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: JQ719

Calculation Name: 3VZ6-A-Xray372

Preferred Name: 60 kDa chaperonin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3VZ6

Chain ID: A

ChEMBL ID: CHEMBL4296299

UniProt ID: P0A6F5

Base Structure: X-ray

Registration Date: 2023-09-23

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004097.937036
FMO2-HF: Nuclear repulsion 1931585.266261
FMO2-HF: Total energy -72512.670775
FMO2-MP2: Total energy -72724.984874


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:184:ILE)


Summations of interaction energy for fragment #1(A:184:ILE)
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.
-6.001-1.6021.029-2.434-2.993-0.013
Interaction energy analysis for fragmet #1(A:184:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.011
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].
3A186LEU00.0440.0162.612-5.549-1.2151.030-2.430-2.934-0.013
4A187THR0-0.074-0.0595.0480.5740.639-0.001-0.004-0.0590.000
5A188GLY00.0290.0198.622-0.023-0.0230.0000.0000.0000.000
6A189SER0-0.055-0.02911.6510.0680.0680.0000.0000.0000.000
7A190ALA00.0120.00814.2910.0810.0810.0000.0000.0000.000
8A191GLU-1-0.896-0.94612.033-0.715-0.7150.0000.0000.0000.000
9A192GLY00.0250.01515.5330.0650.0650.0000.0000.0000.000
10A193MET0-0.0380.00116.410-0.038-0.0380.0000.0000.0000.000
11A194GLN0-0.038-0.02216.7190.0370.0370.0000.0000.0000.000
12A195PHE0-0.025-0.04418.131-0.017-0.0170.0000.0000.0000.000
13A196ASP-1-0.809-0.89518.948-0.320-0.3200.0000.0000.0000.000
14A197ARG10.7940.88622.0240.2090.2090.0000.0000.0000.000
15A198GLY00.0760.07425.492-0.015-0.0150.0000.0000.0000.000
16A199TYR0-0.037-0.02227.3340.0050.0050.0000.0000.0000.000
17A200LEU0-0.003-0.00730.5900.0070.0070.0000.0000.0000.000
18A201SER00.005-0.00633.7790.0100.0100.0000.0000.0000.000
19A202PRO00.0180.01434.162-0.007-0.0070.0000.0000.0000.000
20A203TYR0-0.020-0.02335.228-0.001-0.0010.0000.0000.0000.000
21A204PHE00.0000.00133.6210.0020.0020.0000.0000.0000.000
22A205ILE0-0.084-0.01631.827-0.007-0.0070.0000.0000.0000.000
23A206ASN0-0.038-0.02831.8250.0020.0020.0000.0000.0000.000
24A207LYS10.9110.99128.8100.1760.1760.0000.0000.0000.000
25A208PRO00.014-0.00331.394-0.002-0.0020.0000.0000.0000.000
26A209GLU-1-0.893-0.95630.666-0.133-0.1330.0000.0000.0000.000
27A210THR0-0.008-0.00826.4950.0000.0000.0000.0000.0000.000
28A211GLY0-0.0180.00028.122-0.004-0.0040.0000.0000.0000.000
29A212ALA00.000-0.00926.835-0.007-0.0070.0000.0000.0000.000
30A213VAL00.008-0.00728.1540.0130.0130.0000.0000.0000.000
31A214GLU-1-0.841-0.91226.383-0.233-0.2330.0000.0000.0000.000
32A215LEU0-0.014-0.00128.4540.0180.0180.0000.0000.0000.000
33A216GLU-1-0.747-0.85528.430-0.232-0.2320.0000.0000.0000.000
34A217SER0-0.020-0.01129.6690.0130.0130.0000.0000.0000.000
35A218PRO0-0.059-0.00428.9740.0130.0130.0000.0000.0000.000
36A219PHE00.0600.01131.187-0.006-0.0060.0000.0000.0000.000
37A220ILE0-0.012-0.01827.318-0.004-0.0040.0000.0000.0000.000
38A221LEU00.0300.02231.6010.0020.0020.0000.0000.0000.000
39A222LEU00.000-0.00328.647-0.007-0.0070.0000.0000.0000.000
40A223ALA00.0070.00832.7420.0080.0080.0000.0000.0000.000
41A224ASP-1-0.829-0.89233.289-0.123-0.1230.0000.0000.0000.000
42A225LYS10.8450.94634.4180.0940.0940.0000.0000.0000.000
43A226LYS10.7720.88736.7410.0860.0860.0000.0000.0000.000
44A227ILE00.0200.01136.9770.0040.0040.0000.0000.0000.000
45A228SER00.0560.01040.5000.0000.0000.0000.0000.0000.000
46A229ASN0-0.061-0.03743.8180.0060.0060.0000.0000.0000.000
47A230ILE00.0650.02342.783-0.001-0.0010.0000.0000.0000.000
48A231ARG10.9040.95045.2360.0680.0680.0000.0000.0000.000
49A232GLU-1-0.857-0.93443.898-0.084-0.0840.0000.0000.0000.000
50A233MET00.0220.01438.756-0.003-0.0030.0000.0000.0000.000
51A234LEU0-0.024-0.01143.251-0.002-0.0020.0000.0000.0000.000
52A235PRO00.0140.01445.110-0.001-0.0010.0000.0000.0000.000
53A236VAL00.0820.04139.865-0.001-0.0010.0000.0000.0000.000
54A237LEU0-0.031-0.01140.582-0.004-0.0040.0000.0000.0000.000
55A238GLU-1-0.800-0.90542.399-0.082-0.0820.0000.0000.0000.000
56A239ALA0-0.0140.00142.3480.0000.0000.0000.0000.0000.000
57A240VAL00.008-0.00737.682-0.002-0.0020.0000.0000.0000.000
58A241ALA0-0.017-0.00440.636-0.002-0.0020.0000.0000.0000.000
59A242LYS10.7590.86943.2540.0820.0820.0000.0000.0000.000
60A243ALA0-0.0220.00240.1650.0010.0010.0000.0000.0000.000
61A244GLY0-0.0180.00740.494-0.004-0.0040.0000.0000.0000.000
62A245LYS10.8040.89733.6130.1570.1570.0000.0000.0000.000
63A246PRO0-0.025-0.01833.3230.0050.0050.0000.0000.0000.000
64A247LEU0-0.0200.00034.174-0.003-0.0030.0000.0000.0000.000
65A248LEU00.0060.01027.4010.0040.0040.0000.0000.0000.000
66A249ILE0-0.021-0.02031.7940.0040.0040.0000.0000.0000.000
67A250ILE00.0020.00827.232-0.002-0.0020.0000.0000.0000.000
68A251ALA00.0580.03631.2220.0040.0040.0000.0000.0000.000
69A252GLU-1-0.893-0.94132.272-0.108-0.1080.0000.0000.0000.000
70A253ASP-1-0.770-0.89833.878-0.107-0.1070.0000.0000.0000.000
71A254VAL0-0.029-0.00635.953-0.001-0.0010.0000.0000.0000.000
72A255GLU-1-0.862-0.92138.490-0.079-0.0790.0000.0000.0000.000
73A256GLY00.000-0.00741.724-0.001-0.0010.0000.0000.0000.000
74A257GLU-1-0.883-0.93543.144-0.068-0.0680.0000.0000.0000.000
75A258ALA0-0.0050.00342.401-0.001-0.0010.0000.0000.0000.000
76A259LEU00.0030.00237.245-0.003-0.0030.0000.0000.0000.000
77A260ALA00.0370.01440.854-0.003-0.0030.0000.0000.0000.000
78A261THR0-0.041-0.02943.6070.0010.0010.0000.0000.0000.000
79A262LEU00.0210.01337.895-0.001-0.0010.0000.0000.0000.000
80A263VAL00.0100.01539.120-0.003-0.0030.0000.0000.0000.000
81A264VAL00.0120.00541.1490.0000.0000.0000.0000.0000.000
82A265ASN0-0.048-0.04443.3620.0030.0030.0000.0000.0000.000
83A266THR00.0410.02737.566-0.003-0.0030.0000.0000.0000.000
84A267MET0-0.049-0.02340.938-0.001-0.0010.0000.0000.0000.000
85A268ARG10.9130.95542.7990.0730.0730.0000.0000.0000.000
86A269GLY0-0.018-0.00942.6730.0020.0020.0000.0000.0000.000
87A270ILE0-0.038-0.01143.167-0.003-0.0030.0000.0000.0000.000
88A271VAL00.0620.03540.414-0.001-0.0010.0000.0000.0000.000
89A272LYS10.8020.91436.2170.1130.1130.0000.0000.0000.000
90A273VAL00.0410.01435.557-0.004-0.0040.0000.0000.0000.000
91A274ALA00.0140.00531.6730.0010.0010.0000.0000.0000.000
92A275ALA00.0040.01732.801-0.005-0.0050.0000.0000.0000.000
93A276VAL00.0200.00328.0070.0020.0020.0000.0000.0000.000
94A277LYS10.8240.89929.7540.1220.1220.0000.0000.0000.000
95A278ALA00.0700.02628.046-0.015-0.0150.0000.0000.0000.000
96A279PRO00.005-0.00323.0200.0120.0120.0000.0000.0000.000
97A280GLY00.0240.00524.2420.0060.0060.0000.0000.0000.000
98A281PHE00.000-0.01224.8710.0100.0100.0000.0000.0000.000
99A282GLY00.0420.01327.481-0.006-0.0060.0000.0000.0000.000
100A283ASP-1-0.830-0.91728.715-0.117-0.1170.0000.0000.0000.000
101A284ARG10.7830.86618.4050.2720.2720.0000.0000.0000.000
102A285ARG10.8850.96925.0040.1210.1210.0000.0000.0000.000
103A286LYS10.8380.89727.1850.1030.1030.0000.0000.0000.000
104A287ALA0-0.031-0.01224.684-0.007-0.0070.0000.0000.0000.000
105A288MET0-0.015-0.01721.339-0.023-0.0230.0000.0000.0000.000
106A289LEU0-0.019-0.00324.112-0.016-0.0160.0000.0000.0000.000
107A290GLN00.0340.01727.284-0.007-0.0070.0000.0000.0000.000
108A291ASP-1-0.759-0.84721.733-0.302-0.3020.0000.0000.0000.000
109A292ILE00.0180.00023.695-0.014-0.0140.0000.0000.0000.000
110A293ALA0-0.0380.00824.930-0.001-0.0010.0000.0000.0000.000
111A294THR00.010-0.00425.1800.0050.0050.0000.0000.0000.000
112A295LEU0-0.033-0.02120.5470.0000.0000.0000.0000.0000.000
113A296THR0-0.062-0.05324.2470.0020.0020.0000.0000.0000.000
114A297GLY00.0390.03227.1040.0120.0120.0000.0000.0000.000
115A298GLY00.0050.01529.9140.0120.0120.0000.0000.0000.000
116A299THR0-0.032-0.02531.615-0.005-0.0050.0000.0000.0000.000
117A300VAL0-0.068-0.03130.9930.0010.0010.0000.0000.0000.000
118A301ILE0-0.003-0.01033.8320.0080.0080.0000.0000.0000.000
119A302SER00.024-0.03336.3900.0010.0010.0000.0000.0000.000
120A303GLU-1-0.815-0.91438.479-0.089-0.0890.0000.0000.0000.000
121A304GLU-1-0.912-0.92836.213-0.098-0.0980.0000.0000.0000.000
122A305ILE0-0.028-0.01636.4290.0020.0020.0000.0000.0000.000
123A306GLY0-0.030-0.00840.3600.0000.0000.0000.0000.0000.000
124A307MET0-0.061-0.00838.3390.0010.0010.0000.0000.0000.000
125A308GLU-1-0.756-0.87442.387-0.080-0.0800.0000.0000.0000.000
126A309LEU0-0.020-0.00339.478-0.002-0.0020.0000.0000.0000.000
127A310GLH0-0.054-0.07042.553-0.002-0.0020.0000.0000.0000.000
128A311LYS10.8570.92044.7460.0800.0800.0000.0000.0000.000
129A312ALA00.0300.04940.022-0.001-0.0010.0000.0000.0000.000
130A313THR0-0.056-0.05740.7080.0040.0040.0000.0000.0000.000
131A314LEU0-0.013-0.03639.020-0.004-0.0040.0000.0000.0000.000
132A315GLU-1-0.947-0.95937.226-0.119-0.1190.0000.0000.0000.000
133A316ASP-1-0.814-0.89036.297-0.121-0.1210.0000.0000.0000.000
134A317LEU0-0.096-0.03634.520-0.008-0.0080.0000.0000.0000.000
135A318GLY00.1070.06430.411-0.001-0.0010.0000.0000.0000.000
136A319GLN0-0.056-0.04329.7940.0100.0100.0000.0000.0000.000
137A320ALA00.0450.01725.247-0.016-0.0160.0000.0000.0000.000
138A321LYS10.8200.92121.2860.3720.3720.0000.0000.0000.000
139A322ARG10.7380.81623.9260.2640.2640.0000.0000.0000.000
140A323VAL0-0.0030.00824.772-0.021-0.0210.0000.0000.0000.000
141A324VAL0-0.017-0.01022.7270.0160.0160.0000.0000.0000.000
142A325ILE0-0.009-0.00523.844-0.015-0.0150.0000.0000.0000.000
143A326ASN0-0.008-0.01522.2750.0230.0230.0000.0000.0000.000
144A327LYS10.9010.95626.4510.1680.1680.0000.0000.0000.000
145A328ASP-1-0.894-0.94223.305-0.171-0.1710.0000.0000.0000.000
146A329THR0-0.053-0.02519.809-0.013-0.0130.0000.0000.0000.000
147A330THR00.007-0.01322.7480.0220.0220.0000.0000.0000.000
148A331THR0-0.0170.00519.006-0.033-0.0330.0000.0000.0000.000
149A332ILE0-0.0040.00421.0980.0310.0310.0000.0000.0000.000
150A333ILE00.0210.00119.678-0.033-0.0330.0000.0000.0000.000
151A334ASP-1-0.755-0.87720.857-0.342-0.3420.0000.0000.0000.000
152A335GLY0-0.0060.00522.5000.0330.0330.0000.0000.0000.000
153A336VAL0-0.032-0.02424.561-0.009-0.0090.0000.0000.0000.000
154A337GLY00.0110.01826.1360.0180.0180.0000.0000.0000.000
155A338GLU-1-0.947-0.97826.306-0.191-0.1910.0000.0000.0000.000
156A339GLU-1-0.894-0.95523.283-0.328-0.3280.0000.0000.0000.000
157A340ALA0-0.029-0.01723.855-0.017-0.0170.0000.0000.0000.000
158A341ALA00.0410.03025.577-0.001-0.0010.0000.0000.0000.000
159A342ILE00.0390.02520.865-0.007-0.0070.0000.0000.0000.000
160A343GLN00.0340.01218.014-0.028-0.0280.0000.0000.0000.000
161A344GLY00.0100.01321.4290.0000.0000.0000.0000.0000.000
162A345ARG10.8320.89722.5140.2500.2500.0000.0000.0000.000
163A346VAL00.012-0.01116.702-0.001-0.0010.0000.0000.0000.000
164A347ALA0-0.032-0.01919.063-0.008-0.0080.0000.0000.0000.000
165A348GLN00.0280.02320.8340.0100.0100.0000.0000.0000.000
166A349ILE0-0.037-0.00817.6800.0190.0190.0000.0000.0000.000
167A350ARG10.8820.93415.3710.4340.4340.0000.0000.0000.000
168A351GLN0-0.025-0.01518.0300.0110.0110.0000.0000.0000.000
169A352GLN00.005-0.01421.0590.0010.0010.0000.0000.0000.000
170A353ILE0-0.049-0.01714.3710.0140.0140.0000.0000.0000.000
171A354GLU-1-0.905-0.94516.723-0.077-0.0770.0000.0000.0000.000
172A355GLU-1-0.921-0.95619.471-0.079-0.0790.0000.0000.0000.000
173A356ALA0-0.0430.00219.7570.0140.0140.0000.0000.0000.000
174A357THR0-0.011-0.02121.8470.0150.0150.0000.0000.0000.000
175A358SER0-0.074-0.06821.3840.0220.0220.0000.0000.0000.000
176A359ASP-1-0.865-0.94615.0680.0010.0010.0000.0000.0000.000
177A360TYR00.0120.00916.485-0.047-0.0470.0000.0000.0000.000
178A361ASP-1-0.853-0.89718.056-0.135-0.1350.0000.0000.0000.000
179A362ARG10.8640.93615.1380.0230.0230.0000.0000.0000.000
180A363GLU-1-0.799-0.88512.416-0.485-0.4850.0000.0000.0000.000
181A364LYS10.7490.85014.5500.2250.2250.0000.0000.0000.000
182A365LEU0-0.0150.01516.937-0.010-0.0100.0000.0000.0000.000
183A366GLN00.0790.0269.9360.0600.0600.0000.0000.0000.000
184A367GLU-1-0.770-0.86013.219-0.443-0.4430.0000.0000.0000.000
185A368ARG10.8390.90014.4200.2520.2520.0000.0000.0000.000
186A369VAL0-0.0080.00613.229-0.002-0.0020.0000.0000.0000.000
187A370ALA0-0.019-0.00911.292-0.048-0.0480.0000.0000.0000.000
188A371LYS10.8330.91912.9670.4160.4160.0000.0000.0000.000
189A372LEU0-0.017-0.01816.0030.0270.0270.0000.0000.0000.000
190A373ALA0-0.020-0.01213.0850.0200.0200.0000.0000.0000.000
191A374GLY00.0020.00814.025-0.035-0.0350.0000.0000.0000.000
192A375GLY0-0.017-0.00914.7090.0400.0400.0000.0000.0000.000
193A376VAL0-0.0120.00717.1450.0600.0600.0000.0000.0000.000