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: 43RJN

Calculation Name: 3NXH-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NXH

Chain ID: A

ChEMBL ID:

UniProt ID: P96499

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 231
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2732017.393429
FMO2-HF: Nuclear repulsion 2643903.414779
FMO2-HF: Total energy -88113.97865
FMO2-MP2: Total energy -88372.065975


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:72:MET )


Summations of interaction energy for fragment #1(A:72:MET )
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.
-7.883-3.50111.455-3.813-12.026-0.025
Interaction energy analysis for fragmet #1(A:72:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.012
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].
3A74LYS 10.9620.9622.506-2.1090.6441.497-1.895-2.355-0.015
4A75LYS 10.9090.9494.6591.2711.4740.000-0.014-0.1880.000
5A76PRO 00.0860.0485.674-0.509-0.5090.0000.0000.0000.000
6A77PHE 0-0.054-0.0224.3210.0320.2530.001-0.017-0.2050.000
7A78SER 00.0520.0018.603-0.065-0.0650.0000.0000.0000.000
8A79ILE 0-0.032-0.0167.8470.1270.1270.0000.0000.0000.000
9A80LEU 00.0160.00611.986-0.051-0.0510.0000.0000.0000.000
10A81PHE 00.006-0.01111.5870.0540.0540.0000.0000.0000.000
11A82MET 0-0.070-0.03916.787-0.017-0.0170.0000.0000.0000.000
12A83GLY 00.0330.03120.3000.0140.0140.0000.0000.0000.000
13A84ILE 0-0.057-0.04722.772-0.009-0.0090.0000.0000.0000.000
14A85GLU -1-0.850-0.92625.6970.0100.0100.0000.0000.0000.000
15A86ASP -1-0.827-0.91528.2660.0460.0460.0000.0000.0000.000
16A87TYR 00.0780.05021.7280.0060.0060.0000.0000.0000.000
17A88ALA 0-0.012-0.01327.1250.0070.0070.0000.0000.0000.000
18A89THR 0-0.0520.04128.388-0.004-0.0040.0000.0000.0000.000
19A90LYS 10.8830.92231.088-0.065-0.0650.0000.0000.0000.000
20A91GLY 00.0570.03533.844-0.001-0.0010.0000.0000.0000.000
21A92GLN 0-0.025-0.02534.557-0.004-0.0040.0000.0000.0000.000
22A93LYS 10.8040.87032.974-0.035-0.0350.0000.0000.0000.000
23A94GLY 00.018-0.00631.2530.0010.0010.0000.0000.0000.000
24A95ARG 10.9020.93529.3500.0160.0160.0000.0000.0000.000
25A96SER 00.0790.05524.9090.0030.0030.0000.0000.0000.000
26A97ASP -1-0.939-0.96826.162-0.040-0.0400.0000.0000.0000.000
27A98SER 0-0.014-0.01622.097-0.012-0.0120.0000.0000.0000.000
28A99LEU 0-0.033-0.01821.1350.0170.0170.0000.0000.0000.000
29A100ILE 00.0170.01716.931-0.019-0.0190.0000.0000.0000.000
30A101VAL 00.0200.02015.2040.0190.0190.0000.0000.0000.000
31A102VAL 00.0010.00610.674-0.029-0.0290.0000.0000.0000.000
32A103THR 0-0.010-0.01811.3480.0520.0520.0000.0000.0000.000
33A104LEU 0-0.009-0.0105.822-0.079-0.0790.0000.0000.0000.000
34A105ASP -1-0.773-0.8858.035-1.481-1.4810.0000.0000.0000.000
35A106PRO 00.0270.0113.592-0.362-0.0700.007-0.049-0.2500.000
36A107LYS 10.9060.9585.9731.3701.3700.0000.0000.0000.000
37A108ASN 0-0.062-0.0268.2630.2910.2910.0000.0000.0000.000
38A109LYS 10.8470.9398.6501.7191.7190.0000.0000.0000.000
39A110THR 00.0120.0139.9010.2300.2300.0000.0000.0000.000
40A111MET 0-0.0020.0169.207-0.149-0.1490.0000.0000.0000.000
41A112LYS 10.8540.94612.1460.5800.5800.0000.0000.0000.000
42A113MET 00.0170.00714.219-0.001-0.0010.0000.0000.0000.000
43A114LEU 00.0070.01316.6880.0200.0200.0000.0000.0000.000
44A115SER 00.0190.00219.5200.0090.0090.0000.0000.0000.000
45A116ILE 0-0.056-0.02121.3840.0000.0000.0000.0000.0000.000
46A117PRO 00.0490.03624.3380.0110.0110.0000.0000.0000.000
47A118ARG 10.8990.99427.7190.0460.0460.0000.0000.0000.000
48A119ASP -1-0.910-0.98128.878-0.033-0.0330.0000.0000.0000.000
49A120THR 0-0.022-0.07028.502-0.003-0.0030.0000.0000.0000.000
50A121ARG 10.8180.89730.6900.0490.0490.0000.0000.0000.000
51A122VAL 00.0200.00627.906-0.006-0.0060.0000.0000.0000.000
52A123GLN 0-0.038-0.03131.0360.0030.0030.0000.0000.0000.000
53A124LEU 0-0.040-0.03029.266-0.002-0.0020.0000.0000.0000.000
54A125ALA 00.0240.04226.131-0.002-0.0020.0000.0000.0000.000
55A126GLY 00.0780.03427.9320.0010.0010.0000.0000.0000.000
56A127ASP -1-0.970-0.96229.3100.0110.0110.0000.0000.0000.000
57A128THR 00.003-0.01733.0310.0050.0050.0000.0000.0000.000
58A129THR 00.0330.03236.180-0.002-0.0020.0000.0000.0000.000
59A130GLY 0-0.069-0.02938.156-0.003-0.0030.0000.0000.0000.000
60A131SER 0-0.058-0.06836.006-0.001-0.0010.0000.0000.0000.000
61A132LYS 10.8630.94637.746-0.002-0.0020.0000.0000.0000.000
62A133THR 00.0210.01434.5430.0000.0000.0000.0000.0000.000
63A134LYS 10.8380.92534.0380.0050.0050.0000.0000.0000.000
64A135ILE 00.0450.03132.095-0.002-0.0020.0000.0000.0000.000
65A136ASN 00.0800.04025.3040.0060.0060.0000.0000.0000.000
66A137ALA 0-0.058-0.02828.3240.0010.0010.0000.0000.0000.000
67A138ALA 00.040-0.00326.5110.0060.0060.0000.0000.0000.000
68A139TYR 0-0.0140.02422.7710.0030.0030.0000.0000.0000.000
69A140SER 0-0.064-0.01927.0410.0070.0070.0000.0000.0000.000
70A141LYS 10.8890.94130.419-0.013-0.0130.0000.0000.0000.000
71A142GLY 00.1040.04028.222-0.003-0.0030.0000.0000.0000.000
72A143GLY 0-0.0020.01725.8050.0120.0120.0000.0000.0000.000
73A144LYS 10.9370.93517.549-0.229-0.2290.0000.0000.0000.000
74A145ASP -1-0.847-0.93420.4510.1530.1530.0000.0000.0000.000
75A146GLU -1-0.787-0.86322.1400.0250.0250.0000.0000.0000.000
76A147THR 0-0.098-0.05722.263-0.019-0.0190.0000.0000.0000.000
77A148VAL 00.030-0.00417.801-0.020-0.0200.0000.0000.0000.000
78A149GLU -1-0.866-0.91520.4230.0180.0180.0000.0000.0000.000
79A150THR 0-0.056-0.03422.580-0.018-0.0180.0000.0000.0000.000
80A151VAL 0-0.033-0.03319.694-0.017-0.0170.0000.0000.0000.000
81A152GLU -1-0.806-0.88317.590-0.024-0.0240.0000.0000.0000.000
82A153ASN 00.0080.00520.777-0.022-0.0220.0000.0000.0000.000
83A154PHE 0-0.045-0.01824.127-0.013-0.0130.0000.0000.0000.000
84A155LEU 0-0.016-0.02618.967-0.012-0.0120.0000.0000.0000.000
85A156GLN 0-0.107-0.05421.233-0.028-0.0280.0000.0000.0000.000
86A157ILE 0-0.008-0.00115.680-0.027-0.0270.0000.0000.0000.000
87A158PRO 00.0280.02314.5560.0280.0280.0000.0000.0000.000
88A159ILE 0-0.029-0.00714.438-0.063-0.0630.0000.0000.0000.000
89A160ASP -1-0.897-0.9409.813-0.149-0.1490.0000.0000.0000.000
90A161LYS 10.7880.9006.645-0.934-0.9340.0000.0000.0000.000
91A162TYR 00.0410.02611.039-0.092-0.0920.0000.0000.0000.000
92A163VAL 0-0.017-0.01212.8360.0790.0790.0000.0000.0000.000
93A164THR 0-0.022-0.00215.348-0.055-0.0550.0000.0000.0000.000
94A165VAL 00.0080.01419.0410.0220.0220.0000.0000.0000.000
95A166ASP -1-0.796-0.90320.9250.0500.0500.0000.0000.0000.000
96A167PHE 00.027-0.00724.359-0.011-0.0110.0000.0000.0000.000
97A168ASP -1-0.854-0.92626.8530.0340.0340.0000.0000.0000.000
98A169GLY 00.0310.00623.111-0.004-0.0040.0000.0000.0000.000
99A170PHE 0-0.0040.02821.291-0.002-0.0020.0000.0000.0000.000
100A171LYS 10.9100.96022.706-0.028-0.0280.0000.0000.0000.000
101A172ASP -1-0.904-0.93722.6420.0710.0710.0000.0000.0000.000
102A173VAL 00.0580.02617.471-0.006-0.0060.0000.0000.0000.000
103A174ILE 0-0.030-0.00620.191-0.015-0.0150.0000.0000.0000.000
104A175ASN 00.0160.00021.928-0.023-0.0230.0000.0000.0000.000
105A176GLU -1-0.890-0.94319.8960.0550.0550.0000.0000.0000.000
106A177VAL 0-0.095-0.03816.681-0.009-0.0090.0000.0000.0000.000
107A178GLY 0-0.045-0.02119.508-0.025-0.0250.0000.0000.0000.000
108A179GLY 00.0000.01222.588-0.003-0.0030.0000.0000.0000.000
109A180ILE 0-0.097-0.05820.390-0.015-0.0150.0000.0000.0000.000
110A181ASP -1-0.865-0.92823.292-0.128-0.1280.0000.0000.0000.000
111A182VAL 0-0.111-0.03923.922-0.014-0.0140.0000.0000.0000.000
112A183NME 0-0.0140.10026.0600.0050.0050.0000.0000.0000.000
113A183ACE 00.079-0.09428.6090.0000.0000.0000.0000.0000.000
114A184VAL 0-0.045-0.05428.541-0.003-0.0030.0000.0000.0000.000
115A185PRO 00.0020.02431.3290.0000.0000.0000.0000.0000.000
116A186NME 00.0010.00034.4580.0060.0060.0000.0000.0000.000
117A205ACE 0-0.042-0.03227.501-0.004-0.0040.0000.0000.0000.000
118A206GLU -1-0.867-0.90628.307-0.110-0.1100.0000.0000.0000.000
119A207MET 0-0.087-0.02329.4980.0070.0070.0000.0000.0000.000
120A208HIS 00.000-0.01225.1150.0020.0020.0000.0000.0000.000
121A209LEU 00.017-0.00126.6790.0040.0040.0000.0000.0000.000
122A210ASN 00.0110.01026.7480.0030.0030.0000.0000.0000.000
123A211GLY 00.0830.04325.921-0.002-0.0020.0000.0000.0000.000
124A212GLU -1-0.947-0.98526.900-0.008-0.0080.0000.0000.0000.000
125A213GLU -1-0.912-0.95329.697-0.053-0.0530.0000.0000.0000.000
126A214ALA 00.0690.01525.233-0.003-0.0030.0000.0000.0000.000
127A215LEU 0-0.018-0.03226.576-0.002-0.0020.0000.0000.0000.000
128A216ALA 00.011-0.00427.6010.0020.0020.0000.0000.0000.000
129A217TYR 0-0.184-0.05626.865-0.005-0.0050.0000.0000.0000.000
130A218ALA 0-0.069-0.04627.118-0.010-0.0100.0000.0000.0000.000
131A219NME 0-0.0200.00528.8850.0020.0020.0000.0000.0000.000
132A227ACE 00.0570.01535.5050.0010.0010.0000.0000.0000.000
133A228ASP -1-0.852-0.93929.545-0.069-0.0690.0000.0000.0000.000
134A229PHE 00.029-0.00628.445-0.001-0.0010.0000.0000.0000.000
135A230GLY 00.0330.04130.321-0.006-0.0060.0000.0000.0000.000
136A231ARG 10.8750.92529.3580.0390.0390.0000.0000.0000.000
137A232ASN 00.0000.00825.934-0.013-0.0130.0000.0000.0000.000
138A233ASP -1-0.899-0.94824.682-0.159-0.1590.0000.0000.0000.000
139A234ARG 10.9310.96325.0970.0650.0650.0000.0000.0000.000
140A235GLN 00.0700.03922.675-0.015-0.0150.0000.0000.0000.000
141A236LYS 10.9810.99420.1590.1750.1750.0000.0000.0000.000
142A237GLN 0-0.0170.00920.176-0.028-0.0280.0000.0000.0000.000
143A238ILE 00.0320.02220.448-0.013-0.0130.0000.0000.0000.000
144A239LEU 0-0.014-0.00615.114-0.007-0.0070.0000.0000.0000.000
145A240ASN 00.017-0.02316.738-0.057-0.0570.0000.0000.0000.000
146A241ALA 00.0050.02817.634-0.028-0.0280.0000.0000.0000.000
147A242LEU 00.0180.00615.115-0.006-0.0060.0000.0000.0000.000
148A243ILE 0-0.026-0.03212.198-0.027-0.0270.0000.0000.0000.000
149A244ASP -1-0.769-0.88213.813-0.409-0.4090.0000.0000.0000.000
150A245ARG 10.7820.89016.5150.1370.1370.0000.0000.0000.000
151A246MET 0-0.105-0.03311.9050.0390.0390.0000.0000.0000.000
152A247SER 0-0.022-0.02012.005-0.043-0.0430.0000.0000.0000.000
153A248NME 0-0.057-0.03113.0640.0250.0250.0000.0000.0000.000
154A255ACE 00.038-0.00412.820-0.011-0.0110.0000.0000.0000.000
155A256ASP -1-0.886-0.95113.1770.1040.1040.0000.0000.0000.000
156A257LYS 10.8690.92514.689-0.200-0.2000.0000.0000.0000.000
157A258ILE 00.0680.04415.6340.0160.0160.0000.0000.0000.000
158A259ALA 0-0.020-0.00112.1490.0050.0050.0000.0000.0000.000
159A260GLU -1-0.921-0.97314.1350.4610.4610.0000.0000.0000.000
160A261LYS 10.7630.88015.885-0.108-0.1080.0000.0000.0000.000
161A262ALA 00.0380.00116.0730.0040.0040.0000.0000.0000.000
162A263SER 0-0.073-0.03413.4460.0210.0210.0000.0000.0000.000
163A264GLU -1-0.946-0.96315.5120.3510.3510.0000.0000.0000.000
164A265ASN 00.0040.01118.478-0.019-0.0190.0000.0000.0000.000
165A266VAL 0-0.037-0.01715.322-0.035-0.0350.0000.0000.0000.000
166A267GLU -1-0.872-0.92617.6730.1940.1940.0000.0000.0000.000
167A268THR 00.007-0.01812.2110.0220.0220.0000.0000.0000.000
168A269ASN 00.0040.01011.5060.0340.0340.0000.0000.0000.000
169A270ILE 0-0.039-0.0206.6680.2350.2350.0000.0000.0000.000
170A271ARG 10.9160.9633.715-2.726-2.5360.001-0.025-0.1660.000
171A272ILE 00.1250.0527.4090.2990.2990.0000.0000.0000.000
172A273THR 0-0.038-0.0264.6070.1770.2850.000-0.012-0.0970.000
173A274GLU -1-0.831-0.9352.6330.9561.5183.898-1.722-2.7380.002
174A275GLY 00.0750.0463.795-0.489-1.2800.0631.483-0.756-0.006
175A276LEU 00.0180.0086.409-0.592-0.5920.0000.0000.0000.000
176A277ALA 0-0.051-0.0342.587-1.157-1.5263.252-0.882-2.001-0.001
177A278LEU 0-0.032-0.0222.260-3.602-2.9202.150-0.495-2.338-0.005
178A279GLN 00.1140.0633.951-0.0490.0820.004-0.041-0.0940.000
179A280GLN 0-0.017-0.0016.523-0.059-0.0590.0000.0000.0000.000
180A281ILE 0-0.095-0.0532.635-0.452-0.0520.582-0.144-0.8380.000
181A282TYR 0-0.093-0.1035.1940.1090.1090.0000.0000.0000.000
182A283SER 00.0290.0408.4270.2300.2300.0000.0000.0000.000
183A284GLY 00.0200.01711.3560.1170.1170.0000.0000.0000.000
184A285PHE 00.009-0.03711.964-0.094-0.0940.0000.0000.0000.000
185A286THR 00.0300.01811.5100.0450.0450.0000.0000.0000.000
186A287SER 0-0.0180.01813.8430.0430.0430.0000.0000.0000.000
187A288LYS 10.9460.97716.6440.2760.2760.0000.0000.0000.000
188A289LYS 10.8180.91215.9690.5870.5870.0000.0000.0000.000
189A290ILE 0-0.0290.00214.014-0.023-0.0230.0000.0000.0000.000
190A291ASP -1-0.833-0.90116.302-0.327-0.3270.0000.0000.0000.000
191A292THR 0-0.023-0.01318.1360.0000.0000.0000.0000.0000.000
192A293LEU 0-0.0040.00619.1840.0220.0220.0000.0000.0000.000
193A294SER 0-0.017-0.04222.0050.0170.0170.0000.0000.0000.000
194A295ILE 00.0210.03124.266-0.002-0.0020.0000.0000.0000.000
195A296THR 0-0.038-0.03726.8650.0060.0060.0000.0000.0000.000
196A297GLY 00.0650.03830.4510.0010.0010.0000.0000.0000.000
197A298SER 0-0.084-0.01933.3780.0000.0000.0000.0000.0000.000
198A299ASP -1-0.852-0.93936.342-0.060-0.0600.0000.0000.0000.000
199A300LEU 0-0.025-0.00338.5430.0020.0020.0000.0000.0000.000
200A301TYR 0-0.0130.00139.7730.0020.0020.0000.0000.0000.000
201A302LEU 0-0.025-0.01540.2970.0010.0010.0000.0000.0000.000
202A303GLY 0-0.010-0.00943.8900.0020.0020.0000.0000.0000.000
203A304PRO 00.016-0.00746.842-0.002-0.0020.0000.0000.0000.000
204A305ASN 0-0.024-0.01843.690-0.002-0.0020.0000.0000.0000.000
205A306ASN 00.0030.01444.839-0.002-0.0020.0000.0000.0000.000
206A307THR 0-0.027-0.00939.4360.0000.0000.0000.0000.0000.000
207A308TYR 0-0.018-0.01034.832-0.001-0.0010.0000.0000.0000.000
208A309TYR 0-0.040-0.01835.5350.0050.0050.0000.0000.0000.000
209A310PHE 00.0150.01829.925-0.003-0.0030.0000.0000.0000.000
210A311GLU -1-0.786-0.88733.246-0.051-0.0510.0000.0000.0000.000
211A312PRO 0-0.041-0.00630.013-0.005-0.0050.0000.0000.0000.000
212A313ASP -1-0.821-0.95531.936-0.097-0.0970.0000.0000.0000.000
213A314ALA 00.0100.00831.176-0.008-0.0080.0000.0000.0000.000
214A315THR 00.0200.02630.718-0.013-0.0130.0000.0000.0000.000
215A316ASN 00.016-0.01627.094-0.009-0.0090.0000.0000.0000.000
216A317LEU 00.0490.04025.624-0.017-0.0170.0000.0000.0000.000
217A318GLU -1-0.920-0.96625.665-0.127-0.1270.0000.0000.0000.000
218A319LYS 10.8690.94225.9290.1330.1330.0000.0000.0000.000
219A320VAL 00.0050.04021.615-0.028-0.0280.0000.0000.0000.000
220A321ARG 10.8800.94721.3120.0930.0930.0000.0000.0000.000
221A322LYS 10.9901.01120.7840.1860.1860.0000.0000.0000.000
222A323THR 0-0.033-0.06219.230-0.027-0.0270.0000.0000.0000.000
223A324LEU 0-0.011-0.01316.192-0.049-0.0490.0000.0000.0000.000
224A325GLN 0-0.032-0.01416.014-0.055-0.0550.0000.0000.0000.000
225A326GLU -1-0.950-0.97416.667-0.398-0.3980.0000.0000.0000.000
226A327HIS 0-0.049-0.00411.5770.0130.0130.0000.0000.0000.000
227A328LEU 0-0.036-0.02611.120-0.145-0.1450.0000.0000.0000.000
228A329ASP -1-1.028-0.99412.699-0.600-0.6000.0000.0000.0000.000
229A330TYR 0-0.008-0.01614.8330.0440.0440.0000.0000.0000.000
230A331THR 0-0.041-0.03116.8490.0180.0180.0000.0000.0000.000
231A1NME 00.0150.01920.6570.0220.0220.0000.0000.0000.000