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: NN19Q

Calculation Name: 5LEJ-A-Xray372

Preferred Name: Listeriolysin regulatory protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5LEJ

Chain ID: A

ChEMBL ID: CHEMBL4295575

UniProt ID: P22262

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3050422.977483
FMO2-HF: Nuclear repulsion 2955803.994229
FMO2-HF: Total energy -94618.983254
FMO2-MP2: Total energy -94896.817759


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:2:ASN)


Summations of interaction energy for fragment #1(A:2: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.
-1.352.7830.085-1.419-2.80.005
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.005
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].
3A4GLN00.020-0.0033.610-1.4860.9890.004-1.077-1.4020.004
4A5ALA00.0010.0053.167-1.521-0.6410.083-0.248-0.7160.001
5A6GLU-1-0.827-0.8954.2353.0863.6240.000-0.068-0.4700.000
6A7GLU-1-0.942-0.9596.4130.5860.5860.0000.0000.0000.000
7A8PHE0-0.006-0.0188.074-0.348-0.3480.0000.0000.0000.000
8A9LYS10.9070.9638.283-1.989-1.9890.0000.0000.0000.000
9A10LYS10.9860.9829.895-1.375-1.3750.0000.0000.0000.000
10A11TYR0-0.012-0.00512.173-0.202-0.2020.0000.0000.0000.000
11A12LEU00.0110.00012.158-0.158-0.1580.0000.0000.0000.000
12A13GLU-1-1.020-1.00213.4820.9670.9670.0000.0000.0000.000
13A14THR0-0.056-0.02815.942-0.092-0.0920.0000.0000.0000.000
14A15ASN0-0.027-0.02218.306-0.050-0.0500.0000.0000.0000.000
15A16GLY0-0.012-0.00120.025-0.029-0.0290.0000.0000.0000.000
16A17ILE00.0070.02117.484-0.027-0.0270.0000.0000.0000.000
17A18LYS10.9610.97216.775-0.405-0.4050.0000.0000.0000.000
18A19PRO0-0.015-0.00114.138-0.026-0.0260.0000.0000.0000.000
19A20LYS10.9580.98716.228-0.458-0.4580.0000.0000.0000.000
20A21GLN0-0.022-0.01516.7800.1170.1170.0000.0000.0000.000
21A22PHE0-0.008-0.00317.335-0.049-0.0490.0000.0000.0000.000
22A23HIS00.0020.00418.9930.0100.0100.0000.0000.0000.000
23A24LYS10.9010.94821.307-0.172-0.1720.0000.0000.0000.000
24A25LYS10.8980.94322.219-0.156-0.1560.0000.0000.0000.000
25A26GLU-1-0.866-0.90922.0320.3130.3130.0000.0000.0000.000
26A27LEU0-0.013-0.01921.9350.0130.0130.0000.0000.0000.000
27A28ILE0-0.0230.00016.7830.0080.0080.0000.0000.0000.000
28A29PHE00.0160.00418.0140.0030.0030.0000.0000.0000.000
29A30ASN00.004-0.00822.816-0.021-0.0210.0000.0000.0000.000
30A31GLN00.0400.03325.5970.0060.0060.0000.0000.0000.000
31A32TRP0-0.003-0.01327.861-0.005-0.0050.0000.0000.0000.000
32A33ASP-1-0.905-0.93629.6190.1650.1650.0000.0000.0000.000
33A34PRO0-0.061-0.02827.0460.0190.0190.0000.0000.0000.000
34A35GLN0-0.044-0.02725.551-0.015-0.0150.0000.0000.0000.000
35A36GLU-1-0.874-0.93523.6210.2530.2530.0000.0000.0000.000
36A37TYR0-0.037-0.03619.7170.0180.0180.0000.0000.0000.000
37A38CYS0-0.034-0.00815.3270.0120.0120.0000.0000.0000.000
38A39ILE0-0.018-0.00313.8340.0570.0570.0000.0000.0000.000
39A40PHE00.0480.0156.8570.0250.0250.0000.0000.0000.000
40A41LEU0-0.015-0.01410.4630.0770.0770.0000.0000.0000.000
41A42TYR0-0.045-0.0616.237-0.335-0.3350.0000.0000.0000.000
42A43ASP-1-0.917-0.9627.1981.4721.4720.0000.0000.0000.000
43A44GLY00.0820.0489.658-0.177-0.1770.0000.0000.0000.000
44A45ILE0-0.086-0.05911.547-0.028-0.0280.0000.0000.0000.000
45A46THR00.0140.00614.1650.0040.0040.0000.0000.0000.000
46A47LYS10.8900.95715.951-0.161-0.1610.0000.0000.0000.000
47A48LEU00.0220.01918.0580.0190.0190.0000.0000.0000.000
48A49THR0-0.032-0.02519.767-0.028-0.0280.0000.0000.0000.000
49A50SER00.0480.01023.5440.0130.0130.0000.0000.0000.000
50A51ILE0-0.048-0.01326.763-0.012-0.0120.0000.0000.0000.000
51A52SER00.0110.01130.3280.0040.0040.0000.0000.0000.000
52A53GLU-1-0.864-0.94133.1710.0670.0670.0000.0000.0000.000
53A54ASN0-0.045-0.02836.504-0.002-0.0020.0000.0000.0000.000
54A55GLY00.0230.01034.906-0.004-0.0040.0000.0000.0000.000
55A56THR0-0.077-0.03433.1360.0030.0030.0000.0000.0000.000
56A57ILE00.0310.02127.3940.0070.0070.0000.0000.0000.000
57A58MET0-0.054-0.01225.052-0.016-0.0160.0000.0000.0000.000
58A59ASN0-0.015-0.02322.3330.0280.0280.0000.0000.0000.000
59A60LEU00.0250.02220.986-0.021-0.0210.0000.0000.0000.000
60A61GLN00.0100.02214.285-0.040-0.0400.0000.0000.0000.000
61A62TYR0-0.0030.00815.5180.0290.0290.0000.0000.0000.000
62A63TYR0-0.024-0.05211.471-0.031-0.0310.0000.0000.0000.000
63A64LYS10.9220.9637.9060.3180.3180.0000.0000.0000.000
64A65GLY0-0.0160.0417.893-0.118-0.1180.0000.0000.0000.000
65A66ALA0-0.014-0.0273.956-0.268-0.098-0.001-0.022-0.1470.000
66A67PHE0-0.054-0.0465.362-0.387-0.3870.0000.0000.0000.000
67A68VAL00.0100.0077.8270.1310.1310.0000.0000.0000.000
68A69ILE0-0.028-0.00510.991-0.119-0.1190.0000.0000.0000.000
69A70MET0-0.032-0.01614.5010.0560.0560.0000.0000.0000.000
70A71SER00.0190.00817.534-0.043-0.0430.0000.0000.0000.000
71A72GLY00.0880.01020.815-0.031-0.0310.0000.0000.0000.000
72A73PHE0-0.074-0.03321.3790.0290.0290.0000.0000.0000.000
73A74ILE00.010-0.00319.7070.0110.0110.0000.0000.0000.000
74A75ASP-1-0.912-0.95723.1240.2220.2220.0000.0000.0000.000
75A76THR0-0.014-0.02326.5630.0000.0000.0000.0000.0000.000
76A77GLU-1-0.879-0.94125.7830.2470.2470.0000.0000.0000.000
77A78THR0-0.0160.00626.851-0.004-0.0040.0000.0000.0000.000
78A79SER00.0430.03025.2690.0160.0160.0000.0000.0000.000
79A80VAL0-0.066-0.01321.060-0.013-0.0130.0000.0000.0000.000
80A81GLY0-0.009-0.01324.395-0.019-0.0190.0000.0000.0000.000
81A82TYR0-0.035-0.00525.0870.0140.0140.0000.0000.0000.000
82A83TYR0-0.003-0.00722.402-0.016-0.0160.0000.0000.0000.000
83A84ASN0-0.006-0.01923.3460.0220.0220.0000.0000.0000.000
84A85LEU0-0.0120.00915.722-0.013-0.0130.0000.0000.0000.000
85A86GLU-1-0.891-0.95119.9610.1900.1900.0000.0000.0000.000
86A87VAL00.0090.00717.3940.0040.0040.0000.0000.0000.000
87A88ILE0-0.017-0.01617.655-0.036-0.0360.0000.0000.0000.000
88A89SER0-0.037-0.01515.938-0.035-0.0350.0000.0000.0000.000
89A90GLU-1-0.891-0.96418.0470.2080.2080.0000.0000.0000.000
90A91GLN0-0.002-0.01417.1730.0210.0210.0000.0000.0000.000
91A92ALA0-0.0030.00814.1270.0240.0240.0000.0000.0000.000
92A93THR0-0.0020.00812.193-0.043-0.0430.0000.0000.0000.000
93A94ALA0-0.007-0.01212.0820.1360.1360.0000.0000.0000.000
94A95TYR0-0.0080.01610.8700.0270.0270.0000.0000.0000.000
95A96VAL00.0010.00114.7730.0050.0050.0000.0000.0000.000
96A97ILE00.0260.01915.063-0.014-0.0140.0000.0000.0000.000
97A98LYS10.9790.99218.901-0.355-0.3550.0000.0000.0000.000
98A99ILE00.0210.01220.9650.0280.0280.0000.0000.0000.000
99A100ASN00.0240.01022.5170.0280.0280.0000.0000.0000.000
100A101GLU-1-0.906-0.94922.0190.4170.4170.0000.0000.0000.000
101A102LEU0-0.015-0.01216.1710.0260.0260.0000.0000.0000.000
102A103LYS10.9460.97319.874-0.224-0.2240.0000.0000.0000.000
103A104GLU-1-0.927-0.95822.2420.3190.3190.0000.0000.0000.000
104A105LEU0-0.018-0.01518.1340.0120.0120.0000.0000.0000.000
105A106LEU0-0.013-0.01115.1150.0410.0410.0000.0000.0000.000
106A107SER0-0.016-0.00618.195-0.021-0.0210.0000.0000.0000.000
107A108LYS10.8610.96319.508-0.379-0.3790.0000.0000.0000.000
108A109ASN00.0600.05815.040-0.051-0.0510.0000.0000.0000.000
109A110LEU00.0900.03316.5620.0480.0480.0000.0000.0000.000
110A111THR0-0.054-0.05612.6110.0480.0480.0000.0000.0000.000
111A112HIS00.010-0.01010.1420.2030.2030.0000.0000.0000.000
112A113PHE00.0350.03112.3420.0700.0700.0000.0000.0000.000
113A114PHE00.0340.01112.995-0.003-0.0030.0000.0000.0000.000
114A115TYR0-0.0200.0124.772-0.213-0.143-0.001-0.004-0.0650.000
115A116VAL00.0630.0189.7970.0050.0050.0000.0000.0000.000
116A117PHE0-0.0120.00511.589-0.113-0.1130.0000.0000.0000.000
117A118GLN0-0.015-0.0118.456-0.259-0.2590.0000.0000.0000.000
118A119THR0-0.079-0.0487.025-0.145-0.1450.0000.0000.0000.000
119A120LEU00.1000.0459.759-0.134-0.1340.0000.0000.0000.000
120A121GLN00.0180.01113.394-0.063-0.0630.0000.0000.0000.000
121A122LYS10.9050.9616.2950.1580.1580.0000.0000.0000.000
122A123GLN00.0350.03812.251-0.036-0.0360.0000.0000.0000.000
123A124VAL00.0110.00114.197-0.043-0.0430.0000.0000.0000.000
124A125SER0-0.011-0.00714.689-0.048-0.0480.0000.0000.0000.000
125A126TYR0-0.0110.00714.143-0.009-0.0090.0000.0000.0000.000
126A127SER00.024-0.00116.228-0.003-0.0030.0000.0000.0000.000
127A128LEU0-0.0030.00719.304-0.008-0.0080.0000.0000.0000.000
128A129ALA00.0230.01418.845-0.005-0.0050.0000.0000.0000.000
129A130LYS10.8910.93519.0900.0200.0200.0000.0000.0000.000
130A131PHE0-0.011-0.00321.2910.0040.0040.0000.0000.0000.000
131A132ASN0-0.0460.00623.8510.0010.0010.0000.0000.0000.000
132A133ASP-1-0.727-0.88022.945-0.153-0.1530.0000.0000.0000.000
133A134PHE0-0.095-0.05722.6350.0020.0020.0000.0000.0000.000
134A135SER0-0.026-0.02926.9350.0110.0110.0000.0000.0000.000
135A136ILE0-0.0490.00029.3990.0040.0040.0000.0000.0000.000
136A137ASN00.0280.00630.0390.0080.0080.0000.0000.0000.000
137A138GLY00.0310.02532.1830.0010.0010.0000.0000.0000.000
138A139LYS10.8990.94730.6780.0100.0100.0000.0000.0000.000
139A140LEU00.0250.01430.358-0.002-0.0020.0000.0000.0000.000
140A141GLY00.0850.03028.982-0.009-0.0090.0000.0000.0000.000
141A142SER00.0120.00426.482-0.008-0.0080.0000.0000.0000.000
142A143ILE0-0.049-0.02125.492-0.003-0.0030.0000.0000.0000.000
143A144CYS0-0.050-0.02425.443-0.010-0.0100.0000.0000.0000.000
144A145GLY00.0890.03923.075-0.021-0.0210.0000.0000.0000.000
145A146GLN00.0360.00819.175-0.012-0.0120.0000.0000.0000.000
146A147LEU0-0.002-0.01020.587-0.011-0.0110.0000.0000.0000.000
147A148LEU00.0060.03618.719-0.024-0.0240.0000.0000.0000.000
148A149ILE0-0.012-0.01015.689-0.047-0.0470.0000.0000.0000.000
149A150LEU0-0.049-0.02916.073-0.042-0.0420.0000.0000.0000.000
150A151THR0-0.032-0.04416.627-0.011-0.0110.0000.0000.0000.000
151A152TYR0-0.065-0.05513.747-0.053-0.0530.0000.0000.0000.000
152A153VAL0-0.066-0.02310.863-0.124-0.1240.0000.0000.0000.000
153A154TYR0-0.039-0.04311.969-0.018-0.0180.0000.0000.0000.000
154A155GLY00.0310.04014.6500.0580.0580.0000.0000.0000.000
155A156LYS10.8970.93713.3750.2030.2030.0000.0000.0000.000
156A157GLU-1-0.876-0.93717.047-0.439-0.4390.0000.0000.0000.000
157A158THR0-0.087-0.05319.8730.0180.0180.0000.0000.0000.000
158A159PRO00.002-0.00522.972-0.002-0.0020.0000.0000.0000.000
159A160ASP-1-0.882-0.92526.520-0.150-0.1500.0000.0000.0000.000
160A161GLY0-0.025-0.02425.4370.0070.0070.0000.0000.0000.000
161A162ILE00.0140.01519.057-0.011-0.0110.0000.0000.0000.000
162A163LYS10.9430.97320.4070.1830.1830.0000.0000.0000.000
163A164ILE00.0420.01718.890-0.026-0.0260.0000.0000.0000.000
164A165THR0-0.068-0.04816.6240.0220.0220.0000.0000.0000.000
165A166LEU0-0.013-0.01217.5930.0240.0240.0000.0000.0000.000
166A167ASP-1-0.931-0.94920.1460.0640.0640.0000.0000.0000.000
167A168ASN00.000-0.00322.880-0.019-0.0190.0000.0000.0000.000
168A169LEU00.0380.01621.9800.0020.0020.0000.0000.0000.000
169A170THR00.0150.00524.944-0.014-0.0140.0000.0000.0000.000
170A171MET00.0240.00027.933-0.005-0.0050.0000.0000.0000.000
171A172GLN0-0.041-0.01730.105-0.005-0.0050.0000.0000.0000.000
172A173GLU-1-0.806-0.90724.5720.0730.0730.0000.0000.0000.000
173A174LEU00.0070.00424.123-0.001-0.0010.0000.0000.0000.000
174A175GLY0-0.016-0.01426.438-0.004-0.0040.0000.0000.0000.000
175A176TYR00.0690.03226.414-0.001-0.0010.0000.0000.0000.000
176A177SER0-0.0300.00222.9630.0070.0070.0000.0000.0000.000
177A178SER0-0.009-0.00124.665-0.006-0.0060.0000.0000.0000.000
178A179GLY00.0540.03427.278-0.003-0.0030.0000.0000.0000.000
179A180ILE0-0.144-0.06929.998-0.002-0.0020.0000.0000.0000.000
180A181ALA00.0660.02931.9220.0030.0030.0000.0000.0000.000
181A182HIS00.0480.02534.3990.0030.0030.0000.0000.0000.000
182A183SER00.0710.02433.728-0.007-0.0070.0000.0000.0000.000
183A184SER00.0250.00634.736-0.007-0.0070.0000.0000.0000.000
184A185ALA0-0.024-0.01435.696-0.006-0.0060.0000.0000.0000.000
185A186VAL00.0360.02230.152-0.007-0.0070.0000.0000.0000.000
186A187SER00.0400.02133.121-0.011-0.0110.0000.0000.0000.000
187A188ARG10.9760.99134.9670.0200.0200.0000.0000.0000.000
188A189ILE0-0.003-0.00331.867-0.005-0.0050.0000.0000.0000.000
189A190ILE00.0420.01829.063-0.009-0.0090.0000.0000.0000.000
190A191SER0-0.062-0.04032.737-0.007-0.0070.0000.0000.0000.000
191A192LYS10.9510.98735.4720.0690.0690.0000.0000.0000.000
192A193LEU00.0290.01229.083-0.005-0.0050.0000.0000.0000.000
193A194LYS10.9390.96632.4690.0530.0530.0000.0000.0000.000
194A195GLN0-0.035-0.00733.957-0.006-0.0060.0000.0000.0000.000
195A196GLU-1-0.942-0.97034.330-0.099-0.0990.0000.0000.0000.000
196A197LYS10.8960.94833.5750.0950.0950.0000.0000.0000.000
197A198VAL00.0050.01728.186-0.013-0.0130.0000.0000.0000.000
198A199ILE00.001-0.00926.570-0.015-0.0150.0000.0000.0000.000
199A200VAL0-0.015-0.00728.5440.0130.0130.0000.0000.0000.000
200A201TYR0-0.052-0.02528.455-0.002-0.0020.0000.0000.0000.000
201A202LYS10.9500.98428.8500.1300.1300.0000.0000.0000.000
202A203ASN00.0330.00328.376-0.001-0.0010.0000.0000.0000.000
203A204SER00.0140.00628.5250.0030.0030.0000.0000.0000.000
204A205CYS00.0090.02523.513-0.001-0.0010.0000.0000.0000.000
205A206PHE00.015-0.00423.932-0.006-0.0060.0000.0000.0000.000
206A207TYR0-0.036-0.00823.610-0.016-0.0160.0000.0000.0000.000
207A208VAL00.0120.00122.6800.0180.0180.0000.0000.0000.000
208A209GLN0-0.008-0.01824.481-0.012-0.0120.0000.0000.0000.000
209A210ASN00.0080.01626.987-0.017-0.0170.0000.0000.0000.000
210A211LEU00.0730.03019.8810.0200.0200.0000.0000.0000.000
211A212ASP-1-0.828-0.92124.181-0.272-0.2720.0000.0000.0000.000
212A213TYR0-0.081-0.05126.2330.0140.0140.0000.0000.0000.000
213A214LEU0-0.018-0.02023.2070.0160.0160.0000.0000.0000.000
214A215LYS10.9110.95020.8400.3940.3940.0000.0000.0000.000
215A216ARG10.8900.96224.6970.1720.1720.0000.0000.0000.000
216A217TYR0-0.055-0.02827.6130.0160.0160.0000.0000.0000.000
217A218ALA0-0.0210.00122.5750.0170.0170.0000.0000.0000.000
218A219PRO00.0160.01622.744-0.028-0.0280.0000.0000.0000.000
219A220LYS10.9090.95621.9550.1310.1310.0000.0000.0000.000
220A221LEU0-0.030-0.02118.025-0.020-0.0200.0000.0000.0000.000
221A222ASP-1-0.802-0.86617.620-0.446-0.4460.0000.0000.0000.000
222A223GLU-1-0.876-0.93818.016-0.268-0.2680.0000.0000.0000.000
223A224TRP0-0.033-0.02811.003-0.074-0.0740.0000.0000.0000.000
224A225PHE0-0.018-0.02112.404-0.045-0.0450.0000.0000.0000.000
225A226TYR0-0.0140.00612.903-0.135-0.1350.0000.0000.0000.000
226A227LEU0-0.011-0.00613.810-0.086-0.0860.0000.0000.0000.000
227A228ALA0-0.0250.00111.137-0.023-0.0230.0000.0000.0000.000
228A229CYS0-0.129-0.0688.633-0.118-0.1180.0000.0000.0000.000
229A230PRO00.1230.0678.709-0.085-0.0850.0000.0000.0000.000
230A231ALA0-0.017-0.0147.114-0.006-0.0060.0000.0000.0000.000
231A232THR0-0.048-0.0458.568-0.028-0.0280.0000.0000.0000.000
232A233TRP00.0460.02810.1510.1260.1260.0000.0000.0000.000
233A234GLY00.0260.01512.6450.1110.1110.0000.0000.0000.000
234A235LYS10.8710.9358.2191.6301.6300.0000.0000.0000.000
235A236LEU0-0.0050.01213.8800.0870.0870.0000.0000.0000.000
236A237ASN0-0.0090.01716.8810.1540.1540.0000.0000.0000.000