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: 49LLN

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 OptH
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 -3576152.016412
FMO2-HF: Nuclear repulsion 3466851.881486
FMO2-HF: Total energy -109300.134926
FMO2-MP2: Total energy -109622.514043


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.
-61.934-58.3970.133-1.453-2.2180.006
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 : -0.898 / 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].
3A150VAL0-0.009-0.0223.650-12.610-10.1830.002-1.147-1.2820.006
4A151ASP-1-0.880-0.9322.88432.59333.4060.132-0.194-0.7510.000
5A152HIS0-0.042-0.0014.124-3.700-3.403-0.001-0.112-0.1850.000
6A153SER00.0350.0105.871-4.086-4.0860.0000.0000.0000.000
7A154GLU-1-0.926-0.9608.59620.28420.2840.0000.0000.0000.000
8A155THR0-0.024-0.0118.961-3.246-3.2460.0000.0000.0000.000
9A156LEU00.0030.0059.472-2.156-2.1560.0000.0000.0000.000
10A157GLN00.0270.00211.248-2.349-2.3490.0000.0000.0000.000
11A158LYS10.9550.98413.970-19.259-19.2590.0000.0000.0000.000
12A159LEU0-0.024-0.01212.132-1.354-1.3540.0000.0000.0000.000
13A160VAL00.011-0.00414.914-1.094-1.0940.0000.0000.0000.000
14A161LEU0-0.017-0.00317.288-1.071-1.0710.0000.0000.0000.000
15A162LEU0-0.059-0.02018.264-0.876-0.8760.0000.0000.0000.000
16A163GLY0-0.019-0.00520.448-0.681-0.6810.0000.0000.0000.000
17A164VAL0-0.072-0.03516.656-0.460-0.4600.0000.0000.0000.000
18A165ASP-1-0.809-0.88818.51815.49315.4930.0000.0000.0000.000
19A166LEU00.0570.00912.755-0.307-0.3070.0000.0000.0000.000
20A167SER00.0140.01316.1530.1560.1560.0000.0000.0000.000
21A168LYS10.7760.87118.236-14.041-14.0410.0000.0000.0000.000
22A169ILE00.0020.00514.823-0.366-0.3660.0000.0000.0000.000
23A170GLU-1-0.842-0.93613.27122.73922.7390.0000.0000.0000.000
24A171LYS10.8450.93415.708-15.016-15.0160.0000.0000.0000.000
25A172HIS10.8180.92117.370-16.262-16.2620.0000.0000.0000.000
26A173PRO00.0990.04914.4210.6110.6110.0000.0000.0000.000
27A174GLU-1-0.871-0.92213.03423.30623.3060.0000.0000.0000.000
28A175ALA0-0.006-0.00113.1951.0711.0710.0000.0000.0000.000
29A176ALA0-0.018-0.01112.3170.7890.7890.0000.0000.0000.000
30A177ASN00.0220.0008.5775.6555.6550.0000.0000.0000.000
31A178LEU00.0360.0208.5453.3403.3400.0000.0000.0000.000
32A179LEU0-0.014-0.0099.4591.0791.0790.0000.0000.0000.000
33A180LEU0-0.023-0.0196.028-0.401-0.4010.0000.0000.0000.000
34A181ARG10.8480.9204.974-40.773-40.7730.0000.0000.0000.000
35A182LEU0-0.058-0.0086.228-2.247-2.2470.0000.0000.0000.000
36A183ASP-1-0.803-0.9158.35224.58824.5880.0000.0000.0000.000
37A184PHE00.001-0.0269.706-2.106-2.1060.0000.0000.0000.000
38A185GLU-1-0.903-0.95912.93714.30314.3030.0000.0000.0000.000
39A186LYS10.8450.90811.420-22.734-22.7340.0000.0000.0000.000
40A187ASP-1-0.810-0.88710.95121.98521.9850.0000.0000.0000.000
41A188ILE0-0.0210.00011.910-1.012-1.0120.0000.0000.0000.000
42A189LYS10.9430.97315.466-15.045-15.0450.0000.0000.0000.000
43A190GLN0-0.008-0.00717.834-1.311-1.3110.0000.0000.0000.000
44A191MET00.0270.02718.765-0.958-0.9580.0000.0000.0000.000
45A192LEU0-0.024-0.01918.073-0.739-0.7390.0000.0000.0000.000
46A193LEU0-0.014-0.01021.522-0.626-0.6260.0000.0000.0000.000
47A194PHE00.0240.02123.819-0.593-0.5930.0000.0000.0000.000
48A195LEU0-0.021-0.01422.318-0.476-0.4760.0000.0000.0000.000
49A196LYS10.9030.93725.712-11.109-11.1090.0000.0000.0000.000
50A197ASP-1-0.953-0.96127.6609.2729.2720.0000.0000.0000.000
51A198VAL0-0.108-0.04928.583-0.396-0.3960.0000.0000.0000.000
52A199GLY0-0.007-0.01230.418-0.286-0.2860.0000.0000.0000.000
53A200ILE0-0.122-0.05026.145-0.155-0.1550.0000.0000.0000.000
54A201GLU-1-0.886-0.95827.9649.4779.4770.0000.0000.0000.000
55A202ASP-1-0.779-0.89425.67611.57511.5750.0000.0000.0000.000
56A203ASN0-0.029-0.02025.3750.4000.4000.0000.0000.0000.000
57A204GLN0-0.041-0.01927.4910.0040.0040.0000.0000.0000.000
58A205LEU00.0270.01421.9860.1580.1580.0000.0000.0000.000
59A206GLY00.0680.05821.4530.4150.4150.0000.0000.0000.000
60A207ALA00.003-0.00522.3670.2940.2940.0000.0000.0000.000
61A208PHE0-0.023-0.01222.974-0.055-0.0550.0000.0000.0000.000
62A209LEU00.0200.00018.2930.0130.0130.0000.0000.0000.000
63A210THR0-0.0070.01320.0110.6850.6850.0000.0000.0000.000
64A211LYS10.8600.94121.344-11.297-11.2970.0000.0000.0000.000
65A212ASN0-0.046-0.05622.9020.3940.3940.0000.0000.0000.000
66A213HIS00.0500.00918.4560.7480.7480.0000.0000.0000.000
67A214ALA00.0100.00318.1240.7460.7460.0000.0000.0000.000
68A215ILE0-0.0110.00219.173-0.062-0.0620.0000.0000.0000.000
69A216PHE00.031-0.00615.458-0.286-0.2860.0000.0000.0000.000
70A217SER0-0.022-0.00117.1700.7100.7100.0000.0000.0000.000
71A218GLU-1-0.916-0.94018.64911.90511.9050.0000.0000.0000.000
72A219ASP-1-0.836-0.92321.06412.64012.6400.0000.0000.0000.000
73A220LEU00.0700.01221.982-0.550-0.5500.0000.0000.0000.000
74A221GLU-1-0.815-0.90523.94410.40710.4070.0000.0000.0000.000
75A222ASN0-0.0030.00126.440-0.799-0.7990.0000.0000.0000.000
76A223LEU0-0.044-0.01723.305-0.486-0.4860.0000.0000.0000.000
77A224LYS10.8740.93027.160-11.209-11.2090.0000.0000.0000.000
78A225THR0-0.0050.00129.945-0.482-0.4820.0000.0000.0000.000
79A226ARG10.7780.88426.897-11.325-11.3250.0000.0000.0000.000
80A227VAL00.0250.01530.786-0.301-0.3010.0000.0000.0000.000
81A228ALA00.0180.01633.434-0.309-0.3090.0000.0000.0000.000
82A229TYR0-0.026-0.04235.680-0.267-0.2670.0000.0000.0000.000
83A230LEU00.0060.00534.438-0.300-0.3000.0000.0000.0000.000
84A231HIS0-0.028-0.03336.509-0.074-0.0740.0000.0000.0000.000
85A232SER0-0.065-0.03039.691-0.266-0.2660.0000.0000.0000.000
86A233LYS10.8910.95641.207-7.364-7.3640.0000.0000.0000.000
87A234ASN0-0.061-0.03943.059-0.090-0.0900.0000.0000.0000.000
88A235PHE0-0.049-0.00939.555-0.108-0.1080.0000.0000.0000.000
89A236SER00.0290.01940.4580.1440.1440.0000.0000.0000.000
90A237LYS11.0481.00036.925-8.040-8.0400.0000.0000.0000.000
91A238ALA00.0400.03036.9230.1960.1960.0000.0000.0000.000
92A239ASP-1-0.860-0.93537.9557.5617.5610.0000.0000.0000.000
93A240VAL00.013-0.00733.5090.1450.1450.0000.0000.0000.000
94A241ALA00.0870.06533.1280.2490.2490.0000.0000.0000.000
95A242GLN0-0.100-0.04833.1900.2320.2320.0000.0000.0000.000
96A243MET0-0.082-0.06334.6650.1100.1100.0000.0000.0000.000
97A244VAL00.0500.02728.7610.1510.1510.0000.0000.0000.000
98A245ARG11.0131.01529.821-8.902-8.9020.0000.0000.0000.000
99A246LYS10.8450.91730.516-8.186-8.1860.0000.0000.0000.000
100A247ALA0-0.056-0.02031.659-0.043-0.0430.0000.0000.0000.000
101A248PRO00.0470.02526.303-0.012-0.0120.0000.0000.0000.000
102A249PHE0-0.014-0.00424.0400.1330.1330.0000.0000.0000.000
103A250LEU0-0.0030.00027.991-0.037-0.0370.0000.0000.0000.000
104A251LEU00.0180.00427.631-0.209-0.2090.0000.0000.0000.000
105A252ASN00.0820.05423.7410.0150.0150.0000.0000.0000.000
106A253PHE0-0.113-0.03927.400-0.036-0.0360.0000.0000.0000.000
107A254SER00.0620.02030.913-0.094-0.0940.0000.0000.0000.000
108A255VAL00.0970.03532.341-0.144-0.1440.0000.0000.0000.000
109A256GLU-1-0.905-0.94135.3738.1158.1150.0000.0000.0000.000
110A257ARG10.9520.96930.561-9.952-9.9520.0000.0000.0000.000
111A258LEU0-0.033-0.01633.243-0.182-0.1820.0000.0000.0000.000
112A259ASP-1-0.821-0.87536.9547.2707.2700.0000.0000.0000.000
113A260ASN00.0260.00539.754-0.328-0.3280.0000.0000.0000.000
114A261ARG10.7830.88035.853-8.968-8.9680.0000.0000.0000.000
115A262LEU00.009-0.00140.003-0.175-0.1750.0000.0000.0000.000
116A263GLY00.0190.01442.372-0.197-0.1970.0000.0000.0000.000
117A264PHE0-0.007-0.00743.055-0.170-0.1700.0000.0000.0000.000
118A265PHE00.000-0.01740.407-0.143-0.1430.0000.0000.0000.000
119A266GLN0-0.066-0.05145.610-0.133-0.1330.0000.0000.0000.000
120A267LYS10.9580.97348.236-6.381-6.3810.0000.0000.0000.000
121A268GLU-1-0.927-0.95747.4776.4296.4290.0000.0000.0000.000
122A269LEU0-0.033-0.02946.640-0.078-0.0780.0000.0000.0000.000
123A270GLU-1-0.925-0.93850.6895.6275.6270.0000.0000.0000.000
124A271LEU0-0.044-0.00748.926-0.116-0.1160.0000.0000.0000.000
125A272SER00.0430.03052.2310.0170.0170.0000.0000.0000.000
126A273VAL00.1240.05348.8020.1140.1140.0000.0000.0000.000
127A274LYS10.8560.92048.454-6.260-6.2600.0000.0000.0000.000
128A275LYS10.9780.98148.397-5.720-5.7200.0000.0000.0000.000
129A276THR00.0510.02945.4170.0950.0950.0000.0000.0000.000
130A277ARG10.9550.98643.929-6.656-6.6560.0000.0000.0000.000
131A278ASP-1-0.835-0.91143.7216.7176.7170.0000.0000.0000.000
132A279LEU0-0.037-0.01344.2260.1220.1220.0000.0000.0000.000
133A280VAL0-0.016-0.01539.9020.1500.1500.0000.0000.0000.000
134A281VAL00.0730.04639.5620.2490.2490.0000.0000.0000.000
135A282ARG10.9380.98639.972-6.723-6.7230.0000.0000.0000.000
136A283LEU0-0.105-0.06238.4910.1430.1430.0000.0000.0000.000
137A284PRO00.0920.05335.2870.0150.0150.0000.0000.0000.000
138A285ARG10.9300.95434.487-8.356-8.3560.0000.0000.0000.000
139A286LEU0-0.072-0.02635.6000.0740.0740.0000.0000.0000.000
140A287LEU00.0440.01536.123-0.046-0.0460.0000.0000.0000.000
141A288THR0-0.0020.01431.5300.0750.0750.0000.0000.0000.000
142A289GLY0-0.0240.01132.9960.2650.2650.0000.0000.0000.000
143A290SER00.0440.01835.184-0.133-0.1330.0000.0000.0000.000
144A291LEU00.0280.00337.033-0.096-0.0960.0000.0000.0000.000
145A292GLU-1-0.962-0.97739.5707.8377.8370.0000.0000.0000.000
146A293PRO00.0400.02439.699-0.187-0.1870.0000.0000.0000.000
147A294VAL0-0.0110.00142.048-0.156-0.1560.0000.0000.0000.000
148A295LYS10.9620.99043.093-7.490-7.4900.0000.0000.0000.000
149A296GLU-1-0.944-0.97543.9937.1357.1350.0000.0000.0000.000
150A297ASN0-0.032-0.03745.305-0.211-0.2110.0000.0000.0000.000
151A298MET0-0.0090.01048.367-0.139-0.1390.0000.0000.0000.000
152A299LYS10.9290.96450.176-6.505-6.5050.0000.0000.0000.000
153A300VAL00.0360.03149.742-0.125-0.1250.0000.0000.0000.000
154A301TYR0-0.003-0.02548.471-0.148-0.1480.0000.0000.0000.000
155A302ARG10.9790.98654.165-5.754-5.7540.0000.0000.0000.000
156A303LEU0-0.075-0.04955.329-0.109-0.1090.0000.0000.0000.000
157A304GLU-1-0.877-0.92553.2536.0646.0640.0000.0000.0000.000
158A305LEU0-0.025-0.01153.493-0.065-0.0650.0000.0000.0000.000
159A306GLY00.0240.04657.558-0.091-0.0910.0000.0000.0000.000
160A307PHE0-0.081-0.03056.164-0.087-0.0870.0000.0000.0000.000
161A308LYS10.9870.97159.062-4.928-4.9280.0000.0000.0000.000
162A309HIS00.0510.01153.7500.0500.0500.0000.0000.0000.000
163A310ASN00.0330.00656.7010.1380.1380.0000.0000.0000.000
164A311GLU-1-0.875-0.93557.7215.3285.3280.0000.0000.0000.000
165A312ILE00.0340.02052.5990.0810.0810.0000.0000.0000.000
166A313GLN0-0.005-0.01352.9290.0430.0430.0000.0000.0000.000
167A314HIS0-0.018-0.00453.0930.0550.0550.0000.0000.0000.000
168A315MET0-0.0330.00452.8520.0630.0630.0000.0000.0000.000
169A316ILE00.0290.01948.5130.1230.1230.0000.0000.0000.000
170A317THR0-0.063-0.03848.2710.1280.1280.0000.0000.0000.000
171A318ARG10.8880.95848.938-5.747-5.7470.0000.0000.0000.000
172A319ILE0-0.0410.00046.7360.1390.1390.0000.0000.0000.000
173A320PRO00.0700.03143.5640.0520.0520.0000.0000.0000.000
174A321LYS10.9220.94840.129-7.756-7.7560.0000.0000.0000.000
175A322MET00.0340.02943.6420.0750.0750.0000.0000.0000.000
176A323LEU00.0390.02744.155-0.028-0.0280.0000.0000.0000.000
177A324THR0-0.058-0.02640.1380.1460.1460.0000.0000.0000.000
178A325ALA0-0.0150.02241.9680.1610.1610.0000.0000.0000.000
179A326ASN00.0560.01742.334-0.170-0.1700.0000.0000.0000.000
180A327LYS11.0271.01444.163-6.494-6.4940.0000.0000.0000.000
181A328MET00.0020.01746.094-0.130-0.1300.0000.0000.0000.000
182A329LYS10.9850.98743.164-7.494-7.4940.0000.0000.0000.000
183A330LEU0-0.0150.00347.632-0.119-0.1190.0000.0000.0000.000
184A331THR00.019-0.00150.191-0.162-0.1620.0000.0000.0000.000
185A332GLU-1-0.898-0.94850.2776.3836.3830.0000.0000.0000.000
186A333THR0-0.034-0.01951.118-0.096-0.0960.0000.0000.0000.000
187A334PHE0-0.019-0.02253.692-0.108-0.1080.0000.0000.0000.000
188A335ASP-1-0.858-0.90956.1085.3795.3790.0000.0000.0000.000
189A336PHE00.0370.01656.815-0.102-0.1020.0000.0000.0000.000
190A337VAL00.017-0.01456.426-0.098-0.0980.0000.0000.0000.000
191A338HIS0-0.113-0.07259.362-0.139-0.1390.0000.0000.0000.000
192A339ASN0-0.036-0.03360.896-0.168-0.1680.0000.0000.0000.000
193A340VAL0-0.0180.00561.043-0.076-0.0760.0000.0000.0000.000
194A341MET0-0.103-0.04360.158-0.017-0.0170.0000.0000.0000.000
195A342SER00.0120.02263.693-0.088-0.0880.0000.0000.0000.000
196A343ILE0-0.0130.00361.355-0.068-0.0680.0000.0000.0000.000
197A344PRO00.0440.02563.1750.0680.0680.0000.0000.0000.000
198A345HIS10.9170.92059.905-5.229-5.2290.0000.0000.0000.000
199A346HIS00.0500.02161.1930.0960.0960.0000.0000.0000.000
200A347ILE0-0.007-0.00562.0320.0350.0350.0000.0000.0000.000
201A348ILE00.0410.01956.9630.0810.0810.0000.0000.0000.000
202A349VAL0-0.029-0.02657.3990.1090.1090.0000.0000.0000.000
203A350LYS10.9400.96557.292-4.938-4.9380.0000.0000.0000.000
204A351PHE0-0.038-0.00356.5270.0280.0280.0000.0000.0000.000
205A352PRO00.0690.03452.1640.0530.0530.0000.0000.0000.000
206A353GLN00.0680.00950.7570.1600.1600.0000.0000.0000.000
207A354VAL00.0350.03951.1210.1110.1110.0000.0000.0000.000
208A355PHE0-0.035-0.02949.7250.0500.0500.0000.0000.0000.000
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210A357THR0-0.0030.00247.2090.0920.0920.0000.0000.0000.000
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