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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: VR141

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1731236.101834
FMO2-HF: Nuclear repulsion 1658642.875178
FMO2-HF: Total energy -72593.226656
FMO2-MP2: Total energy -72802.319405


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.
-10.041-14.35821.498-8.491-8.689-0.052
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 : 0.002 / 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].
3A27GLY0-0.020-0.0173.8820.8503.1760.270-1.065-1.5310.002
4A28GLN00.0000.0071.886-11.006-18.32021.223-7.260-6.649-0.053
5A29CYS0-0.048-0.0093.4790.3820.9530.006-0.151-0.425-0.001
6A30GLN00.0340.0064.4460.7900.890-0.001-0.015-0.0840.000
7A31TYR0-0.0010.0058.0410.0740.0740.0000.0000.0000.000
8A32THR0-0.019-0.02410.9580.0130.0130.0000.0000.0000.000
9A33ALA00.0310.01313.255-0.001-0.0010.0000.0000.0000.000
10A34GLU-1-0.804-0.90216.316-0.275-0.2750.0000.0000.0000.000
11A35GLU-1-0.790-0.87111.703-0.614-0.6140.0000.0000.0000.000
12A36TYR00.0250.00815.2660.0320.0320.0000.0000.0000.000
13A37GLN0-0.043-0.02216.5630.0400.0400.0000.0000.0000.000
14A38ALA0-0.009-0.00318.9320.0250.0250.0000.0000.0000.000
15A39ILE00.0560.02715.0050.0270.0270.0000.0000.0000.000
16A40GLN00.0210.03119.1240.0510.0510.0000.0000.0000.000
17A41LYS10.8890.94421.0170.1540.1540.0000.0000.0000.000
18A42ALA0-0.006-0.00421.5270.0170.0170.0000.0000.0000.000
19A43LEU00.0490.01318.6210.0220.0220.0000.0000.0000.000
20A44ARG10.8770.93023.0860.2000.2000.0000.0000.0000.000
21A45GLN0-0.031-0.00226.4540.0130.0130.0000.0000.0000.000
22A46ARG10.8510.90728.0160.0900.0900.0000.0000.0000.000
23A47LEU00.0120.02326.6810.0030.0030.0000.0000.0000.000
24A48GLY00.0700.06030.6420.0030.0030.0000.0000.0000.000
25A49PRO0-0.005-0.02033.227-0.001-0.0010.0000.0000.0000.000
26A50GLU-1-0.820-0.91232.825-0.047-0.0470.0000.0000.0000.000
27A51TYR0-0.020-0.01226.8780.0020.0020.0000.0000.0000.000
28A52ILE0-0.074-0.02731.532-0.001-0.0010.0000.0000.0000.000
29A53SER00.011-0.00534.2230.0040.0040.0000.0000.0000.000
30A54SER0-0.072-0.05536.097-0.003-0.0030.0000.0000.0000.000
31A55ARG10.9750.99435.9130.0320.0320.0000.0000.0000.000
32A56MET00.0420.02140.454-0.002-0.0020.0000.0000.0000.000
33A57ALA00.0050.01242.2300.0000.0000.0000.0000.0000.000
34A58GLY00.0230.00343.1900.0020.0020.0000.0000.0000.000
35A59GLY00.0200.01945.2200.0000.0000.0000.0000.0000.000
36A60GLY0-0.005-0.00446.342-0.001-0.0010.0000.0000.0000.000
37A61GLN00.000-0.00444.4870.0010.0010.0000.0000.0000.000
38A62LYS10.9110.95742.7380.0350.0350.0000.0000.0000.000
39A63VAL0-0.007-0.00737.077-0.003-0.0030.0000.0000.0000.000
40A64CYS0-0.016-0.01836.5590.0030.0030.0000.0000.0000.000
41A65TYR0-0.067-0.03432.178-0.002-0.0020.0000.0000.0000.000
42A66ILE00.0670.04427.7340.0020.0020.0000.0000.0000.000
43A67GLU-1-0.806-0.86629.472-0.027-0.0270.0000.0000.0000.000
44A68GLY00.0670.01925.573-0.006-0.0060.0000.0000.0000.000
45A69HIS00.012-0.00724.294-0.008-0.0080.0000.0000.0000.000
46A70ARG10.8370.91024.5200.0310.0310.0000.0000.0000.000
47A71VAL00.0220.00622.366-0.007-0.0070.0000.0000.0000.000
48A72ILE00.0090.00919.313-0.015-0.0150.0000.0000.0000.000
49A73ASN0-0.006-0.01019.748-0.010-0.0100.0000.0000.0000.000
50A74LEU0-0.0250.00120.987-0.007-0.0070.0000.0000.0000.000
51A75ALA00.0240.00517.358-0.018-0.0180.0000.0000.0000.000
52A76ASN0-0.033-0.01416.268-0.043-0.0430.0000.0000.0000.000
53A77GLU-1-0.925-0.95616.613-0.091-0.0910.0000.0000.0000.000
54A78MET0-0.109-0.03618.142-0.014-0.0140.0000.0000.0000.000
55A79PHE0-0.006-0.02113.071-0.031-0.0310.0000.0000.0000.000
56A80GLY00.0880.05712.573-0.062-0.0620.0000.0000.0000.000
57A81TYR0-0.023-0.03411.218-0.030-0.0300.0000.0000.0000.000
58A82ASN0-0.016-0.0047.4020.0030.0030.0000.0000.0000.000
59A83GLY00.0350.0247.985-0.224-0.2240.0000.0000.0000.000
60A84TRP0-0.062-0.04710.093-0.102-0.1020.0000.0000.0000.000
61A85ALA00.0260.01910.1370.0660.0660.0000.0000.0000.000
62A86HIS0-0.010-0.02212.233-0.038-0.0380.0000.0000.0000.000
63A87SER00.0210.01414.2790.0490.0490.0000.0000.0000.000
64A88ILE0-0.023-0.01616.252-0.027-0.0270.0000.0000.0000.000
65A89THR0-0.039-0.03118.6920.0230.0230.0000.0000.0000.000
66A90GLN00.0160.01419.7170.0130.0130.0000.0000.0000.000
67A91GLN0-0.029-0.00323.4000.0020.0020.0000.0000.0000.000
68A92ASN0-0.038-0.02526.4100.0020.0020.0000.0000.0000.000
69A93VAL0-0.006-0.01530.058-0.001-0.0010.0000.0000.0000.000
70A94ASP-1-0.772-0.84433.284-0.017-0.0170.0000.0000.0000.000
71A95PHE00.0220.01735.6810.0000.0000.0000.0000.0000.000
72A96VAL0-0.055-0.05237.8130.0020.0020.0000.0000.0000.000
73A97ASP-1-0.854-0.90440.422-0.003-0.0030.0000.0000.0000.000
74A98LEU0-0.061-0.04544.0690.0010.0010.0000.0000.0000.000
75A99ASN00.0040.00546.8760.0000.0000.0000.0000.0000.000
76A100ASN0-0.005-0.01549.7280.0010.0010.0000.0000.0000.000
77A101GLY00.0260.02250.8600.0000.0000.0000.0000.0000.000
78A102ALA0-0.036-0.00646.6010.0010.0010.0000.0000.0000.000
79A103PHE0-0.016-0.02642.2510.0000.0000.0000.0000.0000.000
80A104TYR0-0.013-0.01042.295-0.001-0.0010.0000.0000.0000.000
81A105VAL0-0.035-0.02236.2640.0010.0010.0000.0000.0000.000
82A106GLY00.0420.03036.150-0.002-0.0020.0000.0000.0000.000
83A107VAL0-0.052-0.03629.9360.0040.0040.0000.0000.0000.000
84A108CYS0-0.0220.00129.678-0.004-0.0040.0000.0000.0000.000
85A109ALA0-0.008-0.02524.9760.0090.0090.0000.0000.0000.000
86A110PHE00.0010.00023.031-0.010-0.0100.0000.0000.0000.000
87A111VAL0-0.023-0.01219.5810.0140.0140.0000.0000.0000.000
88A112ARG10.8690.95012.7270.1970.1970.0000.0000.0000.000
89A113VAL0-0.002-0.01415.6710.0290.0290.0000.0000.0000.000
90A114GLN00.0200.0038.4850.0460.0460.0000.0000.0000.000
91A115LEU0-0.028-0.00510.9430.0610.0610.0000.0000.0000.000
92A116LYS10.8370.8956.2580.9260.9260.0000.0000.0000.000
93A117ASP-1-0.785-0.8695.696-2.178-2.1780.0000.0000.0000.000
94A118GLY0-0.0080.0067.801-0.013-0.0130.0000.0000.0000.000
95A119SER0-0.088-0.0569.6320.2850.2850.0000.0000.0000.000
96A120TYR0-0.006-0.03012.9880.0450.0450.0000.0000.0000.000
97A121HIS0-0.033-0.00615.3840.0170.0170.0000.0000.0000.000
98A122GLU-1-0.818-0.89118.077-0.103-0.1030.0000.0000.0000.000
99A123ASP-1-0.790-0.85920.307-0.101-0.1010.0000.0000.0000.000
100A124VAL00.0090.01223.6360.0100.0100.0000.0000.0000.000
101A125GLY0-0.007-0.01026.412-0.008-0.0080.0000.0000.0000.000
102A126TYR0-0.085-0.07527.8430.0060.0060.0000.0000.0000.000
103A127GLY0-0.032-0.00931.046-0.001-0.0010.0000.0000.0000.000
104A128VAL00.009-0.00132.6430.0010.0010.0000.0000.0000.000
105A129SER0-0.051-0.01936.2780.0020.0020.0000.0000.0000.000
106A130GLU-1-0.875-0.93838.761-0.013-0.0130.0000.0000.0000.000
107A131GLY00.0090.01442.5450.0000.0000.0000.0000.0000.000
108A132LEU0-0.007-0.00439.8070.0020.0020.0000.0000.0000.000
109A133ALA00.0620.03143.9590.0000.0000.0000.0000.0000.000
110A134SER0-0.005-0.00141.2630.0020.0020.0000.0000.0000.000
111A135LYS11.0121.01439.542-0.016-0.0160.0000.0000.0000.000
112A136ALA00.0010.00437.4600.0000.0000.0000.0000.0000.000
113A137LEU00.0640.02236.2450.0000.0000.0000.0000.0000.000
114A138SER0-0.008-0.00536.401-0.003-0.0030.0000.0000.0000.000
115A139LEU00.0130.00534.145-0.002-0.0020.0000.0000.0000.000
116A140GLU-1-0.882-0.91831.9390.0270.0270.0000.0000.0000.000
117A141LYS10.8160.88131.4900.0080.0080.0000.0000.0000.000
118A142ALA00.0340.02231.887-0.002-0.0020.0000.0000.0000.000
119A143ARG10.9190.93727.642-0.031-0.0310.0000.0000.0000.000
120A144LYS10.8790.92927.178-0.029-0.0290.0000.0000.0000.000
121A145GLU-1-0.845-0.89327.210-0.018-0.0180.0000.0000.0000.000
122A146ALA00.0370.02528.458-0.006-0.0060.0000.0000.0000.000
123A147VAL00.0090.00422.222-0.008-0.0080.0000.0000.0000.000
124A148THR0-0.026-0.02523.764-0.009-0.0090.0000.0000.0000.000
125A149ASP-1-0.848-0.92125.333-0.063-0.0630.0000.0000.0000.000
126A150GLY00.0650.02824.333-0.010-0.0100.0000.0000.0000.000
127A151LEU0-0.0140.00518.992-0.016-0.0160.0000.0000.0000.000
128A152LYS10.8170.89222.0410.0340.0340.0000.0000.0000.000
129A153ARG10.7870.88424.5970.0630.0630.0000.0000.0000.000
130A154ALA00.0400.02720.107-0.011-0.0110.0000.0000.0000.000
131A155LEU00.0100.00317.700-0.026-0.0260.0000.0000.0000.000
132A156ARG10.8220.89221.0230.1000.1000.0000.0000.0000.000
133A157SER0-0.032-0.01721.8840.0040.0040.0000.0000.0000.000
134A158PHE00.0220.02715.957-0.008-0.0080.0000.0000.0000.000
135A159GLY00.0350.01220.997-0.010-0.0100.0000.0000.0000.000
136A160ASN0-0.090-0.05624.1370.0160.0160.0000.0000.0000.000
137A161ALA00.0010.01223.8290.0120.0120.0000.0000.0000.000
138A162LEU00.0410.02219.5580.0050.0050.0000.0000.0000.000
139A163GLY00.0330.00924.0380.0080.0080.0000.0000.0000.000
140A164ASN0-0.054-0.01526.8010.0100.0100.0000.0000.0000.000
141A165CYS0-0.032-0.01728.4360.0060.0060.0000.0000.0000.000
142A166ILE0-0.0030.00530.5840.0070.0070.0000.0000.0000.000
143A167LEU0-0.003-0.01531.1890.0080.0080.0000.0000.0000.000
144A168ASP-1-0.752-0.84834.152-0.078-0.0780.0000.0000.0000.000
145A169LYS10.9290.94535.7970.0670.0670.0000.0000.0000.000
146A170ASP-1-0.776-0.85038.931-0.057-0.0570.0000.0000.0000.000
147A171TYR0-0.021-0.02533.2650.0030.0030.0000.0000.0000.000
148A172LEU00.0120.00336.5850.0050.0050.0000.0000.0000.000
149A173ARG10.7950.87839.1790.0590.0590.0000.0000.0000.000
150A174SER0-0.015-0.02139.3070.0030.0030.0000.0000.0000.000
151A175LEU00.0110.00335.6420.0030.0030.0000.0000.0000.000
152A176ASN0-0.094-0.05540.0350.0060.0060.0000.0000.0000.000
153A177LYS10.9230.95943.2350.0410.0410.0000.0000.0000.000
154A178LEU00.0180.02638.9200.0000.0000.0000.0000.0000.000
155A179PRO0-0.010-0.01143.1410.0010.0010.0000.0000.0000.000
156A180ARG10.8880.95838.1940.0340.0340.0000.0000.0000.000
157A181GLN00.0480.02039.7590.0030.0030.0000.0000.0000.000
158A182LEU00.0210.01642.0530.0010.0010.0000.0000.0000.000
159A183PRO0-0.028-0.01438.694-0.003-0.0030.0000.0000.0000.000
160A184LEU00.0000.00033.388-0.001-0.0010.0000.0000.0000.000
161A185GLU-1-0.899-0.94436.652-0.009-0.0090.0000.0000.0000.000
162A186VAL0-0.008-0.01432.294-0.002-0.0020.0000.0000.0000.000
163A187ASP-1-0.761-0.84434.0650.0110.0110.0000.0000.0000.000
164A188LEU00.012-0.00232.8090.0020.0020.0000.0000.0000.000
165A189THR0-0.081-0.06634.3320.0050.0050.0000.0000.0000.000
166A190LYS10.8710.92430.332-0.008-0.0080.0000.0000.0000.000
167A191ALA0-0.0140.01429.6310.0020.0020.0000.0000.0000.000
168A192LYS10.8010.87423.278-0.085-0.0850.0000.0000.0000.000
169A193ARG10.8860.92628.534-0.034-0.0340.0000.0000.0000.000
170A194GLN00.0230.01728.3940.0000.0000.0000.0000.0000.000
171A195ASP-1-0.865-0.93124.5630.0930.0930.0000.0000.0000.000
172A196LEU0-0.007-0.00223.7250.0060.0060.0000.0000.0000.000
173A197GLU-1-0.824-0.90121.0230.0730.0730.0000.0000.0000.000
174A198PRO00.001-0.00321.7560.0140.0140.0000.0000.0000.000
175A199SER00.0250.02621.1440.0130.0130.0000.0000.0000.000
176A200VAL00.0400.01116.1270.0120.0120.0000.0000.0000.000
177A201GLU-1-0.832-0.88517.5610.2520.2520.0000.0000.0000.000
178A202ALA0-0.0030.00219.5180.0200.0200.0000.0000.0000.000
179A203ALA0-0.014-0.01015.8640.0140.0140.0000.0000.0000.000
180A204ARG10.8580.90414.654-0.230-0.2300.0000.0000.0000.000
181A205TYR00.0290.02415.7830.0470.0470.0000.0000.0000.000
182A206ASN0-0.066-0.03917.730-0.004-0.0040.0000.0000.0000.000
183A207SER0-0.062-0.03112.3020.0230.0230.0000.0000.0000.000
184A208CYS0-0.064-0.02313.3750.0700.0700.0000.0000.0000.000