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: K35R3

Calculation Name: 1W9Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1W9Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YWN5

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 257
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3051072.851046
FMO2-HF: Nuclear repulsion 2953177.6151
FMO2-HF: Total energy -97895.235945
FMO2-MP2: Total energy -98177.866295


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:27:ALA)


Summations of interaction energy for fragment #1(A:27:ALA)
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.
-25.9-23.71412.771-6.703-8.2540.02
Interaction energy analysis for fragmet #1(A:27:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.021
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].
3A29PRO0-0.0010.0111.964-1.4420.3042.016-1.588-2.174-0.006
4A30SER00.0160.0085.121-0.823-0.847-0.001-0.0050.0310.000
5A31ASN00.014-0.0138.014-0.387-0.3870.0000.0000.0000.000
6A32VAL0-0.0210.0018.1060.3620.3620.0000.0000.0000.000
7A33LYS10.9440.9608.4280.3440.3440.0000.0000.0000.000
8A34LEU00.0450.0455.1810.0880.0880.0000.0000.0000.000
9A35SER0-0.045-0.0497.9470.1810.1810.0000.0000.0000.000
10A36LYS10.8360.8778.722-0.272-0.2720.0000.0000.0000.000
11A37GLY00.0350.0218.961-0.065-0.0650.0000.0000.0000.000
12A38GLU-1-0.826-0.8884.2960.0370.110-0.001-0.008-0.0640.000
13A39VAL00.000-0.0094.983-0.708-0.620-0.001-0.002-0.0850.000
14A40GLU-1-0.846-0.9127.5480.1230.1230.0000.0000.0000.000
15A41LYS10.9070.9722.295-22.224-21.0605.202-2.648-3.7180.033
16A42ILE0-0.068-0.0321.907-1.382-2.2435.556-2.452-2.244-0.007
17A43ALA0-0.029-0.0065.651-0.005-0.0050.0000.0000.0000.000
18A44VAL00.0490.0399.4060.1460.1460.0000.0000.0000.000
19A45THR0-0.066-0.07411.678-0.042-0.0420.0000.0000.0000.000
20A46LYS10.9750.95914.1400.1940.1940.0000.0000.0000.000
21A47LYS10.7990.88916.044-0.124-0.1240.0000.0000.0000.000
22A48GLU-1-0.728-0.83312.3530.0500.0500.0000.0000.0000.000
23A49MET0-0.034-0.01416.279-0.008-0.0080.0000.0000.0000.000
24A50PHE0-0.075-0.03419.1320.0020.0020.0000.0000.0000.000
25A51ASP-1-0.781-0.89218.3930.1380.1380.0000.0000.0000.000
26A52GLU-1-0.952-0.95418.6380.0240.0240.0000.0000.0000.000
27A53LEU0-0.042-0.03521.755-0.001-0.0010.0000.0000.0000.000
28A54ALA0-0.0440.00423.772-0.001-0.0010.0000.0000.0000.000
29A55GLN00.013-0.00525.5590.0030.0030.0000.0000.0000.000
30A56CYS0-0.047-0.03728.364-0.001-0.0010.0000.0000.0000.000
31A57ASN0-0.015-0.00226.1620.0010.0010.0000.0000.0000.000
32A58LEU00.0370.03027.5220.0000.0000.0000.0000.0000.000
33A59PRO0-0.008-0.00927.175-0.001-0.0010.0000.0000.0000.000
34A60THR0-0.029-0.01127.402-0.009-0.0090.0000.0000.0000.000
35A61ILE0-0.0040.00625.0560.0050.0050.0000.0000.0000.000
36A62GLU-1-0.745-0.87529.1180.0140.0140.0000.0000.0000.000
37A63LEU0-0.0010.00032.487-0.007-0.0070.0000.0000.0000.000
38A64ILE0-0.001-0.01335.154-0.006-0.0060.0000.0000.0000.000
39A65THR0-0.0140.00029.767-0.004-0.0040.0000.0000.0000.000
40A66ARG10.8790.92530.109-0.003-0.0030.0000.0000.0000.000
41A67GLU-1-0.890-0.94531.913-0.022-0.0220.0000.0000.0000.000
42A68HIS0-0.043-0.02233.215-0.007-0.0070.0000.0000.0000.000
43A69THR00.0310.01928.568-0.006-0.0060.0000.0000.0000.000
44A70PHE0-0.009-0.01329.328-0.006-0.0060.0000.0000.0000.000
45A71ASN0-0.034-0.01929.5280.0000.0000.0000.0000.0000.000
46A72GLY00.0180.00526.610-0.001-0.0010.0000.0000.0000.000
47A73ASP-1-0.877-0.92324.587-0.115-0.1150.0000.0000.0000.000
48A74VAL00.0950.02722.052-0.004-0.0040.0000.0000.0000.000
49A75ILE00.0010.00819.611-0.001-0.0010.0000.0000.0000.000
50A76ARG10.8570.93123.6750.1040.1040.0000.0000.0000.000
51A77PHE0-0.008-0.01426.9230.0040.0040.0000.0000.0000.000
52A78ALA0-0.0050.00425.3390.0050.0050.0000.0000.0000.000
53A79ALA0-0.024-0.01726.6950.0030.0030.0000.0000.0000.000
54A80TRP0-0.013-0.02428.3490.0070.0070.0000.0000.0000.000
55A81LEU00.0040.02230.9030.0040.0040.0000.0000.0000.000
56A82PHE0-0.008-0.01231.7590.0050.0050.0000.0000.0000.000
57A83LEU00.000-0.00232.0330.0010.0010.0000.0000.0000.000
58A84MET0-0.0470.00234.9020.0010.0010.0000.0000.0000.000
59A85ASN0-0.059-0.02936.1850.0070.0070.0000.0000.0000.000
60A86GLY00.0280.01237.622-0.002-0.0020.0000.0000.0000.000
61A87GLN00.0420.01636.6730.0000.0000.0000.0000.0000.000
62A88LYS10.9230.96937.7300.0520.0520.0000.0000.0000.000
63A89LEU0-0.013-0.01141.4510.0040.0040.0000.0000.0000.000
64A90MET0-0.0100.02139.751-0.001-0.0010.0000.0000.0000.000
65A91ILE0-0.055-0.02943.5570.0030.0030.0000.0000.0000.000
66A92ALA0-0.050-0.03646.0470.0000.0000.0000.0000.0000.000
67A93ASN0-0.044-0.00744.0680.0010.0010.0000.0000.0000.000
68A94ASN00.0410.00440.162-0.001-0.0010.0000.0000.0000.000
69A95VAL0-0.028-0.01643.2600.0030.0030.0000.0000.0000.000
70A96ALA00.0080.00139.217-0.004-0.0040.0000.0000.0000.000
71A97VAL0-0.0080.01040.4400.0020.0020.0000.0000.0000.000
72A98ARG10.8510.95233.4910.0420.0420.0000.0000.0000.000
73A99MET00.0180.01437.5220.0050.0050.0000.0000.0000.000
74A100GLY0-0.027-0.00637.6180.0000.0000.0000.0000.0000.000
75A101MET00.0100.01636.2820.0030.0030.0000.0000.0000.000
76A102GLN0-0.016-0.00240.3700.0000.0000.0000.0000.0000.000
77A103TYR0-0.009-0.02542.7490.0000.0000.0000.0000.0000.000
78A104ALA00.0260.02042.270-0.002-0.0020.0000.0000.0000.000
79A105THR00.0290.01442.6350.0020.0020.0000.0000.0000.000
80A106ASN00.009-0.01044.717-0.003-0.0030.0000.0000.0000.000
81A107LEU00.0450.01746.843-0.001-0.0010.0000.0000.0000.000
82A108ALA0-0.079-0.01948.9580.0000.0000.0000.0000.0000.000
83A109GLY00.0220.01945.8840.0010.0010.0000.0000.0000.000
84A110ASN0-0.048-0.01945.9890.0030.0030.0000.0000.0000.000
85A111ASN00.0000.00742.896-0.004-0.0040.0000.0000.0000.000
86A112VAL0-0.017-0.00946.6580.0020.0020.0000.0000.0000.000
87A113LYS10.9570.96947.0790.0130.0130.0000.0000.0000.000
88A114ILE0-0.0270.01242.846-0.001-0.0010.0000.0000.0000.000
89A115THR0-0.052-0.01047.2710.0030.0030.0000.0000.0000.000
90A116TYR0-0.036-0.04841.505-0.002-0.0020.0000.0000.0000.000
91A117VAL0-0.0050.00147.2720.0020.0020.0000.0000.0000.000
92A118THR0-0.015-0.01547.455-0.003-0.0030.0000.0000.0000.000
93A119SER00.0130.01148.1020.0010.0010.0000.0000.0000.000
94A120ASN00.010-0.00147.9750.0000.0000.0000.0000.0000.000
95A121ASN0-0.031-0.02447.4690.0010.0010.0000.0000.0000.000
96A122VAL00.0120.02442.5140.0000.0000.0000.0000.0000.000
97A123VAL0-0.006-0.00642.7670.0010.0010.0000.0000.0000.000
98A124LYS10.8050.90442.7780.0530.0530.0000.0000.0000.000
99A125LEU00.0100.00143.155-0.003-0.0030.0000.0000.0000.000
100A126GLY00.0360.01744.3350.0030.0030.0000.0000.0000.000
101A127HIS0-0.032-0.01545.673-0.002-0.0020.0000.0000.0000.000
102A128ILE00.0240.01146.0510.0020.0020.0000.0000.0000.000
103A129ALA00.0320.01849.501-0.001-0.0010.0000.0000.0000.000
104A130ALA00.0200.01350.7970.0000.0000.0000.0000.0000.000
105A131GLY0-0.011-0.01551.0330.0000.0000.0000.0000.0000.000
106A132VAL0-0.004-0.02353.454-0.001-0.0010.0000.0000.0000.000
107A133LEU00.0100.01850.0010.0000.0000.0000.0000.0000.000
108A134ALA0-0.024-0.00752.3950.0010.0010.0000.0000.0000.000
109A135ASN0-0.029-0.02152.4780.0010.0010.0000.0000.0000.000
110A136PRO00.0430.02452.710-0.001-0.0010.0000.0000.0000.000
111A137TYR00.0400.01548.473-0.001-0.0010.0000.0000.0000.000
112A138SER0-0.021-0.03551.1200.0010.0010.0000.0000.0000.000
113A139ASN0-0.029-0.03350.271-0.002-0.0020.0000.0000.0000.000
114A140LYS10.8790.98650.2900.0450.0450.0000.0000.0000.000
115A141GLY00.0860.04246.737-0.003-0.0030.0000.0000.0000.000
116A142SER0-0.017-0.03944.183-0.001-0.0010.0000.0000.0000.000
117A143GLY0-0.007-0.00945.3220.0010.0010.0000.0000.0000.000
118A144LEU0-0.0340.00041.405-0.001-0.0010.0000.0000.0000.000
119A145PHE00.006-0.01645.1660.0010.0010.0000.0000.0000.000
120A146ILE0-0.0040.00243.180-0.001-0.0010.0000.0000.0000.000
121A147THR00.0200.00147.4090.0010.0010.0000.0000.0000.000
122A148TYR00.012-0.00550.198-0.002-0.0020.0000.0000.0000.000
123A149GLU-1-0.800-0.87351.674-0.029-0.0290.0000.0000.0000.000
124A150HIS0-0.030-0.00754.2770.0030.0030.0000.0000.0000.000
125A151ASN00.0260.00954.688-0.002-0.0020.0000.0000.0000.000
126A152LEU00.011-0.01251.8520.0010.0010.0000.0000.0000.000
127A153ILE0-0.036-0.00454.9170.0010.0010.0000.0000.0000.000
128A154SER0-0.007-0.00357.7360.0010.0010.0000.0000.0000.000
129A155ASN0-0.029-0.01259.3630.0010.0010.0000.0000.0000.000
130A156GLN0-0.040-0.01960.2200.0020.0020.0000.0000.0000.000
131A157ILE0-0.003-0.01258.683-0.001-0.0010.0000.0000.0000.000
132A158GLU-1-0.843-0.89056.406-0.040-0.0400.0000.0000.0000.000
133A159THR0-0.002-0.02156.551-0.001-0.0010.0000.0000.0000.000
134A160GLY0-0.012-0.01154.474-0.001-0.0010.0000.0000.0000.000
135A161LYS10.9010.96752.5390.0390.0390.0000.0000.0000.000
136A162VAL0-0.004-0.00146.8750.0020.0020.0000.0000.0000.000
137A163CYS0-0.031-0.00150.241-0.001-0.0010.0000.0000.0000.000
138A164VAL00.0210.00945.5550.0000.0000.0000.0000.0000.000
139A165LEU0-0.017-0.00948.2490.0010.0010.0000.0000.0000.000
140A166PHE00.0230.01344.381-0.001-0.0010.0000.0000.0000.000
141A167ILE0-0.021-0.00847.7740.0010.0010.0000.0000.0000.000
142A168THR00.0310.00847.162-0.002-0.0020.0000.0000.0000.000
143A169SER0-0.043-0.01849.0300.0030.0030.0000.0000.0000.000
144A170LEU0-0.016-0.01849.058-0.003-0.0030.0000.0000.0000.000
145A171SER0-0.028-0.01450.438-0.003-0.0030.0000.0000.0000.000
146A172THR00.0540.04046.9910.0010.0010.0000.0000.0000.000
147A173THR0-0.018-0.03046.5790.0040.0040.0000.0000.0000.000
148A174ALA0-0.062-0.02649.0450.0020.0020.0000.0000.0000.000
149A175SER0-0.067-0.02550.7140.0030.0030.0000.0000.0000.000
150A176SER0-0.031-0.03353.3380.0020.0020.0000.0000.0000.000
151A177THR0-0.012-0.02855.9260.0020.0020.0000.0000.0000.000
152A178ASN0-0.027-0.00355.608-0.003-0.0030.0000.0000.0000.000
153A179SER00.0470.01755.1880.0010.0010.0000.0000.0000.000
154A180PHE0-0.0140.00851.997-0.002-0.0020.0000.0000.0000.000
155A181ALA00.0530.02352.5780.0010.0010.0000.0000.0000.000
156A182TYR00.0490.00951.051-0.001-0.0010.0000.0000.0000.000
157A183SER00.0220.02448.565-0.001-0.0010.0000.0000.0000.000
158A184ALA00.016-0.00150.0450.0000.0000.0000.0000.0000.000
159A185CYS0-0.050-0.00348.572-0.002-0.0020.0000.0000.0000.000
160A186SER00.035-0.01850.9000.0000.0000.0000.0000.0000.000
161A187VAL0-0.027-0.00746.613-0.001-0.0010.0000.0000.0000.000
162A188PRO00.0090.01349.9690.0030.0030.0000.0000.0000.000
163A189ILE00.0370.01747.932-0.003-0.0030.0000.0000.0000.000
164A190GLU-1-0.904-0.97547.846-0.045-0.0450.0000.0000.0000.000
165A191ASP-1-0.888-0.95146.587-0.056-0.0560.0000.0000.0000.000
166A192TRP0-0.062-0.02142.887-0.004-0.0040.0000.0000.0000.000
167A193ASP-1-0.756-0.89738.812-0.083-0.0830.0000.0000.0000.000
168A194PHE0-0.024-0.00738.349-0.001-0.0010.0000.0000.0000.000
169A195ASN0-0.011-0.00533.798-0.006-0.0060.0000.0000.0000.000
170A196MET0-0.0380.00936.569-0.007-0.0070.0000.0000.0000.000
171A197ILE0-0.008-0.00139.2830.0030.0030.0000.0000.0000.000
172A198LYS10.8630.93035.1380.1170.1170.0000.0000.0000.000
173A199LEU00.0010.00538.8590.0040.0040.0000.0000.0000.000
174A200THR0-0.017-0.01938.337-0.008-0.0080.0000.0000.0000.000
175A201ALA00.0320.00138.7400.0060.0060.0000.0000.0000.000
176A202GLU-1-0.867-0.91835.687-0.129-0.1290.0000.0000.0000.000
177A203THR0-0.012-0.01037.3230.0010.0010.0000.0000.0000.000
178A204SER00.0130.00939.6340.0070.0070.0000.0000.0000.000
179A205CYS00.0330.02743.2070.0010.0010.0000.0000.0000.000
180A206ALA00.0520.02945.7690.0010.0010.0000.0000.0000.000
181A207SER00.0180.00846.5240.0010.0010.0000.0000.0000.000
182A208LEU00.0480.01442.2850.0020.0020.0000.0000.0000.000
183A209THR0-0.0140.00446.2660.0010.0010.0000.0000.0000.000
184A210ALA00.000-0.00149.0850.0020.0020.0000.0000.0000.000
185A211MET00.0310.01847.9420.0030.0030.0000.0000.0000.000
186A212THR0-0.036-0.03847.2620.0000.0000.0000.0000.0000.000
187A213ASN0-0.046-0.03149.3220.0000.0000.0000.0000.0000.000
188A214LEU0-0.008-0.00252.5790.0020.0020.0000.0000.0000.000
189A215VAL0-0.0040.00148.5050.0020.0020.0000.0000.0000.000
190A216ASN0-0.033-0.03050.4150.0010.0010.0000.0000.0000.000
191A217SER0-0.0250.00853.4110.0020.0020.0000.0000.0000.000
192A218LEU0-0.0210.00552.7510.0030.0030.0000.0000.0000.000
193A219VAL00.0590.02455.292-0.002-0.0020.0000.0000.0000.000
194A220PRO00.019-0.00852.090-0.001-0.0010.0000.0000.0000.000
195A221GLY00.0030.00850.742-0.002-0.0020.0000.0000.0000.000
196A222GLU-1-0.835-0.89450.437-0.048-0.0480.0000.0000.0000.000
197A223ARG10.8270.92149.2230.0620.0620.0000.0000.0000.000
198A224THR00.0210.00145.447-0.002-0.0020.0000.0000.0000.000
199A225ARG10.9240.96237.1970.1040.1040.0000.0000.0000.000
200A226PRO00.0100.00644.0720.0000.0000.0000.0000.0000.000
201A227VAL0-0.016-0.01841.447-0.005-0.0050.0000.0000.0000.000
202A228GLY0-0.0060.00243.2400.0050.0050.0000.0000.0000.000
203A229LEU0-0.036-0.02843.101-0.004-0.0040.0000.0000.0000.000
204A230TYR0-0.069-0.07039.6490.0010.0010.0000.0000.0000.000
205A231VAL0-0.001-0.02142.2310.0000.0000.0000.0000.0000.000
206A232ASP-1-0.909-0.92140.814-0.092-0.0920.0000.0000.0000.000
207A233ILE00.0300.01142.414-0.001-0.0010.0000.0000.0000.000
208A234PRO00.0210.00544.9280.0020.0020.0000.0000.0000.000
209A235GLY0-0.0010.00247.8180.0020.0020.0000.0000.0000.000
210A236VAL0-0.021-0.00848.3390.0030.0030.0000.0000.0000.000
211A237THR0-0.0060.01149.847-0.002-0.0020.0000.0000.0000.000
212A238VAL0-0.036-0.02847.5300.0020.0020.0000.0000.0000.000
213A239THR0-0.027-0.00150.6840.0000.0000.0000.0000.0000.000
214A240THR0-0.016-0.02050.938-0.001-0.0010.0000.0000.0000.000
215A241SER0-0.035-0.00653.3560.0010.0010.0000.0000.0000.000
216A242ALA00.0420.01955.850-0.002-0.0020.0000.0000.0000.000
217A243SER00.0030.00056.5070.0000.0000.0000.0000.0000.000
218A244SER0-0.049-0.02457.2470.0020.0020.0000.0000.0000.000
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