0.01937.153-0.001-0.0010.0000.0000.0000.000
26A44LYS10.8680.91640.0100.0870.0870.0000.0000.0000.000
27A45ASP-1-0.817-0.91333.837-0.161-0.1610.0000.0000.0000.000
28A46VAL0-0.033-0.01434.8600.0060.0060.0000.0000.0000.000
29A47GLU-1-0.869-0.93430.999-0.151-0.1510.0000.0000.0000.000
30A48ILE0-0.0100.00331.7550.0110.0110.0000.0000.0000.000
31A49THR0-0.0050.00130.527-0.012-0.0120.0000.0000.0000.000
32A50THR0-0.032-0.03227.0240.0070.0070.0000.0000.0000.000
33A51GLU-1-0.898-0.95529.513-0.055-0.0550.0000.0000.0000.000
34A52ASP-1-0.809-0.86024.365-0.107-0.1070.0000.0000.0000.000
35A53ASN0-0.048-0.03526.377-0.009-0.0090.0000.0000.0000.000
36A54VAL0-0.0150.00423.508-0.015-0.0150.0000.0000.0000.000
37A55LYS10.8450.92026.2790.1320.1320.0000.0000.0000.000
38A56LEU0-0.008-0.00225.831-0.023-0.0230.0000.0000.0000.000
39A57SER00.0400.02327.9950.0090.0090.0000.0000.0000.000
40A58GLY00.010-0.01629.633-0.007-0.0070.0000.0000.0000.000
41A59TRP0-0.046-0.01132.3180.0010.0010.0000.0000.0000.000
42A60TRP00.0190.00135.6030.0010.0010.0000.0000.0000.000
43A61ILE0-0.005-0.01437.390-0.001-0.0010.0000.0000.0000.000
44A62ASP-1-0.838-0.89641.054-0.066-0.0660.0000.0000.0000.000
45A63ASN0-0.023-0.03144.4740.0000.0000.0000.0000.0000.000
46A64GLY00.0020.01346.4340.0030.0030.0000.0000.0000.000
47A65SER0-0.0250.00046.6630.0050.0050.0000.0000.0000.000
48A66ASP-1-0.803-0.87248.037-0.048-0.0480.0000.0000.0000.000
49A67LYS10.8280.90945.2040.0510.0510.0000.0000.0000.000
50A68THR00.019-0.00839.260-0.004-0.0040.0000.0000.0000.000
51A69VAL0-0.010-0.00537.5700.0030.0030.0000.0000.0000.000
52A70ILE00.003-0.00233.014-0.004-0.0040.0000.0000.0000.000
53A71PRO0-0.0260.00033.0280.0020.0020.0000.0000.0000.000
54A72LEU0-0.021-0.01728.480-0.010-0.0100.0000.0000.0000.000
55A73HIS00.0450.01722.9730.0100.0100.0000.0000.0000.000
56A74GLY00.0270.00923.8910.0070.0070.0000.0000.0000.000
57A75TYR00.0440.00213.279-0.031-0.0310.0000.0000.0000.000
58A76THR0-0.098-0.05215.913-0.025-0.0250.0000.0000.0000.000
59A77SER0-0.062-0.01618.933-0.017-0.0170.0000.0000.0000.000
60A78SER00.005-0.03022.572-0.010-0.0100.0000.0000.0000.000
61A79ARG10.8420.90225.3650.1980.1980.0000.0000.0000.000
62A80TRP00.0120.00327.5900.0040.0040.0000.0000.0000.000
63A81ALA0-0.0130.01526.5070.0050.0050.0000.0000.0000.000
64A82GLU-1-0.788-0.90628.180-0.158-0.1580.0000.0000.0000.000
65A83HIS0-0.037-0.01725.4680.0160.0160.0000.0000.0000.000
66A84TYR00.0430.00625.1010.0060.0060.0000.0000.0000.000
67A85MET0-0.0360.00628.9920.0120.0120.0000.0000.0000.000
68A86ARG10.9080.95931.8330.1520.1520.0000.0000.0000.000
69A87PRO0-0.003-0.00233.5440.0090.0090.0000.0000.0000.000
70A88VAL00.0040.00533.6880.0090.0090.0000.0000.0000.000
71A89ILE0-0.004-0.00133.3400.0070.0070.0000.0000.0000.000
72A90GLU-1-0.847-0.92437.324-0.086-0.0860.0000.0000.0000.000
73A91PHE0-0.005-0.01539.3350.0040.0040.0000.0000.0000.000
74A92LEU0-0.008-0.00537.4650.0050.0050.0000.0000.0000.000
75A93LEU00.0010.00340.1220.0040.0040.0000.0000.0000.000
76A94LYS10.8740.92843.2400.0860.0860.0000.0000.0000.000
77A95GLU-1-0.899-0.93143.999-0.058-0.0580.0000.0000.0000.000
78A96GLY00.0000.01546.1320.0040.0040.0000.0000.0000.000
79A97TYR0-0.103-0.06542.7830.0030.0030.0000.0000.0000.000
80A98ASN00.0260.00842.915-0.004-0.0040.0000.0000.0000.000
81A99VAL0-0.006-0.00536.9490.0000.0000.0000.0000.0000.000
82A100LEU0-0.0120.00934.763-0.001-0.0010.0000.0000.0000.000
83A101ALA00.0170.00132.8280.0000.0000.0000.0000.0000.000
84A102PHE00.009-0.00428.036-0.001-0.0010.0000.0000.0000.000
85A103ASP-1-0.740-0.85325.072-0.231-0.2310.0000.0000.0000.000
86A104PHE00.0130.00323.0280.0120.0120.0000.0000.0000.000
87A105ARG10.8200.84920.5960.1240.1240.0000.0000.0000.000
88A106ALA0-0.085-0.03917.663-0.019-0.0190.0000.0000.0000.000
89A107HIS00.0130.01819.002-0.076-0.0760.0000.0000.0000.000
90A108GLY00.0230.01221.3740.0280.0280.0000.0000.0000.000
91A109LYS10.8150.88623.5230.1650.1650.0000.0000.0000.000
92A110SER0-0.0080.00824.2630.0190.0190.0000.0000.0000.000
93A111GLY00.0390.03823.008-0.037-0.0370.0000.0000.0000.000
94A112GLY00.0280.00521.3210.0040.0040.0000.0000.0000.000
95A113LYS10.8860.93116.1080.2320.2320.0000.0000.0000.000
96A114TYR0-0.002-0.03714.1200.0340.0340.0000.0000.0000.000
97A115THR0-0.020-0.01713.8140.0330.0330.0000.0000.0000.000
98A116THR00.0350.02714.307-0.048-0.0480.0000.0000.0000.000
99A117VAL00.0080.00215.219-0.035-0.0350.0000.0000.0000.000
100A118GLY0-0.012-0.00617.6300.0310.0310.0000.0000.0000.000
101A119ASP-1-0.944-0.95719.819-0.021-0.0210.0000.0000.0000.000
102A120LYS11.0000.98320.6020.0860.0860.0000.0000.0000.000
103A121GLU-1-0.780-0.86720.383-0.181-0.1810.0000.0000.0000.000
104A122ILE0-0.013-0.01124.3960.0000.0000.0000.0000.0000.000
105A123LEU00.001-0.00325.2600.0040.0040.0000.0000.0000.000
106A124ASP-1-0.762-0.86824.653-0.163-0.1630.0000.0000.0000.000
107A125LEU00.0060.00728.0620.0030.0030.0000.0000.0000.000
108A126LYS10.8830.93530.7300.0510.0510.0000.0000.0000.000
109A127ALA00.0140.02030.9790.0050.0050.0000.0000.0000.000
110A128GLY00.0060.00732.3240.0010.0010.0000.0000.0000.000
111A129VAL00.001-0.01434.0250.0040.0040.0000.0000.0000.000
112A130LYS10.8190.88636.0140.0630.0630.0000.0000.0000.000
113A131TRP00.0590.03436.0950.0030.0030.0000.0000.0000.000
114A132LEU00.0370.01238.0220.0020.0020.0000.0000.0000.000
115A133LYS10.8220.91340.3420.0550.0550.0000.0000.0000.000
116A134ASP-1-0.835-0.90040.003-0.057-0.0570.0000.0000.0000.000
117A135ASN0-0.086-0.04440.0700.0030.0030.0000.0000.0000.000
118A136TYR0-0.0050.00541.912-0.002-0.0020.0000.0000.0000.000
119A137PRO00.0560.04344.8510.0000.0000.0000.0000.0000.000
120A138GLU-1-0.876-0.96146.268-0.056-0.0560.0000.0000.0000.000
121A139LYS10.8120.90844.8090.0640.0640.0000.0000.0000.000
122A140SER0-0.015-0.00542.477-0.002-0.0020.0000.0000.0000.000
123A141LYS10.9060.95644.4190.0440.0440.0000.0000.0000.000
124A142ARG10.8560.93644.9190.0430.0430.0000.0000.0000.000
125A143ILE00.0520.01638.427-0.003-0.0030.0000.0000.0000.000
126A144GLY00.0580.03139.5610.0050.0050.0000.0000.0000.000
127A145VAL0-0.047-0.01433.897-0.005-0.0050.0000.0000.0000.000
128A146ILE00.0440.02133.7180.0060.0060.0000.0000.0000.000
129A147GLY0-0.0040.01330.331-0.009-0.0090.0000.0000.0000.000
130A148PHE00.0320.00828.3720.0080.0080.0000.0000.0000.000
131A149SER00.000-0.01423.590-0.021-0.0210.0000.0000.0000.000
132A150MET0-0.044-0.01918.6210.0080.0080.0000.0000.0000.000
133A151GLY00.0630.02823.6610.0130.0130.0000.0000.0000.000
134A152ALA0-0.051-0.00826.6670.0130.0130.0000.0000.0000.000
135A153LEU00.0050.00323.3940.0120.0120.0000.0000.0000.000
136A154VAL00.0010.00325.3220.0110.0110.0000.0000.0000.000
137A155ALA00.0110.00827.8910.0080.0080.0000.0000.0000.000
138A156ILE0-0.012-0.00430.1150.0070.0070.0000.0000.0000.000
139A157ARG10.8500.92224.9220.0450.0450.0000.0000.0000.000
140A158GLY00.027-0.00730.8610.0050.0050.0000.0000.0000.000
141A159LEU0-0.040-0.00632.9840.0040.0040.0000.0000.0000.000
142A160SER0-0.0140.01133.7910.0070.0070.0000.0000.0000.000
143A161GLU-1-0.829-0.89630.526-0.029-0.0290.0000.0000.0000.000
144A162VAL0-0.016-0.00733.6610.0000.0000.0000.0000.0000.000
145A163LYS10.9310.97636.4600.0330.0330.0000.0000.0000.000
146A164GLU-1-0.881-0.96739.206-0.044-0.0440.0000.0000.0000.000
147A165ILE0-0.0290.01235.077-0.002-0.0020.0000.0000.0000.000
148A166CYS0-0.029-0.01339.5250.0040.0040.0000.0000.0000.000
149A167CYS0-0.035-0.00340.3770.0020.0020.0000.0000.0000.000
150A168GLY00.0490.01136.598-0.005-0.0050.0000.0000.0000.000
151A169VAL0-0.0080.01235.4960.0050.0050.0000.0000.0000.000
152A170ALA00.001-0.01131.681-0.007-0.0070.0000.0000.0000.000
153A171ASP-1-0.803-0.88831.689-0.089-0.0890.0000.0000.0000.000
154A172SER0-0.001-0.03528.100-0.013-0.0130.0000.0000.0000.000
155A173PRO00.0110.00427.134-0.011-0.0110.0000.0000.0000.000
156A174PRO00.001-0.01122.7500.0110.0110.0000.0000.0000.000
157A175ILE0-0.0020.01225.1350.0040.0040.0000.0000.0000.000
158A176TYR00.0330.00223.2600.0140.0140.0000.0000.0000.000
159A177LEU00.0530.03219.2740.0020.0020.0000.0000.0000.000
160A178ASP-1-0.731-0.85217.4770.0920.0920.0000.0000.0000.000
161A179LYS10.8640.93917.762-0.081-0.0810.0000.0000.0000.000
162A180THR00.008-0.01019.9630.0010.0010.0000.0000.0000.000
163A181GLY00.0280.01216.344-0.028-0.0280.0000.0000.0000.000
164A182ALA0-0.020-0.01715.407-0.015-0.0150.0000.0000.0000.000
165A183ARG10.7090.81016.4750.0070.0070.0000.0000.0000.000
166A184GLY00.0550.02917.098-0.010-0.0100.0000.0000.0000.000
167A185MET00.013-0.00110.406-0.026-0.0260.0000.0000.0000.000
168A186LYS10.8860.95414.723-0.076-0.0760.0000.0000.0000.000
169A187TYR0-0.047-0.02417.0770.0130.0130.0000.0000.0000.000
170A188PHE00.001-0.00911.999-0.056-0.0560.0000.0000.0000.000
171A189ALA0-0.0100.00313.488-0.048-0.0480.0000.0000.0000.000
172A190LYS10.9520.96714.8500.1130.1130.0000.0000.0000.000
173A191LEU0-0.0380.00313.4550.0080.0080.0000.0000.0000.000
174A192PRO00.0550.04014.5970.0250.0250.0000.0000.0000.000
175A193GLU-1-0.797-0.91210.469-0.580-0.5800.0000.0000.0000.000
176A194TRP00.015-0.01310.305-0.336-0.3360.0000.0000.0000.000
177A195LEU0-0.025-0.00611.184-0.211-0.2110.0000.0000.0000.000
178A196TYR00.0040.0036.415-0.032-0.0320.0000.0000.0000.000
179A197SER00.010-0.0096.051-0.290-0.2900.0000.0000.0000.000
180A198PHE0-0.039-0.0026.721-0.680-0.6800.0000.0000.0000.000
181A199VAL00.006-0.0069.458-0.029-0.0290.0000.0000.0000.000
182A200LYS10.8480.9214.126-1.543-1.2460.000-0.080-0.2170.001
183A201PRO00.0220.0155.0140.5910.5910.0000.0000.0000.000
184A202PHE00.0360.0107.0210.5360.5360.0000.0000.0000.000
185A203SER00.0090.0069.9870.2530.2530.0000.0000.0000.000
186A204GLU-1-0.852-0.9265.4102.6562.764-0.001-0.002-0.1050.000
187A205LEU0-0.0100.0259.1630.1850.1850.0000.0000.0000.000
188A206PHE0-0.035-0.00210.5280.1120.1120.0000.0000.0000.000
189A207SER0-0.074-0.04311.9540.0970.0970.0000.0000.0000.000
190A208GLY00.0650.00613.678-0.054-0.0540.0000.0000.0000.000
191A209GLY0-0.077-0.05017.394-0.005-0.0050.0000.0000.0000.000
192A210ARG10.8060.86919.142-0.133-0.1330.0000.0000.0000.000
193A211PRO00.0290.02217.063-0.005-0.0050.0000.0000.0000.000
194A212ILE00.0410.03920.371-0.013-0.0130.0000.0000.0000.000
195A213ASN0-0.022-0.00423.174-0.002-0.0020.0000.0000.0000.000
196A214VAL00.0470.01825.359-0.006-0.0060.0000.0000.0000.000
197A215LEU00.0570.01827.985-0.005-0.0050.0000.0000.0000.000
198A216ASN0-0.0060.01730.2650.0010.0010.0000.0000.0000.000
199A217TYR0-0.003-0.01728.435-0.001-0.0010.0000.0000.0000.000
200A218THR0-0.086-0.03433.324-0.002-0.0020.0000.0000.0000.000
201A219ASN00.0190.01335.3380.0000.0000.0000.0000.0000.000
202A220SER0-0.029-0.04135.3070.0010.0010.0000.0000.0000.000
203A221ILE0-0.025-0.00133.954-0.003-0.0030.0000.0000.0000.000
204A222LYS10.9170.96238.2810.0100.0100.0000.0000.0000.000
205A223LYS10.8360.93240.0000.0370.0370.0000.0000.0000.000
206A224PRO00.0340.02540.8050.0000.0000.0000.0000.0000.000
207A225LEU0-0.007-0.00435.006-0.004-0.0040.0000.0000.0000.000
208A226PHE00.0150.01638.1360.0030.0030.0000.0000.0000.000
209A227LEU0-0.002-0.00433.698-0.006-0.0060.0000.0000.0000.000
210A228ILE00.0430.02234.3290.0030.0030.0000.0000.0000.000
211A229ILE0-0.003-0.00229.692-0.005-0.0050.0000.0000.0000.000
212A230GLY00.0260.03831.6840.0050.0050.0000.0000.0000.000
213A231ARG10.8460.86531.6260.0420.0420.0000.0000.0000.000
214A232ARG10.8790.94730.9460.0720.0720.0000.0000.0000.000
215A233ASP-1-0.764-0.86626.247-0.111-0.1110.0000.0000.0000.000
216A234THR0-0.031-0.00923.6960.0100.0100.0000.0000.0000.000
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