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: 6Y1QZ

Calculation Name: 1SGV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SGV

Chain ID: A

ChEMBL ID:

UniProt ID: P9WHP7

Base Structure: X-ray

Registration Date: 2023-09-24

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 262
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3017601.596359
FMO2-HF: Nuclear repulsion 2919375.288732
FMO2-HF: Total energy -98226.307627
FMO2-MP2: Total energy -98512.52961


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:ALA)


Summations of interaction energy for fragment #1(A:3: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.
-0.8411.4590.005-1.033-1.2710.001
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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].
3A5GLY00.0100.0253.086-1.8950.004-0.003-0.926-0.9700.001
4A6PRO0-0.049-0.0325.0550.7750.799-0.001-0.004-0.0180.000
5A7GLY00.0500.0147.846-0.116-0.1160.0000.0000.0000.000
6A8ILE0-0.010-0.00510.3740.0870.0870.0000.0000.0000.000
7A9VAL00.0260.00811.3870.0200.0200.0000.0000.0000.000
8A10VAL0-0.0030.01213.394-0.022-0.0220.0000.0000.0000.000
9A11ILE0-0.024-0.01213.6980.0250.0250.0000.0000.0000.000
10A12ASP-1-0.763-0.84417.7550.1340.1340.0000.0000.0000.000
11A13LYS10.7310.87020.708-0.139-0.1390.0000.0000.0000.000
12A14PRO00.0300.00920.921-0.018-0.0180.0000.0000.0000.000
13A15ALA00.0910.04323.9870.0010.0010.0000.0000.0000.000
14A16GLY00.0290.02726.6240.0050.0050.0000.0000.0000.000
15A17MET0-0.070-0.03020.0490.0110.0110.0000.0000.0000.000
16A18THR00.048-0.00323.1090.0010.0010.0000.0000.0000.000
17A19SER00.0610.00020.9180.0210.0210.0000.0000.0000.000
18A20HIS0-0.075-0.03619.2150.0290.0290.0000.0000.0000.000
19A21ASP-1-0.787-0.86818.1820.2030.2030.0000.0000.0000.000
20A22VAL00.0520.03416.0800.0320.0320.0000.0000.0000.000
21A23VAL00.0130.01913.9240.0680.0680.0000.0000.0000.000
22A24GLY0-0.012-0.00913.4150.0620.0620.0000.0000.0000.000
23A25ARG10.9150.95413.677-0.243-0.2430.0000.0000.0000.000
24A26CYS00.0230.01210.8930.0600.0600.0000.0000.0000.000
25A27ARG10.8330.9149.069-0.077-0.0770.0000.0000.0000.000
26A28ARG10.9160.9608.469-0.224-0.2240.0000.0000.0000.000
27A29ILE00.0090.0188.0910.0060.0060.0000.0000.0000.000
28A30PHE00.013-0.0045.091-0.043-0.0430.0000.0000.0000.000
29A31ALA0-0.023-0.0013.6540.6931.0700.009-0.103-0.2830.000
30A32THR00.009-0.0115.143-0.604-0.6040.0000.0000.0000.000
31A33ARG10.9880.9836.8200.0190.0190.0000.0000.0000.000
32A34ARG10.7910.9158.677-0.127-0.1270.0000.0000.0000.000
33A35VAL00.0350.0238.8870.1040.1040.0000.0000.0000.000
34A36GLY0-0.008-0.00311.282-0.094-0.0940.0000.0000.0000.000
35A37HIS00.0350.01014.5570.0470.0470.0000.0000.0000.000
36A38ALA00.0320.01817.351-0.024-0.0240.0000.0000.0000.000
37A39GLY00.0520.02919.786-0.025-0.0250.0000.0000.0000.000
38A40THR0-0.030-0.00723.0040.0130.0130.0000.0000.0000.000
39A41LEU0-0.0250.00523.769-0.010-0.0100.0000.0000.0000.000
40A42ASP-1-0.769-0.86925.5370.1040.1040.0000.0000.0000.000
41A43PRO00.0120.00027.0520.0070.0070.0000.0000.0000.000
42A44MET00.0190.02028.0860.0080.0080.0000.0000.0000.000
43A45ALA0-0.0030.01528.591-0.002-0.0020.0000.0000.0000.000
44A46THR0-0.049-0.02126.0220.0080.0080.0000.0000.0000.000
45A47GLY00.0330.01924.697-0.010-0.0100.0000.0000.0000.000
46A48VAL00.0020.00421.6230.0210.0210.0000.0000.0000.000
47A49LEU0-0.023-0.00318.903-0.015-0.0150.0000.0000.0000.000
48A50VAL00.0190.01816.7020.0320.0320.0000.0000.0000.000
49A51ILE0-0.006-0.01312.072-0.022-0.0220.0000.0000.0000.000
50A52GLY00.0160.00812.178-0.004-0.0040.0000.0000.0000.000
51A53ILE00.0180.0055.801-0.075-0.0750.0000.0000.0000.000
52A54GLU-1-0.732-0.8805.437-0.101-0.1010.0000.0000.0000.000
53A55ARG10.9310.9678.3140.0800.0800.0000.0000.0000.000
54A56ALA00.0520.05010.705-0.036-0.0360.0000.0000.0000.000
55A57THR0-0.032-0.04211.974-0.040-0.0400.0000.0000.0000.000
56A58LYS10.8080.89614.157-0.040-0.0400.0000.0000.0000.000
57A59ILE00.0410.02215.648-0.019-0.0190.0000.0000.0000.000
58A60LEU0-0.0170.00815.008-0.004-0.0040.0000.0000.0000.000
59A61GLY00.0110.00318.697-0.005-0.0050.0000.0000.0000.000
60A62LEU0-0.030-0.02021.435-0.008-0.0080.0000.0000.0000.000
61A63LEU0-0.0090.00018.125-0.002-0.0020.0000.0000.0000.000
62A64THR0-0.021-0.01822.449-0.007-0.0070.0000.0000.0000.000
63A65ALA0-0.018-0.01024.442-0.004-0.0040.0000.0000.0000.000
64A66ALA0-0.0110.01825.664-0.007-0.0070.0000.0000.0000.000
65A67PRO00.0380.02527.5540.0030.0030.0000.0000.0000.000
66A68LYS10.7710.86126.489-0.087-0.0870.0000.0000.0000.000
67A69SER00.0250.00529.447-0.005-0.0050.0000.0000.0000.000
68A70TYR0-0.030-0.03629.2050.0130.0130.0000.0000.0000.000
69A71ALA00.0790.06532.062-0.006-0.0060.0000.0000.0000.000
70A72ALA0-0.038-0.03733.3910.0060.0060.0000.0000.0000.000
71A73THR0-0.022-0.01336.000-0.002-0.0020.0000.0000.0000.000
72A74ILE00.0180.00838.8560.0020.0020.0000.0000.0000.000
73A75ARG10.8370.92241.694-0.050-0.0500.0000.0000.0000.000
74A76LEU00.0360.01244.6870.0000.0000.0000.0000.0000.000
75A77GLY00.0440.00348.036-0.001-0.0010.0000.0000.0000.000
76A78GLN0-0.003-0.01147.1000.0010.0010.0000.0000.0000.000
77A79THR00.0330.05045.9660.0020.0020.0000.0000.0000.000
78A80THR00.017-0.02341.692-0.002-0.0020.0000.0000.0000.000
79A81SER0-0.009-0.01541.8870.0000.0000.0000.0000.0000.000
80A82THR0-0.036-0.04038.106-0.001-0.0010.0000.0000.0000.000
81A83GLU-1-0.840-0.90438.8360.0550.0550.0000.0000.0000.000
82A84ASP-1-0.788-0.86936.0180.0730.0730.0000.0000.0000.000
83A85ALA00.0550.02237.774-0.003-0.0030.0000.0000.0000.000
84A86GLU-1-0.976-0.96333.6520.0810.0810.0000.0000.0000.000
85A87GLY0-0.041-0.00737.742-0.001-0.0010.0000.0000.0000.000
86A88GLN0-0.009-0.01141.017-0.002-0.0020.0000.0000.0000.000
87A89VAL00.013-0.00444.6130.0000.0000.0000.0000.0000.000
88A90LEU0-0.040-0.00946.495-0.001-0.0010.0000.0000.0000.000
89A91GLN0-0.049-0.02549.415-0.003-0.0030.0000.0000.0000.000
90A92SER00.024-0.00350.2690.0020.0020.0000.0000.0000.000
91A93VAL0-0.0240.00252.440-0.002-0.0020.0000.0000.0000.000
92A94PRO0-0.039-0.02853.5880.0010.0010.0000.0000.0000.000
93A95ALA00.0870.04051.7860.0000.0000.0000.0000.0000.000
94A96LYS10.8390.92253.848-0.027-0.0270.0000.0000.0000.000
95A97HIS00.0380.01955.480-0.001-0.0010.0000.0000.0000.000
96A98LEU0-0.0110.01452.068-0.001-0.0010.0000.0000.0000.000
97A99THR00.0140.00154.8370.0010.0010.0000.0000.0000.000
98A100ILE00.029-0.00549.8270.0010.0010.0000.0000.0000.000
99A101GLU-1-0.903-0.94651.4110.0260.0260.0000.0000.0000.000
100A102ALA0-0.023-0.00753.1030.0000.0000.0000.0000.0000.000
101A103ILE0-0.005-0.00747.7870.0010.0010.0000.0000.0000.000
102A104ASP-1-0.870-0.94147.3350.0380.0380.0000.0000.0000.000
103A105ALA00.0140.01148.7120.0010.0010.0000.0000.0000.000
104A106ALA0-0.032-0.01749.9200.0000.0000.0000.0000.0000.000
105A107MET0-0.042-0.01243.0190.0010.0010.0000.0000.0000.000
106A108GLU-1-0.811-0.88645.7220.0370.0370.0000.0000.0000.000
107A109ARG10.8280.91547.506-0.030-0.0300.0000.0000.0000.000
108A110LEU0-0.016-0.00844.747-0.001-0.0010.0000.0000.0000.000
109A111ARG10.8150.91142.276-0.038-0.0380.0000.0000.0000.000
110A112GLY0-0.019-0.00742.686-0.003-0.0030.0000.0000.0000.000
111A113GLU-1-0.904-0.95241.4910.0390.0390.0000.0000.0000.000
112A114ILE00.0110.01240.778-0.001-0.0010.0000.0000.0000.000
113A143DLE00.0020.00134.4640.0010.0010.0000.0000.0000.000
114A144GLU-1-0.944-0.98337.3950.0340.0340.0000.0000.0000.000
115A145ALA0-0.013-0.00538.1640.0030.0030.0000.0000.0000.000
116A146ARG10.8580.91731.579-0.069-0.0690.0000.0000.0000.000
117A147PRO00.0500.02537.4580.0010.0010.0000.0000.0000.000
118A148ILE0-0.086-0.03434.9020.0050.0050.0000.0000.0000.000
119A149ARG10.7990.87836.618-0.044-0.0440.0000.0000.0000.000
120A150ILE00.0060.00136.8490.0050.0050.0000.0000.0000.000
121A151ASP-1-0.816-0.90537.4020.0460.0460.0000.0000.0000.000
122A152ARG10.6910.79936.708-0.058-0.0580.0000.0000.0000.000
123A153PHE00.0430.00139.0860.0040.0040.0000.0000.0000.000
124A154GLU-1-0.815-0.88140.7780.0430.0430.0000.0000.0000.000
125A155LEU00.0280.00341.4850.0030.0030.0000.0000.0000.000
126A156LEU0-0.033-0.00137.416-0.001-0.0010.0000.0000.0000.000
127A157ALA0-0.028-0.01942.031-0.002-0.0020.0000.0000.0000.000
128A158ALA00.0360.01644.2650.0010.0010.0000.0000.0000.000
129A159ARG10.7380.82541.158-0.052-0.0520.0000.0000.0000.000
130A160ARG10.9150.95747.285-0.030-0.0300.0000.0000.0000.000
131A161ARG10.8290.91045.410-0.041-0.0410.0000.0000.0000.000
132A162ASP-1-0.790-0.88549.6520.0300.0300.0000.0000.0000.000
133A163GLN0-0.016-0.01153.300-0.001-0.0010.0000.0000.0000.000
134A164LEU00.0060.01948.6920.0000.0000.0000.0000.0000.000
135A165ILE0-0.018-0.01247.970-0.001-0.0010.0000.0000.0000.000
136A166ASP-1-0.785-0.85343.3520.0500.0500.0000.0000.0000.000
137A167ILE0-0.006-0.01343.234-0.002-0.0020.0000.0000.0000.000
138A168ASP-1-0.773-0.83639.4540.0580.0580.0000.0000.0000.000
139A169VAL00.011-0.00838.802-0.003-0.0030.0000.0000.0000.000
140A170GLU-1-0.834-0.90635.4840.0690.0690.0000.0000.0000.000
141A171ILE0-0.007-0.00235.622-0.003-0.0030.0000.0000.0000.000
142A172ASP-1-0.811-0.87134.1160.0710.0710.0000.0000.0000.000
143A173CYS0-0.032-0.00933.001-0.002-0.0020.0000.0000.0000.000
144A174SER00.0560.03132.4930.0050.0050.0000.0000.0000.000
145A175SER0-0.010-0.03130.9100.0080.0080.0000.0000.0000.000
146A176GLY00.0800.04030.916-0.004-0.0040.0000.0000.0000.000
147A177THR0-0.086-0.03930.7230.0000.0000.0000.0000.0000.000
148A178TYR00.0520.02532.6530.0010.0010.0000.0000.0000.000
149A179ILE00.0420.03333.308-0.003-0.0030.0000.0000.0000.000
150A180ARG10.7420.84432.885-0.081-0.0810.0000.0000.0000.000
151A181ALA00.0510.02838.444-0.003-0.0030.0000.0000.0000.000
152A182LEU00.0110.01739.200-0.002-0.0020.0000.0000.0000.000
153A183ALA0-0.002-0.00640.462-0.002-0.0020.0000.0000.0000.000
154A184ARG10.7860.86942.316-0.047-0.0470.0000.0000.0000.000
155A185ASP-1-0.840-0.90144.5260.0400.0400.0000.0000.0000.000
156A186LEU0-0.0080.00144.686-0.002-0.0020.0000.0000.0000.000
157A187GLY00.0250.00846.651-0.002-0.0020.0000.0000.0000.000
158A188ASP-1-0.911-0.97248.5150.0360.0360.0000.0000.0000.000
159A189ALA0-0.044-0.01549.904-0.002-0.0020.0000.0000.0000.000
160A190LEU0-0.068-0.02849.186-0.002-0.0020.0000.0000.0000.000
161A191GLY0-0.025-0.00552.718-0.001-0.0010.0000.0000.0000.000
162A192VAL0-0.109-0.06550.711-0.001-0.0010.0000.0000.0000.000
163A193GLY00.0580.03749.2710.0000.0000.0000.0000.0000.000
164A194GLY00.010-0.02445.8870.0000.0000.0000.0000.0000.000
165A195HIS0-0.102-0.04341.2150.0010.0010.0000.0000.0000.000
166A196VAL00.0120.00935.8890.0000.0000.0000.0000.0000.000
167A197THR0-0.032-0.03438.4780.0010.0010.0000.0000.0000.000
168A198ALA00.0140.01534.2850.0030.0030.0000.0000.0000.000
169A199LEU00.0010.00231.558-0.003-0.0030.0000.0000.0000.000
170A200ARG10.8490.87925.073-0.123-0.1230.0000.0000.0000.000
171A201ARG10.7810.88423.326-0.149-0.1490.0000.0000.0000.000
172A202THR00.0620.01426.6710.0130.0130.0000.0000.0000.000
173A203ARG10.8540.90726.301-0.078-0.0780.0000.0000.0000.000
174A204VAL0-0.040-0.02522.985-0.001-0.0010.0000.0000.0000.000
175A205GLY00.0170.00224.1380.0060.0060.0000.0000.0000.000
176A206ARG10.8630.93523.206-0.070-0.0700.0000.0000.0000.000
177A207PHE0-0.0210.00519.0970.0010.0010.0000.0000.0000.000
178A208GLU-1-0.776-0.88422.9830.0860.0860.0000.0000.0000.000
179A209LEU0-0.019-0.02922.4230.0170.0170.0000.0000.0000.000
180A210ASP-1-0.845-0.89522.8190.1240.1240.0000.0000.0000.000
181A211GLN0-0.050-0.03919.1750.0110.0110.0000.0000.0000.000
182A212ALA0-0.074-0.03117.7690.0360.0360.0000.0000.0000.000
183A213ARG10.8800.93411.402-0.415-0.4150.0000.0000.0000.000
184A214SER00.028-0.00617.3080.0130.0130.0000.0000.0000.000
185A215LEU0-0.028-0.05114.2940.0330.0330.0000.0000.0000.000
186A216ASP-1-0.852-0.89114.4840.2740.2740.0000.0000.0000.000
187A217ASP-1-0.786-0.88414.7100.3010.3010.0000.0000.0000.000
188A218LEU0-0.009-0.01510.3940.0280.0280.0000.0000.0000.000
189A219ALA0-0.051-0.03410.0700.1470.1470.0000.0000.0000.000
190A220GLU-1-0.974-0.97310.7900.1940.1940.0000.0000.0000.000
191A221ARG10.8240.8969.332-0.271-0.2710.0000.0000.0000.000
192A222PRO0-0.017-0.0015.1960.0520.0520.0000.0000.0000.000
193A223ALA00.0320.0205.8190.1080.1080.0000.0000.0000.000
194A224LEU0-0.051-0.0137.371-0.008-0.0080.0000.0000.0000.000
195A225SER0-0.0040.0139.844-0.078-0.0780.0000.0000.0000.000
196A226LEU00.0290.02012.957-0.063-0.0630.0000.0000.0000.000
197A227SER0-0.004-0.03710.5360.0820.0820.0000.0000.0000.000
198A228LEU0-0.032-0.03911.0060.0090.0090.0000.0000.0000.000
199A229ASP-1-0.793-0.89612.917-0.117-0.1170.0000.0000.0000.000
200A230GLU-1-0.789-0.85813.6960.0450.0450.0000.0000.0000.000
201A231ALA0-0.021-0.00815.0530.0050.0050.0000.0000.0000.000
202A232CYS0-0.057-0.03616.385-0.001-0.0010.0000.0000.0000.000
203A233LEU00.006-0.00819.012-0.004-0.0040.0000.0000.0000.000
204A234LEU0-0.0050.02420.021-0.002-0.0020.0000.0000.0000.000
205A235MET0-0.066-0.03720.1610.0070.0070.0000.0000.0000.000
206A236PHE0-0.041-0.01220.2090.0000.0000.0000.0000.0000.000
207A237ALA00.0780.05224.846-0.003-0.0030.0000.0000.0000.000
208A238ARG10.8110.86121.9320.0320.0320.0000.0000.0000.000
209A239ARG10.8240.90125.9580.0130.0130.0000.0000.0000.000
210A240ASP-1-0.799-0.86126.124-0.034-0.0340.0000.0000.0000.000
211A241LEU0-0.053-0.01525.2610.0040.0040.0000.0000.0000.000
212A242THR00.008-0.02527.722-0.006-0.0060.0000.0000.0000.000
213A243ALA00.0410.00326.979-0.001-0.0010.0000.0000.0000.000
214A244ALA00.0170.01927.605-0.002-0.0020.0000.0000.0000.000
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