Manual

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: YYK22

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 OptHSide
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 -1728758.988634
FMO2-HF: Nuclear repulsion 1656166.129714
FMO2-HF: Total energy -72592.85892
FMO2-MP2: Total energy -72802.002565


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.
-8.148-7.99414.201-6.621-7.731-0.035
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 : 0.005 / q_NPA : 0.003
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].
3A27GLY0-0.023-0.0133.8190.4403.1180.333-1.323-1.6870.003
4A28GLN0-0.016-0.0031.923-8.641-11.69713.864-5.202-5.605-0.038
5A29CYS0-0.037-0.0103.2830.0450.5070.005-0.088-0.3780.000
6A30GLN00.0270.0064.7020.6940.764-0.001-0.008-0.0610.000
7A31TYR0-0.011-0.0018.3870.0400.0400.0000.0000.0000.000
8A32THR0-0.002-0.01611.0560.0300.0300.0000.0000.0000.000
9A33ALA00.0390.02013.1350.0090.0090.0000.0000.0000.000
10A34GLU-1-0.823-0.90815.900-0.295-0.2950.0000.0000.0000.000
11A35GLU-1-0.790-0.87411.529-0.639-0.6390.0000.0000.0000.000
12A36TYR00.0060.00015.2500.0320.0320.0000.0000.0000.000
13A37GLN0-0.033-0.01916.3550.0390.0390.0000.0000.0000.000
14A38ALA0-0.009-0.00918.8620.0260.0260.0000.0000.0000.000
15A39ILE00.0690.03314.8630.0290.0290.0000.0000.0000.000
16A40GLN00.0140.03319.0350.0530.0530.0000.0000.0000.000
17A41LYS10.9040.94521.0010.1620.1620.0000.0000.0000.000
18A42ALA00.0130.00621.5390.0190.0190.0000.0000.0000.000
19A43LEU00.0370.00718.8380.0210.0210.0000.0000.0000.000
20A44ARG10.8890.94323.2420.2010.2010.0000.0000.0000.000
21A45GLN0-0.043-0.00226.3980.0080.0080.0000.0000.0000.000
22A46ARG10.8640.92228.2210.0900.0900.0000.0000.0000.000
23A47LEU00.0090.01427.0260.0030.0030.0000.0000.0000.000
24A48GLY00.0600.05231.0170.0040.0040.0000.0000.0000.000
25A49PRO00.001-0.01233.470-0.001-0.0010.0000.0000.0000.000
26A50GLU-1-0.835-0.91332.535-0.050-0.0500.0000.0000.0000.000
27A51TYR0-0.029-0.02826.8280.0010.0010.0000.0000.0000.000
28A52ILE0-0.084-0.02831.651-0.001-0.0010.0000.0000.0000.000
29A53SER00.008-0.00634.3040.0040.0040.0000.0000.0000.000
30A54SER0-0.063-0.04636.115-0.003-0.0030.0000.0000.0000.000
31A55ARG10.9810.99236.3000.0340.0340.0000.0000.0000.000
32A56MET00.0410.01540.573-0.002-0.0020.0000.0000.0000.000
33A57ALA0-0.0020.01142.3710.0010.0010.0000.0000.0000.000
34A58GLY00.0440.01243.3700.0010.0010.0000.0000.0000.000
35A59GLY00.0150.01445.669-0.001-0.0010.0000.0000.0000.000
36A60GLY0-0.013-0.00746.610-0.001-0.0010.0000.0000.0000.000
37A61GLN0-0.025-0.01044.5050.0010.0010.0000.0000.0000.000
38A62LYS10.9330.96842.7100.0370.0370.0000.0000.0000.000
39A63VAL00.0020.00537.235-0.003-0.0030.0000.0000.0000.000
40A64CYS0-0.036-0.02636.4750.0030.0030.0000.0000.0000.000
41A65TYR0-0.063-0.03132.268-0.003-0.0030.0000.0000.0000.000
42A66ILE00.0710.04927.7920.0020.0020.0000.0000.0000.000
43A67GLU-1-0.807-0.88829.808-0.029-0.0290.0000.0000.0000.000
44A68GLY00.0690.01926.117-0.006-0.0060.0000.0000.0000.000
45A69HIS0-0.001-0.01124.660-0.009-0.0090.0000.0000.0000.000
46A70ARG10.8690.93824.5610.0370.0370.0000.0000.0000.000
47A71VAL00.0220.01022.142-0.008-0.0080.0000.0000.0000.000
48A72ILE00.0060.00819.332-0.015-0.0150.0000.0000.0000.000
49A73ASN0-0.017-0.00719.707-0.011-0.0110.0000.0000.0000.000
50A74LEU0-0.0130.00020.748-0.009-0.0090.0000.0000.0000.000
51A75ALA00.0250.00717.314-0.019-0.0190.0000.0000.0000.000
52A76ASN0-0.011-0.00715.920-0.049-0.0490.0000.0000.0000.000
53A77GLU-1-0.947-0.96116.317-0.099-0.0990.0000.0000.0000.000
54A78MET0-0.101-0.03118.005-0.016-0.0160.0000.0000.0000.000
55A79PHE0-0.003-0.02413.141-0.029-0.0290.0000.0000.0000.000
56A80GLY00.0780.05512.423-0.080-0.0800.0000.0000.0000.000
57A81TYR00.000-0.01610.627-0.020-0.0200.0000.0000.0000.000
58A82ASN0-0.037-0.0146.746-0.016-0.0160.0000.0000.0000.000
59A83GLY00.0310.0147.895-0.254-0.2540.0000.0000.0000.000
60A84TRP0-0.085-0.06110.153-0.083-0.0830.0000.0000.0000.000
61A85ALA00.0220.02010.2220.0640.0640.0000.0000.0000.000
62A86HIS00.009-0.01612.375-0.029-0.0290.0000.0000.0000.000
63A87SER00.0210.02514.5700.0410.0410.0000.0000.0000.000
64A88ILE0-0.023-0.02316.445-0.025-0.0250.0000.0000.0000.000
65A89THR0-0.051-0.04419.3490.0210.0210.0000.0000.0000.000
66A90GLN00.0230.01420.1890.0150.0150.0000.0000.0000.000
67A91GLN0-0.0220.00523.7900.0000.0000.0000.0000.0000.000
68A92ASN0-0.035-0.02426.7890.0020.0020.0000.0000.0000.000
69A93VAL0-0.020-0.01830.365-0.002-0.0020.0000.0000.0000.000
70A94ASP-1-0.786-0.85233.618-0.019-0.0190.0000.0000.0000.000
71A95PHE00.0050.00135.9450.0010.0010.0000.0000.0000.000
72A96VAL0-0.071-0.05038.2620.0010.0010.0000.0000.0000.000
73A97ASP-1-0.859-0.91540.699-0.004-0.0040.0000.0000.0000.000
74A98LEU0-0.058-0.03144.3180.0000.0000.0000.0000.0000.000
75A99ASN00.0050.00146.9550.0000.0000.0000.0000.0000.000
76A100ASN0-0.005-0.01749.7930.0000.0000.0000.0000.0000.000
77A101GLY00.0120.00950.4260.0000.0000.0000.0000.0000.000
78A102ALA0-0.0150.01446.6560.0010.0010.0000.0000.0000.000
79A103PHE0-0.025-0.03642.1290.0000.0000.0000.0000.0000.000
80A104TYR0-0.020-0.01142.162-0.002-0.0020.0000.0000.0000.000
81A105VAL0-0.023-0.01636.1070.0020.0020.0000.0000.0000.000
82A106GLY00.0510.03936.295-0.002-0.0020.0000.0000.0000.000
83A107VAL0-0.068-0.03830.1330.0040.0040.0000.0000.0000.000
84A108CYS00.0070.01829.763-0.004-0.0040.0000.0000.0000.000
85A109ALA0-0.014-0.02425.0090.0090.0090.0000.0000.0000.000
86A110PHE00.0060.01123.082-0.010-0.0100.0000.0000.0000.000
87A111VAL0-0.0060.00219.7370.0130.0130.0000.0000.0000.000
88A112ARG10.9390.97412.4520.1930.1930.0000.0000.0000.000
89A113VAL0-0.013-0.01815.8100.0200.0200.0000.0000.0000.000
90A114GLN0-0.008-0.0058.4990.0920.0920.0000.0000.0000.000
91A115LEU0-0.0140.00211.4090.0330.0330.0000.0000.0000.000
92A116LYS10.8500.9046.3350.9640.9640.0000.0000.0000.000
93A117ASP-1-0.789-0.8786.158-1.845-1.8450.0000.0000.0000.000
94A118GLY0-0.0130.0038.2880.0640.0640.0000.0000.0000.000
95A119SER0-0.083-0.05510.2140.2520.2520.0000.0000.0000.000
96A120TYR0-0.003-0.02813.3740.0330.0330.0000.0000.0000.000
97A121HIS0-0.041-0.01215.5930.0160.0160.0000.0000.0000.000
98A122GLU-1-0.859-0.90718.612-0.086-0.0860.0000.0000.0000.000
99A123ASP-1-0.812-0.86720.594-0.105-0.1050.0000.0000.0000.000
100A124VAL0-0.001-0.00223.9620.0090.0090.0000.0000.0000.000
101A125GLY0-0.006-0.00526.664-0.006-0.0060.0000.0000.0000.000
102A126TYR0-0.089-0.08428.2010.0060.0060.0000.0000.0000.000
103A127GLY0-0.045-0.01231.428-0.001-0.0010.0000.0000.0000.000
104A128VAL00.0270.00932.7570.0020.0020.0000.0000.0000.000
105A129SER0-0.030-0.00936.4480.0010.0010.0000.0000.0000.000
106A130GLU-1-0.925-0.96438.675-0.015-0.0150.0000.0000.0000.000
107A131GLY00.0340.01742.4220.0000.0000.0000.0000.0000.000
108A132LEU0-0.030-0.00739.7490.0010.0010.0000.0000.0000.000
109A133ALA00.1020.04843.8730.0000.0000.0000.0000.0000.000
110A134SER0-0.0210.00041.2660.0010.0010.0000.0000.0000.000
111A135LYS11.0301.01939.620-0.015-0.0150.0000.0000.0000.000
112A136ALA0-0.014-0.00437.6630.0000.0000.0000.0000.0000.000
113A137LEU00.0450.01336.5320.0000.0000.0000.0000.0000.000
114A138SER00.001-0.00336.680-0.002-0.0020.0000.0000.0000.000
115A139LEU00.014-0.00134.398-0.002-0.0020.0000.0000.0000.000
116A140GLU-1-0.874-0.90731.7350.0220.0220.0000.0000.0000.000
117A141LYS10.8270.89431.6630.0100.0100.0000.0000.0000.000
118A142ALA00.0320.01932.311-0.003-0.0030.0000.0000.0000.000
119A143ARG10.9320.94728.224-0.024-0.0240.0000.0000.0000.000
120A144LYS10.8780.91827.352-0.026-0.0260.0000.0000.0000.000
121A145GLU-1-0.843-0.90827.473-0.022-0.0220.0000.0000.0000.000
122A146ALA00.0370.02228.620-0.007-0.0070.0000.0000.0000.000
123A147VAL00.0060.00722.405-0.008-0.0080.0000.0000.0000.000
124A148THR0-0.023-0.01324.128-0.010-0.0100.0000.0000.0000.000
125A149ASP-1-0.849-0.91925.398-0.065-0.0650.0000.0000.0000.000
126A150GLY00.0800.03124.858-0.010-0.0100.0000.0000.0000.000
127A151LEU0-0.028-0.00619.167-0.014-0.0140.0000.0000.0000.000
128A152LYS10.7990.88322.3400.0380.0380.0000.0000.0000.000
129A153ARG10.7870.88024.8500.0670.0670.0000.0000.0000.000
130A154ALA00.0390.03420.313-0.010-0.0100.0000.0000.0000.000
131A155LEU00.0290.01017.704-0.023-0.0230.0000.0000.0000.000
132A156ARG10.8420.91221.1520.1020.1020.0000.0000.0000.000
133A157SER0-0.027-0.02022.0540.0070.0070.0000.0000.0000.000
134A158PHE00.0090.01016.206-0.008-0.0080.0000.0000.0000.000
135A159GLY00.0280.01421.177-0.010-0.0100.0000.0000.0000.000
136A160ASN0-0.102-0.06724.3260.0120.0120.0000.0000.0000.000
137A161ALA00.0050.01123.8460.0110.0110.0000.0000.0000.000
138A162LEU00.0320.01819.6060.0100.0100.0000.0000.0000.000
139A163GLY00.0350.00524.0910.0070.0070.0000.0000.0000.000
140A164ASN0-0.055-0.01226.7750.0120.0120.0000.0000.0000.000
141A165CYS0-0.041-0.01528.5050.0050.0050.0000.0000.0000.000
142A166ILE00.0040.00730.5870.0070.0070.0000.0000.0000.000
143A167LEU0-0.009-0.01531.8450.0080.0080.0000.0000.0000.000
144A168ASP-1-0.759-0.87234.436-0.079-0.0790.0000.0000.0000.000
145A169LYS10.9550.96236.1040.0660.0660.0000.0000.0000.000
146A170ASP-1-0.794-0.86939.098-0.059-0.0590.0000.0000.0000.000
147A171TYR0-0.041-0.05533.5370.0020.0020.0000.0000.0000.000
148A172LEU0-0.003-0.00736.7140.0040.0040.0000.0000.0000.000
149A173ARG10.8120.90239.3290.0600.0600.0000.0000.0000.000
150A174SER00.009-0.00939.6080.0030.0030.0000.0000.0000.000
151A175LEU00.0020.01535.8940.0030.0030.0000.0000.0000.000
152A176ASN0-0.059-0.04640.1600.0060.0060.0000.0000.0000.000
153A177LYS10.8800.95543.5890.0430.0430.0000.0000.0000.000
154A178LEU00.0310.02639.2670.0000.0000.0000.0000.0000.000
155A179PRO0-0.005-0.00643.4850.0010.0010.0000.0000.0000.000
156A180ARG10.9310.97138.7640.0350.0350.0000.0000.0000.000
157A181GLN00.0200.00539.9890.0030.0030.0000.0000.0000.000
158A182LEU00.0200.01341.7790.0000.0000.0000.0000.0000.000
159A183PRO0-0.036-0.01138.404-0.003-0.0030.0000.0000.0000.000
160A184LEU00.0100.00633.1920.0000.0000.0000.0000.0000.000
161A185GLU-1-0.898-0.94637.026-0.012-0.0120.0000.0000.0000.000
162A186VAL0-0.038-0.02932.076-0.001-0.0010.0000.0000.0000.000
163A187ASP-1-0.797-0.87534.1070.0070.0070.0000.0000.0000.000
164A188LEU0-0.028-0.02232.3420.0020.0020.0000.0000.0000.000
165A189THR0-0.032-0.03934.1240.0060.0060.0000.0000.0000.000
166A190LYS10.9100.95130.111-0.012-0.0120.0000.0000.0000.000
167A191ALA0-0.0120.01329.4610.0010.0010.0000.0000.0000.000
168A192LYS10.8070.87923.400-0.081-0.0810.0000.0000.0000.000
169A193ARG10.9090.94328.350-0.031-0.0310.0000.0000.0000.000
170A194GLN0-0.0050.00528.4660.0020.0020.0000.0000.0000.000
171A195ASP-1-0.830-0.91624.8420.0900.0900.0000.0000.0000.000
172A196LEU0-0.032-0.01823.9800.0070.0070.0000.0000.0000.000
173A197GLU-1-0.814-0.88920.8280.0720.0720.0000.0000.0000.000
174A198PRO00.0070.00521.6030.0150.0150.0000.0000.0000.000
175A199SER00.0290.02220.8990.0150.0150.0000.0000.0000.000
176A200VAL00.0390.01316.0240.0140.0140.0000.0000.0000.000
177A201GLU-1-0.812-0.87617.4850.2640.2640.0000.0000.0000.000
178A202ALA0-0.027-0.01319.3620.0190.0190.0000.0000.0000.000
179A203ALA0-0.019-0.01615.7100.0170.0170.0000.0000.0000.000
180A204ARG10.8410.89214.449-0.231-0.2310.0000.0000.0000.000
181A205TYR00.0180.02515.4950.0490.0490.0000.0000.0000.000
182A206ASN0-0.068-0.03617.4450.0010.0010.0000.0000.0000.000
183A207SER0-0.072-0.04512.3250.0290.0290.0000.0000.0000.000
184A208CYS0-0.033-0.00413.0700.0860.0860.0000.0000.0000.000