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: LZ4Z9

Calculation Name: 4NS4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NS4

Chain ID: A

ChEMBL ID:

UniProt ID: Q1QEU6

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:


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 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3830169.015062
FMO2-HF: Nuclear repulsion 3725654.398374
FMO2-HF: Total energy -104514.616687
FMO2-MP2: Total energy -104823.220721


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:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-9.749-7.565-0.014-0.934-1.2350.003
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.013
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].
3A5THR00.0410.0243.9090.7172.356-0.017-0.794-0.8280.002
4A6GLN00.0890.0496.8740.1600.1600.0000.0000.0000.000
5A7LYS10.9570.9764.069-4.204-3.8690.004-0.126-0.2130.001
6A8ILE0-0.021-0.0174.347-0.657-0.447-0.001-0.014-0.1940.000
7A9ILE00.0170.0147.019-0.564-0.5640.0000.0000.0000.000
8A10GLN00.0300.01110.012-0.340-0.3400.0000.0000.0000.000
9A11TYR0-0.037-0.0178.455-0.286-0.2860.0000.0000.0000.000
10A12GLU-1-0.757-0.85510.3901.3271.3270.0000.0000.0000.000
11A13ARG10.8550.90512.823-1.415-1.4150.0000.0000.0000.000
12A14SER00.0170.00513.282-0.089-0.0890.0000.0000.0000.000
13A15LYS10.9260.98113.267-1.340-1.3400.0000.0000.0000.000
14A16SER0-0.126-0.06915.744-0.069-0.0690.0000.0000.0000.000
15A17ASP-1-0.868-0.91918.4410.6280.6280.0000.0000.0000.000
16A18LEU0-0.043-0.02218.610-0.065-0.0650.0000.0000.0000.000
17A19THR0-0.053-0.03118.4330.0840.0840.0000.0000.0000.000
18A20THR0-0.063-0.04118.458-0.007-0.0070.0000.0000.0000.000
19A21GLN0-0.0250.00420.582-0.029-0.0290.0000.0000.0000.000
20A22SER0-0.017-0.02623.8250.0090.0090.0000.0000.0000.000
21A23PHE00.0290.02326.175-0.019-0.0190.0000.0000.0000.000
22A24THR0-0.058-0.03229.8450.0050.0050.0000.0000.0000.000
23A25LEU0-0.002-0.00232.354-0.006-0.0060.0000.0000.0000.000
24A26SER00.006-0.02935.005-0.014-0.0140.0000.0000.0000.000
25A27SER0-0.069-0.04935.863-0.007-0.0070.0000.0000.0000.000
26A28GLY00.0160.01235.212-0.009-0.0090.0000.0000.0000.000
27A29ASP-1-0.884-0.92632.2000.2330.2330.0000.0000.0000.000
28A30LYS10.8580.92727.758-0.243-0.2430.0000.0000.0000.000
29A31ILE00.0240.01828.0500.0090.0090.0000.0000.0000.000
30A32VAL00.0040.00321.529-0.008-0.0080.0000.0000.0000.000
31A33TYR00.0110.00524.172-0.004-0.0040.0000.0000.0000.000
32A34ALA00.0090.01220.7800.0210.0210.0000.0000.0000.000
33A35GLU-1-0.760-0.86422.5850.3590.3590.0000.0000.0000.000
34A36ASN00.0480.01022.8760.0270.0270.0000.0000.0000.000
35A37GLY00.0040.02024.401-0.007-0.0070.0000.0000.0000.000
36A38ASN0-0.0180.00427.063-0.047-0.0470.0000.0000.0000.000
37A39VAL0-0.010-0.03329.203-0.013-0.0130.0000.0000.0000.000
38A40ALA0-0.030-0.00332.293-0.017-0.0170.0000.0000.0000.000
39A41GLY00.0160.03232.972-0.010-0.0100.0000.0000.0000.000
40A42GLU-1-0.844-0.91233.9650.2470.2470.0000.0000.0000.000
41A43PRO00.0110.00432.8340.0210.0210.0000.0000.0000.000
42A44LEU0-0.043-0.02730.158-0.011-0.0110.0000.0000.0000.000
43A45LEU0-0.0110.00130.1320.0270.0270.0000.0000.0000.000
44A46LEU0-0.020-0.00726.213-0.008-0.0080.0000.0000.0000.000
45A47VAL00.0240.00327.7020.0240.0240.0000.0000.0000.000
46A48HIS0-0.050-0.00325.103-0.006-0.0060.0000.0000.0000.000
47A49GLY00.1010.03326.819-0.035-0.0350.0000.0000.0000.000
48A50PHE0-0.036-0.02727.1020.0240.0240.0000.0000.0000.000
49A51GLY00.0010.01325.7190.0090.0090.0000.0000.0000.000
50A52GLY0-0.053-0.01422.7340.0470.0470.0000.0000.0000.000
51A53ASN0-0.007-0.02418.310-0.002-0.0020.0000.0000.0000.000
52A54LYS10.8870.91018.809-0.790-0.7900.0000.0000.0000.000
53A55ASP-1-0.816-0.87616.6191.1821.1820.0000.0000.0000.000
54A56ASN0-0.101-0.04818.8270.0040.0040.0000.0000.0000.000
55A57PHE00.0660.01721.325-0.021-0.0210.0000.0000.0000.000
56A58THR00.0120.00715.865-0.054-0.0540.0000.0000.0000.000
57A59ARG10.8210.89113.376-1.508-1.5080.0000.0000.0000.000
58A60ILE00.0140.01319.273-0.029-0.0290.0000.0000.0000.000
59A61ALA00.0180.02321.229-0.051-0.0510.0000.0000.0000.000
60A62ARG10.8160.87515.392-1.209-1.2090.0000.0000.0000.000
61A63GLN0-0.048-0.01221.851-0.070-0.0700.0000.0000.0000.000
62A64LEU00.0070.00225.173-0.052-0.0520.0000.0000.0000.000
63A65GLU-1-0.779-0.88825.5760.4340.4340.0000.0000.0000.000
64A66ASN0-0.048-0.02326.919-0.025-0.0250.0000.0000.0000.000
65A67TYR00.0100.00429.478-0.023-0.0230.0000.0000.0000.000
66A68ASN00.0070.01529.0850.0470.0470.0000.0000.0000.000
67A69LEU0-0.020-0.01425.033-0.009-0.0090.0000.0000.0000.000
68A70ILE00.0150.00726.9180.0160.0160.0000.0000.0000.000
69A71ILE0-0.017-0.01922.882-0.012-0.0120.0000.0000.0000.000
70A72PRO00.0150.00124.3240.0390.0390.0000.0000.0000.000
71A73ASP-1-0.754-0.84421.7950.7050.7050.0000.0000.0000.000
72A74LEU00.0040.00824.968-0.042-0.0420.0000.0000.0000.000
73A75LEU00.0630.03227.6170.0130.0130.0000.0000.0000.000
74A76GLY0-0.022-0.00729.023-0.009-0.0090.0000.0000.0000.000
75A77PHE0-0.023-0.02525.2180.0000.0000.0000.0000.0000.000
76A78GLY00.0470.02521.373-0.005-0.0050.0000.0000.0000.000
77A79ASP-1-0.859-0.91719.0490.7560.7560.0000.0000.0000.000
78A80SER0-0.031-0.02122.001-0.036-0.0360.0000.0000.0000.000
79A81SER0-0.0180.00325.7080.0040.0040.0000.0000.0000.000
80A82LYS10.8340.89323.375-0.430-0.4300.0000.0000.0000.000
81A83PRO00.0570.04129.647-0.016-0.0160.0000.0000.0000.000
82A84MET00.0160.00433.2890.0090.0090.0000.0000.0000.000
83A85ALA0-0.019-0.00534.7940.0000.0000.0000.0000.0000.000
84A86ALA0-0.0040.01735.439-0.007-0.0070.0000.0000.0000.000
85A87ASP-1-0.791-0.88237.5540.2010.2010.0000.0000.0000.000
86A88TYR0-0.042-0.07432.1140.0170.0170.0000.0000.0000.000
87A89HIS10.8310.89835.843-0.181-0.1810.0000.0000.0000.000
88A90SER00.008-0.03136.9120.0020.0020.0000.0000.0000.000
89A91GLU-1-0.762-0.86837.9940.1990.1990.0000.0000.0000.000
90A92ALA0-0.0040.00738.5450.0000.0000.0000.0000.0000.000
91A93GLN0-0.026-0.01931.691-0.002-0.0020.0000.0000.0000.000
92A94ALA00.0270.00935.2110.0100.0100.0000.0000.0000.000
93A95THR0-0.064-0.04737.183-0.002-0.0020.0000.0000.0000.000
94A96ARG10.8770.93734.192-0.243-0.2430.0000.0000.0000.000
95A97LEU0-0.0060.00730.8540.0090.0090.0000.0000.0000.000
96A98HIS10.8530.92034.361-0.206-0.2060.0000.0000.0000.000
97A99GLU-1-0.842-0.90836.2570.2110.2110.0000.0000.0000.000
98A100LEU0-0.022-0.00429.534-0.003-0.0030.0000.0000.0000.000
99A101LEU00.0360.00632.8450.0010.0010.0000.0000.0000.000
100A102GLN0-0.014-0.02735.156-0.005-0.0050.0000.0000.0000.000
101A103ALA0-0.0120.00735.064-0.007-0.0070.0000.0000.0000.000
102A104LYS10.7800.87428.613-0.355-0.3550.0000.0000.0000.000
103A105GLY00.0060.00434.7230.0010.0010.0000.0000.0000.000
104A106LEU0-0.038-0.02832.3890.0010.0010.0000.0000.0000.000
105A107ALA0-0.031-0.00636.7770.0050.0050.0000.0000.0000.000
106A108SER00.0020.00338.8980.0020.0020.0000.0000.0000.000
107A109SER0-0.017-0.03040.426-0.011-0.0110.0000.0000.0000.000
108A110ILE0-0.029-0.00134.0390.0110.0110.0000.0000.0000.000
109A111HIS0-0.0160.01935.064-0.006-0.0060.0000.0000.0000.000
110A112VAL00.0280.01334.0320.0170.0170.0000.0000.0000.000
111A113GLY00.0310.01032.172-0.010-0.0100.0000.0000.0000.000
112A114GLY0-0.0080.01130.6070.0170.0170.0000.0000.0000.000
113A115ASN00.0200.00128.2410.0040.0040.0000.0000.0000.000
114A116SER0-0.0200.00530.3050.0060.0060.0000.0000.0000.000
115A117MET00.0180.01029.862-0.022-0.0220.0000.0000.0000.000
116A118GLY00.0600.03930.892-0.019-0.0190.0000.0000.0000.000
117A119GLY0-0.0010.01231.859-0.009-0.0090.0000.0000.0000.000
118A120ALA00.0520.02534.601-0.017-0.0170.0000.0000.0000.000
119A121ILE0-0.044-0.04532.540-0.015-0.0150.0000.0000.0000.000
120A122SER0-0.002-0.01333.963-0.006-0.0060.0000.0000.0000.000
121A123VAL0-0.0090.00636.442-0.011-0.0110.0000.0000.0000.000
122A124ALA0-0.0230.00239.023-0.012-0.0120.0000.0000.0000.000
123A125TYR00.026-0.00836.871-0.009-0.0090.0000.0000.0000.000
124A126ALA0-0.011-0.00939.668-0.010-0.0100.0000.0000.0000.000
125A127ALA0-0.010-0.00341.677-0.010-0.0100.0000.0000.0000.000
126A128LYS10.8050.90542.332-0.197-0.1970.0000.0000.0000.000
127A129TYR0-0.031-0.03140.351-0.010-0.0100.0000.0000.0000.000
128A130PRO00.0310.02443.6740.0040.0040.0000.0000.0000.000
129A131LYS10.9070.96045.729-0.152-0.1520.0000.0000.0000.000
130A132GLU-1-0.819-0.89041.8060.1950.1950.0000.0000.0000.000
131A133VAL0-0.0230.00139.3380.0100.0100.0000.0000.0000.000
132A134LYS10.8490.93540.363-0.204-0.2040.0000.0000.0000.000
133A135SER0-0.028-0.03738.1160.0000.0000.0000.0000.0000.000
134A136LEU00.0040.00637.1240.0110.0110.0000.0000.0000.000
135A137TRP0-0.025-0.00428.9930.0060.0060.0000.0000.0000.000
136A138LEU0-0.009-0.01634.4170.0150.0150.0000.0000.0000.000
137A139ILE0-0.0130.00629.599-0.002-0.0020.0000.0000.0000.000
138A140ASP-1-0.718-0.89332.0560.3800.3800.0000.0000.0000.000
139A141SER0-0.044-0.02733.7360.0110.0110.0000.0000.0000.000
140A142ALA0-0.045-0.02434.980-0.011-0.0110.0000.0000.0000.000
141A143GLY00.0500.02036.704-0.001-0.0010.0000.0000.0000.000
142A144PHE0-0.005-0.00239.922-0.011-0.0110.0000.0000.0000.000
143A145TRP00.015-0.00137.8310.0100.0100.0000.0000.0000.000
144A146SER00.0240.02843.180-0.016-0.0160.0000.0000.0000.000
145A162PRO00.031-0.01034.0950.0060.0060.0000.0000.0000.000
146A163LEU0-0.0100.00130.871-0.009-0.0090.0000.0000.0000.000
147A164LEU00.0710.04929.5610.0230.0230.0000.0000.0000.000
148A165VAL0-0.054-0.02428.6260.0220.0220.0000.0000.0000.000
149A166ASP-1-0.838-0.92523.8660.4450.4450.0000.0000.0000.000
150A167LYS10.8670.94126.508-0.248-0.2480.0000.0000.0000.000
151A168LYS10.8360.89121.566-0.257-0.2570.0000.0000.0000.000
152A169GLU-1-0.758-0.88318.5250.3130.3130.0000.0000.0000.000
153A170ASP-1-0.873-0.92620.4680.3660.3660.0000.0000.0000.000
154A171PHE00.0370.01222.373-0.036-0.0360.0000.0000.0000.000
155A172TYR0-0.051-0.03217.8080.0060.0060.0000.0000.0000.000
156A173ALA00.0310.02022.1350.0080.0080.0000.0000.0000.000
157A174MET00.0350.02622.018-0.025-0.0250.0000.0000.0000.000
158A175TYR0-0.024-0.04117.9700.0730.0730.0000.0000.0000.000
159A176ASP-1-0.865-0.91623.4090.4600.4600.0000.0000.0000.000
160A177PHE0-0.0130.00525.820-0.018-0.0180.0000.0000.0000.000
161A178VAL0-0.036-0.02925.615-0.017-0.0170.0000.0000.0000.000
162A179MET0-0.051-0.01220.8950.0330.0330.0000.0000.0000.000
163A180SER0-0.015-0.01626.222-0.022-0.0220.0000.0000.0000.000
164A181LYS10.8850.95024.723-0.422-0.4220.0000.0000.0000.000
165A182PRO0-0.0030.00220.1460.0480.0480.0000.0000.0000.000
166A183PRO00.0280.02617.8560.0210.0210.0000.0000.0000.000
167A184TYR00.004-0.0159.4840.0080.0080.0000.0000.0000.000
168A185ILE0-0.025-0.01812.4940.1410.1410.0000.0000.0000.000
169A186PRO00.0290.0197.698-0.148-0.1480.0000.0000.0000.000
170A187LYS11.0340.9989.831-0.771-0.7710.0000.0000.0000.000
171A188SER00.0120.0026.039-0.457-0.4570.0000.0000.0000.000
172A189VAL00.0380.0148.525-0.220-0.2200.0000.0000.0000.000
173A190LYS10.9360.98410.820-1.371-1.3710.0000.0000.0000.000
174A191ALA0-0.012-0.00212.139-0.178-0.1780.0000.0000.0000.000
175A192VAL00.0000.00611.248-0.144-0.1440.0000.0000.0000.000
176A193PHE00.0390.00814.059-0.085-0.0850.0000.0000.0000.000
177A194ALA00.0000.01216.655-0.111-0.1110.0000.0000.0000.000
178A195GLN0-0.027-0.03416.749-0.124-0.1240.0000.0000.0000.000
179A196GLU-1-0.904-0.93516.7990.8130.8130.0000.0000.0000.000
180A197ARG10.8000.86020.165-0.533-0.5330.0000.0000.0000.000
181A198ILE0-0.064-0.02520.516-0.067-0.0670.0000.0000.0000.000
182A199ALA0-0.022-0.01821.977-0.051-0.0510.0000.0000.0000.000
183A200ASN00.0150.01323.859-0.059-0.0590.0000.0000.0000.000
184A201LYS10.9340.98325.934-0.276-0.2760.0000.0000.0000.000
185A202ALA0-0.038-0.01628.279-0.016-0.0160.0000.0000.0000.000
186A203LEU00.0450.01429.494-0.014-0.0140.0000.0000.0000.000
187A204GLU-1-0.765-0.84726.1320.4090.4090.0000.0000.0000.000
188A205SER0-0.085-0.05130.553-0.008-0.0080.0000.0000.0000.000
189A206LYS10.8820.94133.623-0.202-0.2020.0000.0000.0000.000
190A207ILE00.0280.02130.675-0.008-0.0080.0000.0000.0000.000
191A208LEU0-0.016-0.01032.428-0.005-0.0050.0000.0000.0000.000
192A209ALA0-0.004-0.00334.759-0.006-0.0060.0000.0000.0000.000
193A210GLN00.0180.00937.265-0.006-0.0060.0000.0000.0000.000
194A211ILE00.009-0.00833.319-0.002-0.0020.0000.0000.0000.000
195A212VAL0-0.066-0.02737.7400.0010.0010.0000.0000.0000.000
196A213GLU-1-0.850-0.89639.1010.1670.1670.0000.0000.0000.000
197A214ASP-1-0.841-0.87739.4140.2110.2110.0000.0000.0000.000
198A215ASN0-0.078-0.04740.8980.0060.0060.0000.0000.0000.000
199A216VAL0-0.001-0.02440.433-0.005-0.0050.0000.0000.0000.000
200A217GLU-1-0.756-0.86343.3640.1760.1760.0000.0000.0000.000
201A218GLN00.0250.01346.113-0.004-0.0040.0000.0000.0000.000
202A219ARG10.8060.87541.632-0.201-0.2010.0000.0000.0000.000
203A220ALA00.0480.02944.1600.0000.0000.0000.0000.0000.000
204A221LYS10.9230.95845.644-0.142-0.1420.0000.0000.0000.000
205A222VAL00.0240.02947.085-0.004-0.0040.0000.0000.0000.000
206A223ILE0-0.006-0.00242.2210.0000.0000.0000.0000.0000.000
207A224THR0-0.023-0.02746.2960.0020.0020.0000.0000.0000.000
208A225GLU-1-0.945-0.95649.1920.1400.1400.0000.0000.0000.000
209A226TYR0-0.049-0.04548.019-0.004-0.0040.0000.0000.0000.000
210A227ASN0-0.044-0.02248.726-0.001-0.0010.0000.0000.0000.000
211A228ILE0-0.011-0.00442.3840.0030.0030.0000.0000.0000.000
212A229PRO00.0320.02542.2050.0030.0030.0000.0000.0000.000
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214A231LEU0-0.0180.01835.327-0.006-0.0060.0000.0000.0000.000
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