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: 2N8ZR

Calculation Name: 4EQY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQY

Chain ID: A

ChEMBL ID:

UniProt ID: Q2SWY6

Base Structure: X-ray

Registration Date: 2023-09-23

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 261
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3114198.238028
FMO2-HF: Nuclear repulsion 3017077.049459
FMO2-HF: Total energy -97121.188569
FMO2-MP2: Total energy -97406.559631


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:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-6.958-1.880.395-2.423-3.0520.004
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.003
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].
3A5ILE00.0530.0402.797-0.3982.0970.049-1.253-1.2920.003
4A6HIS00.0450.0433.1000.6702.0360.120-0.681-0.805-0.005
5A7PRO0-0.008-0.0192.891-2.677-1.4600.226-0.489-0.9550.006
6A8THR0-0.034-0.0275.832-0.674-0.6740.0000.0000.0000.000
7A9ALA0-0.032-0.0027.819-0.235-0.2350.0000.0000.0000.000
8A10ILE0-0.032-0.0229.5920.1210.1210.0000.0000.0000.000
9A11ILE00.0170.0118.745-0.100-0.1000.0000.0000.0000.000
10A12GLU-1-0.831-0.89711.7060.0550.0550.0000.0000.0000.000
11A13PRO0-0.050-0.04415.158-0.042-0.0420.0000.0000.0000.000
12A14GLY00.0220.01716.1210.0070.0070.0000.0000.0000.000
13A15ALA0-0.0080.02313.934-0.021-0.0210.0000.0000.0000.000
14A16GLN0-0.088-0.04714.700-0.021-0.0210.0000.0000.0000.000
15A17LEU00.011-0.0059.894-0.026-0.0260.0000.0000.0000.000
16A18HIS00.0610.06212.377-0.086-0.0860.0000.0000.0000.000
17A19GLU-1-0.867-0.9459.364-0.654-0.6540.0000.0000.0000.000
18A20THR0-0.111-0.0918.058-0.277-0.2770.0000.0000.0000.000
19A21VAL00.0020.0279.782-0.059-0.0590.0000.0000.0000.000
20A22GLU-1-0.908-0.9366.580-2.689-2.6890.0000.0000.0000.000
21A23VAL00.012-0.0057.2420.4500.4500.0000.0000.0000.000
22A24GLY00.0090.0137.305-0.033-0.0330.0000.0000.0000.000
23A25PRO0-0.016-0.0338.7580.1540.1540.0000.0000.0000.000
24A26TYR0-0.004-0.0159.949-0.100-0.1000.0000.0000.0000.000
25A27ALA0-0.0030.03111.419-0.023-0.0230.0000.0000.0000.000
26A28ILE0-0.019-0.01512.1950.0790.0790.0000.0000.0000.000
27A29VAL0-0.005-0.00512.251-0.061-0.0610.0000.0000.0000.000
28A30GLY00.0770.03914.5830.0330.0330.0000.0000.0000.000
29A31SER0-0.050-0.06417.433-0.035-0.0350.0000.0000.0000.000
30A32ASN0-0.091-0.03918.6910.0020.0020.0000.0000.0000.000
31A33VAL0-0.0160.01317.135-0.007-0.0070.0000.0000.0000.000
32A34THR0-0.021-0.01517.496-0.003-0.0030.0000.0000.0000.000
33A35ILE0-0.043-0.02413.5190.0040.0040.0000.0000.0000.000
34A36GLY00.0500.02515.413-0.031-0.0310.0000.0000.0000.000
35A37ALA00.005-0.00813.928-0.081-0.0810.0000.0000.0000.000
36A38ARG10.7100.79412.5040.5600.5600.0000.0000.0000.000
37A39THR0-0.0250.00813.498-0.015-0.0150.0000.0000.0000.000
38A40THR0-0.049-0.02611.485-0.132-0.1320.0000.0000.0000.000
39A41ILE00.0180.00711.8510.1580.1580.0000.0000.0000.000
40A42GLY0-0.006-0.00111.848-0.107-0.1070.0000.0000.0000.000
41A43SER00.008-0.02512.7100.0580.0580.0000.0000.0000.000
42A44HIS0-0.055-0.05513.6170.0440.0440.0000.0000.0000.000
43A45SER0-0.031-0.00415.4550.0400.0400.0000.0000.0000.000
44A46VAL0-0.0110.00515.6760.0120.0120.0000.0000.0000.000
45A47ILE00.0010.00615.636-0.011-0.0110.0000.0000.0000.000
46A48GLU-1-0.874-0.95417.777-0.056-0.0560.0000.0000.0000.000
47A49GLY00.0700.04420.573-0.015-0.0150.0000.0000.0000.000
48A50HIS0-0.023-0.00522.249-0.014-0.0140.0000.0000.0000.000
49A51THR0-0.014-0.02320.7730.0030.0030.0000.0000.0000.000
50A52THR0-0.040-0.02120.839-0.012-0.0120.0000.0000.0000.000
51A53ILE0-0.033-0.01717.8040.0130.0130.0000.0000.0000.000
52A54GLY00.0710.04219.287-0.022-0.0220.0000.0000.0000.000
53A55GLU-1-0.788-0.89017.676-0.467-0.4670.0000.0000.0000.000
54A56ASP-1-0.822-0.88716.792-0.462-0.4620.0000.0000.0000.000
55A57ASN0-0.045-0.02317.7580.0490.0490.0000.0000.0000.000
56A58ARG10.9240.95815.5770.4690.4690.0000.0000.0000.000
57A59ILE00.0310.01516.6030.0700.0700.0000.0000.0000.000
58A60GLY00.0070.00316.334-0.058-0.0580.0000.0000.0000.000
59A61HIS00.0070.02513.8530.0050.0050.0000.0000.0000.000
60A62TYR0-0.032-0.03117.7150.0120.0120.0000.0000.0000.000
61A63ALA0-0.0110.01319.0320.0190.0190.0000.0000.0000.000
62A64SER0-0.027-0.00419.6910.0040.0040.0000.0000.0000.000
63A65VAL00.014-0.01320.0220.0000.0000.0000.0000.0000.000
64A66GLY00.0630.01821.146-0.007-0.0070.0000.0000.0000.000
65A67GLY0-0.0020.01923.7890.0130.0130.0000.0000.0000.000
66A68ARG10.9560.98025.6290.0280.0280.0000.0000.0000.000
67A69PRO0-0.019-0.00528.8070.0000.0000.0000.0000.0000.000
68A70GLN00.0190.01532.1140.0020.0020.0000.0000.0000.000
69A71ASP-1-0.821-0.91534.213-0.049-0.0490.0000.0000.0000.000
70A72MET00.0080.00537.1800.0020.0020.0000.0000.0000.000
71A73LYS10.8260.89639.6400.0500.0500.0000.0000.0000.000
72A74TYR0-0.039-0.00430.6050.0030.0030.0000.0000.0000.000
73A75LYS10.7450.84936.0150.0300.0300.0000.0000.0000.000
74A76ASP-1-0.846-0.93731.246-0.022-0.0220.0000.0000.0000.000
75A77GLU-1-0.772-0.88131.924-0.043-0.0430.0000.0000.0000.000
76A78PRO0-0.0160.01329.291-0.004-0.0040.0000.0000.0000.000
77A79THR0-0.069-0.04830.030-0.006-0.0060.0000.0000.0000.000
78A80ARG10.9600.97227.2950.0970.0970.0000.0000.0000.000
79A81LEU0-0.013-0.00123.6840.0070.0070.0000.0000.0000.000
80A82VAL0-0.034-0.01225.048-0.007-0.0070.0000.0000.0000.000
81A83ILE0-0.023-0.01022.1440.0100.0100.0000.0000.0000.000
82A84GLY00.0760.04923.417-0.014-0.0140.0000.0000.0000.000
83A85ASP-1-0.813-0.90521.850-0.330-0.3300.0000.0000.0000.000
84A86ARG10.7210.80821.0710.2990.2990.0000.0000.0000.000
85A87ASN0-0.0360.00522.0670.0320.0320.0000.0000.0000.000
86A88THR0-0.054-0.02121.164-0.052-0.0520.0000.0000.0000.000
87A89ILE00.0200.01021.1820.0360.0360.0000.0000.0000.000
88A90ARG10.8430.90520.9140.2500.2500.0000.0000.0000.000
89A91GLU-1-0.754-0.85019.538-0.279-0.2790.0000.0000.0000.000
90A92PHE0-0.018-0.01622.4940.0140.0140.0000.0000.0000.000
91A93THR0-0.038-0.00823.2270.0120.0120.0000.0000.0000.000
92A94THR0-0.015-0.02024.3200.0010.0010.0000.0000.0000.000
93A95ILE00.0140.00824.0570.0010.0010.0000.0000.0000.000
94A96HIS00.0280.01225.7490.0010.0010.0000.0000.0000.000
95A97THR00.0360.03526.444-0.007-0.0070.0000.0000.0000.000
96A98GLY00.008-0.00128.8280.0050.0050.0000.0000.0000.000
97A99THR0-0.074-0.06632.4890.0060.0060.0000.0000.0000.000
98A100VAL0-0.019-0.02335.459-0.002-0.0020.0000.0000.0000.000
99A101GLN0-0.050-0.02237.5720.0020.0020.0000.0000.0000.000
100A102ASP-1-0.797-0.86037.586-0.070-0.0700.0000.0000.0000.000
101A103ALA0-0.025-0.02436.1870.0020.0020.0000.0000.0000.000
102A104GLY0-0.0050.00234.395-0.003-0.0030.0000.0000.0000.000
103A105VAL0-0.085-0.05529.409-0.003-0.0030.0000.0000.0000.000
104A106THR0-0.0120.00129.0830.0070.0070.0000.0000.0000.000
105A107THR0-0.033-0.02429.093-0.005-0.0050.0000.0000.0000.000
106A108LEU0-0.004-0.00125.8830.0070.0070.0000.0000.0000.000
107A109GLY00.0410.03027.743-0.007-0.0070.0000.0000.0000.000
108A110ASP-1-0.759-0.86726.213-0.246-0.2460.0000.0000.0000.000
109A111ASP-1-0.807-0.89025.553-0.230-0.2300.0000.0000.0000.000
110A112ASN0-0.045-0.01726.6210.0220.0220.0000.0000.0000.000
111A113TRP0-0.023-0.01423.930-0.028-0.0280.0000.0000.0000.000
112A114ILE00.0100.00025.6570.0220.0220.0000.0000.0000.000
113A115MET0-0.023-0.00425.522-0.013-0.0130.0000.0000.0000.000
114A116ALA00.0530.02325.4780.0020.0020.0000.0000.0000.000
115A117TYR0-0.031-0.03926.5900.0090.0090.0000.0000.0000.000
116A118VAL0-0.0590.00328.2810.0100.0100.0000.0000.0000.000
117A119HIS0-0.0090.01228.262-0.013-0.0130.0000.0000.0000.000
118A120ILE00.0180.00128.2530.0030.0030.0000.0000.0000.000
119A121GLY00.0710.03230.167-0.001-0.0010.0000.0000.0000.000
120A122HIS10.8740.93832.0230.0610.0610.0000.0000.0000.000
121A123ASP-1-0.724-0.83132.702-0.069-0.0690.0000.0000.0000.000
122A124CYS0-0.094-0.01932.5270.0030.0030.0000.0000.0000.000
123A125ARG10.8020.88832.8470.0800.0800.0000.0000.0000.000
124A126VAL0-0.024-0.01831.0720.0060.0060.0000.0000.0000.000
125A127GLY00.0480.03131.905-0.006-0.0060.0000.0000.0000.000
126A128SER00.0370.00830.444-0.014-0.0140.0000.0000.0000.000
127A129HIS0-0.030-0.02129.7350.0190.0190.0000.0000.0000.000
128A130VAL0-0.055-0.00831.3910.0090.0090.0000.0000.0000.000
129A131VAL0-0.039-0.02030.697-0.013-0.0130.0000.0000.0000.000
130A132LEU00.0110.00130.1400.0140.0140.0000.0000.0000.000
131A133SER00.010-0.03230.419-0.012-0.0120.0000.0000.0000.000
132A134SER00.008-0.01930.3280.0000.0000.0000.0000.0000.000
133A135ASN0-0.030-0.03230.8040.0090.0090.0000.0000.0000.000
134A136ALA0-0.0090.02332.6560.0080.0080.0000.0000.0000.000
135A137GLN0-0.052-0.03832.820-0.002-0.0020.0000.0000.0000.000
136A138MET0-0.023-0.01133.2100.0080.0080.0000.0000.0000.000
137A139ALA00.0260.01434.721-0.001-0.0010.0000.0000.0000.000
138A140GLY00.0550.01835.850-0.004-0.0040.0000.0000.0000.000
139A141HIS0-0.055-0.06236.4810.0060.0060.0000.0000.0000.000
140A142VAL0-0.032-0.00136.8080.0010.0010.0000.0000.0000.000
141A143GLU-1-0.860-0.91336.710-0.088-0.0880.0000.0000.0000.000
142A144ILE0-0.025-0.02134.4740.0040.0040.0000.0000.0000.000
143A145GLY00.0460.02735.916-0.006-0.0060.0000.0000.0000.000
144A146ASP-1-0.796-0.91134.687-0.134-0.1340.0000.0000.0000.000
145A147TRP00.003-0.00933.8430.0100.0100.0000.0000.0000.000
146A148ALA0-0.0050.01835.9550.0040.0040.0000.0000.0000.000
147A149ILE0-0.026-0.01735.518-0.008-0.0080.0000.0000.0000.000
148A150VAL00.0280.02035.4980.0090.0090.0000.0000.0000.000
149A151GLY00.0100.01935.397-0.008-0.0080.0000.0000.0000.000
150A152GLY00.0300.00435.0670.0000.0000.0000.0000.0000.000
151A153MET0-0.026-0.00535.4440.0050.0050.0000.0000.0000.000
152A154SER0-0.0130.00137.3370.0070.0070.0000.0000.0000.000
153A155GLY00.0170.01937.503-0.004-0.0040.0000.0000.0000.000
154A156VAL0-0.029-0.01638.5430.0030.0030.0000.0000.0000.000
155A157HIS0-0.029-0.02739.6080.0030.0030.0000.0000.0000.000
156A158GLN00.0280.01240.276-0.004-0.0040.0000.0000.0000.000
157A159TYR0-0.004-0.01240.7220.0050.0050.0000.0000.0000.000
158A160VAL0-0.058-0.00642.0240.0020.0020.0000.0000.0000.000
159A161ARG10.8210.90741.0500.0640.0640.0000.0000.0000.000
160A162ILE0-0.013-0.01038.6330.0040.0040.0000.0000.0000.000
161A163GLY00.0680.03940.274-0.005-0.0050.0000.0000.0000.000
162A164ALA00.0600.03539.567-0.003-0.0030.0000.0000.0000.000
163A165HIS0-0.002-0.01238.8070.0060.0060.0000.0000.0000.000
164A166SER0-0.060-0.01740.5960.0020.0020.0000.0000.0000.000
165A167MET0-0.050-0.03140.107-0.005-0.0050.0000.0000.0000.000
166A168LEU00.0110.01340.0500.0060.0060.0000.0000.0000.000
167A169GLY00.0320.00740.115-0.005-0.0050.0000.0000.0000.000
168A170GLY00.0320.02139.539-0.002-0.0020.0000.0000.0000.000
169A171ALA0-0.035-0.00939.9680.0050.0050.0000.0000.0000.000
170A172SER0-0.045-0.02141.6520.0060.0060.0000.0000.0000.000
171A173ALA0-0.028-0.01342.108-0.003-0.0030.0000.0000.0000.000
172A174LEU00.0080.01042.0210.0040.0040.0000.0000.0000.000
173A175VAL00.036-0.00443.9380.0000.0000.0000.0000.0000.000
174A176GLN0-0.040-0.01746.5710.0030.0030.0000.0000.0000.000
175A177ASP-1-0.709-0.83045.352-0.067-0.0670.0000.0000.0000.000
176A178ILE0-0.015-0.00742.3770.0030.0030.0000.0000.0000.000
177A179PRO00.0130.00344.966-0.003-0.0030.0000.0000.0000.000
178A180PRO00.0310.02744.062-0.003-0.0030.0000.0000.0000.000
179A181PHE0-0.001-0.01543.9060.0030.0030.0000.0000.0000.000
180A182VAL0-0.053-0.00945.3370.0010.0010.0000.0000.0000.000
181A183ILE0-0.015-0.00144.592-0.005-0.0050.0000.0000.0000.000
182A184ALA00.0190.00044.9600.0050.0050.0000.0000.0000.000
183A185ALA00.0170.00844.811-0.004-0.0040.0000.0000.0000.000
184A186GLY00.0470.04246.0710.0030.0030.0000.0000.0000.000
185A187ASN00.0360.02445.985-0.001-0.0010.0000.0000.0000.000
186A188LYS10.8940.93147.9530.0510.0510.0000.0000.0000.000
187A189ALA0-0.016-0.00445.6550.0000.0000.0000.0000.0000.000
188A190GLU-1-0.835-0.87147.804-0.047-0.0470.0000.0000.0000.000
189A191PRO00.0170.00449.360-0.003-0.0030.0000.0000.0000.000
190A192HIS0-0.001-0.00148.4920.0030.0030.0000.0000.0000.000
191A193GLY0-0.0050.00350.1410.0010.0010.0000.0000.0000.000
192A194ILE00.0170.01548.119-0.002-0.0020.0000.0000.0000.000
193A195ASN00.0110.00340.9190.0010.0010.0000.0000.0000.000
194A196VAL0-0.013-0.02344.635-0.004-0.0040.0000.0000.0000.000
195A197GLU-1-0.733-0.84043.605-0.085-0.0850.0000.0000.0000.000
196A198GLY0-0.0450.00440.656-0.005-0.0050.0000.0000.0000.000
197A199LEU00.0070.00440.785-0.005-0.0050.0000.0000.0000.000
198A200ARG10.8610.89442.9090.0810.0810.0000.0000.0000.000
199A201ARG10.8320.88739.1210.1050.1050.0000.0000.0000.000
200A202ARG10.8370.93336.1110.1170.1170.0000.0000.0000.000
201A203GLY00.0120.01939.747-0.001-0.0010.0000.0000.0000.000
202A204PHE0-0.033-0.00941.5710.0040.0040.0000.0000.0000.000
203A205SER00.014-0.03545.4050.0010.0010.0000.0000.0000.000
204A206PRO0-0.002-0.02448.7200.0000.0000.0000.0000.0000.000
205A207ASP-1-0.850-0.92351.434-0.059-0.0590.0000.0000.0000.000
206A208ALA00.0460.03249.0130.0020.0020.0000.0000.0000.000
207A209ILE00.0190.00046.6690.0010.0010.0000.0000.0000.000
208A210SER0-0.081-0.02150.4830.0020.0020.0000.0000.0000.000
209A211ALA00.0580.04653.3340.0020.0020.0000.0000.0000.000
210A212LEU00.0580.02847.8570.0020.0020.0000.0000.0000.000
211A213ARG10.8810.92352.0960.0650.0650.0000.0000.0000.000
212A214SER0-0.054-0.01454.0740.0030.0030.0000.0000.0000.000
213A215ALA00.0690.04353.5670.0020.0020.0000.0000.0000.000
214A216TYR0-0.052-0.04652.1360.0020.0020.0000.0000.0000.000
215A217ARG10.8650.91154.5490.0520.0520.0000.0000.0000.000
216A218ILE00.0360.02958.2400.0020.0020.0000.0000.0000.000
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