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: 894LY

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004442.066728
FMO2-HF: Nuclear repulsion 1931931.147745
FMO2-HF: Total energy -72510.918983
FMO2-MP2: Total energy -72723.466584


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.
-5.397-1.9450.714-1.729-2.436-0.012
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 : -0.012 / q_NPA : -0.018
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].
3A186LEU00.0330.0122.668-4.891-1.5180.715-1.725-2.362-0.012
4A187THR0-0.062-0.0545.3200.6170.696-0.001-0.004-0.0740.000
5A188GLY00.0540.0398.4530.0340.0340.0000.0000.0000.000
6A189SER0-0.049-0.04111.4020.0770.0770.0000.0000.0000.000
7A190ALA00.003-0.00314.6360.0770.0770.0000.0000.0000.000
8A191GLU-1-0.921-0.93711.727-0.783-0.7830.0000.0000.0000.000
9A192GLY00.0130.00715.1940.0450.0450.0000.0000.0000.000
10A193MET0-0.0450.00315.984-0.051-0.0510.0000.0000.0000.000
11A194GLN00.0200.00916.5810.0290.0290.0000.0000.0000.000
12A195PHE0-0.064-0.05018.033-0.016-0.0160.0000.0000.0000.000
13A196ASP-1-0.846-0.91719.421-0.389-0.3890.0000.0000.0000.000
14A197ARG10.7690.89221.9270.2380.2380.0000.0000.0000.000
15A198GLY00.0920.07025.219-0.013-0.0130.0000.0000.0000.000
16A199TYR0-0.060-0.02627.1730.0100.0100.0000.0000.0000.000
17A200LEU00.0210.00630.4870.0020.0020.0000.0000.0000.000
18A201SER00.0190.00033.6100.0090.0090.0000.0000.0000.000
19A202PRO00.0190.01634.215-0.006-0.0060.0000.0000.0000.000
20A203TYR0-0.018-0.02035.293-0.001-0.0010.0000.0000.0000.000
21A204PHE0-0.015-0.00733.4860.0030.0030.0000.0000.0000.000
22A205ILE0-0.064-0.01131.447-0.005-0.0050.0000.0000.0000.000
23A206ASN0-0.033-0.01731.7740.0010.0010.0000.0000.0000.000
24A207LYS10.9100.98729.0990.1820.1820.0000.0000.0000.000
25A208PRO00.013-0.00131.211-0.009-0.0090.0000.0000.0000.000
26A209GLU-1-0.896-0.95630.786-0.159-0.1590.0000.0000.0000.000
27A210THR0-0.003-0.00926.650-0.003-0.0030.0000.0000.0000.000
28A211GLY0-0.041-0.01427.948-0.011-0.0110.0000.0000.0000.000
29A212ALA0-0.014-0.01226.602-0.006-0.0060.0000.0000.0000.000
30A213VAL0-0.008-0.00528.0890.0160.0160.0000.0000.0000.000
31A214GLU-1-0.905-0.96926.291-0.247-0.2470.0000.0000.0000.000
32A215LEU0-0.044-0.02028.4820.0170.0170.0000.0000.0000.000
33A216GLU-1-0.881-0.95528.545-0.204-0.2040.0000.0000.0000.000
34A217SER0-0.023-0.01829.6030.0130.0130.0000.0000.0000.000
35A218PRO0-0.069-0.02928.8440.0120.0120.0000.0000.0000.000
36A219PHE00.0670.02731.079-0.001-0.0010.0000.0000.0000.000
37A220ILE0-0.025-0.03027.258-0.008-0.0080.0000.0000.0000.000
38A221LEU00.0290.02731.5330.0060.0060.0000.0000.0000.000
39A222LEU00.001-0.00628.212-0.009-0.0090.0000.0000.0000.000
40A223ALA00.0220.01432.5070.0090.0090.0000.0000.0000.000
41A224ASP-1-0.899-0.92933.715-0.102-0.1020.0000.0000.0000.000
42A225LYS10.9490.98234.7080.0820.0820.0000.0000.0000.000
43A226LYS10.8850.95136.7000.0920.0920.0000.0000.0000.000
44A227ILE00.0180.00437.1410.0050.0050.0000.0000.0000.000
45A228SER00.0450.00240.422-0.001-0.0010.0000.0000.0000.000
46A229ASN0-0.016-0.02343.8800.0010.0010.0000.0000.0000.000
47A230ILE00.0960.03842.2100.0000.0000.0000.0000.0000.000
48A231ARG10.9730.97144.8010.0620.0620.0000.0000.0000.000
49A232GLU-1-0.899-0.94943.491-0.075-0.0750.0000.0000.0000.000
50A233MET00.0350.01738.132-0.001-0.0010.0000.0000.0000.000
51A234LEU0-0.0120.00243.207-0.002-0.0020.0000.0000.0000.000
52A235PRO00.0080.02245.239-0.001-0.0010.0000.0000.0000.000
53A236VAL00.0780.04640.1640.0000.0000.0000.0000.0000.000
54A237LEU0-0.008-0.01340.316-0.003-0.0030.0000.0000.0000.000
55A238GLU-1-0.927-0.97542.315-0.069-0.0690.0000.0000.0000.000
56A239ALA0-0.034-0.02042.4010.0010.0010.0000.0000.0000.000
57A240VAL0-0.007-0.00238.0790.0000.0000.0000.0000.0000.000
58A241ALA00.004-0.00240.603-0.002-0.0020.0000.0000.0000.000
59A242LYS10.8370.93342.8990.0640.0640.0000.0000.0000.000
60A243ALA0-0.029-0.00640.0200.0010.0010.0000.0000.0000.000
61A244GLY0-0.0090.01340.762-0.001-0.0010.0000.0000.0000.000
62A245LYS10.8160.91733.2100.1180.1180.0000.0000.0000.000
63A246PRO0-0.035-0.01733.2370.0040.0040.0000.0000.0000.000
64A247LEU0-0.011-0.00334.0900.0000.0000.0000.0000.0000.000
65A248LEU0-0.0050.00427.410-0.002-0.0020.0000.0000.0000.000
66A249ILE0-0.013-0.01831.7770.0050.0050.0000.0000.0000.000
67A250ILE0-0.004-0.00126.950-0.009-0.0090.0000.0000.0000.000
68A251ALA00.0540.02830.9610.0070.0070.0000.0000.0000.000
69A252GLU-1-0.978-0.98132.202-0.117-0.1170.0000.0000.0000.000
70A253ASP-1-0.934-1.00733.672-0.129-0.1290.0000.0000.0000.000
71A254VAL0-0.045-0.00935.6370.0050.0050.0000.0000.0000.000
72A255GLU-1-0.856-0.90738.251-0.090-0.0900.0000.0000.0000.000
73A256GLY00.011-0.00441.603-0.001-0.0010.0000.0000.0000.000
74A257GLU-1-0.911-0.95542.968-0.074-0.0740.0000.0000.0000.000
75A258ALA00.004-0.00342.0920.0010.0010.0000.0000.0000.000
76A259LEU00.0150.00037.110-0.002-0.0020.0000.0000.0000.000
77A260ALA00.0190.01540.855-0.002-0.0020.0000.0000.0000.000
78A261THR0-0.014-0.01343.7140.0020.0020.0000.0000.0000.000
79A262LEU00.0270.01337.9600.0010.0010.0000.0000.0000.000
80A263VAL00.0140.00939.297-0.002-0.0020.0000.0000.0000.000
81A264VAL0-0.0060.00841.2900.0000.0000.0000.0000.0000.000
82A265ASN0-0.034-0.03543.1200.0030.0030.0000.0000.0000.000
83A266THR0-0.0070.01437.5290.0000.0000.0000.0000.0000.000
84A267MET0-0.069-0.03740.940-0.001-0.0010.0000.0000.0000.000
85A268ARG10.9020.94842.4210.0740.0740.0000.0000.0000.000
86A269GLY0-0.020-0.01542.3420.0020.0020.0000.0000.0000.000
87A270ILE0-0.0360.00243.3570.0010.0010.0000.0000.0000.000
88A271VAL00.0680.02240.8720.0010.0010.0000.0000.0000.000
89A272LYS10.8690.95336.4160.1120.1120.0000.0000.0000.000
90A273VAL00.0310.01435.514-0.002-0.0020.0000.0000.0000.000
91A274ALA00.0350.01631.691-0.002-0.0020.0000.0000.0000.000
92A275ALA00.0120.02432.8310.0010.0010.0000.0000.0000.000
93A276VAL00.007-0.00127.636-0.003-0.0030.0000.0000.0000.000
94A277LYS10.9310.96529.5250.1600.1600.0000.0000.0000.000
95A278ALA00.0850.04128.065-0.016-0.0160.0000.0000.0000.000
96A279PRO00.0110.01423.1870.0010.0010.0000.0000.0000.000
97A280GLY00.012-0.00424.3940.0140.0140.0000.0000.0000.000
98A281PHE00.014-0.01525.1370.0090.0090.0000.0000.0000.000
99A282GLY00.0540.02327.480-0.003-0.0030.0000.0000.0000.000
100A283ASP-1-0.805-0.90828.496-0.097-0.0970.0000.0000.0000.000
101A284ARG10.8290.90618.2190.2810.2810.0000.0000.0000.000
102A285ARG10.8490.93325.0060.1430.1430.0000.0000.0000.000
103A286LYS11.0060.99826.9910.0960.0960.0000.0000.0000.000
104A287ALA0-0.0080.00724.4580.0010.0010.0000.0000.0000.000
105A288MET0-0.015-0.01421.520-0.018-0.0180.0000.0000.0000.000
106A289LEU0-0.0100.00824.109-0.011-0.0110.0000.0000.0000.000
107A290GLN00.0320.01226.770-0.001-0.0010.0000.0000.0000.000
108A291ASP-1-0.779-0.87421.283-0.204-0.2040.0000.0000.0000.000
109A292ILE0-0.005-0.00923.419-0.006-0.0060.0000.0000.0000.000
110A293ALA0-0.0270.00824.8330.0020.0020.0000.0000.0000.000
111A294THR00.0130.00724.6210.0080.0080.0000.0000.0000.000
112A295LEU0-0.041-0.02220.7430.0040.0040.0000.0000.0000.000
113A296THR0-0.065-0.05224.2000.0040.0040.0000.0000.0000.000
114A297GLY00.0550.04127.0500.0070.0070.0000.0000.0000.000
115A298GLY00.0020.01329.6990.0070.0070.0000.0000.0000.000
116A299THR0-0.012-0.01431.5280.0010.0010.0000.0000.0000.000
117A300VAL0-0.092-0.04730.589-0.003-0.0030.0000.0000.0000.000
118A301ILE0-0.007-0.01833.4550.0070.0070.0000.0000.0000.000
119A302SER00.008-0.02935.904-0.002-0.0020.0000.0000.0000.000
120A303GLU-1-0.837-0.94037.938-0.075-0.0750.0000.0000.0000.000
121A304GLU-1-1.036-1.00036.652-0.064-0.0640.0000.0000.0000.000
122A305ILE0-0.035-0.01936.2730.0040.0040.0000.0000.0000.000
123A306GLY0-0.039-0.01540.1620.0020.0020.0000.0000.0000.000
124A307MET0-0.065-0.00638.1820.0000.0000.0000.0000.0000.000
125A308GLU-1-0.807-0.90142.120-0.062-0.0620.0000.0000.0000.000
126A309LEU00.0220.01339.305-0.001-0.0010.0000.0000.0000.000
127A310GLH0-0.117-0.07542.187-0.002-0.0020.0000.0000.0000.000
128A311LYS10.8570.91844.5870.0540.0540.0000.0000.0000.000
129A312ALA00.0350.05239.8790.0010.0010.0000.0000.0000.000
130A313THR0-0.043-0.03340.8240.0020.0020.0000.0000.0000.000
131A314LEU00.003-0.03438.830-0.004-0.0040.0000.0000.0000.000
132A315GLU-1-0.966-0.96737.231-0.070-0.0700.0000.0000.0000.000
133A316ASP-1-0.824-0.90436.318-0.079-0.0790.0000.0000.0000.000
134A317LEU0-0.105-0.04834.235-0.008-0.0080.0000.0000.0000.000
135A318GLY00.0870.04630.1790.0020.0020.0000.0000.0000.000
136A319GLN0-0.069-0.03929.5380.0020.0020.0000.0000.0000.000
137A320ALA00.0540.01925.076-0.008-0.0080.0000.0000.0000.000
138A321LYS10.8840.96821.8360.2770.2770.0000.0000.0000.000
139A322ARG10.9150.95923.6600.2480.2480.0000.0000.0000.000
140A323VAL00.0050.01524.655-0.017-0.0170.0000.0000.0000.000
141A324VAL00.0000.00322.7830.0150.0150.0000.0000.0000.000
142A325ILE0-0.019-0.00423.846-0.017-0.0170.0000.0000.0000.000
143A326ASN00.0160.01821.8790.0200.0200.0000.0000.0000.000
144A327LYS10.9520.95526.0540.2360.2360.0000.0000.0000.000
145A328ASP-1-0.884-0.94023.289-0.245-0.2450.0000.0000.0000.000
146A329THR0-0.077-0.02319.714-0.017-0.0170.0000.0000.0000.000
147A330THR00.025-0.01222.2920.0290.0290.0000.0000.0000.000
148A331THR0-0.018-0.01018.782-0.038-0.0380.0000.0000.0000.000
149A332ILE0-0.010-0.01120.8950.0300.0300.0000.0000.0000.000
150A333ILE00.012-0.00720.043-0.026-0.0260.0000.0000.0000.000
151A334ASP-1-0.811-0.91720.733-0.255-0.2550.0000.0000.0000.000
152A335GLY0-0.017-0.00722.2780.0230.0230.0000.0000.0000.000
153A336VAL0-0.027-0.02824.3250.0010.0010.0000.0000.0000.000
154A337GLY0-0.0080.01025.9990.0150.0150.0000.0000.0000.000
155A338GLU-1-0.930-0.96726.275-0.074-0.0740.0000.0000.0000.000
156A339GLU-1-0.861-0.94223.807-0.131-0.1310.0000.0000.0000.000
157A340ALA0-0.032-0.02723.471-0.001-0.0010.0000.0000.0000.000
158A341ALA00.0410.03725.2050.0060.0060.0000.0000.0000.000
159A342ILE00.0310.01320.281-0.005-0.0050.0000.0000.0000.000
160A343GLN0-0.049-0.02418.878-0.022-0.0220.0000.0000.0000.000
161A344GLY00.0100.00921.2060.0120.0120.0000.0000.0000.000
162A345ARG10.8530.91222.0190.1390.1390.0000.0000.0000.000
163A346VAL00.015-0.00316.349-0.002-0.0020.0000.0000.0000.000
164A347ALA0-0.044-0.02718.6020.0140.0140.0000.0000.0000.000
165A348GLN00.0080.00020.4710.0030.0030.0000.0000.0000.000
166A349ILE0-0.0050.00317.2640.0080.0080.0000.0000.0000.000
167A350ARG10.9500.97214.2460.0250.0250.0000.0000.0000.000
168A351GLN0-0.0090.00717.8040.0340.0340.0000.0000.0000.000
169A352GLN0-0.007-0.02020.739-0.004-0.0040.0000.0000.0000.000
170A353ILE0-0.044-0.02614.286-0.007-0.0070.0000.0000.0000.000
171A354GLU-1-0.952-0.98216.8120.1680.1680.0000.0000.0000.000
172A355GLU-1-0.922-0.94919.6800.0150.0150.0000.0000.0000.000
173A356ALA0-0.055-0.00119.570-0.007-0.0070.0000.0000.0000.000
174A357THR0-0.009-0.01321.6600.0150.0150.0000.0000.0000.000
175A358SER0-0.067-0.05121.295-0.001-0.0010.0000.0000.0000.000
176A359ASP-1-0.887-0.95215.078-0.125-0.1250.0000.0000.0000.000
177A360TYR00.0080.01216.723-0.050-0.0500.0000.0000.0000.000
178A361ASP-1-0.845-0.92718.312-0.136-0.1360.0000.0000.0000.000
179A362ARG10.9140.95715.235-0.034-0.0340.0000.0000.0000.000
180A363GLU-1-0.897-0.93511.703-0.606-0.6060.0000.0000.0000.000
181A364LYS10.9330.96714.5110.2470.2470.0000.0000.0000.000
182A365LEU0-0.024-0.00517.024-0.026-0.0260.0000.0000.0000.000
183A366GLN00.0740.0329.8160.1070.1070.0000.0000.0000.000
184A367GLU-1-0.874-0.93812.969-0.518-0.5180.0000.0000.0000.000
185A368ARG10.8190.90314.1570.1620.1620.0000.0000.0000.000
186A369VAL0-0.0060.01212.6860.0100.0100.0000.0000.0000.000
187A370ALA0-0.010-0.00511.140-0.015-0.0150.0000.0000.0000.000
188A371LYS10.8630.92712.7810.4120.4120.0000.0000.0000.000
189A372LEU00.001-0.01615.8350.0130.0130.0000.0000.0000.000
190A373ALA0-0.008-0.00413.0990.0210.0210.0000.0000.0000.000
191A374GLY0-0.0050.00414.270-0.012-0.0120.0000.0000.0000.000
192A375GLY0-0.0290.00014.9060.0220.0220.0000.0000.0000.000
193A376VAL0-0.0080.01417.0550.0520.0520.0000.0000.0000.000