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: 39G8L

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 OptHSide
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 -2407341.337159
FMO2-HF: Nuclear repulsion 2323361.840639
FMO2-HF: Total energy -83979.49652
FMO2-MP2: Total energy -84222.045196


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.
0.1681.8420.3940.031-2.0990.003
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 : 0 / q_Mulliken : 0.052 / q_NPA : 0.021
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].
3A46ALA00.0410.0052.7220.6191.6780.3940.180-1.6330.003
4A47ARG10.9400.9774.081-0.707-0.2360.001-0.128-0.3440.000
5A48LEU0-0.027-0.0095.074-0.168-0.024-0.001-0.021-0.1220.000
6A49GLU-1-0.752-0.8556.9430.5190.5190.0000.0000.0000.000
7A50GLU-1-0.887-0.9478.3750.9120.9120.0000.0000.0000.000
8A51ALA0-0.069-0.0389.555-0.043-0.0430.0000.0000.0000.000
9A52VAL00.0320.01011.2330.0050.0050.0000.0000.0000.000
10A53ASN0-0.011-0.03012.283-0.068-0.0680.0000.0000.0000.000
11A54ARG10.8870.94110.991-0.289-0.2890.0000.0000.0000.000
12A55TRP0-0.027-0.01214.148-0.012-0.0120.0000.0000.0000.000
13A56VAL00.0180.00817.0680.0010.0010.0000.0000.0000.000
14A57LEU00.0240.01518.651-0.001-0.0010.0000.0000.0000.000
15A58LYS10.8450.88718.499-0.082-0.0820.0000.0000.0000.000
16A59PHE0-0.036-0.01021.755-0.005-0.0050.0000.0000.0000.000
17A60TYR00.0680.01621.963-0.004-0.0040.0000.0000.0000.000
18A61PHE00.0460.02124.6760.0020.0020.0000.0000.0000.000
19A62HIS0-0.013-0.01726.287-0.001-0.0010.0000.0000.0000.000
20A63GLU-1-0.814-0.88927.915-0.016-0.0160.0000.0000.0000.000
21A64ALA00.0000.01229.135-0.001-0.0010.0000.0000.0000.000
22A65LEU00.0190.00630.4170.0000.0000.0000.0000.0000.000
23A66ARG10.8130.89532.1500.0130.0130.0000.0000.0000.000
24A67ALA0-0.025-0.01933.697-0.001-0.0010.0000.0000.0000.000
25A68PHE00.0100.00835.0070.0000.0000.0000.0000.0000.000
26A69ARG10.8350.89034.122-0.013-0.0130.0000.0000.0000.000
27A70GLY0-0.063-0.01638.410-0.001-0.0010.0000.0000.0000.000
28A71SER0-0.025-0.02640.103-0.002-0.0020.0000.0000.0000.000
29A72ARG10.8260.91534.6690.0040.0040.0000.0000.0000.000
30A73TYR00.018-0.05037.0840.0000.0000.0000.0000.0000.000
31A74GLY0-0.0080.01036.7060.0020.0020.0000.0000.0000.000
32A75ASP-1-0.805-0.89734.079-0.005-0.0050.0000.0000.0000.000
33A76PHE0-0.049-0.02532.4220.0010.0010.0000.0000.0000.000
34A77ARG10.9020.93531.800-0.014-0.0140.0000.0000.0000.000
35A78GLN00.0140.01531.0340.0000.0000.0000.0000.0000.000
36A79ILE0-0.026-0.01827.3120.0000.0000.0000.0000.0000.000
37A80ARG10.7690.84627.134-0.032-0.0320.0000.0000.0000.000
38A81ASP-1-0.820-0.90227.1810.0430.0430.0000.0000.0000.000
39A82ILE0-0.041-0.00422.7660.0050.0050.0000.0000.0000.000
40A83MET0-0.058-0.03122.6740.0070.0070.0000.0000.0000.000
41A84GLN0-0.0080.00422.5320.0280.0280.0000.0000.0000.000
42A85ALA00.0010.00221.6400.0150.0150.0000.0000.0000.000
43A86LEU0-0.022-0.02516.6390.0160.0160.0000.0000.0000.000
44A87LEU0-0.025-0.00517.7550.0370.0370.0000.0000.0000.000
45A88VAL0-0.0220.00517.2950.0310.0310.0000.0000.0000.000
46A89ARG10.8270.91410.748-0.258-0.2580.0000.0000.0000.000
47A90PRO0-0.0140.0099.869-0.006-0.0060.0000.0000.0000.000
48A91LEU00.0940.03212.544-0.053-0.0530.0000.0000.0000.000
49A92GLY0-0.0010.03812.627-0.043-0.0430.0000.0000.0000.000
50A93LYS10.9300.95413.076-0.415-0.4150.0000.0000.0000.000
51A94GLU-1-0.793-0.90016.4200.1230.1230.0000.0000.0000.000
52A95HIS00.0590.01618.638-0.009-0.0090.0000.0000.0000.000
53A96THR00.0170.00020.705-0.010-0.0100.0000.0000.0000.000
54A97VAL00.0230.00918.477-0.013-0.0130.0000.0000.0000.000
55A98SER00.0180.01221.5870.0010.0010.0000.0000.0000.000
56A99ARG10.8670.93423.375-0.087-0.0870.0000.0000.0000.000
57A100LEU00.0180.03022.809-0.007-0.0070.0000.0000.0000.000
58A101LEU00.012-0.01021.972-0.008-0.0080.0000.0000.0000.000
59A102ARG10.8170.89026.121-0.116-0.1160.0000.0000.0000.000
60A103VAL00.0410.01128.997-0.006-0.0060.0000.0000.0000.000
61A104MET00.0020.01327.528-0.007-0.0070.0000.0000.0000.000
62A105GLN0-0.0010.01028.412-0.004-0.0040.0000.0000.0000.000
63A106CYS0-0.055-0.01830.932-0.006-0.0060.0000.0000.0000.000
64A107LEU00.0300.00332.385-0.003-0.0030.0000.0000.0000.000
65A108SER00.004-0.01831.488-0.005-0.0050.0000.0000.0000.000
66A109ARG10.8060.91831.770-0.071-0.0710.0000.0000.0000.000
67A110ILE00.0100.00236.606-0.003-0.0030.0000.0000.0000.000
68A111GLU-1-0.865-0.89836.2500.0210.0210.0000.0000.0000.000
69A112GLU-1-0.779-0.86136.2100.0290.0290.0000.0000.0000.000
70A113GLY0-0.039-0.02339.5180.0000.0000.0000.0000.0000.000
71A114GLU-1-0.960-0.99942.1450.0190.0190.0000.0000.0000.000
72A115ASN0-0.033-0.00140.196-0.003-0.0030.0000.0000.0000.000
73A116LEU0-0.077-0.04742.5640.0030.0030.0000.0000.0000.000
74A117ASP-1-0.893-0.94643.4810.0260.0260.0000.0000.0000.000
75A118CYS0-0.081-0.04038.4120.0010.0010.0000.0000.0000.000
76A119SER00.0110.00938.1230.0020.0020.0000.0000.0000.000
77A120PHE0-0.007-0.02733.3250.0030.0030.0000.0000.0000.000
78A121ASP-1-0.817-0.87033.9530.0730.0730.0000.0000.0000.000
79A122MET00.0210.01332.8300.0000.0000.0000.0000.0000.000
80A123GLU-1-0.929-0.96036.0570.0670.0670.0000.0000.0000.000
81A124ALA00.019-0.01239.593-0.002-0.0020.0000.0000.0000.000
82A125GLU-1-0.866-0.93040.6730.0380.0380.0000.0000.0000.000
83A126LEU0-0.068-0.02139.372-0.003-0.0030.0000.0000.0000.000
84A127THR00.037-0.00241.0850.0000.0000.0000.0000.0000.000
85A128PRO00.0700.03139.0440.0040.0040.0000.0000.0000.000
86A129LEU00.0530.01439.3510.0030.0030.0000.0000.0000.000
87A130GLU-1-0.833-0.88941.6000.0430.0430.0000.0000.0000.000
88A131SER0-0.036-0.05336.4800.0040.0040.0000.0000.0000.000
89A132ALA0-0.023-0.01637.0250.0040.0040.0000.0000.0000.000
90A133ILE0-0.052-0.01538.1030.0010.0010.0000.0000.0000.000
91A134ASN00.011-0.00336.9860.0000.0000.0000.0000.0000.000
92A135VAL00.003-0.00432.3780.0040.0040.0000.0000.0000.000
93A136LEU00.0000.01334.4380.0030.0030.0000.0000.0000.000
94A137GLU-1-0.806-0.88936.7880.0570.0570.0000.0000.0000.000
95A138MET0-0.040-0.00831.9170.0050.0050.0000.0000.0000.000
96A139ILE00.0300.02531.8380.0050.0050.0000.0000.0000.000
97A140LYS10.7840.88733.317-0.057-0.0570.0000.0000.0000.000
98A141THR0-0.044-0.02933.315-0.001-0.0010.0000.0000.0000.000
99A142GLU-1-0.811-0.88328.6240.1210.1210.0000.0000.0000.000
100A143PHE0-0.092-0.03729.3310.0050.0050.0000.0000.0000.000
101A144THR0-0.047-0.01531.897-0.003-0.0030.0000.0000.0000.000
102A145LEU0-0.0200.00634.490-0.005-0.0050.0000.0000.0000.000
103A146THR00.027-0.00237.3060.0000.0000.0000.0000.0000.000
104A147GLU-1-0.748-0.87140.9610.0480.0480.0000.0000.0000.000
105A148ALA0-0.004-0.00443.318-0.001-0.0010.0000.0000.0000.000
106A149VAL0-0.0130.00339.202-0.002-0.0020.0000.0000.0000.000
107A150VAL0-0.002-0.00538.660-0.001-0.0010.0000.0000.0000.000
108A151GLU-1-0.871-0.93741.6730.0340.0340.0000.0000.0000.000
109A152SER0-0.016-0.00745.165-0.001-0.0010.0000.0000.0000.000
110A153SER00.0510.01241.336-0.002-0.0020.0000.0000.0000.000
111A154ARG10.8380.89240.851-0.049-0.0490.0000.0000.0000.000
112A155LYS10.7850.89343.831-0.034-0.0340.0000.0000.0000.000
113A156LEU00.0320.02145.169-0.001-0.0010.0000.0000.0000.000
114A157VAL00.0370.01541.283-0.001-0.0010.0000.0000.0000.000
115A158LYS10.8350.92044.634-0.041-0.0410.0000.0000.0000.000
116A159GLU-1-0.936-0.97747.0830.0230.0230.0000.0000.0000.000
117A160ALA00.0180.00846.014-0.001-0.0010.0000.0000.0000.000
118A161ALA00.0030.00045.418-0.001-0.0010.0000.0000.0000.000
119A162VAL0-0.035-0.01547.100-0.001-0.0010.0000.0000.0000.000
120A163ILE00.0110.00050.793-0.001-0.0010.0000.0000.0000.000
121A164ILE00.0250.02246.717-0.002-0.0020.0000.0000.0000.000
122A165CYS0-0.0060.01048.8950.0000.0000.0000.0000.0000.000
123A166ILE0-0.059-0.03350.761-0.001-0.0010.0000.0000.0000.000
124A167LYS10.8530.91952.403-0.017-0.0170.0000.0000.0000.000
125A168ASN0-0.0170.00149.283-0.002-0.0020.0000.0000.0000.000
126A169LYS10.9000.94452.842-0.015-0.0150.0000.0000.0000.000
127A170GLU-1-0.795-0.88349.1420.0280.0280.0000.0000.0000.000
128A171PHE0-0.014-0.03353.2990.0010.0010.0000.0000.0000.000
129A172GLU-1-0.920-0.96654.4570.0290.0290.0000.0000.0000.000
130A173LYS10.8680.93445.592-0.038-0.0380.0000.0000.0000.000
131A174ALA00.0360.01551.1590.0010.0010.0000.0000.0000.000
132A175SER0-0.020-0.01252.5920.0010.0010.0000.0000.0000.000
133A176LYS10.9120.96348.465-0.036-0.0360.0000.0000.0000.000
134A177ILE0-0.0110.01047.2200.0020.0020.0000.0000.0000.000
135A178LEU00.0140.00549.7030.0010.0010.0000.0000.0000.000
136A179LYN00.0120.01752.5390.0000.0000.0000.0000.0000.000
137A180LYS10.9220.99044.216-0.048-0.0480.0000.0000.0000.000
138A181HIS00.007-0.01043.6700.0020.0020.0000.0000.0000.000
139A182MET00.0080.01548.9710.0000.0000.0000.0000.0000.000
140A183SER0-0.066-0.03552.113-0.001-0.0010.0000.0000.0000.000
141A184LYS10.9300.95651.198-0.037-0.0370.0000.0000.0000.000
142A185ASP-1-0.816-0.89951.0170.0330.0330.0000.0000.0000.000
143A186PRO00.003-0.00253.441-0.001-0.0010.0000.0000.0000.000
144A187THR00.011-0.00152.700-0.002-0.0020.0000.0000.0000.000
145A188THR00.0050.00352.548-0.001-0.0010.0000.0000.0000.000
146A189GLN00.026-0.00155.397-0.001-0.0010.0000.0000.0000.000
147A190LYS10.9170.94558.853-0.020-0.0200.0000.0000.0000.000
148A191LEU00.0840.07953.288-0.001-0.0010.0000.0000.0000.000
149A192ARG10.9490.94055.638-0.027-0.0270.0000.0000.0000.000
150A193ASN0-0.037-0.02657.3460.0010.0010.0000.0000.0000.000
151A194ASP-1-0.870-0.92060.2040.0180.0180.0000.0000.0000.000
152A195LEU00.004-0.01254.2690.0000.0000.0000.0000.0000.000
153A196LEU0-0.028-0.01358.1410.0000.0000.0000.0000.0000.000
154A197ASN0-0.0010.00259.9970.0000.0000.0000.0000.0000.000
155A198ILE00.0190.02459.039-0.001-0.0010.0000.0000.0000.000
156A199ILE0-0.016-0.01355.673-0.001-0.0010.0000.0000.0000.000
157A200ARG10.8740.93659.864-0.019-0.0190.0000.0000.0000.000
158A201GLU-1-0.925-0.96263.1500.0150.0150.0000.0000.0000.000
159A202LYS10.8640.94361.023-0.018-0.0180.0000.0000.0000.000
160A203ASN0-0.016-0.01162.304-0.001-0.0010.0000.0000.0000.000
161A204LEU00.002-0.01157.5580.0000.0000.0000.0000.0000.000
162A205ALA00.0000.00460.1730.0000.0000.0000.0000.0000.000
163A206HIS00.0640.04861.190-0.001-0.0010.0000.0000.0000.000
164A207PRO00.0250.00160.7170.0000.0000.0000.0000.0000.000
165A208VAL00.0250.01356.8110.0000.0000.0000.0000.0000.000
166A209ILE0-0.0060.00455.9550.0010.0010.0000.0000.0000.000
167A210GLN00.001-0.00456.1000.0000.0000.0000.0000.0000.000
168A211ASN0-0.065-0.03857.177-0.001-0.0010.0000.0000.0000.000
169A212PHE0-0.0230.01648.3940.0000.0000.0000.0000.0000.000
170A213SER00.0090.00750.4670.0000.0000.0000.0000.0000.000
171A214TYR00.069-0.01242.0440.0020.0020.0000.0000.0000.000
172A215GLU-1-0.717-0.80544.2230.0150.0150.0000.0000.0000.000
173A216THR0-0.028-0.03645.1840.0000.0000.0000.0000.0000.000
174A217PHE0-0.028-0.01042.8680.0010.0010.0000.0000.0000.000
175A218GLN00.0430.01840.8210.0010.0010.0000.0000.0000.000
176A219GLN00.027-0.00740.8790.0030.0030.0000.0000.0000.000
177A220LYS10.8610.94241.788-0.020-0.0200.0000.0000.0000.000
178A221MET0-0.032-0.00839.5440.0020.0020.0000.0000.0000.000
179A222LEU0-0.0020.01935.0670.0030.0030.0000.0000.0000.000
180A223ARG10.9810.98537.153-0.017-0.0170.0000.0000.0000.000
181A224PHE0-0.0050.01537.5540.0010.0010.0000.0000.0000.000
182A225LEU0-0.005-0.00334.2350.0030.0030.0000.0000.0000.000
183A226GLU-1-0.768-0.88633.6550.0240.0240.0000.0000.0000.000
184A227SER0-0.092-0.03834.1580.0000.0000.0000.0000.0000.000
185A228HIS0-0.026-0.00633.0720.0030.0030.0000.0000.0000.000
186A229LEU0-0.075-0.05628.3230.0100.0100.0000.0000.0000.000
187A230ASP-1-0.880-0.93726.3480.0300.0300.0000.0000.0000.000
188A231ASP-1-0.910-0.96629.3660.0140.0140.0000.0000.0000.000
189A232ALA0-0.094-0.02526.223-0.006-0.0060.0000.0000.0000.000
190A233GLU-1-0.767-0.83227.139-0.031-0.0310.0000.0000.0000.000
191A234PRO0-0.0070.00123.492-0.002-0.0020.0000.0000.0000.000
192A235TYR00.030-0.00517.516-0.001-0.0010.0000.0000.0000.000
193A236LEU00.0460.00318.309-0.011-0.0110.0000.0000.0000.000
194A237LEU00.0180.02622.086-0.007-0.0070.0000.0000.0000.000
195A238THR0-0.036-0.04124.341-0.003-0.0030.0000.0000.0000.000
196A239MET0-0.055-0.03720.545-0.001-0.0010.0000.0000.0000.000
197A240ALA00.0150.02624.206-0.005-0.0050.0000.0000.0000.000
198A241LYS10.8880.91226.3150.0310.0310.0000.0000.0000.000
199A242LYS10.8620.93725.4550.0720.0720.0000.0000.0000.000
200A243ALA0-0.0100.01125.7830.0010.0010.0000.0000.0000.000
201A244LEU00.0310.00027.8150.0000.0000.0000.0000.0000.000
202A245LYS10.8470.92930.7870.0650.0650.0000.0000.0000.000
203A246SER0-0.044-0.01630.6430.0010.0010.0000.0000.0000.000
204A247GLU-1-0.923-0.94030.972-0.075-0.0750.0000.0000.0000.000