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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: N9QLQ

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2211619.90512
FMO2-HF: Nuclear repulsion 2132633.601235
FMO2-HF: Total energy -78986.303886
FMO2-MP2: Total energy -79217.921711


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.
-3.2390.3370.318-1.946-1.948-0.004
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 : 0.010 / q_NPA : 0.004
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].
3A84SER0-0.048-0.0512.847-1.8741.6950.319-1.945-1.943-0.004
4A85THR00.000-0.0195.143-0.676-0.669-0.001-0.001-0.0050.000
5A86SER00.0720.0268.6360.0940.0940.0000.0000.0000.000
6A87LYS10.9740.98411.844-0.422-0.4220.0000.0000.0000.000
7A88HIS00.0110.0037.925-0.327-0.3270.0000.0000.0000.000
8A89GLU-1-0.774-0.8488.5510.6280.6280.0000.0000.0000.000
9A90PHE00.0090.01111.993-0.029-0.0290.0000.0000.0000.000
10A91GLN0-0.0170.00914.1330.0180.0180.0000.0000.0000.000
11A92ALA00.0340.03912.6510.0370.0370.0000.0000.0000.000
12A93GLU-1-0.782-0.89014.8080.0990.0990.0000.0000.0000.000
13A94THR0-0.034-0.04017.232-0.012-0.0120.0000.0000.0000.000
14A95LYS10.8460.91015.798-0.634-0.6340.0000.0000.0000.000
15A96LYS10.8100.88416.189-0.179-0.1790.0000.0000.0000.000
16A97LEU00.0280.02220.082-0.029-0.0290.0000.0000.0000.000
17A98LEU0-0.0100.00722.897-0.019-0.0190.0000.0000.0000.000
18A99ASP-1-0.806-0.89324.3330.1830.1830.0000.0000.0000.000
19A100ILE0-0.031-0.00624.890-0.017-0.0170.0000.0000.0000.000
20A101VAL00.0220.00327.467-0.011-0.0110.0000.0000.0000.000
21A102ALA00.0020.00128.690-0.010-0.0100.0000.0000.0000.000
22A103ARG10.8050.87727.728-0.172-0.1720.0000.0000.0000.000
23A104SER0-0.040-0.01832.211-0.009-0.0090.0000.0000.0000.000
24A105LEU00.0850.03432.204-0.004-0.0040.0000.0000.0000.000
25A106TYR0-0.105-0.07134.616-0.005-0.0050.0000.0000.0000.000
26A107SER0-0.077-0.05236.346-0.007-0.0070.0000.0000.0000.000
27A108GLU-1-0.873-0.91836.5730.0650.0650.0000.0000.0000.000
28A109LYS10.8180.90739.109-0.093-0.0930.0000.0000.0000.000
29A110GLU-1-0.759-0.86440.6310.0520.0520.0000.0000.0000.000
30A111VAL0-0.040-0.01940.641-0.004-0.0040.0000.0000.0000.000
31A112PHE00.0450.02443.903-0.004-0.0040.0000.0000.0000.000
32A113ILE0-0.016-0.00645.382-0.003-0.0030.0000.0000.0000.000
33A114ARG10.8470.90343.985-0.052-0.0520.0000.0000.0000.000
34A115GLU-1-0.851-0.90445.1040.0480.0480.0000.0000.0000.000
35A116LEU00.0180.00347.260-0.003-0.0030.0000.0000.0000.000
36A117ILE0-0.020-0.00250.142-0.003-0.0030.0000.0000.0000.000
37A118SER00.0230.01449.300-0.003-0.0030.0000.0000.0000.000
38A119ASN0-0.018-0.03248.0350.0000.0000.0000.0000.0000.000
39A120ALA0-0.0030.02152.056-0.001-0.0010.0000.0000.0000.000
40A121SER00.0380.00455.263-0.002-0.0020.0000.0000.0000.000
41A122ASP-1-0.812-0.88953.3300.0280.0280.0000.0000.0000.000
42A123ALA00.0190.01455.761-0.001-0.0010.0000.0000.0000.000
43A124LEU0-0.021-0.00257.406-0.001-0.0010.0000.0000.0000.000
44A125GLU-1-0.786-0.85658.3560.0190.0190.0000.0000.0000.000
45A126LYS10.8160.88853.910-0.031-0.0310.0000.0000.0000.000
46A127LEU0-0.040-0.00860.145-0.001-0.0010.0000.0000.0000.000
47A128ARG10.8740.89363.221-0.020-0.0200.0000.0000.0000.000
48A129HIS00.0010.00362.502-0.001-0.0010.0000.0000.0000.000
49A130LYS10.9200.97964.009-0.025-0.0250.0000.0000.0000.000
50A131LEU0-0.041-0.02065.591-0.001-0.0010.0000.0000.0000.000
51A132VAL00.011-0.00368.074-0.001-0.0010.0000.0000.0000.000
52A133SER0-0.081-0.05466.561-0.001-0.0010.0000.0000.0000.000
53A134ASP-1-0.909-0.92969.1440.0160.0160.0000.0000.0000.000
54A135GLY0-0.030-0.00771.6630.0000.0000.0000.0000.0000.000
55A136GLN0-0.110-0.06271.0610.0010.0010.0000.0000.0000.000
56A137ALA0-0.008-0.00972.4440.0000.0000.0000.0000.0000.000
57A138LEU0-0.007-0.00668.0800.0010.0010.0000.0000.0000.000
58A139PRO0-0.0030.00767.6390.0000.0000.0000.0000.0000.000
59A140GLU-1-0.796-0.88467.8170.0260.0260.0000.0000.0000.000
60A141MET0-0.0510.00663.8360.0000.0000.0000.0000.0000.000
61A142GLU-1-0.788-0.86563.2400.0250.0250.0000.0000.0000.000
62A143ILE00.0120.00756.7330.0010.0010.0000.0000.0000.000
63A144HIS0-0.038-0.04359.6540.0010.0010.0000.0000.0000.000
64A145LEU00.0290.00653.6600.0020.0020.0000.0000.0000.000
65A146GLN0-0.067-0.04156.765-0.001-0.0010.0000.0000.0000.000
66A147THR0-0.0090.00554.0670.0020.0020.0000.0000.0000.000
67A148ASN0-0.033-0.03355.362-0.001-0.0010.0000.0000.0000.000
68A149ALA00.0890.04454.3140.0020.0020.0000.0000.0000.000
69A150GLU-1-0.930-0.96854.5610.0510.0510.0000.0000.0000.000
70A151LYS10.9080.96455.047-0.049-0.0490.0000.0000.0000.000
71A152GLY0-0.040-0.00551.1980.0030.0030.0000.0000.0000.000
72A153THR0-0.005-0.00650.4930.0020.0020.0000.0000.0000.000
73A154ILE0-0.002-0.00349.688-0.003-0.0030.0000.0000.0000.000
74A155THR0-0.057-0.03752.6970.0010.0010.0000.0000.0000.000
75A156ILE00.0100.01452.389-0.002-0.0020.0000.0000.0000.000
76A157GLN0-0.020-0.00655.4730.0020.0020.0000.0000.0000.000
77A158ASP-1-0.759-0.87457.0970.0360.0360.0000.0000.0000.000
78A159THR0-0.070-0.07059.7790.0010.0010.0000.0000.0000.000
79A160GLY00.0370.01260.433-0.002-0.0020.0000.0000.0000.000
80A161ILE0-0.062-0.04158.3760.0000.0000.0000.0000.0000.000
81A162GLY00.0250.02258.6080.0000.0000.0000.0000.0000.000
82A163MET0-0.0230.00152.9400.0010.0010.0000.0000.0000.000
83A164THR0-0.041-0.04957.1810.0000.0000.0000.0000.0000.000
84A165GLN00.0260.01656.0600.0030.0030.0000.0000.0000.000
85A166GLU-1-0.807-0.90754.0090.0420.0420.0000.0000.0000.000
86A167GLU-1-0.874-0.91352.3320.0400.0400.0000.0000.0000.000
87A168LEU0-0.0070.00351.2450.0030.0030.0000.0000.0000.000
88A169VAL00.002-0.00549.3120.0030.0030.0000.0000.0000.000
89A170SER0-0.077-0.05247.9060.0040.0040.0000.0000.0000.000
90A171ASN00.0100.00146.5900.0040.0040.0000.0000.0000.000
91A172LEU00.0190.01945.6290.0040.0040.0000.0000.0000.000
92A173GLY00.0430.03044.3760.0050.0050.0000.0000.0000.000
93A174THR0-0.074-0.06341.9050.0070.0070.0000.0000.0000.000
94A175ILE0-0.0230.01640.8630.0050.0050.0000.0000.0000.000
95A176ALA00.0230.02039.9320.0060.0060.0000.0000.0000.000
96A177ARG10.8770.94237.849-0.071-0.0710.0000.0000.0000.000
97A178SER0-0.039-0.04236.5500.0020.0020.0000.0000.0000.000
98A179GLY00.0600.04035.374-0.002-0.0020.0000.0000.0000.000
99A180SER00.010-0.01430.479-0.002-0.0020.0000.0000.0000.000
100A181LYS10.8790.93932.370-0.086-0.0860.0000.0000.0000.000
101A182ALA00.0290.02434.648-0.006-0.0060.0000.0000.0000.000
102A183PHE0-0.002-0.01031.414-0.002-0.0020.0000.0000.0000.000
103A184LEU0-0.042-0.01529.747-0.001-0.0010.0000.0000.0000.000
104A185ASP-1-0.929-0.97532.6530.0500.0500.0000.0000.0000.000
105A186ALA0-0.011-0.00635.812-0.005-0.0050.0000.0000.0000.000
106A187LEU0-0.049-0.01329.9790.0010.0010.0000.0000.0000.000
107A188GLN0-0.072-0.02130.322-0.009-0.0090.0000.0000.0000.000
108A197ILE0-0.026-0.01541.8520.0010.0010.0000.0000.0000.000
109A198ILE0-0.002-0.00246.025-0.002-0.0020.0000.0000.0000.000
110A199GLY00.0670.02049.3780.0030.0030.0000.0000.0000.000
111A200GLN0-0.040-0.01651.462-0.001-0.0010.0000.0000.0000.000
112A201PHE00.002-0.00247.413-0.001-0.0010.0000.0000.0000.000
113A202GLY00.0880.05045.182-0.001-0.0010.0000.0000.0000.000
114A203VAL0-0.012-0.02839.3010.0030.0030.0000.0000.0000.000
115A204GLY00.1030.06240.8040.0060.0060.0000.0000.0000.000
116A205PHE00.0360.02542.0950.0030.0030.0000.0000.0000.000
117A206TYR0-0.0160.00036.1320.0050.0050.0000.0000.0000.000
118A207SER0-0.042-0.03840.2260.0040.0040.0000.0000.0000.000
119A208ALA00.0290.00841.1890.0010.0010.0000.0000.0000.000
120A209PHE0-0.010-0.01940.6600.0010.0010.0000.0000.0000.000
121A210MET0-0.052-0.01434.9060.0060.0060.0000.0000.0000.000
122A211VAL00.0020.00339.4240.0040.0040.0000.0000.0000.000
123A212ALA00.0060.00942.309-0.004-0.0040.0000.0000.0000.000
124A213ASP-1-0.863-0.91642.5730.1060.1060.0000.0000.0000.000
125A214ARG10.8500.92944.400-0.065-0.0650.0000.0000.0000.000
126A215VAL0-0.029-0.01645.538-0.002-0.0020.0000.0000.0000.000
127A216GLU-1-0.772-0.84248.3730.0590.0590.0000.0000.0000.000
128A217VAL0-0.014-0.01950.318-0.001-0.0010.0000.0000.0000.000
129A218TYR0-0.029-0.03253.124-0.001-0.0010.0000.0000.0000.000
130A219SER0-0.001-0.02156.398-0.001-0.0010.0000.0000.0000.000
131A220ARG10.8240.89658.402-0.033-0.0330.0000.0000.0000.000
132A221SER00.0180.02960.519-0.002-0.0020.0000.0000.0000.000
133A222ALA00.031-0.00161.709-0.001-0.0010.0000.0000.0000.000
134A223ALA0-0.026-0.00464.439-0.002-0.0020.0000.0000.0000.000
135A224PRO00.0370.00766.2340.0010.0010.0000.0000.0000.000
136A225GLY0-0.0030.00369.1230.0000.0000.0000.0000.0000.000
137A226SER0-0.040-0.01463.9100.0010.0010.0000.0000.0000.000
138A227LEU00.0170.01864.1360.0000.0000.0000.0000.0000.000
139A228GLY0-0.0040.00061.8490.0000.0000.0000.0000.0000.000
140A229TYR0-0.036-0.03657.5970.0000.0000.0000.0000.0000.000
141A230GLN0-0.004-0.01454.5360.0020.0020.0000.0000.0000.000
142A231TRP00.0400.02245.4250.0010.0010.0000.0000.0000.000
143A232LEU0-0.031-0.01849.946-0.001-0.0010.0000.0000.0000.000
144A233SER00.0090.01144.4400.0030.0030.0000.0000.0000.000
145A234ASP-1-0.808-0.90246.1090.0850.0850.0000.0000.0000.000
146A235GLY00.0460.03942.8720.0010.0010.0000.0000.0000.000
147A236SER0-0.087-0.05941.5340.0080.0080.0000.0000.0000.000
148A237GLY0-0.036-0.02640.4770.0010.0010.0000.0000.0000.000
149A238VAL0-0.051-0.02741.111-0.001-0.0010.0000.0000.0000.000
150A239PHE0-0.030-0.02141.6710.0000.0000.0000.0000.0000.000
151A240GLU-1-0.934-0.96047.2010.0640.0640.0000.0000.0000.000
152A241ILE0-0.047-0.03851.024-0.001-0.0010.0000.0000.0000.000
153A242ALA00.0180.02253.893-0.001-0.0010.0000.0000.0000.000
154A243GLU-1-0.847-0.91857.5600.0360.0360.0000.0000.0000.000
155A244ALA0-0.033-0.02059.9750.0010.0010.0000.0000.0000.000
156A245SER00.0260.01362.065-0.001-0.0010.0000.0000.0000.000
157A246GLY0-0.015-0.00864.6320.0010.0010.0000.0000.0000.000
158A247VAL0-0.022-0.00160.6250.0000.0000.0000.0000.0000.000
159A248ARG10.8420.90763.554-0.031-0.0310.0000.0000.0000.000
160A249THR0-0.005-0.00763.2150.0010.0010.0000.0000.0000.000
161A250GLY00.0370.03760.998-0.001-0.0010.0000.0000.0000.000
162A251THR0-0.018-0.02054.5320.0010.0010.0000.0000.0000.000
163A252LYS10.9110.96556.816-0.044-0.0440.0000.0000.0000.000
164A253ILE00.0090.01650.0050.0010.0010.0000.0000.0000.000
165A254ILE0-0.040-0.02552.743-0.002-0.0020.0000.0000.0000.000
166A255ILE00.0220.01147.1690.0030.0030.0000.0000.0000.000
167A256HIS0-0.016-0.02448.814-0.001-0.0010.0000.0000.0000.000
168A257LEU0-0.022-0.00946.3710.0040.0040.0000.0000.0000.000
169A258LYS10.8890.91638.885-0.108-0.1080.0000.0000.0000.000
170A259SER0-0.005-0.01641.772-0.003-0.0030.0000.0000.0000.000
171A260ASP-1-0.815-0.88039.5510.1030.1030.0000.0000.0000.000
172A261CYS0-0.0480.01341.653-0.001-0.0010.0000.0000.0000.000
173A262LYS10.9560.98244.300-0.080-0.0800.0000.0000.0000.000
174A263GLU-1-0.807-0.87444.2540.0720.0720.0000.0000.0000.000
175A264PHE00.002-0.01444.070-0.005-0.0050.0000.0000.0000.000
176A265SER0-0.027-0.02149.589-0.003-0.0030.0000.0000.0000.000
177A266SER00.001-0.00152.302-0.003-0.0030.0000.0000.0000.000
178A267GLU-1-0.732-0.84453.8750.0360.0360.0000.0000.0000.000
179A268ALA0-0.025-0.02055.139-0.001-0.0010.0000.0000.0000.000
180A269ARG10.8730.93445.165-0.059-0.0590.0000.0000.0000.000
181A270VAL00.0380.02050.9570.0010.0010.0000.0000.0000.000
182A271ARG10.8710.92352.741-0.037-0.0370.0000.0000.0000.000
183A272ASP-1-0.868-0.91452.3410.0360.0360.0000.0000.0000.000
184A273VAL0-0.016-0.00448.879-0.002-0.0020.0000.0000.0000.000
185A274VAL00.0280.00251.433-0.001-0.0010.0000.0000.0000.000
186A275THR0-0.043-0.02154.293-0.002-0.0020.0000.0000.0000.000
187A276LYS10.9250.96051.898-0.030-0.0300.0000.0000.0000.000
188A277TYR00.0280.00249.431-0.002-0.0020.0000.0000.0000.000
189A278SER0-0.017-0.02153.012-0.002-0.0020.0000.0000.0000.000
190A279ASN0-0.074-0.04055.745-0.002-0.0020.0000.0000.0000.000
191A280PHE0-0.063-0.02052.694-0.002-0.0020.0000.0000.0000.000
192A281VAL0-0.0060.00654.7700.0010.0010.0000.0000.0000.000
193A282SER0-0.0070.00157.1330.0000.0000.0000.0000.0000.000
194A283PHE0-0.008-0.00359.885-0.001-0.0010.0000.0000.0000.000
195A284PRO0-0.0180.00061.2420.0010.0010.0000.0000.0000.000
196A285LEU00.0160.01756.1900.0010.0010.0000.0000.0000.000
197A286TYR0-0.043-0.05260.590-0.001-0.0010.0000.0000.0000.000
198A287LEU0-0.0040.00156.5200.0020.0020.0000.0000.0000.000
199A288ASN0-0.048-0.04858.7870.0000.0000.0000.0000.0000.000
200A289GLY00.0270.02061.946-0.001-0.0010.0000.0000.0000.000
201A290ARG10.8650.93062.646-0.034-0.0340.0000.0000.0000.000
202A291ARG10.8780.93662.889-0.023-0.0230.0000.0000.0000.000
203A292MET0-0.066-0.02858.3840.0000.0000.0000.0000.0000.000
204A293ASN00.0350.01659.8680.0000.0000.0000.0000.0000.000
205A294THR00.0320.02161.8490.0000.0000.0000.0000.0000.000