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: 52NNZ

Calculation Name: 3M66-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M66

Chain ID: A

ChEMBL ID:

UniProt ID: Q96E29

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 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 270
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3577434.388787
FMO2-HF: Nuclear repulsion 3468132.50041
FMO2-HF: Total energy -109301.888377
FMO2-MP2: Total energy -109624.25618


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:148:ASP)


Summations of interaction energy for fragment #1(A:148:ASP)
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.
-75.176-71.0260.127-1.736-2.5420.008
Interaction energy analysis for fragmet #1(A:148:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.904 / q_NPA : -0.959
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].
3A150VAL0-0.008-0.0183.650-13.987-11.2000.018-1.384-1.4210.008
4A151ASP-1-0.896-0.9422.93934.17235.0570.111-0.221-0.7750.000
5A152HIS0-0.0340.0004.213-3.963-3.686-0.001-0.106-0.1710.000
6A153SER00.0360.0135.899-4.333-4.3330.0000.0000.0000.000
7A154GLU-1-0.845-0.9098.62518.15918.1590.0000.0000.0000.000
8A155THR0-0.020-0.0099.073-3.380-3.3800.0000.0000.0000.000
9A156LEU00.0050.0069.553-2.276-2.2760.0000.0000.0000.000
10A157GLN00.0230.00211.444-2.517-2.5170.0000.0000.0000.000
11A158LYS10.8440.91513.196-20.943-20.9430.0000.0000.0000.000
12A159LEU0-0.017-0.00812.252-1.384-1.3840.0000.0000.0000.000
13A160VAL00.011-0.00315.175-1.107-1.1070.0000.0000.0000.000
14A161LEU0-0.017-0.00317.499-1.101-1.1010.0000.0000.0000.000
15A162LEU0-0.057-0.01818.255-0.912-0.9120.0000.0000.0000.000
16A163GLY0-0.013-0.00120.642-0.706-0.7060.0000.0000.0000.000
17A164VAL0-0.070-0.03416.982-0.448-0.4480.0000.0000.0000.000
18A165ASP-1-0.777-0.84418.74615.94115.9410.0000.0000.0000.000
19A166LEU00.0590.01213.018-0.345-0.3450.0000.0000.0000.000
20A167SER00.0260.00215.8960.1210.1210.0000.0000.0000.000
21A168LYS10.7670.86017.842-14.549-14.5490.0000.0000.0000.000
22A169ILE00.0020.00014.725-0.416-0.4160.0000.0000.0000.000
23A170GLU-1-0.844-0.93712.97622.80122.8010.0000.0000.0000.000
24A171LYS10.7970.90515.319-16.087-16.0870.0000.0000.0000.000
25A172HIS10.8260.92617.008-16.659-16.6590.0000.0000.0000.000
26A173PRO00.0970.05014.1200.6650.6650.0000.0000.0000.000
27A174GLU-1-0.866-0.92512.74623.52923.5290.0000.0000.0000.000
28A175ALA0-0.0010.00112.9111.1431.1430.0000.0000.0000.000
29A176ALA0-0.025-0.01312.0020.8830.8830.0000.0000.0000.000
30A177ASN00.0300.0108.3276.2616.2610.0000.0000.0000.000
31A178LEU00.0290.0188.2393.5273.5270.0000.0000.0000.000
32A179LEU0-0.020-0.0129.5581.1531.1530.0000.0000.0000.000
33A180LEU0-0.016-0.0125.695-0.363-0.3630.0000.0000.0000.000
34A181ARG10.8550.9194.431-45.014-44.813-0.001-0.025-0.1750.000
35A182LEU0-0.0500.0006.295-2.525-2.5250.0000.0000.0000.000
36A183ASP-1-0.797-0.9198.43324.88824.8880.0000.0000.0000.000
37A184PHE00.011-0.0169.726-2.084-2.0840.0000.0000.0000.000
38A185GLU-1-0.821-0.89712.99414.03714.0370.0000.0000.0000.000
39A186LYS10.8390.89610.718-24.219-24.2190.0000.0000.0000.000
40A187ASP-1-0.789-0.87310.97422.47122.4710.0000.0000.0000.000
41A188ILE0-0.036-0.00911.725-1.046-1.0460.0000.0000.0000.000
42A189LYS10.8330.90215.529-15.635-15.6350.0000.0000.0000.000
43A190GLN00.000-0.00417.378-1.424-1.4240.0000.0000.0000.000
44A191MET00.0190.02118.866-0.996-0.9960.0000.0000.0000.000
45A192LEU0-0.018-0.01718.276-0.757-0.7570.0000.0000.0000.000
46A193LEU0-0.004-0.00421.612-0.668-0.6680.0000.0000.0000.000
47A194PHE00.0210.01523.880-0.626-0.6260.0000.0000.0000.000
48A195LEU0-0.021-0.01322.345-0.500-0.5000.0000.0000.0000.000
49A196LYS10.8820.92125.804-11.338-11.3380.0000.0000.0000.000
50A197ASP-1-0.872-0.91727.7579.1559.1550.0000.0000.0000.000
51A198VAL0-0.082-0.04128.596-0.448-0.4480.0000.0000.0000.000
52A199GLY00.002-0.00630.470-0.293-0.2930.0000.0000.0000.000
53A200ILE0-0.103-0.04526.403-0.164-0.1640.0000.0000.0000.000
54A201GLU-1-0.831-0.90928.0909.5919.5910.0000.0000.0000.000
55A202ASP-1-0.758-0.87925.72611.64711.6470.0000.0000.0000.000
56A203ASN0-0.016-0.01325.5330.4240.4240.0000.0000.0000.000
57A204GLN0-0.087-0.05927.649-0.016-0.0160.0000.0000.0000.000
58A205LEU00.0190.01122.3280.1820.1820.0000.0000.0000.000
59A206GLY00.0750.06021.6440.4400.4400.0000.0000.0000.000
60A207ALA00.002-0.00322.5670.3200.3200.0000.0000.0000.000
61A208PHE0-0.017-0.01323.099-0.042-0.0420.0000.0000.0000.000
62A209LEU00.012-0.00318.4270.0230.0230.0000.0000.0000.000
63A210THR0-0.0150.00320.1980.7140.7140.0000.0000.0000.000
64A211LYS10.8740.94421.550-11.434-11.4340.0000.0000.0000.000
65A212ASN0-0.054-0.05923.0470.4210.4210.0000.0000.0000.000
66A213HIS00.0360.00518.1880.8520.8520.0000.0000.0000.000
67A214ALA00.0250.01118.0630.8180.8180.0000.0000.0000.000
68A215ILE0-0.015-0.00119.356-0.088-0.0880.0000.0000.0000.000
69A216PHE00.031-0.00315.520-0.299-0.2990.0000.0000.0000.000
70A217SER0-0.0170.00017.2310.7330.7330.0000.0000.0000.000
71A218GLU-1-0.851-0.89518.72111.93711.9370.0000.0000.0000.000
72A219ASP-1-0.783-0.87721.10912.50112.5010.0000.0000.0000.000
73A220LEU00.0600.01522.272-0.553-0.5530.0000.0000.0000.000
74A221GLU-1-0.792-0.88823.97010.59510.5950.0000.0000.0000.000
75A222ASN0-0.027-0.02126.452-0.803-0.8030.0000.0000.0000.000
76A223LEU0-0.035-0.00823.325-0.472-0.4720.0000.0000.0000.000
77A224LYS10.8620.90727.020-11.376-11.3760.0000.0000.0000.000
78A225THR0-0.015-0.00929.985-0.475-0.4750.0000.0000.0000.000
79A226ARG10.7260.84526.899-11.537-11.5370.0000.0000.0000.000
80A227VAL00.0230.01130.891-0.291-0.2910.0000.0000.0000.000
81A228ALA00.0250.01933.505-0.308-0.3080.0000.0000.0000.000
82A229TYR0-0.022-0.04735.734-0.270-0.2700.0000.0000.0000.000
83A230LEU00.0010.00534.404-0.303-0.3030.0000.0000.0000.000
84A231HIS0-0.012-0.02536.661-0.071-0.0710.0000.0000.0000.000
85A232SER0-0.065-0.03139.764-0.264-0.2640.0000.0000.0000.000
86A233LYS10.8180.90541.169-7.542-7.5420.0000.0000.0000.000
87A234ASN0-0.056-0.03743.140-0.136-0.1360.0000.0000.0000.000
88A235PHE0-0.058-0.01339.691-0.126-0.1260.0000.0000.0000.000
89A236SER00.024-0.01440.5490.1340.1340.0000.0000.0000.000
90A237LYS10.9290.93733.610-8.942-8.9420.0000.0000.0000.000
91A238ALA00.0200.02437.0310.2100.2100.0000.0000.0000.000
92A239ASP-1-0.842-0.89938.0847.6377.6370.0000.0000.0000.000
93A240VAL00.015-0.00533.5570.1570.1570.0000.0000.0000.000
94A241ALA00.0800.06633.2520.2620.2620.0000.0000.0000.000
95A242GLN0-0.096-0.04833.3300.2600.2600.0000.0000.0000.000
96A243MET0-0.083-0.06334.8200.1120.1120.0000.0000.0000.000
97A244VAL00.0400.02128.8540.1620.1620.0000.0000.0000.000
98A245ARG10.9921.00729.972-8.971-8.9710.0000.0000.0000.000
99A246LYS10.8330.91030.689-8.202-8.2020.0000.0000.0000.000
100A247ALA0-0.060-0.02531.816-0.042-0.0420.0000.0000.0000.000
101A248PRO00.0390.02226.459-0.011-0.0110.0000.0000.0000.000
102A249PHE0-0.0060.00623.6670.1110.1110.0000.0000.0000.000
103A250LEU0-0.006-0.00128.109-0.052-0.0520.0000.0000.0000.000
104A251LEU00.0180.00827.769-0.211-0.2110.0000.0000.0000.000
105A252ASN00.0400.02923.514-0.086-0.0860.0000.0000.0000.000
106A253PHE0-0.119-0.04327.502-0.050-0.0500.0000.0000.0000.000
107A254SER00.0890.03330.924-0.096-0.0960.0000.0000.0000.000
108A255VAL00.0920.03032.400-0.170-0.1700.0000.0000.0000.000
109A256GLU-1-0.899-0.93735.4348.2598.2590.0000.0000.0000.000
110A257ARG10.9680.98930.265-10.147-10.1470.0000.0000.0000.000
111A258LEU0-0.026-0.00933.220-0.196-0.1960.0000.0000.0000.000
112A259ASP-1-0.775-0.83437.0497.2817.2810.0000.0000.0000.000
113A260ASN0-0.016-0.02239.540-0.350-0.3500.0000.0000.0000.000
114A261ARG10.7780.87535.920-9.022-9.0220.0000.0000.0000.000
115A262LEU00.012-0.00339.985-0.170-0.1700.0000.0000.0000.000
116A263GLY00.0170.01342.463-0.197-0.1970.0000.0000.0000.000
117A264PHE00.001-0.00242.646-0.166-0.1660.0000.0000.0000.000
118A265PHE00.001-0.01340.152-0.149-0.1490.0000.0000.0000.000
119A266GLN0-0.045-0.03445.548-0.128-0.1280.0000.0000.0000.000
120A267LYS10.9620.97848.155-6.370-6.3700.0000.0000.0000.000
121A268GLU-1-0.918-0.96047.2206.5186.5180.0000.0000.0000.000
122A269LEU0-0.044-0.03846.498-0.084-0.0840.0000.0000.0000.000
123A270GLU-1-0.872-0.90850.5865.6765.6760.0000.0000.0000.000
124A271LEU0-0.043-0.00749.162-0.118-0.1180.0000.0000.0000.000
125A272SER00.0370.02052.3570.0120.0120.0000.0000.0000.000
126A273VAL00.1270.05148.8730.1130.1130.0000.0000.0000.000
127A274LYS10.8230.89648.611-6.344-6.3440.0000.0000.0000.000
128A275LYS10.9770.98348.526-5.763-5.7630.0000.0000.0000.000
129A276THR00.0440.02745.5480.1020.1020.0000.0000.0000.000
130A277ARG10.9090.96243.954-6.769-6.7690.0000.0000.0000.000
131A278ASP-1-0.793-0.88543.8576.7726.7720.0000.0000.0000.000
132A279LEU0-0.035-0.01044.6440.1210.1210.0000.0000.0000.000
133A280VAL0-0.012-0.01240.0690.1530.1530.0000.0000.0000.000
134A281VAL00.0690.04439.7110.2560.2560.0000.0000.0000.000
135A282ARG10.9180.97740.129-6.738-6.7380.0000.0000.0000.000
136A283LEU0-0.082-0.04938.6130.1460.1460.0000.0000.0000.000
137A284PRO00.0960.05835.4760.0020.0020.0000.0000.0000.000
138A285ARG10.9250.95134.550-8.445-8.4450.0000.0000.0000.000
139A286LEU0-0.088-0.03735.6490.0720.0720.0000.0000.0000.000
140A287LEU00.0520.01836.402-0.050-0.0500.0000.0000.0000.000
141A288THR00.0080.02731.6380.0740.0740.0000.0000.0000.000
142A289GLY0-0.0230.01132.7140.2670.2670.0000.0000.0000.000
143A290SER00.011-0.01434.847-0.127-0.1270.0000.0000.0000.000
144A291LEU00.0210.00236.695-0.106-0.1060.0000.0000.0000.000
145A292GLU-1-0.899-0.94338.5728.0238.0230.0000.0000.0000.000
146A293PRO00.0620.03139.382-0.190-0.1900.0000.0000.0000.000
147A294VAL0-0.0090.00341.644-0.158-0.1580.0000.0000.0000.000
148A295LYS10.9440.99442.478-7.602-7.6020.0000.0000.0000.000
149A296GLU-1-0.970-0.98643.5357.1667.1660.0000.0000.0000.000
150A297ASN0-0.026-0.03844.703-0.254-0.2540.0000.0000.0000.000
151A298MET0-0.0150.00548.007-0.146-0.1460.0000.0000.0000.000
152A299LYS10.9340.97049.278-6.626-6.6260.0000.0000.0000.000
153A300VAL00.0320.03049.333-0.130-0.1300.0000.0000.0000.000
154A301TYR0-0.007-0.02848.162-0.156-0.1560.0000.0000.0000.000
155A302ARG10.9680.98253.794-5.781-5.7810.0000.0000.0000.000
156A303LEU0-0.070-0.04254.934-0.110-0.1100.0000.0000.0000.000
157A304GLU-1-0.802-0.87252.6396.1326.1320.0000.0000.0000.000
158A305LEU0-0.029-0.01052.897-0.063-0.0630.0000.0000.0000.000
159A306GLY00.0560.05857.187-0.091-0.0910.0000.0000.0000.000
160A307PHE0-0.084-0.03855.803-0.088-0.0880.0000.0000.0000.000
161A308LYS10.9280.93658.691-5.054-5.0540.0000.0000.0000.000
162A309HIS0-0.017-0.03253.7470.0640.0640.0000.0000.0000.000
163A310ASN0-0.001-0.00556.5550.0260.0260.0000.0000.0000.000
164A311GLU-1-0.809-0.89857.6955.3435.3430.0000.0000.0000.000
165A312ILE00.0420.02552.3530.0810.0810.0000.0000.0000.000
166A313GLN00.0180.00452.9130.0270.0270.0000.0000.0000.000
167A314HIS0-0.0270.00153.1600.0530.0530.0000.0000.0000.000
168A315MET0-0.0310.01052.7480.0650.0650.0000.0000.0000.000
169A316ILE00.0370.01748.4040.1240.1240.0000.0000.0000.000
170A317THR0-0.047-0.04048.3510.1270.1270.0000.0000.0000.000
171A318ARG10.8700.95049.110-5.777-5.7770.0000.0000.0000.000
172A319ILE0-0.0290.00046.8390.1390.1390.0000.0000.0000.000
173A320PRO00.0830.04043.6650.0420.0420.0000.0000.0000.000
174A321LYS10.8640.91541.197-7.553-7.5530.0000.0000.0000.000
175A322MET00.0090.01443.5550.0700.0700.0000.0000.0000.000
176A323LEU00.0380.02844.003-0.032-0.0320.0000.0000.0000.000
177A324THR0-0.029-0.01039.7960.1450.1450.0000.0000.0000.000
178A325ALA0-0.0220.01941.5850.1690.1690.0000.0000.0000.000
179A326ASN00.0550.01541.695-0.193-0.1930.0000.0000.0000.000
180A327LYS10.9680.96543.784-6.506-6.5060.0000.0000.0000.000
181A328MET00.0110.02746.155-0.140-0.1400.0000.0000.0000.000
182A329LYS10.9860.98943.202-7.517-7.5170.0000.0000.0000.000
183A330LEU0-0.0180.01047.375-0.127-0.1270.0000.0000.0000.000
184A331THR0-0.007-0.02449.802-0.162-0.1620.0000.0000.0000.000
185A332GLU-1-0.885-0.93549.7876.4496.4490.0000.0000.0000.000
186A333THR0-0.050-0.04550.631-0.091-0.0910.0000.0000.0000.000
187A334PHE0-0.021-0.02153.291-0.112-0.1120.0000.0000.0000.000
188A335ASP-1-0.855-0.90155.7135.4295.4290.0000.0000.0000.000
189A336PHE00.0430.01856.399-0.106-0.1060.0000.0000.0000.000
190A337VAL00.012-0.01656.145-0.099-0.0990.0000.0000.0000.000
191A338HIS0-0.081-0.06158.983-0.135-0.1350.0000.0000.0000.000
192A339ASN0-0.033-0.03560.621-0.159-0.1590.0000.0000.0000.000
193A340VAL0-0.0160.00260.482-0.079-0.0790.0000.0000.0000.000
194A341MET0-0.100-0.03859.767-0.017-0.0170.0000.0000.0000.000
195A342SER00.0140.02263.312-0.089-0.0890.0000.0000.0000.000
196A343ILE0-0.0110.00461.144-0.067-0.0670.0000.0000.0000.000
197A344PRO00.0090.01862.8560.0650.0650.0000.0000.0000.000
198A345HIS10.9130.92159.958-5.250-5.2500.0000.0000.0000.000
199A346HIS00.0390.01261.0160.1220.1220.0000.0000.0000.000
200A347ILE00.004-0.00261.9510.0400.0400.0000.0000.0000.000
201A348ILE00.0440.02356.6850.0860.0860.0000.0000.0000.000
202A349VAL0-0.034-0.02857.3210.1070.1070.0000.0000.0000.000
203A350LYS10.9400.96357.315-4.980-4.9800.0000.0000.0000.000
204A351PHE0-0.0190.00456.6080.0290.0290.0000.0000.0000.000
205A352PRO00.0700.03752.1840.0520.0520.0000.0000.0000.000
206A353GLN00.0650.00350.7800.1370.1370.0000.0000.0000.000
207A354VAL00.0290.03151.0750.1160.1160.0000.0000.0000.000
208A355PHE0-0.014-0.01649.5380.0530.0530.0000.0000.0000.000
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210A357THR00.0050.01047.1500.1070.1070.0000.0000.0000.000
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