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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: 53LZZ

Calculation Name: 5JRB-A-Xray372

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: 2023-06-20

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 OptH
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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1728343.256163
FMO2-HF: Nuclear repulsion 1655751.265252
FMO2-HF: Total energy -72591.990911
FMO2-MP2: Total energy -72801.167539


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: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.
-7.953-6.98411.713-5.561-7.12-0.026
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 : 0.016 / q_NPA : 0.013
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].
3A27GLY0-0.031-0.0213.8190.1902.8380.240-1.310-1.5780.003
4A28GLN0-0.015-0.0031.977-8.210-10.41611.469-4.160-5.104-0.029
5A29CYS0-0.038-0.0123.284-0.0210.4380.005-0.083-0.3800.000
6A30GLN00.0180.0024.6720.6610.729-0.001-0.008-0.0580.000
7A31TYR0-0.013-0.0028.3600.0620.0620.0000.0000.0000.000
8A32THR00.0400.02111.0450.0260.0260.0000.0000.0000.000
9A33ALA00.0410.02113.1430.0020.0020.0000.0000.0000.000
10A34GLU-1-0.873-0.95116.429-0.238-0.2380.0000.0000.0000.000
11A35GLU-1-0.811-0.89411.725-0.527-0.5270.0000.0000.0000.000
12A36TYR00.0060.00115.3190.0250.0250.0000.0000.0000.000
13A37GLN0-0.025-0.01616.3470.0300.0300.0000.0000.0000.000
14A38ALA0-0.016-0.01418.9510.0230.0230.0000.0000.0000.000
15A39ILE00.0630.03414.8370.0270.0270.0000.0000.0000.000
16A40GLN0-0.0300.00119.0290.0480.0480.0000.0000.0000.000
17A41LYS10.9060.94120.9830.1500.1500.0000.0000.0000.000
18A42ALA0-0.007-0.00121.5550.0180.0180.0000.0000.0000.000
19A43LEU00.0650.02118.9470.0190.0190.0000.0000.0000.000
20A44ARG10.9170.97323.2250.1870.1870.0000.0000.0000.000
21A45GLN0-0.044-0.00425.9380.0040.0040.0000.0000.0000.000
22A46ARG10.9420.96928.2050.0900.0900.0000.0000.0000.000
23A47LEU00.0130.01126.9940.0030.0030.0000.0000.0000.000
24A48GLY00.0550.05331.0390.0040.0040.0000.0000.0000.000
25A49PRO0-0.009-0.01633.486-0.002-0.0020.0000.0000.0000.000
26A50GLU-1-0.835-0.91732.694-0.048-0.0480.0000.0000.0000.000
27A51TYR0-0.054-0.03426.4610.0020.0020.0000.0000.0000.000
28A52ILE0-0.084-0.03031.660-0.001-0.0010.0000.0000.0000.000
29A53SER00.0080.00834.3100.0060.0060.0000.0000.0000.000
30A54SER0-0.051-0.03736.115-0.002-0.0020.0000.0000.0000.000
31A55ARG10.9960.99236.6880.0380.0380.0000.0000.0000.000
32A56MET00.0360.01440.535-0.001-0.0010.0000.0000.0000.000
33A57ALA0-0.0050.01042.1450.0000.0000.0000.0000.0000.000
34A58GLY00.0390.01243.2630.0020.0020.0000.0000.0000.000
35A59GLY00.0190.01645.555-0.001-0.0010.0000.0000.0000.000
36A60GLY0-0.016-0.00946.488-0.001-0.0010.0000.0000.0000.000
37A61GLN0-0.026-0.01144.4660.0010.0010.0000.0000.0000.000
38A62LYS10.9720.99642.6470.0380.0380.0000.0000.0000.000
39A63VAL0-0.0020.00037.264-0.003-0.0030.0000.0000.0000.000
40A64CYS0-0.028-0.02636.4800.0030.0030.0000.0000.0000.000
41A65TYR0-0.057-0.02232.181-0.003-0.0030.0000.0000.0000.000
42A66ILE00.0760.05327.8630.0020.0020.0000.0000.0000.000
43A67GLU-1-0.853-0.94429.801-0.033-0.0330.0000.0000.0000.000
44A68GLY00.0560.01426.068-0.006-0.0060.0000.0000.0000.000
45A69HIS00.0040.00024.651-0.009-0.0090.0000.0000.0000.000
46A70ARG10.9520.98624.5550.0390.0390.0000.0000.0000.000
47A71VAL00.0290.01122.130-0.007-0.0070.0000.0000.0000.000
48A72ILE00.0150.01419.335-0.015-0.0150.0000.0000.0000.000
49A73ASN0-0.021-0.00919.706-0.011-0.0110.0000.0000.0000.000
50A74LEU0-0.029-0.00920.757-0.007-0.0070.0000.0000.0000.000
51A75ALA00.0320.01417.252-0.016-0.0160.0000.0000.0000.000
52A76ASN00.0040.00415.844-0.053-0.0530.0000.0000.0000.000
53A77GLU-1-0.941-0.95916.333-0.089-0.0890.0000.0000.0000.000
54A78MET0-0.098-0.03018.033-0.010-0.0100.0000.0000.0000.000
55A79PHE0-0.005-0.02013.128-0.023-0.0230.0000.0000.0000.000
56A80GLY00.0800.05312.451-0.072-0.0720.0000.0000.0000.000
57A81TYR0-0.002-0.01510.340-0.024-0.0240.0000.0000.0000.000
58A82ASN0-0.041-0.0166.563-0.042-0.0420.0000.0000.0000.000
59A83GLY00.0290.0147.903-0.256-0.2560.0000.0000.0000.000
60A84TRP0-0.086-0.06810.171-0.090-0.0900.0000.0000.0000.000
61A85ALA00.0200.01810.1250.0540.0540.0000.0000.0000.000
62A86HIS00.008-0.01612.273-0.015-0.0150.0000.0000.0000.000
63A87SER0-0.0180.01014.4940.0410.0410.0000.0000.0000.000
64A88ILE00.007-0.01116.296-0.019-0.0190.0000.0000.0000.000
65A89THR0-0.0220.00019.2240.0170.0170.0000.0000.0000.000
66A90GLN00.003-0.00120.3350.0180.0180.0000.0000.0000.000
67A91GLN0-0.0090.01523.9470.0000.0000.0000.0000.0000.000
68A92ASN0-0.024-0.01226.8330.0010.0010.0000.0000.0000.000
69A93VAL0-0.031-0.02530.489-0.002-0.0020.0000.0000.0000.000
70A94ASP-1-0.809-0.87233.605-0.029-0.0290.0000.0000.0000.000
71A95PHE0-0.006-0.00736.0550.0010.0010.0000.0000.0000.000
72A96VAL0-0.071-0.05238.1160.0010.0010.0000.0000.0000.000
73A97ASP-1-0.856-0.90940.561-0.011-0.0110.0000.0000.0000.000
74A98LEU0-0.060-0.04444.1790.0000.0000.0000.0000.0000.000
75A99ASN00.0230.00946.8300.0010.0010.0000.0000.0000.000
76A100ASN0-0.018-0.01949.6670.0000.0000.0000.0000.0000.000
77A101GLY00.0110.00850.3230.0000.0000.0000.0000.0000.000
78A102ALA0-0.0090.01946.3770.0010.0010.0000.0000.0000.000
79A103PHE0-0.041-0.03642.0040.0000.0000.0000.0000.0000.000
80A104TYR0-0.019-0.00942.043-0.001-0.0010.0000.0000.0000.000
81A105VAL0-0.025-0.01835.9830.0010.0010.0000.0000.0000.000
82A106GLY00.0530.04136.154-0.002-0.0020.0000.0000.0000.000
83A107VAL0-0.061-0.03329.9650.0030.0030.0000.0000.0000.000
84A108CYS00.0450.04229.817-0.004-0.0040.0000.0000.0000.000
85A109ALA0-0.023-0.03024.8100.0080.0080.0000.0000.0000.000
86A110PHE00.0100.01323.247-0.008-0.0080.0000.0000.0000.000
87A111VAL0-0.0070.00819.4830.0090.0090.0000.0000.0000.000
88A112ARG10.9920.99412.2630.2360.2360.0000.0000.0000.000
89A113VAL0-0.031-0.02715.6380.0120.0120.0000.0000.0000.000
90A114GLN0-0.022-0.0138.0520.1340.1340.0000.0000.0000.000
91A115LEU0-0.0160.00311.4090.0250.0250.0000.0000.0000.000
92A116LYS10.9040.9326.1790.8640.8640.0000.0000.0000.000
93A117ASP-1-0.802-0.8636.105-1.805-1.8050.0000.0000.0000.000
94A118GLY0-0.0050.0088.2320.0720.0720.0000.0000.0000.000
95A119SER0-0.073-0.07510.1560.2340.2340.0000.0000.0000.000
96A120TYR0-0.047-0.04013.3550.0240.0240.0000.0000.0000.000
97A121HIS0-0.021-0.00215.6060.0220.0220.0000.0000.0000.000
98A122GLU-1-0.895-0.95218.684-0.111-0.1110.0000.0000.0000.000
99A123ASP-1-0.820-0.88520.667-0.112-0.1120.0000.0000.0000.000
100A124VAL0-0.006-0.00724.0740.0070.0070.0000.0000.0000.000
101A125GLY0-0.020-0.01326.776-0.005-0.0050.0000.0000.0000.000
102A126TYR0-0.103-0.09028.0940.0060.0060.0000.0000.0000.000
103A127GLY0-0.026-0.01331.281-0.001-0.0010.0000.0000.0000.000
104A128VAL00.0220.00232.6310.0020.0020.0000.0000.0000.000
105A129SER0-0.044-0.02536.3260.0010.0010.0000.0000.0000.000
106A130GLU-1-0.931-0.96438.568-0.021-0.0210.0000.0000.0000.000
107A131GLY00.0300.01242.3120.0000.0000.0000.0000.0000.000
108A132LEU0-0.030-0.01039.6170.0020.0020.0000.0000.0000.000
109A133ALA00.1070.05343.7880.0000.0000.0000.0000.0000.000
110A134SER0-0.0180.00541.0390.0010.0010.0000.0000.0000.000
111A135LYS11.0301.01839.531-0.006-0.0060.0000.0000.0000.000
112A136ALA0-0.017-0.00637.584-0.001-0.0010.0000.0000.0000.000
113A137LEU00.0410.00736.454-0.001-0.0010.0000.0000.0000.000
114A138SER0-0.004-0.00636.603-0.002-0.0020.0000.0000.0000.000
115A139LEU00.0170.00234.287-0.002-0.0020.0000.0000.0000.000
116A140GLU-1-0.866-0.90931.6380.0090.0090.0000.0000.0000.000
117A141LYS10.8350.90831.5800.0170.0170.0000.0000.0000.000
118A142ALA00.0390.02432.219-0.003-0.0030.0000.0000.0000.000
119A143ARG10.9320.94428.760-0.006-0.0060.0000.0000.0000.000
120A144LYS10.8740.91827.264-0.013-0.0130.0000.0000.0000.000
121A145GLU-1-0.842-0.90227.379-0.033-0.0330.0000.0000.0000.000
122A146ALA00.0450.02828.403-0.007-0.0070.0000.0000.0000.000
123A147VAL0-0.006-0.00122.297-0.008-0.0080.0000.0000.0000.000
124A148THR0-0.027-0.01224.010-0.011-0.0110.0000.0000.0000.000
125A149ASP-1-0.882-0.93625.293-0.072-0.0720.0000.0000.0000.000
126A150GLY00.0730.02624.713-0.009-0.0090.0000.0000.0000.000
127A151LEU0-0.038-0.01218.867-0.015-0.0150.0000.0000.0000.000
128A152LYS10.8540.92022.2190.0470.0470.0000.0000.0000.000
129A153ARG10.8110.90024.7550.0780.0780.0000.0000.0000.000
130A154ALA00.0400.03920.285-0.009-0.0090.0000.0000.0000.000
131A155LEU00.0190.00217.739-0.021-0.0210.0000.0000.0000.000
132A156ARG10.8530.92321.1520.1110.1110.0000.0000.0000.000
133A157SER0-0.029-0.01521.9420.0080.0080.0000.0000.0000.000
134A158PHE0-0.0020.00315.961-0.008-0.0080.0000.0000.0000.000
135A159GLY00.0230.00821.137-0.008-0.0080.0000.0000.0000.000
136A160ASN0-0.106-0.07024.2930.0110.0110.0000.0000.0000.000
137A161ALA00.0030.00723.8100.0100.0100.0000.0000.0000.000
138A162LEU00.0220.01419.5800.0100.0100.0000.0000.0000.000
139A163GLY00.0260.00424.1070.0050.0050.0000.0000.0000.000
140A164ASN0-0.042-0.01326.6710.0130.0130.0000.0000.0000.000
141A165CYS0-0.031-0.00228.4690.0050.0050.0000.0000.0000.000
142A166ILE0-0.015-0.00230.6120.0070.0070.0000.0000.0000.000
143A167LEU0-0.005-0.01931.8900.0080.0080.0000.0000.0000.000
144A168ASP-1-0.839-0.91234.324-0.079-0.0790.0000.0000.0000.000
145A169LYS10.9610.96036.0670.0670.0670.0000.0000.0000.000
146A170ASP-1-0.829-0.88638.959-0.060-0.0600.0000.0000.0000.000
147A171TYR0-0.036-0.05533.6260.0030.0030.0000.0000.0000.000
148A172LEU0-0.014-0.01836.6890.0040.0040.0000.0000.0000.000
149A173ARG10.8160.90239.3460.0590.0590.0000.0000.0000.000
150A174SER00.017-0.01139.6500.0040.0040.0000.0000.0000.000
151A175LEU00.0250.01935.9770.0030.0030.0000.0000.0000.000
152A176ASN0-0.056-0.03240.1790.0040.0040.0000.0000.0000.000
153A177LYS10.8500.94143.5820.0440.0440.0000.0000.0000.000
154A178LEU00.0340.02939.2230.0000.0000.0000.0000.0000.000
155A179PRO00.0070.00343.5050.0010.0010.0000.0000.0000.000
156A180ARG10.9470.97539.2050.0350.0350.0000.0000.0000.000
157A181GLN0-0.004-0.00939.8780.0020.0020.0000.0000.0000.000
158A182LEU00.0210.01341.6920.0000.0000.0000.0000.0000.000
159A183PRO0-0.033-0.01238.412-0.003-0.0030.0000.0000.0000.000
160A184LEU00.0050.01333.1430.0010.0010.0000.0000.0000.000
161A185GLU-1-0.888-0.94637.032-0.012-0.0120.0000.0000.0000.000
162A186VAL0-0.046-0.03232.117-0.001-0.0010.0000.0000.0000.000
163A187ASP-1-0.819-0.88334.1130.0080.0080.0000.0000.0000.000
164A188LEU0-0.034-0.02232.4530.0020.0020.0000.0000.0000.000
165A189THR0-0.031-0.04734.1170.0050.0050.0000.0000.0000.000
166A190LYS10.9060.94930.088-0.019-0.0190.0000.0000.0000.000
167A191ALA0-0.0010.01829.4560.0020.0020.0000.0000.0000.000
168A192LYS10.8140.88523.499-0.079-0.0790.0000.0000.0000.000
169A193ARG10.9350.96128.335-0.032-0.0320.0000.0000.0000.000
170A194GLN0-0.012-0.00428.4690.0040.0040.0000.0000.0000.000
171A195ASP-1-0.838-0.92424.9570.0860.0860.0000.0000.0000.000
172A196LEU0-0.019-0.01523.9530.0070.0070.0000.0000.0000.000
173A197GLU-1-0.827-0.88920.8620.0760.0760.0000.0000.0000.000
174A198PRO00.0160.01021.5880.0170.0170.0000.0000.0000.000
175A199SER00.0330.02220.9400.0150.0150.0000.0000.0000.000
176A200VAL00.0260.00916.0710.0190.0190.0000.0000.0000.000
177A201GLU-1-0.936-0.96817.4730.2570.2570.0000.0000.0000.000
178A202ALA0-0.020-0.01119.3480.0200.0200.0000.0000.0000.000
179A203ALA0-0.019-0.01715.6900.0190.0190.0000.0000.0000.000
180A204ARG10.9550.97914.086-0.246-0.2460.0000.0000.0000.000
181A205TYR00.0280.04515.4800.0530.0530.0000.0000.0000.000
182A206ASN0-0.067-0.03917.4790.0060.0060.0000.0000.0000.000
183A207SER0-0.075-0.05412.3190.0330.0330.0000.0000.0000.000
184A208CYS0-0.033-0.00713.0630.0870.0870.0000.0000.0000.000