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: JLK79

Calculation Name: 3BU8-A-Xray372

Preferred Name: Telomeric repeat-binding factor 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3BU8

Chain ID: A

ChEMBL ID: CHEMBL4296012

UniProt ID: Q15554

Base Structure: X-ray

Registration Date: 2023-06-26

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405228.025335
FMO2-HF: Nuclear repulsion 2321250.069883
FMO2-HF: Total energy -83977.955452
FMO2-MP2: Total energy -84220.616413


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:44:GLY)


Summations of interaction energy for fragment #1(A:44:GLY)
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.
0.0251.7030.360.065-2.1030.002
Interaction energy analysis for fragmet #1(A:44:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / q_NPA : 0.019
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].
3A46ALA00.0450.0092.7230.2691.3190.3600.218-1.6270.002
4A47ARG10.9580.9914.017-0.642-0.1600.001-0.131-0.3530.000
5A48LEU0-0.036-0.0114.856-0.199-0.053-0.001-0.022-0.1230.000
6A49GLU-1-0.777-0.8886.9450.4620.4620.0000.0000.0000.000
7A50GLU-1-0.923-0.9578.5470.9640.9640.0000.0000.0000.000
8A51ALA0-0.071-0.0449.549-0.041-0.0410.0000.0000.0000.000
9A52VAL00.0280.01211.2300.0060.0060.0000.0000.0000.000
10A53ASN0-0.004-0.01812.297-0.062-0.0620.0000.0000.0000.000
11A54ARG10.9130.97311.402-0.219-0.2190.0000.0000.0000.000
12A55TRP0-0.024-0.01014.552-0.013-0.0130.0000.0000.0000.000
13A56VAL00.0220.01317.0110.0010.0010.0000.0000.0000.000
14A57LEU00.0150.00918.651-0.001-0.0010.0000.0000.0000.000
15A58LYS10.8580.91018.731-0.066-0.0660.0000.0000.0000.000
16A59PHE0-0.031-0.00421.748-0.004-0.0040.0000.0000.0000.000
17A60TYR00.0680.01421.771-0.004-0.0040.0000.0000.0000.000
18A61PHE00.0430.02124.6690.0020.0020.0000.0000.0000.000
19A62HIS00.002-0.00326.283-0.001-0.0010.0000.0000.0000.000
20A63GLU-1-0.855-0.93527.760-0.015-0.0150.0000.0000.0000.000
21A64ALA00.0010.01129.129-0.001-0.0010.0000.0000.0000.000
22A65LEU00.0210.00530.4370.0000.0000.0000.0000.0000.000
23A66ARG10.8430.93232.2110.0090.0090.0000.0000.0000.000
24A67ALA0-0.032-0.02433.698-0.001-0.0010.0000.0000.0000.000
25A68PHE00.0160.01035.0050.0000.0000.0000.0000.0000.000
26A69ARG10.8600.91134.191-0.012-0.0120.0000.0000.0000.000
27A70GLY0-0.060-0.01638.403-0.001-0.0010.0000.0000.0000.000
28A71SER0-0.017-0.01640.118-0.002-0.0020.0000.0000.0000.000
29A72ARG10.8160.91934.8670.0020.0020.0000.0000.0000.000
30A73TYR00.018-0.04337.0840.0000.0000.0000.0000.0000.000
31A74GLY0-0.0090.00736.7330.0020.0020.0000.0000.0000.000
32A75ASP-1-0.796-0.89934.060-0.003-0.0030.0000.0000.0000.000
33A76PHE0-0.034-0.02132.4840.0010.0010.0000.0000.0000.000
34A77ARG10.9440.97531.815-0.013-0.0130.0000.0000.0000.000
35A78GLN00.0010.01331.1340.0010.0010.0000.0000.0000.000
36A79ILE0-0.011-0.01227.3070.0010.0010.0000.0000.0000.000
37A80ARG10.7870.87927.161-0.029-0.0290.0000.0000.0000.000
38A81ASP-1-0.832-0.92127.2050.0390.0390.0000.0000.0000.000
39A82ILE0-0.046-0.00422.8030.0050.0050.0000.0000.0000.000
40A83MET0-0.063-0.03622.6990.0070.0070.0000.0000.0000.000
41A84GLN0-0.0090.00222.5320.0260.0260.0000.0000.0000.000
42A85ALA00.0120.01021.6110.0140.0140.0000.0000.0000.000
43A86LEU0-0.004-0.02416.9160.0150.0150.0000.0000.0000.000
44A87LEU0-0.036-0.00817.7550.0340.0340.0000.0000.0000.000
45A88VAL0-0.0220.00717.4500.0280.0280.0000.0000.0000.000
46A89ARG10.8470.93210.809-0.234-0.2340.0000.0000.0000.000
47A90PRO0-0.0030.0149.856-0.017-0.0170.0000.0000.0000.000
48A91LEU00.0860.02712.544-0.045-0.0450.0000.0000.0000.000
49A92GLY00.0000.01612.617-0.035-0.0350.0000.0000.0000.000
50A93LYS10.9360.95613.069-0.345-0.3450.0000.0000.0000.000
51A94GLU-1-0.795-0.92516.4140.1080.1080.0000.0000.0000.000
52A95HIS00.0380.01518.632-0.010-0.0100.0000.0000.0000.000
53A96THR00.011-0.00320.532-0.009-0.0090.0000.0000.0000.000
54A97VAL00.0420.02218.264-0.011-0.0110.0000.0000.0000.000
55A98SER0-0.011-0.00321.581-0.004-0.0040.0000.0000.0000.000
56A99ARG10.9370.97523.368-0.075-0.0750.0000.0000.0000.000
57A100LEU00.0220.02522.717-0.005-0.0050.0000.0000.0000.000
58A101LEU0-0.001-0.01421.722-0.007-0.0070.0000.0000.0000.000
59A102ARG10.8290.90526.114-0.103-0.1030.0000.0000.0000.000
60A103VAL00.0410.01228.990-0.006-0.0060.0000.0000.0000.000
61A104MET00.0020.00727.324-0.006-0.0060.0000.0000.0000.000
62A105GLN0-0.0090.02028.361-0.003-0.0030.0000.0000.0000.000
63A106CYS0-0.017-0.00330.932-0.005-0.0050.0000.0000.0000.000
64A107LEU00.0230.00132.334-0.003-0.0030.0000.0000.0000.000
65A108SER0-0.012-0.02631.497-0.004-0.0040.0000.0000.0000.000
66A109ARG10.8550.94131.496-0.063-0.0630.0000.0000.0000.000
67A110ILE00.0100.00036.606-0.003-0.0030.0000.0000.0000.000
68A111GLU-1-0.907-0.96036.6970.0190.0190.0000.0000.0000.000
69A112GLU-1-0.786-0.85536.4030.0270.0270.0000.0000.0000.000
70A113GLY0-0.039-0.02939.5180.0000.0000.0000.0000.0000.000
71A114GLU-1-0.985-1.00742.1450.0170.0170.0000.0000.0000.000
72A115ASN0-0.041-0.01140.257-0.003-0.0030.0000.0000.0000.000
73A116LEU0-0.078-0.04642.5780.0020.0020.0000.0000.0000.000
74A117ASP-1-0.883-0.94343.0800.0240.0240.0000.0000.0000.000
75A118CYS0-0.077-0.03338.4030.0010.0010.0000.0000.0000.000
76A119SER00.0200.01138.2220.0020.0020.0000.0000.0000.000
77A120PHE0-0.029-0.03533.2860.0020.0020.0000.0000.0000.000
78A121ASP-1-0.869-0.92733.9530.0650.0650.0000.0000.0000.000
79A122MET00.0090.00332.9440.0000.0000.0000.0000.0000.000
80A123GLU-1-0.924-0.95536.0570.0590.0590.0000.0000.0000.000
81A124ALA0-0.011-0.02539.593-0.001-0.0010.0000.0000.0000.000
82A125GLU-1-0.971-0.97840.6730.0380.0380.0000.0000.0000.000
83A126LEU0-0.087-0.03839.117-0.002-0.0020.0000.0000.0000.000
84A127THR00.022-0.00141.0850.0000.0000.0000.0000.0000.000
85A128PRO00.0690.03239.1040.0030.0030.0000.0000.0000.000
86A129LEU00.0540.01339.3510.0030.0030.0000.0000.0000.000
87A130GLU-1-0.853-0.91641.6000.0370.0370.0000.0000.0000.000
88A131SER0-0.021-0.00436.2240.0030.0030.0000.0000.0000.000
89A132ALA0-0.010-0.02037.0270.0040.0040.0000.0000.0000.000
90A133ILE0-0.059-0.01938.1030.0010.0010.0000.0000.0000.000
91A134ASN00.0310.00636.8740.0000.0000.0000.0000.0000.000
92A135VAL0-0.003-0.00332.4940.0040.0040.0000.0000.0000.000
93A136LEU0-0.0100.00634.4310.0020.0020.0000.0000.0000.000
94A137GLU-1-0.841-0.91136.7810.0500.0500.0000.0000.0000.000
95A138MET0-0.048-0.02131.9170.0050.0050.0000.0000.0000.000
96A139ILE00.0250.02431.9130.0040.0040.0000.0000.0000.000
97A140LYS10.8780.94433.310-0.049-0.0490.0000.0000.0000.000
98A141THR0-0.046-0.02132.811-0.001-0.0010.0000.0000.0000.000
99A142GLU-1-0.829-0.91228.4720.1060.1060.0000.0000.0000.000
100A143PHE0-0.113-0.04129.2750.0040.0040.0000.0000.0000.000
101A144THR0-0.018-0.02131.890-0.003-0.0030.0000.0000.0000.000
102A145LEU0-0.0330.02134.483-0.004-0.0040.0000.0000.0000.000
103A146THR00.026-0.00537.3000.0000.0000.0000.0000.0000.000
104A147GLU-1-0.750-0.87240.9550.0410.0410.0000.0000.0000.000
105A148ALA0-0.0020.00543.312-0.001-0.0010.0000.0000.0000.000
106A149VAL0-0.0240.00139.209-0.002-0.0020.0000.0000.0000.000
107A150VAL00.0150.00638.864-0.001-0.0010.0000.0000.0000.000
108A151GLU-1-0.917-0.97241.6660.0300.0300.0000.0000.0000.000
109A152SER0-0.029-0.01745.159-0.001-0.0010.0000.0000.0000.000
110A153SER00.0530.01641.310-0.002-0.0020.0000.0000.0000.000
111A154ARG10.7920.85941.414-0.043-0.0430.0000.0000.0000.000
112A155LYS10.8770.94743.824-0.028-0.0280.0000.0000.0000.000
113A156LEU00.0260.01644.864-0.001-0.0010.0000.0000.0000.000
114A157VAL00.0510.02241.384-0.001-0.0010.0000.0000.0000.000
115A158LYS10.8300.92044.627-0.035-0.0350.0000.0000.0000.000
116A159GLU-1-0.934-0.96747.0830.0210.0210.0000.0000.0000.000
117A160ALA00.0080.00546.016-0.001-0.0010.0000.0000.0000.000
118A161ALA00.0140.00645.456-0.001-0.0010.0000.0000.0000.000
119A162VAL0-0.034-0.01547.100-0.001-0.0010.0000.0000.0000.000
120A163ILE00.0190.00050.793-0.001-0.0010.0000.0000.0000.000
121A164ILE00.0370.02546.795-0.002-0.0020.0000.0000.0000.000
122A165CYS00.0020.01749.1710.0000.0000.0000.0000.0000.000
123A166ILE0-0.061-0.03150.761-0.001-0.0010.0000.0000.0000.000
124A167LYS10.9010.94952.111-0.016-0.0160.0000.0000.0000.000
125A168ASN0-0.0120.00249.266-0.002-0.0020.0000.0000.0000.000
126A169LYS10.9100.94752.842-0.014-0.0140.0000.0000.0000.000
127A170GLU-1-0.836-0.90549.2530.0250.0250.0000.0000.0000.000
128A171PHE0-0.010-0.03553.2990.0010.0010.0000.0000.0000.000
129A172GLU-1-0.910-0.95854.4210.0240.0240.0000.0000.0000.000
130A173LYS10.9530.99846.034-0.033-0.0330.0000.0000.0000.000
131A174ALA00.0460.01851.1590.0010.0010.0000.0000.0000.000
132A175SER0-0.025-0.01052.5920.0010.0010.0000.0000.0000.000
133A176LYS10.9470.96750.518-0.030-0.0300.0000.0000.0000.000
134A177ILE00.0240.02747.0280.0010.0010.0000.0000.0000.000
135A178LEU00.0080.00649.7030.0010.0010.0000.0000.0000.000
136A179LYN00.0200.01852.5390.0000.0000.0000.0000.0000.000
137A180LYS10.9130.97944.819-0.042-0.0420.0000.0000.0000.000
138A181HIS00.019-0.00143.9000.0010.0010.0000.0000.0000.000
139A182MET0-0.0050.00648.9710.0000.0000.0000.0000.0000.000
140A183SER0-0.070-0.06052.113-0.001-0.0010.0000.0000.0000.000
141A184LYS10.9260.95651.198-0.032-0.0320.0000.0000.0000.000
142A185ASP-1-0.822-0.91251.1600.0290.0290.0000.0000.0000.000
143A186PRO00.0150.00853.434-0.001-0.0010.0000.0000.0000.000
144A187THR00.0190.00752.397-0.002-0.0020.0000.0000.0000.000
145A188THR0-0.026-0.01252.972-0.001-0.0010.0000.0000.0000.000
146A189GLN0-0.014-0.01555.3900.0000.0000.0000.0000.0000.000
147A190LYS10.9460.95358.846-0.017-0.0170.0000.0000.0000.000
148A191LEU00.0830.09153.285-0.001-0.0010.0000.0000.0000.000
149A192ARG10.9730.96355.721-0.024-0.0240.0000.0000.0000.000
150A193ASN0-0.049-0.02857.3460.0010.0010.0000.0000.0000.000
151A194ASP-1-0.884-0.93159.9710.0160.0160.0000.0000.0000.000
152A195LEU00.002-0.01654.3410.0000.0000.0000.0000.0000.000
153A196LEU0-0.033-0.01657.9420.0000.0000.0000.0000.0000.000
154A197ASN00.0280.01459.9970.0000.0000.0000.0000.0000.000
155A198ILE00.0010.01959.014-0.001-0.0010.0000.0000.0000.000
156A199ILE0-0.025-0.01955.8470.0000.0000.0000.0000.0000.000
157A200ARG10.8740.93959.864-0.017-0.0170.0000.0000.0000.000
158A201GLU-1-0.966-0.98663.1500.0130.0130.0000.0000.0000.000
159A202LYS10.8750.95360.890-0.016-0.0160.0000.0000.0000.000
160A203ASN00.0410.01762.304-0.001-0.0010.0000.0000.0000.000
161A204LEU0-0.016-0.01957.5880.0000.0000.0000.0000.0000.000
162A205ALA00.0230.02060.1730.0000.0000.0000.0000.0000.000
163A206HIS00.0180.02961.1880.0000.0000.0000.0000.0000.000
164A207PRO00.0420.00360.7170.0000.0000.0000.0000.0000.000
165A208VAL00.0090.00156.6410.0000.0000.0000.0000.0000.000
166A209ILE0-0.025-0.00855.8440.0010.0010.0000.0000.0000.000
167A210GLN0-0.009-0.01556.1000.0010.0010.0000.0000.0000.000
168A211ASN0-0.054-0.02857.173-0.001-0.0010.0000.0000.0000.000
169A212PHE0-0.0150.01748.2080.0000.0000.0000.0000.0000.000
170A213SER0-0.0010.00950.2800.0000.0000.0000.0000.0000.000
171A214TYR00.074-0.00542.0880.0010.0010.0000.0000.0000.000
172A215GLU-1-0.736-0.82944.5710.0130.0130.0000.0000.0000.000
173A216THR0-0.030-0.03445.1780.0000.0000.0000.0000.0000.000
174A217PHE0-0.036-0.01243.0810.0010.0010.0000.0000.0000.000
175A218GLN00.0490.01740.6650.0000.0000.0000.0000.0000.000
176A219GLN00.0270.00240.6970.0020.0020.0000.0000.0000.000
177A220LYS10.8740.94441.782-0.018-0.0180.0000.0000.0000.000
178A221MET0-0.028-0.00439.4960.0010.0010.0000.0000.0000.000
179A222LEU00.0000.01835.1160.0030.0030.0000.0000.0000.000
180A223ARG10.9790.98537.147-0.015-0.0150.0000.0000.0000.000
181A224PHE00.0030.01237.7030.0010.0010.0000.0000.0000.000
182A225LEU0-0.010-0.01034.1080.0020.0020.0000.0000.0000.000
183A226GLU-1-0.818-0.91433.6490.0210.0210.0000.0000.0000.000
184A227SER0-0.090-0.03334.1520.0000.0000.0000.0000.0000.000
185A228HIS0-0.028-0.00733.0470.0020.0020.0000.0000.0000.000
186A229LEU0-0.094-0.06928.4190.0080.0080.0000.0000.0000.000
187A230ASP-1-0.888-0.92626.6300.0250.0250.0000.0000.0000.000
188A231ASP-1-0.901-0.96729.3620.0130.0130.0000.0000.0000.000
189A232ALA0-0.102-0.03826.232-0.005-0.0050.0000.0000.0000.000
190A233GLU-1-0.788-0.83627.358-0.028-0.0280.0000.0000.0000.000
191A234PRO0-0.0160.00123.538-0.002-0.0020.0000.0000.0000.000
192A235TYR00.0460.00017.564-0.002-0.0020.0000.0000.0000.000
193A236LEU00.039-0.00218.243-0.010-0.0100.0000.0000.0000.000
194A237LEU00.0180.02822.083-0.006-0.0060.0000.0000.0000.000
195A238THR0-0.053-0.05624.280-0.002-0.0020.0000.0000.0000.000
196A239MET0-0.050-0.03820.866-0.001-0.0010.0000.0000.0000.000
197A240ALA00.0050.02024.205-0.004-0.0040.0000.0000.0000.000
198A241LYS10.9110.93026.3150.0270.0270.0000.0000.0000.000
199A242LYS10.8890.94425.5270.0650.0650.0000.0000.0000.000
200A243ALA0-0.0140.00825.8290.0010.0010.0000.0000.0000.000
201A244LEU00.0380.00127.8150.0010.0010.0000.0000.0000.000
202A245LYS10.8360.92829.8440.0610.0610.0000.0000.0000.000
203A246SER0-0.033-0.01730.5710.0030.0030.0000.0000.0000.000
204A247GLU-1-0.932-0.93731.177-0.060-0.0600.0000.0000.0000.000