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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: 9GZJ2

Calculation Name: 3L8I-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L8I

Chain ID: D

ChEMBL ID:

UniProt ID: Q9BUL8

Base Structure: X-ray

Registration Date: 2023-06-19

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2250140.160254
FMO2-HF: Nuclear repulsion 2167416.457077
FMO2-HF: Total energy -82723.703177
FMO2-MP2: Total energy -82965.114715


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(D:8:MET)


Summations of interaction energy for fragment #1(D:8:MET)
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.
-27.885-22.78710.993-7.618-8.474-0.056
Interaction energy analysis for fragmet #1(D:8:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / 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].
3D10ASN0-0.043-0.0362.253-8.125-3.7091.262-2.131-3.5470.008
4D11GLU-1-0.848-0.9301.850-23.149-22.6609.732-5.468-4.754-0.064
5D12ALA0-0.033-0.0044.7620.8861.079-0.001-0.019-0.1730.000
6D13GLU-1-0.947-0.9566.4232.6692.6690.0000.0000.0000.000
7D14THR0-0.020-0.0017.3820.1930.1930.0000.0000.0000.000
8D15THR0-0.013-0.0039.401-0.215-0.2150.0000.0000.0000.000
9D16SER00.0340.02110.716-0.022-0.0220.0000.0000.0000.000
10D17MET00.035-0.00212.5100.1210.1210.0000.0000.0000.000
11D18VAL00.0060.00713.8920.1030.1030.0000.0000.0000.000
12D19SER00.028-0.01214.5490.0180.0180.0000.0000.0000.000
13D20MET0-0.071-0.02916.7690.0810.0810.0000.0000.0000.000
14D21PRO00.0560.01619.6450.0460.0460.0000.0000.0000.000
15D22LEU00.0300.02818.4240.0450.0450.0000.0000.0000.000
16D23TYR0-0.020-0.02316.3420.0650.0650.0000.0000.0000.000
17D24ALA0-0.022-0.00822.5840.0240.0240.0000.0000.0000.000
18D25VAL0-0.027-0.01324.8290.0160.0160.0000.0000.0000.000
19D26MET00.0010.01124.1090.0170.0170.0000.0000.0000.000
20D27TYR00.017-0.00220.3790.0340.0340.0000.0000.0000.000
21D28PRO0-0.0200.00026.1970.0200.0200.0000.0000.0000.000
22D29VAL00.0310.02229.2280.0130.0130.0000.0000.0000.000
23D30PHE00.013-0.00724.3610.0120.0120.0000.0000.0000.000
24D31ASN00.0350.00828.2700.0180.0180.0000.0000.0000.000
25D32GLU-1-0.888-0.91331.276-0.041-0.0410.0000.0000.0000.000
26D33LEU0-0.042-0.01232.0850.0050.0050.0000.0000.0000.000
27D34GLU-1-0.856-0.91730.1040.0110.0110.0000.0000.0000.000
28D35ARG10.7620.86934.1880.0370.0370.0000.0000.0000.000
29D36VAL0-0.011-0.00737.7540.0030.0030.0000.0000.0000.000
30D37ASN0-0.005-0.00436.3360.0080.0080.0000.0000.0000.000
31D38LEU00.0620.03633.345-0.003-0.0030.0000.0000.0000.000
32D39SER00.0300.01432.6290.0020.0020.0000.0000.0000.000
33D40ALA00.0090.01131.8250.0020.0020.0000.0000.0000.000
34D41ALA00.0460.01730.468-0.004-0.0040.0000.0000.0000.000
35D42GLN00.0150.01228.113-0.004-0.0040.0000.0000.0000.000
36D43THR0-0.014-0.01826.7500.0050.0050.0000.0000.0000.000
37D44LEU0-0.023-0.00926.330-0.004-0.0040.0000.0000.0000.000
38D45ARG10.8390.90623.7350.0040.0040.0000.0000.0000.000
39D46ALA00.0140.00222.368-0.015-0.0150.0000.0000.0000.000
40D47ALA0-0.021-0.00421.253-0.002-0.0020.0000.0000.0000.000
41D48PHE00.031-0.00321.169-0.018-0.0180.0000.0000.0000.000
42D49ILE0-0.038-0.00717.508-0.040-0.0400.0000.0000.0000.000
43D50LYS10.7930.87916.711-0.091-0.0910.0000.0000.0000.000
44D51ALA00.0270.01416.000-0.030-0.0300.0000.0000.0000.000
45D52GLU-1-0.735-0.82315.386-0.496-0.4960.0000.0000.0000.000
46D53LYS10.9290.96310.304-0.205-0.2050.0000.0000.0000.000
47D54GLU-1-0.881-0.91911.162-0.085-0.0850.0000.0000.0000.000
48D55ASN0-0.053-0.02711.467-0.131-0.1310.0000.0000.0000.000
49D56PRO00.0140.01210.0980.0670.0670.0000.0000.0000.000
50D57GLY00.013-0.00113.328-0.031-0.0310.0000.0000.0000.000
51D58LEU00.0330.02816.5320.0620.0620.0000.0000.0000.000
52D59THR0-0.037-0.05718.5940.0620.0620.0000.0000.0000.000
53D60GLN00.016-0.00519.8530.0420.0420.0000.0000.0000.000
54D61ASP-1-0.888-0.93320.143-0.293-0.2930.0000.0000.0000.000
55D62ILE0-0.045-0.03022.4800.0300.0300.0000.0000.0000.000
56D63ILE0-0.009-0.01224.4950.0220.0220.0000.0000.0000.000
57D64MET00.003-0.00124.9110.0190.0190.0000.0000.0000.000
58D65LYS10.8020.89426.4840.1750.1750.0000.0000.0000.000
59D66ILE0-0.008-0.00428.5830.0130.0130.0000.0000.0000.000
60D67LEU0-0.036-0.02528.8050.0110.0110.0000.0000.0000.000
61D68GLU-1-0.845-0.89030.901-0.139-0.1390.0000.0000.0000.000
62D69LYS10.9600.98033.1100.0940.0940.0000.0000.0000.000
63D70LYS10.9891.00435.5440.1090.1090.0000.0000.0000.000
64D71SER0-0.001-0.01137.1570.0050.0050.0000.0000.0000.000
65D72VAL00.0390.01938.8220.0050.0050.0000.0000.0000.000
66D73GLU-1-0.876-0.94136.352-0.062-0.0620.0000.0000.0000.000
67D74VAL0-0.100-0.02939.6490.0040.0040.0000.0000.0000.000
68D75ASN00.0310.00042.1570.0030.0030.0000.0000.0000.000
69D76PHE00.0190.01341.2080.0050.0050.0000.0000.0000.000
70D77THR0-0.026-0.02841.6180.0040.0040.0000.0000.0000.000
71D78GLU-1-0.875-0.93844.138-0.043-0.0430.0000.0000.0000.000
72D79SER00.004-0.00446.8740.0030.0030.0000.0000.0000.000
73D80LEU0-0.043-0.01643.8960.0030.0030.0000.0000.0000.000
74D81LEU0-0.042-0.01247.5670.0020.0020.0000.0000.0000.000
75D82ARG10.8110.87349.8570.0390.0390.0000.0000.0000.000
76D83MET00.0060.00950.3490.0010.0010.0000.0000.0000.000
77D84ALA0-0.031-0.00851.1420.0020.0020.0000.0000.0000.000
78D85ALA0-0.045-0.02252.7490.0020.0020.0000.0000.0000.000
79D86ASP-1-0.870-0.93154.772-0.018-0.0180.0000.0000.0000.000
80D87ASP-1-0.942-0.95051.713-0.014-0.0140.0000.0000.0000.000
81D88VAL0-0.052-0.03254.8510.0000.0000.0000.0000.0000.000
82D89GLU-1-0.862-0.94657.585-0.009-0.0090.0000.0000.0000.000
83D90GLU-1-0.845-0.89353.106-0.003-0.0030.0000.0000.0000.000
84D91TYR0-0.125-0.10349.3090.0000.0000.0000.0000.0000.000
85D92MET0-0.0210.00355.3190.0010.0010.0000.0000.0000.000
86D93ILE0-0.008-0.00758.1830.0020.0020.0000.0000.0000.000
87D94GLU-1-0.820-0.88258.6150.0040.0040.0000.0000.0000.000
88D95ARG10.7790.86661.866-0.005-0.0050.0000.0000.0000.000
89D96PRO0-0.018-0.00264.799-0.001-0.0010.0000.0000.0000.000
90D97GLU-1-0.821-0.90567.3840.0040.0040.0000.0000.0000.000
91D98PRO00.0230.00068.318-0.001-0.0010.0000.0000.0000.000
92D99GLU-1-0.832-0.91066.9380.0000.0000.0000.0000.0000.000
93D100PHE00.013-0.01161.539-0.001-0.0010.0000.0000.0000.000
94D101GLN00.0800.04663.731-0.001-0.0010.0000.0000.0000.000
95D102ASP-1-0.850-0.89365.602-0.008-0.0080.0000.0000.0000.000
96D103LEU0-0.043-0.02159.079-0.001-0.0010.0000.0000.0000.000
97D104ASN00.014-0.00560.591-0.001-0.0010.0000.0000.0000.000
98D105GLU-1-0.781-0.83861.157-0.011-0.0110.0000.0000.0000.000
99D106LYS10.8070.87161.9380.0070.0070.0000.0000.0000.000
100D107ALA0-0.048-0.01856.981-0.001-0.0010.0000.0000.0000.000
101D108ARG10.7910.85757.6930.0090.0090.0000.0000.0000.000
102D109ALA00.004-0.00159.461-0.002-0.0020.0000.0000.0000.000
103D110LEU0-0.044-0.03154.707-0.002-0.0020.0000.0000.0000.000
104D111LYS10.8460.92153.5230.0110.0110.0000.0000.0000.000
105D112GLN00.0740.04855.803-0.001-0.0010.0000.0000.0000.000
106D113ILE0-0.046-0.01357.980-0.002-0.0020.0000.0000.0000.000
107D114LEU0-0.030-0.02152.263-0.002-0.0020.0000.0000.0000.000
108D115SER0-0.008-0.01453.588-0.002-0.0020.0000.0000.0000.000
109D116LYS10.8420.90654.6610.0270.0270.0000.0000.0000.000
110D117ILE0-0.041-0.02051.799-0.002-0.0020.0000.0000.0000.000
111D118PRO0-0.018-0.02551.250-0.002-0.0020.0000.0000.0000.000
112D119ASP-1-0.819-0.86553.482-0.033-0.0330.0000.0000.0000.000
113D120GLU-1-0.840-0.89957.101-0.030-0.0300.0000.0000.0000.000
114D121ILE0-0.070-0.03251.017-0.001-0.0010.0000.0000.0000.000
115D122ASN0-0.052-0.03153.418-0.003-0.0030.0000.0000.0000.000
116D123ASP-1-0.772-0.88056.482-0.035-0.0350.0000.0000.0000.000
117D124ARG10.9180.96355.1230.0460.0460.0000.0000.0000.000
118D125VAL00.018-0.00459.6870.0000.0000.0000.0000.0000.000
119D126ARG10.9240.93561.8670.0290.0290.0000.0000.0000.000
120D127PHE00.0200.04152.9740.0010.0010.0000.0000.0000.000
121D128LEU0-0.053-0.04058.6530.0000.0000.0000.0000.0000.000
122D129GLN0-0.086-0.04460.3550.0000.0000.0000.0000.0000.000
123D130THR00.0560.01757.8350.0010.0010.0000.0000.0000.000
124D131ILE0-0.053-0.03654.6540.0010.0010.0000.0000.0000.000
125D132LYS10.9060.95858.0760.0300.0300.0000.0000.0000.000
126D133ASP-1-0.797-0.88861.095-0.022-0.0220.0000.0000.0000.000
127D134ILE00.0110.01654.8130.0010.0010.0000.0000.0000.000
128D135ALA0-0.019-0.01457.9200.0010.0010.0000.0000.0000.000
129D136SER0-0.032-0.02458.7730.0020.0020.0000.0000.0000.000
130D137ALA00.0590.03659.3310.0010.0010.0000.0000.0000.000
131D138ILE0-0.037-0.01654.5800.0010.0010.0000.0000.0000.000
132D139LYS10.9020.95358.2880.0200.0200.0000.0000.0000.000
133D140GLU-1-0.878-0.93361.196-0.012-0.0120.0000.0000.0000.000
134D141LEU00.0130.03056.1060.0020.0020.0000.0000.0000.000
135D142LEU0-0.022-0.02056.5130.0020.0020.0000.0000.0000.000
136D143ASP-1-0.924-0.96259.513-0.006-0.0060.0000.0000.0000.000
137D144THR00.0430.01162.5160.0020.0020.0000.0000.0000.000
138D145VAL00.0080.01357.1770.0020.0020.0000.0000.0000.000
139D146ASN0-0.059-0.05659.7020.0030.0030.0000.0000.0000.000
140D147ASN00.009-0.00362.0110.0020.0020.0000.0000.0000.000
141D148VAL00.0430.03362.3830.0010.0010.0000.0000.0000.000
142D149PHE0-0.050-0.03257.7440.0020.0020.0000.0000.0000.000
143D150LYS10.8760.92361.0130.0030.0030.0000.0000.0000.000
144D151LYS10.9300.98465.2800.0010.0010.0000.0000.0000.000
145D152TYR0-0.065-0.03664.4120.0010.0010.0000.0000.0000.000
146D153GLN0-0.0230.00761.5980.0010.0010.0000.0000.0000.000
147D154TYR0-0.001-0.00858.3890.0010.0010.0000.0000.0000.000
148D155GLN00.0470.03158.7210.0020.0020.0000.0000.0000.000
149D156ASN0-0.0030.03254.6560.0030.0030.0000.0000.0000.000
150D157ARG11.0311.00347.940-0.019-0.0190.0000.0000.0000.000
151D158ARG10.8610.91753.308-0.009-0.0090.0000.0000.0000.000
152D159ALA00.0240.01350.947-0.001-0.0010.0000.0000.0000.000
153D160LEU00.1070.06251.430-0.001-0.0010.0000.0000.0000.000
154D161GLU-1-0.894-0.93454.037-0.004-0.0040.0000.0000.0000.000
155D162HIS0-0.039-0.02645.002-0.001-0.0010.0000.0000.0000.000
156D163GLN00.0390.01647.1620.0000.0000.0000.0000.0000.000
157D164LYS10.8930.94550.4770.0040.0040.0000.0000.0000.000
158D165LYS10.8880.93949.527-0.002-0.0020.0000.0000.0000.000
159D166GLU-1-0.784-0.88044.149-0.019-0.0190.0000.0000.0000.000
160D167PHE00.0530.03248.051-0.003-0.0030.0000.0000.0000.000
161D168VAL00.0160.00350.652-0.002-0.0020.0000.0000.0000.000
162D169LYS10.8050.90642.7810.0190.0190.0000.0000.0000.000
163D170TYR00.015-0.01941.703-0.006-0.0060.0000.0000.0000.000
164D171SER00.0140.03347.675-0.002-0.0020.0000.0000.0000.000
165D172LYS10.8390.88147.5710.0350.0350.0000.0000.0000.000
166D173SER00.0080.00545.022-0.003-0.0030.0000.0000.0000.000
167D174PHE00.0320.02747.211-0.004-0.0040.0000.0000.0000.000
168D175SER0-0.016-0.01649.316-0.002-0.0020.0000.0000.0000.000
169D176ASP-1-0.857-0.90547.214-0.041-0.0410.0000.0000.0000.000
170D177THR0-0.022-0.01345.654-0.004-0.0040.0000.0000.0000.000
171D178LEU00.0210.02047.514-0.003-0.0030.0000.0000.0000.000
172D179LYS10.9140.95151.0280.0380.0380.0000.0000.0000.000
173D180THR0-0.037-0.01944.621-0.002-0.0020.0000.0000.0000.000
174D181TYR00.0360.03047.810-0.004-0.0040.0000.0000.0000.000
175D182PHE0-0.070-0.04649.052-0.001-0.0010.0000.0000.0000.000
176D183LYS10.9060.96448.4310.0560.0560.0000.0000.0000.000
177D184ASP-1-0.808-0.90444.124-0.074-0.0740.0000.0000.0000.000
178D185GLY00.0190.03546.997-0.003-0.0030.0000.0000.0000.000
179D186LYS10.8030.88042.4740.0780.0780.0000.0000.0000.000
180D187ALA00.0480.02245.8020.0010.0010.0000.0000.0000.000
181D188ILE00.0190.01741.5960.0020.0020.0000.0000.0000.000
182D189ASN00.016-0.00541.0500.0000.0000.0000.0000.0000.000
183D190VAL00.0380.01444.0930.0030.0030.0000.0000.0000.000
184D191PHE00.0540.02945.8020.0030.0030.0000.0000.0000.000
185D192VAL00.0110.00840.9210.0030.0030.0000.0000.0000.000
186D193SER0-0.049-0.02644.0900.0050.0050.0000.0000.0000.000
187D194ALA00.0520.02145.9230.0030.0030.0000.0000.0000.000
188D195ASN00.0420.02145.1150.0050.0050.0000.0000.0000.000
189D196ARG10.9060.95738.5380.0540.0540.0000.0000.0000.000
190D197LEU0-0.0100.00145.6480.0030.0030.0000.0000.0000.000
191D198ILE00.0470.01349.1900.0030.0030.0000.0000.0000.000
192D199HIS00.0110.00743.8350.0020.0020.0000.0000.0000.000
193D200GLN0-0.001-0.01244.9070.0050.0050.0000.0000.0000.000
194D201THR0-0.033-0.00948.8410.0020.0020.0000.0000.0000.000
195D202ASN00.0810.04149.4550.0030.0030.0000.0000.0000.000
196D203LEU00.0280.01646.0140.0030.0030.0000.0000.0000.000
197D204ILE0-0.074-0.02349.9630.0030.0030.0000.0000.0000.000
198D205LEU00.0150.01153.2870.0020.0020.0000.0000.0000.000
199D206GLN00.0120.00248.0520.0000.0000.0000.0000.0000.000
200D207THR0-0.055-0.04351.4130.0030.0030.0000.0000.0000.000
201D208PHE0-0.027-0.03453.0890.0020.0020.0000.0000.0000.000
202D209LYS10.8470.94754.833-0.005-0.0050.0000.0000.0000.000
203D210THR0-0.044-0.03551.8700.0010.0010.0000.0000.0000.000