FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Z6MGN

Calculation Name: 5CEN-A-Xray372

Preferred Name: Mitogen-activated protein kinase kinase kinase 12

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5CEN

Chain ID: A

ChEMBL ID: CHEMBL1908389

UniProt ID: Q12852

Base Structure: X-ray

Registration Date: 2023-09-20

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 281
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4019072.633235
FMO2-HF: Nuclear repulsion 3907103.42705
FMO2-HF: Total energy -111969.206185
FMO2-MP2: Total energy -112294.751528


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:117:LEU)


Summations of interaction energy for fragment #1(A:117:LEU)
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.
-13.333-8.8391.468-2.249-3.709-0.017
Interaction energy analysis for fragmet #1(A:117:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.015
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].
3A119GLU-1-0.898-0.9453.129-3.171-0.7390.021-0.998-1.4540.000
4A120VAL0-0.011-0.0112.464-4.833-3.2461.446-1.208-1.824-0.017
5A121PRO00.0380.0293.5950.4940.7940.003-0.032-0.2710.000
6A122PHE00.055-0.0136.4490.1940.1940.0000.0000.0000.000
7A123GLU-1-0.930-0.9668.451-1.619-1.6190.0000.0000.0000.000
8A124GLU-1-0.886-0.9485.959-3.248-3.2480.0000.0000.0000.000
9A125ILE0-0.098-0.0509.6810.1440.1440.0000.0000.0000.000
10A126LEU0-0.014-0.00812.0260.1070.1070.0000.0000.0000.000
11A127ASP-1-0.855-0.92315.288-0.366-0.3660.0000.0000.0000.000
12A128LEU00.0060.00215.6720.0310.0310.0000.0000.0000.000
13A129GLN0-0.009-0.00119.0230.0360.0360.0000.0000.0000.000
14A130TRP0-0.056-0.01822.1320.0050.0050.0000.0000.0000.000
15A131VAL0-0.002-0.01322.4270.0160.0160.0000.0000.0000.000
16A132GLY00.0680.04224.6300.0250.0250.0000.0000.0000.000
17A133SER0-0.098-0.03724.854-0.022-0.0220.0000.0000.0000.000
18A134GLY00.0950.03923.1560.0150.0150.0000.0000.0000.000
19A135ALA0-0.042-0.02624.064-0.006-0.0060.0000.0000.0000.000
20A136GLN0-0.007-0.01623.206-0.010-0.0100.0000.0000.0000.000
21A137GLY00.0220.00521.432-0.028-0.0280.0000.0000.0000.000
22A138ALA0-0.0270.01721.6960.0280.0280.0000.0000.0000.000
23A139VAL0-0.011-0.02519.803-0.041-0.0410.0000.0000.0000.000
24A140PHE0-0.012-0.00218.4780.0210.0210.0000.0000.0000.000
25A141LEU00.0370.03218.475-0.012-0.0120.0000.0000.0000.000
26A142GLY00.0420.01515.903-0.025-0.0250.0000.0000.0000.000
27A143ARG10.8620.92614.5880.4690.4690.0000.0000.0000.000
28A144PHE00.004-0.0035.208-0.041-0.0410.0000.0000.0000.000
29A145HIS10.8360.9094.5082.0672.160-0.001-0.002-0.0890.000
30A146GLY00.0110.00910.0400.1600.1600.0000.0000.0000.000
31A147GLU-1-0.851-0.89911.9190.1960.1960.0000.0000.0000.000
32A148GLU-1-0.918-0.95713.833-0.258-0.2580.0000.0000.0000.000
33A149VAL0-0.066-0.03711.2600.0390.0390.0000.0000.0000.000
34A150ALA00.0370.02914.763-0.015-0.0150.0000.0000.0000.000
35A151VAL00.008-0.01213.695-0.055-0.0550.0000.0000.0000.000
36A152LYS10.8340.91315.6860.2110.2110.0000.0000.0000.000
37A153LYS10.8500.93016.5290.4480.4480.0000.0000.0000.000
38A154VAL00.025-0.00115.9880.0570.0570.0000.0000.0000.000
39A155ARG10.9000.92918.4670.1640.1640.0000.0000.0000.000
40A156ASP-1-0.828-0.91717.846-0.276-0.2760.0000.0000.0000.000
41A157LEU00.0440.01911.989-0.013-0.0130.0000.0000.0000.000
42A158LYS10.9711.00414.8830.0830.0830.0000.0000.0000.000
43A159GLU-1-0.928-0.95817.283-0.147-0.1470.0000.0000.0000.000
44A160THR0-0.059-0.04712.057-0.018-0.0180.0000.0000.0000.000
45A161ASP-1-0.975-0.98212.602-0.074-0.0740.0000.0000.0000.000
46A162ILE00.0470.01512.0070.0740.0740.0000.0000.0000.000
47A163LYS10.9260.9609.1610.3920.3920.0000.0000.0000.000
48A164HIS0-0.0050.00311.7080.1600.1600.0000.0000.0000.000
49A165LEU00.0260.00514.0930.0240.0240.0000.0000.0000.000
50A166ARG10.9460.9944.314-3.137-3.055-0.001-0.009-0.0710.000
51A167LYS10.8790.91911.429-0.632-0.6320.0000.0000.0000.000
52A168LEU0-0.0030.01613.275-0.006-0.0060.0000.0000.0000.000
53A169LYS10.9550.98010.692-1.240-1.2400.0000.0000.0000.000
54A170HIS00.0620.03416.714-0.010-0.0100.0000.0000.0000.000
55A171PRO00.0410.02119.675-0.001-0.0010.0000.0000.0000.000
56A172ASN0-0.0040.00121.443-0.011-0.0110.0000.0000.0000.000
57A173ILE0-0.038-0.00218.017-0.030-0.0300.0000.0000.0000.000
58A174ILE0-0.031-0.00316.4550.0330.0330.0000.0000.0000.000
59A175THR0-0.021-0.00612.0990.0890.0890.0000.0000.0000.000
60A176PHE0-0.013-0.02010.965-0.091-0.0910.0000.0000.0000.000
61A177LYS10.8060.8768.3020.0840.0840.0000.0000.0000.000
62A178GLY00.0090.0106.391-0.184-0.1840.0000.0000.0000.000
63A179VAL0-0.048-0.0157.2840.4210.4210.0000.0000.0000.000
64A180CYS00.0120.0447.162-0.516-0.5160.0000.0000.0000.000
65A181THR0-0.024-0.0357.9580.2430.2430.0000.0000.0000.000
66A182GLN00.0560.0248.4180.0920.0920.0000.0000.0000.000
67A183ALA0-0.0010.02211.0730.0620.0620.0000.0000.0000.000
68A184PRO00.005-0.01014.867-0.024-0.0240.0000.0000.0000.000
69A185CYS0-0.052-0.04413.2340.0980.0980.0000.0000.0000.000
70A186TYR00.0180.03012.970-0.048-0.0480.0000.0000.0000.000
71A187CYS00.0150.01312.5500.0550.0550.0000.0000.0000.000
72A188ILE00.0050.01012.020-0.139-0.1390.0000.0000.0000.000
73A189LEU00.0270.0348.8780.0760.0760.0000.0000.0000.000
74A190MET0-0.042-0.02311.4710.1250.1250.0000.0000.0000.000
75A191GLU-1-0.795-0.91013.5290.1160.1160.0000.0000.0000.000
76A192PHE00.0340.01415.066-0.028-0.0280.0000.0000.0000.000
77A193CYS0-0.068-0.03018.1720.0460.0460.0000.0000.0000.000
78A194ALA00.035-0.00121.629-0.011-0.0110.0000.0000.0000.000
79A195GLN0-0.088-0.05124.111-0.013-0.0130.0000.0000.0000.000
80A196GLY00.0190.03325.270-0.002-0.0020.0000.0000.0000.000
81A197GLN0-0.010-0.02226.2070.0260.0260.0000.0000.0000.000
82A198LEU00.0190.00627.7160.0020.0020.0000.0000.0000.000
83A199TYR0-0.029-0.02230.132-0.001-0.0010.0000.0000.0000.000
84A200GLU-1-0.850-0.93928.670-0.077-0.0770.0000.0000.0000.000
85A201VAL00.0180.01430.2210.0010.0010.0000.0000.0000.000
86A202LEU0-0.030-0.02533.0150.0020.0020.0000.0000.0000.000
87A203ARG10.8430.93735.5370.0190.0190.0000.0000.0000.000
88A204ALA0-0.0190.00235.277-0.002-0.0020.0000.0000.0000.000
89A205GLY0-0.025-0.00337.2180.0010.0010.0000.0000.0000.000
90A206ARG10.8130.90531.730-0.012-0.0120.0000.0000.0000.000
91A207PRO0-0.007-0.01037.4230.0030.0030.0000.0000.0000.000
92A208VAL00.0210.00836.0090.0030.0030.0000.0000.0000.000
93A209THR00.0160.00438.1690.0020.0020.0000.0000.0000.000
94A210PRO00.0440.01538.7390.0030.0030.0000.0000.0000.000
95A211SER00.0430.01336.6950.0020.0020.0000.0000.0000.000
96A212LEU00.0160.02832.7060.0060.0060.0000.0000.0000.000
97A213LEU0-0.0230.00534.3090.0040.0040.0000.0000.0000.000
98A214VAL00.0020.00835.6750.0040.0040.0000.0000.0000.000
99A215ASP-1-0.875-0.93331.2960.0930.0930.0000.0000.0000.000
100A216TRP0-0.045-0.05829.6480.0050.0050.0000.0000.0000.000
101A217SER0-0.035-0.03130.8830.0070.0070.0000.0000.0000.000
102A218MET0-0.001-0.01032.3850.0050.0050.0000.0000.0000.000
103A219GLY00.0400.03628.4000.0130.0130.0000.0000.0000.000
104A220ILE0-0.013-0.01727.4460.0150.0150.0000.0000.0000.000
105A221ALA0-0.005-0.00528.2880.0090.0090.0000.0000.0000.000
106A222GLY00.0230.00528.2680.0080.0080.0000.0000.0000.000
107A223GLY00.005-0.00124.3900.0200.0200.0000.0000.0000.000
108A224MET00.0120.00724.5590.0140.0140.0000.0000.0000.000
109A225ASN0-0.027-0.01326.959-0.002-0.0020.0000.0000.0000.000
110A226TYR0-0.0010.00818.7310.0150.0150.0000.0000.0000.000
111A227LEU00.0190.00220.6160.0190.0190.0000.0000.0000.000
112A228HIS0-0.024-0.02023.7220.0060.0060.0000.0000.0000.000
113A229LEU0-0.053-0.01525.711-0.002-0.0020.0000.0000.0000.000
114A230HIS0-0.104-0.05320.8240.0400.0400.0000.0000.0000.000
115A231LYS10.9060.94922.871-0.154-0.1540.0000.0000.0000.000
116A232ILE0-0.0140.01220.026-0.013-0.0130.0000.0000.0000.000
117A233ILE0-0.045-0.02423.909-0.004-0.0040.0000.0000.0000.000
118A234HIS0-0.008-0.00523.775-0.002-0.0020.0000.0000.0000.000
119A235ARG10.8510.91625.606-0.073-0.0730.0000.0000.0000.000
120A236ASP-1-0.820-0.89626.764-0.034-0.0340.0000.0000.0000.000
121A237LEU00.0050.00127.477-0.004-0.0040.0000.0000.0000.000
122A238LYS10.8710.92429.0540.0290.0290.0000.0000.0000.000
123A239SER0-0.011-0.05829.411-0.002-0.0020.0000.0000.0000.000
124A240PRO0-0.015-0.01629.4140.0000.0000.0000.0000.0000.000
125A241ASN0-0.031-0.01025.398-0.014-0.0140.0000.0000.0000.000
126A242MET0-0.089-0.02124.6620.0210.0210.0000.0000.0000.000
127A243LEU00.0070.00320.987-0.016-0.0160.0000.0000.0000.000
128A244ILE00.0270.01924.7810.0230.0230.0000.0000.0000.000
129A245THR0-0.014-0.02521.398-0.021-0.0210.0000.0000.0000.000
130A246TYR00.0240.00623.574-0.001-0.0010.0000.0000.0000.000
131A247ASP-1-0.886-0.93124.2760.0930.0930.0000.0000.0000.000
132A248ASP-1-0.766-0.84726.8040.0380.0380.0000.0000.0000.000
133A249VAL00.0190.02623.6950.0100.0100.0000.0000.0000.000
134A250VAL0-0.029-0.00325.033-0.010-0.0100.0000.0000.0000.000
135A251LYS10.8470.91619.269-0.162-0.1620.0000.0000.0000.000
136A252ILE0-0.013-0.01422.700-0.026-0.0260.0000.0000.0000.000
137A253SER00.0570.01919.8690.0220.0220.0000.0000.0000.000
138A254ASP-1-0.850-0.90120.679-0.089-0.0890.0000.0000.0000.000
139A255PHE00.0360.00318.8880.0110.0110.0000.0000.0000.000
140A256GLY00.0650.04022.267-0.023-0.0230.0000.0000.0000.000
141A257THR0-0.025-0.01922.9080.0160.0160.0000.0000.0000.000
142A258SER0-0.063-0.05025.5630.0020.0020.0000.0000.0000.000
143A259LYS10.9950.99528.704-0.015-0.0150.0000.0000.0000.000
144A260GLU-1-0.981-0.96631.4290.0080.0080.0000.0000.0000.000
145A261LEU00.0080.00430.6500.0000.0000.0000.0000.0000.000
146A262SER0-0.0050.00131.541-0.006-0.0060.0000.0000.0000.000
147A263ASP-1-0.825-0.90031.939-0.083-0.0830.0000.0000.0000.000
148A264LYS10.9860.96934.5090.0560.0560.0000.0000.0000.000
149A265SER00.0360.00833.4090.0060.0060.0000.0000.0000.000
150A266THR00.0240.01030.718-0.001-0.0010.0000.0000.0000.000
151A267LYS10.8920.97233.0990.0440.0440.0000.0000.0000.000
152A268MET0-0.027-0.01936.3040.0050.0050.0000.0000.0000.000
153A269SER0-0.044-0.02632.7110.0010.0010.0000.0000.0000.000
154A270PHE00.031-0.00829.4090.0030.0030.0000.0000.0000.000
155A271ALA00.0060.00334.9740.0060.0060.0000.0000.0000.000
156A272GLY00.0070.01236.9700.0030.0030.0000.0000.0000.000
157A273THR0-0.034-0.02133.1570.0020.0020.0000.0000.0000.000
158A274VAL00.0180.00735.8310.0060.0060.0000.0000.0000.000
159A275ALA00.0230.02538.2830.0050.0050.0000.0000.0000.000
160A276TRP0-0.018-0.02934.1510.0010.0010.0000.0000.0000.000
161A277MET0-0.055-0.01032.0130.0080.0080.0000.0000.0000.000
162A278ALA00.0330.02036.4110.0000.0000.0000.0000.0000.000
163A279PRO00.0170.00538.346-0.003-0.0030.0000.0000.0000.000
164A280GLU-1-0.744-0.86037.4000.0360.0360.0000.0000.0000.000
165A281VAL0-0.052-0.02334.428-0.001-0.0010.0000.0000.0000.000
166A282ILE0-0.038-0.00637.049-0.005-0.0050.0000.0000.0000.000
167A283ARG10.7180.81339.923-0.021-0.0210.0000.0000.0000.000
168A284ASN0-0.060-0.02236.7100.0000.0000.0000.0000.0000.000
169A285GLU-1-0.795-0.86538.6800.0220.0220.0000.0000.0000.000
170A286PRO00.004-0.01035.5650.0010.0010.0000.0000.0000.000
171A287VAL0-0.022-0.00131.4680.0020.0020.0000.0000.0000.000
172A288SER0-0.008-0.00232.8220.0080.0080.0000.0000.0000.000
173A289GLU-1-0.869-0.95930.1060.1140.1140.0000.0000.0000.000
174A290LYS10.8560.91631.429-0.085-0.0850.0000.0000.0000.000
175A291VAL0-0.011-0.00131.627-0.004-0.0040.0000.0000.0000.000
176A292ASP-1-0.690-0.84228.5260.0730.0730.0000.0000.0000.000
177A293ILE0-0.052-0.01331.858-0.001-0.0010.0000.0000.0000.000
178A294TRP00.0200.02134.7480.0000.0000.0000.0000.0000.000
179A295SER0-0.033-0.03632.524-0.002-0.0020.0000.0000.0000.000
180A296PHE00.015-0.00631.993-0.003-0.0030.0000.0000.0000.000
181A297GLY00.0330.01834.005-0.001-0.0010.0000.0000.0000.000
182A298VAL0-0.047-0.01736.516-0.003-0.0030.0000.0000.0000.000
183A299VAL00.0190.01931.920-0.003-0.0030.0000.0000.0000.000
184A300LEU0-0.012-0.00435.181-0.001-0.0010.0000.0000.0000.000
185A301TRP00.043-0.01337.262-0.002-0.0020.0000.0000.0000.000
186A302GLU-1-0.758-0.83535.2190.0010.0010.0000.0000.0000.000
187A303LEU0-0.062-0.01733.528-0.003-0.0030.0000.0000.0000.000
188A304LEU0-0.023-0.01037.622-0.001-0.0010.0000.0000.0000.000
189A305THR00.011-0.01141.269-0.003-0.0030.0000.0000.0000.000
190A306GLY00.0070.02039.576-0.003-0.0030.0000.0000.0000.000
191A307GLU-1-0.918-0.97840.650-0.013-0.0130.0000.0000.0000.000
192A308ILE0-0.032-0.01439.0500.0010.0010.0000.0000.0000.000
193A309PRO00.005-0.00838.1820.0010.0010.0000.0000.0000.000
194A310TYR0-0.016-0.02341.263-0.002-0.0020.0000.0000.0000.000
195A311LYS10.9470.98843.3980.0180.0180.0000.0000.0000.000
196A312ASP-1-0.904-0.95644.218-0.025-0.0250.0000.0000.0000.000
197A313VAL0-0.0360.00145.6540.0000.0000.0000.0000.0000.000
198A314ASP-1-0.892-0.94845.269-0.027-0.0270.0000.0000.0000.000
199A315SER00.032-0.00242.2280.0040.0040.0000.0000.0000.000
200A316SER00.0130.00644.0640.0030.0030.0000.0000.0000.000
201A317ALA00.0150.01646.7760.0030.0030.0000.0000.0000.000
202A318ILE00.0110.01042.3410.0040.0040.0000.0000.0000.000
203A319ILE0-0.012-0.01141.6290.0040.0040.0000.0000.0000.000
204A320TRP00.0170.01644.3280.0030.0030.0000.0000.0000.000
205A321GLY00.0250.01047.8550.0030.0030.0000.0000.0000.000
206A322VAL0-0.010-0.01741.8240.0030.0030.0000.0000.0000.000
207A323GLY00.0330.01944.3110.0040.0040.0000.0000.0000.000
208A324SER0-0.025-0.00545.2140.0020.0020.0000.0000.0000.000
209A325ASN0-0.102-0.03245.5770.0030.0030.0000.0000.0000.000
210A326SER0-0.035-0.03347.4690.0020.0020.0000.0000.0000.000
211A327LEU0-0.011-0.00146.479-0.002-0.0020.0000.0000.0000.000
212A328HIS0-0.064-0.03844.3700.0030.0030.0000.0000.0000.000
213A329LEU00.0100.02540.853-0.002-0.0020.0000.0000.0000.000
214A330PRO00.0190.03345.2000.0030.0030.0000.0000.0000.000
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