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: 6NVQZ

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 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 203
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2418157.818811
FMO2-HF: Nuclear repulsion 2334446.537593
FMO2-HF: Total energy -83711.281219
FMO2-MP2: Total energy -83950.791326


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.
-10.772-5.7035.44-3.962-6.549-0.013
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 : 0.021 / 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].
3A144GLN0-0.001-0.0013.574-3.415-0.550-0.014-1.406-1.4460.000
4A145LEU00.0490.0252.194-2.390-1.3681.857-1.265-1.615-0.002
5A146LEU0-0.052-0.0282.252-4.186-3.0823.598-1.285-3.417-0.011
6A147MET00.0410.0754.9980.0890.167-0.001-0.006-0.0710.000
7A148ASP-1-0.842-0.9357.5590.5170.5170.0000.0000.0000.000
8A149LEU0-0.074-0.0376.7430.0800.0800.0000.0000.0000.000
9A150ASP-1-0.771-0.8979.054-2.403-2.4030.0000.0000.0000.000
10A151VAL0-0.008-0.00811.8010.2010.2010.0000.0000.0000.000
11A152VAL0-0.049-0.01313.1710.0940.0940.0000.0000.0000.000
12A153MET0-0.036-0.00612.9930.0050.0050.0000.0000.0000.000
13A154ARG00.0420.01713.307-0.067-0.0670.0000.0000.0000.000
14A155SER00.0100.01718.0500.0400.0400.0000.0000.0000.000
15A156SER00.0080.01319.3060.0210.0210.0000.0000.0000.000
16A157ASH0-0.130-0.10222.113-0.010-0.0100.0000.0000.0000.000
17A158CYS00.0630.04723.386-0.014-0.0140.0000.0000.0000.000
18A159PRO00.0000.01124.2880.0030.0030.0000.0000.0000.000
19A160TYR0-0.010-0.01015.405-0.028-0.0280.0000.0000.0000.000
20A161ILE0-0.0020.01617.3400.0470.0470.0000.0000.0000.000
21A162VAL0-0.034-0.02318.327-0.061-0.0610.0000.0000.0000.000
22A163GLN0-0.083-0.04010.8660.0110.0110.0000.0000.0000.000
23A164PHE0-0.039-0.06412.0890.0560.0560.0000.0000.0000.000
24A177CYS0-0.013-0.01712.081-0.031-0.0310.0000.0000.0000.000
25A178MET0-0.006-0.01413.9200.0960.0960.0000.0000.0000.000
26A179GLU-1-0.780-0.84717.664-0.412-0.4120.0000.0000.0000.000
27A180LEU0-0.030-0.02720.739-0.029-0.0290.0000.0000.0000.000
28A181MET0-0.0180.02123.6240.0110.0110.0000.0000.0000.000
29A182SER00.0210.00926.5820.0110.0110.0000.0000.0000.000
30A183THR0-0.012-0.01928.4040.0060.0060.0000.0000.0000.000
31A184SER00.0130.01726.2840.0030.0030.0000.0000.0000.000
32A185PHE00.064-0.00528.1660.0210.0210.0000.0000.0000.000
33A186ASP-1-0.883-0.91529.143-0.272-0.2720.0000.0000.0000.000
34A187LYS10.9500.96428.8120.2700.2700.0000.0000.0000.000
35A188PHE0-0.0100.00732.7960.0130.0130.0000.0000.0000.000
36A189TYR0-0.059-0.07532.5210.0140.0140.0000.0000.0000.000
37A190LYS10.8240.90331.7270.2680.2680.0000.0000.0000.000
38A191TYR0-0.057-0.01737.1010.0080.0080.0000.0000.0000.000
39A192VAL00.0560.03838.9440.0090.0090.0000.0000.0000.000
40A193TYR00.010-0.03239.118-0.005-0.0050.0000.0000.0000.000
41A194SER0-0.122-0.05441.3560.0090.0090.0000.0000.0000.000
42A195VAL0-0.037-0.03643.2670.0050.0050.0000.0000.0000.000
43A196LEU0-0.068-0.03543.0720.0080.0080.0000.0000.0000.000
44A197ASP-1-0.871-0.92645.054-0.129-0.1290.0000.0000.0000.000
45A198ASP-1-0.867-0.93743.639-0.140-0.1400.0000.0000.0000.000
46A199VAL0-0.0010.03643.856-0.006-0.0060.0000.0000.0000.000
47A200ILE0-0.074-0.04537.045-0.002-0.0020.0000.0000.0000.000
48A201PRO00.0250.01841.196-0.003-0.0030.0000.0000.0000.000
49A202GLU-1-0.760-0.86440.751-0.171-0.1710.0000.0000.0000.000
50A203GLU-1-0.909-0.96640.279-0.149-0.1490.0000.0000.0000.000
51A204ILE0-0.026-0.01036.805-0.008-0.0080.0000.0000.0000.000
52A205LEU00.0280.01236.345-0.018-0.0180.0000.0000.0000.000
53A206GLY00.0330.02635.635-0.017-0.0170.0000.0000.0000.000
54A207LYS10.8170.89734.7810.1710.1710.0000.0000.0000.000
55A208ILE00.0280.02330.724-0.020-0.0200.0000.0000.0000.000
56A209THR0-0.024-0.01030.823-0.028-0.0280.0000.0000.0000.000
57A210LEU0-0.0180.00131.221-0.021-0.0210.0000.0000.0000.000
58A211ALA0-0.026-0.01828.573-0.017-0.0170.0000.0000.0000.000
59A212THR00.013-0.02326.538-0.031-0.0310.0000.0000.0000.000
60A213VAL00.0140.00926.230-0.037-0.0370.0000.0000.0000.000
61A214LYS10.9280.97227.0120.2640.2640.0000.0000.0000.000
62A215ALA00.0180.01923.009-0.022-0.0220.0000.0000.0000.000
63A216LEU00.0000.00221.886-0.054-0.0540.0000.0000.0000.000
64A217ASN00.011-0.00922.406-0.047-0.0470.0000.0000.0000.000
65A218HIS10.8380.92320.2800.4980.4980.0000.0000.0000.000
66A219LEU00.0100.00316.137-0.025-0.0250.0000.0000.0000.000
67A220LYS10.8900.95518.3360.4620.4620.0000.0000.0000.000
68A221GLU-1-0.846-0.92420.947-0.432-0.4320.0000.0000.0000.000
69A222ASN0-0.043-0.02119.594-0.001-0.0010.0000.0000.0000.000
70A223LEU00.0350.02914.775-0.006-0.0060.0000.0000.0000.000
71A224LYS10.7980.89717.1900.5170.5170.0000.0000.0000.000
72A225ILE00.0210.01113.681-0.034-0.0340.0000.0000.0000.000
73A226ILE0-0.024-0.01417.2300.0600.0600.0000.0000.0000.000
74A227HIS10.7890.90216.8210.7480.7480.0000.0000.0000.000
75A228ARG10.7960.88715.5620.9050.9050.0000.0000.0000.000
76A229ASP-1-0.752-0.86718.442-0.571-0.5710.0000.0000.0000.000
77A230ILE0-0.045-0.00721.792-0.025-0.0250.0000.0000.0000.000
78A231LYS10.9710.97623.9720.4910.4910.0000.0000.0000.000
79A232PRO00.0880.05126.594-0.023-0.0230.0000.0000.0000.000
80A233SER0-0.036-0.02325.0220.0130.0130.0000.0000.0000.000
81A234ASN0-0.085-0.05622.1630.0000.0000.0000.0000.0000.000
82A235ILE00.0010.00923.570-0.031-0.0310.0000.0000.0000.000
83A236LEU00.000-0.00622.4720.0250.0250.0000.0000.0000.000
84A237LEU00.0330.02726.8670.0040.0040.0000.0000.0000.000
85A238ASP-1-0.733-0.89928.315-0.248-0.2480.0000.0000.0000.000
86A239ARG10.8790.91330.7320.1360.1360.0000.0000.0000.000
87A240SER0-0.026-0.00331.1910.0170.0170.0000.0000.0000.000
88A241GLY00.0170.01832.8830.0060.0060.0000.0000.0000.000
89A242ASN0-0.081-0.03927.6910.0060.0060.0000.0000.0000.000
90A243ILE0-0.008-0.00628.404-0.021-0.0210.0000.0000.0000.000
91A244LYS10.7650.87123.6570.3180.3180.0000.0000.0000.000
92A245LEU0-0.042-0.02920.8460.0040.0040.0000.0000.0000.000
93A246CYS0-0.0330.00320.799-0.032-0.0320.0000.0000.0000.000
94A247ASP-1-0.801-0.92215.776-0.982-0.9820.0000.0000.0000.000
95A248PHE00.0120.00915.0420.0240.0240.0000.0000.0000.000
96A249GLY00.0790.05512.834-0.173-0.1730.0000.0000.0000.000
97A250ILE0-0.0030.0106.151-0.084-0.0840.0000.0000.0000.000
98A251SER0-0.066-0.0439.5390.0000.0000.0000.0000.0000.000
99A252GLY0-0.062-0.0248.7860.2290.2290.0000.0000.0000.000
100A285ASP-1-0.806-0.90223.411-0.487-0.4870.0000.0000.0000.000
101A286VAL00.024-0.01123.7720.0090.0090.0000.0000.0000.000
102A287ARG10.8310.90124.6630.3660.3660.0000.0000.0000.000
103A288SER0-0.0090.01024.3860.0420.0420.0000.0000.0000.000
104A289ASP-1-0.766-0.88422.164-0.594-0.5940.0000.0000.0000.000
105A290VAL0-0.054-0.01525.6520.0180.0180.0000.0000.0000.000
106A291TRP00.0390.02729.0520.0220.0220.0000.0000.0000.000
107A292SER00.0080.00526.0430.0260.0260.0000.0000.0000.000
108A293LEU0-0.0070.01128.0280.0080.0080.0000.0000.0000.000
109A294GLY00.0360.00929.5940.0180.0180.0000.0000.0000.000
110A295ILE0-0.018-0.01131.1690.0170.0170.0000.0000.0000.000
111A296THR0-0.023-0.02928.8940.0050.0050.0000.0000.0000.000
112A297LEU0-0.009-0.01831.4260.0110.0110.0000.0000.0000.000
113A298TYR00.0180.01434.3300.0130.0130.0000.0000.0000.000
114A299GLU-1-0.846-0.92131.584-0.285-0.2850.0000.0000.0000.000
115A300LEU0-0.041-0.02131.8490.0080.0080.0000.0000.0000.000
116A301ALA00.0080.01236.1470.0110.0110.0000.0000.0000.000
117A302THR0-0.0010.00138.9650.0140.0140.0000.0000.0000.000
118A303GLY00.0600.06138.650-0.008-0.0080.0000.0000.0000.000
119A304ARG10.8390.91137.1900.1960.1960.0000.0000.0000.000
120A305PHE00.000-0.00331.2300.0010.0010.0000.0000.0000.000
121A306PRO00.0270.00835.0100.0090.0090.0000.0000.0000.000
122A307TYR0-0.017-0.00636.3680.0120.0120.0000.0000.0000.000
123A308PRO0-0.0330.00036.771-0.010-0.0100.0000.0000.0000.000
124A309LYS10.8400.91539.0490.1500.1500.0000.0000.0000.000
125A310TRP00.1060.03839.1480.0020.0020.0000.0000.0000.000
126A311ASN00.0720.03039.058-0.010-0.0100.0000.0000.0000.000
127A312SER0-0.0200.01036.575-0.002-0.0020.0000.0000.0000.000
128A313VAL00.0720.02830.758-0.001-0.0010.0000.0000.0000.000
129A314PHE00.0090.00733.594-0.010-0.0100.0000.0000.0000.000
130A315ASP-1-0.882-0.94534.573-0.174-0.1740.0000.0000.0000.000
131A316GLN0-0.037-0.04535.0630.0000.0000.0000.0000.0000.000
132A317LEU0-0.0090.01129.846-0.009-0.0090.0000.0000.0000.000
133A318THR0-0.021-0.01333.855-0.004-0.0040.0000.0000.0000.000
134A319GLN0-0.076-0.04336.201-0.005-0.0050.0000.0000.0000.000
135A320VAL00.0170.02033.0990.0040.0040.0000.0000.0000.000
136A321VAL0-0.064-0.02933.499-0.005-0.0050.0000.0000.0000.000
137A322LYS10.9230.93236.7220.1800.1800.0000.0000.0000.000
138A323GLY00.0160.03740.0290.0110.0110.0000.0000.0000.000
139A324ASP-1-0.883-0.93240.412-0.173-0.1730.0000.0000.0000.000
140A325PRO0-0.013-0.00738.718-0.007-0.0070.0000.0000.0000.000
141A326PRO00.0200.00937.6130.0090.0090.0000.0000.0000.000
142A327GLN0-0.017-0.01340.7820.0040.0040.0000.0000.0000.000
143A328LEU00.0650.04640.1230.0050.0050.0000.0000.0000.000
144A329SER0-0.073-0.03442.5890.0090.0090.0000.0000.0000.000
145A330ASN0-0.033-0.00845.6510.0090.0090.0000.0000.0000.000
146A331SER0-0.013-0.00747.3970.0080.0080.0000.0000.0000.000
147A332GLU-1-0.949-0.97448.642-0.135-0.1350.0000.0000.0000.000
148A333GLU-1-0.923-0.95548.252-0.111-0.1110.0000.0000.0000.000
149A334ARG10.8570.93148.4190.1150.1150.0000.0000.0000.000
150A335GLU-1-0.847-0.92947.672-0.124-0.1240.0000.0000.0000.000
151A336PHE0-0.017-0.02143.784-0.006-0.0060.0000.0000.0000.000
152A337SER0-0.009-0.01844.640-0.005-0.0050.0000.0000.0000.000
153A338PRO00.019-0.01345.881-0.005-0.0050.0000.0000.0000.000
154A339SER0-0.020-0.00743.523-0.004-0.0040.0000.0000.0000.000
155A340PHE00.0800.04937.035-0.011-0.0110.0000.0000.0000.000
156A341ILE00.0510.03240.517-0.011-0.0110.0000.0000.0000.000
157A342ASN0-0.026-0.02441.892-0.009-0.0090.0000.0000.0000.000
158A343PHE00.0170.01333.397-0.007-0.0070.0000.0000.0000.000
159A344VAL00.0320.00836.298-0.013-0.0130.0000.0000.0000.000
160A345ASN00.027-0.01036.925-0.016-0.0160.0000.0000.0000.000
161A346LEU0-0.037-0.00137.233-0.003-0.0030.0000.0000.0000.000
162A347CYS0-0.080-0.03032.930-0.013-0.0130.0000.0000.0000.000
163A348LEU0-0.0130.00333.747-0.016-0.0160.0000.0000.0000.000
164A349THR00.001-0.00535.6660.0160.0160.0000.0000.0000.000
165A350LYN00.0330.01235.064-0.018-0.0180.0000.0000.0000.000
166A351ASP-1-0.889-0.94135.198-0.219-0.2190.0000.0000.0000.000
167A352GLU-1-0.736-0.85231.096-0.342-0.3420.0000.0000.0000.000
168A353SER0-0.132-0.07332.8790.0200.0200.0000.0000.0000.000
169A354LYS10.8830.93534.3780.2300.2300.0000.0000.0000.000
170A355ARG10.8580.93829.7020.3230.3230.0000.0000.0000.000
171A356PRO00.0120.01533.159-0.011-0.0110.0000.0000.0000.000
172A357LYS10.8790.92127.1160.3630.3630.0000.0000.0000.000
173A358TYR00.0750.01524.3880.0330.0330.0000.0000.0000.000
174A359LYS10.8010.88929.9910.2700.2700.0000.0000.0000.000
175A360GLU-1-0.781-0.87532.309-0.233-0.2330.0000.0000.0000.000
176A361LEU00.0020.00031.0660.0100.0100.0000.0000.0000.000
177A362LEU0-0.002-0.00429.9770.0060.0060.0000.0000.0000.000
178A363LYS10.9130.95433.5950.2090.2090.0000.0000.0000.000
179A364HIS0-0.0210.00836.8670.0110.0110.0000.0000.0000.000
180A365PRO00.010-0.01338.808-0.001-0.0010.0000.0000.0000.000
181A366PHE00.0240.01637.0050.0040.0040.0000.0000.0000.000
182A367ILE0-0.039-0.00433.9790.0000.0000.0000.0000.0000.000
183A368LEU00.0390.02437.2120.0030.0030.0000.0000.0000.000
184A369MET0-0.0290.00239.0210.0120.0120.0000.0000.0000.000
185A370TYR00.013-0.02737.9100.0070.0070.0000.0000.0000.000
186A371GLU-1-0.943-0.98133.820-0.232-0.2320.0000.0000.0000.000
187A372GLU-1-0.912-0.95736.445-0.164-0.1640.0000.0000.0000.000
188A373ARG10.8070.91438.5440.1660.1660.0000.0000.0000.000
189A374ALA0-0.052-0.00839.556-0.006-0.0060.0000.0000.0000.000
190A375VAL00.0290.01840.6260.0080.0080.0000.0000.0000.000
191A376GLU-1-0.826-0.91440.171-0.148-0.1480.0000.0000.0000.000
192A377VAL0-0.021-0.01535.322-0.006-0.0060.0000.0000.0000.000
193A378ALA00.0530.03236.350-0.003-0.0030.0000.0000.0000.000
194A379CYS0-0.035-0.01237.3390.0030.0030.0000.0000.0000.000
195A380TYR00.0650.02538.3610.0000.0000.0000.0000.0000.000
196A381VAL00.015-0.00433.9340.0000.0000.0000.0000.0000.000
197A382CYS0-0.075-0.03637.3610.0000.0000.0000.0000.0000.000
198A383LYS10.9670.99238.6350.1110.1110.0000.0000.0000.000
199A384ILE00.0080.01038.4840.0060.0060.0000.0000.0000.000
200A385LEU00.0110.00033.763-0.004-0.0040.0000.0000.0000.000
201A386ASP-1-0.837-0.92837.818-0.126-0.1260.0000.0000.0000.000
202A387GLN0-0.095-0.04240.4360.0100.0100.0000.0000.0000.000
203A388MET0-0.0600.01134.586-0.002-0.0020.0000.0000.0000.000