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: 4J6GN

Calculation Name: 1KUT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KUT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0X0

Base Structure: X-ray

Registration Date: 2023-09-23

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2585247.665207
FMO2-HF: Nuclear repulsion 2500127.05722
FMO2-HF: Total energy -85120.607987
FMO2-MP2: Total energy -85370.465419


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:7:THR)


Summations of interaction energy for fragment #1(A:7:THR)
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.
-14.798-6.0482.058-4.715-6.092-0.01
Interaction energy analysis for fragmet #1(A:7:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.021
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].
3A9ILE0-0.049-0.0123.669-1.1532.365-0.013-1.934-1.5700.006
4A10VAL00.0340.0256.230-0.640-0.6400.0000.0000.0000.000
5A11LYS10.9540.9689.342-0.416-0.4160.0000.0000.0000.000
6A12VAL00.0020.00512.666-0.095-0.0950.0000.0000.0000.000
7A13THR0-0.052-0.05016.0570.0160.0160.0000.0000.0000.000
8A14GLY0-0.0050.02518.839-0.031-0.0310.0000.0000.0000.000
9A15ASP-1-0.888-0.94321.1060.0580.0580.0000.0000.0000.000
10A16TYR0-0.031-0.02719.041-0.024-0.0240.0000.0000.0000.000
11A17ALA0-0.006-0.00314.0590.0510.0510.0000.0000.0000.000
12A18LEU00.0040.00613.780-0.073-0.0730.0000.0000.0000.000
13A19LEU0-0.008-0.0097.0730.1870.1870.0000.0000.0000.000
14A20GLU-1-0.913-0.9578.129-0.105-0.1050.0000.0000.0000.000
15A21PHE00.017-0.0135.4220.1620.1620.0000.0000.0000.000
16A22LYS10.8930.9413.525-5.513-4.1590.021-0.561-0.8140.002
17A23ASP-1-0.842-0.9242.635-8.864-7.2970.433-1.005-0.994-0.013
18A24ASP-1-0.704-0.7332.304-1.0561.0781.619-1.200-2.553-0.005
19A36LEU0-0.202-0.2145.943-0.116-0.1160.0000.0000.0000.000
20A37THR0-0.042-0.0497.641-0.052-0.0520.0000.0000.0000.000
21A38GLY00.0360.0377.8990.2060.2060.0000.0000.0000.000
22A39LYS10.8810.9363.9053.5013.640-0.001-0.014-0.1250.000
23A40GLY00.0260.0235.866-0.157-0.1570.0000.0000.0000.000
24A41SER0-0.007-0.0396.4660.3510.3510.0000.0000.0000.000
25A42ILE00.0470.02210.0790.1520.1520.0000.0000.0000.000
26A43CYS0-0.0150.0085.9740.3320.3320.0000.0000.0000.000
27A44ALA00.0170.0348.7080.2510.2510.0000.0000.0000.000
28A45GLU-1-0.804-0.87710.282-0.384-0.3840.0000.0000.0000.000
29A46THR0-0.023-0.04011.6120.1520.1520.0000.0000.0000.000
30A47THR00.0080.00410.0700.1410.1410.0000.0000.0000.000
31A48ALA0-0.019-0.01712.7320.1300.1300.0000.0000.0000.000
32A49ILE0-0.040-0.00615.4710.0870.0870.0000.0000.0000.000
33A50LEU00.0180.00514.9880.0580.0580.0000.0000.0000.000
34A51MET0-0.0250.00112.5890.0710.0710.0000.0000.0000.000
35A52LYS10.9450.98017.3150.2780.2780.0000.0000.0000.000
36A53TYR00.0170.01320.3760.0440.0440.0000.0000.0000.000
37A54LEU0-0.006-0.02418.1950.0320.0320.0000.0000.0000.000
38A55SER0-0.016-0.00320.7440.0330.0330.0000.0000.0000.000
39A56GLU-1-0.943-0.95123.148-0.179-0.1790.0000.0000.0000.000
40A57LYS10.8430.93424.8390.1940.1940.0000.0000.0000.000
41A58GLY0-0.021-0.02326.3980.0110.0110.0000.0000.0000.000
42A59ILE0-0.068-0.02220.7270.0170.0170.0000.0000.0000.000
43A60LYS10.9650.99221.4210.0570.0570.0000.0000.0000.000
44A61THR00.0380.01616.789-0.007-0.0070.0000.0000.0000.000
45A62HIS0-0.008-0.02811.2540.0990.0990.0000.0000.0000.000
46A63LEU00.0200.01615.2330.0050.0050.0000.0000.0000.000
47A64VAL0-0.099-0.02717.0660.0330.0330.0000.0000.0000.000
48A65GLU-1-0.944-0.99818.007-0.171-0.1710.0000.0000.0000.000
49A66TYR00.0120.00013.1960.0290.0290.0000.0000.0000.000
50A67ILE00.0050.01215.5430.0490.0490.0000.0000.0000.000
51A68PRO0-0.0280.01914.939-0.063-0.0630.0000.0000.0000.000
52A69PRO00.014-0.02012.6380.0610.0610.0000.0000.0000.000
53A70ARG10.9710.9878.2360.8900.8900.0000.0000.0000.000
54A71THR00.0280.0309.541-0.191-0.1910.0000.0000.0000.000
55A72LEU0-0.0160.00810.7950.0120.0120.0000.0000.0000.000
56A73LYS10.9500.99913.5000.1680.1680.0000.0000.0000.000
57A74VAL00.036-0.00812.918-0.034-0.0340.0000.0000.0000.000
58A75ILE0-0.039-0.00916.0800.0490.0490.0000.0000.0000.000
59A76PRO0-0.006-0.00816.3160.0000.0000.0000.0000.0000.000
60A77LEU0-0.005-0.00615.242-0.024-0.0240.0000.0000.0000.000
61A78LYS10.9340.98615.616-0.094-0.0940.0000.0000.0000.000
62A79MET00.0240.01511.745-0.060-0.0600.0000.0000.0000.000
63A80PHE00.0100.00715.0580.0300.0300.0000.0000.0000.000
64A81PRO00.0190.02714.138-0.005-0.0050.0000.0000.0000.000
65A82LEU0-0.029-0.05314.850-0.006-0.0060.0000.0000.0000.000
66A83GLU-1-0.876-0.9339.9520.0350.0350.0000.0000.0000.000
67A84VAL0-0.054-0.03314.1250.0080.0080.0000.0000.0000.000
68A85VAL00.007-0.01015.739-0.043-0.0430.0000.0000.0000.000
69A86VAL0-0.015-0.00317.8890.0260.0260.0000.0000.0000.000
70A87ARG10.8230.89218.5440.0740.0740.0000.0000.0000.000
71A88LEU00.011-0.00422.3090.0130.0130.0000.0000.0000.000
72A89LYS10.8870.95323.8820.1650.1650.0000.0000.0000.000
73A90LYS10.8620.96824.1220.0620.0620.0000.0000.0000.000
74A91ALA00.1070.04821.731-0.005-0.0050.0000.0000.0000.000
75A92GLY00.010-0.00819.6560.0100.0100.0000.0000.0000.000
76A93SER00.024-0.01618.9430.0130.0130.0000.0000.0000.000
77A94PHE00.0010.02020.8990.0120.0120.0000.0000.0000.000
78A95VAL00.0510.03623.7900.0080.0080.0000.0000.0000.000
79A96ARG10.8980.96318.5720.0580.0580.0000.0000.0000.000
80A97ARG10.7730.87021.9430.0330.0330.0000.0000.0000.000
81A98TYR00.000-0.00425.3890.0090.0090.0000.0000.0000.000
82A99GLY00.0120.02828.5610.0000.0000.0000.0000.0000.000
83A100GLY0-0.029-0.02929.361-0.005-0.0050.0000.0000.0000.000
84A101ALA00.004-0.00130.4190.0000.0000.0000.0000.0000.000
85A102GLU-1-0.922-0.97923.869-0.122-0.1220.0000.0000.0000.000
86A103GLY0-0.004-0.01826.418-0.002-0.0020.0000.0000.0000.000
87A104GLU-1-0.977-0.98227.349-0.073-0.0730.0000.0000.0000.000
88A105ASP-1-0.860-0.93228.619-0.127-0.1270.0000.0000.0000.000
89A106LEU0-0.035-0.02226.0470.0110.0110.0000.0000.0000.000
90A107PRO0-0.026-0.01129.681-0.004-0.0040.0000.0000.0000.000
91A108VAL0-0.010-0.00429.607-0.002-0.0020.0000.0000.0000.000
92A109PRO0-0.012-0.00924.7720.0010.0010.0000.0000.0000.000
93A110LEU00.0030.02124.4730.0100.0100.0000.0000.0000.000
94A111VAL0-0.027-0.01521.296-0.012-0.0120.0000.0000.0000.000
95A112GLU-1-0.765-0.85720.447-0.034-0.0340.0000.0000.0000.000
96A113PHE0-0.004-0.00519.090-0.017-0.0170.0000.0000.0000.000
97A114PHE00.0030.00515.687-0.004-0.0040.0000.0000.0000.000
98A115ILE00.0210.01616.041-0.002-0.0020.0000.0000.0000.000
99A116LYS10.8590.9558.502-0.320-0.3200.0000.0000.0000.000
100A117ASP-1-0.875-0.96213.3700.3210.3210.0000.0000.0000.000
101A118ASP-1-0.876-0.94011.1730.3870.3870.0000.0000.0000.000
102A119GLU-1-0.997-0.98313.2790.2450.2450.0000.0000.0000.000
103A120ARG10.8610.93616.230-0.235-0.2350.0000.0000.0000.000
104A121HIS0-0.070-0.03615.705-0.050-0.0500.0000.0000.0000.000
105A122ASP-1-0.865-0.92612.7390.2100.2100.0000.0000.0000.000
106A123PRO0-0.0090.00915.917-0.036-0.0360.0000.0000.0000.000
107A124MET0-0.028-0.02919.341-0.006-0.0060.0000.0000.0000.000
108A125VAL0-0.045-0.01020.7010.0060.0060.0000.0000.0000.000
109A126CYS0-0.011-0.01423.226-0.015-0.0150.0000.0000.0000.000
110A127VAL00.0660.00925.8620.0090.0090.0000.0000.0000.000
111A128ASP-1-0.887-0.95927.3220.0320.0320.0000.0000.0000.000
112A129HIS00.0340.02325.1980.0010.0010.0000.0000.0000.000
113A130LEU00.0130.00221.1970.0100.0100.0000.0000.0000.000
114A131GLU-1-0.816-0.90624.7730.0470.0470.0000.0000.0000.000
115A132ILE0-0.034-0.00927.9870.0070.0070.0000.0000.0000.000
116A133LEU0-0.039-0.02923.1990.0060.0060.0000.0000.0000.000
117A134GLY0-0.028-0.00225.0920.0130.0130.0000.0000.0000.000
118A135ILE0-0.047-0.00920.1170.0070.0070.0000.0000.0000.000
119A136ALA0-0.027-0.03022.2280.0000.0000.0000.0000.0000.000
120A137THR00.0260.01624.286-0.005-0.0050.0000.0000.0000.000
121A138LYS10.9200.94827.141-0.035-0.0350.0000.0000.0000.000
122A139LYS10.9941.00528.672-0.011-0.0110.0000.0000.0000.000
123A140GLN00.0190.02123.972-0.005-0.0050.0000.0000.0000.000
124A141ALA00.0500.02323.770-0.010-0.0100.0000.0000.0000.000
125A142GLU-1-0.932-0.96624.674-0.024-0.0240.0000.0000.0000.000
126A143LYS10.9360.95624.6390.0340.0340.0000.0000.0000.000
127A144MET0-0.036-0.01520.001-0.016-0.0160.0000.0000.0000.000
128A145LYS10.9740.99621.8200.0200.0200.0000.0000.0000.000
129A146GLU-1-0.929-0.96124.114-0.060-0.0600.0000.0000.0000.000
130A147ALA0-0.037-0.01021.729-0.013-0.0130.0000.0000.0000.000
131A148ALA00.0580.03320.080-0.020-0.0200.0000.0000.0000.000
132A149VAL00.0170.02921.002-0.022-0.0220.0000.0000.0000.000
133A150LYS10.9540.97624.0790.1000.1000.0000.0000.0000.000
134A151ILE0-0.0010.00318.233-0.008-0.0080.0000.0000.0000.000
135A152THR00.0490.00620.604-0.026-0.0260.0000.0000.0000.000
136A153LEU0-0.0230.00121.501-0.010-0.0100.0000.0000.0000.000
137A154ALA00.0050.00723.212-0.003-0.0030.0000.0000.0000.000
138A155LEU00.016-0.00816.968-0.012-0.0120.0000.0000.0000.000
139A156LYS10.9050.95421.5710.1380.1380.0000.0000.0000.000
140A157GLU-1-0.937-0.97323.670-0.172-0.1720.0000.0000.0000.000
141A158PHE0-0.047-0.02620.0170.0030.0030.0000.0000.0000.000
142A159PHE00.0540.00017.319-0.005-0.0050.0000.0000.0000.000
143A160GLU-1-0.926-0.95823.273-0.160-0.1600.0000.0000.0000.000
144A161ARG10.9150.96626.6180.2160.2160.0000.0000.0000.000
145A162ALA00.0140.01324.5080.0060.0060.0000.0000.0000.000
146A163ASN0-0.041-0.01926.3180.0040.0040.0000.0000.0000.000
147A164PHE00.0150.00021.314-0.004-0.0040.0000.0000.0000.000
148A165GLU-1-0.827-0.92023.465-0.173-0.1730.0000.0000.0000.000
149A166LEU0-0.010-0.00217.868-0.019-0.0190.0000.0000.0000.000
150A167TRP0-0.080-0.06120.0170.0280.0280.0000.0000.0000.000
151A168ASP-1-0.901-0.96917.618-0.197-0.1970.0000.0000.0000.000
152A169ILE0-0.018-0.01514.300-0.051-0.0510.0000.0000.0000.000
153A170LYS10.8810.9748.6110.3520.3520.0000.0000.0000.000
154A171TYR0-0.016-0.02512.707-0.084-0.0840.0000.0000.0000.000
155A172GLU-1-0.826-0.9219.5600.0430.0430.0000.0000.0000.000
156A173PHE00.0300.00213.456-0.045-0.0450.0000.0000.0000.000
157A174GLY00.0620.01216.0620.0430.0430.0000.0000.0000.000
158A175LEU0-0.069-0.02817.422-0.028-0.0280.0000.0000.0000.000
159A176ASP-1-0.769-0.88520.0900.0190.0190.0000.0000.0000.000
160A177LYS10.8760.92521.587-0.004-0.0040.0000.0000.0000.000
161A178ASP-1-0.899-0.94624.1480.0140.0140.0000.0000.0000.000
162A179GLY0-0.059-0.01624.6690.0010.0010.0000.0000.0000.000
163A180ASN0-0.065-0.04024.953-0.002-0.0020.0000.0000.0000.000
164A181VAL0-0.018-0.01620.8060.0040.0040.0000.0000.0000.000
165A182VAL0-0.051-0.00917.849-0.016-0.0160.0000.0000.0000.000
166A183LEU0-0.018-0.01214.8310.0180.0180.0000.0000.0000.000
167A184GLY00.039-0.00513.3880.0080.0080.0000.0000.0000.000
168A185ASP-1-0.869-0.9297.139-0.679-0.6790.0000.0000.0000.000
169A186GLU-1-0.834-0.9215.333-2.687-2.6870.0000.0000.0000.000
170A187ILE0-0.0030.0059.6170.1160.1160.0000.0000.0000.000
171A188SER0-0.003-0.0217.5160.0520.0520.0000.0000.0000.000
172A189PRO00.0230.0019.6900.1020.1020.0000.0000.0000.000
173A190ASP-1-0.820-0.9285.179-2.481-2.443-0.001-0.001-0.0360.000
174A191THR0-0.089-0.0248.2370.1820.1820.0000.0000.0000.000
175A192PHE00.0470.02110.6630.1200.1200.0000.0000.0000.000
176A193ARG10.8960.96613.8130.2210.2210.0000.0000.0000.000
177A194LEU00.0010.00216.3660.0330.0330.0000.0000.0000.000
178A195ARG10.9200.96117.1020.2740.2740.0000.0000.0000.000
179A196LYS10.9641.01721.4280.2400.2400.0000.0000.0000.000
180A197LYS10.9090.94924.2010.1930.1930.0000.0000.0000.000
181A198GLY00.0200.01427.4740.0030.0030.0000.0000.0000.000
182A199GLU-1-0.956-0.98822.794-0.257-0.2570.0000.0000.0000.000
183A200ILE0-0.0020.00427.1140.0060.0060.0000.0000.0000.000
184A201PHE0-0.013-0.01221.688-0.006-0.0060.0000.0000.0000.000
185A202ASP-1-0.788-0.89325.585-0.134-0.1340.0000.0000.0000.000
186A203LYS10.9560.96925.4600.0880.0880.0000.0000.0000.000
187A204ASP-1-0.929-0.97925.717-0.144-0.1440.0000.0000.0000.000
188A205VAL0-0.010-0.00622.850-0.012-0.0120.0000.0000.0000.000
189A206TYR00.0090.01318.055-0.023-0.0230.0000.0000.0000.000
190A207ARG10.9720.96220.9860.1130.1130.0000.0000.0000.000
191A208ARG10.9731.00322.1770.2150.2150.0000.0000.0000.000
192A209ASP-1-0.873-0.95518.956-0.363-0.3630.0000.0000.0000.000
193A210LEU0-0.0360.01017.611-0.032-0.0320.0000.0000.0000.000
194A211GLY0-0.015-0.00717.7090.0000.0000.0000.0000.0000.000
195A212ASP-1-0.876-0.93216.151-0.518-0.5180.0000.0000.0000.000
196A213PRO00.0440.01511.760-0.037-0.0370.0000.0000.0000.000
197A214LEU0-0.027-0.0389.676-0.089-0.0890.0000.0000.0000.000
198A215LYS10.8320.92512.4640.3170.3170.0000.0000.0000.000
199A216LYS10.9690.99211.3760.7070.7070.0000.0000.0000.000
200A217TYR0-0.058-0.0317.670-0.005-0.0050.0000.0000.0000.000
201A218ARG10.8750.94412.3310.5410.5410.0000.0000.0000.000
202A219GLU-1-0.839-0.91615.250-0.365-0.3650.0000.0000.0000.000
203A220VAL0-0.0060.00213.9860.0360.0360.0000.0000.0000.000
204A221LEU0-0.0190.00813.7510.0360.0360.0000.0000.0000.000
205A222GLU-1-0.942-0.98515.762-0.373-0.3730.0000.0000.0000.000
206A223LEU0-0.0320.00318.8690.0480.0480.0000.0000.0000.000
207A224CYS0-0.040-0.03117.1250.0300.0300.0000.0000.0000.000
208A225ARG10.8380.90317.4280.5660.5660.0000.0000.0000.000
209A226SER00.029-0.00121.0070.0380.0380.0000.0000.0000.000
210A227LEU00.0480.01922.6310.0250.0250.0000.0000.0000.000
211A228ASN0-0.184-0.07121.5730.0390.0390.0000.0000.0000.000
212A229SER0-0.032-0.02823.6740.0190.0190.0000.0000.0000.000
213A230GLN0-0.061-0.00423.3930.0170.0170.0000.0000.0000.000