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: 2296R

Calculation Name: 3L8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L8I

Chain ID: A

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144613.61832
FMO2-HF: Nuclear repulsion 2064423.114368
FMO2-HF: Total energy -80190.503952
FMO2-MP2: Total energy -80425.624467


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:15:THR)


Summations of interaction energy for fragment #1(A:15:THR)
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.
-0.9181.149-0.02-1.109-0.9380.004
Interaction energy analysis for fragmet #1(A:15:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.009
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].
3A17MET00.0340.0053.8271.1453.212-0.020-1.109-0.9380.004
4A18VAL00.0210.0105.999-0.596-0.5960.0000.0000.0000.000
5A19SER00.023-0.0127.502-0.236-0.2360.0000.0000.0000.000
6A20MET0-0.048-0.0239.270-0.254-0.2540.0000.0000.0000.000
7A21PRO00.0470.02210.900-0.160-0.1600.0000.0000.0000.000
8A22LEU00.0310.02812.253-0.150-0.1500.0000.0000.0000.000
9A23TYR0-0.029-0.03410.188-0.095-0.0950.0000.0000.0000.000
10A24ALA0-0.024-0.01414.559-0.104-0.1040.0000.0000.0000.000
11A25VAL00.0010.00516.217-0.090-0.0900.0000.0000.0000.000
12A26MET00.0050.00417.649-0.062-0.0620.0000.0000.0000.000
13A27TYR0-0.010-0.00415.497-0.076-0.0760.0000.0000.0000.000
14A28PRO00.0060.02118.676-0.051-0.0510.0000.0000.0000.000
15A29VAL00.0370.02521.731-0.046-0.0460.0000.0000.0000.000
16A30PHE0-0.011-0.02620.797-0.039-0.0390.0000.0000.0000.000
17A31ASN0-0.017-0.02420.894-0.025-0.0250.0000.0000.0000.000
18A32GLU-1-0.954-0.96824.7850.3110.3110.0000.0000.0000.000
19A33LEU0-0.026-0.00826.867-0.028-0.0280.0000.0000.0000.000
20A34GLU-1-0.817-0.89526.1010.2960.2960.0000.0000.0000.000
21A35ARG10.8960.93329.821-0.189-0.1890.0000.0000.0000.000
22A36VAL0-0.0260.01132.495-0.014-0.0140.0000.0000.0000.000
23A37ASN00.0300.00732.128-0.004-0.0040.0000.0000.0000.000
24A38LEU00.0640.05028.8760.0130.0130.0000.0000.0000.000
25A39SER0-0.013-0.00528.8660.0160.0160.0000.0000.0000.000
26A40ALA00.0460.02828.5910.0140.0140.0000.0000.0000.000
27A41ALA00.0530.03026.2260.0200.0200.0000.0000.0000.000
28A42GLN0-0.030-0.02524.5390.0280.0280.0000.0000.0000.000
29A43THR0-0.029-0.03523.8480.0240.0240.0000.0000.0000.000
30A44LEU0-0.001-0.00123.8500.0110.0110.0000.0000.0000.000
31A45ARG10.8230.90420.261-0.364-0.3640.0000.0000.0000.000
32A46ALA0-0.024-0.00719.1490.0590.0590.0000.0000.0000.000
33A47ALA0-0.0070.00419.3780.0270.0270.0000.0000.0000.000
34A48PHE00.0500.00417.3860.0130.0130.0000.0000.0000.000
35A49ILE0-0.030-0.00514.2250.0820.0820.0000.0000.0000.000
36A50LYS10.7990.89314.357-0.279-0.2790.0000.0000.0000.000
37A51ALA00.0330.01415.5460.0130.0130.0000.0000.0000.000
38A52GLU-1-0.725-0.82010.7711.3081.3080.0000.0000.0000.000
39A53LYS10.8980.94710.666-0.657-0.6570.0000.0000.0000.000
40A54GLU-1-0.859-0.91111.1320.3980.3980.0000.0000.0000.000
41A55ASN0-0.075-0.03212.856-0.101-0.1010.0000.0000.0000.000
42A56PRO00.0200.0097.6360.0420.0420.0000.0000.0000.000
43A57GLY00.0270.0129.809-0.136-0.1360.0000.0000.0000.000
44A58LEU0-0.0060.00411.688-0.144-0.1440.0000.0000.0000.000
45A59THR0-0.014-0.05014.248-0.114-0.1140.0000.0000.0000.000
46A60GLN00.0120.00813.660-0.038-0.0380.0000.0000.0000.000
47A61ASP-1-0.819-0.90615.5350.3200.3200.0000.0000.0000.000
48A62ILE0-0.064-0.03217.917-0.068-0.0680.0000.0000.0000.000
49A63ILE00.0160.00317.068-0.049-0.0490.0000.0000.0000.000
50A64MET0-0.025-0.01518.848-0.039-0.0390.0000.0000.0000.000
51A65LYS10.9020.95020.519-0.366-0.3660.0000.0000.0000.000
52A66ILE0-0.037-0.01323.056-0.030-0.0300.0000.0000.0000.000
53A67LEU0-0.041-0.02522.235-0.028-0.0280.0000.0000.0000.000
54A68GLU-1-0.911-0.95724.0500.2170.2170.0000.0000.0000.000
55A69LYS10.8910.95727.534-0.200-0.2000.0000.0000.0000.000
56A70LYS10.9640.99029.801-0.184-0.1840.0000.0000.0000.000
57A71SER00.020-0.00931.311-0.003-0.0030.0000.0000.0000.000
58A72VAL00.0340.02933.477-0.007-0.0070.0000.0000.0000.000
59A73GLU-1-0.859-0.92731.3970.1790.1790.0000.0000.0000.000
60A74VAL0-0.070-0.03634.082-0.001-0.0010.0000.0000.0000.000
61A75ASN00.0040.00336.470-0.006-0.0060.0000.0000.0000.000
62A76PHE00.0240.01135.966-0.008-0.0080.0000.0000.0000.000
63A77THR0-0.017-0.02435.964-0.002-0.0020.0000.0000.0000.000
64A78GLU-1-0.904-0.94238.5890.1020.1020.0000.0000.0000.000
65A79SER0-0.023-0.01941.589-0.007-0.0070.0000.0000.0000.000
66A80LEU0-0.013-0.00838.394-0.004-0.0040.0000.0000.0000.000
67A81LEU0-0.076-0.01742.400-0.002-0.0020.0000.0000.0000.000
68A82ARG10.7540.82544.060-0.098-0.0980.0000.0000.0000.000
69A83MET0-0.0080.00943.739-0.004-0.0040.0000.0000.0000.000
70A84ALA0-0.005-0.00145.018-0.002-0.0020.0000.0000.0000.000
71A85ALA0-0.034-0.02147.075-0.001-0.0010.0000.0000.0000.000
72A86ASP-1-0.938-0.98350.6060.0750.0750.0000.0000.0000.000
73A87ASP-1-0.835-0.90451.0060.0830.0830.0000.0000.0000.000
74A88VAL0-0.109-0.07652.858-0.002-0.0020.0000.0000.0000.000
75A89GLU-1-0.928-0.96255.9570.0670.0670.0000.0000.0000.000
76A90GLU-1-0.890-0.91250.8300.0880.0880.0000.0000.0000.000
77A91TYR0-0.123-0.08049.012-0.001-0.0010.0000.0000.0000.000
78A92MET00.0430.01054.836-0.001-0.0010.0000.0000.0000.000
79A93ILE0-0.101-0.04458.401-0.001-0.0010.0000.0000.0000.000
80A94GLU-1-0.833-0.91860.7680.0610.0610.0000.0000.0000.000
81A95ARG10.8030.90863.961-0.057-0.0570.0000.0000.0000.000
82A96PRO00.0830.02966.1020.0010.0010.0000.0000.0000.000
83A97GLU-1-0.876-0.92367.3810.0500.0500.0000.0000.0000.000
84A98PRO00.0560.02667.1680.0020.0020.0000.0000.0000.000
85A99GLU-1-0.793-0.90664.8470.0510.0510.0000.0000.0000.000
86A100PHE00.0310.00661.1280.0020.0020.0000.0000.0000.000
87A101GLN00.0320.01462.4640.0010.0010.0000.0000.0000.000
88A102ASP-1-0.779-0.85563.4430.0580.0580.0000.0000.0000.000
89A103LEU0-0.002-0.00356.8460.0020.0020.0000.0000.0000.000
90A104ASN0-0.017-0.02658.5790.0040.0040.0000.0000.0000.000
91A105GLU-1-0.920-0.95958.5580.0570.0570.0000.0000.0000.000
92A106LYS10.8300.91658.462-0.056-0.0560.0000.0000.0000.000
93A107ALA0-0.0090.00054.6870.0020.0020.0000.0000.0000.000
94A108ARG10.9570.97654.473-0.065-0.0650.0000.0000.0000.000
95A109ALA00.0270.01955.2230.0020.0020.0000.0000.0000.000
96A110LEU00.003-0.00150.9860.0010.0010.0000.0000.0000.000
97A111LYS10.8930.94650.518-0.082-0.0820.0000.0000.0000.000
98A112GLN00.0110.00950.7790.0010.0010.0000.0000.0000.000
99A113ILE0-0.0130.01452.1430.0010.0010.0000.0000.0000.000
100A114LEU0-0.010-0.02146.9920.0020.0020.0000.0000.0000.000
101A115SER0-0.041-0.03547.4240.0030.0030.0000.0000.0000.000
102A116LYS10.9350.96248.183-0.070-0.0700.0000.0000.0000.000
103A117ILE0-0.0090.00444.764-0.001-0.0010.0000.0000.0000.000
104A118PRO0-0.019-0.02043.9030.0000.0000.0000.0000.0000.000
105A119ASP-1-0.829-0.87245.4750.0850.0850.0000.0000.0000.000
106A120GLU-1-0.888-0.93348.2510.0670.0670.0000.0000.0000.000
107A121ILE0-0.069-0.02642.464-0.001-0.0010.0000.0000.0000.000
108A122ASN0-0.054-0.03643.6400.0020.0020.0000.0000.0000.000
109A123ASP-1-0.823-0.89946.3190.0610.0610.0000.0000.0000.000
110A124ARG10.9280.94742.971-0.085-0.0850.0000.0000.0000.000
111A125VAL00.0130.00749.9600.0010.0010.0000.0000.0000.000
112A126ARG10.9630.98053.148-0.060-0.0600.0000.0000.0000.000
113A127PHE00.0510.04445.3920.0020.0020.0000.0000.0000.000
114A128LEU0-0.035-0.03449.9430.0020.0020.0000.0000.0000.000
115A129GLN0-0.114-0.05652.243-0.002-0.0020.0000.0000.0000.000
116A130THR00.0710.01050.6690.0000.0000.0000.0000.0000.000
117A131ILE0-0.021-0.00647.4010.0010.0010.0000.0000.0000.000
118A132LYS10.9080.96651.096-0.058-0.0580.0000.0000.0000.000
119A133ASP-1-0.801-0.88954.6060.0620.0620.0000.0000.0000.000
120A134ILE0-0.019-0.00948.7710.0000.0000.0000.0000.0000.000
121A135ALA0-0.031-0.01352.2730.0000.0000.0000.0000.0000.000
122A136SER00.0100.00853.288-0.001-0.0010.0000.0000.0000.000
123A137ALA00.0520.03654.329-0.001-0.0010.0000.0000.0000.000
124A138ILE0-0.033-0.02749.3720.0000.0000.0000.0000.0000.000
125A139LYS10.7910.90653.627-0.061-0.0610.0000.0000.0000.000
126A140GLU-1-0.846-0.94556.5080.0580.0580.0000.0000.0000.000
127A141LEU0-0.023-0.00152.959-0.001-0.0010.0000.0000.0000.000
128A142LEU0-0.012-0.02152.7670.0000.0000.0000.0000.0000.000
129A143ASP-1-0.900-0.95256.5720.0590.0590.0000.0000.0000.000
130A144THR0-0.048-0.04359.090-0.002-0.0020.0000.0000.0000.000
131A145VAL0-0.025-0.00555.1300.0000.0000.0000.0000.0000.000
132A146ASN0-0.023-0.03957.6960.0010.0010.0000.0000.0000.000
133A147ASN0-0.035-0.01660.382-0.003-0.0030.0000.0000.0000.000
134A148VAL00.0460.04160.311-0.002-0.0020.0000.0000.0000.000
135A149PHE00.0140.00456.1060.0000.0000.0000.0000.0000.000
136A150LYS10.7830.86561.902-0.051-0.0510.0000.0000.0000.000
137A151LYS10.8390.93764.717-0.051-0.0510.0000.0000.0000.000
138A152TYR0-0.014-0.00459.3720.0000.0000.0000.0000.0000.000
139A153GLN00.0740.03863.8300.0000.0000.0000.0000.0000.000
140A154TYR00.0480.00362.9190.0020.0020.0000.0000.0000.000
141A155GLN0-0.052-0.02362.0300.0010.0010.0000.0000.0000.000
142A156ASN0-0.064-0.03359.7520.0010.0010.0000.0000.0000.000
143A157ARG10.9790.98958.230-0.058-0.0580.0000.0000.0000.000
144A158ARG10.9410.97951.567-0.077-0.0770.0000.0000.0000.000
145A159ALA00.0460.02252.0730.0030.0030.0000.0000.0000.000
146A160LEU00.0320.03352.3150.0030.0030.0000.0000.0000.000
147A161GLU-1-0.814-0.91053.5090.0770.0770.0000.0000.0000.000
148A162HIS0-0.038-0.01645.427-0.002-0.0020.0000.0000.0000.000
149A163GLN00.0200.00447.5510.0070.0070.0000.0000.0000.000
150A164LYS10.8640.93649.448-0.071-0.0710.0000.0000.0000.000
151A165LYS10.9020.95348.140-0.088-0.0880.0000.0000.0000.000
152A166GLU-1-0.776-0.86843.5420.1220.1220.0000.0000.0000.000
153A167PHE00.0820.03845.5190.0040.0040.0000.0000.0000.000
154A168VAL00.0180.00747.2170.0010.0010.0000.0000.0000.000
155A169LYS10.7860.87642.433-0.119-0.1190.0000.0000.0000.000
156A170TYR00.0280.00739.8380.0060.0060.0000.0000.0000.000
157A171SER00.0110.02243.7230.0010.0010.0000.0000.0000.000
158A172LYS10.9190.94944.309-0.093-0.0930.0000.0000.0000.000
159A173SER00.0350.01939.4600.0030.0030.0000.0000.0000.000
160A174PHE00.0220.03141.1150.0030.0030.0000.0000.0000.000
161A175SER0-0.006-0.01243.128-0.002-0.0020.0000.0000.0000.000
162A176ASP-1-0.869-0.93440.2800.1080.1080.0000.0000.0000.000
163A177THR0-0.058-0.05338.1880.0070.0070.0000.0000.0000.000
164A178LEU00.0150.01640.1260.0010.0010.0000.0000.0000.000
165A179LYS10.8340.91141.720-0.100-0.1000.0000.0000.0000.000
166A180THR0-0.003-0.00736.641-0.001-0.0010.0000.0000.0000.000
167A181TYR00.0390.04038.2440.0010.0010.0000.0000.0000.000
168A182PHE0-0.029-0.02539.965-0.002-0.0020.0000.0000.0000.000
169A183LYS10.9050.96238.224-0.103-0.1030.0000.0000.0000.000
170A184ASP-1-0.853-0.91134.0900.1590.1590.0000.0000.0000.000
171A185GLY00.0300.02636.603-0.002-0.0020.0000.0000.0000.000
172A186LYS10.7990.87730.955-0.175-0.1750.0000.0000.0000.000
173A187ALA00.0560.02136.2550.0030.0030.0000.0000.0000.000
174A188ILE00.0470.02332.254-0.002-0.0020.0000.0000.0000.000
175A189ASN00.0050.00834.3070.0070.0070.0000.0000.0000.000
176A190VAL00.0330.01436.653-0.001-0.0010.0000.0000.0000.000
177A191PHE00.0540.02539.077-0.001-0.0010.0000.0000.0000.000
178A192VAL00.0290.00734.989-0.002-0.0020.0000.0000.0000.000
179A193SER0-0.059-0.03738.357-0.003-0.0030.0000.0000.0000.000
180A194ALA00.0360.01440.210-0.004-0.0040.0000.0000.0000.000
181A195ASN00.0350.03239.866-0.010-0.0100.0000.0000.0000.000
182A196ARG10.9340.96233.765-0.178-0.1780.0000.0000.0000.000
183A197LEU0-0.017-0.00541.783-0.003-0.0030.0000.0000.0000.000
184A198ILE00.0330.01645.072-0.004-0.0040.0000.0000.0000.000
185A199HIS00.0040.00443.365-0.004-0.0040.0000.0000.0000.000
186A200GLN00.012-0.00442.559-0.007-0.0070.0000.0000.0000.000
187A201THR0-0.043-0.01446.595-0.004-0.0040.0000.0000.0000.000
188A202ASN00.0830.04347.464-0.008-0.0080.0000.0000.0000.000
189A203LEU00.0380.02844.474-0.003-0.0030.0000.0000.0000.000
190A204ILE0-0.068-0.01749.110-0.003-0.0030.0000.0000.0000.000
191A205LEU00.0490.02552.000-0.003-0.0030.0000.0000.0000.000
192A206GLN00.0510.04049.0680.0000.0000.0000.0000.0000.000
193A207THR0-0.052-0.02251.025-0.001-0.0010.0000.0000.0000.000
194A208PHE0-0.016-0.03253.332-0.002-0.0020.0000.0000.0000.000
195A209LYS10.8640.94656.101-0.073-0.0730.0000.0000.0000.000
196A210THR0-0.056-0.03654.094-0.002-0.0020.0000.0000.0000.000
197A211VAL0-0.075-0.03355.766-0.001-0.0010.0000.0000.0000.000
198A212ALA0-0.0300.00558.346-0.003-0.0030.0000.0000.0000.000