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: LR4Y9

Calculation Name: 1KN0-A-Xray549

Preferred Name: DNA repair protein RAD52 homolog

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1KN0

Chain ID: A

ChEMBL ID: CHEMBL2362978

UniProt ID: P43351

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -1752424.032398
FMO2-HF: Nuclear repulsion 1679261.003911
FMO2-HF: Total energy -73163.028487
FMO2-MP2: Total energy -73373.815884


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:25:CYS)


Summations of interaction energy for fragment #1(A:25:CYS)
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.
-6.527-7.50313.652-5.183-7.494-0.018
Interaction energy analysis for fragmet #1(A:25:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.037
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].
3A27GLY0-0.013-0.0073.8446.2317.9210.046-0.568-1.1690.000
4A28GLN0-0.030-0.0092.096-4.277-5.3497.008-2.255-3.6820.006
5A29CYS0-0.068-0.0262.493-8.178-10.0516.597-2.252-2.471-0.023
6A30GLN00.0470.0273.9283.3073.5860.001-0.108-0.172-0.001
7A31TYR0-0.010-0.0087.731-0.610-0.6100.0000.0000.0000.000
8A32THR00.010-0.00610.4470.2050.2050.0000.0000.0000.000
9A33ALA00.0250.01012.7920.2200.2200.0000.0000.0000.000
10A34GLU-1-0.848-0.92515.546-2.005-2.0050.0000.0000.0000.000
11A35GLU-1-0.787-0.87211.084-3.542-3.5420.0000.0000.0000.000
12A36TYR00.0400.01914.6340.2330.2330.0000.0000.0000.000
13A37GLN00.001-0.00315.8450.3270.3270.0000.0000.0000.000
14A38ALA0-0.013-0.00718.1170.1640.1640.0000.0000.0000.000
15A39ILE00.0610.03214.2260.1850.1850.0000.0000.0000.000
16A40GLN00.0380.02218.4020.1340.1340.0000.0000.0000.000
17A41LYS10.7920.89920.5410.9710.9710.0000.0000.0000.000
18A42ALA00.0520.03321.0140.0920.0920.0000.0000.0000.000
19A43LEU00.0690.02618.2800.0950.0950.0000.0000.0000.000
20A44ARG10.8860.93122.6750.7530.7530.0000.0000.0000.000
21A45GLN0-0.043-0.00624.6250.0830.0830.0000.0000.0000.000
22A46ARG10.8700.91927.5190.3010.3010.0000.0000.0000.000
23A47LEU0-0.0040.01626.118-0.006-0.0060.0000.0000.0000.000
24A48GLY00.0790.06330.0480.0260.0260.0000.0000.0000.000
25A49PRO00.009-0.02932.6770.0070.0070.0000.0000.0000.000
26A50GLU-1-0.879-0.92931.791-0.286-0.2860.0000.0000.0000.000
27A51TYR0-0.001-0.01026.0330.0040.0040.0000.0000.0000.000
28A52ILE0-0.087-0.02730.8160.0230.0230.0000.0000.0000.000
29A53SER00.008-0.00333.4800.0010.0010.0000.0000.0000.000
30A54SER0-0.042-0.05135.422-0.003-0.0030.0000.0000.0000.000
31A55ARG10.9400.98734.9120.0120.0120.0000.0000.0000.000
32A56MET00.0290.01840.033-0.011-0.0110.0000.0000.0000.000
33A57ALA0-0.0080.00642.0470.0090.0090.0000.0000.0000.000
34A58GLY00.0160.00343.183-0.001-0.0010.0000.0000.0000.000
35A59GLY00.0180.01645.5470.0030.0030.0000.0000.0000.000
36A60GLY0-0.010-0.00145.548-0.003-0.0030.0000.0000.0000.000
37A61GLN00.021-0.00144.3490.0020.0020.0000.0000.0000.000
38A62LYS10.9730.98240.3720.1140.1140.0000.0000.0000.000
39A63VAL0-0.0030.00737.104-0.008-0.0080.0000.0000.0000.000
40A64CYS0-0.022-0.02336.0680.0040.0040.0000.0000.0000.000
41A65TYR0-0.043-0.02131.7820.0120.0120.0000.0000.0000.000
42A66ILE00.0820.05127.457-0.010-0.0100.0000.0000.0000.000
43A67GLU-1-0.802-0.88929.271-0.093-0.0930.0000.0000.0000.000
44A68GLY00.0410.00825.545-0.023-0.0230.0000.0000.0000.000
45A69HIS00.015-0.00724.049-0.044-0.0440.0000.0000.0000.000
46A70ARG10.8600.93923.9360.1540.1540.0000.0000.0000.000
47A71VAL00.0150.00521.843-0.048-0.0480.0000.0000.0000.000
48A72ILE00.0320.02118.865-0.050-0.0500.0000.0000.0000.000
49A73ASN0-0.010-0.00918.969-0.100-0.1000.0000.0000.0000.000
50A74LEU0-0.0230.00020.019-0.073-0.0730.0000.0000.0000.000
51A75ALA00.0190.00516.597-0.095-0.0950.0000.0000.0000.000
52A76ASN0-0.011-0.00515.365-0.190-0.1900.0000.0000.0000.000
53A77GLU-1-0.924-0.95415.654-1.069-1.0690.0000.0000.0000.000
54A78MET0-0.130-0.04717.295-0.081-0.0810.0000.0000.0000.000
55A79PHE0-0.002-0.01512.116-0.055-0.0550.0000.0000.0000.000
56A80GLY00.0840.05511.516-0.484-0.4840.0000.0000.0000.000
57A81TYR0-0.016-0.02910.769-0.005-0.0050.0000.0000.0000.000
58A82ASN0-0.0090.0016.6280.4030.4030.0000.0000.0000.000
59A83GLY00.0120.0147.268-0.761-0.7610.0000.0000.0000.000
60A84TRP0-0.064-0.0519.1150.1300.1300.0000.0000.0000.000
61A85ALA00.0380.0279.9640.1190.1190.0000.0000.0000.000
62A86HIS0-0.011-0.01911.995-0.077-0.0770.0000.0000.0000.000
63A87SER0-0.0200.00414.3560.2240.2240.0000.0000.0000.000
64A88ILE0-0.018-0.02316.194-0.135-0.1350.0000.0000.0000.000
65A89THR0-0.032-0.02919.8230.1200.1200.0000.0000.0000.000
66A90GLN00.0110.00320.6160.0460.0460.0000.0000.0000.000
67A91GLN0-0.021-0.00424.163-0.038-0.0380.0000.0000.0000.000
68A92ASN0-0.030-0.01426.8450.0410.0410.0000.0000.0000.000
69A93VAL0-0.032-0.02530.579-0.024-0.0240.0000.0000.0000.000
70A94ASP-1-0.788-0.85933.6320.2450.2450.0000.0000.0000.000
71A95PHE00.0110.01436.157-0.005-0.0050.0000.0000.0000.000
72A96VAL0-0.053-0.04937.8630.0030.0030.0000.0000.0000.000
73A97ASP-1-0.845-0.90240.5280.1590.1590.0000.0000.0000.000
74A98LEU0-0.062-0.04244.193-0.004-0.0040.0000.0000.0000.000
75A99ASN00.0390.03146.903-0.003-0.0030.0000.0000.0000.000
76A100ASN0-0.007-0.02649.645-0.004-0.0040.0000.0000.0000.000
77A101GLY00.0060.00449.703-0.005-0.0050.0000.0000.0000.000
78A102LYS10.9350.97146.680-0.073-0.0730.0000.0000.0000.000
79A103PHE0-0.001-0.01341.9260.0060.0060.0000.0000.0000.000
80A104TYR0-0.0230.00342.190-0.008-0.0080.0000.0000.0000.000
81A105VAL0-0.022-0.01936.1000.0110.0110.0000.0000.0000.000
82A106GLY00.0580.04236.220-0.015-0.0150.0000.0000.0000.000
83A107VAL0-0.045-0.03030.0160.0220.0220.0000.0000.0000.000
84A108CYS00.0230.02130.028-0.013-0.0130.0000.0000.0000.000
85A109ALA0-0.032-0.02824.8370.0410.0410.0000.0000.0000.000
86A110PHE00.0210.01323.774-0.050-0.0500.0000.0000.0000.000
87A111VAL0-0.035-0.02319.5060.0780.0780.0000.0000.0000.000
88A112ARG10.9480.98713.021-1.056-1.0560.0000.0000.0000.000
89A113VAL0-0.012-0.02115.4710.1150.1150.0000.0000.0000.000
90A114GLN0-0.0070.0028.8770.1380.1380.0000.0000.0000.000
91A115LEU0-0.0180.00410.701-0.097-0.0970.0000.0000.0000.000
92A116LYS10.8510.9015.5365.5805.5800.0000.0000.0000.000
93A117ASP-1-0.805-0.9105.466-4.200-4.2000.0000.0000.0000.000
94A118GLY0-0.020-0.0047.7750.8540.8540.0000.0000.0000.000
95A119SER0-0.039-0.0069.8640.5340.5340.0000.0000.0000.000
96A120TYR0-0.008-0.03212.9820.0790.0790.0000.0000.0000.000
97A121HIS0-0.0230.00215.462-0.018-0.0180.0000.0000.0000.000
98A122GLU-1-0.866-0.92718.5060.6440.6440.0000.0000.0000.000
99A123ASP-1-0.824-0.87220.9520.0110.0110.0000.0000.0000.000
100A124VAL0-0.002-0.00524.0470.0570.0570.0000.0000.0000.000
101A125GLY0-0.015-0.00926.874-0.048-0.0480.0000.0000.0000.000
102A126TYR0-0.088-0.07727.8750.0240.0240.0000.0000.0000.000
103A127GLY0-0.015-0.00531.115-0.021-0.0210.0000.0000.0000.000
104A128VAL00.0080.00532.5670.0140.0140.0000.0000.0000.000
105A129SER0-0.064-0.03136.248-0.017-0.0170.0000.0000.0000.000
106A130GLU-1-0.858-0.93038.8400.0930.0930.0000.0000.0000.000
107A131GLY00.0050.00642.563-0.007-0.0070.0000.0000.0000.000
108A132LEU0-0.011-0.00739.477-0.001-0.0010.0000.0000.0000.000
109A133LYS10.9570.96543.581-0.090-0.0900.0000.0000.0000.000
110A134SER00.0070.01641.0990.0090.0090.0000.0000.0000.000
111A135LYS11.0191.01739.494-0.205-0.2050.0000.0000.0000.000
112A136ALA00.0150.01137.3110.0080.0080.0000.0000.0000.000
113A137LEU00.0800.03036.0720.0080.0080.0000.0000.0000.000
114A138SER0-0.022-0.01236.285-0.009-0.0090.0000.0000.0000.000
115A139LEU00.0090.00834.1140.0020.0020.0000.0000.0000.000
116A140GLU-1-0.861-0.91031.4830.1980.1980.0000.0000.0000.000
117A141LYS10.7810.86531.347-0.084-0.0840.0000.0000.0000.000
118A142ALA00.0250.01432.135-0.006-0.0060.0000.0000.0000.000
119A143ARG10.9200.93928.698-0.363-0.3630.0000.0000.0000.000
120A144LYS10.8730.92427.200-0.185-0.1850.0000.0000.0000.000
121A145GLU-1-0.849-0.89827.2170.0740.0740.0000.0000.0000.000
122A146ALA00.0250.02228.189-0.016-0.0160.0000.0000.0000.000
123A147VAL00.0240.00822.091-0.003-0.0030.0000.0000.0000.000
124A148THR0-0.019-0.01623.553-0.025-0.0250.0000.0000.0000.000
125A149ASP-1-0.913-0.97525.088-0.001-0.0010.0000.0000.0000.000
126A150GLY00.0670.03324.456-0.033-0.0330.0000.0000.0000.000
127A151LEU0-0.0210.00218.616-0.023-0.0230.0000.0000.0000.000
128A152LYS10.8700.93721.547-0.021-0.0210.0000.0000.0000.000
129A153ARG10.7480.86723.987-0.106-0.1060.0000.0000.0000.000
130A154ALA00.0490.02520.203-0.040-0.0400.0000.0000.0000.000
131A155LEU0-0.007-0.00717.261-0.064-0.0640.0000.0000.0000.000
132A156ARG10.9140.95920.7520.0350.0350.0000.0000.0000.000
133A157SER0-0.0100.00221.642-0.035-0.0350.0000.0000.0000.000
134A158PHE00.0220.02415.670-0.041-0.0410.0000.0000.0000.000
135A159GLY00.0290.00920.514-0.076-0.0760.0000.0000.0000.000
136A160ASN0-0.110-0.06323.5710.0750.0750.0000.0000.0000.000
137A161ALA00.0160.01323.0590.0430.0430.0000.0000.0000.000
138A162LEU00.0380.02318.712-0.003-0.0030.0000.0000.0000.000
139A163GLY00.0320.00523.2010.0610.0610.0000.0000.0000.000
140A164ASN0-0.040-0.01226.1270.0720.0720.0000.0000.0000.000
141A165CYS0-0.034-0.00827.7820.0180.0180.0000.0000.0000.000
142A166ILE0-0.049-0.01930.1960.0190.0190.0000.0000.0000.000
143A167LEU00.002-0.00330.4550.0260.0260.0000.0000.0000.000
144A168ASP-1-0.838-0.90133.719-0.202-0.2020.0000.0000.0000.000
145A169LYS11.0150.98635.3860.0830.0830.0000.0000.0000.000
146A170ASP-1-0.810-0.87938.635-0.152-0.1520.0000.0000.0000.000
147A171TYR0-0.034-0.03432.620-0.001-0.0010.0000.0000.0000.000
148A172LEU0-0.001-0.00636.0680.0010.0010.0000.0000.0000.000
149A173ARG10.8460.89838.6100.1520.1520.0000.0000.0000.000
150A174SER0-0.066-0.04738.8430.0030.0030.0000.0000.0000.000
151A175LEU00.0140.00935.1240.0000.0000.0000.0000.0000.000
152A176ASN0-0.086-0.04539.3620.0050.0050.0000.0000.0000.000
153A177LYS10.9190.96942.7480.1580.1580.0000.0000.0000.000
154A178LEU00.0250.02838.336-0.007-0.0070.0000.0000.0000.000
155A179PRO00.0290.00742.1410.0110.0110.0000.0000.0000.000
156A180ARG10.9370.97739.7910.1310.1310.0000.0000.0000.000
157A181GLN00.0050.00236.2940.0080.0080.0000.0000.0000.000
158A182LEU00.004-0.00140.5980.0080.0080.0000.0000.0000.000
159A183PRO0-0.039-0.03537.526-0.013-0.0130.0000.0000.0000.000
160A184LEU00.0140.01333.9620.0040.0040.0000.0000.0000.000
161A185GLU-1-0.919-0.94836.224-0.165-0.1650.0000.0000.0000.000
162A186VAL0-0.030-0.02131.487-0.021-0.0210.0000.0000.0000.000
163A187ASP-1-0.804-0.87833.267-0.233-0.2330.0000.0000.0000.000
164A188LEU00.0030.00331.903-0.013-0.0130.0000.0000.0000.000
165A189THR0-0.036-0.04233.8400.0070.0070.0000.0000.0000.000
166A190LYS10.9620.97429.9330.3550.3550.0000.0000.0000.000
167A191ALA00.0030.02329.277-0.021-0.0210.0000.0000.0000.000
168A192LYS10.7950.87223.2600.2220.2220.0000.0000.0000.000
169A193ARG10.8190.88828.1760.1880.1880.0000.0000.0000.000
170A194GLN0-0.002-0.00226.6710.0400.0400.0000.0000.0000.000
171A195ASP-1-0.847-0.92824.653-0.039-0.0390.0000.0000.0000.000
172A196LEU0-0.0110.01623.331-0.020-0.0200.0000.0000.0000.000
173A197GLU-1-0.822-0.89920.398-0.384-0.3840.0000.0000.0000.000
174A198PRO0-0.007-0.00921.322-0.038-0.0380.0000.0000.0000.000
175A199SER00.0410.02720.898-0.035-0.0350.0000.0000.0000.000
176A200VAL00.004-0.00315.794-0.070-0.0700.0000.0000.0000.000
177A201GLU-1-0.901-0.94417.284-0.210-0.2100.0000.0000.0000.000
178A202GLU-1-0.949-0.96519.303-0.525-0.5250.0000.0000.0000.000
179A203ALA00.0170.00115.676-0.024-0.0240.0000.0000.0000.000
180A204ARG10.8550.92114.4010.1780.1780.0000.0000.0000.000
181A205TYR00.0010.00015.3760.0180.0180.0000.0000.0000.000
182A206ASN0-0.068-0.04417.6350.0110.0110.0000.0000.0000.000
183A207SER0-0.077-0.03611.479-0.288-0.2880.0000.0000.0000.000
184A208CYS-1-0.985-0.96712.539-0.301-0.3010.0000.0000.0000.000