FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4LN6N

Calculation Name: 1JEY-A-Xray372

Preferred Name: DNA-PK/Ku70/Ku85

Target Type: PROTEIN COMPLEX

Ligand Name:

ligand 3-letter code:

PDB ID: 1JEY

Chain ID: A

ChEMBL ID: CHEMBL4106136

UniProt ID: P13010

Base Structure: X-ray

Registration Date: 2023-09-26

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 493
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8908630.886135
FMO2-HF: Nuclear repulsion 8710308.202218
FMO2-HF: Total energy -198322.683917
FMO2-MP2: Total energy -198900.414193


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:34:GLY)


Summations of interaction energy for fragment #1(A:34: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.
-1.8371.840.269-1.668-2.279-0.006
Interaction energy analysis for fragmet #1(A:34:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.017
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].
3A36ASP-1-0.691-0.7843.692-1.302-0.0030.000-0.561-0.738-0.001
4A37SER0-0.027-0.0255.7630.5570.5570.0000.0000.0000.000
5A38LEU0-0.032-0.0148.951-0.067-0.0670.0000.0000.0000.000
6A39ILE00.0170.02212.6160.0260.0260.0000.0000.0000.000
7A40PHE00.013-0.00315.712-0.020-0.0200.0000.0000.0000.000
8A41LEU0-0.010-0.00518.8650.0240.0240.0000.0000.0000.000
9A42VAL0-0.007-0.00721.715-0.011-0.0110.0000.0000.0000.000
10A43ASP-1-0.725-0.79825.272-0.025-0.0250.0000.0000.0000.000
11A44ALA00.0300.01028.505-0.004-0.0040.0000.0000.0000.000
12A45SER00.021-0.03531.4760.0060.0060.0000.0000.0000.000
13A46LYS10.8310.89034.1590.0230.0230.0000.0000.0000.000
14A47ALA00.0260.01535.938-0.001-0.0010.0000.0000.0000.000
15A48MET0-0.0070.04028.757-0.005-0.0050.0000.0000.0000.000
16A49PHE0-0.068-0.03232.554-0.003-0.0030.0000.0000.0000.000
17A50GLU-1-0.790-0.89536.202-0.027-0.0270.0000.0000.0000.000
18A51SER0-0.0020.00337.710-0.001-0.0010.0000.0000.0000.000
19A52GLN0-0.033-0.03936.5020.0000.0000.0000.0000.0000.000
20A53SER0-0.070-0.02641.1920.0020.0020.0000.0000.0000.000
21A54GLU-1-0.801-0.86839.545-0.055-0.0550.0000.0000.0000.000
22A55ASP-1-0.956-0.97541.520-0.044-0.0440.0000.0000.0000.000
23A56GLU-1-0.868-0.93534.894-0.078-0.0780.0000.0000.0000.000
24A57LEU0-0.045-0.03732.0840.0040.0040.0000.0000.0000.000
25A58THR0-0.012-0.00234.636-0.001-0.0010.0000.0000.0000.000
26A59PRO00.0300.00931.810-0.005-0.0050.0000.0000.0000.000
27A60PHE00.0130.02229.264-0.008-0.0080.0000.0000.0000.000
28A61ASP-1-0.767-0.87229.234-0.067-0.0670.0000.0000.0000.000
29A62MET0-0.0300.00529.203-0.010-0.0100.0000.0000.0000.000
30A63SER00.025-0.01525.639-0.013-0.0130.0000.0000.0000.000
31A64ILE0-0.027-0.00124.989-0.012-0.0120.0000.0000.0000.000
32A65GLN0-0.029-0.02925.344-0.014-0.0140.0000.0000.0000.000
33A66CYS0-0.0130.02322.500-0.015-0.0150.0000.0000.0000.000
34A67ILE0-0.017-0.00320.065-0.022-0.0220.0000.0000.0000.000
35A68GLN0-0.043-0.05120.747-0.019-0.0190.0000.0000.0000.000
36A69SER0-0.012-0.01022.072-0.009-0.0090.0000.0000.0000.000
37A70VAL0-0.0150.02616.280-0.019-0.0190.0000.0000.0000.000
38A71TYR0-0.019-0.04317.544-0.041-0.0410.0000.0000.0000.000
39A72ILE00.0220.01318.198-0.014-0.0140.0000.0000.0000.000
40A73SER0-0.007-0.00918.641-0.006-0.0060.0000.0000.0000.000
41A74LYS10.7870.88810.8590.7820.7820.0000.0000.0000.000
42A75ILE0-0.0030.01414.875-0.032-0.0320.0000.0000.0000.000
43A76ILE0-0.042-0.01917.2190.0000.0000.0000.0000.0000.000
44A77SER0-0.085-0.06514.954-0.016-0.0160.0000.0000.0000.000
45A78SER0-0.091-0.04614.309-0.018-0.0180.0000.0000.0000.000
46A79ASP-1-0.847-0.90110.157-1.112-1.1120.0000.0000.0000.000
47A80ARG10.8490.8973.5511.8622.2160.015-0.149-0.2200.000
48A81ASP-1-0.830-0.9027.412-1.709-1.7090.0000.0000.0000.000
49A82LEU0-0.083-0.0228.2500.2230.2230.0000.0000.0000.000
50A83LEU0-0.008-0.00910.518-0.041-0.0410.0000.0000.0000.000
51A84ALA00.0380.01613.9820.0570.0570.0000.0000.0000.000
52A85VAL0-0.026-0.00316.698-0.032-0.0320.0000.0000.0000.000
53A86VAL0-0.003-0.00319.6840.0210.0210.0000.0000.0000.000
54A87PHE00.0310.01822.420-0.015-0.0150.0000.0000.0000.000
55A88TYR00.007-0.02925.6350.0090.0090.0000.0000.0000.000
56A89GLY00.0590.03628.260-0.006-0.0060.0000.0000.0000.000
57A90THR0-0.068-0.03330.044-0.003-0.0030.0000.0000.0000.000
58A91GLU-1-0.931-0.95232.5160.0080.0080.0000.0000.0000.000
59A92LYS10.8700.95032.237-0.011-0.0110.0000.0000.0000.000
60A93ASP-1-0.821-0.89529.4410.0290.0290.0000.0000.0000.000
61A94LYS10.8150.88723.038-0.057-0.0570.0000.0000.0000.000
62A95ASN0-0.029-0.03324.0360.0060.0060.0000.0000.0000.000
63A96SER00.011-0.00121.479-0.011-0.0110.0000.0000.0000.000
64A97VAL0-0.0090.00224.1620.0040.0040.0000.0000.0000.000
65A98ASN0-0.057-0.02326.692-0.009-0.0090.0000.0000.0000.000
66A99PHE00.0100.01125.652-0.005-0.0050.0000.0000.0000.000
67A100LYS10.8380.90829.372-0.033-0.0330.0000.0000.0000.000
68A101ASN0-0.009-0.00930.6020.0000.0000.0000.0000.0000.000
69A102ILE00.0260.01125.019-0.006-0.0060.0000.0000.0000.000
70A103TYR00.0100.00526.6260.0120.0120.0000.0000.0000.000
71A104VAL00.0190.00420.496-0.011-0.0110.0000.0000.0000.000
72A105LEU0-0.0230.00523.2490.0080.0080.0000.0000.0000.000
73A106GLN0-0.035-0.01619.134-0.003-0.0030.0000.0000.0000.000
74A107GLU-1-0.773-0.87917.1900.0760.0760.0000.0000.0000.000
75A108LEU0-0.038-0.01811.190-0.032-0.0320.0000.0000.0000.000
76A109ASP-1-0.817-0.89112.9150.1840.1840.0000.0000.0000.000
77A110ASN0-0.038-0.03311.156-0.156-0.1560.0000.0000.0000.000
78A111PRO00.0310.03313.1300.0420.0420.0000.0000.0000.000
79A112GLY00.025-0.00916.0950.0010.0010.0000.0000.0000.000
80A113ALA00.0380.01719.1690.0040.0040.0000.0000.0000.000
81A114LYS11.0060.99722.923-0.006-0.0060.0000.0000.0000.000
82A115ARG10.8310.92717.402-0.019-0.0190.0000.0000.0000.000
83A116ILE00.0280.02320.406-0.005-0.0050.0000.0000.0000.000
84A117LEU00.0460.01423.5140.0020.0020.0000.0000.0000.000
85A118GLU-1-0.863-0.93124.248-0.004-0.0040.0000.0000.0000.000
86A119LEU00.0180.00821.7310.0020.0020.0000.0000.0000.000
87A120ASP-1-0.792-0.87926.339-0.069-0.0690.0000.0000.0000.000
88A121GLN0-0.095-0.04629.3260.0060.0060.0000.0000.0000.000
89A122PHE0-0.002-0.01827.1210.0050.0050.0000.0000.0000.000
90A123LYS10.8610.95128.8090.0740.0740.0000.0000.0000.000
91A124GLY00.0370.01331.7200.0050.0050.0000.0000.0000.000
92A125GLN0-0.012-0.00835.1460.0020.0020.0000.0000.0000.000
93A126GLN00.019-0.00637.5060.0010.0010.0000.0000.0000.000
94A127GLY00.0310.01833.6770.0040.0040.0000.0000.0000.000
95A128GLN00.0330.01934.0080.0000.0000.0000.0000.0000.000
96A129LYS10.8290.89135.2460.0150.0150.0000.0000.0000.000
97A130ARG10.8890.94434.2050.0320.0320.0000.0000.0000.000
98A131PHE00.0120.00128.6460.0040.0040.0000.0000.0000.000
99A132GLN0-0.019-0.01233.3400.0050.0050.0000.0000.0000.000
100A133ASP-1-0.811-0.87736.188-0.006-0.0060.0000.0000.0000.000
101A134MET0-0.072-0.01531.1660.0040.0040.0000.0000.0000.000
102A135MET0-0.072-0.04527.9530.0060.0060.0000.0000.0000.000
103A136GLY00.1090.06533.5360.0020.0020.0000.0000.0000.000
104A137HIS0-0.054-0.04334.127-0.001-0.0010.0000.0000.0000.000
105A138GLY0-0.047-0.02135.2260.0020.0020.0000.0000.0000.000
106A139SER0-0.0330.00034.9170.0020.0020.0000.0000.0000.000
107A140ASP-1-0.813-0.90634.960-0.002-0.0020.0000.0000.0000.000
108A141TYR00.008-0.00230.2630.0020.0020.0000.0000.0000.000
109A142SER0-0.032-0.06130.389-0.003-0.0030.0000.0000.0000.000
110A143LEU00.0530.00125.8020.0050.0050.0000.0000.0000.000
111A144SER0-0.0010.00225.5320.0010.0010.0000.0000.0000.000
112A145GLU-1-0.849-0.88425.2200.0330.0330.0000.0000.0000.000
113A146VAL00.0180.01623.3080.0090.0090.0000.0000.0000.000
114A147LEU00.0220.00920.6640.0040.0040.0000.0000.0000.000
115A148TRP00.010-0.00420.3660.0150.0150.0000.0000.0000.000
116A149VAL00.0040.00920.6860.0220.0220.0000.0000.0000.000
117A150CYS0-0.050-0.03317.8220.0130.0130.0000.0000.0000.000
118A151ALA00.008-0.00416.2940.0160.0160.0000.0000.0000.000
119A152ASN0-0.058-0.01815.9760.0370.0370.0000.0000.0000.000
120A153LEU00.0510.03515.6920.0450.0450.0000.0000.0000.000
121A154PHE0-0.058-0.04110.8140.0410.0410.0000.0000.0000.000
122A155SER0-0.061-0.04111.7810.1270.1270.0000.0000.0000.000
123A156ASP-1-0.853-0.92114.3360.2810.2810.0000.0000.0000.000
124A157VAL0-0.069-0.0209.4200.0220.0220.0000.0000.0000.000
125A158GLN00.0700.02811.2080.1570.1570.0000.0000.0000.000
126A159PHE0-0.032-0.0256.3850.1060.1060.0000.0000.0000.000
127A160LYS10.9590.9704.107-2.133-1.9330.003-0.051-0.1510.000
128A161MET00.0310.0323.8061.9022.2330.035-0.199-0.1680.001
129A162SER0-0.079-0.0672.985-3.705-2.3360.211-0.677-0.904-0.006
130A163HIS0-0.016-0.0063.8350.7960.9200.005-0.031-0.0980.000
131A164LYS10.8980.9456.527-0.281-0.2810.0000.0000.0000.000
132A165ARG10.8060.9019.9900.3860.3860.0000.0000.0000.000
133A166ILE00.0280.02312.8720.0120.0120.0000.0000.0000.000
134A167MET0-0.025-0.00416.381-0.024-0.0240.0000.0000.0000.000
135A168LEU00.0070.01118.6890.0110.0110.0000.0000.0000.000
136A169PHE00.0160.00220.674-0.011-0.0110.0000.0000.0000.000
137A170THR00.008-0.05225.2550.0100.0100.0000.0000.0000.000
138A171ASN00.003-0.00928.750-0.005-0.0050.0000.0000.0000.000
139A172GLU-1-0.807-0.88931.577-0.033-0.0330.0000.0000.0000.000
140A173ASP-1-0.790-0.90131.347-0.047-0.0470.0000.0000.0000.000
141A174ASN00.019-0.02332.5940.0010.0010.0000.0000.0000.000
142A175PRO00.0120.00930.2370.0040.0040.0000.0000.0000.000
143A176HIS0-0.010-0.00231.3160.0060.0060.0000.0000.0000.000
144A177GLY00.0380.03135.0890.0020.0020.0000.0000.0000.000
145A178ASN0-0.035-0.01337.856-0.001-0.0010.0000.0000.0000.000
146A179ASP-1-0.824-0.91736.7430.0030.0030.0000.0000.0000.000
147A180SER00.0650.02536.3070.0000.0000.0000.0000.0000.000
148A181ALA0-0.0050.01836.0210.0010.0010.0000.0000.0000.000
149A182LYS10.8300.91032.8270.0020.0020.0000.0000.0000.000
150A183ALA00.0160.00431.6790.0000.0000.0000.0000.0000.000
151A184SER0-0.044-0.03531.448-0.001-0.0010.0000.0000.0000.000
152A185ARG10.9170.96229.967-0.017-0.0170.0000.0000.0000.000
153A186ALA00.0260.01627.3850.0030.0030.0000.0000.0000.000
154A187ARG10.8270.90326.3710.0270.0270.0000.0000.0000.000
155A188THR0-0.040-0.03026.474-0.002-0.0020.0000.0000.0000.000
156A189LYS10.7920.90020.309-0.063-0.0630.0000.0000.0000.000
157A190ALA00.0380.01222.1470.0020.0020.0000.0000.0000.000
158A191GLY0-0.030-0.01021.665-0.011-0.0110.0000.0000.0000.000
159A192ASP-1-0.811-0.89420.9600.0560.0560.0000.0000.0000.000
160A193LEU0-0.023-0.00217.2370.0110.0110.0000.0000.0000.000
161A194ARG10.8790.94316.8710.0560.0560.0000.0000.0000.000
162A195ASP-1-0.931-0.95717.339-0.037-0.0370.0000.0000.0000.000
163A196THR0-0.091-0.05114.6560.0190.0190.0000.0000.0000.000
164A197GLY0-0.051-0.02013.1800.0250.0250.0000.0000.0000.000
165A198ILE0-0.101-0.04812.251-0.044-0.0440.0000.0000.0000.000
166A199PHE00.003-0.01311.598-0.018-0.0180.0000.0000.0000.000
167A200LEU00.0150.00715.1430.0090.0090.0000.0000.0000.000
168A201ASP-1-0.791-0.87716.478-0.262-0.2620.0000.0000.0000.000
169A202LEU0-0.027-0.01319.3550.0140.0140.0000.0000.0000.000
170A203MET0-0.059-0.02620.119-0.011-0.0110.0000.0000.0000.000
171A204HIS00.0140.02124.3390.0050.0050.0000.0000.0000.000
172A205LEU0-0.032-0.02227.422-0.006-0.0060.0000.0000.0000.000
173A206LYS10.8690.91330.6190.0610.0610.0000.0000.0000.000
174A207LYS10.8380.91834.3670.0440.0440.0000.0000.0000.000
175A208PRO0-0.024-0.00836.683-0.001-0.0010.0000.0000.0000.000
176A209GLY0-0.018-0.01240.5460.0020.0020.0000.0000.0000.000
177A210GLY0-0.0220.00736.999-0.001-0.0010.0000.0000.0000.000
178A211PHE0-0.037-0.01229.3870.0020.0020.0000.0000.0000.000
179A212ASP-1-0.793-0.87833.533-0.059-0.0590.0000.0000.0000.000
180A213ILE00.000-0.02127.7750.0030.0030.0000.0000.0000.000
181A214SER0-0.144-0.09731.1350.0030.0030.0000.0000.0000.000
182A215LEU00.0030.01533.4430.0030.0030.0000.0000.0000.000
183A216PHE0-0.042-0.03228.9690.0060.0060.0000.0000.0000.000
184A217TYR00.0400.01826.056-0.001-0.0010.0000.0000.0000.000
185A218ARG10.9670.99426.7170.0490.0490.0000.0000.0000.000
186A219ASP-1-0.837-0.88727.468-0.047-0.0470.0000.0000.0000.000
187A220ILE0-0.051-0.01923.7190.0050.0050.0000.0000.0000.000
188A221ILE00.0150.01322.087-0.004-0.0040.0000.0000.0000.000
189A222SER0-0.061-0.02717.728-0.022-0.0220.0000.0000.0000.000
190A231VAL00.0150.00627.4050.0040.0040.0000.0000.0000.000
191A232HIS0-0.092-0.05224.348-0.019-0.0190.0000.0000.0000.000
192A233PHE00.008-0.00321.722-0.001-0.0010.0000.0000.0000.000
193A234GLU-1-0.766-0.86127.155-0.082-0.0820.0000.0000.0000.000
194A235GLU-1-0.814-0.90228.944-0.075-0.0750.0000.0000.0000.000
195A236SER0-0.051-0.04127.385-0.004-0.0040.0000.0000.0000.000
196A237SER00.0390.01730.5200.0040.0040.0000.0000.0000.000
197A238LYS10.8600.91732.3040.0940.0940.0000.0000.0000.000
198A239LEU00.0430.02027.955-0.008-0.0080.0000.0000.0000.000
199A240GLU-1-0.802-0.88228.502-0.106-0.1060.0000.0000.0000.000
200A241ASP-1-0.787-0.88427.957-0.121-0.1210.0000.0000.0000.000
201A242LEU00.0060.01525.134-0.011-0.0110.0000.0000.0000.000
202A243LEU00.0450.00623.040-0.018-0.0180.0000.0000.0000.000
203A244ARG10.7410.84923.0850.1110.1110.0000.0000.0000.000
204A245LYS10.8190.89922.8820.0990.0990.0000.0000.0000.000
205A246VAL00.030-0.00319.097-0.022-0.0220.0000.0000.0000.000
206A247ARG10.8980.93118.5130.1560.1560.0000.0000.0000.000
207A248ALA0-0.059-0.01518.084-0.042-0.0420.0000.0000.0000.000
208A249LYS10.8290.90315.7030.2070.2070.0000.0000.0000.000
209A250GLU-1-0.877-0.94214.235-0.391-0.3910.0000.0000.0000.000
210A251THR00.0100.00511.092-0.112-0.1120.0000.0000.0000.000
211A252ARG10.8230.9038.8240.8520.8520.0000.0000.0000.000
212A253LYS10.9290.97011.5350.3230.3230.0000.0000.0000.000
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