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: J3V89

Calculation Name: 4UQF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UQF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y5X1

Base Structure: X-ray

Registration Date: 2023-03-14

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1898394.054063
FMO2-HF: Nuclear repulsion 1823777.045444
FMO2-HF: Total energy -74617.008619
FMO2-MP2: Total energy -74830.194569


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-22.578-21.12810.925-5.755-6.6190.044
Interaction energy analysis for fragmet #1(A:3:GLN)
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 : 0.020
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].
3A5ASP-1-0.812-0.8953.6426.2288.4930.040-0.979-1.3250.000
4A6LYS10.8150.8611.806-28.802-32.9319.600-2.780-2.6920.036
5A7GLN0-0.0100.0086.906-0.604-0.6040.0000.0000.0000.000
6A8LYS10.9140.9539.037-1.167-1.1670.0000.0000.0000.000
7A9ILE0-0.024-0.0028.519-0.216-0.2160.0000.0000.0000.000
8A10ALA00.0210.01010.982-0.251-0.2510.0000.0000.0000.000
9A11ASP-1-0.847-0.93512.8670.9840.9840.0000.0000.0000.000
10A12ALA0-0.012-0.00814.529-0.148-0.1480.0000.0000.0000.000
11A13VAL0-0.022-0.01414.793-0.100-0.1000.0000.0000.0000.000
12A14LYS10.8250.90917.086-0.661-0.6610.0000.0000.0000.000
13A15VAL00.0410.02419.139-0.074-0.0740.0000.0000.0000.000
14A16ILE0-0.048-0.02318.286-0.059-0.0590.0000.0000.0000.000
15A17LEU0-0.030-0.02020.194-0.048-0.0480.0000.0000.0000.000
16A18GLU-1-0.854-0.94923.1070.4680.4680.0000.0000.0000.000
17A19ALA0-0.051-0.02024.647-0.043-0.0430.0000.0000.0000.000
18A20VAL0-0.082-0.03525.334-0.028-0.0280.0000.0000.0000.000
19A21GLY0-0.017-0.00127.866-0.021-0.0210.0000.0000.0000.000
20A22GLU-1-0.796-0.84625.1680.4100.4100.0000.0000.0000.000
21A23ASN00.004-0.01327.0150.0210.0210.0000.0000.0000.000
22A24PRO0-0.009-0.02521.4430.0110.0110.0000.0000.0000.000
23A25ASP-1-0.829-0.89522.2880.5740.5740.0000.0000.0000.000
24A26ARG10.7870.86824.237-0.454-0.4540.0000.0000.0000.000
25A27GLU-1-0.868-0.94824.5270.4380.4380.0000.0000.0000.000
26A28GLY0-0.042-0.02023.3630.0370.0370.0000.0000.0000.000
27A29LEU0-0.079-0.04921.2700.0510.0510.0000.0000.0000.000
28A30ILE00.0890.06119.2120.0900.0900.0000.0000.0000.000
29A31ASP-1-0.769-0.86815.2741.1861.1860.0000.0000.0000.000
30A32THR0-0.038-0.00715.6090.1480.1480.0000.0000.0000.000
31A33PRO00.0330.02215.0910.1330.1330.0000.0000.0000.000
32A34MET00.0880.0429.3110.4980.4980.0000.0000.0000.000
33A35ARG10.7630.89311.146-0.516-0.5160.0000.0000.0000.000
34A36VAL00.0270.02112.9070.1070.1070.0000.0000.0000.000
35A37ALA00.0050.0098.8400.1090.1090.0000.0000.0000.000
36A38ARG10.8080.8548.255-1.260-1.2600.0000.0000.0000.000
37A39MET00.0060.0149.322-0.087-0.0870.0000.0000.0000.000
38A40TYR00.000-0.01410.735-0.113-0.1130.0000.0000.0000.000
39A41GLU-1-0.851-0.9103.27610.68512.3050.108-0.843-0.884-0.005
40A42GLU-1-0.893-0.9357.4240.7830.7830.0000.0000.0000.000
41A43VAL0-0.017-0.0259.969-0.183-0.1830.0000.0000.0000.000
42A44PHE00.004-0.0119.507-0.238-0.2380.0000.0000.0000.000
43A45ALA00.0370.0277.4750.2200.2200.0000.0000.0000.000
44A46GLY00.0370.0148.0790.0290.0290.0000.0000.0000.000
45A47LEU0-0.075-0.0338.534-0.231-0.2310.0000.0000.0000.000
46A48LYS10.8030.9092.743-8.916-7.2221.177-1.153-1.7180.013
47A49LYS10.8200.9026.927-0.978-0.9780.0000.0000.0000.000
48A50ASP-1-0.754-0.82910.0680.0940.0940.0000.0000.0000.000
49A51PRO0-0.025-0.02113.658-0.050-0.0500.0000.0000.0000.000
50A52SER0-0.018-0.05415.615-0.045-0.0450.0000.0000.0000.000
51A53VAL00.0480.02113.914-0.024-0.0240.0000.0000.0000.000
52A54HIS0-0.095-0.04914.612-0.094-0.0940.0000.0000.0000.000
53A55PHE0-0.021-0.03318.7510.0060.0060.0000.0000.0000.000
54A56ASP-1-0.845-0.88919.518-0.145-0.1450.0000.0000.0000.000
55A57THR0-0.069-0.05321.551-0.038-0.0380.0000.0000.0000.000
56A58ILE0-0.0090.00423.8000.0100.0100.0000.0000.0000.000
57A59PHE0-0.017-0.00426.2220.0040.0040.0000.0000.0000.000
58A60GLU-1-0.791-0.89827.780-0.071-0.0710.0000.0000.0000.000
59A61GLU-1-0.955-0.97331.327-0.049-0.0490.0000.0000.0000.000
60A62GLN0-0.086-0.03735.1600.0060.0060.0000.0000.0000.000
61A63HIS00.0220.02136.720-0.002-0.0020.0000.0000.0000.000
62A64GLU-1-0.939-0.99637.332-0.022-0.0220.0000.0000.0000.000
63A65GLU-1-0.912-0.94439.6980.0120.0120.0000.0000.0000.000
64A66LEU0-0.049-0.03837.0130.0010.0010.0000.0000.0000.000
65A67VAL0-0.0010.01432.821-0.001-0.0010.0000.0000.0000.000
66A68LEU0-0.020-0.02133.5960.0070.0070.0000.0000.0000.000
67A69VAL0-0.019-0.00228.224-0.004-0.0040.0000.0000.0000.000
68A70LYS10.8330.90730.785-0.095-0.0950.0000.0000.0000.000
69A71ASP-1-0.863-0.95130.5660.1380.1380.0000.0000.0000.000
70A72ILE0-0.014-0.00124.2300.0070.0070.0000.0000.0000.000
71A73ARG10.9380.96324.943-0.182-0.1820.0000.0000.0000.000
72A74PHE0-0.0020.01421.3070.0040.0040.0000.0000.0000.000
73A75SER0-0.022-0.01819.2180.0140.0140.0000.0000.0000.000
74A76SER00.033-0.00218.0060.0200.0200.0000.0000.0000.000
75A77MET00.0030.01315.976-0.025-0.0250.0000.0000.0000.000
76A78CYS0-0.027-0.00319.044-0.013-0.0130.0000.0000.0000.000
77A79GLU-1-0.737-0.86019.5420.4460.4460.0000.0000.0000.000
78A80HIS0-0.028-0.01420.5020.0260.0260.0000.0000.0000.000
79A81HIS0-0.015-0.02422.480-0.041-0.0410.0000.0000.0000.000
80A82LEU0-0.0160.01016.1590.0340.0340.0000.0000.0000.000
81A83VAL00.0230.01619.1120.0530.0530.0000.0000.0000.000
82A84PRO00.054-0.00120.134-0.021-0.0210.0000.0000.0000.000
83A85PHE0-0.039-0.01021.515-0.048-0.0480.0000.0000.0000.000
84A86PHE00.0200.00422.4500.0310.0310.0000.0000.0000.000
85A87GLY00.0100.00424.493-0.024-0.0240.0000.0000.0000.000
86A88VAL0-0.051-0.01626.3540.0040.0040.0000.0000.0000.000
87A89ALA00.0090.01125.5920.0030.0030.0000.0000.0000.000
88A90HIS00.0240.00827.590-0.016-0.0160.0000.0000.0000.000
89A91VAL0-0.007-0.00526.7840.0040.0040.0000.0000.0000.000
90A92ALA00.0310.01830.247-0.008-0.0080.0000.0000.0000.000
91A93TYR00.004-0.00730.5120.0000.0000.0000.0000.0000.000
92A94LEU00.0490.03533.856-0.002-0.0020.0000.0000.0000.000
93A95PRO00.0380.02634.454-0.001-0.0010.0000.0000.0000.000
94A96GLN00.0120.00735.194-0.003-0.0030.0000.0000.0000.000
95A97ASN00.0130.00635.726-0.006-0.0060.0000.0000.0000.000
96A98GLY00.0620.05036.837-0.007-0.0070.0000.0000.0000.000
97A99ARG10.7980.88131.0210.0340.0340.0000.0000.0000.000
98A100VAL00.0360.02131.3500.0120.0120.0000.0000.0000.000
99A101ALA00.0170.01226.365-0.013-0.0130.0000.0000.0000.000
100A102GLY00.013-0.00227.0210.0110.0110.0000.0000.0000.000
101A103LEU00.0250.00225.6180.0070.0070.0000.0000.0000.000
102A104SER0-0.008-0.01222.5320.0190.0190.0000.0000.0000.000
103A105LYS10.8180.91321.0660.1020.1020.0000.0000.0000.000
104A106LEU00.0700.02621.0370.0220.0220.0000.0000.0000.000
105A107ALA0-0.003-0.00422.2730.0280.0280.0000.0000.0000.000
106A108ARG10.9410.97416.3550.0580.0580.0000.0000.0000.000
107A109VAL00.0150.02517.3190.0510.0510.0000.0000.0000.000
108A110VAL00.000-0.00218.8080.0450.0450.0000.0000.0000.000
109A111ASP-1-0.803-0.86316.9480.5020.5020.0000.0000.0000.000
110A112ASP-1-0.762-0.87212.8360.4800.4800.0000.0000.0000.000
111A113VAL0-0.053-0.01714.4530.0810.0810.0000.0000.0000.000
112A114SER0-0.006-0.01017.1080.0290.0290.0000.0000.0000.000
113A115ARG10.7560.88712.394-0.635-0.6350.0000.0000.0000.000
114A116ARG10.8970.92912.180-0.446-0.4460.0000.0000.0000.000
115A117PRO0-0.0030.00613.344-0.082-0.0820.0000.0000.0000.000
116A118GLN0-0.019-0.01416.581-0.079-0.0790.0000.0000.0000.000
117A119LEU00.0100.01819.668-0.008-0.0080.0000.0000.0000.000
118A120GLN00.0450.00723.1050.0180.0180.0000.0000.0000.000
119A121GLU-1-0.832-0.92225.1410.2440.2440.0000.0000.0000.000
120A122ARG10.8000.88420.230-0.395-0.3950.0000.0000.0000.000
121A123ILE00.0090.02420.189-0.016-0.0160.0000.0000.0000.000
122A124THR00.004-0.00522.526-0.029-0.0290.0000.0000.0000.000
123A125THR0-0.041-0.04425.957-0.020-0.0200.0000.0000.0000.000
124A126THR0-0.023-0.02119.696-0.018-0.0180.0000.0000.0000.000
125A127VAL00.0130.00421.945-0.022-0.0220.0000.0000.0000.000
126A128ALA00.0100.00423.769-0.024-0.0240.0000.0000.0000.000
127A129GLU-1-0.778-0.85524.7290.0760.0760.0000.0000.0000.000
128A130ILE00.0370.02119.476-0.019-0.0190.0000.0000.0000.000
129A131MET0-0.027-0.00823.744-0.018-0.0180.0000.0000.0000.000
130A132MET0-0.062-0.03226.603-0.015-0.0150.0000.0000.0000.000
131A133GLU-1-0.963-0.98323.3890.0190.0190.0000.0000.0000.000
132A134LYS10.7830.86720.0480.0710.0710.0000.0000.0000.000
133A135LEU00.0120.01425.613-0.013-0.0130.0000.0000.0000.000
134A136LYS10.8860.97028.7670.0160.0160.0000.0000.0000.000
135A137PRO00.0390.03430.591-0.005-0.0050.0000.0000.0000.000
136A138LEU0-0.018-0.01933.6140.0000.0000.0000.0000.0000.000
137A139GLY0-0.014-0.01734.5710.0030.0030.0000.0000.0000.000
138A140VAL0-0.010-0.00529.327-0.003-0.0030.0000.0000.0000.000
139A141MET0-0.0160.00132.6930.0000.0000.0000.0000.0000.000
140A142VAL0-0.0010.01326.759-0.001-0.0010.0000.0000.0000.000
141A143ILE00.005-0.01530.1970.0000.0000.0000.0000.0000.000
142A144MET0-0.042-0.01023.5930.0040.0040.0000.0000.0000.000
143A145GLU-1-0.858-0.91529.2150.1760.1760.0000.0000.0000.000
144A146ALA0-0.008-0.00626.5670.0110.0110.0000.0000.0000.000
145A147GLU-1-0.794-0.86128.3140.2470.2470.0000.0000.0000.000
146A148HIS0-0.005-0.02126.0000.0480.0480.0000.0000.0000.000
147A149MET00.0400.02724.778-0.020-0.0200.0000.0000.0000.000
148A151MET0-0.061-0.03427.288-0.018-0.0180.0000.0000.0000.000
149A152THR0-0.026-0.03329.692-0.012-0.0120.0000.0000.0000.000
150A153ILE00.0130.00825.808-0.008-0.0080.0000.0000.0000.000
151A154ARG10.8750.95127.350-0.331-0.3310.0000.0000.0000.000
152A155GLY00.0360.00631.262-0.014-0.0140.0000.0000.0000.000
153A156VAL0-0.0240.00432.940-0.013-0.0130.0000.0000.0000.000
154A157ASN00.0000.00534.571-0.013-0.0130.0000.0000.0000.000
155A158LYS10.8500.91634.506-0.217-0.2170.0000.0000.0000.000
156A159PRO00.0680.04733.7300.0070.0070.0000.0000.0000.000
157A160GLY00.0000.00333.869-0.015-0.0150.0000.0000.0000.000
158A161THR0-0.077-0.05833.345-0.016-0.0160.0000.0000.0000.000
159A162LYS10.8700.93032.196-0.193-0.1930.0000.0000.0000.000
160A163THR00.0230.02029.668-0.018-0.0180.0000.0000.0000.000
161A164ILE00.0070.01031.1360.0070.0070.0000.0000.0000.000
162A165THR00.0030.00028.600-0.002-0.0020.0000.0000.0000.000
163A166SER0-0.039-0.03331.457-0.008-0.0080.0000.0000.0000.000
164A167ALA00.0040.01029.8570.0020.0020.0000.0000.0000.000
165A168VAL00.0030.00831.856-0.005-0.0050.0000.0000.0000.000
166A169ARG10.7370.82429.434-0.096-0.0960.0000.0000.0000.000
167A170GLY00.0780.03433.998-0.002-0.0020.0000.0000.0000.000
168A171ALA00.0530.01536.5740.0050.0050.0000.0000.0000.000
169A172PHE00.0670.04236.1050.0030.0030.0000.0000.0000.000
170A173LYS10.9410.97535.249-0.053-0.0530.0000.0000.0000.000
171A174ASN0-0.069-0.04338.8290.0030.0030.0000.0000.0000.000
172A175ASP-1-0.812-0.89241.9340.0380.0380.0000.0000.0000.000
173A176ASP-1-0.835-0.92342.2950.0530.0530.0000.0000.0000.000
174A177LYS10.8330.91144.310-0.039-0.0390.0000.0000.0000.000
175A178LEU00.0810.04839.2960.0040.0040.0000.0000.0000.000
176A179ARG10.8400.89938.807-0.060-0.0600.0000.0000.0000.000
177A180SER0-0.007-0.00440.4410.0060.0060.0000.0000.0000.000
178A181GLU-1-0.949-0.97242.4260.0450.0450.0000.0000.0000.000
179A182VAL00.0060.00135.9460.0030.0030.0000.0000.0000.000
180A183LEU0-0.005-0.00637.6050.0060.0060.0000.0000.0000.000
181A184ALA0-0.018-0.00339.6660.0050.0050.0000.0000.0000.000
182A185LEU0-0.012-0.00739.1020.0020.0020.0000.0000.0000.000
183A186ILE0-0.001-0.01034.5560.0030.0030.0000.0000.0000.000
184A187LYS10.8850.95637.439-0.074-0.0740.0000.0000.0000.000
185A188HIS00.0210.03139.0900.0050.0050.0000.0000.0000.000