Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QV1MY

Calculation Name: 1EF7-A-Xray372

Preferred Name: Cathepsin Z

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1EF7

Chain ID: A

ChEMBL ID: CHEMBL4160

UniProt ID: Q9UBR2

Base Structure: X-ray

Registration Date: 2023-09-21

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3112954.612137
FMO2-HF: Nuclear repulsion 3015077.766348
FMO2-HF: Total energy -97876.845789
FMO2-MP2: Total energy -98154.830489


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-2.6881.6577.872-2.583-9.634-0.01
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.024
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].
3A3LYS10.9610.9623.4980.2762.4510.007-1.096-1.0860.004
4A4SER0-0.017-0.0116.0300.4750.4750.0000.0000.0000.000
5A5TRP00.0210.0185.627-0.191-0.1910.0000.0000.0000.000
6A6ASP-1-0.712-0.8517.595-0.253-0.2530.0000.0000.0000.000
7A7TRP00.0320.0278.417-0.001-0.0010.0000.0000.0000.000
8A8ARG10.8440.90712.2290.2910.2910.0000.0000.0000.000
9A9ASN0-0.095-0.06413.9430.0370.0370.0000.0000.0000.000
10A10VAL00.0250.03111.254-0.063-0.0630.0000.0000.0000.000
11A11ASP-1-0.926-0.95913.527-0.198-0.1980.0000.0000.0000.000
12A12GLY0-0.036-0.02515.6020.0330.0330.0000.0000.0000.000
13A13VAL0-0.048-0.01416.8460.0200.0200.0000.0000.0000.000
14A14ASN00.0380.02916.331-0.029-0.0290.0000.0000.0000.000
15A15TYR0-0.004-0.01214.7600.0400.0400.0000.0000.0000.000
16A16ALA0-0.035-0.00516.8240.0220.0220.0000.0000.0000.000
17A17SER0-0.018-0.01718.085-0.001-0.0010.0000.0000.0000.000
18A18ILE0-0.007-0.00821.369-0.013-0.0130.0000.0000.0000.000
19A19THR00.0150.00823.3350.0040.0040.0000.0000.0000.000
20A20ARG10.8770.94924.2410.0140.0140.0000.0000.0000.000
21A21ASN00.025-0.01426.351-0.005-0.0050.0000.0000.0000.000
22A22GLN00.0330.03026.5520.0010.0010.0000.0000.0000.000
23A23HIS0-0.0230.00429.3200.0060.0060.0000.0000.0000.000
24A24ILE00.0010.00232.482-0.001-0.0010.0000.0000.0000.000
25A25PRO00.000-0.00834.1330.0000.0000.0000.0000.0000.000
26A26GLN0-0.046-0.00836.6190.0010.0010.0000.0000.0000.000
27A27TYR00.0230.00832.077-0.002-0.0020.0000.0000.0000.000
28A28CYS0-0.0370.00331.6390.0020.0020.0000.0000.0000.000
29A29GLY00.0280.03030.143-0.004-0.0040.0000.0000.0000.000
30A30SER00.0470.01128.5910.0040.0040.0000.0000.0000.000
31A31CYS0-0.0240.00123.9830.0030.0030.0000.0000.0000.000
32A32TRP00.0230.02123.1930.0010.0010.0000.0000.0000.000
33A33ALA00.0520.03923.4180.0080.0080.0000.0000.0000.000
34A34HIS0-0.0200.00323.935-0.001-0.0010.0000.0000.0000.000
35A35ALA00.0120.00718.805-0.003-0.0030.0000.0000.0000.000
36A36SER00.0220.00518.9080.0010.0010.0000.0000.0000.000
37A37THR0-0.004-0.03119.7690.0040.0040.0000.0000.0000.000
38A38SER0-0.005-0.00419.835-0.002-0.0020.0000.0000.0000.000
39A39ALA00.0080.01215.441-0.005-0.0050.0000.0000.0000.000
40A40MET0-0.0130.00616.6500.0120.0120.0000.0000.0000.000
41A41ALA0-0.003-0.00218.9070.0090.0090.0000.0000.0000.000
42A42ASP-1-0.768-0.87915.638-0.040-0.0400.0000.0000.0000.000
43A43ARG10.8040.90210.940-0.198-0.1980.0000.0000.0000.000
44A44ILE0-0.037-0.01116.0530.0170.0170.0000.0000.0000.000
45A45ASN0-0.009-0.00118.0310.0130.0130.0000.0000.0000.000
46A46ILE00.0050.00211.814-0.002-0.0020.0000.0000.0000.000
47A47LYS10.8380.92215.510-0.195-0.1950.0000.0000.0000.000
48A48ARG10.7930.90217.441-0.035-0.0350.0000.0000.0000.000
49A49LYS10.9280.95217.351-0.119-0.1190.0000.0000.0000.000
50A50GLY00.0320.03018.912-0.015-0.0150.0000.0000.0000.000
51A51ALA0-0.048-0.00720.504-0.009-0.0090.0000.0000.0000.000
52A52TRP00.0120.03123.9760.0020.0020.0000.0000.0000.000
53A53PRO0-0.039-0.03326.7800.0070.0070.0000.0000.0000.000
54A54SER00.0330.00723.2500.0070.0070.0000.0000.0000.000
55A55THR0-0.014-0.03222.2450.0040.0040.0000.0000.0000.000
56A56LEU00.003-0.00223.667-0.007-0.0070.0000.0000.0000.000
57A57LEU0-0.0070.01123.2480.0030.0030.0000.0000.0000.000
58A58SER00.007-0.00326.861-0.005-0.0050.0000.0000.0000.000
59A59VAL00.0050.00326.4530.0040.0040.0000.0000.0000.000
60A60GLN0-0.0100.00028.792-0.001-0.0010.0000.0000.0000.000
61A61ASN00.0290.02831.4470.0060.0060.0000.0000.0000.000
62A62VAL0-0.0010.00426.8500.0030.0030.0000.0000.0000.000
63A63ILE0-0.058-0.04030.1200.0020.0020.0000.0000.0000.000
64A64ASP-1-0.740-0.85731.9980.0180.0180.0000.0000.0000.000
65A65CYS0-0.089-0.06834.0050.0000.0000.0000.0000.0000.000
66A66GLY00.0460.02530.5000.0040.0040.0000.0000.0000.000
67A67ASN0-0.076-0.03330.6040.0010.0010.0000.0000.0000.000
68A68ALA00.0380.01127.4580.0040.0040.0000.0000.0000.000
69A69GLY0-0.013-0.01728.6990.0000.0000.0000.0000.0000.000
70A70SER00.0180.01131.029-0.001-0.0010.0000.0000.0000.000
71A72GLU-1-0.909-0.95333.2190.0040.0040.0000.0000.0000.000
72A73GLY0-0.051-0.01629.740-0.001-0.0010.0000.0000.0000.000
73A74GLY00.002-0.01028.2460.0020.0020.0000.0000.0000.000
74A75ASN0-0.0070.00323.3460.0040.0040.0000.0000.0000.000
75A76ASP-1-0.733-0.88119.2760.0630.0630.0000.0000.0000.000
76A77LEU0-0.013-0.01519.3290.0060.0060.0000.0000.0000.000
77A78SER0-0.0100.00121.8600.0060.0060.0000.0000.0000.000
78A79VAL0-0.0200.00523.163-0.001-0.0010.0000.0000.0000.000
79A80TRP00.0000.01016.8990.0060.0060.0000.0000.0000.000
80A81ASP-1-0.830-0.85421.9510.1030.1030.0000.0000.0000.000
81A82TYR00.0190.00224.6480.0010.0010.0000.0000.0000.000
82A83ALA0-0.037-0.02523.229-0.003-0.0030.0000.0000.0000.000
83A84HIS0-0.089-0.05322.869-0.005-0.0050.0000.0000.0000.000
84A85GLN0-0.040-0.01425.068-0.006-0.0060.0000.0000.0000.000
85A86HIS0-0.082-0.03028.706-0.005-0.0050.0000.0000.0000.000
86A87GLY00.0050.00227.3110.0000.0000.0000.0000.0000.000
87A88ILE0-0.0020.00124.717-0.005-0.0050.0000.0000.0000.000
88A89PRO00.0140.01228.3010.0020.0020.0000.0000.0000.000
89A90ASP-1-0.836-0.88929.1080.0110.0110.0000.0000.0000.000
90A91GLU-1-0.780-0.92129.3140.0000.0000.0000.0000.0000.000
91A92THR0-0.092-0.08031.0100.0000.0000.0000.0000.0000.000
92A93CYS0-0.140-0.06833.6780.0010.0010.0000.0000.0000.000
93A94ASN0-0.041-0.03134.347-0.002-0.0020.0000.0000.0000.000
94A95ASN00.0560.04433.7660.0010.0010.0000.0000.0000.000
95A96TYR0-0.062-0.03231.2000.0000.0000.0000.0000.0000.000
96A97GLN0-0.009-0.01633.631-0.004-0.0040.0000.0000.0000.000
97A98ALA0-0.047-0.01733.953-0.001-0.0010.0000.0000.0000.000
98A99LYS10.9530.97434.891-0.004-0.0040.0000.0000.0000.000
99A100ASP-1-0.768-0.89236.0070.0130.0130.0000.0000.0000.000
100A101GLN0-0.143-0.09137.720-0.004-0.0040.0000.0000.0000.000
101A102GLU-1-0.915-0.94438.8530.0230.0230.0000.0000.0000.000
102A104ASP-1-0.849-0.92339.5040.0210.0210.0000.0000.0000.000
103A105LYS10.9270.93240.383-0.034-0.0340.0000.0000.0000.000
104A106PHE0-0.022-0.00940.5070.0010.0010.0000.0000.0000.000
105A107ASN00.0040.01538.088-0.002-0.0020.0000.0000.0000.000
106A108GLN0-0.085-0.05135.4620.0010.0010.0000.0000.0000.000
107A110GLY00.0540.04737.9150.0010.0010.0000.0000.0000.000
108A111THR0-0.064-0.02340.268-0.002-0.0020.0000.0000.0000.000
109A112CYS00.0740.03342.8490.0000.0000.0000.0000.0000.000
110A113ASN0-0.020-0.01346.0110.0000.0000.0000.0000.0000.000
111A114GLU-1-0.900-0.97447.2230.0020.0020.0000.0000.0000.000
112A115PHE00.0000.00850.1780.0000.0000.0000.0000.0000.000
113A116LYS10.9020.96751.681-0.006-0.0060.0000.0000.0000.000
114A117GLU-1-0.974-0.99249.0450.0110.0110.0000.0000.0000.000
115A119HIS0-0.052-0.00146.2250.0020.0020.0000.0000.0000.000
116A120ALA00.0560.01442.4100.0000.0000.0000.0000.0000.000
117A121ILE0-0.037-0.01039.5250.0000.0000.0000.0000.0000.000
118A122ARG10.9410.94940.453-0.023-0.0230.0000.0000.0000.000
119A123ASN0-0.064-0.04038.1130.0050.0050.0000.0000.0000.000
120A124TYR00.0310.01833.983-0.003-0.0030.0000.0000.0000.000
121A125THR00.000-0.00329.5120.0030.0030.0000.0000.0000.000
122A126LEU0-0.0090.00730.308-0.003-0.0030.0000.0000.0000.000
123A127TRP0-0.017-0.00924.1700.0080.0080.0000.0000.0000.000
124A128ARG10.9490.96625.158-0.084-0.0840.0000.0000.0000.000
125A129VAL0-0.003-0.00319.4270.0030.0030.0000.0000.0000.000
126A130GLY0-0.0200.00420.386-0.007-0.0070.0000.0000.0000.000
127A131ASP-1-0.853-0.92317.0460.2520.2520.0000.0000.0000.000
128A132TYR0-0.088-0.11717.064-0.002-0.0020.0000.0000.0000.000
129A133GLY0-0.0110.01316.4510.0030.0030.0000.0000.0000.000
130A134SER00.004-0.00715.265-0.022-0.0220.0000.0000.0000.000
131A135LEU0-0.070-0.0258.7610.0490.0490.0000.0000.0000.000
132A136SER00.0020.00411.874-0.032-0.0320.0000.0000.0000.000
133A137GLY00.0440.02610.8920.0530.0530.0000.0000.0000.000
134A138ARG10.7820.8516.1590.5280.5280.0000.0000.0000.000
135A139GLU-1-0.830-0.9104.8680.0910.0910.0000.0000.0000.000
136A140LYS10.9500.9794.435-0.422-0.254-0.001-0.012-0.1550.000
137A141MET00.0030.0205.7600.0580.0580.0000.0000.0000.000
138A142MET0-0.035-0.0182.208-1.103-0.4632.221-0.648-2.2140.001
139A143ALA0-0.028-0.0211.986-1.894-1.1354.646-2.920-2.485-0.002
140A144GLU-1-0.793-0.9082.7643.5610.4160.1373.288-0.280-0.002
141A145ILE0-0.025-0.0175.956-0.058-0.0580.0000.0000.0000.000
142A146TYR0-0.067-0.0363.010-2.442-0.0160.640-0.812-2.254-0.009
143A147ALA0-0.034-0.0024.9430.0270.103-0.001-0.003-0.0710.000
144A148ASN0-0.029-0.0116.723-0.055-0.0550.0000.0000.0000.000
145A149GLY00.0310.0159.309-0.052-0.0520.0000.0000.0000.000
146A150PRO0-0.090-0.03810.3940.0180.0180.0000.0000.0000.000
147A151ILE00.0220.0259.1320.0410.0410.0000.0000.0000.000
148A152SER0-0.037-0.02412.706-0.046-0.0460.0000.0000.0000.000
149A153CYS0-0.0210.00812.623-0.005-0.0050.0000.0000.0000.000
150A154GLY00.0620.04415.805-0.012-0.0120.0000.0000.0000.000
151A155ILE0-0.012-0.01317.753-0.011-0.0110.0000.0000.0000.000
152A156MET0-0.0060.03520.0710.0070.0070.0000.0000.0000.000
153A157ALA0-0.002-0.02223.339-0.011-0.0110.0000.0000.0000.000
154A158THR0-0.021-0.03325.2260.0050.0050.0000.0000.0000.000
155A159GLU-1-0.889-0.95927.666-0.045-0.0450.0000.0000.0000.000
156A160ARG10.8540.93324.9160.1010.1010.0000.0000.0000.000
157A161LEU0-0.015-0.00222.276-0.006-0.0060.0000.0000.0000.000
158A162ALA00.0360.00525.936-0.005-0.0050.0000.0000.0000.000
159A163ASN00.0030.00128.4920.0020.0020.0000.0000.0000.000
160A164TYR0-0.091-0.04521.120-0.003-0.0030.0000.0000.0000.000
161A165THR0-0.013-0.01426.7320.0020.0020.0000.0000.0000.000
162A166GLY00.0280.01223.783-0.002-0.0020.0000.0000.0000.000
163A167GLY0-0.057-0.01822.1470.0050.0050.0000.0000.0000.000
164A168ILE0-0.033-0.01316.6180.0010.0010.0000.0000.0000.000
165A169TYR00.017-0.00919.6660.0100.0100.0000.0000.0000.000
166A170ALA00.006-0.01119.343-0.013-0.0130.0000.0000.0000.000
167A171GLU-1-0.830-0.88921.431-0.065-0.0650.0000.0000.0000.000
168A172TYR0-0.061-0.02423.5870.0030.0030.0000.0000.0000.000
169A173GLN00.0320.00924.6830.0100.0100.0000.0000.0000.000
170A174ASP-1-1.017-1.00625.253-0.024-0.0240.0000.0000.0000.000
171A175THR00.0070.00726.8690.0080.0080.0000.0000.0000.000
172A176THR0-0.016-0.02322.215-0.006-0.0060.0000.0000.0000.000
173A177TYR0-0.006-0.01924.6980.0060.0060.0000.0000.0000.000
174A178ILE0-0.0020.00519.879-0.007-0.0070.0000.0000.0000.000
175A179ASN0-0.018-0.00323.5090.0020.0020.0000.0000.0000.000
176A180HIS0-0.012-0.00122.5090.0050.0050.0000.0000.0000.000
177A181VAL00.0190.00919.0250.0040.0040.0000.0000.0000.000
178A182VAL0-0.0320.00116.759-0.008-0.0080.0000.0000.0000.000
179A183SER0-0.008-0.00214.9340.0090.0090.0000.0000.0000.000
180A184VAL00.000-0.00610.003-0.029-0.0290.0000.0000.0000.000
181A185ALA0-0.004-0.01511.1310.0320.0320.0000.0000.0000.000
182A186GLY00.0560.0168.136-0.014-0.0140.0000.0000.0000.000
183A187TRP0-0.051-0.0302.692-0.9320.3140.223-0.380-1.089-0.002
184A188GLY00.019-0.0058.967-0.110-0.1100.0000.0000.0000.000
185A189ILE0-0.012-0.0029.8050.0310.0310.0000.0000.0000.000
186A190SER0-0.052-0.02012.2950.0070.0070.0000.0000.0000.000
187A191ASP-1-0.886-0.94016.026-0.289-0.2890.0000.0000.0000.000
188A192GLY0-0.035-0.01915.3010.0250.0250.0000.0000.0000.000
189A193THR0-0.027-0.00715.2840.0070.0070.0000.0000.0000.000
190A194GLU-1-0.733-0.8118.449-0.716-0.7160.0000.0000.0000.000
191A195TYR0-0.054-0.04311.5700.0790.0790.0000.0000.0000.000
192A196TRP00.0070.0066.761-0.115-0.1150.0000.0000.0000.000
193A197ILE0-0.052-0.02411.3480.0300.0300.0000.0000.0000.000
194A198VAL0-0.028-0.03412.9110.0180.0180.0000.0000.0000.000
195A199ARG10.8770.94315.4180.0510.0510.0000.0000.0000.000
196A200ASN00.0230.01218.1670.0230.0230.0000.0000.0000.000
197A201SER0-0.035-0.04221.311-0.002-0.0020.0000.0000.0000.000
198A202TRP00.011-0.00624.3960.0040.0040.0000.0000.0000.000
199A203GLY00.0270.00726.7770.0020.0020.0000.0000.0000.000
200A204GLU-1-0.886-0.92826.602-0.086-0.0860.0000.0000.0000.000
201A205PRO0-0.016-0.02327.687-0.006-0.0060.0000.0000.0000.000
202A206TRP0-0.0130.02922.112-0.005-0.0050.0000.0000.0000.000
203A207GLY00.0180.02524.367-0.006-0.0060.0000.0000.0000.000
204A208GLU-1-0.740-0.84420.218-0.208-0.2080.0000.0000.0000.000
205A209ARG10.8180.88822.4610.1000.1000.0000.0000.0000.000
206A210GLY00.0270.00523.7760.0020.0020.0000.0000.0000.000
207A211TRP0-0.076-0.03715.217-0.002-0.0020.0000.0000.0000.000
208A212LEU00.0150.00517.9680.0010.0010.0000.0000.0000.000
209A213ARG10.7920.89615.8120.2490.2490.0000.0000.0000.000
210A214ILE00.0120.01115.2060.0160.0160.0000.0000.0000.000
211A215VAL0-0.009-0.00814.600-0.032-0.0320.0000.0000.0000.000
212A216THR0-0.027-0.0339.8480.0470.0470.0000.0000.0000.000
213A217SER0-0.009-0.02611.422-0.007-0.0070.0000.0000.0000.000
214A218THR0-0.004-0.02010.9430.0500.0500.0000.0000.0000.000
215A219TYR0-0.0200.01213.570-0.006-0.0060.0000.0000.0000.000
216A220LYS10.9060.93016.5850.1550.1550.0000.0000.0000.000
217A221ASP-1-0.908-0.95217.918-0.139-0.1390.0000.0000.0000.000
218A222GLY00.0220.02615.6940.0260.0260.0000.0000.0000.000
219A223LYS10.8790.94316.7550.1100.1100.0000.0000.0000.000
220A224GLY00.0500.02316.4210.0080.0080.0000.0000.0000.000
221A225ALA00.0230.00816.5780.0020.0020.0000.0000.0000.000
222A226ARG10.9030.96017.6560.0550.0550.0000.0000.0000.000
223A227TYR0-0.029-0.02719.6720.0030.0030.0000.0000.0000.000
224A228ASN0-0.010-0.00514.4340.0160.0160.0000.0000.0000.000
225A229LEU00.0280.02317.7120.0040.0040.0000.0000.0000.000
226A230ALA00.1050.05018.3510.0070.0070.0000.0000.0000.000
227A231ILE00.0050.00913.4010.0130.0130.0000.0000.0000.000
228A232GLU-1-0.781-0.91511.812-0.089-0.0890.0000.0000.0000.000
229A233GLU-1-0.955-0.97313.4660.0680.0680.0000.0000.0000.000
230A234HIS0-0.001-0.00816.2100.0300.0300.0000.0000.0000.000
231A236THR00.004-0.00114.6180.0320.0320.0000.0000.0000.000
232A237PHE0-0.015-0.02912.397-0.015-0.0150.0000.0000.0000.000
233A238GLY00.0700.00614.919-0.001-0.0010.0000.0000.0000.000
234A239ASP-1-0.840-0.89215.4000.2570.2570.0000.0000.0000.000
235A240PRO0-0.0260.01216.511-0.013-0.0130.0000.0000.0000.000
236A241ILE00.013-0.02119.3460.0160.0160.0000.0000.0000.000
237A242VAL0-0.036-0.01320.499-0.011-0.0110.0000.0000.0000.000