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: 6NM2Z

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2586951.780035
FMO2-HF: Nuclear repulsion 2495474.389028
FMO2-HF: Total energy -91477.391007
FMO2-MP2: Total energy -91742.261289


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.
-0.4931.04-0.021-0.54-0.9690.001
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 : -0.023 / q_NPA : -0.034
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].
3A4LYS10.9510.9843.838-1.450-0.161-0.019-0.515-0.7540.001
4A5LEU00.0460.0135.891-0.081-0.0810.0000.0000.0000.000
5A6ILE0-0.078-0.0379.6760.0750.0750.0000.0000.0000.000
6A7LEU00.028-0.00312.427-0.041-0.0410.0000.0000.0000.000
7A8ASN00.0150.02615.6130.0150.0150.0000.0000.0000.000
8A20ALA00.0110.0074.801-0.499-0.4990.0000.0000.0000.000
9A21VAL0-0.053-0.0365.7500.9961.085-0.0010.000-0.0870.000
10A22ASP-1-0.826-0.9077.7420.3310.3310.0000.0000.0000.000
11A23ALA00.0370.0037.8780.0090.0090.0000.0000.0000.000
12A24ALA00.0520.0348.688-0.060-0.0600.0000.0000.0000.000
13A25THR0-0.060-0.04710.010-0.079-0.0790.0000.0000.0000.000
14A26ALA0-0.016-0.0156.841-0.051-0.0510.0000.0000.0000.000
15A27GLU-1-0.808-0.8848.505-0.139-0.1390.0000.0000.0000.000
16A28LYS10.9050.95711.6690.0150.0150.0000.0000.0000.000
17A29VAL0-0.053-0.0369.428-0.016-0.0160.0000.0000.0000.000
18A30PHE00.0070.0016.1740.0080.0080.0000.0000.0000.000
19A31LYS10.8940.95212.0500.0490.0490.0000.0000.0000.000
20A32GLN0-0.025-0.01615.1900.0200.0200.0000.0000.0000.000
21A33TYR0-0.034-0.00713.381-0.031-0.0310.0000.0000.0000.000
22A34ALA0-0.0010.01015.401-0.001-0.0010.0000.0000.0000.000
23A35ASN00.007-0.00117.606-0.001-0.0010.0000.0000.0000.000
24A36ASP-1-0.910-0.93818.153-0.185-0.1850.0000.0000.0000.000
25A37ASN0-0.039-0.03717.4040.0010.0010.0000.0000.0000.000
26A38GLY00.014-0.02120.4430.0080.0080.0000.0000.0000.000
27A39VAL0-0.021-0.02519.6850.0100.0100.0000.0000.0000.000
28A40ASP-1-0.993-0.99820.913-0.038-0.0380.0000.0000.0000.000
29A41GLY0-0.0060.01620.3050.0090.0090.0000.0000.0000.000
30A42GLU-1-0.927-0.97020.5600.0150.0150.0000.0000.0000.000
31A43TRP00.0120.00112.900-0.001-0.0010.0000.0000.0000.000
32A44THR00.0020.00715.4110.0060.0060.0000.0000.0000.000
33A45TYR0-0.057-0.03511.5270.0160.0160.0000.0000.0000.000
34A46ASP-1-0.840-0.91711.1510.2190.2190.0000.0000.0000.000
35A47ASP-1-0.921-0.9779.696-0.222-0.2220.0000.0000.0000.000
36A48ALA0-0.042-0.0149.155-0.109-0.1090.0000.0000.0000.000
37A49THR0-0.063-0.0458.675-0.008-0.0080.0000.0000.0000.000
38A50LYS10.8710.9594.3480.7860.941-0.001-0.025-0.1280.000
39A51THR0-0.025-0.0195.300-0.142-0.1420.0000.0000.0000.000
40A52PHE00.005-0.0037.956-0.005-0.0050.0000.0000.0000.000
41A53THR0-0.071-0.02810.9800.0470.0470.0000.0000.0000.000
42A54VAL00.0770.06613.858-0.021-0.0210.0000.0000.0000.000
43A55THR0-0.067-0.06916.8450.0050.0050.0000.0000.0000.000
44A56GLU-1-0.889-0.95020.4020.0300.0300.0000.0000.0000.000
45A57LEU0-0.0200.00223.522-0.002-0.0020.0000.0000.0000.000
46A58GLU-1-0.886-0.96423.973-0.036-0.0360.0000.0000.0000.000
47A59VAL0-0.023-0.01325.8400.0050.0050.0000.0000.0000.000
48A60LEU0-0.0340.03324.097-0.004-0.0040.0000.0000.0000.000
49A61PHE0-0.028-0.00527.4370.0020.0020.0000.0000.0000.000
50A62GLN0-0.060-0.03722.9090.0030.0030.0000.0000.0000.000
51A63GLY00.0950.02122.094-0.002-0.0020.0000.0000.0000.000
52A64PRO0-0.083-0.05918.3510.0110.0110.0000.0000.0000.000
53A65LEU0-0.0300.06221.4330.0170.0170.0000.0000.0000.000
54A66ASP-1-0.820-0.94924.789-0.026-0.0260.0000.0000.0000.000
55A67PRO0-0.0290.00424.854-0.004-0.0040.0000.0000.0000.000
56A68ASN00.0480.01826.076-0.005-0.0050.0000.0000.0000.000
57A69SER0-0.0520.00426.832-0.009-0.0090.0000.0000.0000.000
58A101MET00.0160.03718.528-0.021-0.0210.0000.0000.0000.000
59A102ALA0-0.048-0.05223.498-0.011-0.0110.0000.0000.0000.000
60A103THR0-0.066-0.05525.7460.0020.0020.0000.0000.0000.000
61A104TYR00.005-0.00719.201-0.010-0.0100.0000.0000.0000.000
62A105GLU-1-0.813-0.90022.113-0.151-0.1510.0000.0000.0000.000
63A106VAL00.0150.00224.622-0.002-0.0020.0000.0000.0000.000
64A107LEU0-0.007-0.00724.896-0.002-0.0020.0000.0000.0000.000
65A108CYS00.0030.00321.778-0.016-0.0160.0000.0000.0000.000
66A109GLU-1-0.902-0.94024.028-0.127-0.1270.0000.0000.0000.000
67A110VAL0-0.003-0.00126.3590.0020.0020.0000.0000.0000.000
68A111ALA0-0.003-0.00525.1090.0010.0010.0000.0000.0000.000
69A112ARG10.8030.86521.2770.1690.1690.0000.0000.0000.000
70A113LYS10.8630.95625.5170.1020.1020.0000.0000.0000.000
71A114LEU0-0.0100.00628.8950.0090.0090.0000.0000.0000.000
72A115GLY00.0260.01229.4660.0060.0060.0000.0000.0000.000
73A116THR0-0.034-0.05430.0720.0040.0040.0000.0000.0000.000
74A117ASP-1-0.839-0.91431.307-0.105-0.1050.0000.0000.0000.000
75A118ASP-1-0.814-0.90233.421-0.094-0.0940.0000.0000.0000.000
76A119ARG10.8240.89826.2430.1820.1820.0000.0000.0000.000
77A120GLU-1-0.750-0.85731.292-0.116-0.1160.0000.0000.0000.000
78A121VAL00.0650.04333.6590.0030.0030.0000.0000.0000.000
79A122VAL00.004-0.01531.4650.0030.0030.0000.0000.0000.000
80A123LEU0-0.032-0.02928.1750.0010.0010.0000.0000.0000.000
81A124PHE0-0.0150.01932.4790.0030.0030.0000.0000.0000.000
82A125LEU0-0.024-0.02536.0390.0050.0050.0000.0000.0000.000
83A126LEU0-0.043-0.02631.8630.0050.0050.0000.0000.0000.000
84A127ASN0-0.057-0.02033.480-0.006-0.0060.0000.0000.0000.000
85A128VAL00.0310.01029.2550.0000.0000.0000.0000.0000.000
86A129PHE00.0230.02231.289-0.007-0.0070.0000.0000.0000.000
87A130ILE0-0.028-0.02525.976-0.003-0.0030.0000.0000.0000.000
88A131PRO00.0050.00530.1670.0010.0010.0000.0000.0000.000
89A132GLN0-0.081-0.03930.004-0.013-0.0130.0000.0000.0000.000
90A133PRO00.0090.03926.712-0.015-0.0150.0000.0000.0000.000
91A134THR00.014-0.01522.1250.0010.0010.0000.0000.0000.000
92A135LEU00.0220.00221.5530.0040.0040.0000.0000.0000.000
93A136ALA00.0240.00218.2550.0070.0070.0000.0000.0000.000
94A137GLN0-0.0090.01319.9660.0020.0020.0000.0000.0000.000
95A138LEU00.0450.02422.8400.0100.0100.0000.0000.0000.000
96A139ILE0-0.027-0.02219.9210.0110.0110.0000.0000.0000.000
97A140GLY00.0120.01020.8870.0060.0060.0000.0000.0000.000
98A141ALA00.0430.02021.5520.0130.0130.0000.0000.0000.000
99A142LEU0-0.013-0.00925.2310.0150.0150.0000.0000.0000.000
100A143ARG10.8280.90920.0980.1980.1980.0000.0000.0000.000
101A144ALA00.0190.01823.8560.0070.0070.0000.0000.0000.000
102A145LEU00.0590.02524.9700.0140.0140.0000.0000.0000.000
103A146LYS10.7960.88526.1270.1130.1130.0000.0000.0000.000
104A147GLU-1-0.748-0.87223.262-0.121-0.1210.0000.0000.0000.000
105A148GLU-1-0.927-0.95126.731-0.112-0.1120.0000.0000.0000.000
106A149GLY0-0.034-0.00229.5610.0090.0090.0000.0000.0000.000
107A150ARG10.9090.95231.9840.0940.0940.0000.0000.0000.000
108A151LEU0-0.038-0.01529.4490.0040.0040.0000.0000.0000.000
109A152THR00.0380.02032.7710.0030.0030.0000.0000.0000.000
110A153PHE00.0610.01733.658-0.003-0.0030.0000.0000.0000.000
111A154PRO0-0.002-0.02135.646-0.001-0.0010.0000.0000.0000.000
112A155LEU00.0150.04035.0540.0000.0000.0000.0000.0000.000
113A156LEU00.0090.00631.775-0.002-0.0020.0000.0000.0000.000
114A157ALA00.0370.01235.376-0.002-0.0020.0000.0000.0000.000
115A158GLU-1-0.734-0.85838.167-0.057-0.0570.0000.0000.0000.000
116A159CYS0-0.051-0.01334.514-0.001-0.0010.0000.0000.0000.000
117A160LEU00.0340.00533.201-0.002-0.0020.0000.0000.0000.000
118A161PHE0-0.056-0.03337.0620.0020.0020.0000.0000.0000.000
119A162ARG10.8320.91540.5060.0570.0570.0000.0000.0000.000
120A163ALA00.0250.02036.9260.0010.0010.0000.0000.0000.000
121A164GLY00.0430.03938.9130.0000.0000.0000.0000.0000.000
122A165ARG10.8150.92133.1180.0980.0980.0000.0000.0000.000
123A166ARG10.8690.89238.0680.0500.0500.0000.0000.0000.000
124A167ASP-1-0.851-0.91737.137-0.073-0.0730.0000.0000.0000.000
125A168LEU00.0310.00932.1500.0020.0020.0000.0000.0000.000
126A169LEU0-0.053-0.00635.5810.0010.0010.0000.0000.0000.000
127A170ARG10.8890.94538.1580.0470.0470.0000.0000.0000.000
128A171ASP-1-0.960-0.98533.573-0.067-0.0670.0000.0000.0000.000
129A172LEU0-0.0110.00429.9480.0000.0000.0000.0000.0000.000
130A173LEU0-0.057-0.02433.3900.0020.0020.0000.0000.0000.000
131A174HIS00.0000.01234.0740.0080.0080.0000.0000.0000.000
132A175LEU0-0.015-0.00438.3810.0050.0050.0000.0000.0000.000
133A176ASP-1-0.874-0.95541.064-0.039-0.0390.0000.0000.0000.000
134A177PRO00.0320.00642.2740.0010.0010.0000.0000.0000.000
135A178ARG10.9340.97944.7180.0390.0390.0000.0000.0000.000
136A179PHE0-0.029-0.01644.8590.0020.0020.0000.0000.0000.000
137A180LEU00.0500.01541.3350.0010.0010.0000.0000.0000.000
138A181GLU-1-0.841-0.90945.874-0.045-0.0450.0000.0000.0000.000
139A182ARG10.9100.96148.3440.0330.0330.0000.0000.0000.000
140A183HIS0-0.019-0.00445.3600.0030.0030.0000.0000.0000.000
141A184LEU0-0.017-0.01744.1530.0000.0000.0000.0000.0000.000
142A185ALA0-0.0380.00948.4430.0000.0000.0000.0000.0000.000
143A186GLY0-0.032-0.01552.2120.0010.0010.0000.0000.0000.000
144A187THR0-0.038-0.03547.6080.0020.0020.0000.0000.0000.000
145A188MET0-0.047-0.00547.8900.0000.0000.0000.0000.0000.000
146A189SER0-0.026-0.02344.754-0.001-0.0010.0000.0000.0000.000
147A190TYR00.008-0.02240.8500.0010.0010.0000.0000.0000.000
148A191PHE0-0.050-0.01638.090-0.003-0.0030.0000.0000.0000.000
149A192SER00.0340.01943.1570.0040.0040.0000.0000.0000.000
150A193PRO00.0590.01645.692-0.001-0.0010.0000.0000.0000.000
151A194TYR00.0200.02642.9900.0010.0010.0000.0000.0000.000
152A195GLN0-0.016-0.00439.4490.0030.0030.0000.0000.0000.000
153A196LEU00.003-0.01243.544-0.002-0.0020.0000.0000.0000.000
154A197THR0-0.022-0.01445.5160.0010.0010.0000.0000.0000.000
155A198VAL00.0040.00142.5200.0000.0000.0000.0000.0000.000
156A199LEU00.0010.00440.698-0.001-0.0010.0000.0000.0000.000
157A200HIS0-0.025-0.01943.505-0.001-0.0010.0000.0000.0000.000
158A201VAL0-0.039-0.02846.8650.0010.0010.0000.0000.0000.000
159A202ASP-1-0.941-0.99040.930-0.080-0.0800.0000.0000.0000.000
160A203GLY00.0040.02844.134-0.001-0.0010.0000.0000.0000.000
161A204GLU-1-0.923-0.96845.271-0.051-0.0510.0000.0000.0000.000
162A205LEU0-0.073-0.02346.0000.0020.0020.0000.0000.0000.000
163A206CYS0-0.042-0.00246.081-0.002-0.0020.0000.0000.0000.000
164A207ALA00.0590.00443.929-0.002-0.0020.0000.0000.0000.000
165A208ARG10.8950.92844.9720.0500.0500.0000.0000.0000.000
166A209ASP-1-0.785-0.90247.784-0.054-0.0540.0000.0000.0000.000
167A210ILE00.0760.03741.5680.0000.0000.0000.0000.0000.000
168A211ARG10.9220.96343.1800.0690.0690.0000.0000.0000.000
169A212SER0-0.041-0.02044.8730.0000.0000.0000.0000.0000.000
170A213LEU00.0480.03543.2120.0010.0010.0000.0000.0000.000
171A214ILE00.0110.01940.3720.0010.0010.0000.0000.0000.000
172A215PHE0-0.039-0.03843.896-0.001-0.0010.0000.0000.0000.000
173A216LEU00.0460.01546.7770.0010.0010.0000.0000.0000.000
174A217SER0-0.027-0.01243.470-0.001-0.0010.0000.0000.0000.000
175A218LYS10.8540.92444.2160.0650.0650.0000.0000.0000.000
176A219ASP-1-0.910-0.93845.522-0.052-0.0520.0000.0000.0000.000
177A220THR0-0.098-0.03945.2260.0010.0010.0000.0000.0000.000
178A221ILE0-0.0430.02239.352-0.004-0.0040.0000.0000.0000.000
179A222GLY00.0400.01040.3550.0030.0030.0000.0000.0000.000
180A223SER0-0.029-0.05537.363-0.006-0.0060.0000.0000.0000.000
181A224ARG10.9460.98732.3630.1000.1000.0000.0000.0000.000
182A225SER0-0.033-0.03532.6660.0030.0030.0000.0000.0000.000
183A226THR00.0420.04135.4300.0010.0010.0000.0000.0000.000
184A227PRO00.0290.00436.601-0.006-0.0060.0000.0000.0000.000
185A228GLN0-0.052-0.02734.0920.0040.0040.0000.0000.0000.000
186A229THR00.001-0.02636.2580.0020.0020.0000.0000.0000.000
187A230PHE00.019-0.00338.8420.0010.0010.0000.0000.0000.000
188A231LEU00.0960.04237.4420.0020.0020.0000.0000.0000.000
189A232HIS0-0.032-0.00234.753-0.007-0.0070.0000.0000.0000.000
190A233TRP00.000-0.01837.4470.0000.0000.0000.0000.0000.000
191A234VAL00.0030.00340.8650.0020.0020.0000.0000.0000.000
192A235TYR00.0600.04032.980-0.001-0.0010.0000.0000.0000.000
193A236CYS0-0.071-0.03638.237-0.002-0.0020.0000.0000.0000.000
194A237MET00.0090.00539.5480.0030.0030.0000.0000.0000.000
195A238GLU-1-0.876-0.94839.973-0.075-0.0750.0000.0000.0000.000
196A239ASN0-0.045-0.01735.5740.0020.0020.0000.0000.0000.000
197A240LEU0-0.076-0.04439.9400.0020.0020.0000.0000.0000.000
198A241ASP-1-0.952-0.95242.992-0.057-0.0570.0000.0000.0000.000
199A242LEU0-0.067-0.03445.2180.0030.0030.0000.0000.0000.000
200A243LEU0-0.057-0.02544.7120.0020.0020.0000.0000.0000.000
201A244GLY00.0760.03345.229-0.002-0.0020.0000.0000.0000.000
202A245PRO0-0.062-0.04544.7440.0020.0020.0000.0000.0000.000
203A246THR0-0.023-0.01447.6410.0010.0010.0000.0000.0000.000
204A247ASP-1-0.884-0.93349.906-0.043-0.0430.0000.0000.0000.000
205A248VAL00.0510.01248.748-0.002-0.0020.0000.0000.0000.000
206A249ASP-1-0.915-0.96050.922-0.041-0.0410.0000.0000.0000.000
207A250ALA00.0630.02648.9960.0000.0000.0000.0000.0000.000
208A251LEU00.0040.01446.909-0.001-0.0010.0000.0000.0000.000
209A252MET0-0.056-0.02849.7590.0010.0010.0000.0000.0000.000
210A253SER0-0.069-0.03951.6960.0010.0010.0000.0000.0000.000
211A254MET00.0340.02747.8100.0010.0010.0000.0000.0000.000
212A255LEU00.018-0.00349.7960.0010.0010.0000.0000.0000.000
213A256ARG10.8700.93152.7120.0420.0420.0000.0000.0000.000
214A257SER0-0.081-0.03853.2470.0010.0010.0000.0000.0000.000
215A258LEU00.0270.01648.809-0.001-0.0010.0000.0000.0000.000
216A259SER0-0.032-0.03053.2960.0000.0000.0000.0000.0000.000
217A260ARG10.8370.95551.0350.0510.0510.0000.0000.0000.000
218A261VAL00.044-0.00455.1010.0000.0000.0000.0000.0000.000
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