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: 5JYGZ

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 OptHSide
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 -2585128.581885
FMO2-HF: Nuclear repulsion 2500005.639651
FMO2-HF: Total energy -85122.942234
FMO2-MP2: Total energy -85372.591921


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.
-7.999-0.6333.358-4.613-6.1110
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 : 0.014 / q_NPA : 0.011
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].
3A9ILE0-0.037-0.0043.763-1.4522.002-0.017-1.908-1.5290.006
4A10VAL00.0290.0206.343-0.463-0.4630.0000.0000.0000.000
5A11LYS10.9520.9649.428-0.203-0.2030.0000.0000.0000.000
6A12VAL0-0.0070.00012.767-0.063-0.0630.0000.0000.0000.000
7A13THR0-0.039-0.02816.1460.0130.0130.0000.0000.0000.000
8A14GLY00.0050.00818.937-0.016-0.0160.0000.0000.0000.000
9A15ASP-1-0.909-0.95221.1820.0100.0100.0000.0000.0000.000
10A16TYR0-0.033-0.02019.151-0.013-0.0130.0000.0000.0000.000
11A17ALA0-0.017-0.00514.1820.0320.0320.0000.0000.0000.000
12A18LEU00.0030.00813.869-0.046-0.0460.0000.0000.0000.000
13A19LEU0-0.012-0.0137.0160.1210.1210.0000.0000.0000.000
14A20GLU-1-0.909-0.9568.243-0.175-0.1750.0000.0000.0000.000
15A21PHE00.010-0.0095.383-0.091-0.0910.0000.0000.0000.000
16A22LYS10.8800.9213.582-3.273-2.2660.008-0.386-0.6290.001
17A23ASP-1-0.824-0.9023.022-5.540-4.5160.229-0.634-0.619-0.005
18A24ASP-1-0.878-0.9272.0742.0173.7123.139-1.665-3.168-0.002
19A36LEU00.0120.0046.8610.0180.0180.0000.0000.0000.000
20A37THR0-0.049-0.0497.7670.1270.1270.0000.0000.0000.000
21A38GLY00.0210.0308.0310.0900.0900.0000.0000.0000.000
22A39LYS10.8740.9003.8300.6300.7950.000-0.019-0.1470.000
23A40GLY00.0120.0205.491-0.149-0.1490.0000.0000.0000.000
24A41SER00.010-0.0296.2340.1950.1950.0000.0000.0000.000
25A42ILE00.0410.0209.7580.0970.0970.0000.0000.0000.000
26A43CYS0-0.0140.0066.2630.2130.2130.0000.0000.0000.000
27A44ALA00.0140.0368.5060.1590.1590.0000.0000.0000.000
28A45GLU-1-0.774-0.8619.930-0.206-0.2060.0000.0000.0000.000
29A46THR0-0.019-0.03311.5030.1120.1120.0000.0000.0000.000
30A47THR00.0040.00310.0020.1040.1040.0000.0000.0000.000
31A48ALA0-0.026-0.01612.6890.0830.0830.0000.0000.0000.000
32A49ILE0-0.026-0.00315.3470.0570.0570.0000.0000.0000.000
33A50LEU00.0200.00814.9310.0380.0380.0000.0000.0000.000
34A51MET0-0.0100.00512.6570.0390.0390.0000.0000.0000.000
35A52LYS10.9510.99717.2970.1660.1660.0000.0000.0000.000
36A53TYR0-0.009-0.01220.3430.0270.0270.0000.0000.0000.000
37A54LEU00.022-0.01218.0330.0200.0200.0000.0000.0000.000
38A55SER0-0.012-0.00920.6760.0180.0180.0000.0000.0000.000
39A56GLU-1-0.939-0.95523.125-0.098-0.0980.0000.0000.0000.000
40A57LYS10.8250.93424.9460.1060.1060.0000.0000.0000.000
41A58GLY0-0.028-0.03226.3740.0080.0080.0000.0000.0000.000
42A59ILE0-0.067-0.02320.6530.0090.0090.0000.0000.0000.000
43A60LYS10.8860.94221.5410.0350.0350.0000.0000.0000.000
44A61THR00.0230.00116.863-0.005-0.0050.0000.0000.0000.000
45A62HIS0-0.018-0.00911.2250.0620.0620.0000.0000.0000.000
46A63LEU00.0080.01915.123-0.008-0.0080.0000.0000.0000.000
47A64VAL0-0.066-0.01917.0510.0260.0260.0000.0000.0000.000
48A65GLU-1-0.862-0.93417.987-0.122-0.1220.0000.0000.0000.000
49A66TYR00.0200.00312.7490.0210.0210.0000.0000.0000.000
50A67ILE0-0.0080.00315.3400.0400.0400.0000.0000.0000.000
51A68PRO0-0.0220.02314.915-0.051-0.0510.0000.0000.0000.000
52A69PRO00.016-0.01412.7560.0380.0380.0000.0000.0000.000
53A70ARG10.8830.9308.4810.7790.7790.0000.0000.0000.000
54A71THR00.0340.0259.519-0.198-0.1980.0000.0000.0000.000
55A72LEU0-0.0190.00910.9850.0340.0340.0000.0000.0000.000
56A73LYS10.8800.94413.4780.1490.1490.0000.0000.0000.000
57A74VAL00.034-0.01012.952-0.015-0.0150.0000.0000.0000.000
58A75ILE0-0.013-0.01216.0770.0320.0320.0000.0000.0000.000
59A76PRO0-0.003-0.00516.345-0.003-0.0030.0000.0000.0000.000
60A77LEU0-0.007-0.00115.179-0.008-0.0080.0000.0000.0000.000
61A78LYS10.9260.97915.627-0.031-0.0310.0000.0000.0000.000
62A79MET00.0200.01111.543-0.031-0.0310.0000.0000.0000.000
63A80PHE00.0210.00515.0240.0170.0170.0000.0000.0000.000
64A81PRO00.0020.02114.069-0.002-0.0020.0000.0000.0000.000
65A82LEU0-0.008-0.04214.823-0.001-0.0010.0000.0000.0000.000
66A83GLU-1-0.837-0.8949.6170.1470.1470.0000.0000.0000.000
67A84VAL0-0.056-0.04014.0580.0020.0020.0000.0000.0000.000
68A85VAL0-0.008-0.01415.504-0.015-0.0150.0000.0000.0000.000
69A86VAL0-0.0080.00217.8910.0030.0030.0000.0000.0000.000
70A87ARG10.7890.88218.171-0.031-0.0310.0000.0000.0000.000
71A88LEU00.011-0.00622.297-0.001-0.0010.0000.0000.0000.000
72A89LYS10.8310.91623.8620.0340.0340.0000.0000.0000.000
73A90LYS10.7570.89624.0810.0040.0040.0000.0000.0000.000
74A91ALA00.0900.03921.643-0.002-0.0020.0000.0000.0000.000
75A92GLY00.004-0.00419.5260.0060.0060.0000.0000.0000.000
76A93SER00.006-0.02018.751-0.002-0.0020.0000.0000.0000.000
77A94PHE00.0030.02020.7740.0000.0000.0000.0000.0000.000
78A95VAL00.0460.03423.668-0.001-0.0010.0000.0000.0000.000
79A96ARG10.9090.96118.288-0.061-0.0610.0000.0000.0000.000
80A97ARG10.7740.86222.152-0.040-0.0400.0000.0000.0000.000
81A98TYR0-0.009-0.01125.2360.0010.0010.0000.0000.0000.000
82A99GLY00.0110.02828.433-0.003-0.0030.0000.0000.0000.000
83A100GLY0-0.008-0.01629.235-0.001-0.0010.0000.0000.0000.000
84A101ALA0-0.013-0.00730.2900.0020.0020.0000.0000.0000.000
85A102GLU-1-0.889-0.96823.3250.0110.0110.0000.0000.0000.000
86A103GLY0-0.009-0.01126.556-0.003-0.0030.0000.0000.0000.000
87A104GLU-1-0.857-0.91327.611-0.007-0.0070.0000.0000.0000.000
88A105ASP-1-0.840-0.91028.591-0.027-0.0270.0000.0000.0000.000
89A106LEU0-0.024-0.01725.8300.0040.0040.0000.0000.0000.000
90A107PRO0-0.025-0.01329.666-0.003-0.0030.0000.0000.0000.000
91A108VAL0-0.005-0.00230.080-0.003-0.0030.0000.0000.0000.000
92A109PRO0-0.010-0.00824.7270.0020.0020.0000.0000.0000.000
93A110LEU00.0010.02124.5390.0030.0030.0000.0000.0000.000
94A111VAL0-0.017-0.01221.389-0.002-0.0020.0000.0000.0000.000
95A112GLU-1-0.756-0.84420.3310.0370.0370.0000.0000.0000.000
96A113PHE0-0.002-0.00919.004-0.005-0.0050.0000.0000.0000.000
97A114PHE0-0.0010.00215.628-0.002-0.0020.0000.0000.0000.000
98A115ILE00.0100.01315.978-0.002-0.0020.0000.0000.0000.000
99A116LYS10.7550.8728.759-0.155-0.1550.0000.0000.0000.000
100A117ASP-1-0.899-0.97913.3240.1720.1720.0000.0000.0000.000
101A118ASP-1-0.883-0.94011.0240.2180.2180.0000.0000.0000.000
102A119GLU-1-0.886-0.91813.1730.1270.1270.0000.0000.0000.000
103A120ARG10.7710.87216.129-0.135-0.1350.0000.0000.0000.000
104A121HIS0-0.076-0.03515.579-0.022-0.0220.0000.0000.0000.000
105A122ASP-1-0.871-0.92512.6930.1790.1790.0000.0000.0000.000
106A123PRO00.0080.01515.842-0.014-0.0140.0000.0000.0000.000
107A124MET0-0.033-0.02919.268-0.002-0.0020.0000.0000.0000.000
108A125VAL0-0.040-0.01120.461-0.001-0.0010.0000.0000.0000.000
109A126CYS0-0.020-0.01423.156-0.006-0.0060.0000.0000.0000.000
110A127VAL00.0620.00125.8030.0030.0030.0000.0000.0000.000
111A128ASP-1-0.868-0.94727.2650.0280.0280.0000.0000.0000.000
112A129HIS00.0520.03125.3080.0010.0010.0000.0000.0000.000
113A130LEU00.0170.01021.2960.0030.0030.0000.0000.0000.000
114A131GLU-1-0.812-0.90224.7330.0310.0310.0000.0000.0000.000
115A132ILE0-0.037-0.01127.9570.0020.0020.0000.0000.0000.000
116A133LEU0-0.038-0.02423.2220.0020.0020.0000.0000.0000.000
117A134GLY0-0.022-0.00225.0770.0060.0060.0000.0000.0000.000
118A135ILE0-0.050-0.01019.9730.0030.0030.0000.0000.0000.000
119A136ALA0-0.038-0.03022.169-0.001-0.0010.0000.0000.0000.000
120A137THR00.0240.00024.220-0.002-0.0020.0000.0000.0000.000
121A138LYS10.8860.92927.084-0.029-0.0290.0000.0000.0000.000
122A139LYS10.9770.99228.696-0.007-0.0070.0000.0000.0000.000
123A140GLN00.0290.04223.945-0.002-0.0020.0000.0000.0000.000
124A141ALA00.0490.02623.791-0.005-0.0050.0000.0000.0000.000
125A142GLU-1-0.851-0.93224.6920.0010.0010.0000.0000.0000.000
126A143LYS10.8570.90824.9360.0150.0150.0000.0000.0000.000
127A144MET0-0.028-0.00919.975-0.008-0.0080.0000.0000.0000.000
128A145LYS10.8770.94821.837-0.011-0.0110.0000.0000.0000.000
129A146GLU-1-0.863-0.91424.116-0.022-0.0220.0000.0000.0000.000
130A147ALA0-0.025-0.00621.788-0.006-0.0060.0000.0000.0000.000
131A148ALA00.0570.03020.022-0.010-0.0100.0000.0000.0000.000
132A149VAL00.0210.02920.998-0.008-0.0080.0000.0000.0000.000
133A150LYS10.9380.97224.0700.0500.0500.0000.0000.0000.000
134A151ILE0-0.0050.00318.079-0.005-0.0050.0000.0000.0000.000
135A152THR00.0460.01220.562-0.010-0.0100.0000.0000.0000.000
136A153LEU0-0.0170.00621.479-0.003-0.0030.0000.0000.0000.000
137A154ALA0-0.011-0.00723.216-0.001-0.0010.0000.0000.0000.000
138A155LEU00.013-0.00216.885-0.007-0.0070.0000.0000.0000.000
139A156LYS10.8370.90621.5360.0470.0470.0000.0000.0000.000
140A157GLU-1-0.817-0.89223.635-0.087-0.0870.0000.0000.0000.000
141A158PHE0-0.002-0.00220.2540.0000.0000.0000.0000.0000.000
142A159PHE00.0530.00117.301-0.002-0.0020.0000.0000.0000.000
143A160GLU-1-0.784-0.84223.411-0.051-0.0510.0000.0000.0000.000
144A161ARG10.7840.87826.0160.1030.1030.0000.0000.0000.000
145A162ALA00.0080.00624.5900.0010.0010.0000.0000.0000.000
146A163ASN0-0.048-0.01926.4470.0030.0030.0000.0000.0000.000
147A164PHE00.013-0.00221.0500.0020.0020.0000.0000.0000.000
148A165GLU-1-0.825-0.92823.742-0.042-0.0420.0000.0000.0000.000
149A166LEU0-0.024-0.00517.847-0.002-0.0020.0000.0000.0000.000
150A167TRP0-0.071-0.05820.2250.0120.0120.0000.0000.0000.000
151A168ASP-1-0.845-0.94218.1340.0120.0120.0000.0000.0000.000
152A169ILE0-0.033-0.01414.390-0.013-0.0130.0000.0000.0000.000
153A170LYS10.8650.9548.4230.0340.0340.0000.0000.0000.000
154A171TYR0-0.013-0.03912.697-0.043-0.0430.0000.0000.0000.000
155A172GLU-1-0.773-0.8649.3050.0720.0720.0000.0000.0000.000
156A173PHE00.0300.00613.472-0.034-0.0340.0000.0000.0000.000
157A174GLY00.0770.02016.0440.0240.0240.0000.0000.0000.000
158A175LEU0-0.061-0.02017.388-0.014-0.0140.0000.0000.0000.000
159A176ASP-1-0.716-0.84820.086-0.008-0.0080.0000.0000.0000.000
160A177LYS10.8380.89321.5880.0160.0160.0000.0000.0000.000
161A178ASP-1-0.866-0.91624.164-0.005-0.0050.0000.0000.0000.000
162A179GLY0-0.0200.00424.6540.0020.0020.0000.0000.0000.000
163A180ASN0-0.112-0.06024.534-0.006-0.0060.0000.0000.0000.000
164A181VAL00.009-0.01220.7150.0000.0000.0000.0000.0000.000
165A182VAL0-0.036-0.00217.895-0.008-0.0080.0000.0000.0000.000
166A183LEU0-0.014-0.01014.8990.0090.0090.0000.0000.0000.000
167A184GLY00.0510.00013.399-0.004-0.0040.0000.0000.0000.000
168A185ASP-1-0.850-0.9207.139-0.422-0.4220.0000.0000.0000.000
169A186GLU-1-0.788-0.8765.188-1.780-1.759-0.001-0.001-0.0190.000
170A187ILE0-0.026-0.0129.5960.1140.1140.0000.0000.0000.000
171A188SER00.021-0.0267.6390.0420.0420.0000.0000.0000.000
172A189PRO00.0610.0229.6790.0880.0880.0000.0000.0000.000
173A190ASP-1-0.784-0.8465.737-0.291-0.2910.0000.0000.0000.000
174A191THR0-0.042-0.0148.2340.0950.0950.0000.0000.0000.000
175A192PHE00.0430.03110.6380.0270.0270.0000.0000.0000.000
176A193ARG10.9120.96714.184-0.026-0.0260.0000.0000.0000.000
177A194LEU00.0000.00016.7460.0010.0010.0000.0000.0000.000
178A195ARG10.9340.98118.3480.0330.0330.0000.0000.0000.000
179A196LYS10.9090.96521.7540.0690.0690.0000.0000.0000.000
180A197LYS10.8380.89024.4650.0670.0670.0000.0000.0000.000
181A198GLY00.0120.00927.768-0.001-0.0010.0000.0000.0000.000
182A199GLU-1-0.886-0.92923.071-0.067-0.0670.0000.0000.0000.000
183A200ILE00.0070.00127.4480.0050.0050.0000.0000.0000.000
184A201PHE0-0.028-0.01922.129-0.002-0.0020.0000.0000.0000.000
185A202ASP-1-0.784-0.89325.960-0.031-0.0310.0000.0000.0000.000
186A203LYS10.9460.96825.8320.0160.0160.0000.0000.0000.000
187A204ASP-1-0.916-0.97326.078-0.034-0.0340.0000.0000.0000.000
188A205VAL0-0.007-0.00623.124-0.004-0.0040.0000.0000.0000.000
189A206TYR0-0.0060.00318.276-0.003-0.0030.0000.0000.0000.000
190A207ARG10.9740.96821.3020.0190.0190.0000.0000.0000.000
191A208ARG10.8830.95622.4560.0710.0710.0000.0000.0000.000
192A209ASP-1-0.832-0.91920.585-0.103-0.1030.0000.0000.0000.000
193A210LEU0-0.069-0.02017.601-0.007-0.0070.0000.0000.0000.000
194A211GLY0-0.008-0.00517.9590.0060.0060.0000.0000.0000.000
195A212ASP-1-0.835-0.89415.944-0.214-0.2140.0000.0000.0000.000
196A213PRO00.0350.01111.712-0.005-0.0050.0000.0000.0000.000
197A214LEU0-0.040-0.02310.056-0.014-0.0140.0000.0000.0000.000
198A215LYS10.8350.93212.4930.0840.0840.0000.0000.0000.000
199A216LYS10.8970.96010.5770.0620.0620.0000.0000.0000.000
200A217TYR0-0.064-0.0777.876-0.016-0.0160.0000.0000.0000.000
201A218ARG10.8500.90512.3720.2050.2050.0000.0000.0000.000
202A219GLU-1-0.798-0.89015.179-0.128-0.1280.0000.0000.0000.000
203A220VAL00.0140.00914.1620.0120.0120.0000.0000.0000.000
204A221LEU0-0.0120.01613.5140.0090.0090.0000.0000.0000.000
205A222GLU-1-0.940-0.98515.657-0.197-0.1970.0000.0000.0000.000
206A223LEU0-0.0240.01018.8210.0200.0200.0000.0000.0000.000
207A224CYS0-0.048-0.04517.1690.0120.0120.0000.0000.0000.000
208A225ARG10.8210.88616.8470.3230.3230.0000.0000.0000.000
209A226SER00.0180.00520.8320.0180.0180.0000.0000.0000.000
210A227LEU00.0490.02222.8220.0120.0120.0000.0000.0000.000
211A228ASN0-0.191-0.07021.4150.0100.0100.0000.0000.0000.000
212A229SER0-0.029-0.03123.5260.0070.0070.0000.0000.0000.000
213A230GLN0-0.057-0.00923.0600.0080.0080.0000.0000.0000.000