FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: JVKZ9

Calculation Name: 3BU8-A-Xray547

Preferred Name: Telomeric repeat-binding factor 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BU8

Chain ID: A

ChEMBL ID: CHEMBL4296012

UniProt ID: Q15554

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2407134.123288
FMO2-HF: Nuclear repulsion 2323154.804021
FMO2-HF: Total energy -83979.319268
FMO2-MP2: Total energy -84221.6858


3D Structure Molmil
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.
71.85874.0160.025-0.882-1.302-0.003
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 : 1 / q_Mulliken : 0.820 / q_NPA : 0.888
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].
3A46ALA00.0330.0192.78112.62014.2920.027-0.748-0.952-0.003
4A47ARG10.9390.9734.07741.84742.206-0.001-0.118-0.2400.000
5A48LEU0-0.021-0.0085.2935.6405.767-0.001-0.016-0.1100.000
6A49GLU-1-0.765-0.8667.318-25.109-25.1090.0000.0000.0000.000
7A50GLU-1-0.865-0.9428.840-25.465-25.4650.0000.0000.0000.000
8A51ALA0-0.058-0.01910.3532.6192.6190.0000.0000.0000.000
9A52VAL00.0250.01611.6162.2742.2740.0000.0000.0000.000
10A53ASN0-0.018-0.03012.4112.6932.6930.0000.0000.0000.000
11A54ARG10.8900.93511.61124.06924.0690.0000.0000.0000.000
12A55TRP0-0.042-0.02614.5030.9510.9510.0000.0000.0000.000
13A56VAL00.0230.01017.4641.1511.1510.0000.0000.0000.000
14A57LEU00.0130.01419.0660.9580.9580.0000.0000.0000.000
15A58LYS10.8620.90618.88516.83616.8360.0000.0000.0000.000
16A59PHE0-0.025-0.01322.0790.6680.6680.0000.0000.0000.000
17A60TYR00.0450.00722.1740.7560.7560.0000.0000.0000.000
18A61PHE00.0570.01725.0610.5450.5450.0000.0000.0000.000
19A62HIS0-0.019-0.01026.8040.6580.6580.0000.0000.0000.000
20A63GLU-1-0.804-0.88128.034-10.102-10.1020.0000.0000.0000.000
21A64ALA00.0130.01129.4410.4160.4160.0000.0000.0000.000
22A65LEU00.0040.00130.5310.4400.4400.0000.0000.0000.000
23A66ARG10.8380.89632.18010.19510.1950.0000.0000.0000.000
24A67ALA0-0.048-0.01833.9330.2910.2910.0000.0000.0000.000
25A68PHE00.0140.00435.3770.3030.3030.0000.0000.0000.000
26A69ARG10.8540.90134.4649.2309.2300.0000.0000.0000.000
27A70GLY0-0.039-0.00738.9870.1910.1910.0000.0000.0000.000
28A71SER0-0.009-0.02740.7300.1100.1100.0000.0000.0000.000
29A72ARG10.8090.91934.8539.0549.0540.0000.0000.0000.000
30A73TYR0-0.026-0.06537.244-0.387-0.3870.0000.0000.0000.000
31A74GLY00.0030.00636.648-0.189-0.1890.0000.0000.0000.000
32A75ASP-1-0.801-0.89234.177-9.246-9.2460.0000.0000.0000.000
33A76PHE0-0.011-0.02032.575-0.409-0.4090.0000.0000.0000.000
34A77ARG10.8790.92631.8658.2458.2450.0000.0000.0000.000
35A78GLN00.0220.01630.934-0.388-0.3880.0000.0000.0000.000
36A79ILE0-0.021-0.01427.462-0.508-0.5080.0000.0000.0000.000
37A80ARG10.7760.84827.0829.3849.3840.0000.0000.0000.000
38A81ASP-1-0.833-0.89027.212-10.980-10.9800.0000.0000.0000.000
39A82ILE0-0.037-0.01523.119-0.553-0.5530.0000.0000.0000.000
40A83MET0-0.060-0.03122.830-0.610-0.6100.0000.0000.0000.000
41A84GLN0-0.013-0.00422.725-0.898-0.8980.0000.0000.0000.000
42A85ALA00.0030.00221.721-0.420-0.4200.0000.0000.0000.000
43A86LEU0-0.013-0.01416.898-0.966-0.9660.0000.0000.0000.000
44A87LEU0-0.045-0.01518.085-0.990-0.9900.0000.0000.0000.000
45A88VAL0-0.0140.00417.831-0.249-0.2490.0000.0000.0000.000
46A89ARG10.8330.91510.95923.27623.2760.0000.0000.0000.000
47A90PRO0-0.0180.0099.8380.9050.9050.0000.0000.0000.000
48A91LEU00.1060.03512.623-0.741-0.7410.0000.0000.0000.000
49A92GLY0-0.0150.02312.6860.4870.4870.0000.0000.0000.000
50A93LYS10.9310.95713.38317.88817.8880.0000.0000.0000.000
51A94GLU-1-0.801-0.90116.893-16.999-16.9990.0000.0000.0000.000
52A95HIS00.0550.01719.0670.1420.1420.0000.0000.0000.000
53A96THR00.0010.00321.3380.5360.5360.0000.0000.0000.000
54A97VAL00.0360.01018.9000.3360.3360.0000.0000.0000.000
55A98SER00.0180.01822.1070.1810.1810.0000.0000.0000.000
56A99ARG10.8660.92024.11811.01111.0110.0000.0000.0000.000
57A100LEU00.0310.03423.1370.3310.3310.0000.0000.0000.000
58A101LEU00.014-0.00122.1440.3620.3620.0000.0000.0000.000
59A102ARG10.7900.86826.41311.21511.2150.0000.0000.0000.000
60A103VAL00.0420.01629.3730.3700.3700.0000.0000.0000.000
61A104MET00.0080.01027.8010.3570.3570.0000.0000.0000.000
62A105GLN00.0120.02828.7950.3720.3720.0000.0000.0000.000
63A106CYS0-0.0240.00431.2600.3820.3820.0000.0000.0000.000
64A107LEU00.0390.01232.7270.2510.2510.0000.0000.0000.000
65A108SER0-0.036-0.04331.6440.1350.1350.0000.0000.0000.000
66A109ARG10.8200.91831.8709.7359.7350.0000.0000.0000.000
67A110ILE00.0020.00536.9660.2640.2640.0000.0000.0000.000
68A111GLU-1-0.847-0.89336.714-8.481-8.4810.0000.0000.0000.000
69A112GLU-1-0.767-0.84936.273-8.608-8.6080.0000.0000.0000.000
70A113GLY0-0.028-0.01239.5710.1060.1060.0000.0000.0000.000
71A114GLU-1-0.947-0.99842.169-6.746-6.7460.0000.0000.0000.000
72A115ASN0-0.051-0.02340.1470.3230.3230.0000.0000.0000.000
73A116LEU0-0.061-0.04442.412-0.163-0.1630.0000.0000.0000.000
74A117ASP-1-0.908-0.94343.502-7.465-7.4650.0000.0000.0000.000
75A118CYS0-0.066-0.03938.349-0.144-0.1440.0000.0000.0000.000
76A119SER00.0200.01337.8230.0820.0820.0000.0000.0000.000
77A120PHE00.000-0.02833.789-0.302-0.3020.0000.0000.0000.000
78A121ASP-1-0.875-0.89434.316-9.143-9.1430.0000.0000.0000.000
79A122MET00.001-0.00433.480-0.080-0.0800.0000.0000.0000.000
80A123GLU-1-0.896-0.94836.224-8.461-8.4610.0000.0000.0000.000
81A124ALA0-0.025-0.01739.4940.1030.1030.0000.0000.0000.000
82A125GLU-1-0.937-0.96440.703-6.990-6.9900.0000.0000.0000.000
83A126LEU0-0.093-0.03039.5980.1960.1960.0000.0000.0000.000
84A127THR00.047-0.00641.583-0.105-0.1050.0000.0000.0000.000
85A128PRO00.0390.02239.371-0.129-0.1290.0000.0000.0000.000
86A129LEU00.0050.00139.708-0.158-0.1580.0000.0000.0000.000
87A130GLU-1-0.809-0.88142.165-7.176-7.1760.0000.0000.0000.000
88A131SER00.011-0.02036.804-0.198-0.1980.0000.0000.0000.000
89A132ALA0-0.020-0.01337.556-0.221-0.2210.0000.0000.0000.000
90A133ILE0-0.063-0.02538.591-0.045-0.0450.0000.0000.0000.000
91A134ASN00.0250.00837.3310.0780.0780.0000.0000.0000.000
92A135VAL0-0.005-0.01232.736-0.190-0.1900.0000.0000.0000.000
93A136LEU0-0.0020.01634.806-0.163-0.1630.0000.0000.0000.000
94A137GLU-1-0.830-0.90337.244-7.826-7.8260.0000.0000.0000.000
95A138MET0-0.0410.00132.068-0.204-0.2040.0000.0000.0000.000
96A139ILE00.0070.00832.376-0.188-0.1880.0000.0000.0000.000
97A140LYS10.8700.92733.6967.6637.6630.0000.0000.0000.000
98A141THR0-0.040-0.02333.2110.1080.1080.0000.0000.0000.000
99A142GLU-1-0.838-0.90428.541-11.126-11.1260.0000.0000.0000.000
100A143PHE0-0.064-0.02930.047-0.340-0.3400.0000.0000.0000.000
101A144THR0-0.061-0.02332.4930.0990.0990.0000.0000.0000.000
102A145LEU0-0.0070.01335.0550.2170.2170.0000.0000.0000.000
103A146THR00.015-0.00938.0320.0900.0900.0000.0000.0000.000
104A147GLU-1-0.775-0.88241.737-7.276-7.2760.0000.0000.0000.000
105A148ALA00.0100.00544.188-0.019-0.0190.0000.0000.0000.000
106A149VAL0-0.0200.00439.7890.0530.0530.0000.0000.0000.000
107A150VAL00.0070.00039.483-0.080-0.0800.0000.0000.0000.000
108A151GLU-1-0.841-0.91942.284-6.531-6.5310.0000.0000.0000.000
109A152SER0-0.021-0.00145.7980.1210.1210.0000.0000.0000.000
110A153SER00.0600.01741.6250.1410.1410.0000.0000.0000.000
111A154ARG10.8090.87641.6757.4697.4690.0000.0000.0000.000
112A155LYS10.7740.88144.4596.5026.5020.0000.0000.0000.000
113A156LEU00.0280.01745.5860.0670.0670.0000.0000.0000.000
114A157VAL00.0320.00541.5290.0460.0460.0000.0000.0000.000
115A158LYS10.8430.92444.8636.8966.8960.0000.0000.0000.000
116A159GLU-1-0.952-0.97747.614-6.198-6.1980.0000.0000.0000.000
117A160ALA00.0120.00646.1820.0930.0930.0000.0000.0000.000
118A161ALA00.0070.00445.7050.0420.0420.0000.0000.0000.000
119A162VAL0-0.037-0.01547.3400.0820.0820.0000.0000.0000.000
120A163ILE00.005-0.00351.1030.1100.1100.0000.0000.0000.000
121A164ILE00.0290.02146.7510.1290.1290.0000.0000.0000.000
122A165CYS0-0.0140.01149.1610.0100.0100.0000.0000.0000.000
123A166ILE0-0.064-0.03450.9810.1200.1200.0000.0000.0000.000
124A167LYS10.8490.92252.3696.1946.1940.0000.0000.0000.000
125A168ASN0-0.0060.00749.1700.0670.0670.0000.0000.0000.000
126A169LYS10.9120.95152.7815.5185.5180.0000.0000.0000.000
127A170GLU-1-0.788-0.88049.333-6.544-6.5440.0000.0000.0000.000
128A171PHE0-0.041-0.04053.599-0.031-0.0310.0000.0000.0000.000
129A172GLU-1-0.909-0.95854.358-5.841-5.8410.0000.0000.0000.000
130A173LYS10.8530.92246.0417.0017.0010.0000.0000.0000.000
131A174ALA00.0560.02451.093-0.074-0.0740.0000.0000.0000.000
132A175SER0-0.004-0.00352.798-0.018-0.0180.0000.0000.0000.000
133A176LYS10.9290.95650.6916.2916.2910.0000.0000.0000.000
134A177ILE00.0210.01947.480-0.050-0.0500.0000.0000.0000.000
135A178LEU00.0090.00149.978-0.033-0.0330.0000.0000.0000.000
136A179LYS00.0090.01652.9700.0240.0240.0000.0000.0000.000
137A180LYS10.9350.99345.1347.0587.0580.0000.0000.0000.000
138A181HIS00.0240.01044.212-0.063-0.0630.0000.0000.0000.000
139A182MET00.0170.01549.3870.0060.0060.0000.0000.0000.000
140A183SER0-0.086-0.04952.5210.1070.1070.0000.0000.0000.000
141A184LYS10.9170.94951.3246.0786.0780.0000.0000.0000.000
142A185ASP-1-0.805-0.89351.350-6.251-6.2510.0000.0000.0000.000
143A186PRO00.0160.00753.5040.0620.0620.0000.0000.0000.000
144A187THR00.0210.00753.2030.1330.1330.0000.0000.0000.000
145A188THR00.0250.00953.2160.0410.0410.0000.0000.0000.000
146A189GLN0-0.036-0.01855.7210.0150.0150.0000.0000.0000.000
147A190LYS10.9440.95759.1495.1015.1010.0000.0000.0000.000
148A191LEU00.0810.06953.3800.0560.0560.0000.0000.0000.000
149A192ARG10.9250.92855.8555.6295.6290.0000.0000.0000.000
150A193ASN0-0.030-0.02857.481-0.046-0.0460.0000.0000.0000.000
151A194ASP-1-0.872-0.92160.458-5.150-5.1500.0000.0000.0000.000
152A195LEU00.006-0.00454.5490.0240.0240.0000.0000.0000.000
153A196LEU0-0.023-0.01358.4610.0010.0010.0000.0000.0000.000
154A197ASN0-0.009-0.00160.3650.0430.0430.0000.0000.0000.000
155A198ILE00.0050.00859.1200.0410.0410.0000.0000.0000.000
156A199ILE0-0.020-0.01655.9130.0130.0130.0000.0000.0000.000
157A200ARG10.8870.94760.0024.9994.9990.0000.0000.0000.000
158A201GLU-1-0.930-0.97663.394-4.826-4.8260.0000.0000.0000.000
159A202LYS10.8700.94861.4015.2605.2600.0000.0000.0000.000
160A203ASN00.0120.01662.475-0.043-0.0430.0000.0000.0000.000
161A204LEU00.011-0.01657.687-0.029-0.0290.0000.0000.0000.000
162A205ALA0-0.0010.01060.488-0.050-0.0500.0000.0000.0000.000
163A206HIS00.0550.03861.5100.0000.0000.0000.0000.0000.000
164A207PRO00.004-0.00860.907-0.106-0.1060.0000.0000.0000.000
165A208VAL00.0290.01456.832-0.073-0.0730.0000.0000.0000.000
166A209ILE00.0050.00856.098-0.126-0.1260.0000.0000.0000.000
167A210GLN00.0130.00456.325-0.175-0.1750.0000.0000.0000.000
168A211ASN0-0.066-0.04257.368-0.045-0.0450.0000.0000.0000.000
169A212PHE0-0.0280.00948.770-0.078-0.0780.0000.0000.0000.000
170A213SER00.0280.01851.018-0.086-0.0860.0000.0000.0000.000
171A214TYR00.061-0.00142.250-0.003-0.0030.0000.0000.0000.000
172A215GLU-1-0.697-0.79144.470-7.567-7.5670.0000.0000.0000.000
173A216THR0-0.060-0.04245.607-0.095-0.0950.0000.0000.0000.000
174A217PHE0-0.007-0.00843.188-0.041-0.0410.0000.0000.0000.000
175A218GLN00.0340.01441.1370.0130.0130.0000.0000.0000.000
176A219GLN00.007-0.02341.219-0.304-0.3040.0000.0000.0000.000
177A220LYS10.8630.93842.4036.5916.5910.0000.0000.0000.000
178A221MET0-0.0080.00639.906-0.049-0.0490.0000.0000.0000.000
179A222LEU00.0000.01735.635-0.208-0.2080.0000.0000.0000.000
180A223ARG10.9770.98437.6527.3447.3440.0000.0000.0000.000
181A224PHE0-0.0070.00738.259-0.065-0.0650.0000.0000.0000.000
182A225LEU0-0.007-0.00434.588-0.156-0.1560.0000.0000.0000.000
183A226GLU-1-0.801-0.89934.248-9.126-9.1260.0000.0000.0000.000
184A227SER0-0.092-0.04734.731-0.112-0.1120.0000.0000.0000.000
185A228HIS00.0000.01233.446-0.113-0.1130.0000.0000.0000.000
186A229LEU0-0.065-0.03728.899-0.456-0.4560.0000.0000.0000.000
187A230ASP-1-0.866-0.93626.973-11.163-11.1630.0000.0000.0000.000
188A231ASP-1-0.900-0.95229.887-9.273-9.2730.0000.0000.0000.000
189A232ALA0-0.100-0.03126.9680.0180.0180.0000.0000.0000.000
190A233GLU-1-0.791-0.85327.343-11.123-11.1230.0000.0000.0000.000
191A234PRO0-0.0110.00623.854-0.546-0.5460.0000.0000.0000.000
192A235TYR00.0400.00117.6810.4240.4240.0000.0000.0000.000
193A236LEU00.0390.00718.3590.0020.0020.0000.0000.0000.000
194A237LEU00.0170.02122.3720.2640.2640.0000.0000.0000.000
195A238THR0-0.036-0.04324.6200.1890.1890.0000.0000.0000.000
196A239MET0-0.065-0.03520.6360.4690.4690.0000.0000.0000.000
197A240ALA00.0140.01824.2470.1940.1940.0000.0000.0000.000
198A241LYS10.8750.91026.47010.58010.5800.0000.0000.0000.000
199A242LYS10.8620.93325.30512.19812.1980.0000.0000.0000.000
200A243ALA0-0.005-0.00325.7010.2110.2110.0000.0000.0000.000
201A244LEU00.018-0.00427.6290.1860.1860.0000.0000.0000.000
202A245LYS10.8660.95130.28710.57810.5780.0000.0000.0000.000
203A246SER0-0.052-0.03630.2660.2790.2790.0000.0000.0000.000
204A247GLU-2-1.884-1.90831.111-18.967-18.9670.0000.0000.0000.000