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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VR291

Calculation Name: 5JRB-A-Xray323

Preferred Name: DNA repair protein RAD52 homolog

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5JRB

Chain ID: A

ChEMBL ID: CHEMBL2362978

UniProt ID: P43351

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1735040.161121
FMO2-HF: Nuclear repulsion 1662277.292934
FMO2-HF: Total energy -72762.868187
FMO2-MP2: Total energy -72972.562689


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:24:ACE )


Summations of interaction energy for fragment #1(A:24:ACE )
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.
0.6182.2150.055-0.703-0.948-0.002
Interaction energy analysis for fragmet #1(A:24:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.006
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].
3A26PHE 00.0080.0053.8101.0741.871-0.007-0.390-0.4000.000
4A27GLY 0-0.030-0.0197.2450.0470.0470.0000.0000.0000.000
5A28GLN 0-0.020-0.0053.265-0.834-0.2360.062-0.295-0.365-0.002
6A29CYS 0-0.043-0.0144.6080.6030.8050.000-0.018-0.1830.000
7A30GLN 00.0190.0025.432-0.192-0.1920.0000.0000.0000.000
8A31TYR 0-0.013-0.0028.519-0.047-0.0470.0000.0000.0000.000
9A32THR 00.0390.02010.9260.0400.0400.0000.0000.0000.000
10A33ALA 00.0420.02212.880-0.034-0.0340.0000.0000.0000.000
11A34GLU -1-0.874-0.95115.9080.1090.1090.0000.0000.0000.000
12A35GLU -1-0.810-0.89412.374-0.081-0.0810.0000.0000.0000.000
13A36TYR 00.0070.00115.661-0.019-0.0190.0000.0000.0000.000
14A37GLN 0-0.023-0.01616.849-0.013-0.0130.0000.0000.0000.000
15A38ALA 0-0.018-0.01419.570-0.010-0.0100.0000.0000.0000.000
16A39ILE 00.0640.03415.962-0.005-0.0050.0000.0000.0000.000
17A40GLN 0-0.0300.00120.040-0.005-0.0050.0000.0000.0000.000
18A41LYS 10.9060.94121.924-0.004-0.0040.0000.0000.0000.000
19A42ALA 0-0.007-0.00222.714-0.002-0.0020.0000.0000.0000.000
20A43LEU 00.0620.02020.426-0.003-0.0030.0000.0000.0000.000
21A44ARG 10.9200.97424.601-0.012-0.0120.0000.0000.0000.000
22A45GLN 0-0.042-0.00327.198-0.001-0.0010.0000.0000.0000.000
23A46ARG 10.9440.97029.7130.0090.0090.0000.0000.0000.000
24A47LEU 00.0130.01129.0760.0010.0010.0000.0000.0000.000
25A48GLY 00.0540.05332.9050.0030.0030.0000.0000.0000.000
26A49PRO 0-0.006-0.01535.708-0.003-0.0030.0000.0000.0000.000
27A50GLU -1-0.838-0.91735.081-0.033-0.0330.0000.0000.0000.000
28A51TYR 0-0.053-0.03328.857-0.002-0.0020.0000.0000.0000.000
29A52ILE 0-0.083-0.03034.258-0.002-0.0020.0000.0000.0000.000
30A53SER 00.0060.00836.9560.0000.0000.0000.0000.0000.000
31A54SER 0-0.051-0.03739.0510.0020.0020.0000.0000.0000.000
32A55ARG 10.9960.99239.9160.0370.0370.0000.0000.0000.000
33A56MET 00.0360.01343.6890.0010.0010.0000.0000.0000.000
34A57ALA 0-0.0060.01045.251-0.002-0.0020.0000.0000.0000.000
35A58GLY 00.0400.01246.5470.0010.0010.0000.0000.0000.000
36A59GLY 00.0180.01649.0950.0010.0010.0000.0000.0000.000
37A60GLY 0-0.015-0.00849.4460.0010.0010.0000.0000.0000.000
38A61GLN 0-0.027-0.01347.011-0.002-0.0020.0000.0000.0000.000
39A62LYS 10.9720.99645.3760.0190.0190.0000.0000.0000.000
40A63VAL 0-0.0030.00040.0530.0010.0010.0000.0000.0000.000
41A64CYS 0-0.027-0.02639.013-0.001-0.0010.0000.0000.0000.000
42A65TYR 0-0.055-0.02135.3100.0010.0010.0000.0000.0000.000
43A66ILE 00.0760.05230.5990.0010.0010.0000.0000.0000.000
44A67GLU -1-0.855-0.94532.933-0.056-0.0560.0000.0000.0000.000
45A68GLY 00.0550.01429.453-0.002-0.0020.0000.0000.0000.000
46A69HIS 00.0060.00228.040-0.009-0.0090.0000.0000.0000.000
47A70ARG 10.9540.98727.9070.0500.0500.0000.0000.0000.000
48A71VAL 00.0250.00925.077-0.001-0.0010.0000.0000.0000.000
49A72ILE 00.0160.01422.900-0.005-0.0050.0000.0000.0000.000
50A73ASN 0-0.014-0.00722.863-0.017-0.0170.0000.0000.0000.000
51A74LEU 0-0.034-0.01123.524-0.001-0.0010.0000.0000.0000.000
52A75ALA 00.0300.01320.0590.0020.0020.0000.0000.0000.000
53A76ASN 00.0070.00618.852-0.028-0.0280.0000.0000.0000.000
54A77GLU -1-0.942-0.96018.897-0.108-0.1080.0000.0000.0000.000
55A78MET 0-0.100-0.03019.5980.0100.0100.0000.0000.0000.000
56A79PHE 0-0.008-0.02215.2030.0110.0110.0000.0000.0000.000
57A80GLY 00.0840.05314.447-0.029-0.0290.0000.0000.0000.000
58A81TYR 0-0.003-0.01513.790-0.038-0.0380.0000.0000.0000.000
59A82ASN 0-0.039-0.0149.7810.0730.0730.0000.0000.0000.000
60A83GLY 00.0270.01311.009-0.091-0.0910.0000.0000.0000.000
61A84TRP 0-0.083-0.06812.6990.0410.0410.0000.0000.0000.000
62A85ALA 00.0180.01714.166-0.033-0.0330.0000.0000.0000.000
63A86HIS 00.006-0.01616.1050.0450.0450.0000.0000.0000.000
64A87SER 0-0.0150.01119.013-0.012-0.0120.0000.0000.0000.000
65A88ILE 00.003-0.01320.7570.0150.0150.0000.0000.0000.000
66A89THR 0-0.0190.00123.137-0.009-0.0090.0000.0000.0000.000
67A90GLN 00.002-0.00224.4520.0050.0050.0000.0000.0000.000
68A91GLN 0-0.0100.01528.1460.0000.0000.0000.0000.0000.000
69A92ASN 0-0.023-0.01231.1830.0000.0000.0000.0000.0000.000
70A93VAL 0-0.032-0.02634.7520.0000.0000.0000.0000.0000.000
71A94ASP -1-0.811-0.87238.042-0.040-0.0400.0000.0000.0000.000
72A95PHE 0-0.004-0.00640.2200.0020.0020.0000.0000.0000.000
73A96VAL 0-0.073-0.05342.826-0.002-0.0020.0000.0000.0000.000
74A97ASP -1-0.855-0.90945.185-0.029-0.0290.0000.0000.0000.000
75A98LEU 0-0.061-0.04348.748-0.001-0.0010.0000.0000.0000.000
76A99ASN 00.0230.00951.5580.0020.0020.0000.0000.0000.000
77A100ASN 0-0.016-0.01854.3040.0000.0000.0000.0000.0000.000
78A101GLY 00.0090.00855.2670.0000.0000.0000.0000.0000.000
79A102ALA 0-0.0070.01951.143-0.001-0.0010.0000.0000.0000.000
80A103PHE 0-0.044-0.03846.8460.0000.0000.0000.0000.0000.000
81A104TYR 0-0.020-0.00946.6300.0000.0000.0000.0000.0000.000
82A105VAL 0-0.023-0.01840.5950.0000.0000.0000.0000.0000.000
83A106GLY 00.0560.04240.4840.0000.0000.0000.0000.0000.000
84A107VAL 0-0.061-0.03334.409-0.001-0.0010.0000.0000.0000.000
85A108CYS 00.0460.04233.631-0.001-0.0010.0000.0000.0000.000
86A109ALA 0-0.023-0.03029.106-0.004-0.0040.0000.0000.0000.000
87A110PHE 00.0120.01326.9740.0040.0040.0000.0000.0000.000
88A111VAL 0-0.0120.00723.557-0.010-0.0100.0000.0000.0000.000
89A112ARG 10.9950.99515.4600.1370.1370.0000.0000.0000.000
90A113VAL 0-0.033-0.02718.301-0.022-0.0220.0000.0000.0000.000
91A114GLN 0-0.021-0.01211.2630.0490.0490.0000.0000.0000.000
92A115LEU 0-0.0140.00313.403-0.035-0.0350.0000.0000.0000.000
93A116LYS 10.9000.9328.1210.1480.1480.0000.0000.0000.000
94A117ASP -1-0.803-0.8627.963-0.087-0.0870.0000.0000.0000.000
95A118GLY 0-0.0050.0089.6560.0600.0600.0000.0000.0000.000
96A119SER 0-0.073-0.07511.8480.0010.0010.0000.0000.0000.000
97A120TYR 0-0.044-0.03915.164-0.040-0.0400.0000.0000.0000.000
98A121HIS 0-0.023-0.00317.8310.0270.0270.0000.0000.0000.000
99A122GLU -1-0.892-0.95121.483-0.091-0.0910.0000.0000.0000.000
100A123ASP -1-0.819-0.88423.747-0.036-0.0360.0000.0000.0000.000
101A124VAL 0-0.009-0.00827.362-0.007-0.0070.0000.0000.0000.000
102A125GLY 0-0.023-0.01430.2200.0020.0020.0000.0000.0000.000
103A126TYR 0-0.099-0.08831.8540.0000.0000.0000.0000.0000.000
104A127GLY 0-0.024-0.01235.270-0.002-0.0020.0000.0000.0000.000
105A128VAL 00.0180.00036.9710.0010.0010.0000.0000.0000.000
106A129SER 0-0.048-0.02640.712-0.002-0.0020.0000.0000.0000.000
107A130GLU -1-0.928-0.96343.186-0.031-0.0310.0000.0000.0000.000
108A131GLY 00.0280.01246.8680.0000.0000.0000.0000.0000.000
109A132LEU 0-0.029-0.01044.4420.0010.0010.0000.0000.0000.000
110A133ALA 00.1080.05448.6490.0000.0000.0000.0000.0000.000
111A134SER 0-0.0190.00446.2500.0000.0000.0000.0000.0000.000
112A135LYS 11.0291.01844.6070.0370.0370.0000.0000.0000.000
113A136ALA 0-0.016-0.00542.790-0.002-0.0020.0000.0000.0000.000
114A137LEU 00.0430.00841.595-0.002-0.0020.0000.0000.0000.000
115A138SER 0-0.007-0.00741.579-0.001-0.0010.0000.0000.0000.000
116A139LEU 00.0180.00239.309-0.002-0.0020.0000.0000.0000.000
117A140GLU -1-0.864-0.90936.716-0.068-0.0680.0000.0000.0000.000
118A141LYS 10.8340.90836.5290.0440.0440.0000.0000.0000.000
119A142ALA 00.0400.02436.930-0.002-0.0020.0000.0000.0000.000
120A143ARG 10.9330.94533.5200.0640.0640.0000.0000.0000.000
121A144LYS 10.8750.91732.0940.0720.0720.0000.0000.0000.000
122A145GLU -1-0.847-0.90431.985-0.054-0.0540.0000.0000.0000.000
123A146ALA 00.0510.03032.894-0.001-0.0010.0000.0000.0000.000
124A147VAL 0-0.008-0.00126.889-0.002-0.0020.0000.0000.0000.000
125A148THR 0-0.027-0.01328.175-0.005-0.0050.0000.0000.0000.000
126A149ASP -1-0.882-0.93629.034-0.055-0.0550.0000.0000.0000.000
127A150GLY 00.0760.02628.5410.0030.0030.0000.0000.0000.000
128A151LEU 0-0.037-0.01222.402-0.001-0.0010.0000.0000.0000.000
129A152LYS 10.8480.91825.3250.0620.0620.0000.0000.0000.000
130A153ARG 10.8120.90027.4850.0500.0500.0000.0000.0000.000
131A154ALA 00.0450.04123.0930.0060.0060.0000.0000.0000.000
132A155LEU 00.0160.00120.5110.0040.0040.0000.0000.0000.000
133A156ARG 10.8520.92323.5950.0490.0490.0000.0000.0000.000
134A157SER 0-0.031-0.01523.8850.0100.0100.0000.0000.0000.000
135A158PHE 0-0.0030.00217.9090.0070.0070.0000.0000.0000.000
136A159GLY 00.0230.00822.8640.0080.0080.0000.0000.0000.000
137A160ASN 0-0.106-0.07125.913-0.006-0.0060.0000.0000.0000.000
138A161ALA 00.0080.00925.404-0.003-0.0030.0000.0000.0000.000
139A162LEU 00.0190.01421.558-0.005-0.0050.0000.0000.0000.000
140A163GLY 00.0240.00326.205-0.003-0.0030.0000.0000.0000.000
141A164ASN 0-0.046-0.01328.4580.0010.0010.0000.0000.0000.000
142A165CYS 0-0.025-0.00130.3060.0030.0030.0000.0000.0000.000
143A166ILE 0-0.016-0.00232.8150.0020.0020.0000.0000.0000.000
144A167LEU 0-0.005-0.01933.9730.0010.0010.0000.0000.0000.000
145A168ASP -1-0.840-0.91336.023-0.011-0.0110.0000.0000.0000.000
146A169LYS 10.9610.96137.8220.0210.0210.0000.0000.0000.000
147A170ASP -1-0.829-0.88640.520-0.009-0.0090.0000.0000.0000.000
148A171TYR 0-0.037-0.05535.5890.0000.0000.0000.0000.0000.000
149A172LEU 0-0.019-0.01938.869-0.001-0.0010.0000.0000.0000.000
150A173ARG 10.8220.90441.2400.0100.0100.0000.0000.0000.000
151A174SER 00.016-0.01141.2370.0010.0010.0000.0000.0000.000
152A175LEU 00.0240.01938.1040.0000.0000.0000.0000.0000.000
153A176ASN 0-0.055-0.03242.114-0.001-0.0010.0000.0000.0000.000
154A177LYS 10.8510.94145.4170.0130.0130.0000.0000.0000.000
155A178LEU 00.0340.02941.1170.0010.0010.0000.0000.0000.000
156A179PRO 00.0050.00245.422-0.001-0.0010.0000.0000.0000.000
157A180ARG 10.9490.97641.7840.0250.0250.0000.0000.0000.000
158A181GLN 0-0.005-0.00942.255-0.001-0.0010.0000.0000.0000.000
159A182LEU 00.0200.01344.3230.0000.0000.0000.0000.0000.000
160A183PRO 0-0.034-0.01241.279-0.001-0.0010.0000.0000.0000.000
161A184LEU 00.0050.01335.8090.0010.0010.0000.0000.0000.000
162A185GLU -1-0.887-0.94639.847-0.035-0.0350.0000.0000.0000.000
163A186VAL 0-0.046-0.03235.237-0.001-0.0010.0000.0000.0000.000
164A187ASP -1-0.819-0.88337.022-0.042-0.0420.0000.0000.0000.000
165A188LEU 0-0.035-0.02235.766-0.003-0.0030.0000.0000.0000.000
166A189THR 0-0.032-0.04737.303-0.002-0.0020.0000.0000.0000.000
167A190LYS 10.9070.94932.7550.0490.0490.0000.0000.0000.000
168A191ALA 0-0.0020.01832.464-0.005-0.0050.0000.0000.0000.000
169A192LYS 10.8150.88526.9530.1140.1140.0000.0000.0000.000
170A193ARG 10.9340.96231.7320.0570.0570.0000.0000.0000.000
171A194GLN 0-0.011-0.00531.6600.0030.0030.0000.0000.0000.000
172A195ASP -1-0.838-0.92528.473-0.103-0.1030.0000.0000.0000.000
173A196LEU 0-0.020-0.01527.346-0.010-0.0100.0000.0000.0000.000
174A197GLU -1-0.827-0.88923.925-0.110-0.1100.0000.0000.0000.000
175A198PRO 00.0160.01024.154-0.009-0.0090.0000.0000.0000.000
176A199SER 00.0330.02223.018-0.004-0.0040.0000.0000.0000.000
177A200VAL 00.0260.00918.850-0.010-0.0100.0000.0000.0000.000
178A201GLU -1-0.936-0.96819.609-0.168-0.1680.0000.0000.0000.000
179A202ALA 0-0.018-0.01120.943-0.002-0.0020.0000.0000.0000.000
180A203ALA 0-0.020-0.01717.1650.0000.0000.0000.0000.0000.000
181A204ARG 10.9560.97915.9900.2160.2160.0000.0000.0000.000
182A205TYR 00.0280.04516.543-0.013-0.0130.0000.0000.0000.000
183A206ASN 0-0.067-0.03817.4330.0120.0120.0000.0000.0000.000
184A207SER 0-0.079-0.05712.716-0.005-0.0050.0000.0000.0000.000
185A208CYS 0-0.044-0.01912.889-0.049-0.0490.0000.0000.0000.000
186A209NME 00.0120.01214.8930.0310.0310.0000.0000.0000.000