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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: 85MQY

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 OptHSide
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 -2208735.577273
FMO2-HF: Nuclear repulsion 2129749.665373
FMO2-HF: Total energy -78985.9119
FMO2-MP2: Total energy -79217.581315


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.
-3.758-0.0580.218-1.903-2.014-0.004
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 : 0.006 / 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].
3A84SER0-0.027-0.0422.889-1.5662.1140.219-1.901-1.997-0.004
4A85THR0-0.013-0.0145.133-0.582-0.562-0.001-0.002-0.0170.000
5A86SER00.0960.0378.3270.0240.0240.0000.0000.0000.000
6A87LYS10.9700.98011.608-0.546-0.5460.0000.0000.0000.000
7A88HIS00.001-0.0207.561-0.387-0.3870.0000.0000.0000.000
8A89GLU-1-0.777-0.8498.665-0.010-0.0100.0000.0000.0000.000
9A90PHE0-0.0090.00611.968-0.050-0.0500.0000.0000.0000.000
10A91GLN0-0.031-0.01614.2570.0120.0120.0000.0000.0000.000
11A92ALA00.0050.00912.718-0.021-0.0210.0000.0000.0000.000
12A93GLU-1-0.767-0.88214.861-0.115-0.1150.0000.0000.0000.000
13A94THR0-0.038-0.02717.091-0.008-0.0080.0000.0000.0000.000
14A95LYS10.9130.95915.641-0.578-0.5780.0000.0000.0000.000
15A96LYS10.8070.89316.0230.0320.0320.0000.0000.0000.000
16A97LEU00.0070.00520.192-0.024-0.0240.0000.0000.0000.000
17A98LEU0-0.0110.00622.963-0.009-0.0090.0000.0000.0000.000
18A99ASP-1-0.801-0.89124.7970.1140.1140.0000.0000.0000.000
19A100ILE0-0.036-0.02224.599-0.009-0.0090.0000.0000.0000.000
20A101VAL00.0340.01827.498-0.008-0.0080.0000.0000.0000.000
21A102ALA00.0000.00128.819-0.005-0.0050.0000.0000.0000.000
22A103ARG10.8260.89027.836-0.098-0.0980.0000.0000.0000.000
23A104SER0-0.0130.00532.263-0.007-0.0070.0000.0000.0000.000
24A105LEU00.0530.02832.288-0.002-0.0020.0000.0000.0000.000
25A106TYR0-0.101-0.07034.682-0.005-0.0050.0000.0000.0000.000
26A107SER0-0.090-0.05436.481-0.005-0.0050.0000.0000.0000.000
27A108GLU-1-0.863-0.92936.9830.0310.0310.0000.0000.0000.000
28A109LYS10.8610.93639.419-0.063-0.0630.0000.0000.0000.000
29A110GLU-1-0.775-0.87740.9860.0310.0310.0000.0000.0000.000
30A111VAL0-0.035-0.01841.002-0.003-0.0030.0000.0000.0000.000
31A112PHE00.0360.02044.032-0.002-0.0020.0000.0000.0000.000
32A113ILE0-0.017-0.00545.412-0.002-0.0020.0000.0000.0000.000
33A114ARG10.8670.91244.169-0.031-0.0310.0000.0000.0000.000
34A115GLU-1-0.871-0.91545.1920.0370.0370.0000.0000.0000.000
35A116LEU00.0080.00047.249-0.001-0.0010.0000.0000.0000.000
36A117ILE0-0.026-0.00850.202-0.002-0.0020.0000.0000.0000.000
37A118SER00.0130.00549.891-0.002-0.0020.0000.0000.0000.000
38A119ASN0-0.044-0.04648.1050.0010.0010.0000.0000.0000.000
39A120ALA00.0000.01152.120-0.001-0.0010.0000.0000.0000.000
40A121SER00.033-0.00155.359-0.002-0.0020.0000.0000.0000.000
41A122ASP-1-0.833-0.90053.1770.0230.0230.0000.0000.0000.000
42A123ALA00.0130.01155.718-0.001-0.0010.0000.0000.0000.000
43A124LEU0-0.018-0.00957.412-0.001-0.0010.0000.0000.0000.000
44A125GLU-1-0.777-0.84858.5960.0140.0140.0000.0000.0000.000
45A126LYS10.8060.89753.968-0.025-0.0250.0000.0000.0000.000
46A127LEU0-0.039-0.01360.085-0.001-0.0010.0000.0000.0000.000
47A128ARG10.8610.88563.223-0.015-0.0150.0000.0000.0000.000
48A129HIS00.0140.01162.508-0.001-0.0010.0000.0000.0000.000
49A130LYS10.9460.98964.119-0.022-0.0220.0000.0000.0000.000
50A131LEU0-0.027-0.01365.6880.0000.0000.0000.0000.0000.000
51A132VAL00.002-0.00667.970-0.001-0.0010.0000.0000.0000.000
52A133SER0-0.080-0.05066.650-0.001-0.0010.0000.0000.0000.000
53A134ASP-1-0.919-0.93769.3380.0150.0150.0000.0000.0000.000
54A135GLY0-0.0240.00771.6620.0000.0000.0000.0000.0000.000
55A136GLN0-0.123-0.07871.5580.0000.0000.0000.0000.0000.000
56A137ALA0-0.019-0.01672.5350.0000.0000.0000.0000.0000.000
57A138LEU00.001-0.00368.2530.0010.0010.0000.0000.0000.000
58A139PRO0-0.0020.00967.8450.0000.0000.0000.0000.0000.000
59A140GLU-1-0.811-0.90368.3510.0200.0200.0000.0000.0000.000
60A141MET0-0.0480.00063.8930.0010.0010.0000.0000.0000.000
61A142GLU-1-0.808-0.87563.5690.0180.0180.0000.0000.0000.000
62A143ILE00.0190.01156.9640.0010.0010.0000.0000.0000.000
63A144HIS0-0.067-0.05159.8490.0000.0000.0000.0000.0000.000
64A145LEU00.0420.01753.8660.0020.0020.0000.0000.0000.000
65A146GLN0-0.018-0.01757.0770.0000.0000.0000.0000.0000.000
66A147THR0-0.0030.00954.1930.0020.0020.0000.0000.0000.000
67A148ASN0-0.045-0.03855.593-0.001-0.0010.0000.0000.0000.000
68A149ALA00.0790.03454.9410.0020.0020.0000.0000.0000.000
69A150GLU-1-0.939-0.96255.2030.0380.0380.0000.0000.0000.000
70A151LYS10.8840.93955.592-0.038-0.0380.0000.0000.0000.000
71A152GLY00.0050.02451.7220.0030.0030.0000.0000.0000.000
72A153THR0-0.010-0.01251.0380.0020.0020.0000.0000.0000.000
73A154ILE0-0.025-0.01750.108-0.003-0.0030.0000.0000.0000.000
74A155THR0-0.046-0.01852.7190.0020.0020.0000.0000.0000.000
75A156ILE0-0.0030.00352.188-0.002-0.0020.0000.0000.0000.000
76A157GLN0-0.013-0.01455.4040.0020.0020.0000.0000.0000.000
77A158ASP-1-0.755-0.86957.0050.0290.0290.0000.0000.0000.000
78A159THR0-0.063-0.05759.8040.0010.0010.0000.0000.0000.000
79A160GLY00.0410.01060.499-0.001-0.0010.0000.0000.0000.000
80A161ILE0-0.064-0.03358.4880.0000.0000.0000.0000.0000.000
81A162GLY00.0210.01458.5320.0000.0000.0000.0000.0000.000
82A163MET0-0.054-0.01053.2740.0010.0010.0000.0000.0000.000
83A164THR0-0.043-0.05457.1160.0000.0000.0000.0000.0000.000
84A165GLN00.0260.01956.0870.0030.0030.0000.0000.0000.000
85A166GLU-1-0.828-0.91954.1780.0410.0410.0000.0000.0000.000
86A167GLU-1-0.857-0.90152.4480.0380.0380.0000.0000.0000.000
87A168LEU0-0.0090.00351.3320.0020.0020.0000.0000.0000.000
88A169VAL00.012-0.00149.6200.0030.0030.0000.0000.0000.000
89A170SER0-0.069-0.04748.0100.0030.0030.0000.0000.0000.000
90A171ASN00.0040.00746.6670.0020.0020.0000.0000.0000.000
91A172LEU00.0310.01245.8660.0030.0030.0000.0000.0000.000
92A173GLY00.0160.01444.5910.0040.0040.0000.0000.0000.000
93A174THR0-0.090-0.07242.0290.0070.0070.0000.0000.0000.000
94A175ILE0-0.0280.00840.9240.0060.0060.0000.0000.0000.000
95A176ALA00.0190.02140.1770.0050.0050.0000.0000.0000.000
96A177ARG10.9200.97037.880-0.075-0.0750.0000.0000.0000.000
97A178SER0-0.076-0.05536.6750.0050.0050.0000.0000.0000.000
98A179GLY00.0630.03634.937-0.004-0.0040.0000.0000.0000.000
99A180SER00.014-0.01030.101-0.004-0.0040.0000.0000.0000.000
100A181LYS10.9220.96432.363-0.086-0.0860.0000.0000.0000.000
101A182ALA00.0460.02934.743-0.007-0.0070.0000.0000.0000.000
102A183PHE0-0.002-0.00831.707-0.004-0.0040.0000.0000.0000.000
103A184LEU0-0.058-0.02629.621-0.004-0.0040.0000.0000.0000.000
104A185ASP-1-0.940-0.98432.6300.0350.0350.0000.0000.0000.000
105A186ALA0-0.0110.00235.873-0.006-0.0060.0000.0000.0000.000
106A187LEU0-0.061-0.02529.946-0.003-0.0030.0000.0000.0000.000
107A188GLN0-0.059-0.00930.509-0.009-0.0090.0000.0000.0000.000
108A197ILE0-0.014-0.01741.8230.0020.0020.0000.0000.0000.000
109A198ILE0-0.019-0.01146.183-0.002-0.0020.0000.0000.0000.000
110A199GLY00.0490.01749.7450.0030.0030.0000.0000.0000.000
111A200GLN0-0.038-0.01351.399-0.001-0.0010.0000.0000.0000.000
112A201PHE00.0060.00147.272-0.001-0.0010.0000.0000.0000.000
113A202GLY00.1090.06145.1680.0010.0010.0000.0000.0000.000
114A203VAL00.007-0.02139.1680.0030.0030.0000.0000.0000.000
115A204GLY00.1060.06340.9050.0050.0050.0000.0000.0000.000
116A205PHE00.0410.02742.2900.0010.0010.0000.0000.0000.000
117A206TYR0-0.048-0.01936.1650.0040.0040.0000.0000.0000.000
118A207SER0-0.024-0.02640.5310.0030.0030.0000.0000.0000.000
119A208ALA00.0260.00141.5000.0010.0010.0000.0000.0000.000
120A209PHE00.007-0.01540.7830.0010.0010.0000.0000.0000.000
121A210MET0-0.055-0.00835.1420.0060.0060.0000.0000.0000.000
122A211VAL00.0060.00639.7170.0020.0020.0000.0000.0000.000
123A212ALA0-0.0090.00942.569-0.003-0.0030.0000.0000.0000.000
124A213ASP-1-0.885-0.94443.0540.0860.0860.0000.0000.0000.000
125A214ARG10.8440.92844.848-0.057-0.0570.0000.0000.0000.000
126A215VAL0-0.026-0.01645.794-0.003-0.0030.0000.0000.0000.000
127A216GLU-1-0.778-0.84548.6190.0520.0520.0000.0000.0000.000
128A217VAL0-0.007-0.01050.324-0.002-0.0020.0000.0000.0000.000
129A218TYR0-0.061-0.05253.2550.0000.0000.0000.0000.0000.000
130A219SER00.0310.00456.316-0.001-0.0010.0000.0000.0000.000
131A220ARG10.8220.90358.331-0.029-0.0290.0000.0000.0000.000
132A221SER00.0320.02560.640-0.002-0.0020.0000.0000.0000.000
133A222ALA00.042-0.00261.811-0.001-0.0010.0000.0000.0000.000
134A223ALA0-0.071-0.01664.239-0.002-0.0020.0000.0000.0000.000
135A224PRO00.0560.02366.1370.0010.0010.0000.0000.0000.000
136A225GLY0-0.0060.00168.8660.0000.0000.0000.0000.0000.000
137A226SER0-0.017-0.00763.8410.0010.0010.0000.0000.0000.000
138A227LEU0-0.0050.00963.921-0.001-0.0010.0000.0000.0000.000
139A228GLY0-0.011-0.00561.8650.0000.0000.0000.0000.0000.000
140A229TYR00.0260.01357.4450.0000.0000.0000.0000.0000.000
141A230GLN00.002-0.01354.6030.0010.0010.0000.0000.0000.000
142A231TRP00.0280.01445.4300.0010.0010.0000.0000.0000.000
143A232LEU0-0.022-0.00950.120-0.001-0.0010.0000.0000.0000.000
144A233SER0-0.001-0.00244.5140.0040.0040.0000.0000.0000.000
145A234ASP-1-0.805-0.90446.3760.0770.0770.0000.0000.0000.000
146A235GLY00.0160.02342.7110.0010.0010.0000.0000.0000.000
147A236SER0-0.054-0.03741.6280.0080.0080.0000.0000.0000.000
148A237GLY0-0.039-0.03240.8100.0010.0010.0000.0000.0000.000
149A238VAL0-0.058-0.03241.5210.0000.0000.0000.0000.0000.000
150A239PHE0-0.023-0.00941.888-0.001-0.0010.0000.0000.0000.000
151A240GLU-1-0.930-0.95447.3350.0630.0630.0000.0000.0000.000
152A241ILE0-0.041-0.02951.129-0.001-0.0010.0000.0000.0000.000
153A242ALA00.0210.01253.9800.0000.0000.0000.0000.0000.000
154A243GLU-1-0.916-0.96257.6360.0350.0350.0000.0000.0000.000
155A244ALA0-0.014-0.01559.8610.0010.0010.0000.0000.0000.000
156A245SER00.0130.00961.921-0.001-0.0010.0000.0000.0000.000
157A246GLY0-0.017-0.01964.8870.0000.0000.0000.0000.0000.000
158A247VAL00.0210.02260.6890.0000.0000.0000.0000.0000.000
159A248ARG10.8210.90963.578-0.025-0.0250.0000.0000.0000.000
160A249THR0-0.005-0.00762.9410.0010.0010.0000.0000.0000.000
161A250GLY00.0350.04060.613-0.001-0.0010.0000.0000.0000.000
162A251THR00.007-0.01954.5240.0020.0020.0000.0000.0000.000
163A252LYS10.9040.96757.083-0.038-0.0380.0000.0000.0000.000
164A253ILE00.0140.01050.3630.0020.0020.0000.0000.0000.000
165A254ILE0-0.041-0.02553.213-0.002-0.0020.0000.0000.0000.000
166A255ILE00.0280.01947.3620.0030.0030.0000.0000.0000.000
167A256HIS0-0.025-0.03049.124-0.002-0.0020.0000.0000.0000.000
168A257LEU0-0.029-0.01046.6660.0030.0030.0000.0000.0000.000
169A258LYS10.9220.95039.491-0.088-0.0880.0000.0000.0000.000
170A259SER0-0.018-0.02141.834-0.003-0.0030.0000.0000.0000.000
171A260ASP-1-0.849-0.90239.5620.0760.0760.0000.0000.0000.000
172A261CYS0-0.047-0.00141.955-0.002-0.0020.0000.0000.0000.000
173A262LYS10.9760.98644.651-0.062-0.0620.0000.0000.0000.000
174A263GLU-1-0.793-0.87744.5380.0490.0490.0000.0000.0000.000
175A264PHE0-0.015-0.02144.181-0.004-0.0040.0000.0000.0000.000
176A265SER0-0.038-0.02849.628-0.001-0.0010.0000.0000.0000.000
177A266SER00.006-0.00352.347-0.002-0.0020.0000.0000.0000.000
178A267GLU-1-0.763-0.86154.0280.0230.0230.0000.0000.0000.000
179A268ALA0-0.028-0.02455.381-0.001-0.0010.0000.0000.0000.000
180A269ARG10.8820.94445.419-0.036-0.0360.0000.0000.0000.000
181A270VAL00.0280.00951.2530.0000.0000.0000.0000.0000.000
182A271ARG10.8780.93052.858-0.023-0.0230.0000.0000.0000.000
183A272ASP-1-0.891-0.92052.3770.0200.0200.0000.0000.0000.000
184A273VAL0-0.024-0.01348.950-0.002-0.0020.0000.0000.0000.000
185A274VAL00.012-0.00851.475-0.001-0.0010.0000.0000.0000.000
186A275THR0-0.044-0.03354.262-0.002-0.0020.0000.0000.0000.000
187A276LYS10.9410.96752.077-0.011-0.0110.0000.0000.0000.000
188A277TYR00.0630.02549.696-0.001-0.0010.0000.0000.0000.000
189A278SER0-0.0050.00353.101-0.001-0.0010.0000.0000.0000.000
190A279ASN0-0.076-0.04955.869-0.002-0.0020.0000.0000.0000.000
191A280PHE0-0.062-0.02152.495-0.002-0.0020.0000.0000.0000.000
192A281VAL0-0.0170.00855.2780.0010.0010.0000.0000.0000.000
193A282SER0-0.0050.00457.376-0.001-0.0010.0000.0000.0000.000
194A283PHE00.002-0.00560.108-0.001-0.0010.0000.0000.0000.000
195A284PRO0-0.024-0.00861.4420.0000.0000.0000.0000.0000.000
196A285LEU00.0240.02156.4540.0010.0010.0000.0000.0000.000
197A286TYR0-0.054-0.06761.097-0.002-0.0020.0000.0000.0000.000
198A287LEU00.0050.00056.6840.0020.0020.0000.0000.0000.000
199A288ASN0-0.041-0.04258.7370.0000.0000.0000.0000.0000.000
200A289GLY00.0030.00862.005-0.001-0.0010.0000.0000.0000.000
201A290ARG10.9210.96163.323-0.022-0.0220.0000.0000.0000.000
202A291ARG10.8870.95663.095-0.014-0.0140.0000.0000.0000.000
203A292MET0-0.049-0.01658.4970.0000.0000.0000.0000.0000.000
204A293ASN00.0270.02559.913-0.001-0.0010.0000.0000.0000.000
205A294THR00.0310.00961.9680.0010.0010.0000.0000.0000.000