FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: KZ2Q3

Calculation Name: 4U9P-C-Xray549

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4U9P

Chain ID: C

ChEMBL ID:

UniProt ID: Q58499

Base Structure: X-ray

Registration Date: 2025-10-12

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2822908.764029
FMO2-HF: Nuclear repulsion 2734884.679825
FMO2-HF: Total energy -88024.084204
FMO2-MP2: Total energy -88280.831131


3D Structure Molmil
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(C:0:HIS)


Summations of interaction energy for fragment #1(C:0:HIS)
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.
-171.375-165.56214.419-9.02-11.213-0.083
Interaction energy analysis for fragmet #1(C:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.741 / q_NPA : 0.855
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].
3C2ILE00.0140.0143.3912.0315.3120.437-1.381-2.337-0.005
4C3LEU00.011-0.0015.1390.7520.858-0.001-0.009-0.0960.000
23C22ASP-1-0.779-0.8644.973-27.223-27.027-0.001-0.007-0.1870.000
199C198LYS10.9070.9363.22156.80357.3140.020-0.123-0.409-0.001
200C199GLU-1-0.885-0.9195.130-30.512-30.488-0.001-0.001-0.0220.000
232C231LYS10.8410.9132.22125.74327.2480.845-0.767-1.5830.007
233C232GLU-1-0.947-0.9754.404-34.494-34.358-0.001-0.016-0.1200.000
235C234CYS-1-0.876-0.8931.822-108.509-108.45513.121-6.716-6.459-0.084
5C4LEU0-0.023-0.0017.1432.5032.5030.0000.0000.0000.000
6C5VAL00.020-0.00310.7070.1730.1730.0000.0000.0000.000
7C6SER0-0.056-0.03513.2220.4240.4240.0000.0000.0000.000
8C7PRO0-0.037-0.01516.4050.3970.3970.0000.0000.0000.000
9C8ILE0-0.040-0.02619.0080.2800.2800.0000.0000.0000.000
10C9ASP-1-0.788-0.86422.116-10.949-10.9490.0000.0000.0000.000
11C10VAL00.0750.00821.534-0.468-0.4680.0000.0000.0000.000
12C11GLU-1-0.853-0.89721.592-11.405-11.4050.0000.0000.0000.000
13C12GLU-1-0.719-0.84119.252-13.513-13.5130.0000.0000.0000.000
14C13ALA00.0330.01517.187-0.754-0.7540.0000.0000.0000.000
15C14LYS10.8440.91716.26810.54710.5470.0000.0000.0000.000
16C15GLU-1-0.826-0.89316.465-13.826-13.8260.0000.0000.0000.000
17C16ALA00.006-0.00613.195-0.757-0.7570.0000.0000.0000.000
18C17ILE0-0.014-0.00311.853-1.082-1.0820.0000.0000.0000.000
19C18ALA0-0.041-0.02112.144-0.629-0.6290.0000.0000.0000.000
20C19GLY0-0.009-0.01111.6220.0110.0110.0000.0000.0000.000
21C20GLY0-0.032-0.0078.086-1.473-1.4730.0000.0000.0000.000
22C21ALA0-0.025-0.0216.823-2.193-2.1930.0000.0000.0000.000
24C23ILE0-0.035-0.0177.9281.0141.0140.0000.0000.0000.000
25C24ILE00.0060.01111.039-0.107-0.1070.0000.0000.0000.000
26C25ASP-1-0.794-0.87214.440-15.967-15.9670.0000.0000.0000.000
27C26VAL00.007-0.00816.6900.5070.5070.0000.0000.0000.000
28C27LYS10.9180.96219.65714.99614.9960.0000.0000.0000.000
29C28ASN0-0.047-0.03222.7420.1950.1950.0000.0000.0000.000
30C29PRO00.013-0.00524.1480.2040.2040.0000.0000.0000.000
31C30LYS10.9160.96626.7369.3449.3440.0000.0000.0000.000
32C31GLU-1-0.921-0.95529.325-9.416-9.4160.0000.0000.0000.000
33C32GLY00.0130.01028.5450.0200.0200.0000.0000.0000.000
34C33SER0-0.111-0.06723.901-0.385-0.3850.0000.0000.0000.000
35C34LEU0-0.016-0.03020.343-0.653-0.6530.0000.0000.0000.000
36C35GLY00.0480.03623.8960.1740.1740.0000.0000.0000.000
37C36ALA00.0340.02725.428-0.424-0.4240.0000.0000.0000.000
38C37ASN0-0.013-0.00524.7350.6730.6730.0000.0000.0000.000
39C38PHE00.0360.00926.7280.0880.0880.0000.0000.0000.000
40C39PRO00.0450.02427.261-0.240-0.2400.0000.0000.0000.000
41C40TRP00.023-0.00627.282-0.173-0.1730.0000.0000.0000.000
42C41MET0-0.0160.00824.273-0.120-0.1200.0000.0000.0000.000
43C42ILE00.001-0.00221.964-0.324-0.3240.0000.0000.0000.000
44C43LYS11.0051.00722.4819.3479.3470.0000.0000.0000.000
45C44ALA0-0.035-0.01523.980-0.099-0.0990.0000.0000.0000.000
46C45ILE00.005-0.00318.643-0.146-0.1460.0000.0000.0000.000
47C46ARG10.7340.84615.39114.23414.2340.0000.0000.0000.000
48C47GLU-1-0.948-0.96020.095-11.020-11.0200.0000.0000.0000.000
49C48VAL0-0.080-0.03719.352-0.016-0.0160.0000.0000.0000.000
50C49THR0-0.017-0.01914.620-0.502-0.5020.0000.0000.0000.000
51C50PRO00.0010.01014.3440.3500.3500.0000.0000.0000.000
52C51LYS10.9430.95415.06711.55411.5540.0000.0000.0000.000
53C52ASP-1-0.881-0.92711.980-16.704-16.7040.0000.0000.0000.000
54C53LEU0-0.0100.0179.378-1.090-1.0900.0000.0000.0000.000
55C54LEU00.0210.00910.2210.9360.9360.0000.0000.0000.000
56C55VAL00.0110.00913.134-0.255-0.2550.0000.0000.0000.000
57C56SER0-0.043-0.03315.023-0.115-0.1150.0000.0000.0000.000
58C57ALA00.0190.00716.7720.4830.4830.0000.0000.0000.000
59C58THR0-0.036-0.02020.465-0.250-0.2500.0000.0000.0000.000
60C59VAL0-0.008-0.01122.6660.4960.4960.0000.0000.0000.000
61C60GLY0-0.025-0.01425.4280.5130.5130.0000.0000.0000.000
62C61ASP-1-0.746-0.84126.223-12.472-12.4720.0000.0000.0000.000
63C62VAL0-0.030-0.00627.3390.5050.5050.0000.0000.0000.000
64C63PRO00.0110.00129.9820.0590.0590.0000.0000.0000.000
65C64TYR00.0320.00232.603-0.049-0.0490.0000.0000.0000.000
66C65LYS10.9270.95533.4148.5928.5920.0000.0000.0000.000
67C66PRO00.0760.03832.050-0.082-0.0820.0000.0000.0000.000
68C67GLY00.0470.04632.162-0.184-0.1840.0000.0000.0000.000
69C68THR0-0.009-0.01433.633-0.015-0.0150.0000.0000.0000.000
70C69ILE00.0210.00627.770-0.041-0.0410.0000.0000.0000.000
71C70SER00.0400.01228.766-0.383-0.3830.0000.0000.0000.000
72C71LEU0-0.012-0.00629.656-0.098-0.0980.0000.0000.0000.000
73C72ALA0-0.007-0.00128.982-0.026-0.0260.0000.0000.0000.000
74C73ALA00.0020.01025.426-0.240-0.2400.0000.0000.0000.000
75C74VAL00.0360.02325.745-0.238-0.2380.0000.0000.0000.000
76C75GLY0-0.0010.00127.695-0.041-0.0410.0000.0000.0000.000
77C76ALA00.0020.00723.417-0.020-0.0200.0000.0000.0000.000
78C77ALA00.0340.01823.025-0.237-0.2370.0000.0000.0000.000
79C78ILE0-0.016-0.01024.099-0.040-0.0400.0000.0000.0000.000
80C79SER0-0.116-0.07725.3660.2850.2850.0000.0000.0000.000
81C80GLY0-0.016-0.00822.673-0.056-0.0560.0000.0000.0000.000
82C81ALA0-0.009-0.00319.725-0.453-0.4530.0000.0000.0000.000
83C82ASP-1-0.798-0.88415.526-14.545-14.5450.0000.0000.0000.000
84C83TYR00.0080.0059.826-0.645-0.6450.0000.0000.0000.000
85C84ILE0-0.002-0.00616.7200.6220.6220.0000.0000.0000.000
86C85LYS10.8530.92216.95316.57316.5730.0000.0000.0000.000
87C86VAL00.014-0.00520.4370.7220.7220.0000.0000.0000.000
88C87GLY00.0730.04422.981-0.540-0.5400.0000.0000.0000.000
89C88LEU0-0.039-0.02623.5890.7890.7890.0000.0000.0000.000
90C89TYR00.015-0.00226.6720.2360.2360.0000.0000.0000.000
91C90GLY0-0.021-0.02429.5330.2820.2820.0000.0000.0000.000
92C91VAL0-0.056-0.02228.6630.3570.3570.0000.0000.0000.000
93C92LYS10.8980.94531.0629.3599.3590.0000.0000.0000.000
94C93ASN00.005-0.00331.125-0.183-0.1830.0000.0000.0000.000
95C94TYR00.025-0.02526.4090.1750.1750.0000.0000.0000.000
96C95TYR00.0440.02429.404-0.155-0.1550.0000.0000.0000.000
97C96GLN00.0210.01332.016-0.160-0.1600.0000.0000.0000.000
98C97ALA00.0310.01626.968-0.006-0.0060.0000.0000.0000.000
99C98VAL00.0170.01326.637-0.195-0.1950.0000.0000.0000.000
100C99GLU-1-0.878-0.93028.382-9.491-9.4910.0000.0000.0000.000
101C100LEU0-0.051-0.03227.9170.1220.1220.0000.0000.0000.000
102C101MET00.0060.00422.5900.0710.0710.0000.0000.0000.000
103C102LYS10.9330.98126.26710.80910.8090.0000.0000.0000.000
104C103ASN0-0.111-0.05628.3860.1900.1900.0000.0000.0000.000
105C104VAL00.0100.00124.2390.0560.0560.0000.0000.0000.000
106C105VAL00.0150.00222.770-0.080-0.0800.0000.0000.0000.000
107C106ARG10.8250.90425.0479.2289.2280.0000.0000.0000.000
108C107ALA0-0.036-0.01827.8800.0680.0680.0000.0000.0000.000
109C108VAL0-0.001-0.01021.4640.1640.1640.0000.0000.0000.000
110C109LYS10.9460.99223.41211.88811.8880.0000.0000.0000.000
111C110ASP-1-0.840-0.91225.073-9.595-9.5950.0000.0000.0000.000
112C111ILE0-0.128-0.05225.7320.3580.3580.0000.0000.0000.000
113C112ASP-1-0.819-0.93121.583-12.533-12.5330.0000.0000.0000.000
114C113GLU-1-0.899-0.96422.378-12.124-12.1240.0000.0000.0000.000
115C114ASN0-0.110-0.05217.867-0.861-0.8610.0000.0000.0000.000
116C115LYS10.7870.91217.19012.33512.3350.0000.0000.0000.000
117C116ILE00.0040.01413.6910.0160.0160.0000.0000.0000.000
118C117VAL0-0.005-0.02116.9510.2820.2820.0000.0000.0000.000
119C118VAL0-0.009-0.01615.543-0.693-0.6930.0000.0000.0000.000
120C119ALA00.0200.01018.2280.9130.9130.0000.0000.0000.000
121C120ALA00.011-0.00119.525-0.813-0.8130.0000.0000.0000.000
122C121GLY00.0090.01220.6030.9650.9650.0000.0000.0000.000
123C122TYR0-0.046-0.06421.548-0.370-0.3700.0000.0000.0000.000
124C123ALA00.0580.02420.1040.3220.3220.0000.0000.0000.000
125C124ASP-1-0.733-0.84821.957-12.498-12.4980.0000.0000.0000.000
126C125ALA00.0140.01225.5130.5510.5510.0000.0000.0000.000
127C126TYR00.0390.01327.3690.3340.3340.0000.0000.0000.000
128C127ARG10.7640.86927.37111.80411.8040.0000.0000.0000.000
129C128VAL0-0.034-0.01429.4290.2590.2590.0000.0000.0000.000
130C129GLY0-0.0220.00632.2920.2060.2060.0000.0000.0000.000
131C130ALA0-0.034-0.00628.4790.2150.2150.0000.0000.0000.000
132C131VAL0-0.056-0.02226.3170.0810.0810.0000.0000.0000.000
133C132GLU-1-0.843-0.92125.241-12.806-12.8060.0000.0000.0000.000
134C133PRO00.002-0.00521.580-0.235-0.2350.0000.0000.0000.000
135C134LEU00.0380.00621.423-0.638-0.6380.0000.0000.0000.000
136C135ILE0-0.038-0.00822.3790.0110.0110.0000.0000.0000.000
137C136VAL0-0.035-0.01519.5620.1840.1840.0000.0000.0000.000
138C137PRO00.0510.03117.6330.0600.0600.0000.0000.0000.000
139C138LYS10.9230.97219.32513.05513.0550.0000.0000.0000.000
140C139ILE0-0.037-0.02522.7100.4030.4030.0000.0000.0000.000
141C140ALA00.0100.00119.0620.4000.4000.0000.0000.0000.000
142C141ARG10.8540.91820.35713.62613.6260.0000.0000.0000.000
143C142ASP-1-0.801-0.84221.437-12.024-12.0240.0000.0000.0000.000
144C143ALA0-0.067-0.05324.2650.6730.6730.0000.0000.0000.000
145C144GLY0-0.0230.00422.8030.4300.4300.0000.0000.0000.000
146C145CYS0-0.091-0.03819.8370.3070.3070.0000.0000.0000.000
147C146ASP-1-0.784-0.87615.164-16.869-16.8690.0000.0000.0000.000
148C147VAL0-0.046-0.02813.175-1.562-1.5620.0000.0000.0000.000
149C148ALA00.0070.02514.9871.4941.4940.0000.0000.0000.000
150C149MET0-0.013-0.01414.780-1.387-1.3870.0000.0000.0000.000
151C150LEU00.0010.01616.3411.4161.4160.0000.0000.0000.000
152C151ASP-1-0.785-0.90517.246-16.968-16.9680.0000.0000.0000.000
153C152THR0-0.030-0.00619.8690.2620.2620.0000.0000.0000.000
154C153ALA0-0.015-0.00322.9520.0480.0480.0000.0000.0000.000
155C154ILE0-0.035-0.01326.3970.2960.2960.0000.0000.0000.000
156C155LYS10.8440.92021.95613.87613.8760.0000.0000.0000.000
157C156ASP-1-0.785-0.87926.809-11.052-11.0520.0000.0000.0000.000
158C157GLY0-0.025-0.01525.4000.1480.1480.0000.0000.0000.000
159C158LYS10.8620.93924.52410.40910.4090.0000.0000.0000.000
160C159THR0-0.087-0.07619.732-0.516-0.5160.0000.0000.0000.000
161C160LEU00.0110.00514.9630.6330.6330.0000.0000.0000.000
162C161PHE00.0330.00113.4000.2410.2410.0000.0000.0000.000
163C162ASP-1-0.862-0.89019.532-13.380-13.3800.0000.0000.0000.000
164C163PHE0-0.067-0.04622.1810.8300.8300.0000.0000.0000.000
165C164GLN0-0.002-0.00319.2650.1680.1680.0000.0000.0000.000
166C165SER00.0270.01519.395-0.746-0.7460.0000.0000.0000.000
167C166LYS10.8470.89012.52223.59923.5990.0000.0000.0000.000
168C167GLU-1-0.920-0.94115.310-18.870-18.8700.0000.0000.0000.000
169C168ILE00.0380.01917.071-0.463-0.4630.0000.0000.0000.000
170C169LEU0-0.039-0.02514.185-0.268-0.2680.0000.0000.0000.000
171C170ALA00.0360.02112.750-1.465-1.4650.0000.0000.0000.000
172C171GLU-1-0.895-0.94913.796-15.954-15.9540.0000.0000.0000.000
173C172PHE0-0.035-0.02714.6100.1250.1250.0000.0000.0000.000
174C173VAL0-0.009-0.0289.275-0.075-0.0750.0000.0000.0000.000
175C174ASP-1-0.887-0.94011.985-25.715-25.7150.0000.0000.0000.000
176C175GLU-1-0.820-0.88313.725-14.485-14.4850.0000.0000.0000.000
177C176ALA00.004-0.00113.4140.5940.5940.0000.0000.0000.000
178C177HIS10.8120.8988.24732.67832.6780.0000.0000.0000.000
179C178SER0-0.083-0.04212.8620.8350.8350.0000.0000.0000.000
180C179TYR0-0.099-0.10416.3241.5181.5180.0000.0000.0000.000
181C180GLY0-0.0100.00114.4780.6850.6850.0000.0000.0000.000
182C181LEU0-0.059-0.00914.341-0.355-0.3550.0000.0000.0000.000
183C182LYS10.8650.9317.06034.36334.3630.0000.0000.0000.000
184C183CYS00.0180.01810.0183.0183.0180.0000.0000.0000.000
185C184ALA0-0.015-0.0089.991-3.206-3.2060.0000.0000.0000.000
186C185LEU00.011-0.00411.3992.2042.2040.0000.0000.0000.000
187C186ALA00.0360.01713.237-1.148-1.1480.0000.0000.0000.000
188C187GLY00.0470.01616.0970.4320.4320.0000.0000.0000.000
189C188SER0-0.095-0.06219.314-0.056-0.0560.0000.0000.0000.000
190C189ILE00.0280.02613.2850.6470.6470.0000.0000.0000.000
191C190LYS10.8810.95216.38016.14416.1440.0000.0000.0000.000
192C191LYS10.8670.93513.66317.57817.5780.0000.0000.0000.000
193C192GLU-1-0.810-0.92812.974-19.826-19.8260.0000.0000.0000.000
194C193HIS0-0.012-0.01313.908-0.609-0.6090.0000.0000.0000.000
195C194ILE00.0260.0208.005-0.947-0.9470.0000.0000.0000.000
196C195PRO00.0170.0028.611-3.886-3.8860.0000.0000.0000.000
197C196ILE00.0020.0058.894-1.980-1.9800.0000.0000.0000.000
198C197LEU00.0180.0069.085-0.171-0.1710.0000.0000.0000.000
201C200ILE0-0.040-0.0187.7660.8070.8070.0000.0000.0000.000
202C201GLY00.0340.0285.1501.5501.5500.0000.0000.0000.000
203C202THR0-0.043-0.0466.1792.1762.1760.0000.0000.0000.000
204C203ASP-1-0.813-0.8845.374-47.619-47.6190.0000.0000.0000.000
205C204ILE0-0.017-0.0106.433-2.890-2.8900.0000.0000.0000.000
206C205VAL00.0430.0247.7612.3482.3480.0000.0000.0000.000
207C206GLY0-0.0010.00310.3050.8030.8030.0000.0000.0000.000
208C207VAL0-0.050-0.03511.7021.1041.1040.0000.0000.0000.000
209C208ARG10.8110.86314.25013.87313.8730.0000.0000.0000.000
210C209GLY0-0.014-0.00916.8080.1210.1210.0000.0000.0000.000
211C210ALA00.0310.01314.2270.5000.5000.0000.0000.0000.000
212C211ALA00.0210.00813.729-0.381-0.3810.0000.0000.0000.000
213C212CYS0-0.067-0.01915.5730.8550.8550.0000.0000.0000.000
214C213LYS10.8640.91819.21113.69713.6970.0000.0000.0000.000
215C214GLY00.0040.00121.4760.2990.2990.0000.0000.0000.000
216C215GLY00.0270.01825.0210.3090.3090.0000.0000.0000.000
217C216ASP-1-0.845-0.93726.717-9.367-9.3670.0000.0000.0000.000
218C217ARG10.8840.95529.0309.7109.7100.0000.0000.0000.000
219C218ASN0-0.058-0.04630.2960.3210.3210.0000.0000.0000.000
220C219ASN0-0.064-0.02226.894-0.230-0.2300.0000.0000.0000.000
221C220GLY00.027-0.00224.543-0.121-0.1210.0000.0000.0000.000
222C221ARG10.8220.89022.12911.46811.4680.0000.0000.0000.000
223C222ILE0-0.022-0.00115.660-0.288-0.2880.0000.0000.0000.000
224C223ASP-1-0.756-0.87517.056-13.841-13.8410.0000.0000.0000.000
225C224ARG10.9070.94114.24212.28812.2880.0000.0000.0000.000
226C225GLU-1-0.935-0.95013.416-14.911-14.9110.0000.0000.0000.000
227C226LEU0-0.003-0.00713.702-1.085-1.0850.0000.0000.0000.000
228C227VAL0-0.038-0.02210.093-1.199-1.1990.0000.0000.0000.000
229C228LYS10.9921.0049.25016.69716.6970.0000.0000.0000.000
230C229GLU-1-0.882-0.9308.855-20.278-20.2780.0000.0000.0000.000
231C230LEU0-0.042-0.0299.234-1.251-1.2510.0000.0000.0000.000
234C233LEU0-0.055-0.0216.937-1.198-1.1980.0000.0000.0000.000