Manual

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: 5J6RZ

Calculation Name: 3K6Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K6Y

Chain ID: A

ChEMBL ID:

UniProt ID: P9WHR9

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2403134.269488
FMO2-HF: Nuclear repulsion 2322857.933984
FMO2-HF: Total energy -80276.335504
FMO2-MP2: Total energy -80514.168714


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:171:ALA)


Summations of interaction energy for fragment #1(A:171:ALA)
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.
-0.6610.688-0.009-0.515-0.8240.002
Interaction energy analysis for fragmet #1(A:171:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.030
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].
3A173LEU0-0.035-0.0263.813-0.4050.944-0.009-0.515-0.8240.002
4A174GLU-1-0.874-0.9475.421-0.280-0.2800.0000.0000.0000.000
5A175PRO0-0.054-0.0048.1900.1730.1730.0000.0000.0000.000
6A176PHE00.0310.00911.4100.0100.0100.0000.0000.0000.000
7A177SER0-0.046-0.02814.4930.0030.0030.0000.0000.0000.000
8A178ARG10.9570.97616.6530.1770.1770.0000.0000.0000.000
9A179THR0-0.009-0.00520.154-0.021-0.0210.0000.0000.0000.000
10A180PRO0-0.016-0.00622.8870.0090.0090.0000.0000.0000.000
11A181VAL00.0680.04225.3820.0070.0070.0000.0000.0000.000
12A182ILE00.0060.00728.935-0.005-0.0050.0000.0000.0000.000
13A183PRO0-0.016-0.00329.6010.0060.0060.0000.0000.0000.000
14A184VAL0-0.0120.00632.5740.0040.0040.0000.0000.0000.000
15A185ALA00.0040.00036.359-0.002-0.0020.0000.0000.0000.000
16A186SER00.0450.01039.403-0.001-0.0010.0000.0000.0000.000
17A187PRO00.0150.02940.5360.0020.0020.0000.0000.0000.000
18A188ASP-1-0.837-0.91543.454-0.041-0.0410.0000.0000.0000.000
19A189PRO00.012-0.00546.9140.0020.0020.0000.0000.0000.000
20A190ALA00.001-0.00648.8650.0020.0020.0000.0000.0000.000
21A191LEU0-0.021-0.01547.0790.0020.0020.0000.0000.0000.000
22A192VAL0-0.0240.00050.5520.0010.0010.0000.0000.0000.000
23A193ASN0-0.031-0.01352.6140.0020.0020.0000.0000.0000.000
24A194ASN00.0010.00753.3870.0020.0020.0000.0000.0000.000
25A195PRO00.022-0.00655.4530.0000.0000.0000.0000.0000.000
26A196VAL0-0.0040.02052.8070.0010.0010.0000.0000.0000.000
27A197VAL00.0260.02452.8010.0010.0010.0000.0000.0000.000
28A198ALA00.0290.00955.3230.0010.0010.0000.0000.0000.000
29A199ALA0-0.054-0.03058.6100.0010.0010.0000.0000.0000.000
30A200THR0-0.015-0.01653.3420.0010.0010.0000.0000.0000.000
31A201GLU-1-0.935-0.96556.018-0.023-0.0230.0000.0000.0000.000
32A202PRO0-0.029-0.00657.0270.0000.0000.0000.0000.0000.000
33A203SER0-0.042-0.04256.6240.0010.0010.0000.0000.0000.000
34A204VAL0-0.036-0.00851.9840.0000.0000.0000.0000.0000.000
35A205VAL0-0.0060.01353.9830.0000.0000.0000.0000.0000.000
36A206LYS10.9070.96853.2350.0220.0220.0000.0000.0000.000
37A207ILE0-0.044-0.02350.7600.0020.0020.0000.0000.0000.000
38A208ARG10.9010.94352.2830.0190.0190.0000.0000.0000.000
39A209SER00.028-0.00150.8230.0020.0020.0000.0000.0000.000
40A210LEU0-0.0270.00152.211-0.001-0.0010.0000.0000.0000.000
41A211ALA00.0740.01849.5270.0010.0010.0000.0000.0000.000
42A212PRO00.0270.01750.791-0.001-0.0010.0000.0000.0000.000
43A213ARG10.8580.92147.5180.0110.0110.0000.0000.0000.000
44A214CYS0-0.049-0.01844.1180.0000.0000.0000.0000.0000.000
45A215GLN0-0.036-0.01447.465-0.002-0.0020.0000.0000.0000.000
46A216LYS10.9740.99442.6330.0270.0270.0000.0000.0000.000
47A217VAL0-0.024-0.01249.8150.0020.0020.0000.0000.0000.000
48A218LEU0-0.037-0.00545.567-0.002-0.0020.0000.0000.0000.000
49A219GLU-1-0.808-0.91748.610-0.023-0.0230.0000.0000.0000.000
50A220GLY0-0.012-0.00147.997-0.002-0.0020.0000.0000.0000.000
51A221THR0-0.0060.01648.2120.0010.0010.0000.0000.0000.000
52A222GLY00.0310.02249.0620.0000.0000.0000.0000.0000.000
53A223PHE00.0140.00947.8070.0000.0000.0000.0000.0000.000
54A224VAL00.0020.01752.9070.0010.0010.0000.0000.0000.000
55A225ILE0-0.018-0.00851.2100.0000.0000.0000.0000.0000.000
56A226SER0-0.019-0.02954.5490.0010.0010.0000.0000.0000.000
57A227PRO00.0440.01957.8970.0000.0000.0000.0000.0000.000
58A228ASP-1-0.809-0.89460.682-0.010-0.0100.0000.0000.0000.000
59A229ARG10.8000.89855.6550.0090.0090.0000.0000.0000.000
60A230VAL00.0380.02652.809-0.001-0.0010.0000.0000.0000.000
61A231MET0-0.0170.01547.7180.0010.0010.0000.0000.0000.000
62A232THR00.041-0.00748.004-0.001-0.0010.0000.0000.0000.000
63A233ASN0-0.010-0.01442.263-0.001-0.0010.0000.0000.0000.000
64A234ALA00.0150.01942.9450.0010.0010.0000.0000.0000.000
65A235HIS10.7860.83740.6760.0330.0330.0000.0000.0000.000
66A236VAL0-0.040-0.00743.365-0.001-0.0010.0000.0000.0000.000
67A237VAL00.0090.00446.4840.0010.0010.0000.0000.0000.000
68A238ALA00.0090.01844.2970.0020.0020.0000.0000.0000.000
69A239GLY0-0.037-0.02146.201-0.001-0.0010.0000.0000.0000.000
70A240SER0-0.081-0.05647.9140.0010.0010.0000.0000.0000.000
71A241ASN0-0.047-0.03951.1590.0000.0000.0000.0000.0000.000
72A242ASN0-0.009-0.00554.6680.0000.0000.0000.0000.0000.000
73A243VAL00.0420.02353.047-0.001-0.0010.0000.0000.0000.000
74A244THR0-0.0220.00455.6640.0010.0010.0000.0000.0000.000
75A245VAL00.0190.00755.567-0.001-0.0010.0000.0000.0000.000
76A246TYR0-0.021-0.02857.0330.0010.0010.0000.0000.0000.000
77A247ALA00.0570.02058.176-0.001-0.0010.0000.0000.0000.000
78A248GLY00.0250.01060.6310.0010.0010.0000.0000.0000.000
79A249ASP-1-0.921-0.94861.769-0.019-0.0190.0000.0000.0000.000
80A250LYS10.8900.95563.0510.0130.0130.0000.0000.0000.000
81A251PRO0-0.037-0.01761.6970.0000.0000.0000.0000.0000.000
82A252PHE0-0.023-0.01861.0610.0010.0010.0000.0000.0000.000
83A253GLU-1-0.921-0.95960.495-0.010-0.0100.0000.0000.0000.000
84A254ALA00.0200.00556.8890.0000.0000.0000.0000.0000.000
85A255THR0-0.045-0.00757.1650.0010.0010.0000.0000.0000.000
86A256VAL00.0450.01650.7800.0000.0000.0000.0000.0000.000
87A257VAL00.0040.00453.8870.0010.0010.0000.0000.0000.000
88A258SER0-0.047-0.03249.0010.0020.0020.0000.0000.0000.000
89A259TYR00.0420.01144.674-0.001-0.0010.0000.0000.0000.000
90A260ASP-1-0.776-0.86541.623-0.009-0.0090.0000.0000.0000.000
91A261PRO00.001-0.00840.510-0.002-0.0020.0000.0000.0000.000
92A262SER0-0.004-0.00437.482-0.002-0.0020.0000.0000.0000.000
93A263VAL00.0300.00337.437-0.003-0.0030.0000.0000.0000.000
94A264ASP-1-0.754-0.85439.225-0.031-0.0310.0000.0000.0000.000
95A265VAL00.0000.00041.195-0.002-0.0020.0000.0000.0000.000
96A266ALA0-0.017-0.00944.7080.0020.0020.0000.0000.0000.000
97A267ILE0-0.015-0.00948.173-0.001-0.0010.0000.0000.0000.000
98A268LEU0-0.021-0.01651.4930.0010.0010.0000.0000.0000.000
99A269ALA0-0.010-0.00454.6270.0000.0000.0000.0000.0000.000
100A270VAL0-0.013-0.02857.6210.0000.0000.0000.0000.0000.000
101A271PRO0-0.007-0.00660.3590.0000.0000.0000.0000.0000.000
102A272HIS0-0.039-0.01664.0440.0000.0000.0000.0000.0000.000
103A273LEU00.0010.00958.8110.0000.0000.0000.0000.0000.000
104A274PRO0-0.047-0.03363.3490.0000.0000.0000.0000.0000.000
105A275PRO0-0.0100.01560.2090.0000.0000.0000.0000.0000.000
106A276PRO00.0330.02360.6540.0010.0010.0000.0000.0000.000
107A277PRO0-0.018-0.00357.229-0.001-0.0010.0000.0000.0000.000
108A278LEU00.0100.01552.8260.0000.0000.0000.0000.0000.000
109A279VAL0-0.037-0.01753.3480.0010.0010.0000.0000.0000.000
110A280PHE00.009-0.00547.420-0.001-0.0010.0000.0000.0000.000
111A281ALA00.0170.00547.3570.0010.0010.0000.0000.0000.000
112A282ALA0-0.033-0.01947.7640.0000.0000.0000.0000.0000.000
113A283GLU-1-0.932-0.96445.375-0.018-0.0180.0000.0000.0000.000
114A284PRO0-0.039-0.00940.649-0.001-0.0010.0000.0000.0000.000
115A285ALA00.0080.00341.5660.0000.0000.0000.0000.0000.000
116A286LYS10.9500.95939.8040.0320.0320.0000.0000.0000.000
117A287THR0-0.004-0.02735.4850.0010.0010.0000.0000.0000.000
118A288GLY0-0.046-0.03138.2290.0010.0010.0000.0000.0000.000
119A289ALA0-0.0310.00140.2590.0010.0010.0000.0000.0000.000
120A290ASP-1-0.845-0.92042.985-0.044-0.0440.0000.0000.0000.000
121A291VAL0-0.054-0.03742.6120.0020.0020.0000.0000.0000.000
122A292VAL00.002-0.00245.871-0.002-0.0020.0000.0000.0000.000
123A293VAL00.0080.01642.9570.0010.0010.0000.0000.0000.000
124A294LEU0-0.0170.00246.2660.0000.0000.0000.0000.0000.000
125A295GLY00.0690.01048.8220.0010.0010.0000.0000.0000.000
126A296TYR0-0.065-0.03649.7310.0000.0000.0000.0000.0000.000
127A297PRO00.0690.04747.5340.0010.0010.0000.0000.0000.000
128A298GLY0-0.015-0.02047.9050.0010.0010.0000.0000.0000.000
129A299GLY0-0.052-0.01649.5400.0010.0010.0000.0000.0000.000
130A300GLY0-0.058-0.02852.1850.0020.0020.0000.0000.0000.000
131A301ASN00.005-0.01654.2450.0020.0020.0000.0000.0000.000
132A302PHE00.0620.02853.455-0.001-0.0010.0000.0000.0000.000
133A303THR0-0.022-0.01349.6510.0000.0000.0000.0000.0000.000
134A304ALA0-0.0060.00250.2710.0000.0000.0000.0000.0000.000
135A305THR00.0320.00044.2040.0000.0000.0000.0000.0000.000
136A306PRO0-0.033-0.00945.8660.0000.0000.0000.0000.0000.000
137A307ALA00.0200.00541.946-0.003-0.0030.0000.0000.0000.000
138A308ARG10.7900.89139.7680.0540.0540.0000.0000.0000.000
139A309ILE0-0.0130.01338.004-0.003-0.0030.0000.0000.0000.000
140A310ARG10.8630.93332.7970.0810.0810.0000.0000.0000.000
141A311GLU-1-0.880-0.96230.076-0.082-0.0820.0000.0000.0000.000
142A312ALA0-0.0200.00634.4750.0010.0010.0000.0000.0000.000
143A313ILE0-0.0010.00629.656-0.002-0.0020.0000.0000.0000.000
144A314ARG10.8980.94629.6700.0280.0280.0000.0000.0000.000
145A315LEU0-0.024-0.00328.781-0.006-0.0060.0000.0000.0000.000
146A316SER00.0300.00226.5300.0080.0080.0000.0000.0000.000
147A317GLY0-0.0100.00027.844-0.010-0.0100.0000.0000.0000.000
148A318PRO00.0110.02928.8150.0060.0060.0000.0000.0000.000
149A319ASH0-0.022-0.05731.427-0.004-0.0040.0000.0000.0000.000
150A320ILE0-0.009-0.01934.941-0.002-0.0020.0000.0000.0000.000
151A321TYR0-0.062-0.04637.378-0.001-0.0010.0000.0000.0000.000
152A322GLY0-0.0320.00233.0750.0000.0000.0000.0000.0000.000
153A323ASP-1-0.856-0.88433.297-0.008-0.0080.0000.0000.0000.000
154A324PRO0-0.053-0.04030.950-0.002-0.0020.0000.0000.0000.000
155A325GLU-1-0.935-0.95529.8090.0090.0090.0000.0000.0000.000
156A326PRO0-0.062-0.01527.091-0.004-0.0040.0000.0000.0000.000
157A327VAL00.0150.00230.3160.0050.0050.0000.0000.0000.000
158A328THR0-0.023-0.03229.235-0.003-0.0030.0000.0000.0000.000
159A329ARG10.8570.94031.8090.0360.0360.0000.0000.0000.000
160A330ASP-1-0.872-0.93033.390-0.030-0.0300.0000.0000.0000.000
161A331VAL0-0.035-0.03933.2100.0010.0010.0000.0000.0000.000
162A332TYR00.0180.01635.313-0.001-0.0010.0000.0000.0000.000
163A333THR00.0010.00731.364-0.001-0.0010.0000.0000.0000.000
164A334ILE00.004-0.00634.7860.0010.0010.0000.0000.0000.000
165A335ARG10.7470.86836.3010.0690.0690.0000.0000.0000.000
166A336ALA00.018-0.02137.7150.0040.0040.0000.0000.0000.000
167A337ASP-1-0.892-0.93338.807-0.063-0.0630.0000.0000.0000.000
168A338VAL0-0.041-0.01839.5540.0030.0030.0000.0000.0000.000
169A339GLU-1-0.908-0.95140.825-0.044-0.0440.0000.0000.0000.000
170A340GLN0-0.043-0.03740.8050.0030.0030.0000.0000.0000.000
171A341GLY00.0310.02443.9160.0010.0010.0000.0000.0000.000
172A342ASP-1-0.771-0.88743.972-0.037-0.0370.0000.0000.0000.000
173A343SER0-0.096-0.04342.0960.0010.0010.0000.0000.0000.000
174A344GLY00.0210.00944.1730.0020.0020.0000.0000.0000.000
175A345GLY00.0360.01546.1760.0020.0020.0000.0000.0000.000
176A346PRO0-0.0470.00045.971-0.001-0.0010.0000.0000.0000.000
177A347LEU00.0080.00141.726-0.002-0.0020.0000.0000.0000.000
178A348ILE0-0.008-0.01145.7110.0020.0020.0000.0000.0000.000
179A349ASP-1-0.763-0.90147.613-0.029-0.0290.0000.0000.0000.000
180A350LEU0-0.008-0.02248.7550.0010.0010.0000.0000.0000.000
181A351ASN0-0.080-0.03051.6000.0010.0010.0000.0000.0000.000
182A352GLY0-0.003-0.00752.5000.0010.0010.0000.0000.0000.000
183A353GLN0-0.063-0.02251.0230.0010.0010.0000.0000.0000.000
184A354VAL0-0.015-0.00847.351-0.002-0.0020.0000.0000.0000.000
185A355LEU00.016-0.00343.8020.0010.0010.0000.0000.0000.000
186A356GLY00.018-0.01342.9560.0000.0000.0000.0000.0000.000
187A357VAL0-0.034-0.00242.8540.0000.0000.0000.0000.0000.000
188A358VAL00.0410.02541.212-0.002-0.0020.0000.0000.0000.000
189A359PHE0-0.039-0.02634.8950.0020.0020.0000.0000.0000.000
190A360GLY0-0.008-0.01236.8290.0010.0010.0000.0000.0000.000
191A361ALA00.0370.02635.9550.0000.0000.0000.0000.0000.000
192A362ALA0-0.057-0.01530.8210.0000.0000.0000.0000.0000.000
193A363ILE0-0.048-0.02629.3860.0020.0020.0000.0000.0000.000
194A364ASP-1-0.904-0.96025.820-0.124-0.1240.0000.0000.0000.000
195A365ASP-1-0.926-0.92229.056-0.107-0.1070.0000.0000.0000.000
196A366ALA00.031-0.00630.4790.0060.0060.0000.0000.0000.000
197A367GLU-1-0.773-0.86333.964-0.066-0.0660.0000.0000.0000.000
198A368THR0-0.026-0.05432.0250.0020.0020.0000.0000.0000.000
199A369GLY00.0010.01334.8420.0010.0010.0000.0000.0000.000
200A370PHE0-0.021-0.02030.532-0.003-0.0030.0000.0000.0000.000
201A371VAL00.0110.00136.3700.0030.0030.0000.0000.0000.000
202A372LEU0-0.0100.00737.787-0.001-0.0010.0000.0000.0000.000
203A373THR00.0220.01838.1080.0020.0020.0000.0000.0000.000
204A374ALA00.0560.01440.8180.0020.0020.0000.0000.0000.000
205A375GLY0-0.008-0.00742.0260.0020.0020.0000.0000.0000.000
206A376GLU-1-0.835-0.91837.546-0.018-0.0180.0000.0000.0000.000
207A377VAL0-0.005-0.00840.6500.0020.0020.0000.0000.0000.000
208A378ALA00.0190.01843.8270.0020.0020.0000.0000.0000.000
209A379GLY00.0020.00044.5290.0010.0010.0000.0000.0000.000
210A380GLN0-0.041-0.03643.2400.0020.0020.0000.0000.0000.000
211A381LEU00.002-0.00347.2260.0010.0010.0000.0000.0000.000
212A382ALA0-0.0040.01449.4700.0010.0010.0000.0000.0000.000
213A383LYS10.8840.95550.3260.0050.0050.0000.0000.0000.000
214A384ILE00.0340.01352.2830.0000.0000.0000.0000.0000.000
215A385GLY0-0.0080.00154.4380.0000.0000.0000.0000.0000.000
216A386ALA0-0.045-0.01454.8930.0010.0010.0000.0000.0000.000
217A387THR00.007-0.01656.819-0.001-0.0010.0000.0000.0000.000
218A388GLN0-0.035-0.00957.7570.0000.0000.0000.0000.0000.000
219A389PRO00.0360.02056.0850.0000.0000.0000.0000.0000.000
220A390VAL0-0.045-0.00950.6140.0010.0010.0000.0000.0000.000
221A391GLY0-0.014-0.01450.781-0.001-0.0010.0000.0000.0000.000
222A392THR0-0.003-0.00848.5890.0000.0000.0000.0000.0000.000
223A393GLY00.0320.03245.553-0.001-0.0010.0000.0000.0000.000
224A394ALA00.0070.01242.4100.0000.0000.0000.0000.0000.000
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