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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: G6GV1

Calculation Name: 5F3K-A-Xray372

Preferred Name: Heat shock protein 75 kDa, mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5F3K

Chain ID: A

ChEMBL ID: CHEMBL1075132

UniProt ID: Q12931

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:


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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2207285.926028
FMO2-HF: Nuclear repulsion 2128301.033561
FMO2-HF: Total energy -78984.892467
FMO2-MP2: Total energy -79216.55624


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:82:GLN)


Summations of interaction energy for fragment #1(A:82: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.
-2.574-0.0270000000000010.057-1.205-1.399-0.004
Interaction energy analysis for fragmet #1(A:82:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.027
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].
3A84SER0-0.029-0.0373.158-0.0182.5290.057-1.205-1.399-0.004
4A85THR0-0.016-0.0205.591-0.277-0.2770.0000.0000.0000.000
5A86SER00.1080.0368.632-0.107-0.1070.0000.0000.0000.000
6A87LYS10.9590.98111.975-0.721-0.7210.0000.0000.0000.000
7A88HIS0-0.001-0.0167.827-0.371-0.3710.0000.0000.0000.000
8A89GLU-1-0.779-0.8528.716-0.501-0.5010.0000.0000.0000.000
9A90PHE0-0.0130.00512.380-0.068-0.0680.0000.0000.0000.000
10A91GLN0-0.042-0.03014.601-0.058-0.0580.0000.0000.0000.000
11A92ALA0-0.021-0.00413.003-0.033-0.0330.0000.0000.0000.000
12A93GLU-1-0.875-0.95514.811-0.241-0.2410.0000.0000.0000.000
13A94THR0-0.056-0.02416.994-0.012-0.0120.0000.0000.0000.000
14A95LYS10.9610.97515.622-0.403-0.4030.0000.0000.0000.000
15A96LYS10.9290.97716.1150.1880.1880.0000.0000.0000.000
16A97LEU00.0190.00420.006-0.021-0.0210.0000.0000.0000.000
17A98LEU0-0.0060.00923.0160.0010.0010.0000.0000.0000.000
18A99ASP-1-0.896-0.95224.807-0.007-0.0070.0000.0000.0000.000
19A100ILE0-0.070-0.03124.109-0.002-0.0020.0000.0000.0000.000
20A101VAL00.0360.01527.2540.0000.0000.0000.0000.0000.000
21A102ALA00.0130.00528.9030.0020.0020.0000.0000.0000.000
22A103ARG10.9320.96127.6300.0260.0260.0000.0000.0000.000
23A104SER00.0400.03132.100-0.003-0.0030.0000.0000.0000.000
24A105LEU00.0370.01932.6270.0010.0010.0000.0000.0000.000
25A106TYR0-0.067-0.03334.836-0.002-0.0020.0000.0000.0000.000
26A107SER0-0.112-0.06736.561-0.002-0.0020.0000.0000.0000.000
27A108GLU-1-0.886-0.93737.8670.0040.0040.0000.0000.0000.000
28A109LYS10.9170.97339.744-0.012-0.0120.0000.0000.0000.000
29A110GLU-1-0.842-0.92941.2320.0060.0060.0000.0000.0000.000
30A111VAL0-0.032-0.02241.1830.0000.0000.0000.0000.0000.000
31A112PHE00.0260.01344.4150.0010.0010.0000.0000.0000.000
32A113ILE0-0.0050.00245.7930.0000.0000.0000.0000.0000.000
33A114ARG10.8950.94343.860-0.011-0.0110.0000.0000.0000.000
34A115GLU-1-0.910-0.94245.4740.0330.0330.0000.0000.0000.000
35A116LEU0-0.001-0.00847.5790.0010.0010.0000.0000.0000.000
36A117ILE0-0.027-0.00650.5660.0000.0000.0000.0000.0000.000
37A118SER0-0.019-0.00549.938-0.001-0.0010.0000.0000.0000.000
38A119ASN00.0350.00348.8310.0020.0020.0000.0000.0000.000
39A120ALA00.0110.01452.4540.0000.0000.0000.0000.0000.000
40A121SER00.022-0.00755.611-0.001-0.0010.0000.0000.0000.000
41A122ASP-1-0.897-0.93552.7320.0250.0250.0000.0000.0000.000
42A123ALA0-0.040-0.01956.1230.0000.0000.0000.0000.0000.000
43A124LEU0-0.011-0.00957.7550.0000.0000.0000.0000.0000.000
44A125GLU-1-0.766-0.86059.0330.0180.0180.0000.0000.0000.000
45A126LYS10.9140.96254.768-0.031-0.0310.0000.0000.0000.000
46A127LEU0-0.035-0.01360.5650.0000.0000.0000.0000.0000.000
47A128ARG10.8730.91563.618-0.017-0.0170.0000.0000.0000.000
48A129HIS00.0110.01162.996-0.001-0.0010.0000.0000.0000.000
49A130LYS10.9460.97764.549-0.025-0.0250.0000.0000.0000.000
50A131LEU0-0.032-0.01466.1670.0000.0000.0000.0000.0000.000
51A132VAL00.004-0.00268.417-0.001-0.0010.0000.0000.0000.000
52A133SER0-0.081-0.05067.161-0.001-0.0010.0000.0000.0000.000
53A134ASP-1-0.910-0.93269.8140.0210.0210.0000.0000.0000.000
54A135GLY0-0.0190.01072.1300.0000.0000.0000.0000.0000.000
55A136GLN0-0.133-0.08271.739-0.001-0.0010.0000.0000.0000.000
56A137ALA0-0.017-0.01372.9950.0000.0000.0000.0000.0000.000
57A138LEU0-0.007-0.01168.8160.0010.0010.0000.0000.0000.000
58A139PRO0-0.0030.01068.158-0.001-0.0010.0000.0000.0000.000
59A140GLU-1-0.905-0.96568.5040.0140.0140.0000.0000.0000.000
60A141MET0-0.065-0.00864.6410.0010.0010.0000.0000.0000.000
61A142GLU-1-0.857-0.91763.8450.0120.0120.0000.0000.0000.000
62A143ILE00.0200.00857.2700.0010.0010.0000.0000.0000.000
63A144HIS0-0.069-0.05060.229-0.002-0.0020.0000.0000.0000.000
64A145LEU00.0330.01154.1740.0020.0020.0000.0000.0000.000
65A146GLN0-0.017-0.01757.484-0.001-0.0010.0000.0000.0000.000
66A147THR00.0070.01254.6260.0010.0010.0000.0000.0000.000
67A148ASN0-0.039-0.02156.018-0.001-0.0010.0000.0000.0000.000
68A149ALA00.0770.02755.3790.0010.0010.0000.0000.0000.000
69A150GLU-1-0.940-0.96255.6380.0100.0100.0000.0000.0000.000
70A151LYS10.8570.92255.960-0.018-0.0180.0000.0000.0000.000
71A152GLY00.0260.03552.1350.0020.0020.0000.0000.0000.000
72A153THR0-0.023-0.02051.4410.0010.0010.0000.0000.0000.000
73A154ILE00.000-0.00150.449-0.003-0.0030.0000.0000.0000.000
74A155THR0-0.057-0.02753.1030.0030.0030.0000.0000.0000.000
75A156ILE00.0120.01352.670-0.002-0.0020.0000.0000.0000.000
76A157GLN0-0.030-0.03055.7780.0020.0020.0000.0000.0000.000
77A158ASP-1-0.758-0.87757.3990.0240.0240.0000.0000.0000.000
78A159THR0-0.068-0.06160.1490.0010.0010.0000.0000.0000.000
79A160GLY00.0380.01060.814-0.001-0.0010.0000.0000.0000.000
80A161ILE0-0.064-0.03558.7710.0000.0000.0000.0000.0000.000
81A162GLY00.0150.01158.8180.0000.0000.0000.0000.0000.000
82A163MET0-0.032-0.00153.1480.0020.0020.0000.0000.0000.000
83A164THR00.009-0.00257.3690.0000.0000.0000.0000.0000.000
84A165GLN00.0130.01456.1790.0020.0020.0000.0000.0000.000
85A166GLU-1-0.876-0.96054.3540.0440.0440.0000.0000.0000.000
86A167GLU-1-0.893-0.94252.6430.0420.0420.0000.0000.0000.000
87A168LEU00.0020.00251.5590.0020.0020.0000.0000.0000.000
88A169VAL00.0110.00349.6760.0020.0020.0000.0000.0000.000
89A170SER0-0.067-0.03048.2010.0040.0040.0000.0000.0000.000
90A171ASN00.0200.01746.8760.0010.0010.0000.0000.0000.000
91A172LEU00.0360.01146.1100.0020.0020.0000.0000.0000.000
92A173GLY00.0070.01144.8190.0030.0030.0000.0000.0000.000
93A174THR0-0.082-0.05842.1810.0070.0070.0000.0000.0000.000
94A175ILE0-0.0290.00841.1560.0050.0050.0000.0000.0000.000
95A176ALA00.0260.02340.4480.0030.0030.0000.0000.0000.000
96A177ARG10.9230.96838.102-0.079-0.0790.0000.0000.0000.000
97A178SER0-0.076-0.05636.9120.0080.0080.0000.0000.0000.000
98A179GLY00.0590.02835.232-0.003-0.0030.0000.0000.0000.000
99A180SER00.011-0.01330.141-0.006-0.0060.0000.0000.0000.000
100A181LYS10.9320.96932.649-0.098-0.0980.0000.0000.0000.000
101A182ALA00.0460.03235.044-0.005-0.0050.0000.0000.0000.000
102A183PHE0-0.003-0.01232.252-0.005-0.0050.0000.0000.0000.000
103A184LEU0-0.056-0.02630.067-0.004-0.0040.0000.0000.0000.000
104A185ASP-1-0.938-0.98333.0410.0390.0390.0000.0000.0000.000
105A186ALA00.0020.00636.081-0.005-0.0050.0000.0000.0000.000
106A187LEU0-0.073-0.02930.065-0.005-0.0050.0000.0000.0000.000
107A188GLN0-0.067-0.01231.134-0.007-0.0070.0000.0000.0000.000
108A197ILE0-0.040-0.04442.2500.0010.0010.0000.0000.0000.000
109A198ILE00.0040.01646.535-0.003-0.0030.0000.0000.0000.000
110A199GLY00.0430.01449.9770.0010.0010.0000.0000.0000.000
111A200GLN0-0.041-0.01851.7000.0000.0000.0000.0000.0000.000
112A201PHE0-0.001-0.00247.491-0.002-0.0020.0000.0000.0000.000
113A202GLY00.0930.04745.5420.0020.0020.0000.0000.0000.000
114A203VAL00.006-0.02239.6690.0010.0010.0000.0000.0000.000
115A204GLY00.1170.06841.2190.0020.0020.0000.0000.0000.000
116A205PHE00.0460.02642.623-0.002-0.0020.0000.0000.0000.000
117A206TYR0-0.059-0.01836.5770.0010.0010.0000.0000.0000.000
118A207SER0-0.022-0.02040.9080.0000.0000.0000.0000.0000.000
119A208ALA00.0290.00341.871-0.002-0.0020.0000.0000.0000.000
120A209PHE00.006-0.01441.0840.0000.0000.0000.0000.0000.000
121A210MET0-0.064-0.01335.4520.0040.0040.0000.0000.0000.000
122A211VAL00.0140.00240.094-0.002-0.0020.0000.0000.0000.000
123A212ALA0-0.0240.00042.966-0.003-0.0030.0000.0000.0000.000
124A213ASP-1-0.945-0.97143.4110.0430.0430.0000.0000.0000.000
125A214ARG10.8620.92445.204-0.037-0.0370.0000.0000.0000.000
126A215VAL0-0.025-0.01846.112-0.003-0.0030.0000.0000.0000.000
127A216GLU-1-0.822-0.88648.9460.0350.0350.0000.0000.0000.000
128A217VAL00.000-0.00550.635-0.002-0.0020.0000.0000.0000.000
129A218TYR0-0.049-0.03353.5590.0010.0010.0000.0000.0000.000
130A219SER00.026-0.00156.588-0.001-0.0010.0000.0000.0000.000
131A220ARG10.8150.89158.614-0.026-0.0260.0000.0000.0000.000
132A221SER00.0340.02660.882-0.002-0.0020.0000.0000.0000.000
133A222ALA00.0440.00262.066-0.001-0.0010.0000.0000.0000.000
134A223ALA0-0.071-0.02464.489-0.001-0.0010.0000.0000.0000.000
135A224PRO00.0350.00366.3750.0000.0000.0000.0000.0000.000
136A225GLY0-0.0010.00769.0900.0010.0010.0000.0000.0000.000
137A226SER0-0.0170.00564.1220.0010.0010.0000.0000.0000.000
138A227LEU00.0050.01464.023-0.001-0.0010.0000.0000.0000.000
139A228GLY0-0.017-0.00762.1280.0000.0000.0000.0000.0000.000
140A229TYR00.0340.01557.5970.0000.0000.0000.0000.0000.000
141A230GLN00.008-0.01254.864-0.001-0.0010.0000.0000.0000.000
142A231TRP00.0250.01145.8260.0010.0010.0000.0000.0000.000
143A232LEU0-0.017-0.00850.175-0.003-0.0030.0000.0000.0000.000
144A233SER0-0.007-0.00444.2770.0040.0040.0000.0000.0000.000
145A234ASP-1-0.811-0.89846.6860.0530.0530.0000.0000.0000.000
146A235GLY00.0220.02343.010-0.001-0.0010.0000.0000.0000.000
147A236SER0-0.057-0.04341.9130.0060.0060.0000.0000.0000.000
148A237GLY0-0.044-0.03541.0410.0020.0020.0000.0000.0000.000
149A238VAL0-0.050-0.02841.7450.0030.0030.0000.0000.0000.000
150A239PHE0-0.020-0.00642.185-0.002-0.0020.0000.0000.0000.000
151A240GLU-1-0.933-0.95847.5640.0510.0510.0000.0000.0000.000
152A241ILE0-0.026-0.02151.355-0.001-0.0010.0000.0000.0000.000
153A242ALA00.0110.00554.2040.0000.0000.0000.0000.0000.000
154A243GLU-1-0.925-0.96157.8640.0310.0310.0000.0000.0000.000
155A244ALA0-0.005-0.01160.1610.0000.0000.0000.0000.0000.000
156A245SER00.0160.00762.186-0.001-0.0010.0000.0000.0000.000
157A246GLY0-0.024-0.02265.1760.0000.0000.0000.0000.0000.000
158A247VAL00.0240.02661.027-0.001-0.0010.0000.0000.0000.000
159A248ARG10.9320.98763.876-0.019-0.0190.0000.0000.0000.000
160A249THR00.000-0.00563.2450.0010.0010.0000.0000.0000.000
161A250GLY00.0330.03960.916-0.001-0.0010.0000.0000.0000.000
162A251THR00.0160.00054.7980.0020.0020.0000.0000.0000.000
163A252LYS10.9100.96757.409-0.025-0.0250.0000.0000.0000.000
164A253ILE00.0070.01250.6870.0020.0020.0000.0000.0000.000
165A254ILE0-0.047-0.02853.533-0.003-0.0030.0000.0000.0000.000
166A255ILE00.0220.01547.6700.0030.0030.0000.0000.0000.000
167A256HIS0-0.004-0.00949.507-0.004-0.0040.0000.0000.0000.000
168A257LEU0-0.026-0.01347.0640.0030.0030.0000.0000.0000.000
169A258LYS10.9810.99639.743-0.050-0.0500.0000.0000.0000.000
170A259SER0-0.017-0.02442.492-0.002-0.0020.0000.0000.0000.000
171A260ASP-1-0.906-0.95339.5030.0240.0240.0000.0000.0000.000
172A261CYS0-0.0150.01742.406-0.002-0.0020.0000.0000.0000.000
173A262LYS10.9870.99045.091-0.021-0.0210.0000.0000.0000.000
174A263GLU-1-0.871-0.92544.9350.0090.0090.0000.0000.0000.000
175A264PHE0-0.015-0.01944.576-0.002-0.0020.0000.0000.0000.000
176A265SER0-0.038-0.02450.0720.0010.0010.0000.0000.0000.000
177A266SER00.002-0.00452.804-0.001-0.0010.0000.0000.0000.000
178A267GLU-1-0.842-0.92754.3380.0050.0050.0000.0000.0000.000
179A268ALA0-0.043-0.03255.4630.0000.0000.0000.0000.0000.000
180A269ARG10.9140.97145.410-0.004-0.0040.0000.0000.0000.000
181A270VAL00.0360.01551.4660.0000.0000.0000.0000.0000.000
182A271ARG10.9670.98953.018-0.001-0.0010.0000.0000.0000.000
183A272ASP-1-0.898-0.94152.147-0.001-0.0010.0000.0000.0000.000
184A273VAL0-0.010-0.00148.8120.0000.0000.0000.0000.0000.000
185A274VAL00.009-0.00851.3840.0010.0010.0000.0000.0000.000
186A275THR0-0.038-0.02254.2530.0000.0000.0000.0000.0000.000
187A276LYS10.9260.96151.9690.0040.0040.0000.0000.0000.000
188A277TYR00.0730.02349.8900.0000.0000.0000.0000.0000.000
189A278SER0-0.0030.01252.9700.0010.0010.0000.0000.0000.000
190A279ASN0-0.053-0.03655.6500.0000.0000.0000.0000.0000.000
191A280PHE0-0.066-0.02152.165-0.001-0.0010.0000.0000.0000.000
192A281VAL0-0.0150.00955.3840.0020.0020.0000.0000.0000.000
193A282SER0-0.0030.00457.465-0.001-0.0010.0000.0000.0000.000
194A283PHE0-0.023-0.01060.2430.0000.0000.0000.0000.0000.000
195A284PRO0-0.023-0.00861.521-0.001-0.0010.0000.0000.0000.000
196A285LEU00.0310.02656.6570.0010.0010.0000.0000.0000.000
197A286TYR0-0.021-0.02461.231-0.002-0.0020.0000.0000.0000.000
198A287LEU00.006-0.00357.0670.0010.0010.0000.0000.0000.000
199A288ASN0-0.030-0.03159.0540.0000.0000.0000.0000.0000.000
200A289GLY0-0.0030.00662.416-0.001-0.0010.0000.0000.0000.000
201A290ARG10.9250.95863.567-0.005-0.0050.0000.0000.0000.000
202A291ARG10.9180.97063.238-0.007-0.0070.0000.0000.0000.000
203A292MET0-0.060-0.01958.358-0.001-0.0010.0000.0000.0000.000
204A293ASN00.0250.02359.855-0.001-0.0010.0000.0000.0000.000
205A294THR00.0230.00561.8200.0000.0000.0000.0000.0000.000