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: 524LZ

Calculation Name: 5DE2-A-Xray372

Preferred Name: Serine/threonine-protein kinase NEK7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5DE2

Chain ID: A

ChEMBL ID: CHEMBL4849

UniProt ID: Q8TDX7

Base Structure: X-ray

Registration Date: 2023-09-19

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 267
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3718498.895117
FMO2-HF: Nuclear repulsion 3608472.087326
FMO2-HF: Total energy -110026.807791
FMO2-MP2: Total energy -110339.878241


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:20:LYS)


Summations of interaction energy for fragment #1(A:20:LYS)
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.
-86.248-82.47115.955-10.851-8.881-0.113
Interaction energy analysis for fragmet #1(A:20:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.885 / q_NPA : 0.925
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].
3A22LEU00.0250.0083.847-3.821-1.469-0.020-1.225-1.1080.005
4A23ARG10.9250.9554.34742.84942.996-0.001-0.004-0.1410.000
5A24PRO00.011-0.0028.663-0.213-0.2130.0000.0000.0000.000
6A25ASP-1-0.883-0.93911.139-22.518-22.5180.0000.0000.0000.000
7A26MET0-0.0240.0128.875-0.595-0.5950.0000.0000.0000.000
8A27GLY00.0210.01412.0340.8210.8210.0000.0000.0000.000
9A28TYR0-0.039-0.06611.371-2.350-2.3500.0000.0000.0000.000
10A29ASN0-0.055-0.03511.105-0.540-0.5400.0000.0000.0000.000
11A30THR0-0.006-0.0235.765-2.168-2.1680.0000.0000.0000.000
12A31LEU0-0.029-0.0233.1273.0283.5820.018-0.145-0.427-0.001
13A32ALA0-0.044-0.0152.9650.3991.2690.254-0.258-0.8660.000
14A33ASN0-0.014-0.0053.9742.3172.3880.003-0.012-0.0610.000
15A34PHE0-0.0050.0086.7464.7714.7710.0000.0000.0000.000
16A35ARG10.9020.9557.15017.41817.4180.0000.0000.0000.000
17A36ILE00.000-0.0237.7792.6582.6580.0000.0000.0000.000
18A37GLU-1-0.822-0.89011.198-16.946-16.9460.0000.0000.0000.000
19A38LYS10.8880.93114.79617.28417.2840.0000.0000.0000.000
20A39LYS10.8800.95314.55919.69819.6980.0000.0000.0000.000
21A40ILE0-0.058-0.04117.0340.9450.9450.0000.0000.0000.000
22A41GLY00.0340.02218.7270.9410.9410.0000.0000.0000.000
23A42ARG10.8600.92218.00214.85914.8590.0000.0000.0000.000
24A43GLY00.0080.01619.1400.8940.8940.0000.0000.0000.000
25A44GLN0-0.020-0.01420.207-0.537-0.5370.0000.0000.0000.000
26A45PHE00.0380.01518.314-0.062-0.0620.0000.0000.0000.000
27A46SER00.0430.02815.432-0.861-0.8610.0000.0000.0000.000
28A47GLU-1-0.796-0.87213.736-17.738-17.7380.0000.0000.0000.000
29A48VAL0-0.019-0.01014.220-1.362-1.3620.0000.0000.0000.000
30A49TYR00.027-0.00111.9540.7650.7650.0000.0000.0000.000
31A50ARG10.8440.91714.77815.87515.8750.0000.0000.0000.000
32A51ALA0-0.007-0.01211.530-1.070-1.0700.0000.0000.0000.000
33A52ALA00.0000.00612.4541.6171.6170.0000.0000.0000.000
34A53CYS00.0010.01511.466-2.755-2.7550.0000.0000.0000.000
35A54LEU0-0.020-0.0327.3501.6251.6250.0000.0000.0000.000
36A55LEU0-0.061-0.01010.8200.9820.9820.0000.0000.0000.000
37A56ASP-1-0.760-0.87813.054-17.123-17.1230.0000.0000.0000.000
38A57GLY0-0.0060.01115.1420.9380.9380.0000.0000.0000.000
39A58VAL0-0.038-0.01316.3630.6220.6220.0000.0000.0000.000
40A59PRO0-0.059-0.02716.251-1.229-1.2290.0000.0000.0000.000
41A60VAL00.001-0.01013.7010.7120.7120.0000.0000.0000.000
42A61ALA0-0.005-0.00615.915-0.386-0.3860.0000.0000.0000.000
43A62LEU0-0.020-0.0088.418-0.488-0.4880.0000.0000.0000.000
44A63LYS10.8600.93013.05116.24716.2470.0000.0000.0000.000
45A64LYS10.8810.9595.12745.50345.5030.0000.0000.0000.000
46A65VAL00.007-0.01711.7831.5011.5010.0000.0000.0000.000
47A66GLN00.0530.01812.394-0.716-0.7160.0000.0000.0000.000
48A67ILE0-0.002-0.01913.6171.4211.4210.0000.0000.0000.000
49A68PHE0-0.050-0.01711.9711.5241.5240.0000.0000.0000.000
50A69ASP-1-0.863-0.93113.042-21.632-21.6320.0000.0000.0000.000
51A70LEU0-0.0170.00116.2180.9600.9600.0000.0000.0000.000
52A71MET0-0.055-0.00618.4570.7300.7300.0000.0000.0000.000
53A72ASP-1-0.810-0.90220.056-13.056-13.0560.0000.0000.0000.000
54A73ALA0-0.006-0.02622.190-0.295-0.2950.0000.0000.0000.000
55A74LYS10.8450.90723.12310.90310.9030.0000.0000.0000.000
56A75ALA00.0520.02722.878-0.060-0.0600.0000.0000.0000.000
57A76ARG10.9040.94017.86216.20016.2000.0000.0000.0000.000
58A77ALA0-0.021-0.01020.331-0.493-0.4930.0000.0000.0000.000
59A78ASP-1-0.795-0.88622.782-11.731-11.7310.0000.0000.0000.000
60A79CYS0-0.042-0.00618.488-0.145-0.1450.0000.0000.0000.000
61A80ILE00.0250.00217.265-0.182-0.1820.0000.0000.0000.000
62A81LYS10.8190.91519.87514.26614.2660.0000.0000.0000.000
63A82GLU-1-0.776-0.87323.081-11.759-11.7590.0000.0000.0000.000
64A83ILE0-0.010-0.01017.0750.0160.0160.0000.0000.0000.000
65A84ASP-1-0.828-0.92020.140-15.590-15.5900.0000.0000.0000.000
66A85LEU00.0000.01021.7830.2860.2860.0000.0000.0000.000
67A86LEU00.0210.00522.0250.2690.2690.0000.0000.0000.000
68A87LYS10.8430.93417.77317.24817.2480.0000.0000.0000.000
69A88GLN0-0.057-0.03521.4780.4750.4750.0000.0000.0000.000
70A89LEU0-0.0380.01124.9030.6440.6440.0000.0000.0000.000
71A90ASN0-0.052-0.05125.379-0.694-0.6940.0000.0000.0000.000
72A91HIS00.0770.04427.7990.1590.1590.0000.0000.0000.000
73A92PRO00.0180.01528.888-0.362-0.3620.0000.0000.0000.000
74A93ASN0-0.033-0.03730.0760.0940.0940.0000.0000.0000.000
75A94VAL0-0.0140.00625.8970.0800.0800.0000.0000.0000.000
76A95ILE0-0.058-0.01221.642-0.073-0.0730.0000.0000.0000.000
77A96LYS10.8800.94521.93313.74513.7450.0000.0000.0000.000
78A97PHE00.0130.00818.578-0.780-0.7800.0000.0000.0000.000
79A98TYR00.012-0.01416.3160.6400.6400.0000.0000.0000.000
80A99ALA00.0420.02713.2870.0710.0710.0000.0000.0000.000
81A100SER0-0.025-0.03713.3110.5800.5800.0000.0000.0000.000
82A101PHE00.0020.0306.3591.9571.9570.0000.0000.0000.000
83A102ILE00.0210.0139.765-1.043-1.0430.0000.0000.0000.000
84A103GLU-1-0.768-0.8894.382-58.165-58.021-0.001-0.019-0.1240.000
85A104ASP-1-0.865-0.9201.777-137.215-137.60715.703-9.183-6.129-0.117
86A105ASN0-0.011-0.0015.0704.3844.415-0.001-0.005-0.0250.000
87A106GLU-1-0.832-0.9077.670-31.779-31.7790.0000.0000.0000.000
88A107LEU0-0.003-0.0059.664-1.298-1.2980.0000.0000.0000.000
89A108ASN0-0.033-0.0297.331-0.494-0.4940.0000.0000.0000.000
90A109ILE0-0.014-0.01810.4670.8970.8970.0000.0000.0000.000
91A110VAL0-0.0120.01011.387-0.332-0.3320.0000.0000.0000.000
92A111LEU0-0.013-0.01513.9541.2271.2270.0000.0000.0000.000
93A112GLU-1-0.771-0.86117.516-13.316-13.3160.0000.0000.0000.000
94A113LEU0-0.013-0.00618.8120.0130.0130.0000.0000.0000.000
95A114ALA00.001-0.01320.9020.5730.5730.0000.0000.0000.000
96A115ASP-1-0.834-0.89423.015-13.315-13.3150.0000.0000.0000.000
97A116ALA0-0.056-0.02124.9200.3160.3160.0000.0000.0000.000
98A117GLY00.0020.00728.2020.4350.4350.0000.0000.0000.000
99A118ASP-1-0.787-0.88929.416-10.684-10.6840.0000.0000.0000.000
100A119LEU00.0660.02731.3910.3050.3050.0000.0000.0000.000
101A120SER00.0150.00732.7340.4540.4540.0000.0000.0000.000
102A121ARG10.8590.93028.11611.08511.0850.0000.0000.0000.000
103A122MET0-0.0150.00134.5950.3060.3060.0000.0000.0000.000
104A123ILE00.0320.01337.4270.2610.2610.0000.0000.0000.000
105A124LYS10.9070.95336.6828.7788.7780.0000.0000.0000.000
106A125HIS0-0.0030.01738.5170.1080.1080.0000.0000.0000.000
107A126PHE00.017-0.00540.2630.2060.2060.0000.0000.0000.000
108A127LYS10.8690.93342.5317.5027.5020.0000.0000.0000.000
109A128LYS10.9120.95638.9508.2338.2330.0000.0000.0000.000
110A129GLN0-0.033-0.00344.0060.1570.1570.0000.0000.0000.000
111A130LYS10.9240.96346.2586.5836.5830.0000.0000.0000.000
112A131ARG10.9350.97746.2407.0037.0030.0000.0000.0000.000
113A132LEU00.0570.04046.739-0.159-0.1590.0000.0000.0000.000
114A133ILE0-0.023-0.00741.4830.0030.0030.0000.0000.0000.000
115A134PRO00.0220.01245.7790.0740.0740.0000.0000.0000.000
116A135GLU-1-0.635-0.77846.584-6.583-6.5830.0000.0000.0000.000
117A136ARG10.9100.96646.8386.4186.4180.0000.0000.0000.000
118A137THR0-0.039-0.03142.135-0.102-0.1020.0000.0000.0000.000
119A138VAL00.0150.00742.451-0.227-0.2270.0000.0000.0000.000
120A139TRP00.053-0.00442.043-0.332-0.3320.0000.0000.0000.000
121A140LYS10.9460.99039.8937.8767.8760.0000.0000.0000.000
122A141TYR0-0.033-0.01336.300-0.085-0.0850.0000.0000.0000.000
123A142PHE00.0750.03037.554-0.242-0.2420.0000.0000.0000.000
124A143VAL00.0350.02039.038-0.133-0.1330.0000.0000.0000.000
125A144GLN00.006-0.00735.219-0.342-0.3420.0000.0000.0000.000
126A145LEU0-0.0040.01033.448-0.266-0.2660.0000.0000.0000.000
127A146CYS0-0.044-0.01835.158-0.105-0.1050.0000.0000.0000.000
128A147SER0-0.004-0.00735.839-0.127-0.1270.0000.0000.0000.000
129A148ALA0-0.017-0.00731.224-0.110-0.1100.0000.0000.0000.000
130A149LEU00.020-0.00332.311-0.231-0.2310.0000.0000.0000.000
131A150GLU-1-0.855-0.92934.093-8.188-8.1880.0000.0000.0000.000
132A151HIS00.0300.01730.042-0.330-0.3300.0000.0000.0000.000
133A152MET0-0.027-0.00227.721-0.118-0.1180.0000.0000.0000.000
134A153HIS0-0.019-0.02631.5220.1570.1570.0000.0000.0000.000
135A154SER0-0.072-0.02734.4030.0660.0660.0000.0000.0000.000
136A155ARG10.8600.93228.14710.84410.8440.0000.0000.0000.000
137A156ARG10.9050.95131.1778.4178.4170.0000.0000.0000.000
138A157VAL00.0350.01627.161-0.215-0.2150.0000.0000.0000.000
139A158MET0-0.054-0.01130.1630.2490.2490.0000.0000.0000.000
140A159HIS0-0.028-0.02027.416-0.136-0.1360.0000.0000.0000.000
141A160ARG10.8240.87927.26210.74610.7460.0000.0000.0000.000
142A161ASP-1-0.796-0.87228.076-11.043-11.0430.0000.0000.0000.000
143A162ILE00.0170.02430.014-0.199-0.1990.0000.0000.0000.000
144A163LYS10.8580.89728.40511.36011.3600.0000.0000.0000.000
145A164PRO00.0350.00631.966-0.277-0.2770.0000.0000.0000.000
146A165ALA0-0.028-0.02029.156-0.087-0.0870.0000.0000.0000.000
147A166ASN0-0.021-0.01026.716-0.683-0.6830.0000.0000.0000.000
148A167VAL0-0.0110.01128.428-0.156-0.1560.0000.0000.0000.000
149A168PHE00.0120.00125.2820.1690.1690.0000.0000.0000.000
150A169ILE0-0.041-0.03029.2800.3050.3050.0000.0000.0000.000
151A170THR00.007-0.00228.012-0.126-0.1260.0000.0000.0000.000
152A171ALA00.0590.01030.3590.3290.3290.0000.0000.0000.000
153A172THR0-0.022-0.00731.9660.2990.2990.0000.0000.0000.000
154A173GLY0-0.037-0.01034.0960.3000.3000.0000.0000.0000.000
155A174VAL0-0.015-0.00431.4540.1690.1690.0000.0000.0000.000
156A175VAL0-0.0200.00031.876-0.263-0.2630.0000.0000.0000.000
157A176LYS10.8130.89826.23111.82011.8200.0000.0000.0000.000
158A177LEU0-0.0140.00228.401-0.110-0.1100.0000.0000.0000.000
159A178GLY00.0550.00624.823-0.355-0.3550.0000.0000.0000.000
160A179ASP-1-0.860-0.94322.870-13.266-13.2660.0000.0000.0000.000
161A180LEU0-0.054-0.01621.248-0.874-0.8740.0000.0000.0000.000
162A181GLY0-0.0180.01122.509-0.033-0.0330.0000.0000.0000.000
163A196LEU00.000-0.00938.079-0.087-0.0870.0000.0000.0000.000
164A197VAL0-0.011-0.00936.2100.1300.1300.0000.0000.0000.000
165A198GLY00.0160.01232.880-0.025-0.0250.0000.0000.0000.000
166A199THR00.0150.01433.050-0.050-0.0500.0000.0000.0000.000
167A200PRO0-0.009-0.01932.303-0.179-0.1790.0000.0000.0000.000
168A201TYR0-0.081-0.03532.6930.0890.0890.0000.0000.0000.000
169A202TYR0-0.004-0.03434.4390.2090.2090.0000.0000.0000.000
170A203MET0-0.0090.01037.146-0.161-0.1610.0000.0000.0000.000
171A204SER00.0630.03138.0730.1500.1500.0000.0000.0000.000
172A205PRO00.0610.03440.403-0.045-0.0450.0000.0000.0000.000
173A206GLU-1-0.729-0.80438.620-7.948-7.9480.0000.0000.0000.000
174A207ARG10.7820.87434.8258.6848.6840.0000.0000.0000.000
175A208ILE00.004-0.00338.652-0.062-0.0620.0000.0000.0000.000
176A209HIS0-0.067-0.03941.8470.2080.2080.0000.0000.0000.000
177A210GLU-1-0.885-0.92138.153-8.426-8.4260.0000.0000.0000.000
178A211ASN00.0090.01338.846-0.045-0.0450.0000.0000.0000.000
179A212GLY0-0.0040.01135.737-0.075-0.0750.0000.0000.0000.000
180A213TYR0-0.080-0.07533.0220.1870.1870.0000.0000.0000.000
181A214ASN00.0530.00235.034-0.010-0.0100.0000.0000.0000.000
182A215PHE00.0510.01233.232-0.016-0.0160.0000.0000.0000.000
183A216LYS10.8720.93036.7687.2917.2910.0000.0000.0000.000
184A217SER0-0.013-0.02236.0600.1160.1160.0000.0000.0000.000
185A218ASP-1-0.760-0.84833.147-9.856-9.8560.0000.0000.0000.000
186A219ILE0-0.0060.00136.095-0.030-0.0300.0000.0000.0000.000
187A220TRP00.0280.02339.1310.1390.1390.0000.0000.0000.000
188A221SER0-0.004-0.00735.3360.1730.1730.0000.0000.0000.000
189A222LEU0-0.0050.00736.949-0.004-0.0040.0000.0000.0000.000
190A223GLY00.0520.01938.6920.0990.0990.0000.0000.0000.000
191A224CYS0-0.059-0.03039.6140.1720.1720.0000.0000.0000.000
192A225LEU0-0.010-0.00235.1480.0550.0550.0000.0000.0000.000
193A226LEU00.0040.00239.2260.0270.0270.0000.0000.0000.000
194A227TYR0-0.008-0.01542.1490.0640.0640.0000.0000.0000.000
195A228GLU-1-0.793-0.87838.713-8.357-8.3570.0000.0000.0000.000
196A229MET0-0.126-0.04739.331-0.038-0.0380.0000.0000.0000.000
197A230ALA00.0130.01242.1600.0510.0510.0000.0000.0000.000
198A231ALA00.0220.01045.3570.1340.1340.0000.0000.0000.000
199A232LEU0-0.060-0.03542.7430.0320.0320.0000.0000.0000.000
200A233GLN0-0.026-0.01342.091-0.154-0.1540.0000.0000.0000.000
201A234SER00.0250.00139.6280.0260.0260.0000.0000.0000.000
202A235PRO00.0220.01941.9090.1160.1160.0000.0000.0000.000
203A236PHE00.021-0.00742.7640.1230.1230.0000.0000.0000.000
204A237TYR0-0.084-0.04442.579-0.142-0.1420.0000.0000.0000.000
205A238GLY00.005-0.01544.2090.1940.1940.0000.0000.0000.000
206A239ASP-1-0.875-0.91945.187-6.809-6.8090.0000.0000.0000.000
207A240LYS10.9280.95846.1536.3156.3150.0000.0000.0000.000
208A241MET0-0.0110.03043.0450.1260.1260.0000.0000.0000.000
209A242ASN0-0.033-0.02743.486-0.118-0.1180.0000.0000.0000.000
210A243LEU00.1070.03840.3260.0920.0920.0000.0000.0000.000
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