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: Z6J8N

Calculation Name: 5LDE-A-Xray372

Preferred Name: NF-kappa-B essential modulator

Target Type: SINGLE PROTEIN

Ligand Name: l-isovaline

ligand 3-letter code: 6ZS

PDB ID: 5LDE

Chain ID: A

ChEMBL ID: CHEMBL4967

UniProt ID: Q9Y6K9

Base Structure: X-ray

Registration Date: 2023-09-20

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2588014.718198
FMO2-HF: Nuclear repulsion 2496536.265546
FMO2-HF: Total energy -91478.452652
FMO2-MP2: Total energy -91743.366224


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:2:GLN)


Summations of interaction energy for fragment #1(A:2:GLN)
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.
-2.45-0.117-0.025-1.012-1.2970.005
Interaction energy analysis for fragmet #1(A:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.007
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].
3A4LYS10.9400.9783.838-1.9490.095-0.022-0.979-1.0430.005
4A5LEU00.0410.0145.870-0.209-0.2090.0000.0000.0000.000
5A6ILE0-0.060-0.0329.6170.1740.1740.0000.0000.0000.000
6A7LEU00.018-0.00212.402-0.075-0.0750.0000.0000.0000.000
7A8ASN0-0.0120.00615.5350.0660.0660.0000.0000.0000.000
8A20ALA00.0140.0104.625-0.131-0.065-0.001-0.005-0.0600.000
9A21VAL0-0.045-0.0354.8790.0050.087-0.001-0.001-0.0800.000
10A22ASP-1-0.832-0.9047.178-0.991-0.9910.0000.0000.0000.000
11A23ALA00.0620.0207.442-0.200-0.2000.0000.0000.0000.000
12A24ALA00.0440.0288.2590.0850.0850.0000.0000.0000.000
13A25THR0-0.069-0.0549.1030.1400.1400.0000.0000.0000.000
14A26ALA0-0.028-0.0246.3410.0790.0790.0000.0000.0000.000
15A27GLU-1-0.791-0.8688.362-0.476-0.4760.0000.0000.0000.000
16A28LYS10.9000.95211.6160.7230.7230.0000.0000.0000.000
17A29VAL0-0.061-0.0379.4410.1030.1030.0000.0000.0000.000
18A30PHE00.0100.0036.0740.1040.1040.0000.0000.0000.000
19A31LYS10.8710.93812.0610.5620.5620.0000.0000.0000.000
20A32GLN0-0.022-0.00815.1940.0230.0230.0000.0000.0000.000
21A33TYR0-0.050-0.02413.4140.0190.0190.0000.0000.0000.000
22A34ALA0-0.0050.00815.4140.0400.0400.0000.0000.0000.000
23A35ASN00.0140.00017.6220.0300.0300.0000.0000.0000.000
24A36ASP-1-0.923-0.94318.164-0.282-0.2820.0000.0000.0000.000
25A37ASN0-0.028-0.02817.4320.0420.0420.0000.0000.0000.000
26A38GLY00.022-0.00920.4600.0270.0270.0000.0000.0000.000
27A39VAL0-0.024-0.02219.2530.0110.0110.0000.0000.0000.000
28A40ASP-1-0.970-0.98820.906-0.252-0.2520.0000.0000.0000.000
29A41GLY0-0.0260.00820.3220.0230.0230.0000.0000.0000.000
30A42GLU-1-0.897-0.96220.577-0.201-0.2010.0000.0000.0000.000
31A43TRP00.0140.00513.296-0.045-0.0450.0000.0000.0000.000
32A44THR00.0030.00715.9540.0140.0140.0000.0000.0000.000
33A45TYR0-0.056-0.04411.4150.0070.0070.0000.0000.0000.000
34A46ASP-1-0.795-0.86311.531-0.041-0.0410.0000.0000.0000.000
35A47ASP-1-0.878-0.9539.936-1.253-1.2530.0000.0000.0000.000
36A48ALA0-0.0190.0029.364-0.179-0.1790.0000.0000.0000.000
37A49THR0-0.081-0.0848.4570.0350.0350.0000.0000.0000.000
38A50LYS10.7790.9084.5011.7131.854-0.001-0.027-0.1140.000
39A51THR0-0.005-0.0125.515-0.101-0.1010.0000.0000.0000.000
40A52PHE00.0090.0048.021-0.029-0.0290.0000.0000.0000.000
41A53THR0-0.073-0.03611.0700.1060.1060.0000.0000.0000.000
42A54VAL00.0590.05213.911-0.044-0.0440.0000.0000.0000.000
43A55THR0-0.072-0.05816.8440.0370.0370.0000.0000.0000.000
44A56GLU-1-0.876-0.95920.403-0.059-0.0590.0000.0000.0000.000
45A57LEU0-0.0130.01523.5080.0100.0100.0000.0000.0000.000
46A58GLU-1-0.895-0.96623.897-0.098-0.0980.0000.0000.0000.000
47A59VAL0-0.021-0.01425.7610.0110.0110.0000.0000.0000.000
48A60LEU0-0.0180.01924.176-0.009-0.0090.0000.0000.0000.000
49A61PHE0-0.0150.01127.2830.0080.0080.0000.0000.0000.000
50A62GLN0-0.068-0.02823.0910.0180.0180.0000.0000.0000.000
51A63GLY00.0980.02722.360-0.008-0.0080.0000.0000.0000.000
52A64PRO0-0.078-0.05318.4950.0170.0170.0000.0000.0000.000
53A65LEU0-0.0320.06021.6000.0120.0120.0000.0000.0000.000
54A66ASP-1-0.835-0.95724.667-0.043-0.0430.0000.0000.0000.000
55A67PRO0-0.0200.01525.2240.0070.0070.0000.0000.0000.000
56A68ASN00.0540.01826.675-0.001-0.0010.0000.0000.0000.000
57A69SER0-0.066-0.00927.2310.0010.0010.0000.0000.0000.000
58A101MET00.0170.03219.087-0.023-0.0230.0000.0000.0000.000
59A102ALA0-0.054-0.05324.0520.0010.0010.0000.0000.0000.000
60A103THR0-0.065-0.05926.3140.0060.0060.0000.0000.0000.000
61A104TYR0-0.002-0.01019.705-0.006-0.0060.0000.0000.0000.000
62A105GLU-1-0.791-0.88422.253-0.045-0.0450.0000.0000.0000.000
63A106VAL00.0040.00225.1090.0030.0030.0000.0000.0000.000
64A107LEU0-0.005-0.00825.8540.0010.0010.0000.0000.0000.000
65A108CYS0-0.043-0.02122.316-0.012-0.0120.0000.0000.0000.000
66A109GLU-1-0.787-0.89324.417-0.027-0.0270.0000.0000.0000.000
67A110VAL0-0.034-0.01926.7350.0030.0030.0000.0000.0000.000
68A111ALA0-0.009-0.00825.4590.0010.0010.0000.0000.0000.000
69A112ARG10.7620.85021.0620.0530.0530.0000.0000.0000.000
70A113LYS10.8700.95425.7810.0240.0240.0000.0000.0000.000
71A114LEU0-0.0200.00829.1430.0040.0040.0000.0000.0000.000
72A115GLY00.0350.01329.7460.0050.0050.0000.0000.0000.000
73A116THR0-0.049-0.06830.2270.0000.0000.0000.0000.0000.000
74A117ASP-1-0.839-0.90331.511-0.068-0.0680.0000.0000.0000.000
75A118ASP-1-0.782-0.88333.636-0.053-0.0530.0000.0000.0000.000
76A119ARG10.8360.90026.8780.1000.1000.0000.0000.0000.000
77A120GLU-1-0.740-0.83431.571-0.090-0.0900.0000.0000.0000.000
78A121VAL00.0540.03733.905-0.002-0.0020.0000.0000.0000.000
79A122VAL00.009-0.01031.8210.0000.0000.0000.0000.0000.000
80A123LEU0-0.028-0.03028.376-0.002-0.0020.0000.0000.0000.000
81A124PHE0-0.0270.01332.785-0.002-0.0020.0000.0000.0000.000
82A125LEU0-0.011-0.01236.3240.0010.0010.0000.0000.0000.000
83A126LEU0-0.052-0.03132.3860.0020.0020.0000.0000.0000.000
84A127ASN0-0.019-0.00933.824-0.012-0.0120.0000.0000.0000.000
85A128VAL00.0130.01229.5210.0010.0010.0000.0000.0000.000
86A129PHE00.0300.02831.580-0.003-0.0030.0000.0000.0000.000
87A130ILE0-0.044-0.02826.155-0.005-0.0050.0000.0000.0000.000
88A131PRO00.005-0.00430.3590.0050.0050.0000.0000.0000.000
89A132GLN0-0.070-0.04730.123-0.005-0.0050.0000.0000.0000.000
90A133PRO0-0.0100.03426.922-0.010-0.0100.0000.0000.0000.000
91A134THR00.022-0.01322.0740.0070.0070.0000.0000.0000.000
92A135LEU00.0320.00421.858-0.002-0.0020.0000.0000.0000.000
93A136ALA00.0180.00318.4820.0020.0020.0000.0000.0000.000
94A137GLN0-0.0080.00920.226-0.011-0.0110.0000.0000.0000.000
95A138LEU00.0380.02423.0810.0000.0000.0000.0000.0000.000
96A139ILE0-0.015-0.01820.5530.0040.0040.0000.0000.0000.000
97A140GLY00.0150.01321.2620.0010.0010.0000.0000.0000.000
98A141ALA00.0340.01521.9090.0000.0000.0000.0000.0000.000
99A142LEU0-0.004-0.00925.5750.0080.0080.0000.0000.0000.000
100A143ARG10.8460.91820.5490.1980.1980.0000.0000.0000.000
101A144ALA00.0200.01324.171-0.001-0.0010.0000.0000.0000.000
102A145LEU00.0300.01725.3810.0070.0070.0000.0000.0000.000
103A146LYS10.8200.89026.7820.1220.1220.0000.0000.0000.000
104A147GLU-1-0.763-0.88223.690-0.144-0.1440.0000.0000.0000.000
105A148GLU-1-0.899-0.93527.071-0.145-0.1450.0000.0000.0000.000
106A149GLY0-0.040-0.00929.6860.0060.0060.0000.0000.0000.000
107A150ARG10.8720.93932.4390.1160.1160.0000.0000.0000.000
108A151LEU0-0.038-0.01429.9380.0080.0080.0000.0000.0000.000
109A152THR00.0420.01833.2340.0030.0030.0000.0000.0000.000
110A153PHE00.0470.01334.1000.0000.0000.0000.0000.0000.000
111A154PRO00.009-0.01636.1100.0010.0010.0000.0000.0000.000
112A155LEU00.0110.03735.8470.0020.0020.0000.0000.0000.000
113A156LEU00.0170.00432.2030.0000.0000.0000.0000.0000.000
114A157ALA00.0320.01235.8330.0020.0020.0000.0000.0000.000
115A158GLU-1-0.721-0.82338.570-0.045-0.0450.0000.0000.0000.000
116A159CYS0-0.058-0.01635.0550.0010.0010.0000.0000.0000.000
117A160LEU00.0350.01033.6570.0000.0000.0000.0000.0000.000
118A161PHE0-0.061-0.03337.4380.0030.0030.0000.0000.0000.000
119A162ARG10.8140.88340.9540.0440.0440.0000.0000.0000.000
120A163ALA00.0250.02137.2320.0010.0010.0000.0000.0000.000
121A164GLY00.0340.03139.2560.0010.0010.0000.0000.0000.000
122A165ARG10.7600.87333.6530.0460.0460.0000.0000.0000.000
123A166ARG10.8600.88938.3940.0250.0250.0000.0000.0000.000
124A167ASP-1-0.834-0.89836.747-0.028-0.0280.0000.0000.0000.000
125A168LEU00.0540.02732.8180.0030.0030.0000.0000.0000.000
126A169LEU0-0.050-0.00535.9640.0010.0010.0000.0000.0000.000
127A170ARG10.8760.93838.5430.0120.0120.0000.0000.0000.000
128A171ASP-1-0.961-0.98233.892-0.008-0.0080.0000.0000.0000.000
129A172LEU0-0.0190.00230.3250.0020.0020.0000.0000.0000.000
130A173LEU0-0.066-0.02833.6650.0000.0000.0000.0000.0000.000
131A174HIS00.0100.01234.7570.0020.0020.0000.0000.0000.000
132A175LEU0-0.0140.00238.8340.0020.0020.0000.0000.0000.000
133A176ASP-1-0.828-0.93341.505-0.015-0.0150.0000.0000.0000.000
134A177PRO00.0150.00142.597-0.001-0.0010.0000.0000.0000.000
135A178ARG10.8970.95145.1010.0150.0150.0000.0000.0000.000
136A179PHE0-0.037-0.02345.2160.0000.0000.0000.0000.0000.000
137A180LEU00.0380.01241.671-0.001-0.0010.0000.0000.0000.000
138A181GLU-1-0.816-0.89246.282-0.025-0.0250.0000.0000.0000.000
139A182ARG10.9130.96448.7200.0170.0170.0000.0000.0000.000
140A183HIS0-0.018-0.00246.2210.0020.0020.0000.0000.0000.000
141A184LEU0-0.016-0.01444.538-0.001-0.0010.0000.0000.0000.000
142A185ALA0-0.0440.00648.876-0.001-0.0010.0000.0000.0000.000
143A186GLY0-0.029-0.01252.6480.0000.0000.0000.0000.0000.000
144A187THR0-0.039-0.03247.8590.0000.0000.0000.0000.0000.000
145A188MET0-0.054-0.01148.2840.0010.0010.0000.0000.0000.000
146A189SER0-0.014-0.03245.369-0.002-0.0020.0000.0000.0000.000
147A190TYR00.010-0.01741.287-0.001-0.0010.0000.0000.0000.000
148A191PHE0-0.037-0.01238.517-0.003-0.0030.0000.0000.0000.000
149A192SER00.0450.01543.5370.0040.0040.0000.0000.0000.000
150A193PRO00.0520.01346.0430.0000.0000.0000.0000.0000.000
151A194TYR0-0.005-0.01343.2320.0030.0030.0000.0000.0000.000
152A195GLN0-0.0060.00139.7390.0030.0030.0000.0000.0000.000
153A196LEU00.001-0.01043.8450.0000.0000.0000.0000.0000.000
154A197THR0-0.015-0.01745.8400.0030.0030.0000.0000.0000.000
155A198VAL0-0.0030.00242.5440.0020.0020.0000.0000.0000.000
156A199LEU0-0.006-0.00241.0120.0000.0000.0000.0000.0000.000
157A200HIS0-0.026-0.00943.7850.0010.0010.0000.0000.0000.000
158A201VAL0-0.035-0.02947.1530.0020.0020.0000.0000.0000.000
159A202ASP-1-0.909-0.97641.067-0.055-0.0550.0000.0000.0000.000
160A203GLY0-0.0070.01744.3470.0000.0000.0000.0000.0000.000
161A204GLU-1-0.915-0.96445.516-0.029-0.0290.0000.0000.0000.000
162A205LEU0-0.073-0.01446.0570.0020.0020.0000.0000.0000.000
163A206CYS0-0.050-0.00146.2600.0000.0000.0000.0000.0000.000
164A207ALA00.0550.00444.041-0.002-0.0020.0000.0000.0000.000
165A208ARG10.9070.92745.0600.0260.0260.0000.0000.0000.000
166A209ASP-1-0.762-0.89247.862-0.035-0.0350.0000.0000.0000.000
167A210ILE00.0770.03941.679-0.001-0.0010.0000.0000.0000.000
168A211ARG10.9240.96342.6150.0360.0360.0000.0000.0000.000
169A212SER0-0.020-0.01144.9200.0000.0000.0000.0000.0000.000
170A213LEU00.0150.01743.5360.0000.0000.0000.0000.0000.000
171A214ILE00.0090.01940.378-0.001-0.0010.0000.0000.0000.000
172A215PHE0-0.034-0.03643.929-0.001-0.0010.0000.0000.0000.000
173A216LEU00.0440.01746.7740.0000.0000.0000.0000.0000.000
174A217SER0-0.018-0.00843.477-0.002-0.0020.0000.0000.0000.000
175A218LYS10.8650.94344.2620.0450.0450.0000.0000.0000.000
176A219ASP-1-0.916-0.93845.501-0.047-0.0470.0000.0000.0000.000
177A220THR0-0.096-0.04545.2120.0000.0000.0000.0000.0000.000
178A221ILE0-0.048-0.00539.822-0.005-0.0050.0000.0000.0000.000
179A222GLY00.0460.01840.3080.0030.0030.0000.0000.0000.000
180A223SER0-0.034-0.05537.312-0.004-0.0040.0000.0000.0000.000
181A224ARG10.9510.99232.5610.1070.1070.0000.0000.0000.000
182A225SER0-0.027-0.03232.387-0.003-0.0030.0000.0000.0000.000
183A226THR00.0490.04435.401-0.001-0.0010.0000.0000.0000.000
184A227PRO00.0160.02036.617-0.004-0.0040.0000.0000.0000.000
185A228GLN0-0.067-0.04534.1200.0060.0060.0000.0000.0000.000
186A229THR00.000-0.03236.3480.0040.0040.0000.0000.0000.000
187A230PHE00.022-0.00238.962-0.001-0.0010.0000.0000.0000.000
188A231LEU00.0730.03737.692-0.001-0.0010.0000.0000.0000.000
189A232HIS0-0.037-0.00934.748-0.007-0.0070.0000.0000.0000.000
190A233TRP0-0.004-0.02337.582-0.002-0.0020.0000.0000.0000.000
191A234VAL00.0040.00741.0350.0000.0000.0000.0000.0000.000
192A235TYR00.0610.04032.835-0.002-0.0020.0000.0000.0000.000
193A236CYS0-0.080-0.03838.302-0.004-0.0040.0000.0000.0000.000
194A237MET00.0120.00439.6520.0000.0000.0000.0000.0000.000
195A238GLU-1-0.821-0.89140.072-0.075-0.0750.0000.0000.0000.000
196A239ASN0-0.058-0.02335.965-0.002-0.0020.0000.0000.0000.000
197A240LEU0-0.081-0.04940.071-0.001-0.0010.0000.0000.0000.000
198A241ASP-1-0.971-0.95943.087-0.069-0.0690.0000.0000.0000.000
199A242LEU0-0.054-0.02745.3560.0040.0040.0000.0000.0000.000
200A243LEU0-0.074-0.03244.9730.0040.0040.0000.0000.0000.000
201A244GLY00.0870.03745.452-0.004-0.0040.0000.0000.0000.000
202A245PRO0-0.058-0.04144.9870.0030.0030.0000.0000.0000.000
203A246THR0-0.016-0.00747.9060.0020.0020.0000.0000.0000.000
204A247ASP-1-0.868-0.92050.134-0.046-0.0460.0000.0000.0000.000
205A248VAL00.0550.01049.053-0.002-0.0020.0000.0000.0000.000
206A249ASP-1-0.921-0.97051.132-0.039-0.0390.0000.0000.0000.000
207A250ALA00.0680.02649.1500.0020.0020.0000.0000.0000.000
208A251LEU0-0.0030.00947.4900.0010.0010.0000.0000.0000.000
209A252MET0-0.044-0.02449.9310.0030.0030.0000.0000.0000.000
210A253SER0-0.060-0.03451.8490.0020.0020.0000.0000.0000.000
211A254MET00.0370.03647.5620.0020.0020.0000.0000.0000.000
212A255LEU00.011-0.00649.9560.0020.0020.0000.0000.0000.000
213A256ARG10.8640.93252.8590.0380.0380.0000.0000.0000.000
214A257SER0-0.073-0.04253.4490.0010.0010.0000.0000.0000.000
215A258LEU00.0310.01448.9100.0000.0000.0000.0000.0000.000
216A259SER0-0.051-0.03353.3970.0010.0010.0000.0000.0000.000
217A260ARG10.7980.91451.0700.0340.0340.0000.0000.0000.000
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