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: LZR99

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2412790.664664
FMO2-HF: Nuclear repulsion 2328810.564783
FMO2-HF: Total energy -83980.099881
FMO2-MP2: Total energy -84222.564653


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.
-0.941.4050.065-1.039-1.3710.004
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 : 0.022 / q_NPA : 0.002
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].
3A46ALA00.0120.0063.148-1.1010.6480.064-0.841-0.9720.004
4A47ARG10.8970.9513.819-0.558-0.1160.002-0.171-0.2740.000
5A48LEU0-0.012-0.0034.9040.0990.253-0.001-0.027-0.1250.000
6A49GLU-1-0.768-0.8677.0230.5880.5880.0000.0000.0000.000
7A50GLU-1-0.846-0.9278.4510.5050.5050.0000.0000.0000.000
8A51ALA0-0.047-0.0159.8220.0230.0230.0000.0000.0000.000
9A52VAL00.0260.01111.3660.0410.0410.0000.0000.0000.000
10A53ASN0-0.011-0.02512.611-0.020-0.0200.0000.0000.0000.000
11A54ARG10.8650.91910.812-0.081-0.0810.0000.0000.0000.000
12A55TRP0-0.040-0.02513.7070.0000.0000.0000.0000.0000.000
13A56VAL00.0120.00517.2950.0100.0100.0000.0000.0000.000
14A57LEU00.0240.01818.7530.0070.0070.0000.0000.0000.000
15A58LYS10.8470.90118.3770.0080.0080.0000.0000.0000.000
16A59PHE0-0.032-0.01721.7480.0000.0000.0000.0000.0000.000
17A60TYR00.0430.00921.9280.0000.0000.0000.0000.0000.000
18A61PHE00.0550.01524.6630.0040.0040.0000.0000.0000.000
19A62HIS0-0.012-0.01126.3510.0020.0020.0000.0000.0000.000
20A63GLU-1-0.792-0.86627.970-0.034-0.0340.0000.0000.0000.000
21A64ALA00.0100.01429.1130.0020.0020.0000.0000.0000.000
22A65LEU00.0150.00730.4980.0020.0020.0000.0000.0000.000
23A66ARG10.8000.87032.0980.0330.0330.0000.0000.0000.000
24A67ALA0-0.0240.00333.719-0.002-0.0020.0000.0000.0000.000
25A68PHE00.0230.00535.0030.0010.0010.0000.0000.0000.000
26A69ARG10.8270.89033.8860.0070.0070.0000.0000.0000.000
27A70GLY0-0.038-0.01538.542-0.001-0.0010.0000.0000.0000.000
28A71SER0-0.015-0.02540.551-0.002-0.0020.0000.0000.0000.000
29A72ARG10.8060.90834.3060.0180.0180.0000.0000.0000.000
30A73TYR0-0.006-0.05937.0520.0000.0000.0000.0000.0000.000
31A74GLY00.0140.01236.6020.0020.0020.0000.0000.0000.000
32A75ASP-1-0.828-0.89034.107-0.015-0.0150.0000.0000.0000.000
33A76PHE0-0.028-0.02732.267-0.001-0.0010.0000.0000.0000.000
34A77ARG10.8940.94031.766-0.009-0.0090.0000.0000.0000.000
35A78GLN0-0.005-0.00731.1080.0000.0000.0000.0000.0000.000
36A79ILE0-0.028-0.01627.3900.0010.0010.0000.0000.0000.000
37A80ARG10.7430.83427.061-0.024-0.0240.0000.0000.0000.000
38A81ASP-1-0.814-0.89127.3780.0350.0350.0000.0000.0000.000
39A82ILE0-0.034-0.01123.3970.0050.0050.0000.0000.0000.000
40A83MET0-0.066-0.03723.0610.0040.0040.0000.0000.0000.000
41A84GLN0-0.011-0.00422.9050.0210.0210.0000.0000.0000.000
42A85ALA0-0.005-0.00122.4390.0160.0160.0000.0000.0000.000
43A86LEU0-0.034-0.01817.0310.0130.0130.0000.0000.0000.000
44A87LEU0-0.025-0.01118.3510.0240.0240.0000.0000.0000.000
45A88VAL0-0.0270.00718.5910.0290.0290.0000.0000.0000.000
46A89ARG10.8430.90911.828-0.261-0.2610.0000.0000.0000.000
47A90PRO0-0.0100.01810.150-0.005-0.0050.0000.0000.0000.000
48A91LEU00.1000.02412.385-0.086-0.0860.0000.0000.0000.000
49A92GLY0-0.0280.01812.189-0.057-0.0570.0000.0000.0000.000
50A93LYS10.9280.95412.941-0.275-0.2750.0000.0000.0000.000
51A94GLU-1-0.802-0.89716.4350.0200.0200.0000.0000.0000.000
52A95HIS00.0530.01618.651-0.002-0.0020.0000.0000.0000.000
53A96THR00.0280.01420.943-0.002-0.0020.0000.0000.0000.000
54A97VAL00.0280.00718.343-0.007-0.0070.0000.0000.0000.000
55A98SER00.0190.01821.5590.0060.0060.0000.0000.0000.000
56A99ARG10.8680.92223.456-0.046-0.0460.0000.0000.0000.000
57A100LEU00.0130.02422.820-0.003-0.0030.0000.0000.0000.000
58A101LEU00.0180.00222.237-0.005-0.0050.0000.0000.0000.000
59A102ARG10.7920.86425.774-0.084-0.0840.0000.0000.0000.000
60A103VAL00.0360.01828.740-0.003-0.0030.0000.0000.0000.000
61A104MET00.0040.01127.337-0.005-0.0050.0000.0000.0000.000
62A105GLN00.0170.02727.897-0.003-0.0030.0000.0000.0000.000
63A106CYS0-0.038-0.01030.870-0.003-0.0030.0000.0000.0000.000
64A107LEU00.0280.00632.075-0.002-0.0020.0000.0000.0000.000
65A108SER0-0.012-0.03131.434-0.003-0.0030.0000.0000.0000.000
66A109ARG10.7750.89432.244-0.056-0.0560.0000.0000.0000.000
67A110ILE00.0070.00836.643-0.002-0.0020.0000.0000.0000.000
68A111GLU-1-0.827-0.88335.7450.0130.0130.0000.0000.0000.000
69A112GLU-1-0.763-0.85636.5200.0230.0230.0000.0000.0000.000
70A113GLY0-0.015-0.01339.6700.0010.0010.0000.0000.0000.000
71A114GLU-1-0.941-0.99642.0740.0130.0130.0000.0000.0000.000
72A115ASN0-0.051-0.01740.418-0.002-0.0020.0000.0000.0000.000
73A116LEU0-0.057-0.04542.7000.0030.0030.0000.0000.0000.000
74A117ASP-1-0.907-0.94344.0980.0240.0240.0000.0000.0000.000
75A118CYS0-0.066-0.04138.7980.0020.0020.0000.0000.0000.000
76A119SER0-0.022-0.01139.0760.0020.0020.0000.0000.0000.000
77A120PHE00.029-0.00733.9670.0020.0020.0000.0000.0000.000
78A121ASP-1-0.832-0.86734.4980.0610.0610.0000.0000.0000.000
79A122MET00.0010.00333.9060.0010.0010.0000.0000.0000.000
80A123GLU-1-0.909-0.95936.8190.0620.0620.0000.0000.0000.000
81A124ALA00.016-0.00540.284-0.003-0.0030.0000.0000.0000.000
82A125GLU-1-0.787-0.86241.2940.0330.0330.0000.0000.0000.000
83A126LEU0-0.084-0.02739.558-0.003-0.0030.0000.0000.0000.000
84A127THR00.0570.00141.2050.0000.0000.0000.0000.0000.000
85A128PRO00.0270.02639.3480.0030.0030.0000.0000.0000.000
86A129LEU00.0380.01639.5810.0020.0020.0000.0000.0000.000
87A130GLU-1-0.826-0.88741.7660.0350.0350.0000.0000.0000.000
88A131SER0-0.009-0.03436.9190.0030.0030.0000.0000.0000.000
89A132ALA0-0.011-0.00837.1700.0030.0030.0000.0000.0000.000
90A133ILE0-0.053-0.02138.0690.0000.0000.0000.0000.0000.000
91A134ASN00.002-0.00337.2270.0000.0000.0000.0000.0000.000
92A135VAL00.012-0.00332.3140.0030.0030.0000.0000.0000.000
93A136LEU0-0.0050.01534.3620.0010.0010.0000.0000.0000.000
94A137GLU-1-0.808-0.88436.8030.0410.0410.0000.0000.0000.000
95A138MET0-0.0250.00831.7880.0050.0050.0000.0000.0000.000
96A139ILE00.0240.01431.7300.0030.0030.0000.0000.0000.000
97A140LYS10.7760.87233.133-0.042-0.0420.0000.0000.0000.000
98A141THR0-0.038-0.02032.895-0.001-0.0010.0000.0000.0000.000
99A142GLU-1-0.818-0.88828.2980.0880.0880.0000.0000.0000.000
100A143PHE0-0.076-0.03229.5240.0010.0010.0000.0000.0000.000
101A144THR0-0.059-0.02531.805-0.003-0.0030.0000.0000.0000.000
102A145LEU0-0.0210.00834.374-0.004-0.0040.0000.0000.0000.000
103A146THR00.027-0.00337.2760.0010.0010.0000.0000.0000.000
104A147GLU-1-0.744-0.86140.9490.0340.0340.0000.0000.0000.000
105A148ALA00.0280.00743.264-0.001-0.0010.0000.0000.0000.000
106A149VAL0-0.0240.00439.315-0.002-0.0020.0000.0000.0000.000
107A150VAL0-0.003-0.00738.586-0.001-0.0010.0000.0000.0000.000
108A151GLU-1-0.873-0.93841.7310.0240.0240.0000.0000.0000.000
109A152SER0-0.026-0.00845.097-0.001-0.0010.0000.0000.0000.000
110A153SER00.0580.02041.114-0.001-0.0010.0000.0000.0000.000
111A154ARG10.8310.88340.417-0.036-0.0360.0000.0000.0000.000
112A155LYS10.7480.87343.803-0.023-0.0230.0000.0000.0000.000
113A156LEU00.0390.02345.263-0.001-0.0010.0000.0000.0000.000
114A157VAL00.0150.00341.012-0.001-0.0010.0000.0000.0000.000
115A158LYS10.8600.93244.389-0.030-0.0300.0000.0000.0000.000
116A159GLU-1-0.950-0.98247.1460.0150.0150.0000.0000.0000.000
117A160ALA00.0250.01145.720-0.001-0.0010.0000.0000.0000.000
118A161ALA00.0150.00645.4260.0000.0000.0000.0000.0000.000
119A162VAL0-0.037-0.01847.0970.0000.0000.0000.0000.0000.000
120A163ILE0-0.004-0.00850.865-0.001-0.0010.0000.0000.0000.000
121A164ILE00.0220.02446.675-0.001-0.0010.0000.0000.0000.000
122A165CYS0-0.0140.00449.0510.0000.0000.0000.0000.0000.000
123A166ILE0-0.064-0.03550.922-0.001-0.0010.0000.0000.0000.000
124A167LYS10.8190.89952.369-0.011-0.0110.0000.0000.0000.000
125A168ASN0-0.0010.00949.363-0.002-0.0020.0000.0000.0000.000
126A169LYS10.9010.94852.983-0.012-0.0120.0000.0000.0000.000
127A170GLU-1-0.779-0.87549.5250.0240.0240.0000.0000.0000.000
128A171PHE0-0.027-0.04253.6340.0010.0010.0000.0000.0000.000
129A172GLU-1-0.926-0.96554.0140.0260.0260.0000.0000.0000.000
130A173LYS10.8560.91146.003-0.033-0.0330.0000.0000.0000.000
131A174ALA00.0420.01651.0280.0010.0010.0000.0000.0000.000
132A175SER0-0.024-0.01052.6380.0000.0000.0000.0000.0000.000
133A176LYS10.8340.90649.237-0.032-0.0320.0000.0000.0000.000
134A177ILE0-0.0050.00747.3530.0010.0010.0000.0000.0000.000
135A178LEU00.0160.00749.7160.0010.0010.0000.0000.0000.000
136A179LYN00.0140.01952.6050.0000.0000.0000.0000.0000.000
137A180LYS10.8960.97244.207-0.039-0.0390.0000.0000.0000.000
138A181HIS00.0480.02143.6490.0020.0020.0000.0000.0000.000
139A182MET00.0080.01548.7820.0000.0000.0000.0000.0000.000
140A183SER0-0.071-0.03351.954-0.001-0.0010.0000.0000.0000.000
141A184LYS10.8790.92350.960-0.029-0.0290.0000.0000.0000.000
142A185ASP-1-0.786-0.88250.3040.0240.0240.0000.0000.0000.000
143A186PRO00.0200.00653.066-0.001-0.0010.0000.0000.0000.000
144A187THR00.0110.00252.897-0.001-0.0010.0000.0000.0000.000
145A188THR00.0490.02452.565-0.001-0.0010.0000.0000.0000.000
146A189GLN0-0.0010.00555.144-0.001-0.0010.0000.0000.0000.000
147A190LYS10.9050.93958.384-0.015-0.0150.0000.0000.0000.000
148A191LEU00.0900.06353.3060.0000.0000.0000.0000.0000.000
149A192ARG10.8940.91155.115-0.021-0.0210.0000.0000.0000.000
150A193ASN00.000-0.00556.8580.0010.0010.0000.0000.0000.000
151A194ASP-1-0.837-0.91760.3180.0130.0130.0000.0000.0000.000
152A195LEU00.0070.00254.0690.0000.0000.0000.0000.0000.000
153A196LEU0-0.016-0.00958.0580.0000.0000.0000.0000.0000.000
154A197ASN0-0.019-0.00260.0470.0000.0000.0000.0000.0000.000
155A198ILE00.0330.01758.7980.0000.0000.0000.0000.0000.000
156A199ILE0-0.010-0.00655.6870.0000.0000.0000.0000.0000.000
157A200ARG10.8800.94259.984-0.016-0.0160.0000.0000.0000.000
158A201GLU-1-0.893-0.95663.5140.0120.0120.0000.0000.0000.000
159A202LYS10.8610.94761.388-0.016-0.0160.0000.0000.0000.000
160A203ASN0-0.021-0.01062.428-0.001-0.0010.0000.0000.0000.000
161A204LEU00.011-0.02057.6730.0000.0000.0000.0000.0000.000
162A205ALA0-0.0120.00560.3230.0000.0000.0000.0000.0000.000
163A206HIS00.0250.02861.231-0.001-0.0010.0000.0000.0000.000
164A207PRO00.012-0.00360.5860.0000.0000.0000.0000.0000.000
165A208VAL00.0170.00956.4090.0000.0000.0000.0000.0000.000
166A209ILE00.0070.01355.9090.0000.0000.0000.0000.0000.000
167A210GLN00.0110.00856.0930.0000.0000.0000.0000.0000.000
168A211ASN0-0.056-0.04356.927-0.001-0.0010.0000.0000.0000.000
169A212PHE0-0.0250.01648.1430.0000.0000.0000.0000.0000.000
170A213SER00.0330.01550.6930.0000.0000.0000.0000.0000.000
171A214TYR00.053-0.00841.7500.0010.0010.0000.0000.0000.000
172A215GLU-1-0.682-0.78243.9250.0040.0040.0000.0000.0000.000
173A216THR0-0.045-0.03345.058-0.001-0.0010.0000.0000.0000.000
174A217PHE0-0.025-0.01542.5590.0000.0000.0000.0000.0000.000
175A218GLN00.0270.01741.0140.0000.0000.0000.0000.0000.000
176A219GLN00.015-0.02140.7320.0010.0010.0000.0000.0000.000
177A220LYS10.8600.93941.726-0.011-0.0110.0000.0000.0000.000
178A221MET0-0.015-0.00139.1610.0010.0010.0000.0000.0000.000
179A222LEU00.0080.02535.2590.0020.0020.0000.0000.0000.000
180A223ARG10.9690.97837.037-0.003-0.0030.0000.0000.0000.000
181A224PHE0-0.0170.00737.6810.0000.0000.0000.0000.0000.000
182A225LEU0-0.0050.00034.0750.0020.0020.0000.0000.0000.000
183A226GLU-1-0.772-0.88933.4770.0020.0020.0000.0000.0000.000
184A227SER0-0.101-0.05233.8820.0000.0000.0000.0000.0000.000
185A228HIS00.0040.01232.9540.0020.0020.0000.0000.0000.000
186A229LEU0-0.068-0.04228.1810.0060.0060.0000.0000.0000.000
187A230ASP-1-0.866-0.93525.912-0.010-0.0100.0000.0000.0000.000
188A231ASP-1-0.929-0.96828.974-0.011-0.0110.0000.0000.0000.000
189A232ALA0-0.070-0.01426.227-0.006-0.0060.0000.0000.0000.000
190A233GLU-1-0.774-0.84927.185-0.060-0.0600.0000.0000.0000.000
191A234PRO0-0.0100.00823.440-0.006-0.0060.0000.0000.0000.000
192A235TYR00.029-0.00817.0950.0040.0040.0000.0000.0000.000
193A236LEU00.0620.02318.070-0.009-0.0090.0000.0000.0000.000
194A237LEU00.0180.02622.010-0.004-0.0040.0000.0000.0000.000
195A238THR0-0.028-0.04124.353-0.002-0.0020.0000.0000.0000.000
196A239MET0-0.047-0.01520.0900.0020.0020.0000.0000.0000.000
197A240ALA00.0300.01824.091-0.002-0.0020.0000.0000.0000.000
198A241LYS10.8640.90326.2110.0590.0590.0000.0000.0000.000
199A242LYS10.8160.91125.0450.1070.1070.0000.0000.0000.000
200A243ALA00.0110.00525.5800.0010.0010.0000.0000.0000.000
201A244LEU00.0380.00827.5500.0030.0030.0000.0000.0000.000
202A245LYS10.8820.95630.8170.0840.0840.0000.0000.0000.000
203A246SER0-0.032-0.01529.5870.0060.0060.0000.0000.0000.000
204A247GLU-1-0.982-0.96930.893-0.085-0.0850.0000.0000.0000.000