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: R9Z28

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 OptAll
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 -2595909.950164
FMO2-HF: Nuclear repulsion 2504430.134587
FMO2-HF: Total energy -91479.815577
FMO2-MP2: Total energy -91744.657183


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.
-2.2640.21-0.012-1.219-1.2430.004
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 : -0.013 / 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].
3A4LYS10.9230.9733.813-2.593-0.275-0.011-1.185-1.1220.004
4A5LEU00.0350.0205.672-0.438-0.4380.0000.0000.0000.000
5A6ILE0-0.056-0.0299.3980.3280.3280.0000.0000.0000.000
6A7LEU00.013-0.00212.454-0.118-0.1180.0000.0000.0000.000
7A8ASN0-0.0300.00215.7440.0480.0480.0000.0000.0000.000
8A20ALA00.0220.0145.0480.1150.1150.0000.0000.0000.000
9A21VAL0-0.041-0.0375.409-0.420-0.4200.0000.0000.0000.000
10A22ASP-1-0.828-0.8957.236-1.162-1.1620.0000.0000.0000.000
11A23ALA00.0830.0398.044-0.124-0.1240.0000.0000.0000.000
12A24ALA00.0340.0258.9960.1530.1530.0000.0000.0000.000
13A25THR0-0.082-0.0669.5430.1580.1580.0000.0000.0000.000
14A26ALA0-0.025-0.0156.8680.1190.1190.0000.0000.0000.000
15A27GLU-1-0.791-0.8708.698-0.201-0.2010.0000.0000.0000.000
16A28LYS10.8860.94611.9730.6010.6010.0000.0000.0000.000
17A29VAL0-0.050-0.0329.9440.0950.0950.0000.0000.0000.000
18A30PHE00.0060.0056.3880.1170.1170.0000.0000.0000.000
19A31LYS10.8750.94012.4400.3430.3430.0000.0000.0000.000
20A32GLN0-0.013-0.00415.563-0.003-0.0030.0000.0000.0000.000
21A33TYR0-0.054-0.02613.7550.0370.0370.0000.0000.0000.000
22A34ALA00.0020.00415.7400.0390.0390.0000.0000.0000.000
23A35ASN0-0.007-0.00817.4760.0130.0130.0000.0000.0000.000
24A36ASP-1-0.911-0.94118.522-0.046-0.0460.0000.0000.0000.000
25A37ASN0-0.040-0.03217.5640.0570.0570.0000.0000.0000.000
26A38GLY00.0310.00620.4400.0170.0170.0000.0000.0000.000
27A39VAL0-0.042-0.02519.0990.0070.0070.0000.0000.0000.000
28A40ASP-1-0.897-0.95920.582-0.095-0.0950.0000.0000.0000.000
29A41GLY0-0.0050.00120.6620.0170.0170.0000.0000.0000.000
30A42GLU-1-0.879-0.94520.260-0.066-0.0660.0000.0000.0000.000
31A43TRP00.0010.01113.7240.0010.0010.0000.0000.0000.000
32A44THR0-0.016-0.00216.363-0.013-0.0130.0000.0000.0000.000
33A45TYR0-0.047-0.05411.7500.0200.0200.0000.0000.0000.000
34A46ASP-1-0.771-0.85311.533-0.047-0.0470.0000.0000.0000.000
35A47ASP-1-0.860-0.9269.438-1.458-1.4580.0000.0000.0000.000
36A48ALA0-0.036-0.0149.039-0.244-0.2440.0000.0000.0000.000
37A49THR0-0.082-0.0777.9160.0270.0270.0000.0000.0000.000
38A50LYS10.7710.8994.1312.1192.275-0.001-0.034-0.1210.000
39A51THR0-0.006-0.0146.0390.1290.1290.0000.0000.0000.000
40A52PHE00.002-0.0108.179-0.146-0.1460.0000.0000.0000.000
41A53THR0-0.076-0.04011.0290.2100.2100.0000.0000.0000.000
42A54VAL00.0310.01913.971-0.078-0.0780.0000.0000.0000.000
43A55THR0-0.032-0.03316.9390.0540.0540.0000.0000.0000.000
44A56GLU-1-0.952-0.98420.1000.0590.0590.0000.0000.0000.000
45A57LEU0-0.0070.01123.1860.0140.0140.0000.0000.0000.000
46A58GLU-1-0.843-0.94423.5200.0460.0460.0000.0000.0000.000
47A59VAL0-0.040-0.02325.649-0.003-0.0030.0000.0000.0000.000
48A60LEU0-0.0330.00324.521-0.011-0.0110.0000.0000.0000.000
49A61PHE0-0.0260.00427.582-0.002-0.0020.0000.0000.0000.000
50A62GLN0-0.0050.01223.4720.0000.0000.0000.0000.0000.000
51A63GLY00.0740.01622.3090.0060.0060.0000.0000.0000.000
52A64PRO0-0.082-0.05818.3920.0060.0060.0000.0000.0000.000
53A65LEU0-0.0300.04721.4820.0140.0140.0000.0000.0000.000
54A66ASP-1-0.873-0.96524.5080.1070.1070.0000.0000.0000.000
55A67PRO0-0.0120.01725.3930.0130.0130.0000.0000.0000.000
56A68ASN0-0.004-0.02227.2760.0080.0080.0000.0000.0000.000
57A69SER0-0.041-0.01626.684-0.002-0.0020.0000.0000.0000.000
58A101MET00.0410.05719.452-0.013-0.0130.0000.0000.0000.000
59A102ALA0-0.008-0.02124.6810.0000.0000.0000.0000.0000.000
60A103THR0-0.058-0.06026.647-0.004-0.0040.0000.0000.0000.000
61A104TYR00.000-0.00420.082-0.012-0.0120.0000.0000.0000.000
62A105GLU-1-0.767-0.86322.2200.1380.1380.0000.0000.0000.000
63A106VAL00.0010.00325.133-0.006-0.0060.0000.0000.0000.000
64A107LEU0-0.0080.00026.831-0.007-0.0070.0000.0000.0000.000
65A108CYS0-0.034-0.01922.831-0.011-0.0110.0000.0000.0000.000
66A109GLU-1-0.777-0.88725.0410.0770.0770.0000.0000.0000.000
67A110VAL0-0.025-0.01727.331-0.007-0.0070.0000.0000.0000.000
68A111ALA0-0.014-0.00925.665-0.006-0.0060.0000.0000.0000.000
69A112ARG10.7160.82221.806-0.108-0.1080.0000.0000.0000.000
70A113LYS10.8060.90126.232-0.071-0.0710.0000.0000.0000.000
71A114LEU0-0.0030.01529.487-0.002-0.0020.0000.0000.0000.000
72A115GLY00.0490.02830.232-0.001-0.0010.0000.0000.0000.000
73A116THR0-0.056-0.07330.435-0.002-0.0020.0000.0000.0000.000
74A117ASP-1-0.849-0.90631.977-0.022-0.0220.0000.0000.0000.000
75A118ASP-1-0.793-0.89733.8030.0000.0000.0000.0000.0000.000
76A119ARG10.8290.90327.5470.0240.0240.0000.0000.0000.000
77A120GLU-1-0.726-0.82332.351-0.040-0.0400.0000.0000.0000.000
78A121VAL00.0280.01434.733-0.001-0.0010.0000.0000.0000.000
79A122VAL00.006-0.01832.4930.0000.0000.0000.0000.0000.000
80A123LEU0-0.029-0.02629.2940.0000.0000.0000.0000.0000.000
81A124PHE0-0.0270.01333.780-0.002-0.0020.0000.0000.0000.000
82A125LEU0-0.011-0.00237.3180.0000.0000.0000.0000.0000.000
83A126LEU0-0.025-0.03032.7720.0010.0010.0000.0000.0000.000
84A127ASN00.0110.02335.059-0.004-0.0040.0000.0000.0000.000
85A128VAL0-0.021-0.00730.255-0.004-0.0040.0000.0000.0000.000
86A129PHE0-0.002-0.00131.9020.0000.0000.0000.0000.0000.000
87A130ILE0-0.032-0.01727.064-0.007-0.0070.0000.0000.0000.000
88A131PRO00.0070.01131.1390.0050.0050.0000.0000.0000.000
89A132GLN0-0.070-0.06230.426-0.006-0.0060.0000.0000.0000.000
90A133PRO0-0.0080.03927.504-0.007-0.0070.0000.0000.0000.000
91A134THR00.036-0.00422.3320.0100.0100.0000.0000.0000.000
92A135LEU00.0540.01022.5110.0010.0010.0000.0000.0000.000
93A136ALA00.0030.00719.3620.0080.0080.0000.0000.0000.000
94A137GLN00.0180.01021.1040.0040.0040.0000.0000.0000.000
95A138LEU00.0110.01923.9060.0030.0030.0000.0000.0000.000
96A139ILE00.003-0.00621.0810.0050.0050.0000.0000.0000.000
97A140GLY00.0130.01422.2730.0070.0070.0000.0000.0000.000
98A141ALA00.0260.01222.9370.0020.0020.0000.0000.0000.000
99A142LEU0-0.007-0.00826.5710.0040.0040.0000.0000.0000.000
100A143ARG10.8440.91120.731-0.014-0.0140.0000.0000.0000.000
101A144ALA00.0250.00925.0000.0030.0030.0000.0000.0000.000
102A145LEU00.0210.00826.1010.0030.0030.0000.0000.0000.000
103A146LYS10.8150.90726.718-0.025-0.0250.0000.0000.0000.000
104A147GLU-1-0.737-0.86223.7980.0310.0310.0000.0000.0000.000
105A148GLU-1-0.846-0.90327.400-0.046-0.0460.0000.0000.0000.000
106A149GLY0-0.0230.00130.3070.0000.0000.0000.0000.0000.000
107A150ARG10.7960.87332.4770.0370.0370.0000.0000.0000.000
108A151LEU0-0.044-0.01630.3180.0030.0030.0000.0000.0000.000
109A152THR00.0280.01233.3930.0050.0050.0000.0000.0000.000
110A153PHE00.0380.01134.572-0.001-0.0010.0000.0000.0000.000
111A154PRO00.011-0.00936.4320.0000.0000.0000.0000.0000.000
112A155LEU00.0180.03736.221-0.001-0.0010.0000.0000.0000.000
113A156LEU00.0230.00932.516-0.002-0.0020.0000.0000.0000.000
114A157ALA00.0360.01036.1130.0000.0000.0000.0000.0000.000
115A158GLU-1-0.748-0.83138.7720.0020.0020.0000.0000.0000.000
116A159CYS0-0.066-0.00735.735-0.002-0.0020.0000.0000.0000.000
117A160LEU00.0340.00734.039-0.001-0.0010.0000.0000.0000.000
118A161PHE0-0.047-0.02738.0170.0000.0000.0000.0000.0000.000
119A162ARG10.8270.89441.743-0.003-0.0030.0000.0000.0000.000
120A163ALA00.0270.02137.986-0.002-0.0020.0000.0000.0000.000
121A164GLY00.0210.01940.0190.0000.0000.0000.0000.0000.000
122A165ARG10.7490.86734.103-0.015-0.0150.0000.0000.0000.000
123A166ARG10.8470.86438.631-0.013-0.0130.0000.0000.0000.000
124A167ASP-1-0.819-0.88336.9210.0280.0280.0000.0000.0000.000
125A168LEU00.0470.02632.9680.0050.0050.0000.0000.0000.000
126A169LEU0-0.049-0.01536.2900.0040.0040.0000.0000.0000.000
127A170ARG10.7980.89938.835-0.044-0.0440.0000.0000.0000.000
128A171ASP-1-0.891-0.94133.6550.0630.0630.0000.0000.0000.000
129A172LEU0-0.039-0.01130.9740.0060.0060.0000.0000.0000.000
130A173LEU0-0.047-0.01834.1190.0030.0030.0000.0000.0000.000
131A174HIS00.0160.01035.479-0.004-0.0040.0000.0000.0000.000
132A175LEU00.0420.04239.176-0.001-0.0010.0000.0000.0000.000
133A176ASP-1-0.804-0.90241.9910.0270.0270.0000.0000.0000.000
134A177PRO00.0100.00042.943-0.002-0.0020.0000.0000.0000.000
135A178ARG10.8760.91545.288-0.020-0.0200.0000.0000.0000.000
136A179PHE0-0.035-0.02645.547-0.002-0.0020.0000.0000.0000.000
137A180LEU00.0410.01842.059-0.002-0.0020.0000.0000.0000.000
138A181GLU-1-0.787-0.86346.5310.0130.0130.0000.0000.0000.000
139A182ARG10.9090.95848.949-0.021-0.0210.0000.0000.0000.000
140A183HIS0-0.0080.00646.9160.0000.0000.0000.0000.0000.000
141A184LEU0-0.016-0.01544.828-0.001-0.0010.0000.0000.0000.000
142A185ALA0-0.046-0.00649.347-0.002-0.0020.0000.0000.0000.000
143A186GLY0-0.033-0.01252.501-0.001-0.0010.0000.0000.0000.000
144A187THR0-0.065-0.03348.1910.0000.0000.0000.0000.0000.000
145A188MET0-0.046-0.01248.8790.0000.0000.0000.0000.0000.000
146A189SER0-0.010-0.03245.7560.0000.0000.0000.0000.0000.000
147A190TYR0-0.013-0.02941.9190.0000.0000.0000.0000.0000.000
148A191PHE0-0.012-0.00439.073-0.002-0.0020.0000.0000.0000.000
149A192SER00.0400.01744.2960.0010.0010.0000.0000.0000.000
150A193PRO00.0490.00346.7710.0000.0000.0000.0000.0000.000
151A194TYR0-0.012-0.01843.7800.0010.0010.0000.0000.0000.000
152A195GLN00.0060.00440.4850.0010.0010.0000.0000.0000.000
153A196LEU0-0.007-0.00744.7240.0010.0010.0000.0000.0000.000
154A197THR0-0.002-0.01546.7580.0010.0010.0000.0000.0000.000
155A198VAL0-0.020-0.00543.3130.0000.0000.0000.0000.0000.000
156A199LEU0-0.010-0.00741.6570.0000.0000.0000.0000.0000.000
157A200HIS0-0.040-0.01644.4150.0010.0010.0000.0000.0000.000
158A201VAL0-0.020-0.01947.6750.0000.0000.0000.0000.0000.000
159A202ASP-1-0.890-0.96841.403-0.019-0.0190.0000.0000.0000.000
160A203GLY0-0.0120.00844.6820.0000.0000.0000.0000.0000.000
161A204GLU-1-0.924-0.95045.654-0.003-0.0030.0000.0000.0000.000
162A205LEU0-0.028-0.00446.4180.0000.0000.0000.0000.0000.000
163A206CYS0-0.065-0.02647.1380.0010.0010.0000.0000.0000.000
164A207ALA00.0450.00244.506-0.002-0.0020.0000.0000.0000.000
165A208ARG10.8800.91545.5390.0100.0100.0000.0000.0000.000
166A209ASP-1-0.717-0.83648.271-0.015-0.0150.0000.0000.0000.000
167A210ILE00.0820.04342.100-0.002-0.0020.0000.0000.0000.000
168A211ARG10.9390.97142.5190.0180.0180.0000.0000.0000.000
169A212SER0-0.005-0.00545.273-0.002-0.0020.0000.0000.0000.000
170A213LEU00.0190.01544.350-0.001-0.0010.0000.0000.0000.000
171A214ILE00.0050.01240.703-0.002-0.0020.0000.0000.0000.000
172A215PHE0-0.050-0.03544.245-0.003-0.0030.0000.0000.0000.000
173A216LEU00.0320.00046.975-0.001-0.0010.0000.0000.0000.000
174A217SER0-0.026-0.01343.722-0.002-0.0020.0000.0000.0000.000
175A218LYS10.8640.95345.0340.0330.0330.0000.0000.0000.000
176A219ASP-1-0.918-0.94846.165-0.036-0.0360.0000.0000.0000.000
177A220THR0-0.078-0.04345.7950.0000.0000.0000.0000.0000.000
178A221ILE0-0.0250.00439.894-0.003-0.0030.0000.0000.0000.000
179A222GLY00.0460.00940.6100.0010.0010.0000.0000.0000.000
180A223SER0-0.045-0.04337.973-0.002-0.0020.0000.0000.0000.000
181A224ARG10.9200.97532.6590.0800.0800.0000.0000.0000.000
182A225SER00.009-0.01432.639-0.003-0.0030.0000.0000.0000.000
183A226THR00.0250.03235.7630.0010.0010.0000.0000.0000.000
184A227PRO00.0340.02737.001-0.002-0.0020.0000.0000.0000.000
185A228GLN0-0.071-0.04834.6440.0020.0020.0000.0000.0000.000
186A229THR0-0.005-0.03036.9650.0020.0020.0000.0000.0000.000
187A230PHE00.0200.00039.723-0.002-0.0020.0000.0000.0000.000
188A231LEU00.0610.03838.383-0.002-0.0020.0000.0000.0000.000
189A232HIS0-0.027-0.01635.291-0.005-0.0050.0000.0000.0000.000
190A233TRP0-0.007-0.01338.244-0.003-0.0030.0000.0000.0000.000
191A234VAL00.0040.00941.656-0.001-0.0010.0000.0000.0000.000
192A235TYR00.0800.04433.403-0.004-0.0040.0000.0000.0000.000
193A236CYS0-0.082-0.03539.097-0.004-0.0040.0000.0000.0000.000
194A237MET0-0.001-0.00340.368-0.002-0.0020.0000.0000.0000.000
195A238GLU-1-0.815-0.88340.691-0.034-0.0340.0000.0000.0000.000
196A239ASN0-0.091-0.05636.887-0.004-0.0040.0000.0000.0000.000
197A240LEU0-0.093-0.04340.626-0.002-0.0020.0000.0000.0000.000
198A241ASP-1-0.957-0.96443.849-0.039-0.0390.0000.0000.0000.000
199A242LEU0-0.043-0.01945.9020.0020.0020.0000.0000.0000.000
200A243LEU0-0.072-0.04245.8110.0030.0030.0000.0000.0000.000
201A244GLY00.0630.03245.888-0.002-0.0020.0000.0000.0000.000
202A245PRO0-0.052-0.04445.4720.0020.0020.0000.0000.0000.000
203A246THR0-0.007-0.00148.4360.0010.0010.0000.0000.0000.000
204A247ASP-1-0.893-0.93450.685-0.024-0.0240.0000.0000.0000.000
205A248VAL00.0790.02949.621-0.001-0.0010.0000.0000.0000.000
206A249ASP-1-0.773-0.86951.859-0.019-0.0190.0000.0000.0000.000
207A250ALA00.0780.05050.1210.0000.0000.0000.0000.0000.000
208A251LEU00.0120.01348.1450.0000.0000.0000.0000.0000.000
209A252MET0-0.059-0.02750.4290.0020.0020.0000.0000.0000.000
210A253SER0-0.041-0.03152.7550.0010.0010.0000.0000.0000.000
211A254MET00.0560.05547.6920.0010.0010.0000.0000.0000.000
212A255LEU0-0.010-0.01150.2970.0010.0010.0000.0000.0000.000
213A256ARG10.7130.81853.3500.0200.0200.0000.0000.0000.000
214A257SER0-0.052-0.03553.9130.0000.0000.0000.0000.0000.000
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216A259SER0-0.041-0.02054.0250.0010.0010.0000.0000.0000.000
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