FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 72VRK

Calculation Name: 3VUT-A-Xray372

Preferred Name: Dual specificity mitogen-activated protein kinase kinase 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3VUT

Chain ID: A

ChEMBL ID: CHEMBL2897

UniProt ID: P45985

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2420208.842437
FMO2-HF: Nuclear repulsion 2336502.199011
FMO2-HF: Total energy -83706.643426
FMO2-MP2: Total energy -83946.929398


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:142:GLN)


Summations of interaction energy for fragment #1(A:142: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.
-12.79-9.92311.171-5.687-8.35-0.01
Interaction energy analysis for fragmet #1(A:142:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.002
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].
3A144GLN00.0290.0013.676-4.384-2.245-0.002-1.017-1.1190.003
4A145LEU0-0.0060.0092.042-3.595-3.3835.667-2.795-3.084-0.005
5A146LEU0-0.018-0.0342.132-3.976-3.5835.506-1.846-4.053-0.008
6A147MET0-0.0220.0424.3840.3740.4970.000-0.029-0.0940.000
7A148ASP-1-0.878-0.9556.9650.0380.0380.0000.0000.0000.000
8A149LEU0-0.108-0.0525.9450.0110.0110.0000.0000.0000.000
9A150ASP-1-0.825-0.9358.692-2.211-2.2110.0000.0000.0000.000
10A151VAL00.0390.04011.1820.2240.2240.0000.0000.0000.000
11A152VAL0-0.053-0.01313.0930.0580.0580.0000.0000.0000.000
12A153MET0-0.0280.00012.3230.0130.0130.0000.0000.0000.000
13A154ARG0-0.019-0.04012.537-0.095-0.0950.0000.0000.0000.000
14A155SER00.0350.04517.6030.0560.0560.0000.0000.0000.000
15A156SER0-0.028-0.00619.0720.0260.0260.0000.0000.0000.000
16A157ASH00.003-0.03621.582-0.018-0.0180.0000.0000.0000.000
17A158CYS00.1530.13723.092-0.009-0.0090.0000.0000.0000.000
18A159PRO0-0.038-0.00924.0240.0100.0100.0000.0000.0000.000
19A160TYR00.0060.03315.819-0.042-0.0420.0000.0000.0000.000
20A161ILE0-0.0270.00317.9050.0380.0380.0000.0000.0000.000
21A162VAL0-0.026-0.01517.966-0.048-0.0480.0000.0000.0000.000
22A163GLN0-0.039-0.01810.5100.0220.0220.0000.0000.0000.000
23A164PHE00.0490.00512.1990.0280.0280.0000.0000.0000.000
24A177CYS0-0.048-0.01912.754-0.028-0.0280.0000.0000.0000.000
25A178MET0-0.013-0.01514.4460.0890.0890.0000.0000.0000.000
26A179GLU-1-0.735-0.83017.926-0.317-0.3170.0000.0000.0000.000
27A180LEU0-0.032-0.01921.069-0.030-0.0300.0000.0000.0000.000
28A181MET0-0.069-0.00423.7770.0120.0120.0000.0000.0000.000
29A182SER0-0.005-0.00926.5110.0270.0270.0000.0000.0000.000
30A183THR0-0.036-0.02928.5900.0050.0050.0000.0000.0000.000
31A184SER00.0120.01726.762-0.002-0.0020.0000.0000.0000.000
32A185PHE00.0950.00328.3660.0200.0200.0000.0000.0000.000
33A186ASP-1-0.962-0.96729.402-0.216-0.2160.0000.0000.0000.000
34A187LYS10.9690.96929.3900.1690.1690.0000.0000.0000.000
35A188PHE0-0.0320.01232.7830.0110.0110.0000.0000.0000.000
36A189TYR0-0.022-0.02433.1000.0040.0040.0000.0000.0000.000
37A190LYS10.9310.96332.6520.1970.1970.0000.0000.0000.000
38A191TYR0-0.087-0.02737.0720.0090.0090.0000.0000.0000.000
39A192VAL00.0650.03839.0190.0080.0080.0000.0000.0000.000
40A193TYR0-0.033-0.06439.042-0.006-0.0060.0000.0000.0000.000
41A194SER0-0.089-0.03641.6300.0060.0060.0000.0000.0000.000
42A195VAL0-0.029-0.02543.2790.0020.0020.0000.0000.0000.000
43A196LEU0-0.096-0.04542.7120.0070.0070.0000.0000.0000.000
44A197ASP-1-0.872-0.91945.024-0.100-0.1000.0000.0000.0000.000
45A198ASP-1-0.810-0.90743.692-0.117-0.1170.0000.0000.0000.000
46A199VAL0-0.0250.02644.075-0.007-0.0070.0000.0000.0000.000
47A200ILE0-0.064-0.04436.933-0.001-0.0010.0000.0000.0000.000
48A201PRO00.0170.00640.759-0.005-0.0050.0000.0000.0000.000
49A202GLU-1-0.786-0.90640.428-0.167-0.1670.0000.0000.0000.000
50A203GLU-1-0.949-0.99240.103-0.134-0.1340.0000.0000.0000.000
51A204ILE0-0.0070.00836.800-0.005-0.0050.0000.0000.0000.000
52A205LEU00.0280.00336.328-0.016-0.0160.0000.0000.0000.000
53A206GLY00.0020.01135.456-0.019-0.0190.0000.0000.0000.000
54A207LYS10.9180.96534.5890.1600.1600.0000.0000.0000.000
55A208ILE00.0350.03830.787-0.021-0.0210.0000.0000.0000.000
56A209THR0-0.037-0.01530.828-0.029-0.0290.0000.0000.0000.000
57A210LEU0-0.050-0.00431.054-0.026-0.0260.0000.0000.0000.000
58A211ALA0-0.039-0.03828.354-0.023-0.0230.0000.0000.0000.000
59A212THR00.038-0.01526.456-0.035-0.0350.0000.0000.0000.000
60A213VAL00.0340.01825.889-0.048-0.0480.0000.0000.0000.000
61A214LYS10.7410.82426.3520.2800.2800.0000.0000.0000.000
62A215ALA00.0370.01122.791-0.034-0.0340.0000.0000.0000.000
63A216LEU0-0.0050.01121.638-0.060-0.0600.0000.0000.0000.000
64A217ASN00.025-0.00722.031-0.075-0.0750.0000.0000.0000.000
65A218HIS10.8170.91319.5300.5770.5770.0000.0000.0000.000
66A219LEU00.015-0.00516.591-0.036-0.0360.0000.0000.0000.000
67A220LYS10.9851.00818.3460.5620.5620.0000.0000.0000.000
68A221GLU-1-1.021-1.02520.519-0.556-0.5560.0000.0000.0000.000
69A222ASN0-0.069-0.01518.266-0.049-0.0490.0000.0000.0000.000
70A223LEU00.0360.02314.610-0.033-0.0330.0000.0000.0000.000
71A224LYS10.9320.97017.5430.6600.6600.0000.0000.0000.000
72A225ILE0-0.015-0.00413.576-0.075-0.0750.0000.0000.0000.000
73A226ILE0-0.038-0.00716.9810.0770.0770.0000.0000.0000.000
74A227HIS10.8450.91116.6660.7730.7730.0000.0000.0000.000
75A228ARG10.9090.94515.6970.8760.8760.0000.0000.0000.000
76A229ASP-1-0.772-0.86318.608-0.544-0.5440.0000.0000.0000.000
77A230ILE0-0.0280.00421.725-0.018-0.0180.0000.0000.0000.000
78A231LYS10.9410.94423.8030.4450.4450.0000.0000.0000.000
79A232PRO00.0960.05126.376-0.018-0.0180.0000.0000.0000.000
80A233SER0-0.007-0.02125.1600.0060.0060.0000.0000.0000.000
81A234ASN0-0.045-0.02421.042-0.002-0.0020.0000.0000.0000.000
82A235ILE0-0.0030.01123.812-0.027-0.0270.0000.0000.0000.000
83A236LEU00.0200.00122.4900.0320.0320.0000.0000.0000.000
84A237LEU00.0820.02226.8590.0000.0000.0000.0000.0000.000
85A238ASP-1-0.743-0.87628.436-0.161-0.1610.0000.0000.0000.000
86A239ARG11.0200.98530.3340.0680.0680.0000.0000.0000.000
87A240SER0-0.058-0.02431.0430.0120.0120.0000.0000.0000.000
88A241GLY0-0.0040.01432.3560.0030.0030.0000.0000.0000.000
89A242ASN0-0.087-0.05328.074-0.002-0.0020.0000.0000.0000.000
90A243ILE00.0180.01528.137-0.004-0.0040.0000.0000.0000.000
91A244LYS10.7850.88523.1700.2260.2260.0000.0000.0000.000
92A245LEU0-0.045-0.04820.4580.0120.0120.0000.0000.0000.000
93A246CYS0-0.0410.02520.585-0.021-0.0210.0000.0000.0000.000
94A247ASP-1-0.877-0.99315.853-0.820-0.8200.0000.0000.0000.000
95A248PHE0-0.105-0.05314.845-0.026-0.0260.0000.0000.0000.000
96A249GLY00.0370.03113.012-0.111-0.1110.0000.0000.0000.000
97A250ILE00.0260.0346.282-0.204-0.2040.0000.0000.0000.000
98A251SER0-0.056-0.0399.9730.2600.2600.0000.0000.0000.000
99A252GLY0-0.0030.0068.9460.0060.0060.0000.0000.0000.000
100A285ASP-1-0.934-0.97921.690-0.716-0.7160.0000.0000.0000.000
101A286VAL00.0660.02122.727-0.025-0.0250.0000.0000.0000.000
102A287ARG10.8880.95324.4630.4340.4340.0000.0000.0000.000
103A288SER00.0270.02224.0740.0420.0420.0000.0000.0000.000
104A289ASP-1-0.799-0.91022.084-0.647-0.6470.0000.0000.0000.000
105A290VAL0-0.055-0.02225.3860.0220.0220.0000.0000.0000.000
106A291TRP00.0410.02128.6470.0280.0280.0000.0000.0000.000
107A292SER00.0200.00825.7130.0270.0270.0000.0000.0000.000
108A293LEU00.0130.01028.0910.0170.0170.0000.0000.0000.000
109A294GLY00.0370.02329.3800.0220.0220.0000.0000.0000.000
110A295ILE0-0.022-0.01130.9770.0190.0190.0000.0000.0000.000
111A296THR0-0.047-0.03128.8520.0010.0010.0000.0000.0000.000
112A297LEU0-0.014-0.02931.2730.0150.0150.0000.0000.0000.000
113A298TYR0-0.0020.00934.0260.0160.0160.0000.0000.0000.000
114A299GLU-1-0.823-0.94131.534-0.272-0.2720.0000.0000.0000.000
115A300LEU0-0.047-0.01731.9090.0090.0090.0000.0000.0000.000
116A301ALA0-0.033-0.00736.1130.0120.0120.0000.0000.0000.000
117A302THR0-0.0130.00138.7990.0130.0130.0000.0000.0000.000
118A303GLY00.0940.05839.205-0.005-0.0050.0000.0000.0000.000
119A304ARG10.8420.94636.4400.1680.1680.0000.0000.0000.000
120A305PHE00.030-0.00931.120-0.003-0.0030.0000.0000.0000.000
121A306PRO0-0.014-0.00935.0920.0100.0100.0000.0000.0000.000
122A307TYR0-0.085-0.10736.2430.0080.0080.0000.0000.0000.000
123A308PRO0-0.031-0.00436.468-0.007-0.0070.0000.0000.0000.000
124A309LYS10.9360.94638.7050.1340.1340.0000.0000.0000.000
125A310TRP00.0530.02238.7960.0020.0020.0000.0000.0000.000
126A311ASN00.0110.00739.544-0.005-0.0050.0000.0000.0000.000
127A312SER00.0240.02836.314-0.006-0.0060.0000.0000.0000.000
128A313VAL00.1120.03730.820-0.002-0.0020.0000.0000.0000.000
129A314PHE00.019-0.01433.127-0.011-0.0110.0000.0000.0000.000
130A315ASP-1-0.856-0.92134.249-0.176-0.1760.0000.0000.0000.000
131A316GLN0-0.081-0.04834.9240.0040.0040.0000.0000.0000.000
132A317LEU0-0.0400.01029.594-0.009-0.0090.0000.0000.0000.000
133A318THR0-0.110-0.05733.738-0.009-0.0090.0000.0000.0000.000
134A319GLN00.0320.02835.962-0.019-0.0190.0000.0000.0000.000
135A320VAL00.0240.01732.3530.0010.0010.0000.0000.0000.000
136A321VAL0-0.018-0.03533.639-0.001-0.0010.0000.0000.0000.000
137A322LYS10.8630.92836.4270.2060.2060.0000.0000.0000.000
138A323GLY00.0350.03339.4800.0110.0110.0000.0000.0000.000
139A324ASP-1-0.854-0.92540.462-0.184-0.1840.0000.0000.0000.000
140A325PRO0-0.0470.01738.454-0.003-0.0030.0000.0000.0000.000
141A326PRO00.0210.04137.1620.0080.0080.0000.0000.0000.000
142A327GLN00.003-0.02239.9080.0040.0040.0000.0000.0000.000
143A328LEU00.0610.01739.7790.0040.0040.0000.0000.0000.000
144A329SER0-0.078-0.03742.2630.0090.0090.0000.0000.0000.000
145A330ASN00.0010.00945.1820.0090.0090.0000.0000.0000.000
146A331SER00.0340.03047.0400.0050.0050.0000.0000.0000.000
147A332GLU-1-0.968-0.97248.373-0.130-0.1300.0000.0000.0000.000
148A333GLU-1-0.905-0.95947.951-0.103-0.1030.0000.0000.0000.000
149A334ARG10.8230.89747.9290.1100.1100.0000.0000.0000.000
150A335GLU-1-0.884-0.93747.422-0.114-0.1140.0000.0000.0000.000
151A336PHE0-0.004-0.00842.370-0.007-0.0070.0000.0000.0000.000
152A337SER0-0.034-0.01144.969-0.005-0.0050.0000.0000.0000.000
153A338PRO00.040-0.01545.527-0.007-0.0070.0000.0000.0000.000
154A339SER0-0.003-0.00843.314-0.006-0.0060.0000.0000.0000.000
155A340PHE00.0660.05536.880-0.014-0.0140.0000.0000.0000.000
156A341ILE00.0670.03440.552-0.010-0.0100.0000.0000.0000.000
157A342ASN0-0.063-0.03842.097-0.005-0.0050.0000.0000.0000.000
158A343PHE0-0.019-0.00933.351-0.009-0.0090.0000.0000.0000.000
159A344VAL00.0340.00236.269-0.017-0.0170.0000.0000.0000.000
160A345ASN00.0440.00436.828-0.017-0.0170.0000.0000.0000.000
161A346LEU0-0.0210.02237.022-0.005-0.0050.0000.0000.0000.000
162A347CYS0-0.105-0.03832.747-0.018-0.0180.0000.0000.0000.000
163A348LEU0-0.0270.00133.143-0.022-0.0220.0000.0000.0000.000
164A349THR00.0170.00034.6310.0180.0180.0000.0000.0000.000
165A350LYN0-0.0160.01634.550-0.025-0.0250.0000.0000.0000.000
166A351ASP-1-0.875-0.92035.259-0.246-0.2460.0000.0000.0000.000
167A352GLU-1-0.895-0.94431.617-0.339-0.3390.0000.0000.0000.000
168A353SER0-0.162-0.10132.2610.0160.0160.0000.0000.0000.000
169A354LYS10.9730.97633.4790.2490.2490.0000.0000.0000.000
170A355ARG10.8410.93729.0880.3690.3690.0000.0000.0000.000
171A356PRO00.0210.01532.456-0.023-0.0230.0000.0000.0000.000
172A357LYS10.9400.95827.8270.4110.4110.0000.0000.0000.000
173A358TYR00.0880.01424.9430.0150.0150.0000.0000.0000.000
174A359LYS10.9210.98129.4360.3440.3440.0000.0000.0000.000
175A360GLU-1-0.918-0.97431.789-0.263-0.2630.0000.0000.0000.000
176A361LEU00.0190.01631.2180.0150.0150.0000.0000.0000.000
177A362LEU0-0.024-0.00629.3220.0070.0070.0000.0000.0000.000
178A363LYS10.9370.96733.1730.2490.2490.0000.0000.0000.000
179A364HIS00.0390.02336.3650.0130.0130.0000.0000.0000.000
180A365PRO00.021-0.00838.2920.0020.0020.0000.0000.0000.000
181A366PHE00.0580.03536.5580.0080.0080.0000.0000.0000.000
182A367ILE0-0.026-0.00833.6670.0000.0000.0000.0000.0000.000
183A368LEU00.0310.01936.9610.0030.0030.0000.0000.0000.000
184A369MET0-0.066-0.01238.6380.0120.0120.0000.0000.0000.000
185A370TYR00.0750.02137.2770.0090.0090.0000.0000.0000.000
186A371GLU-1-0.948-0.98733.755-0.245-0.2450.0000.0000.0000.000
187A372GLU-1-0.942-0.96236.281-0.148-0.1480.0000.0000.0000.000
188A373ARG10.7990.90737.6900.1720.1720.0000.0000.0000.000
189A374ALA0-0.083-0.04738.375-0.002-0.0020.0000.0000.0000.000
190A375VAL00.0420.03639.8220.0090.0090.0000.0000.0000.000
191A376GLU-1-0.884-0.95939.615-0.119-0.1190.0000.0000.0000.000
192A377VAL00.0340.02034.999-0.003-0.0030.0000.0000.0000.000
193A378ALA00.0580.02136.148-0.001-0.0010.0000.0000.0000.000
194A379CYS0-0.047-0.01737.4410.0060.0060.0000.0000.0000.000
195A380TYR00.0770.02937.7550.0060.0060.0000.0000.0000.000
196A381VAL00.002-0.00834.1480.0020.0020.0000.0000.0000.000
197A382CYS0-0.053-0.02237.3740.0040.0040.0000.0000.0000.000
198A383LYS10.9801.01538.6540.0770.0770.0000.0000.0000.000
199A384ILE0-0.024-0.02238.8410.0050.0050.0000.0000.0000.000
200A385LEU0-0.036-0.02033.895-0.002-0.0020.0000.0000.0000.000
201A386ASP-1-0.911-0.96338.143-0.068-0.0680.0000.0000.0000.000
202A387GLN0-0.069-0.03740.5470.0020.0020.0000.0000.0000.000
203A388MET0-0.0740.00434.867-0.003-0.0030.0000.0000.0000.000