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: 3QY5L

Calculation Name: 4L7A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L7A

Chain ID: A

ChEMBL ID:

UniProt ID: A5ZEW7

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 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 -3694194.747929
FMO2-HF: Nuclear repulsion 3588043.985634
FMO2-HF: Total energy -106150.762295
FMO2-MP2: Total energy -106460.472278


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:37:SER)


Summations of interaction energy for fragment #1(A:37: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.
-47.184-52.19232.253-15.621-11.623-0.059
Interaction energy analysis for fragmet #1(A:37:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.047
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].
3A39PHE00.000-0.0042.107-9.019-4.7794.788-4.181-4.8460.041
4A40ASP-1-0.867-0.8991.619-40.134-49.43627.465-11.408-6.756-0.100
5A41ALA00.0180.0154.0871.0891.1430.000-0.032-0.0210.000
6A42SER0-0.069-0.0737.7910.1300.1300.0000.0000.0000.000
7A43GLU-1-0.763-0.89710.343-0.832-0.8320.0000.0000.0000.000
8A44LYS10.9140.98113.6520.7700.7700.0000.0000.0000.000
9A45GLU-1-0.740-0.8389.760-1.502-1.5020.0000.0000.0000.000
10A46LYS10.8960.93610.1341.4301.4300.0000.0000.0000.000
11A47SER0-0.001-0.01114.1590.1170.1170.0000.0000.0000.000
12A48GLU-1-0.918-0.95816.482-0.331-0.3310.0000.0000.0000.000
13A49PHE00.0300.00514.6000.0720.0720.0000.0000.0000.000
14A50ASP-1-0.772-0.85417.334-0.397-0.3970.0000.0000.0000.000
15A51ARG10.8070.88519.4850.2770.2770.0000.0000.0000.000
16A52TRP00.0400.02819.8370.0340.0340.0000.0000.0000.000
17A53LEU00.0160.00718.3820.0340.0340.0000.0000.0000.000
18A54LEU00.0000.00522.3100.0230.0230.0000.0000.0000.000
19A55GLU-1-0.814-0.86725.032-0.164-0.1640.0000.0000.0000.000
20A56ASN0-0.068-0.04124.0080.0300.0300.0000.0000.0000.000
21A57TYR0-0.024-0.03722.8150.0190.0190.0000.0000.0000.000
22A58VAL00.0060.01425.5180.0090.0090.0000.0000.0000.000
23A59ASN0-0.014-0.01328.1470.0100.0100.0000.0000.0000.000
24A60PRO0-0.0100.00729.3300.0070.0070.0000.0000.0000.000
25A61TYR0-0.031-0.04728.9080.0060.0060.0000.0000.0000.000
26A62ASN0-0.055-0.00730.9930.0120.0120.0000.0000.0000.000
27A63ILE0-0.0130.01026.2810.0030.0030.0000.0000.0000.000
28A64ASP-1-0.854-0.93824.346-0.152-0.1520.0000.0000.0000.000
29A65PHE00.025-0.00318.4080.0180.0180.0000.0000.0000.000
30A66LYS10.8600.94719.4440.1340.1340.0000.0000.0000.000
31A67TYR00.017-0.04112.9360.0130.0130.0000.0000.0000.000
32A68ARG10.8000.89014.3820.5390.5390.0000.0000.0000.000
33A69MET00.0450.05110.2050.0850.0850.0000.0000.0000.000
34A70GLU-1-0.848-0.91415.033-0.518-0.5180.0000.0000.0000.000
35A71HIS0-0.113-0.06217.8500.0110.0110.0000.0000.0000.000
36A72ILE0-0.028-0.01017.2140.0300.0300.0000.0000.0000.000
37A73GLU-1-0.936-0.96020.759-0.100-0.1000.0000.0000.0000.000
38A74SER0-0.065-0.05722.5040.0070.0070.0000.0000.0000.000
39A75ASP-1-0.885-0.92523.723-0.014-0.0140.0000.0000.0000.000
40A76TYR0-0.039-0.01020.477-0.003-0.0030.0000.0000.0000.000
41A77THR00.0250.00121.2240.0120.0120.0000.0000.0000.000
42A78HIS00.021-0.00920.160-0.003-0.0030.0000.0000.0000.000
43A79ASN0-0.0070.01418.4390.0230.0230.0000.0000.0000.000
44A80LEU0-0.0280.00615.7820.0400.0400.0000.0000.0000.000
45A81VAL0-0.024-0.00411.3440.0220.0220.0000.0000.0000.000
46A82PRO00.006-0.0188.399-0.038-0.0380.0000.0000.0000.000
47A83THR00.009-0.02410.2330.1760.1760.0000.0000.0000.000
48A84ASP-1-0.871-0.9168.0790.7840.7840.0000.0000.0000.000
49A85PHE00.0410.0328.006-0.077-0.0770.0000.0000.0000.000
50A86TRP00.0680.0167.3090.1150.1150.0000.0000.0000.000
51A87LEU0-0.019-0.00110.043-0.031-0.0310.0000.0000.0000.000
52A88SER0-0.009-0.03312.067-0.063-0.0630.0000.0000.0000.000
53A89VAL0-0.032-0.00413.119-0.015-0.0150.0000.0000.0000.000
54A90LYS10.8040.89612.597-0.292-0.2920.0000.0000.0000.000
55A91LEU00.0120.00415.669-0.014-0.0140.0000.0000.0000.000
56A92ALA00.0090.01217.847-0.010-0.0100.0000.0000.0000.000
57A93LYS10.8370.92918.6640.0870.0870.0000.0000.0000.000
58A94ILE00.0420.02119.018-0.002-0.0020.0000.0000.0000.000
59A95VAL0-0.009-0.01321.784-0.001-0.0010.0000.0000.0000.000
60A96LYS10.8310.90623.8500.0500.0500.0000.0000.0000.000
61A97HIS0-0.020-0.01925.114-0.007-0.0070.0000.0000.0000.000
62A98CYS0-0.019-0.01125.3860.0050.0050.0000.0000.0000.000
63A99TRP0-0.018-0.00926.5990.0020.0020.0000.0000.0000.000
64A100LEU0-0.0250.00227.095-0.003-0.0030.0000.0000.0000.000
65A101GLU-1-0.759-0.86528.531-0.031-0.0310.0000.0000.0000.000
66A102ALA00.0070.00531.4640.0010.0010.0000.0000.0000.000
67A103TYR0-0.026-0.04633.3500.0010.0010.0000.0000.0000.000
68A104ASP-1-0.765-0.84732.964-0.034-0.0340.0000.0000.0000.000
69A105GLU-1-0.823-0.88434.7180.0010.0010.0000.0000.0000.000
70A106VAL0-0.053-0.03237.1870.0020.0020.0000.0000.0000.000
71A107GLY0-0.006-0.00739.1510.0010.0010.0000.0000.0000.000
72A108GLY0-0.0240.00639.399-0.002-0.0020.0000.0000.0000.000
73A109LEU00.006-0.00534.0220.0010.0010.0000.0000.0000.000
74A110ASP-1-0.906-0.96336.999-0.039-0.0390.0000.0000.0000.000
75A111PHE0-0.0200.00537.7940.0010.0010.0000.0000.0000.000
76A112THR00.025-0.02332.8600.0040.0040.0000.0000.0000.000
77A113ARG10.8430.90434.9140.0570.0570.0000.0000.0000.000
78A114ALA0-0.045-0.00136.132-0.001-0.0010.0000.0000.0000.000
79A115CYS0-0.087-0.05236.2200.0020.0020.0000.0000.0000.000
80A116ALA00.0420.03631.5990.0040.0040.0000.0000.0000.000
81A117PRO0-0.0300.00128.5860.0000.0000.0000.0000.0000.000
82A118LYS10.7720.87630.6170.0640.0640.0000.0000.0000.000
83A119VAL0-0.007-0.01125.458-0.011-0.0110.0000.0000.0000.000
84A120ILE00.0310.02022.0310.0160.0160.0000.0000.0000.000
85A121HIS0-0.020-0.01420.620-0.027-0.0270.0000.0000.0000.000
86A122LEU00.0260.02416.2760.0310.0310.0000.0000.0000.000
87A123ILE00.002-0.00316.003-0.045-0.0450.0000.0000.0000.000
88A124GLY00.0580.03513.0860.0480.0480.0000.0000.0000.000
89A125SER0-0.010-0.03014.055-0.042-0.0420.0000.0000.0000.000
90A126ALA0-0.006-0.00714.6280.0640.0640.0000.0000.0000.000
91A127SER0-0.037-0.01315.6840.0420.0420.0000.0000.0000.000
92A128TRP00.0690.04818.353-0.022-0.0220.0000.0000.0000.000
93A129ASP-1-0.817-0.89421.2560.1860.1860.0000.0000.0000.000
94A130LYS10.7570.85322.261-0.202-0.2020.0000.0000.0000.000
95A131GLY0-0.0010.01624.384-0.020-0.0200.0000.0000.0000.000
96A132THR0-0.022-0.03621.6530.0140.0140.0000.0000.0000.000
97A133TYR0-0.008-0.00322.488-0.005-0.0050.0000.0000.0000.000
98A134THR00.0110.01324.7980.0010.0010.0000.0000.0000.000
99A135LEU00.0020.00326.724-0.006-0.0060.0000.0000.0000.000
100A136GLY00.0400.01929.3890.0010.0010.0000.0000.0000.000
101A137THR0-0.036-0.01531.1060.0000.0000.0000.0000.0000.000
102A138ALA00.0230.00529.761-0.005-0.0050.0000.0000.0000.000
103A139GLU-1-0.876-0.92831.802-0.081-0.0810.0000.0000.0000.000
104A140GLY00.0080.00833.8300.0020.0020.0000.0000.0000.000
105A141GLY0-0.002-0.00534.6200.0050.0050.0000.0000.0000.000
106A142LEU00.0140.01530.736-0.003-0.0030.0000.0000.0000.000
107A143LYS10.8710.94425.1750.0580.0580.0000.0000.0000.000
108A144VAL00.010-0.00425.2570.0100.0100.0000.0000.0000.000
109A145THR0-0.027-0.01221.598-0.021-0.0210.0000.0000.0000.000
110A146LEU0-0.007-0.00220.4010.0150.0150.0000.0000.0000.000
111A147TYR0-0.015-0.01118.474-0.010-0.0100.0000.0000.0000.000
112A148MET0-0.048-0.00212.3710.0360.0360.0000.0000.0000.000
113A149GLY00.1080.03012.4380.0010.0010.0000.0000.0000.000
114A150ASN0-0.010-0.0148.888-0.233-0.2330.0000.0000.0000.000
115A151TRP0-0.021-0.00812.321-0.019-0.0190.0000.0000.0000.000
116A152LEU0-0.036-0.01515.500-0.063-0.0630.0000.0000.0000.000
117A153ASP-1-0.798-0.87116.6910.2750.2750.0000.0000.0000.000
118A154LEU0-0.019-0.03115.658-0.039-0.0390.0000.0000.0000.000
119A155THR00.006-0.01319.666-0.030-0.0300.0000.0000.0000.000
120A156ASN0-0.070-0.03722.457-0.037-0.0370.0000.0000.0000.000
121A157VAL00.0420.01824.493-0.002-0.0020.0000.0000.0000.000
122A158ASP-1-0.867-0.93327.0510.1100.1100.0000.0000.0000.000
123A159ARG10.7850.89023.669-0.160-0.1600.0000.0000.0000.000
124A160MET00.0130.02320.7610.0060.0060.0000.0000.0000.000
125A161ASN0-0.007-0.00924.573-0.017-0.0170.0000.0000.0000.000
126A162GLU-1-0.904-0.94027.0880.1340.1340.0000.0000.0000.000
127A163TYR0-0.018-0.00821.4450.0040.0040.0000.0000.0000.000
128A164TYR00.017-0.01119.4120.0000.0000.0000.0000.0000.000
129A165PHE00.0500.01424.478-0.013-0.0130.0000.0000.0000.000
130A166LYS10.8030.88928.337-0.062-0.0620.0000.0000.0000.000
131A167VAL00.0170.00129.374-0.007-0.0070.0000.0000.0000.000
132A168MET0-0.032-0.00826.034-0.004-0.0040.0000.0000.0000.000
133A169HIS00.0890.04730.416-0.012-0.0120.0000.0000.0000.000
134A170HIS0-0.069-0.03133.594-0.006-0.0060.0000.0000.0000.000
135A171GLU-1-0.872-0.95632.3540.0100.0100.0000.0000.0000.000
136A172PHE0-0.012-0.00729.418-0.005-0.0050.0000.0000.0000.000
137A173ALA00.0300.01635.542-0.004-0.0040.0000.0000.0000.000
138A174HIS00.0110.01637.735-0.004-0.0040.0000.0000.0000.000
139A175ILE0-0.017-0.01134.683-0.003-0.0030.0000.0000.0000.000
140A176LEU0-0.023-0.00738.943-0.003-0.0030.0000.0000.0000.000
141A177HIS0-0.027-0.03741.3040.0010.0010.0000.0000.0000.000
142A178GLN0-0.041-0.02738.880-0.004-0.0040.0000.0000.0000.000
143A179LYS10.8360.93138.8500.0210.0210.0000.0000.0000.000
144A180LYS10.8420.93044.6640.0130.0130.0000.0000.0000.000
145A181ASN00.0280.03546.8260.0030.0030.0000.0000.0000.000
146A182TYR0-0.038-0.02546.361-0.001-0.0010.0000.0000.0000.000
147A183PRO0-0.013-0.02249.088-0.001-0.0010.0000.0000.0000.000
148A184VAL00.0660.02652.2350.0020.0020.0000.0000.0000.000
149A185ASP-1-0.865-0.92653.8660.0080.0080.0000.0000.0000.000
150A186TYR00.029-0.02146.1960.0010.0010.0000.0000.0000.000
151A187ASP-1-0.835-0.90850.7580.0120.0120.0000.0000.0000.000
152A188LYS10.7920.87452.313-0.007-0.0070.0000.0000.0000.000
153A189ILE0-0.0410.00451.4820.0010.0010.0000.0000.0000.000
154A190SER00.0320.02350.7180.0010.0010.0000.0000.0000.000
155A191ALA00.0370.01652.8100.0010.0010.0000.0000.0000.000
156A192GLY0-0.050-0.02954.9330.0010.0010.0000.0000.0000.000
157A193ASN0-0.030-0.00952.0700.0020.0020.0000.0000.0000.000
158A194TYR0-0.030-0.02147.4800.0020.0020.0000.0000.0000.000
159A195THR0-0.035-0.01846.5150.0000.0000.0000.0000.0000.000
160A196PRO00.0530.01546.1340.0020.0020.0000.0000.0000.000
161A197THR0-0.050-0.02744.9580.0000.0000.0000.0000.0000.000
162A198GLY00.0340.01844.469-0.001-0.0010.0000.0000.0000.000
163A199TRP00.0100.01137.3790.0030.0030.0000.0000.0000.000
164A200GLN00.0310.01639.3660.0000.0000.0000.0000.0000.000
165A201ASN0-0.036-0.01740.9560.0060.0060.0000.0000.0000.000
166A202ARG10.8340.93943.662-0.032-0.0320.0000.0000.0000.000
167A203LYS10.9230.94941.274-0.058-0.0580.0000.0000.0000.000
168A204LEU00.0610.02439.803-0.003-0.0030.0000.0000.0000.000
169A205ALA00.004-0.00743.000-0.003-0.0030.0000.0000.0000.000
170A206GLU-1-0.895-0.93946.1820.0420.0420.0000.0000.0000.000
171A207VAL0-0.018-0.02043.639-0.003-0.0030.0000.0000.0000.000
172A208ALA00.0530.04145.108-0.003-0.0030.0000.0000.0000.000
173A209PRO0-0.036-0.02346.944-0.003-0.0030.0000.0000.0000.000
174A210LEU0-0.043-0.01449.786-0.002-0.0020.0000.0000.0000.000
175A211GLY00.0390.01749.274-0.002-0.0020.0000.0000.0000.000
176A212PHE0-0.054-0.01144.765-0.001-0.0010.0000.0000.0000.000
177A213VAL00.0480.01540.7790.0020.0020.0000.0000.0000.000
178A214THR0-0.013-0.03737.3930.0040.0040.0000.0000.0000.000
179A215PRO00.007-0.01139.202-0.003-0.0030.0000.0000.0000.000
180A216TYR00.0210.02536.737-0.002-0.0020.0000.0000.0000.000
181A217ALA00.0170.02540.305-0.004-0.0040.0000.0000.0000.000
182A218GLY00.0370.02342.713-0.003-0.0030.0000.0000.0000.000
183A219SER0-0.044-0.03642.426-0.002-0.0020.0000.0000.0000.000
184A220LYS10.8280.87143.731-0.016-0.0160.0000.0000.0000.000
185A221PRO00.0310.02745.3330.0010.0010.0000.0000.0000.000
186A222SER00.011-0.02344.0360.0000.0000.0000.0000.0000.000
187A223GLU-1-0.737-0.82040.4400.0160.0160.0000.0000.0000.000
188A224ASP-1-0.789-0.84341.4060.0280.0280.0000.0000.0000.000
189A225ILE00.0070.01343.2330.0020.0020.0000.0000.0000.000
190A226ALA00.0180.03238.9790.0000.0000.0000.0000.0000.000
191A227GLU-1-0.741-0.83336.9590.0480.0480.0000.0000.0000.000
192A228VAL0-0.044-0.02239.4330.0030.0030.0000.0000.0000.000
193A229THR0-0.020-0.02439.0660.0010.0010.0000.0000.0000.000
194A230ALA00.0190.01435.1680.0010.0010.0000.0000.0000.000
195A231CYS0-0.065-0.01235.7090.0050.0050.0000.0000.0000.000
196A232PHE00.000-0.00137.4420.0030.0030.0000.0000.0000.000
197A233LEU0-0.045-0.02635.6710.0010.0010.0000.0000.0000.000
198A234THR0-0.036-0.03031.8830.0030.0030.0000.0000.0000.000
199A235TYR0-0.031-0.02133.6230.0070.0070.0000.0000.0000.000
200A236PRO00.0640.03333.549-0.006-0.0060.0000.0000.0000.000
201A237GLU-1-0.836-0.90836.3190.0390.0390.0000.0000.0000.000
202A238ALA00.0290.01438.613-0.002-0.0020.0000.0000.0000.000
203A239GLN00.0220.01134.1900.0000.0000.0000.0000.0000.000
204A240TRP00.0200.00638.663-0.001-0.0010.0000.0000.0000.000
205A241GLU-1-0.811-0.93141.1640.0380.0380.0000.0000.0000.000
206A242ASN0-0.0230.01440.517-0.001-0.0010.0000.0000.0000.000
207A243VAL0-0.011-0.00240.478-0.001-0.0010.0000.0000.0000.000
208A244MET0-0.011-0.00243.331-0.002-0.0020.0000.0000.0000.000
209A245THR0-0.058-0.02846.002-0.003-0.0030.0000.0000.0000.000
210A246LEU0-0.038-0.03242.893-0.001-0.0010.0000.0000.0000.000
211A247ALA00.0010.00847.094-0.001-0.0010.0000.0000.0000.000
212A248GLY00.0120.00349.083-0.002-0.0020.0000.0000.0000.000
213A249GLU-1-0.898-0.96452.1880.0270.0270.0000.0000.0000.000
214A250LYS10.8280.90854.861-0.028-0.0280.0000.0000.0000.000
215A251GLY00.0950.05651.111-0.001-0.0010.0000.0000.0000.000
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