Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JQ1Z9

Calculation Name: 3KBG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KBG

Chain ID: A

ChEMBL ID:

UniProt ID: Q56230

Base Structure: X-ray

Registration Date: 2023-09-24

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2064170.550035
FMO2-HF: Nuclear repulsion 1989239.369844
FMO2-HF: Total energy -74931.180191
FMO2-MP2: Total energy -75150.306674


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:34:LYS)


Summations of interaction energy for fragment #1(A:34:LYS)
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.
74.33381.8689.617-5.865-11.287-0.063
Interaction energy analysis for fragmet #1(A:34:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.950 / q_NPA : 0.982
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].
3A36GLN0-0.035-0.0213.0042.1774.9660.052-1.252-1.5890.004
4A37SER0-0.019-0.0026.0943.7173.7170.0000.0000.0000.000
5A38VAL00.0140.0116.164-1.586-1.5860.0000.0000.0000.000
6A39THR0-0.021-0.0178.9302.6612.6610.0000.0000.0000.000
7A40LEU00.0610.02712.170-0.959-0.9590.0000.0000.0000.000
8A41LEU00.015-0.00314.5920.0330.0330.0000.0000.0000.000
9A42SER0-0.031-0.00310.4480.1600.1600.0000.0000.0000.000
10A43ILE00.0530.0389.385-0.642-0.6420.0000.0000.0000.000
11A44ILE00.0220.01111.7610.3870.3870.0000.0000.0000.000
12A45ARG10.9200.95713.78219.47519.4750.0000.0000.0000.000
13A46ASP-1-0.867-0.9318.728-30.250-30.2500.0000.0000.0000.000
14A47TYR00.0280.01911.5970.1650.1650.0000.0000.0000.000
15A48LEU00.0210.00013.9580.7590.7590.0000.0000.0000.000
16A49LYS10.8470.91011.09725.79125.7910.0000.0000.0000.000
17A50LEU0-0.0430.00012.2120.5390.5390.0000.0000.0000.000
18A51SER0-0.054-0.01715.9380.9310.9310.0000.0000.0000.000
19A52ASP-1-0.796-0.87118.355-13.965-13.9650.0000.0000.0000.000
20A53LYS10.9290.95619.35913.28313.2830.0000.0000.0000.000
21A54GLU-1-0.862-0.91015.934-16.537-16.5370.0000.0000.0000.000
22A55ARG10.7460.81218.24415.02015.0200.0000.0000.0000.000
23A56GLU-1-0.811-0.88421.302-11.924-11.9240.0000.0000.0000.000
24A57ALA00.0050.00918.0720.2400.2400.0000.0000.0000.000
25A58ALA0-0.002-0.00820.0470.1670.1670.0000.0000.0000.000
26A59ARG10.9170.94921.89012.06412.0640.0000.0000.0000.000
27A60ILE00.022-0.00422.1390.4430.4430.0000.0000.0000.000
28A61LEU00.0160.00418.5960.2750.2750.0000.0000.0000.000
29A62ALA0-0.022-0.00222.8360.4180.4180.0000.0000.0000.000
30A63ASN00.0060.00526.0140.6400.6400.0000.0000.0000.000
31A64GLY0-0.016-0.00226.4620.2980.2980.0000.0000.0000.000
32A65LEU0-0.042-0.00725.5660.1630.1630.0000.0000.0000.000
33A66VAL00.0080.01019.490-0.312-0.3120.0000.0000.0000.000
34A67LYS10.8490.92021.89811.80511.8050.0000.0000.0000.000
35A68VAL00.0390.01517.182-0.675-0.6750.0000.0000.0000.000
36A69ASP-1-0.768-0.86818.946-14.425-14.4250.0000.0000.0000.000
37A70GLY00.0300.01921.2360.4900.4900.0000.0000.0000.000
38A71LYS10.9130.96123.35412.44312.4430.0000.0000.0000.000
39A72THR00.0200.00323.292-0.545-0.5450.0000.0000.0000.000
40A73VAL0-0.031-0.01019.7320.2490.2490.0000.0000.0000.000
41A74ARG10.9190.94222.37411.04111.0410.0000.0000.0000.000
42A75GLU-1-0.816-0.87819.874-14.078-14.0780.0000.0000.0000.000
43A76LYS11.0100.99718.24715.64515.6450.0000.0000.0000.000
44A77LYS10.8260.87116.34512.99012.9900.0000.0000.0000.000
45A78PHE0-0.0030.01216.003-0.288-0.2880.0000.0000.0000.000
46A79ALA00.0130.01112.203-0.718-0.7180.0000.0000.0000.000
47A80VAL0-0.015-0.00711.2601.1501.1500.0000.0000.0000.000
48A81GLY00.0600.0019.455-2.281-2.2810.0000.0000.0000.000
49A82PHE00.0210.0169.1011.0571.0570.0000.0000.0000.000
50A83MET0-0.0180.00010.8261.2671.2670.0000.0000.0000.000
51A84ASP-1-0.809-0.87813.756-17.274-17.2740.0000.0000.0000.000
52A85VAL00.0100.00115.601-0.635-0.6350.0000.0000.0000.000
53A86ILE0-0.003-0.00814.2050.3270.3270.0000.0000.0000.000
54A87GLU-1-0.889-0.93418.240-11.653-11.6530.0000.0000.0000.000
55A88ILE00.012-0.00417.721-0.084-0.0840.0000.0000.0000.000
56A89ASN0-0.038-0.03222.2900.1570.1570.0000.0000.0000.000
57A90GLY00.0390.03025.9310.2920.2920.0000.0000.0000.000
58A91GLU-1-0.775-0.87423.476-12.321-12.3210.0000.0000.0000.000
59A92SER0-0.0110.00321.714-0.140-0.1400.0000.0000.0000.000
60A93TYR0-0.0080.00116.701-0.077-0.0770.0000.0000.0000.000
61A94ARG10.7820.87814.87515.96615.9660.0000.0000.0000.000
62A95VAL0-0.0170.0039.863-1.071-1.0710.0000.0000.0000.000
63A96VAL00.006-0.01610.8151.1041.1040.0000.0000.0000.000
64A97TYR0-0.017-0.0294.456-0.1380.008-0.001-0.015-0.1300.000
65A98ASN00.0530.0304.705-1.803-1.662-0.001-0.005-0.1350.000
66A99ASP-1-0.800-0.9046.465-29.532-29.5320.0000.0000.0000.000
67A100GLN0-0.073-0.0322.904-2.239-1.5180.122-0.261-0.581-0.001
68A101GLY00.0230.0062.280-20.955-18.8914.472-2.559-3.978-0.041
69A102ALA0-0.058-0.0332.505-6.996-5.4624.930-1.979-4.485-0.024
70A103LEU0-0.0050.0073.5827.4157.5550.0430.206-0.389-0.001
71A104VAL0-0.005-0.0096.177-0.881-0.8810.0000.0000.0000.000
72A105LEU0-0.020-0.0029.4821.6841.6840.0000.0000.0000.000
73A106MET00.0000.01413.142-0.595-0.5950.0000.0000.0000.000
74A107LYS10.8110.89215.64714.21814.2180.0000.0000.0000.000
75A108GLU-1-0.777-0.88619.146-14.651-14.6510.0000.0000.0000.000
76A109THR0-0.010-0.00720.9440.6100.6100.0000.0000.0000.000
77A110LYS10.8830.89424.26911.62911.6290.0000.0000.0000.000
78A111GLU-1-0.910-0.93826.670-10.251-10.2510.0000.0000.0000.000
79A112ARG10.9630.98822.07812.81912.8190.0000.0000.0000.000
80A113ALA0-0.037-0.01822.133-0.339-0.3390.0000.0000.0000.000
81A114SER0-0.043-0.00623.206-0.034-0.0340.0000.0000.0000.000
82A115MET00.0120.02021.4740.3360.3360.0000.0000.0000.000
83A116LYS10.7720.86616.48315.33715.3370.0000.0000.0000.000
84A117LEU0-0.0310.01317.5870.6020.6020.0000.0000.0000.000
85A118LEU00.001-0.00817.289-0.875-0.8750.0000.0000.0000.000
86A119LYS10.8560.93812.80518.50218.5020.0000.0000.0000.000
87A120VAL00.000-0.00217.422-0.156-0.1560.0000.0000.0000.000
88A121ARG10.9300.96612.70217.22717.2270.0000.0000.0000.000
89A122SER00.0190.00417.013-0.217-0.2170.0000.0000.0000.000
90A123LYS10.8530.92119.85410.66410.6640.0000.0000.0000.000
91A124VAL00.0140.02223.604-0.060-0.0600.0000.0000.0000.000
92A125ILE0-0.031-0.02226.4670.1100.1100.0000.0000.0000.000
93A126ALA00.0250.02729.5920.0820.0820.0000.0000.0000.000
94A127PRO00.0400.00032.9020.0170.0170.0000.0000.0000.000
95A128GLY00.0290.01236.355-0.037-0.0370.0000.0000.0000.000
96A129ASN0-0.041-0.01933.938-0.073-0.0730.0000.0000.0000.000
97A130ARG10.9941.01931.5568.6718.6710.0000.0000.0000.000
98A131ILE0-0.020-0.01627.546-0.198-0.1980.0000.0000.0000.000
99A132GLN00.0180.02226.1060.3270.3270.0000.0000.0000.000
100A133LEU00.011-0.00423.535-0.228-0.2280.0000.0000.0000.000
101A134GLY00.0460.02420.6310.0980.0980.0000.0000.0000.000
102A135THR00.030-0.02018.615-0.103-0.1030.0000.0000.0000.000
103A136HIS0-0.051-0.04012.2930.5570.5570.0000.0000.0000.000
104A137ASP-1-0.742-0.85613.920-15.799-15.7990.0000.0000.0000.000
105A138GLY0-0.047-0.02315.8140.1350.1350.0000.0000.0000.000
106A139ARG10.8210.90918.23314.23314.2330.0000.0000.0000.000
107A140THR0-0.023-0.01921.346-0.171-0.1710.0000.0000.0000.000
108A141PHE00.0070.01322.4370.2580.2580.0000.0000.0000.000
109A142ILE0-0.016-0.01326.767-0.090-0.0900.0000.0000.0000.000
110A143THR0-0.010-0.00328.6340.2180.2180.0000.0000.0000.000
111A144ASP-1-0.836-0.92331.060-8.191-8.1910.0000.0000.0000.000
112A145ASP-1-0.787-0.87031.055-8.963-8.9630.0000.0000.0000.000
113A146LYS10.9260.95230.2887.5757.5750.0000.0000.0000.000
114A147SER0-0.101-0.06830.038-0.277-0.2770.0000.0000.0000.000
115A148ILE00.0210.01124.741-0.294-0.2940.0000.0000.0000.000
116A149LYS10.8430.91723.8149.9119.9110.0000.0000.0000.000
117A150VAL00.0250.01218.076-0.202-0.2020.0000.0000.0000.000
118A151GLY0-0.025-0.01817.7600.0410.0410.0000.0000.0000.000
119A152ASP-1-0.754-0.85518.811-11.494-11.4940.0000.0000.0000.000
120A153VAL0-0.030-0.02318.004-0.484-0.4840.0000.0000.0000.000
121A154LEU0-0.0100.01220.7750.6290.6290.0000.0000.0000.000
122A155ALA00.0060.01321.633-0.641-0.6410.0000.0000.0000.000
123A156VAL00.009-0.00722.1390.5000.5000.0000.0000.0000.000
124A157SER0-0.004-0.01324.267-0.398-0.3980.0000.0000.0000.000
125A158VAL0-0.004-0.02222.326-0.026-0.0260.0000.0000.0000.000
126A159PRO0-0.034-0.02625.1260.0440.0440.0000.0000.0000.000
127A160ASP-1-0.795-0.87328.568-9.409-9.4090.0000.0000.0000.000
128A161MET0-0.057-0.02023.606-0.044-0.0440.0000.0000.0000.000
129A162LYS10.8730.95127.1468.9918.9910.0000.0000.0000.000
130A163ILE0-0.001-0.00726.020-0.301-0.3010.0000.0000.0000.000
131A164SER00.008-0.00227.3900.2470.2470.0000.0000.0000.000
132A165GLU-1-0.828-0.91126.775-9.658-9.6580.0000.0000.0000.000
133A166ILE0-0.0070.00325.125-0.387-0.3870.0000.0000.0000.000
134A167ILE0-0.053-0.02821.3790.3300.3300.0000.0000.0000.000
135A168LYS10.8630.93022.79110.03610.0360.0000.0000.0000.000
136A169MET00.012-0.00116.859-0.090-0.0900.0000.0000.0000.000
137A170GLN0-0.052-0.02522.3160.2720.2720.0000.0000.0000.000
138A171PRO00.031-0.01124.576-0.305-0.3050.0000.0000.0000.000
139A172GLY0-0.0120.00625.8710.3010.3010.0000.0000.0000.000
140A173ASN0-0.044-0.02123.4560.3060.3060.0000.0000.0000.000
141A174LYS10.9060.96320.16412.74912.7490.0000.0000.0000.000
142A175ALA0-0.009-0.01316.6000.0380.0380.0000.0000.0000.000
143A176TYR00.022-0.0099.828-0.080-0.0800.0000.0000.0000.000
144A177ILE0-0.0220.0019.9950.1460.1460.0000.0000.0000.000
145A178THR00.0150.0017.909-0.721-0.7210.0000.0000.0000.000
146A179ALA0-0.008-0.0035.132-3.738-3.7380.0000.0000.0000.000
147A180GLY00.0170.0095.4833.0173.0170.0000.0000.0000.000
148A181SER00.018-0.0087.458-1.556-1.5560.0000.0000.0000.000
149A182HIS10.8760.9279.75019.52519.5250.0000.0000.0000.000
150A183VAL00.0010.0145.3151.1421.1420.0000.0000.0000.000
151A184ASN0-0.020-0.0128.5310.9580.9580.0000.0000.0000.000
152A185GLN00.0530.06910.3272.7182.7180.0000.0000.0000.000
153A186THR0-0.007-0.02213.580-0.019-0.0190.0000.0000.0000.000
154A187GLY0-0.011-0.00116.6370.1580.1580.0000.0000.0000.000
155A188THR0-0.054-0.05519.581-0.004-0.0040.0000.0000.0000.000
156A189ILE0-0.0300.00319.9690.0270.0270.0000.0000.0000.000
157A190SER0-0.011-0.01722.7700.4480.4480.0000.0000.0000.000
158A191LYS10.8880.92823.89411.46111.4610.0000.0000.0000.000
159A192ILE0-0.005-0.00221.281-0.571-0.5710.0000.0000.0000.000
160A193GLU-1-0.808-0.86922.397-10.974-10.9740.0000.0000.0000.000
161A194ALA0-0.010-0.01022.153-0.507-0.5070.0000.0000.0000.000
162A195LYS10.9250.97023.33910.12910.1290.0000.0000.0000.000
163A196GLU-1-0.913-0.94923.904-9.843-9.8430.0000.0000.0000.000
164A197GLY00.0410.01423.8800.1320.1320.0000.0000.0000.000
165A198SER00.006-0.00720.028-0.013-0.0130.0000.0000.0000.000
166A199SER00.008-0.00519.973-0.133-0.1330.0000.0000.0000.000
167A200ALA00.0720.06217.895-0.680-0.6800.0000.0000.0000.000
168A201ASN0-0.114-0.07818.3380.2870.2870.0000.0000.0000.000
169A202LEU0-0.020-0.01016.729-0.774-0.7740.0000.0000.0000.000
170A203VAL0-0.035-0.01217.4200.7460.7460.0000.0000.0000.000
171A204HIS0-0.020-0.03218.466-0.694-0.6940.0000.0000.0000.000
172A205PHE00.0130.00116.4840.2260.2260.0000.0000.0000.000
173A206GLN00.008-0.01021.6170.1670.1670.0000.0000.0000.000
174A207GLU-1-0.800-0.88720.479-13.035-13.0350.0000.0000.0000.000
175A208GLY00.0060.02121.859-0.216-0.2160.0000.0000.0000.000
176A209PHE0-0.028-0.01815.273-0.516-0.5160.0000.0000.0000.000
177A210SER00.0190.00417.8900.2830.2830.0000.0000.0000.000
178A211THR0-0.0060.00012.589-0.963-0.9630.0000.0000.0000.000
179A212ILE00.0450.02710.7410.8400.8400.0000.0000.0000.000
180A213LYS11.0211.00113.57812.12512.1250.0000.0000.0000.000
181A214ASP-1-0.914-0.95310.932-17.719-17.7190.0000.0000.0000.000
182A215HIS0-0.012-0.0128.073-1.148-1.1480.0000.0000.0000.000
183A216VAL0-0.0030.02110.705-0.447-0.4470.0000.0000.0000.000
184A217PHE0-0.0070.00212.5530.5850.5850.0000.0000.0000.000
185A218MET0-0.0160.00514.718-0.140-0.1400.0000.0000.0000.000
186A219ILE00.014-0.01516.572-0.132-0.1320.0000.0000.0000.000
187A220GLY0-0.0010.00819.4870.2830.2830.0000.0000.0000.000
188A221SER0-0.027-0.01623.1070.0740.0740.0000.0000.0000.000
189A222SER00.034-0.00226.396-0.015-0.0150.0000.0000.0000.000
190A223LYS10.8350.92328.58910.15610.1560.0000.0000.0000.000
191A224PHE00.0370.02323.4790.0190.0190.0000.0000.0000.000
192A225SER00.004-0.00724.109-0.395-0.3950.0000.0000.0000.000
193A226PHE00.0050.01417.9700.1080.1080.0000.0000.0000.000
194A227VAL00.0040.00320.2220.1230.1230.0000.0000.0000.000