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: NNJ4Q

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2003521.398398
FMO2-HF: Nuclear repulsion 1931009.153521
FMO2-HF: Total energy -72512.244877
FMO2-MP2: Total energy -72724.659743


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.
-5.07-0.8620.369-2.165-2.413-0.004
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 : 0.015 / q_NPA : 0.010
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].
3A186LEU00.0390.0132.836-4.742-0.5340.369-2.165-2.413-0.004
4A187THR0-0.074-0.0595.4890.5700.5700.0000.0000.0000.000
5A188GLY00.0460.0388.5890.0790.0790.0000.0000.0000.000
6A189SER0-0.042-0.03711.6120.0730.0730.0000.0000.0000.000
7A190ALA00.0110.00414.8210.0790.0790.0000.0000.0000.000
8A191GLU-1-0.930-0.94611.873-0.746-0.7460.0000.0000.0000.000
9A192GLY00.0180.00715.3720.0600.0600.0000.0000.0000.000
10A193MET0-0.0430.00316.149-0.045-0.0450.0000.0000.0000.000
11A194GLN0-0.007-0.01316.7200.0390.0390.0000.0000.0000.000
12A195PHE0-0.032-0.04118.135-0.017-0.0170.0000.0000.0000.000
13A196ASP-1-0.864-0.92819.159-0.329-0.3290.0000.0000.0000.000
14A197ARG10.7980.90721.9770.2180.2180.0000.0000.0000.000
15A198GLY00.0880.06925.296-0.015-0.0150.0000.0000.0000.000
16A199TYR0-0.056-0.02727.2400.0070.0070.0000.0000.0000.000
17A200LEU00.0170.00630.5670.0060.0060.0000.0000.0000.000
18A201SER00.011-0.00233.6820.0100.0100.0000.0000.0000.000
19A202PRO00.0210.01634.282-0.007-0.0070.0000.0000.0000.000
20A203TYR0-0.022-0.02435.362-0.001-0.0010.0000.0000.0000.000
21A204PHE0-0.017-0.00933.6000.0010.0010.0000.0000.0000.000
22A205ILE0-0.064-0.01031.592-0.007-0.0070.0000.0000.0000.000
23A206ASN0-0.035-0.02531.9130.0020.0020.0000.0000.0000.000
24A207LYS10.9210.99729.1470.1810.1810.0000.0000.0000.000
25A208PRO00.009-0.00631.301-0.005-0.0050.0000.0000.0000.000
26A209GLU-1-0.907-0.95531.058-0.140-0.1400.0000.0000.0000.000
27A210THR00.001-0.00826.8000.0000.0000.0000.0000.0000.000
28A211GLY0-0.034-0.01428.014-0.007-0.0070.0000.0000.0000.000
29A212ALA0-0.008-0.01126.699-0.005-0.0050.0000.0000.0000.000
30A213VAL0-0.005-0.00628.2020.0140.0140.0000.0000.0000.000
31A214GLU-1-0.852-0.92426.597-0.238-0.2380.0000.0000.0000.000
32A215LEU0-0.036-0.01228.6330.0170.0170.0000.0000.0000.000
33A216GLU-1-0.778-0.88028.857-0.233-0.2330.0000.0000.0000.000
34A217SER0-0.013-0.01429.7880.0130.0130.0000.0000.0000.000
35A218PRO0-0.058-0.01329.0960.0140.0140.0000.0000.0000.000
36A219PHE00.0610.02331.265-0.006-0.0060.0000.0000.0000.000
37A220ILE0-0.029-0.03127.374-0.004-0.0040.0000.0000.0000.000
38A221LEU00.0420.03131.6970.0030.0030.0000.0000.0000.000
39A222LEU00.008-0.00128.408-0.006-0.0060.0000.0000.0000.000
40A223ALA00.0250.01732.6440.0080.0080.0000.0000.0000.000
41A224ASP-1-0.882-0.92433.822-0.120-0.1200.0000.0000.0000.000
42A225LYS10.9000.96734.8410.0960.0960.0000.0000.0000.000
43A226LYS10.7910.91036.7930.0920.0920.0000.0000.0000.000
44A227ILE00.0200.00237.0260.0040.0040.0000.0000.0000.000
45A228SER00.0500.01640.5190.0010.0010.0000.0000.0000.000
46A229ASN0-0.038-0.03143.9680.0020.0020.0000.0000.0000.000
47A230ILE00.1040.03542.308-0.001-0.0010.0000.0000.0000.000
48A231ARG10.9800.98944.9180.0680.0680.0000.0000.0000.000
49A232GLU-1-0.911-0.95944.072-0.085-0.0850.0000.0000.0000.000
50A233MET00.0400.01338.774-0.003-0.0030.0000.0000.0000.000
51A234LEU0-0.009-0.00243.352-0.003-0.0030.0000.0000.0000.000
52A235PRO00.0080.01945.500-0.001-0.0010.0000.0000.0000.000
53A236VAL00.0850.04640.1360.0000.0000.0000.0000.0000.000
54A237LEU0-0.025-0.01040.610-0.004-0.0040.0000.0000.0000.000
55A238GLU-1-0.857-0.92742.471-0.082-0.0820.0000.0000.0000.000
56A239ALA0-0.028-0.01842.7310.0000.0000.0000.0000.0000.000
57A240VAL00.010-0.00237.945-0.001-0.0010.0000.0000.0000.000
58A241ALA0-0.004-0.00440.778-0.002-0.0020.0000.0000.0000.000
59A242LYS10.7790.88543.0700.0810.0810.0000.0000.0000.000
60A243ALA0-0.032-0.00640.2400.0010.0010.0000.0000.0000.000
61A244GLY0-0.0080.01340.956-0.002-0.0020.0000.0000.0000.000
62A245LYS10.7950.89733.5050.1560.1560.0000.0000.0000.000
63A246PRO0-0.035-0.01833.4920.0050.0050.0000.0000.0000.000
64A247LEU0-0.020-0.00534.257-0.003-0.0030.0000.0000.0000.000
65A248LEU00.0040.00927.5340.0020.0020.0000.0000.0000.000
66A249ILE0-0.019-0.02331.9220.0020.0020.0000.0000.0000.000
67A250ILE00.0010.00527.070-0.004-0.0040.0000.0000.0000.000
68A251ALA00.0540.02831.0790.0040.0040.0000.0000.0000.000
69A252GLU-1-0.890-0.94232.289-0.113-0.1130.0000.0000.0000.000
70A253ASP-1-0.771-0.90833.737-0.116-0.1160.0000.0000.0000.000
71A254VAL0-0.044-0.00635.7090.0010.0010.0000.0000.0000.000
72A255GLU-1-0.862-0.91938.333-0.083-0.0830.0000.0000.0000.000
73A256GLY00.008-0.00441.675-0.002-0.0020.0000.0000.0000.000
74A257GLU-1-0.907-0.95343.034-0.071-0.0710.0000.0000.0000.000
75A258ALA00.0070.00042.2160.0000.0000.0000.0000.0000.000
76A259LEU00.002-0.00437.187-0.003-0.0030.0000.0000.0000.000
77A260ALA00.0280.01940.945-0.003-0.0030.0000.0000.0000.000
78A261THR0-0.030-0.02143.8030.0010.0010.0000.0000.0000.000
79A262LEU00.0220.01938.0130.0000.0000.0000.0000.0000.000
80A263VAL00.0090.00239.330-0.002-0.0020.0000.0000.0000.000
81A264VAL00.0050.00541.3940.0000.0000.0000.0000.0000.000
82A265ASN0-0.035-0.03543.3190.0020.0020.0000.0000.0000.000
83A266THR00.0450.03737.660-0.002-0.0020.0000.0000.0000.000
84A267MET0-0.067-0.03641.069-0.001-0.0010.0000.0000.0000.000
85A268ARG10.9060.95242.5390.0750.0750.0000.0000.0000.000
86A269GLY0-0.047-0.02242.4280.0020.0020.0000.0000.0000.000
87A270ILE0-0.035-0.00143.5020.0000.0000.0000.0000.0000.000
88A271VAL00.0670.03040.820-0.001-0.0010.0000.0000.0000.000
89A272LYS10.8550.94536.5770.1150.1150.0000.0000.0000.000
90A273VAL00.0290.00935.640-0.004-0.0040.0000.0000.0000.000
91A274ALA00.0230.01531.8340.0010.0010.0000.0000.0000.000
92A275ALA00.0060.01832.936-0.002-0.0020.0000.0000.0000.000
93A276VAL00.005-0.00227.6330.0020.0020.0000.0000.0000.000
94A277LYS10.8300.90129.5750.1310.1310.0000.0000.0000.000
95A278ALA00.0500.01928.149-0.015-0.0150.0000.0000.0000.000
96A279PRO00.0300.01123.2980.0090.0090.0000.0000.0000.000
97A280GLY00.011-0.00424.5790.0090.0090.0000.0000.0000.000
98A281PHE00.008-0.01525.2010.0100.0100.0000.0000.0000.000
99A282GLY00.0490.02127.633-0.005-0.0050.0000.0000.0000.000
100A283ASP-1-0.823-0.91628.458-0.116-0.1160.0000.0000.0000.000
101A284ARG10.7990.87618.2000.2910.2910.0000.0000.0000.000
102A285ARG10.8650.95825.1970.1300.1300.0000.0000.0000.000
103A286LYS10.8880.92827.1840.1040.1040.0000.0000.0000.000
104A287ALA0-0.020-0.00124.603-0.005-0.0050.0000.0000.0000.000
105A288MET0-0.011-0.01021.714-0.023-0.0230.0000.0000.0000.000
106A289LEU0-0.0160.00224.287-0.015-0.0150.0000.0000.0000.000
107A290GLN00.0290.01127.144-0.008-0.0080.0000.0000.0000.000
108A291ASP-1-0.757-0.85421.577-0.293-0.2930.0000.0000.0000.000
109A292ILE00.006-0.00423.595-0.013-0.0130.0000.0000.0000.000
110A293ALA0-0.0280.01324.9870.0000.0000.0000.0000.0000.000
111A294THR00.0110.00225.1190.0050.0050.0000.0000.0000.000
112A295LEU0-0.045-0.02420.8230.0010.0010.0000.0000.0000.000
113A296THR0-0.058-0.05324.3880.0040.0040.0000.0000.0000.000
114A297GLY00.0480.04027.2400.0110.0110.0000.0000.0000.000
115A298GLY00.0050.01329.8770.0110.0110.0000.0000.0000.000
116A299THR0-0.025-0.01731.729-0.003-0.0030.0000.0000.0000.000
117A300VAL0-0.084-0.04430.7840.0010.0010.0000.0000.0000.000
118A301ILE00.001-0.00833.5960.0080.0080.0000.0000.0000.000
119A302SER00.025-0.02036.0660.0010.0010.0000.0000.0000.000
120A303GLU-1-0.827-0.93438.131-0.090-0.0900.0000.0000.0000.000
121A304GLU-1-0.965-0.95936.550-0.093-0.0930.0000.0000.0000.000
122A305ILE0-0.035-0.02536.3970.0030.0030.0000.0000.0000.000
123A306GLY0-0.030-0.00740.3960.0010.0010.0000.0000.0000.000
124A307MET0-0.065-0.00838.4600.0000.0000.0000.0000.0000.000
125A308GLU-1-0.796-0.89442.350-0.076-0.0760.0000.0000.0000.000
126A309LEU00.0100.01739.355-0.003-0.0030.0000.0000.0000.000
127A310GLH0-0.097-0.07442.323-0.003-0.0030.0000.0000.0000.000
128A311LYS10.8500.90944.7430.0760.0760.0000.0000.0000.000
129A312ALA00.0140.03940.0050.0000.0000.0000.0000.0000.000
130A313THR0-0.058-0.04740.9880.0040.0040.0000.0000.0000.000
131A314LEU00.013-0.02639.034-0.004-0.0040.0000.0000.0000.000
132A315GLU-1-0.965-0.96937.419-0.112-0.1120.0000.0000.0000.000
133A316ASP-1-0.807-0.89236.505-0.118-0.1180.0000.0000.0000.000
134A317LEU0-0.098-0.04334.420-0.008-0.0080.0000.0000.0000.000
135A318GLY00.0830.04330.354-0.001-0.0010.0000.0000.0000.000
136A319GLN0-0.066-0.04129.7240.0100.0100.0000.0000.0000.000
137A320ALA00.0530.01925.302-0.015-0.0150.0000.0000.0000.000
138A321LYS10.8260.92721.7920.3550.3550.0000.0000.0000.000
139A322ARG10.7820.84923.9740.2690.2690.0000.0000.0000.000
140A323VAL0-0.0010.01224.832-0.021-0.0210.0000.0000.0000.000
141A324VAL00.0000.00022.9250.0180.0180.0000.0000.0000.000
142A325ILE0-0.024-0.00923.968-0.016-0.0160.0000.0000.0000.000
143A326ASN0-0.014-0.00922.0750.0250.0250.0000.0000.0000.000
144A327LYS10.9400.96026.2340.1840.1840.0000.0000.0000.000
145A328ASP-1-0.886-0.93923.209-0.188-0.1880.0000.0000.0000.000
146A329THR0-0.030-0.00419.590-0.015-0.0150.0000.0000.0000.000
147A330THR00.010-0.01322.3880.0240.0240.0000.0000.0000.000
148A331THR0-0.023-0.00618.760-0.035-0.0350.0000.0000.0000.000
149A332ILE0-0.010-0.00821.0530.0310.0310.0000.0000.0000.000
150A333ILE0-0.001-0.01220.215-0.035-0.0350.0000.0000.0000.000
151A334ASP-1-0.761-0.88020.938-0.334-0.3340.0000.0000.0000.000
152A335GLY0-0.0010.00422.4820.0320.0320.0000.0000.0000.000
153A336VAL0-0.025-0.02624.528-0.006-0.0060.0000.0000.0000.000
154A337GLY0-0.0070.01026.2160.0160.0160.0000.0000.0000.000
155A338GLU-1-0.932-0.96926.494-0.174-0.1740.0000.0000.0000.000
156A339GLU-1-0.877-0.94923.448-0.296-0.2960.0000.0000.0000.000
157A340ALA0-0.027-0.02423.549-0.016-0.0160.0000.0000.0000.000
158A341ALA00.0390.03425.2520.0010.0010.0000.0000.0000.000
159A342ILE00.0310.01620.567-0.008-0.0080.0000.0000.0000.000
160A343GLN0-0.021-0.01618.273-0.034-0.0340.0000.0000.0000.000
161A344GLY00.0050.01021.2610.0000.0000.0000.0000.0000.000
162A345ARG10.8350.89922.4430.2350.2350.0000.0000.0000.000
163A346VAL00.019-0.00316.350-0.003-0.0030.0000.0000.0000.000
164A347ALA0-0.043-0.02618.771-0.003-0.0030.0000.0000.0000.000
165A348GLN00.0180.01320.5030.0080.0080.0000.0000.0000.000
166A349ILE0-0.019-0.00717.4980.0200.0200.0000.0000.0000.000
167A350ARG10.9470.97314.6630.3980.3980.0000.0000.0000.000
168A351GLN0-0.027-0.01117.9030.0170.0170.0000.0000.0000.000
169A352GLN00.013-0.00821.0060.0000.0000.0000.0000.0000.000
170A353ILE0-0.042-0.02014.5260.0140.0140.0000.0000.0000.000
171A354GLU-1-0.936-0.97116.833-0.035-0.0350.0000.0000.0000.000
172A355GLU-1-0.929-0.94519.691-0.061-0.0610.0000.0000.0000.000
173A356ALA0-0.056-0.00719.6430.0110.0110.0000.0000.0000.000
174A357THR0-0.017-0.01621.7780.0160.0160.0000.0000.0000.000
175A358SER0-0.061-0.07121.2790.0180.0180.0000.0000.0000.000
176A359ASP-1-0.875-0.94415.219-0.007-0.0070.0000.0000.0000.000
177A360TYR00.0070.01116.681-0.049-0.0490.0000.0000.0000.000
178A361ASP-1-0.842-0.90018.282-0.135-0.1350.0000.0000.0000.000
179A362ARG10.8930.94515.2750.0030.0030.0000.0000.0000.000
180A363GLU-1-0.820-0.89812.154-0.503-0.5030.0000.0000.0000.000
181A364LYS10.7790.87114.5470.2460.2460.0000.0000.0000.000
182A365LEU0-0.0110.00817.249-0.036-0.0360.0000.0000.0000.000
183A366GLN00.0710.0299.8210.0680.0680.0000.0000.0000.000
184A367GLU-1-0.799-0.87413.147-0.474-0.4740.0000.0000.0000.000
185A368ARG10.8380.90014.3370.2410.2410.0000.0000.0000.000
186A369VAL0-0.0170.00513.2170.0030.0030.0000.0000.0000.000
187A370ALA0-0.017-0.00911.324-0.041-0.0410.0000.0000.0000.000
188A371LYS10.8660.93712.9780.4350.4350.0000.0000.0000.000
189A372LEU0-0.003-0.01215.9770.0190.0190.0000.0000.0000.000
190A373ALA0-0.016-0.01113.3100.0210.0210.0000.0000.0000.000
191A374GLY0-0.0010.00614.472-0.017-0.0170.0000.0000.0000.000
192A375GLY0-0.0250.00115.1000.0420.0420.0000.0000.0000.000
193A376VAL00.0030.02017.3750.0610.0610.0000.0000.0000.000