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: 52JMZ

Calculation Name: 2HZ6-A-Xray372

Preferred Name: Serine/threonine-protein kinase/endoribonuclease IRE1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZ6

Chain ID: A

ChEMBL ID: CHEMBL1163101

UniProt ID: O75460

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptH
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 268
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3655143.327074
FMO2-HF: Nuclear repulsion 3549250.675022
FMO2-HF: Total energy -105892.652052
FMO2-MP2: Total energy -106204.785796


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:29:PRO)


Summations of interaction energy for fragment #1(A:29:PRO)
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.
-2.929-1.60812.859-4.71-9.467-0.015
Interaction energy analysis for fragmet #1(A:29:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.022
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].
3A31THR0-0.033-0.0112.694-0.7812.1590.069-1.311-1.6990.004
4A32LEU0-0.057-0.0212.5030.1001.1140.553-0.500-1.0660.001
5A33LEU0-0.0150.0094.918-0.549-0.574-0.001-0.0050.0320.000
6A34PHE0-0.045-0.0184.6790.1290.238-0.001-0.006-0.1020.000
7A35VAL00.013-0.0019.774-0.051-0.0510.0000.0000.0000.000
8A36SER00.0430.04313.3010.0600.0600.0000.0000.0000.000
9A37THR0-0.016-0.00815.813-0.001-0.0010.0000.0000.0000.000
10A38LEU00.043-0.00418.9980.0000.0000.0000.0000.0000.000
11A39ASP-1-0.833-0.90820.8080.0590.0590.0000.0000.0000.000
12A40GLY0-0.007-0.00419.7450.0100.0100.0000.0000.0000.000
13A41SER0-0.127-0.05516.8270.0170.0170.0000.0000.0000.000
14A42LEU00.0100.01710.396-0.037-0.0370.0000.0000.0000.000
15A43HIS00.0120.00511.8370.1240.1240.0000.0000.0000.000
16A44ALA00.0460.0516.661-0.114-0.1140.0000.0000.0000.000
17A45VAL0-0.0020.0038.2710.2030.2030.0000.0000.0000.000
18A46SER0-0.069-0.0158.117-0.129-0.1290.0000.0000.0000.000
19A47LYS10.8910.9436.3731.0651.0650.0000.0000.0000.000
20A48ARG10.9100.95210.1220.0200.0200.0000.0000.0000.000
21A49THR00.0250.01112.305-0.015-0.0150.0000.0000.0000.000
22A50GLY00.1180.03312.429-0.037-0.0370.0000.0000.0000.000
23A51SER0-0.022-0.05213.203-0.034-0.0340.0000.0000.0000.000
24A52ILE00.0100.00711.2940.0780.0780.0000.0000.0000.000
25A53LYS10.8250.9317.352-1.511-1.5110.0000.0000.0000.000
26A54TRP00.0740.0095.469-0.208-0.2080.0000.0000.0000.000
27A55THR00.002-0.01810.679-0.050-0.0500.0000.0000.0000.000
28A56LEU0-0.0220.00111.2990.0260.0260.0000.0000.0000.000
29A57LYS10.8330.93714.121-0.122-0.1220.0000.0000.0000.000
30A58GLU-1-0.852-0.93216.6500.0720.0720.0000.0000.0000.000
31A59ASP-1-0.895-0.93819.303-0.008-0.0080.0000.0000.0000.000
32A60PRO0-0.016-0.00220.936-0.014-0.0140.0000.0000.0000.000
33A61VAL00.0040.00620.172-0.007-0.0070.0000.0000.0000.000
34A62LEU00.0130.01922.699-0.011-0.0110.0000.0000.0000.000
35A63GLN00.010-0.00226.4960.0040.0040.0000.0000.0000.000
36A64VAL0-0.036-0.01429.397-0.001-0.0010.0000.0000.0000.000
37A65PRO00.0230.05232.4840.0040.0040.0000.0000.0000.000
38A66THR0-0.043-0.05235.0890.0020.0020.0000.0000.0000.000
39A67HIS0-0.025-0.01036.8010.0000.0000.0000.0000.0000.000
40A68VAL00.0210.02441.081-0.001-0.0010.0000.0000.0000.000
41A69GLU-1-1.001-0.99743.389-0.017-0.0170.0000.0000.0000.000
42A70GLU-1-0.925-0.96639.648-0.013-0.0130.0000.0000.0000.000
43A71PRO0-0.044-0.00839.129-0.002-0.0020.0000.0000.0000.000
44A72ALA00.020-0.00938.5610.0000.0000.0000.0000.0000.000
45A73PHE0-0.035-0.03235.170-0.002-0.0020.0000.0000.0000.000
46A74LEU0-0.062-0.03633.9060.0020.0020.0000.0000.0000.000
47A75PRO00.026-0.00529.328-0.005-0.0050.0000.0000.0000.000
48A76ASP-1-0.736-0.87926.354-0.091-0.0910.0000.0000.0000.000
49A77PRO0-0.051-0.06424.189-0.010-0.0100.0000.0000.0000.000
50A78ASN0-0.065-0.05021.9810.0000.0000.0000.0000.0000.000
51A79ASP-1-0.785-0.83522.437-0.148-0.1480.0000.0000.0000.000
52A80GLY00.0130.01123.7190.0020.0020.0000.0000.0000.000
53A81SER0-0.121-0.11926.6240.0080.0080.0000.0000.0000.000
54A82LEU0-0.017-0.01129.2030.0080.0080.0000.0000.0000.000
55A83TYR00.004-0.00531.0880.0000.0000.0000.0000.0000.000
56A84THR0-0.0290.00535.5620.0020.0020.0000.0000.0000.000
57A85LEU00.0630.02139.020-0.001-0.0010.0000.0000.0000.000
58A86GLY0-0.003-0.00241.7580.0010.0010.0000.0000.0000.000
59A87SER0-0.009-0.01741.5480.0010.0010.0000.0000.0000.000
60A88LYS10.8320.91540.8930.0510.0510.0000.0000.0000.000
61A89ASN00.012-0.02542.6060.0000.0000.0000.0000.0000.000
62A90ASN0-0.045-0.00846.4860.0000.0000.0000.0000.0000.000
63A91GLH00.0300.01844.8030.0010.0010.0000.0000.0000.000
64A92GLY00.0210.03344.5510.0010.0010.0000.0000.0000.000
65A93LEU00.0350.02536.9780.0000.0000.0000.0000.0000.000
66A94THR00.0080.00639.444-0.002-0.0020.0000.0000.0000.000
67A95LYS10.9910.99830.2920.1010.1010.0000.0000.0000.000
68A96LEU0-0.051-0.01535.4050.0010.0010.0000.0000.0000.000
69A97PRO0-0.029-0.03435.109-0.003-0.0030.0000.0000.0000.000
70A98PHE00.0230.02832.627-0.003-0.0030.0000.0000.0000.000
71A99THR00.0240.01627.3310.0080.0080.0000.0000.0000.000
72A100ILE00.0150.01527.5720.0060.0060.0000.0000.0000.000
73A101PRO00.0300.00124.4690.0060.0060.0000.0000.0000.000
74A102GLU-1-0.870-0.93027.355-0.119-0.1190.0000.0000.0000.000
75A103LEU0-0.018-0.00129.9720.0060.0060.0000.0000.0000.000
76A104VAL0-0.0220.01028.8740.0080.0080.0000.0000.0000.000
77A105GLN0-0.111-0.04925.3530.0010.0010.0000.0000.0000.000
78A106ALA0-0.039-0.03730.464-0.003-0.0030.0000.0000.0000.000
79A107SER0-0.034-0.00534.1500.0080.0080.0000.0000.0000.000
80A108PRO0-0.018-0.02735.412-0.002-0.0020.0000.0000.0000.000
81A109CYS0-0.0100.03138.500-0.001-0.0010.0000.0000.0000.000
82A110ARG10.9570.96640.5770.0440.0440.0000.0000.0000.000
83A111SER0-0.005-0.00942.961-0.002-0.0020.0000.0000.0000.000
84A112SER0-0.018-0.02445.1010.0020.0020.0000.0000.0000.000
85A113ASP-1-0.748-0.83141.095-0.046-0.0460.0000.0000.0000.000
86A114GLY00.0290.02342.2230.0030.0030.0000.0000.0000.000
87A115ILE0-0.112-0.06843.151-0.001-0.0010.0000.0000.0000.000
88A116LEU0-0.025-0.02942.446-0.001-0.0010.0000.0000.0000.000
89A117TYR0-0.0030.01736.7600.0030.0030.0000.0000.0000.000
90A118MET0-0.010-0.01036.484-0.002-0.0020.0000.0000.0000.000
91A119GLY00.0570.02332.677-0.001-0.0010.0000.0000.0000.000
92A120LYS10.9310.94328.2000.0590.0590.0000.0000.0000.000
93A121LYS10.8490.90122.1590.1590.1590.0000.0000.0000.000
94A122GLN0-0.077-0.00523.013-0.013-0.0130.0000.0000.0000.000
95A123ASP-1-0.758-0.87219.547-0.175-0.1750.0000.0000.0000.000
96A124ILE0-0.0050.00417.5510.0150.0150.0000.0000.0000.000
97A125TRP0-0.004-0.01511.679-0.041-0.0410.0000.0000.0000.000
98A126TYR0-0.022-0.01812.4970.0370.0370.0000.0000.0000.000
99A127VAL0-0.009-0.00811.164-0.077-0.0770.0000.0000.0000.000
100A128ILE00.003-0.0018.2950.0530.0530.0000.0000.0000.000
101A129ASP-1-0.877-0.9287.4200.5770.5770.0000.0000.0000.000
102A130LEU0-0.051-0.0061.9912.727-1.6628.590-1.535-2.665-0.007
103A153LEU0-0.031-0.0336.3590.2080.2080.0000.0000.0000.000
104A154LEU0-0.066-0.0272.925-0.802-0.3800.076-0.113-0.3850.000
105A155TYR00.0260.0056.4180.2380.2380.0000.0000.0000.000
106A156LEU0-0.013-0.0068.680-0.124-0.1240.0000.0000.0000.000
107A157GLY00.0720.04010.2450.0970.0970.0000.0000.0000.000
108A158ARG10.8250.92613.8710.0500.0500.0000.0000.0000.000
109A159THR0-0.017-0.00816.6030.0110.0110.0000.0000.0000.000
110A160GLU-1-0.870-0.91920.288-0.048-0.0480.0000.0000.0000.000
111A161TYR0-0.026-0.01421.7280.0060.0060.0000.0000.0000.000
112A162THR0-0.031-0.01726.0630.0100.0100.0000.0000.0000.000
113A163ILE0-0.0050.01729.557-0.003-0.0030.0000.0000.0000.000
114A164THR0-0.051-0.03832.5940.0070.0070.0000.0000.0000.000
115A165MET0-0.0170.02836.298-0.003-0.0030.0000.0000.0000.000
116A166TYR00.0580.00239.4660.0030.0030.0000.0000.0000.000
117A167ASP-1-0.757-0.86142.853-0.032-0.0320.0000.0000.0000.000
118A168THR00.010-0.00546.5200.0010.0010.0000.0000.0000.000
119A169LYS10.8120.90648.8750.0320.0320.0000.0000.0000.000
120A170THR00.0130.00948.2030.0010.0010.0000.0000.0000.000
121A171ARG10.8530.90948.5550.0230.0230.0000.0000.0000.000
122A172GLU-1-0.818-0.88044.161-0.017-0.0170.0000.0000.0000.000
123A173LEU0-0.039-0.03938.742-0.003-0.0030.0000.0000.0000.000
124A174ARG10.7640.87141.6640.0380.0380.0000.0000.0000.000
125A175TRP00.0630.01632.716-0.001-0.0010.0000.0000.0000.000
126A176ASN00.022-0.01033.8770.0000.0000.0000.0000.0000.000
127A177ALA00.0390.01530.6600.0010.0010.0000.0000.0000.000
128A178THR00.0210.00026.682-0.001-0.0010.0000.0000.0000.000
129A179TYR0-0.079-0.02121.8480.0100.0100.0000.0000.0000.000
130A180PHE00.0630.02820.331-0.015-0.0150.0000.0000.0000.000
131A181ASP-1-0.859-0.94218.356-0.217-0.2170.0000.0000.0000.000
132A182TYR0-0.009-0.00713.0290.0060.0060.0000.0000.0000.000
133A183ALA0-0.0030.00014.647-0.008-0.0080.0000.0000.0000.000
134A184ALA0-0.023-0.02812.909-0.072-0.0720.0000.0000.0000.000
135A185SER0-0.044-0.02012.7950.0560.0560.0000.0000.0000.000
136A186LEU00.043-0.00515.155-0.009-0.0090.0000.0000.0000.000
137A187PRO0-0.083-0.02216.842-0.036-0.0360.0000.0000.0000.000
138A188GLU-1-0.915-0.95717.412-0.314-0.3140.0000.0000.0000.000
139A189ASP-1-0.896-0.94517.961-0.288-0.2880.0000.0000.0000.000
140A190ASP-1-0.796-0.88314.739-0.526-0.5260.0000.0000.0000.000
141A191DVA0-0.026-0.02117.555-0.005-0.0050.0000.0000.0000.000
142A192ASP-1-0.938-0.97812.874-0.608-0.6080.0000.0000.0000.000
143A193TYR0-0.044-0.02512.104-0.054-0.0540.0000.0000.0000.000
144A194LYS10.8360.89915.6310.2840.2840.0000.0000.0000.000
145A195MET0-0.0330.00112.2400.0470.0470.0000.0000.0000.000
146A196SER00.0550.02117.294-0.016-0.0160.0000.0000.0000.000
147A197HIS00.0030.01613.775-0.025-0.0250.0000.0000.0000.000
148A198PHE0-0.0240.00219.169-0.008-0.0080.0000.0000.0000.000
149A199VAL00.0470.02020.0280.0140.0140.0000.0000.0000.000
150A200SER00.0100.02222.7630.0010.0010.0000.0000.0000.000
151A201ASN00.0120.01625.150-0.001-0.0010.0000.0000.0000.000
152A202GLY0-0.018-0.00827.2130.0060.0060.0000.0000.0000.000
153A203ASP-1-0.860-0.96426.0350.0320.0320.0000.0000.0000.000
154A204GLY00.0080.03222.096-0.012-0.0120.0000.0000.0000.000
155A205LEU0-0.0150.01921.3140.0140.0140.0000.0000.0000.000
156A206VAL0-0.024-0.01917.216-0.018-0.0180.0000.0000.0000.000
157A207VAL0-0.017-0.02620.5230.0200.0200.0000.0000.0000.000
158A208THR0-0.002-0.00815.573-0.036-0.0360.0000.0000.0000.000
159A209VAL0-0.035-0.00518.7470.0230.0230.0000.0000.0000.000
160A210ASP-1-0.820-0.93519.333-0.143-0.1430.0000.0000.0000.000
161A211SER0-0.009-0.00619.7270.0170.0170.0000.0000.0000.000
162A212GLU-1-0.912-0.92821.004-0.176-0.1760.0000.0000.0000.000
163A213SER0-0.065-0.06423.2780.0130.0130.0000.0000.0000.000
164A214GLY00.0450.03024.5000.0020.0020.0000.0000.0000.000
165A215ASP-1-0.894-0.92923.622-0.031-0.0310.0000.0000.0000.000
166A216VAL0-0.021-0.03822.347-0.009-0.0090.0000.0000.0000.000
167A217LEU0-0.061-0.02716.1170.0100.0100.0000.0000.0000.000
168A218TRP0-0.036-0.01513.4210.0430.0430.0000.0000.0000.000
169A219ILE00.0040.01819.235-0.022-0.0220.0000.0000.0000.000
170A220GLN0-0.041-0.02516.3350.0190.0190.0000.0000.0000.000
171A221ASN00.0270.01419.703-0.034-0.0340.0000.0000.0000.000
172A222TYR0-0.050-0.03814.5270.0050.0050.0000.0000.0000.000
173A223ALA0-0.006-0.00619.784-0.012-0.0120.0000.0000.0000.000
174A224SER00.0470.02821.058-0.010-0.0100.0000.0000.0000.000
175A225PRO0-0.023-0.01621.1060.0010.0010.0000.0000.0000.000
176A226VAL00.0160.00017.3670.0000.0000.0000.0000.0000.000
177A227VAL0-0.037-0.01518.741-0.006-0.0060.0000.0000.0000.000
178A228ALA00.004-0.00417.013-0.018-0.0180.0000.0000.0000.000
179A229PHE00.0340.02113.6880.0260.0260.0000.0000.0000.000
180A230TYR00.0040.00010.289-0.020-0.0200.0000.0000.0000.000
181A231VAL00.0450.0148.243-0.023-0.0230.0000.0000.0000.000
182A232TRP00.0220.0192.359-2.501-1.2513.574-1.236-3.588-0.013
183A233GLN00.0150.0155.148-0.651-0.651-0.001-0.0040.0060.000
184A234ARG10.8520.9147.3210.9840.9840.0000.0000.0000.000
185A235GLU-1-0.927-0.9565.460-1.115-1.1150.0000.0000.0000.000
186A236GLY00.0620.0125.9960.3810.3810.0000.0000.0000.000
187A237LEU0-0.061-0.0287.173-0.111-0.1110.0000.0000.0000.000
188A238ARG10.8290.9249.1960.7150.7150.0000.0000.0000.000
189A239LYS10.9670.99011.7890.2390.2390.0000.0000.0000.000
190A240VAL0-0.006-0.00612.7540.0010.0010.0000.0000.0000.000
191A241MET0-0.053-0.01115.4810.0430.0430.0000.0000.0000.000
192A242HIS00.0170.00718.657-0.016-0.0160.0000.0000.0000.000
193A243ILE0-0.020-0.02320.4990.0080.0080.0000.0000.0000.000
194A244ASN00.0080.01923.7850.0040.0040.0000.0000.0000.000
195A245VAL0-0.049-0.02125.9970.0020.0020.0000.0000.0000.000
196A246ALA00.1050.05027.8210.0030.0030.0000.0000.0000.000
197A247VAL00.0300.02228.0650.0020.0020.0000.0000.0000.000
198A248GLU-1-0.883-0.93029.783-0.007-0.0070.0000.0000.0000.000
199A249THR00.021-0.01631.4600.0030.0030.0000.0000.0000.000
200A250LEU00.0180.01624.277-0.001-0.0010.0000.0000.0000.000
201A251ARG10.9250.99628.559-0.011-0.0110.0000.0000.0000.000
202A252TYR0-0.014-0.02330.2140.0040.0040.0000.0000.0000.000
203A253LEU00.0170.00229.1120.0010.0010.0000.0000.0000.000
204A254THR0-0.036-0.05226.2750.0010.0010.0000.0000.0000.000
205A255PHE0-0.043-0.01728.7320.0050.0050.0000.0000.0000.000
206A256MET00.0150.01132.1310.0030.0030.0000.0000.0000.000
207A257SER0-0.065-0.03128.1420.0040.0040.0000.0000.0000.000
208A258GLY00.0700.02330.4650.0020.0020.0000.0000.0000.000
209A259GLU-1-0.823-0.86431.1640.0240.0240.0000.0000.0000.000
210A260VAL0-0.011-0.01933.1340.0010.0010.0000.0000.0000.000
211A261GLY00.020-0.00531.3320.0000.0000.0000.0000.0000.000
212A262ARG10.7650.85731.990-0.023-0.0230.0000.0000.0000.000
213A263ILE0-0.031-0.02634.5660.0010.0010.0000.0000.0000.000
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