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: LJY89

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2247170.22983
FMO2-HF: Nuclear repulsion 2164448.281828
FMO2-HF: Total energy -82721.948002
FMO2-MP2: Total energy -82963.357192


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.
-16.599-6.8972.073-5.107-6.668-0.022
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 : 0.045 / q_NPA : 0.013
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].
3D10ASN00.006-0.0052.191-6.061-1.4121.328-2.489-3.4890.005
4D11GLU-1-0.863-0.9502.648-12.920-8.0540.746-2.597-3.015-0.027
5D12ALA0-0.0250.0024.6620.7820.969-0.001-0.021-0.1640.000
6D13GLU-1-1.016-0.9956.3311.4251.4250.0000.0000.0000.000
7D14THR0-0.062-0.0096.9030.2560.2560.0000.0000.0000.000
8D15THR00.0090.0039.385-0.217-0.2170.0000.0000.0000.000
9D16SER00.0650.03010.6210.0850.0850.0000.0000.0000.000
10D17MET00.012-0.00412.5630.0970.0970.0000.0000.0000.000
11D18VAL00.0010.00313.9320.0830.0830.0000.0000.0000.000
12D19SER00.037-0.00814.5050.0040.0040.0000.0000.0000.000
13D20MET0-0.076-0.03316.6700.0580.0580.0000.0000.0000.000
14D21PRO00.0490.01419.5330.0390.0390.0000.0000.0000.000
15D22LEU00.0260.02618.2820.0390.0390.0000.0000.0000.000
16D23TYR0-0.008-0.01817.0450.0210.0210.0000.0000.0000.000
17D24ALA0-0.024-0.01122.4730.0260.0260.0000.0000.0000.000
18D25VAL0-0.019-0.00924.7240.0190.0190.0000.0000.0000.000
19D26MET00.0030.01224.0610.0170.0170.0000.0000.0000.000
20D27TYR0-0.002-0.01320.5030.0240.0240.0000.0000.0000.000
21D28PRO0-0.024-0.00526.0970.0170.0170.0000.0000.0000.000
22D29VAL00.0670.04629.1460.0130.0130.0000.0000.0000.000
23D30PHE0-0.009-0.02024.5720.0100.0100.0000.0000.0000.000
24D31ASN00.0290.00128.1660.0100.0100.0000.0000.0000.000
25D32GLU-1-1.036-1.00531.177-0.079-0.0790.0000.0000.0000.000
26D33LEU0-0.037-0.00531.8120.0070.0070.0000.0000.0000.000
27D34GLU-1-0.873-0.92930.476-0.072-0.0720.0000.0000.0000.000
28D35ARG10.8910.94434.1010.0690.0690.0000.0000.0000.000
29D36VAL00.000-0.00137.6700.0040.0040.0000.0000.0000.000
30D37ASN00.004-0.00336.1830.0050.0050.0000.0000.0000.000
31D38LEU00.0670.03233.432-0.006-0.0060.0000.0000.0000.000
32D39SER00.0280.01932.560-0.005-0.0050.0000.0000.0000.000
33D40ALA0-0.0050.00131.767-0.006-0.0060.0000.0000.0000.000
34D41ALA00.0530.01730.385-0.010-0.0100.0000.0000.0000.000
35D42GLN0-0.0020.00928.044-0.012-0.0120.0000.0000.0000.000
36D43THR0-0.007-0.01126.688-0.010-0.0100.0000.0000.0000.000
37D44LEU0-0.008-0.00326.280-0.014-0.0140.0000.0000.0000.000
38D45ARG10.8630.93223.4950.0950.0950.0000.0000.0000.000
39D46ALA00.008-0.00122.305-0.026-0.0260.0000.0000.0000.000
40D47ALA0-0.020-0.00621.202-0.025-0.0250.0000.0000.0000.000
41D48PHE00.026-0.00221.125-0.021-0.0210.0000.0000.0000.000
42D49ILE0-0.038-0.00717.353-0.043-0.0430.0000.0000.0000.000
43D50LYS10.9070.94916.6500.1760.1760.0000.0000.0000.000
44D51ALA00.0420.01915.964-0.056-0.0560.0000.0000.0000.000
45D52GLU-1-0.729-0.81315.141-0.570-0.5700.0000.0000.0000.000
46D53LYS10.9340.96410.9860.4390.4390.0000.0000.0000.000
47D54GLU-1-1.001-0.99211.115-0.557-0.5570.0000.0000.0000.000
48D55ASN0-0.048-0.02211.454-0.162-0.1620.0000.0000.0000.000
49D56PRO00.0100.00710.0440.1010.1010.0000.0000.0000.000
50D57GLY00.015-0.00213.264-0.002-0.0020.0000.0000.0000.000
51D58LEU00.0260.02716.4670.0720.0720.0000.0000.0000.000
52D59THR0-0.044-0.06818.5450.0670.0670.0000.0000.0000.000
53D60GLN00.0420.01219.7680.0430.0430.0000.0000.0000.000
54D61ASP-1-0.907-0.94519.741-0.320-0.3200.0000.0000.0000.000
55D62ILE0-0.044-0.03022.5160.0340.0340.0000.0000.0000.000
56D63ILE0-0.008-0.01124.4300.0260.0260.0000.0000.0000.000
57D64MET00.001-0.00624.7720.0240.0240.0000.0000.0000.000
58D65LYS10.9480.98625.7690.2100.2100.0000.0000.0000.000
59D66ILE0-0.019-0.00828.5050.0140.0140.0000.0000.0000.000
60D67LEU0-0.050-0.03229.2260.0130.0130.0000.0000.0000.000
61D68GLU-1-0.949-0.95830.987-0.136-0.1360.0000.0000.0000.000
62D69LYS10.9380.97033.0550.1200.1200.0000.0000.0000.000
63D70LYS10.9971.00635.4760.1100.1100.0000.0000.0000.000
64D71SER0-0.026-0.02237.0920.0040.0040.0000.0000.0000.000
65D72VAL00.0530.02838.8120.0050.0050.0000.0000.0000.000
66D73GLU-1-0.891-0.95336.553-0.087-0.0870.0000.0000.0000.000
67D74VAL0-0.090-0.02939.5890.0040.0040.0000.0000.0000.000
68D75ASN00.0500.01042.0890.0040.0040.0000.0000.0000.000
69D76PHE00.0150.00841.8170.0040.0040.0000.0000.0000.000
70D77THR0-0.017-0.01841.4620.0030.0030.0000.0000.0000.000
71D78GLU-1-0.903-0.95644.072-0.054-0.0540.0000.0000.0000.000
72D79SER0-0.030-0.01746.6890.0040.0040.0000.0000.0000.000
73D80LEU0-0.004-0.00243.7580.0020.0020.0000.0000.0000.000
74D81LEU0-0.055-0.01147.5070.0020.0020.0000.0000.0000.000
75D82ARG10.8170.87849.7880.0490.0490.0000.0000.0000.000
76D83MET00.0160.01250.3000.0020.0020.0000.0000.0000.000
77D84ALA0-0.0190.00251.1390.0010.0010.0000.0000.0000.000
78D85ALA0-0.064-0.03052.6860.0020.0020.0000.0000.0000.000
79D86ASP-1-0.871-0.93254.794-0.038-0.0380.0000.0000.0000.000
80D87ASP-1-0.952-0.96051.965-0.042-0.0420.0000.0000.0000.000
81D88VAL0-0.074-0.04654.7880.0000.0000.0000.0000.0000.000
82D89GLU-1-0.938-1.00257.521-0.027-0.0270.0000.0000.0000.000
83D90GLU-1-0.848-0.89253.099-0.033-0.0330.0000.0000.0000.000
84D91TYR0-0.140-0.10849.018-0.001-0.0010.0000.0000.0000.000
85D92MET0-0.0200.00055.2590.0010.0010.0000.0000.0000.000
86D93ILE0-0.010-0.00958.1880.0010.0010.0000.0000.0000.000
87D94GLU-1-0.928-0.95358.948-0.024-0.0240.0000.0000.0000.000
88D95ARG10.7900.88361.8080.0190.0190.0000.0000.0000.000
89D96PRO0-0.0100.00664.736-0.001-0.0010.0000.0000.0000.000
90D97GLU-1-0.848-0.92767.601-0.017-0.0170.0000.0000.0000.000
91D98PRO00.017-0.00268.249-0.001-0.0010.0000.0000.0000.000
92D99GLU-1-0.856-0.93866.755-0.017-0.0170.0000.0000.0000.000
93D100PHE0-0.004-0.01861.636-0.001-0.0010.0000.0000.0000.000
94D101GLN00.0620.02863.659-0.002-0.0020.0000.0000.0000.000
95D102ASP-1-0.926-0.94865.530-0.022-0.0220.0000.0000.0000.000
96D103LEU0-0.060-0.02858.768-0.001-0.0010.0000.0000.0000.000
97D104ASN00.0330.01460.405-0.002-0.0020.0000.0000.0000.000
98D105GLU-1-0.807-0.87961.086-0.027-0.0270.0000.0000.0000.000
99D106LYS10.9160.94261.7730.0220.0220.0000.0000.0000.000
100D107ALA0-0.053-0.01956.859-0.001-0.0010.0000.0000.0000.000
101D108ARG10.9220.97457.6170.0260.0260.0000.0000.0000.000
102D109ALA0-0.009-0.00959.388-0.001-0.0010.0000.0000.0000.000
103D110LEU0-0.044-0.03154.472-0.001-0.0010.0000.0000.0000.000
104D111LYS10.8640.92253.1950.0350.0350.0000.0000.0000.000
105D112GLN00.0630.03955.729-0.001-0.0010.0000.0000.0000.000
106D113ILE0-0.037-0.01257.631-0.001-0.0010.0000.0000.0000.000
107D114LEU0-0.025-0.02351.953-0.001-0.0010.0000.0000.0000.000
108D115SER0-0.008-0.00753.518-0.002-0.0020.0000.0000.0000.000
109D116LYS10.9780.99154.5880.0340.0340.0000.0000.0000.000
110D117ILE0-0.045-0.01851.8440.0000.0000.0000.0000.0000.000
111D118PRO0-0.027-0.03051.2590.0000.0000.0000.0000.0000.000
112D119ASP-1-0.871-0.90853.408-0.042-0.0420.0000.0000.0000.000
113D120GLU-1-0.876-0.92057.030-0.035-0.0350.0000.0000.0000.000
114D121ILE0-0.075-0.03550.9510.0000.0000.0000.0000.0000.000
115D122ASN0-0.053-0.03753.071-0.001-0.0010.0000.0000.0000.000
116D123ASP-1-0.819-0.90456.400-0.034-0.0340.0000.0000.0000.000
117D124ARG10.9210.96355.2610.0410.0410.0000.0000.0000.000
118D125VAL00.0340.00159.5940.0000.0000.0000.0000.0000.000
119D126ARG10.9280.94561.8410.0340.0340.0000.0000.0000.000
120D127PHE00.0320.03453.0240.0000.0000.0000.0000.0000.000
121D128LEU0-0.060-0.03858.5430.0000.0000.0000.0000.0000.000
122D129GLN0-0.064-0.02260.2580.0010.0010.0000.0000.0000.000
123D130THR00.0640.03557.5190.0000.0000.0000.0000.0000.000
124D131ILE0-0.030-0.02754.4220.0000.0000.0000.0000.0000.000
125D132LYS10.8920.94757.9800.0310.0310.0000.0000.0000.000
126D133ASP-1-0.822-0.90761.035-0.029-0.0290.0000.0000.0000.000
127D134ILE00.0140.01954.7350.0000.0000.0000.0000.0000.000
128D135ALA0-0.024-0.01657.8250.0000.0000.0000.0000.0000.000
129D136SER0-0.050-0.03158.6750.0010.0010.0000.0000.0000.000
130D137ALA00.0680.04359.2530.0010.0010.0000.0000.0000.000
131D138ILE0-0.046-0.02154.6380.0000.0000.0000.0000.0000.000
132D139LYS10.9020.94858.1950.0260.0260.0000.0000.0000.000
133D140GLU-1-0.891-0.94261.099-0.025-0.0250.0000.0000.0000.000
134D141LEU00.0330.06155.9180.0010.0010.0000.0000.0000.000
135D142LEU0-0.049-0.03356.1720.0010.0010.0000.0000.0000.000
136D143ASP-1-0.934-0.97559.419-0.019-0.0190.0000.0000.0000.000
137D144THR00.006-0.02662.2260.0010.0010.0000.0000.0000.000
138D145VAL0-0.0020.00757.1060.0010.0010.0000.0000.0000.000
139D146ASN0-0.037-0.04459.7580.0010.0010.0000.0000.0000.000
140D147ASN00.001-0.00261.9190.0020.0020.0000.0000.0000.000
141D148VAL00.0370.02962.1790.0010.0010.0000.0000.0000.000
142D149PHE0-0.043-0.02957.5410.0010.0010.0000.0000.0000.000
143D150LYS10.9130.94161.4870.0190.0190.0000.0000.0000.000
144D151LYS10.9230.97965.1900.0150.0150.0000.0000.0000.000
145D152TYR0-0.036-0.00464.3340.0000.0000.0000.0000.0000.000
146D153GLN0-0.033-0.00661.5900.0000.0000.0000.0000.0000.000
147D154TYR0-0.021-0.03058.9380.0010.0010.0000.0000.0000.000
148D155GLN00.0440.02558.6410.0000.0000.0000.0000.0000.000
149D156ASN0-0.030-0.00253.9380.0000.0000.0000.0000.0000.000
150D157ARG11.0331.01047.7960.0200.0200.0000.0000.0000.000
151D158ARG10.9080.94453.1480.0150.0150.0000.0000.0000.000
152D159ALA00.0190.01350.845-0.001-0.0010.0000.0000.0000.000
153D160LEU00.1040.05651.345-0.002-0.0020.0000.0000.0000.000
154D161GLU-1-0.939-0.97253.826-0.022-0.0220.0000.0000.0000.000
155D162HIS0-0.050-0.03344.8720.0010.0010.0000.0000.0000.000
156D163GLN00.0500.02247.465-0.002-0.0020.0000.0000.0000.000
157D164LYS10.9731.00250.3890.0240.0240.0000.0000.0000.000
158D165LYS10.8720.93149.4050.0230.0230.0000.0000.0000.000
159D166GLU-1-0.899-0.95344.047-0.045-0.0450.0000.0000.0000.000
160D167PHE00.0560.03147.955-0.002-0.0020.0000.0000.0000.000
161D168VAL0-0.010-0.01150.558-0.001-0.0010.0000.0000.0000.000
162D169LYS10.9030.97042.6500.0440.0440.0000.0000.0000.000
163D170TYR00.016-0.01741.837-0.004-0.0040.0000.0000.0000.000
164D171SER00.0200.03347.576-0.002-0.0020.0000.0000.0000.000
165D172LYS10.9300.95748.1340.0390.0390.0000.0000.0000.000
166D173SER0-0.031-0.01444.771-0.002-0.0020.0000.0000.0000.000
167D174PHE00.0690.03047.108-0.002-0.0020.0000.0000.0000.000
168D175SER0-0.024-0.02049.2170.0000.0000.0000.0000.0000.000
169D176ASP-1-0.925-0.96547.142-0.045-0.0450.0000.0000.0000.000
170D177THR0-0.0210.00345.675-0.003-0.0030.0000.0000.0000.000
171D178LEU00.0080.01147.411-0.001-0.0010.0000.0000.0000.000
172D179LYS10.8880.94050.9250.0380.0380.0000.0000.0000.000
173D180THR0-0.046-0.01944.5270.0000.0000.0000.0000.0000.000
174D181TYR00.0430.03547.704-0.002-0.0020.0000.0000.0000.000
175D182PHE0-0.071-0.05348.9500.0000.0000.0000.0000.0000.000
176D183LYS10.8970.95648.3590.0480.0480.0000.0000.0000.000
177D184ASP-1-0.845-0.92244.696-0.065-0.0650.0000.0000.0000.000
178D185GLY00.0060.01846.898-0.002-0.0020.0000.0000.0000.000
179D186LYS10.9000.92942.1460.0740.0740.0000.0000.0000.000
180D187ALA00.0350.02345.7090.0000.0000.0000.0000.0000.000
181D188ILE00.0200.01541.4430.0010.0010.0000.0000.0000.000
182D189ASN00.016-0.00840.856-0.002-0.0020.0000.0000.0000.000
183D190VAL00.0420.02044.0010.0010.0010.0000.0000.0000.000
184D191PHE00.0420.02745.7160.0020.0020.0000.0000.0000.000
185D192VAL00.0070.00440.8130.0010.0010.0000.0000.0000.000
186D193SER0-0.028-0.00644.0070.0020.0020.0000.0000.0000.000
187D194ALA00.0670.02445.8330.0020.0020.0000.0000.0000.000
188D195ASN00.0610.03044.7340.0050.0050.0000.0000.0000.000
189D196ARG10.8920.94738.9810.0740.0740.0000.0000.0000.000
190D197LEU0-0.0100.00245.5640.0020.0020.0000.0000.0000.000
191D198ILE00.0530.01149.1030.0020.0020.0000.0000.0000.000
192D199HIS00.0050.00943.8160.0020.0020.0000.0000.0000.000
193D200GLN0-0.008-0.01844.7650.0040.0040.0000.0000.0000.000
194D201THR0-0.037-0.01248.7580.0020.0020.0000.0000.0000.000
195D202ASN00.1210.08249.2410.0040.0040.0000.0000.0000.000
196D203LEU00.0330.02245.9120.0020.0020.0000.0000.0000.000
197D204ILE0-0.0760.00349.8880.0020.0020.0000.0000.0000.000
198D205LEU00.0180.01153.2080.0020.0020.0000.0000.0000.000
199D206GLN00.0290.00848.2400.0010.0010.0000.0000.0000.000
200D207THR0-0.085-0.08051.5550.0010.0010.0000.0000.0000.000
201D208PHE0-0.028-0.03653.0160.0020.0020.0000.0000.0000.000
202D209LYS10.9791.03654.5330.0280.0280.0000.0000.0000.000
203D210THR0-0.016-0.00151.7950.0010.0010.0000.0000.0000.000