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: JL849

Calculation Name: 4RZI-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RZI

Chain ID: B

ChEMBL ID:

UniProt ID: P73826

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 OptAll
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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2757157.689797
FMO2-HF: Nuclear repulsion 2669202.538314
FMO2-HF: Total energy -87955.151483
FMO2-MP2: Total energy -88213.265839


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(B:2:LEU)


Summations of interaction energy for fragment #1(B:2: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.
-0.6271.195-0.016-1.006-0.80.002
Interaction energy analysis for fragmet #1(B:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / 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].
3B4LEU0-0.022-0.0093.8831.2343.056-0.016-1.006-0.8000.002
4B5GLY00.0470.0337.071-0.239-0.2390.0000.0000.0000.000
5B6LEU0-0.054-0.0678.7040.0390.0390.0000.0000.0000.000
6B7GLU-1-0.757-0.8616.164-0.571-0.5710.0000.0000.0000.000
7B8ASP-1-0.882-0.93010.777-0.082-0.0820.0000.0000.0000.000
8B9LYS10.8700.95912.297-0.082-0.0820.0000.0000.0000.000
9B10VAL00.0480.04615.851-0.026-0.0260.0000.0000.0000.000
10B11ILE0-0.020-0.01715.6610.0290.0290.0000.0000.0000.000
11B12VAL00.0280.02620.216-0.015-0.0150.0000.0000.0000.000
12B13VAL0-0.027-0.01521.9240.0110.0110.0000.0000.0000.000
13B14THR00.0410.01724.620-0.003-0.0030.0000.0000.0000.000
14B15GLY0-0.004-0.00827.7120.0000.0000.0000.0000.0000.000
15B16GLY0-0.008-0.01426.557-0.003-0.0030.0000.0000.0000.000
16B17ASN00.003-0.00126.778-0.015-0.0150.0000.0000.0000.000
17B18ARG10.8060.88729.3880.0630.0630.0000.0000.0000.000
18B19GLY00.0110.00628.1380.0020.0020.0000.0000.0000.000
19B20ILE0-0.021-0.02323.648-0.009-0.0090.0000.0000.0000.000
20B21GLY00.0480.03123.662-0.007-0.0070.0000.0000.0000.000
21B22ALA00.0460.02723.838-0.007-0.0070.0000.0000.0000.000
22B23ALA0-0.027-0.01321.427-0.016-0.0160.0000.0000.0000.000
23B24ILE0-0.032-0.02419.402-0.021-0.0210.0000.0000.0000.000
24B25VAL0-0.033-0.01519.100-0.012-0.0120.0000.0000.0000.000
25B26LYS10.8330.89518.2550.2570.2570.0000.0000.0000.000
26B27LEU0-0.014-0.00113.702-0.025-0.0250.0000.0000.0000.000
27B28LEU0-0.024-0.02314.576-0.046-0.0460.0000.0000.0000.000
28B29GLN00.0610.04414.614-0.023-0.0230.0000.0000.0000.000
29B30GLU-1-0.836-0.88714.014-0.360-0.3600.0000.0000.0000.000
30B31MET0-0.086-0.03910.163-0.077-0.0770.0000.0000.0000.000
31B32GLY00.0080.00610.198-0.057-0.0570.0000.0000.0000.000
32B33ALA0-0.030-0.00612.2450.0500.0500.0000.0000.0000.000
33B34LYS10.8030.88114.7960.0910.0910.0000.0000.0000.000
34B35VAL0-0.035-0.02017.8310.0280.0280.0000.0000.0000.000
35B36ALA00.0390.02920.1480.0000.0000.0000.0000.0000.000
36B37PHE0-0.052-0.01623.9320.0050.0050.0000.0000.0000.000
37B38THR00.0300.02226.5390.0020.0020.0000.0000.0000.000
38B39ASP-1-0.840-0.92730.115-0.047-0.0470.0000.0000.0000.000
39B40LEU0-0.015-0.01432.6160.0020.0020.0000.0000.0000.000
40B41ALA0-0.030-0.00634.5710.0010.0010.0000.0000.0000.000
41B42THR00.024-0.00331.5060.0000.0000.0000.0000.0000.000
42B43ASP-1-0.841-0.87932.099-0.067-0.0670.0000.0000.0000.000
43B44GLY00.0220.03129.902-0.002-0.0020.0000.0000.0000.000
44B45GLY0-0.028-0.03929.7560.0030.0030.0000.0000.0000.000
45B46ASN0-0.048-0.04722.156-0.008-0.0080.0000.0000.0000.000
46B47THR00.0350.00226.0750.0060.0060.0000.0000.0000.000
47B48GLU-1-0.955-0.96419.928-0.200-0.2000.0000.0000.0000.000
48B49ALA0-0.0030.00122.049-0.009-0.0090.0000.0000.0000.000
49B50LEU0-0.003-0.00123.6310.0100.0100.0000.0000.0000.000
50B51GLY00.0310.02126.2790.0060.0060.0000.0000.0000.000
51B52VAL0-0.012-0.01528.8280.0020.0020.0000.0000.0000.000
52B53VAL0-0.014-0.01531.5830.0020.0020.0000.0000.0000.000
53B54ALA0-0.001-0.00533.2190.0040.0040.0000.0000.0000.000
54B55ASN00.0440.03735.090-0.002-0.0020.0000.0000.0000.000
55B56VAL00.0560.01031.9910.0030.0030.0000.0000.0000.000
56B57THR0-0.106-0.07535.0460.0040.0040.0000.0000.0000.000
57B58ASP-1-0.866-0.93138.025-0.005-0.0050.0000.0000.0000.000
58B59LEU00.0190.00535.966-0.001-0.0010.0000.0000.0000.000
59B60GLU-1-0.910-0.93237.2940.0000.0000.0000.0000.0000.000
60B61SER0-0.0230.00237.292-0.002-0.0020.0000.0000.0000.000
61B62MET0-0.018-0.00830.496-0.004-0.0040.0000.0000.0000.000
62B63THR0-0.021-0.02932.8840.0010.0010.0000.0000.0000.000
63B64ALA0-0.0100.00133.9280.0000.0000.0000.0000.0000.000
64B65ALA00.0430.01731.423-0.002-0.0020.0000.0000.0000.000
65B66ALA0-0.011-0.00529.295-0.004-0.0040.0000.0000.0000.000
66B67ALA0-0.0180.00229.2780.0000.0000.0000.0000.0000.000
67B68GLU-1-0.831-0.89630.644-0.038-0.0380.0000.0000.0000.000
68B69ILE0-0.009-0.01925.061-0.005-0.0050.0000.0000.0000.000
69B70THR0-0.068-0.05026.014-0.002-0.0020.0000.0000.0000.000
70B71ASP-1-0.991-0.99226.732-0.027-0.0270.0000.0000.0000.000
71B72LYS10.8350.90127.2390.0390.0390.0000.0000.0000.000
72B73LEU0-0.042-0.01021.747-0.011-0.0110.0000.0000.0000.000
73B74GLY00.0140.01721.892-0.004-0.0040.0000.0000.0000.000
74B75PRO0-0.043-0.03721.5340.0020.0020.0000.0000.0000.000
75B76VAL00.0070.01221.5020.0040.0040.0000.0000.0000.000
76B77TYR0-0.049-0.02415.1100.0300.0300.0000.0000.0000.000
77B78GLY00.030-0.00219.5300.0230.0230.0000.0000.0000.000
78B79VAL0-0.0070.00620.435-0.017-0.0170.0000.0000.0000.000
79B80VAL00.0230.00520.4350.0110.0110.0000.0000.0000.000
80B81ALA00.0050.01623.291-0.008-0.0080.0000.0000.0000.000
81B82ASN0-0.047-0.06024.7820.0020.0020.0000.0000.0000.000
82B83ALA0-0.0160.01626.774-0.002-0.0020.0000.0000.0000.000
83B84GLY0-0.014-0.02830.4620.0060.0060.0000.0000.0000.000
84B85ILE0-0.036-0.00533.002-0.004-0.0040.0000.0000.0000.000
85B86THR0-0.031-0.03836.0970.0030.0030.0000.0000.0000.000
86B87LYS10.8820.91538.5410.0110.0110.0000.0000.0000.000
87B88ASP-1-0.784-0.85239.696-0.014-0.0140.0000.0000.0000.000
88B89ASN00.0570.01742.770-0.001-0.0010.0000.0000.0000.000
89B90PHE0-0.013-0.01245.5560.0010.0010.0000.0000.0000.000
90B91PHE00.0800.03146.6320.0000.0000.0000.0000.0000.000
91B92PRO0-0.020-0.01148.4280.0000.0000.0000.0000.0000.000
92B93LYS10.8970.94850.2790.0060.0060.0000.0000.0000.000
93B94LEU0-0.067-0.00144.983-0.001-0.0010.0000.0000.0000.000
94B95THR00.018-0.01748.8130.0010.0010.0000.0000.0000.000
95B96PRO00.0580.00548.6090.0000.0000.0000.0000.0000.000
96B97ALA00.0490.03247.5950.0010.0010.0000.0000.0000.000
97B98ASP-1-0.820-0.87245.135-0.009-0.0090.0000.0000.0000.000
98B99TRP00.0070.00642.8600.0000.0000.0000.0000.0000.000
99B100ASP-1-0.869-0.93042.7680.0010.0010.0000.0000.0000.000
100B101ALA00.0120.00942.3560.0000.0000.0000.0000.0000.000
101B102VAL00.0210.00238.591-0.001-0.0010.0000.0000.0000.000
102B103LEU00.003-0.00637.9740.0010.0010.0000.0000.0000.000
103B104ASN0-0.013-0.01038.4640.0040.0040.0000.0000.0000.000
104B105VAL00.0210.01934.4150.0010.0010.0000.0000.0000.000
105B106ASN0-0.046-0.03133.630-0.002-0.0020.0000.0000.0000.000
106B107LEU0-0.008-0.00433.4280.0030.0030.0000.0000.0000.000
107B108LYS10.8830.94834.749-0.002-0.0020.0000.0000.0000.000
108B109GLY00.0990.04935.0890.0020.0020.0000.0000.0000.000
109B110VAL0-0.0350.00629.349-0.001-0.0010.0000.0000.0000.000
110B111ALA00.0310.00630.8890.0030.0030.0000.0000.0000.000
111B112TYR0-0.042-0.03232.7710.0020.0020.0000.0000.0000.000
112B113SER0-0.016-0.02829.165-0.004-0.0040.0000.0000.0000.000
113B114ILE0-0.0050.00427.2200.0010.0010.0000.0000.0000.000
114B115LYS10.9200.97129.524-0.026-0.0260.0000.0000.0000.000
115B116PRO0-0.010-0.00231.1200.0040.0040.0000.0000.0000.000
116B117PHE00.0410.01826.094-0.002-0.0020.0000.0000.0000.000
117B118ILE0-0.013-0.01026.4570.0070.0070.0000.0000.0000.000
118B119GLU-1-0.883-0.94927.7570.0440.0440.0000.0000.0000.000
119B120GLY00.0530.02727.4080.0040.0040.0000.0000.0000.000
120B121MET0-0.039-0.00922.6060.0110.0110.0000.0000.0000.000
121B122TYR0-0.018-0.02224.2870.0170.0170.0000.0000.0000.000
122B123GLU-1-0.945-0.96726.9580.0560.0560.0000.0000.0000.000
123B124ARG10.8800.93821.912-0.049-0.0490.0000.0000.0000.000
124B125LYS10.7790.89521.904-0.090-0.0900.0000.0000.0000.000
125B126ALA00.0150.01118.0500.0280.0280.0000.0000.0000.000
126B127GLY00.0420.01119.160-0.027-0.0270.0000.0000.0000.000
127B128SER0-0.097-0.04017.0370.0190.0190.0000.0000.0000.000
128B129ILE00.0300.01719.377-0.025-0.0250.0000.0000.0000.000
129B130VAL0-0.012-0.01118.5660.0120.0120.0000.0000.0000.000
130B131ALA00.0300.02121.977-0.014-0.0140.0000.0000.0000.000
131B132ILE00.0050.01222.3990.0020.0020.0000.0000.0000.000
132B133SER00.0120.00525.862-0.001-0.0010.0000.0000.0000.000
133B134SER00.029-0.00328.1070.0040.0040.0000.0000.0000.000
134B135ILE00.0190.03429.5570.0060.0060.0000.0000.0000.000
135B136SER0-0.005-0.02430.8300.0030.0030.0000.0000.0000.000
136B137GLY0-0.0090.01332.6260.0010.0010.0000.0000.0000.000
137B138GLU-1-0.838-0.89927.9650.0290.0290.0000.0000.0000.000
138B139ARG10.8270.93132.4530.0060.0060.0000.0000.0000.000
139B140GLY00.0330.03735.1300.0000.0000.0000.0000.0000.000
140B141ASN0-0.022-0.04737.014-0.001-0.0010.0000.0000.0000.000
141B142VAL00.0090.00639.0590.0010.0010.0000.0000.0000.000
142B143GLY0-0.021-0.00241.781-0.002-0.0020.0000.0000.0000.000
143B144GLN00.0320.02136.5880.0000.0000.0000.0000.0000.000
144B145THR0-0.019-0.00539.5670.0020.0020.0000.0000.0000.000
145B146ASN00.0200.00740.8940.0020.0020.0000.0000.0000.000
146B147TYR00.008-0.00931.8420.0020.0020.0000.0000.0000.000
147B148SER0-0.043-0.02235.9850.0020.0020.0000.0000.0000.000
148B149ALA00.0460.02235.9480.0030.0030.0000.0000.0000.000
149B150THR0-0.047-0.03435.8690.0020.0020.0000.0000.0000.000
150B151LYS10.8630.92329.7260.0060.0060.0000.0000.0000.000
151B152ALA00.0230.01731.4860.0030.0030.0000.0000.0000.000
152B153GLY00.0050.00032.9450.0050.0050.0000.0000.0000.000
153B154VAL0-0.008-0.00728.9050.0050.0050.0000.0000.0000.000
154B155ILE00.0200.02327.7570.0070.0070.0000.0000.0000.000
155B156GLY00.0100.01229.1810.0080.0080.0000.0000.0000.000
156B157MET0-0.0280.00030.6290.0050.0050.0000.0000.0000.000
157B158MET0-0.0020.00525.4330.0060.0060.0000.0000.0000.000
158B159LYS10.8300.90525.786-0.067-0.0670.0000.0000.0000.000
159B160SER0-0.063-0.02928.2760.0050.0050.0000.0000.0000.000
160B161LEU00.0320.00626.9410.0050.0050.0000.0000.0000.000
161B162ALA00.0100.01624.6180.0070.0070.0000.0000.0000.000
162B163ARG10.8940.94225.818-0.078-0.0780.0000.0000.0000.000
163B164GLU-1-0.932-0.95528.5010.0660.0660.0000.0000.0000.000
164B165GLY00.000-0.00225.4960.0020.0020.0000.0000.0000.000
165B166ALA00.0450.02423.9550.0110.0110.0000.0000.0000.000
166B167ARG10.8650.93524.689-0.078-0.0780.0000.0000.0000.000
167B168TYR0-0.041-0.01825.206-0.007-0.0070.0000.0000.0000.000
168B169GLY00.0350.02021.0880.0040.0040.0000.0000.0000.000
169B170VAL0-0.042-0.00220.1640.0170.0170.0000.0000.0000.000
170B171ARG10.7890.88614.478-0.281-0.2810.0000.0000.0000.000
171B172ALA00.0120.00421.206-0.016-0.0160.0000.0000.0000.000
172B173ASN0-0.008-0.01118.9160.0070.0070.0000.0000.0000.000
173B174ALA00.0280.00922.146-0.013-0.0130.0000.0000.0000.000
174B175VAL00.0370.03419.7490.0080.0080.0000.0000.0000.000
175B176ALA0-0.003-0.00622.485-0.005-0.0050.0000.0000.0000.000
176B177PRO00.0210.00724.479-0.001-0.0010.0000.0000.0000.000
177B178GLY00.006-0.00825.8030.0070.0070.0000.0000.0000.000
178B179PHE0-0.017-0.00428.313-0.001-0.0010.0000.0000.0000.000
179B180ILE00.0090.02625.002-0.004-0.0040.0000.0000.0000.000
180B181ASP-1-0.776-0.84028.321-0.060-0.0600.0000.0000.0000.000
181B182THR0-0.012-0.02928.418-0.006-0.0060.0000.0000.0000.000
182B183GLU-1-0.805-0.92330.685-0.066-0.0660.0000.0000.0000.000
183B184MET00.0160.02733.6640.0030.0030.0000.0000.0000.000
184B185THR0-0.020-0.05631.5990.0020.0020.0000.0000.0000.000
185B186LEU0-0.017-0.00631.8150.0010.0010.0000.0000.0000.000
186B187ALA00.0150.02535.5640.0010.0010.0000.0000.0000.000
187B188ILE0-0.072-0.01836.2350.0040.0040.0000.0000.0000.000
188B189ARG10.8550.88339.6710.0230.0230.0000.0000.0000.000
189B190GLU-1-0.776-0.89838.455-0.043-0.0430.0000.0000.0000.000
190B191ASP-1-0.815-0.87540.532-0.025-0.0250.0000.0000.0000.000
191B192ILE0-0.017-0.01039.4640.0010.0010.0000.0000.0000.000
192B193ARG10.8300.90633.1940.0500.0500.0000.0000.0000.000
193B194GLU-1-0.773-0.86336.601-0.034-0.0340.0000.0000.0000.000
194B195LYS10.8280.90738.4710.0160.0160.0000.0000.0000.000
195B196ILE0-0.020-0.01534.0500.0020.0020.0000.0000.0000.000
196B197THR00.003-0.01132.9670.0000.0000.0000.0000.0000.000
197B198LYS10.8330.89434.4760.0260.0260.0000.0000.0000.000
198B199GLU-1-0.844-0.87835.455-0.010-0.0100.0000.0000.0000.000
199B200ILE0-0.027-0.00329.3300.0030.0030.0000.0000.0000.000
200B201PRO0-0.0060.00329.585-0.004-0.0040.0000.0000.0000.000
201B202PHE0-0.034-0.01922.664-0.002-0.0020.0000.0000.0000.000
202B203ARG10.8330.91928.4230.0210.0210.0000.0000.0000.000
203B204ARG10.7850.86522.4240.0860.0860.0000.0000.0000.000
204B205PHE00.0230.01529.0240.0050.0050.0000.0000.0000.000
205B206GLY00.0200.00525.110-0.006-0.0060.0000.0000.0000.000
206B207LYS10.8580.89923.0150.0880.0880.0000.0000.0000.000
207B208PRO00.0490.01022.883-0.002-0.0020.0000.0000.0000.000
208B209GLU-1-0.788-0.89017.128-0.255-0.2550.0000.0000.0000.000
209B210GLU-1-0.769-0.84018.189-0.108-0.1080.0000.0000.0000.000
210B211ILE0-0.023-0.01418.4990.0130.0130.0000.0000.0000.000
211B212ALA00.0330.02718.1110.0160.0160.0000.0000.0000.000
212B213TRP00.0370.0019.7140.0080.0080.0000.0000.0000.000
213B214ALA0-0.034-0.01014.0810.0270.0270.0000.0000.0000.000
214B215VAL00.013-0.00716.1870.0380.0380.0000.0000.0000.000
215B216ALA00.0410.02312.7710.0350.0350.0000.0000.0000.000
216B217PHE0-0.001-0.00210.6030.0500.0500.0000.0000.0000.000
217B218LEU0-0.0300.00412.4880.0930.0930.0000.0000.0000.000
218B219LEU00.0280.02015.0160.0350.0350.0000.0000.0000.000
219B220SER00.0370.0379.1510.1270.1270.0000.0000.0000.000
220B221PRO0-0.037-0.00210.8850.0450.0450.0000.0000.0000.000
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222B223ALA00.005-0.0077.2820.0330.0330.0000.0000.0000.000
223B224SER00.001-0.0238.731-0.124-0.1240.0000.0000.0000.000
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225B226TYR00.0100.00413.879-0.067-0.0670.0000.0000.0000.000
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227B228THR00.0450.01817.690-0.012-0.0120.0000.0000.0000.000
228B229GLY00.0500.02720.939-0.002-0.0020.0000.0000.0000.000
229B230GLU-1-0.857-0.92920.6400.0830.0830.0000.0000.0000.000
230B231VAL0-0.035-0.02922.610-0.007-0.0070.0000.0000.0000.000
231B232LEU00.0080.01416.6250.0000.0000.0000.0000.0000.000
232B233ARG10.8040.86620.913-0.039-0.0390.0000.0000.0000.000
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234B235ASN00.000-0.02022.561-0.009-0.0090.0000.0000.0000.000
235B236GLY00.0630.03324.4480.0000.0000.0000.0000.0000.000
236B237ALA00.0230.00025.8720.0010.0010.0000.0000.0000.000
237B238HIS0-0.048-0.03927.5360.0020.0020.0000.0000.0000.000
238B239HIS0-0.004-0.02229.0620.0000.0000.0000.0000.0000.000
239B240THR00.0490.05427.7490.0030.0030.0000.0000.0000.000