Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 5JVNZ

Calculation Name: 2B0A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B0A

Chain ID: A

ChEMBL ID:

UniProt ID: Q58193

Base Structure: X-ray

Registration Date: 2023-09-23

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063732.713674
FMO2-HF: Nuclear repulsion 1990026.504736
FMO2-HF: Total energy -73706.208938
FMO2-MP2: Total energy -73921.417677


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:1:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-3.8320.497000000000010.414-1.914-2.8270.005
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.920 / q_NPA : -0.969
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].
3A3LEU0-0.023-0.0023.698-4.517-2.836-0.012-0.780-0.8890.003
4A4ASP-1-0.748-0.8576.42722.47222.4720.0000.0000.0000.000
5A5LEU0-0.020-0.0059.341-1.383-1.3830.0000.0000.0000.000
6A6THR0-0.009-0.02012.552-1.788-1.7880.0000.0000.0000.000
7A7GLN00.0200.01715.3220.5010.5010.0000.0000.0000.000
8A8THR0-0.039-0.01518.1800.3870.3870.0000.0000.0000.000
9A9LEU0-0.020-0.01419.037-0.554-0.5540.0000.0000.0000.000
10A10ILE00.024-0.00121.939-0.210-0.2100.0000.0000.0000.000
11A11ASN0-0.002-0.02225.0970.1040.1040.0000.0000.0000.000
12A12PHE0-0.014-0.01126.094-0.211-0.2110.0000.0000.0000.000
13A13PRO00.0340.02228.1580.3610.3610.0000.0000.0000.000
14A14ARG10.9380.98330.258-9.812-9.8120.0000.0000.0000.000
15A15PRO00.0500.01031.741-0.148-0.1480.0000.0000.0000.000
16A16GLY0-0.026-0.01135.291-0.042-0.0420.0000.0000.0000.000
17A17ASP-1-0.940-0.95931.7979.5809.5800.0000.0000.0000.000
18A18PRO0-0.080-0.05432.832-0.076-0.0760.0000.0000.0000.000
19A19GLU-1-0.863-0.91132.1459.1129.1120.0000.0000.0000.000
20A20LEU0-0.080-0.03026.0580.0650.0650.0000.0000.0000.000
21A21ARG10.9250.95730.131-8.817-8.8170.0000.0000.0000.000
22A22ILE00.015-0.00125.9260.1490.1490.0000.0000.0000.000
23A23ILE0-0.058-0.01630.325-0.234-0.2340.0000.0000.0000.000
24A24GLU-1-0.910-0.95630.07810.16610.1660.0000.0000.0000.000
25A25LYS10.9000.94732.708-8.613-8.6130.0000.0000.0000.000
26A26LYS10.9720.98333.943-8.156-8.1560.0000.0000.0000.000
27A27ILE0-0.008-0.02135.578-0.290-0.2900.0000.0000.0000.000
28A28ASP-1-0.900-0.94836.1788.2348.2340.0000.0000.0000.000
29A29GLY0-0.0130.00235.9350.0920.0920.0000.0000.0000.000
30A30PHE0-0.0220.00430.6790.3700.3700.0000.0000.0000.000
31A31ILE0-0.019-0.01129.760-0.318-0.3180.0000.0000.0000.000
32A32VAL0-0.0010.00429.7500.3230.3230.0000.0000.0000.000
33A33SER00.010-0.01728.262-0.085-0.0850.0000.0000.0000.000
34A34GLU-1-0.951-0.96030.2899.0309.0300.0000.0000.0000.000
35A35ILE0-0.012-0.01624.9700.0190.0190.0000.0000.0000.000
36A36ILE00.0050.01229.275-0.121-0.1210.0000.0000.0000.000
37A37MET00.0370.00224.0000.2220.2220.0000.0000.0000.000
38A38GLY00.0520.03829.630-0.170-0.1700.0000.0000.0000.000
39A39SER0-0.055-0.05327.7890.3690.3690.0000.0000.0000.000
40A40HIS10.8480.91526.674-10.296-10.2960.0000.0000.0000.000
41A41LEU00.0020.02625.5140.1140.1140.0000.0000.0000.000
42A42CYS0-0.0240.01421.9340.4810.4810.0000.0000.0000.000
43A43THR00.0210.02117.431-0.085-0.0850.0000.0000.0000.000
44A44HIS10.8310.92220.685-12.266-12.2660.0000.0000.0000.000
45A45ILE0-0.012-0.01720.8400.2190.2190.0000.0000.0000.000
46A46ASP-1-0.799-0.91423.19710.91110.9110.0000.0000.0000.000
47A47TYR0-0.045-0.03923.7160.5250.5250.0000.0000.0000.000
48A48PRO00.0330.00028.451-0.253-0.2530.0000.0000.0000.000
49A49LYS10.8410.91631.731-9.511-9.5110.0000.0000.0000.000
50A50HIS0-0.031-0.00730.795-0.384-0.3840.0000.0000.0000.000
51A51VAL0-0.030-0.00333.128-0.210-0.2100.0000.0000.0000.000
52A52GLY0-0.017-0.01435.704-0.264-0.2640.0000.0000.0000.000
53A53LEU0-0.076-0.03134.876-0.242-0.2420.0000.0000.0000.000
54A54GLU-1-0.904-0.94734.8888.7948.7940.0000.0000.0000.000
55A55ASN0-0.029-0.02129.8780.1300.1300.0000.0000.0000.000
56A56ARG11.0101.00129.750-10.092-10.0920.0000.0000.0000.000
57A57ILE0-0.025-0.01825.5010.3030.3030.0000.0000.0000.000
58A58PRO0-0.0040.01324.4470.0670.0670.0000.0000.0000.000
59A59PHE00.0360.01918.9800.3870.3870.0000.0000.0000.000
60A60LYS10.8970.92320.675-14.530-14.5300.0000.0000.0000.000
61A61ASP-1-0.891-0.93719.93815.23115.2310.0000.0000.0000.000
62A62GLY00.0370.01021.483-0.011-0.0110.0000.0000.0000.000
63A63ILE0-0.075-0.02015.1040.3490.3490.0000.0000.0000.000
64A64ILE00.0040.01416.856-0.241-0.2410.0000.0000.0000.000
65A65LYS10.9440.96713.728-17.344-17.3440.0000.0000.0000.000
66A66GLY00.0300.01613.675-1.624-1.6240.0000.0000.0000.000
67A67LYS10.8720.95113.425-18.260-18.2600.0000.0000.0000.000
68A68GLY00.0430.02312.811-1.498-1.4980.0000.0000.0000.000
69A69TYR0-0.043-0.04513.2870.1910.1910.0000.0000.0000.000
70A70CYS0-0.0570.00013.393-0.782-0.7820.0000.0000.0000.000
71A71ILE0-0.0060.00515.1760.0070.0070.0000.0000.0000.000
72A72SER00.031-0.00818.4170.3870.3870.0000.0000.0000.000
73A73LEU0-0.059-0.03420.191-0.311-0.3110.0000.0000.0000.000
74A74ASP-1-0.864-0.91623.11911.56511.5650.0000.0000.0000.000
75A75ASP-1-0.925-0.95921.23512.12612.1260.0000.0000.0000.000
76A76PHE0-0.072-0.04522.155-0.065-0.0650.0000.0000.0000.000
77A77PRO0-0.0020.01524.808-0.230-0.2300.0000.0000.0000.000
78A78GLY00.006-0.00228.612-0.157-0.1570.0000.0000.0000.000
79A79ASN0-0.026-0.01423.909-0.363-0.3630.0000.0000.0000.000
80A80LYS10.9520.97025.339-11.294-11.2940.0000.0000.0000.000
81A81LEU00.0130.02023.0660.3820.3820.0000.0000.0000.000
82A82PRO00.0160.01418.544-0.123-0.1230.0000.0000.0000.000
83A83ALA0-0.0210.00020.126-0.228-0.2280.0000.0000.0000.000
84A84CYS0-0.091-0.05317.0180.8640.8640.0000.0000.0000.000
85A85ASP-1-0.792-0.87917.52316.17116.1710.0000.0000.0000.000
86A86ILE0-0.022-0.01115.640-0.776-0.7760.0000.0000.0000.000
87A87LEU00.0340.01816.4420.7280.7280.0000.0000.0000.000
88A88LEU0-0.029-0.01312.925-0.254-0.2540.0000.0000.0000.000
89A89ILE00.020-0.00417.034-0.122-0.1220.0000.0000.0000.000
90A90TYR00.0210.00016.7010.0890.0890.0000.0000.0000.000
91A91THR0-0.007-0.04218.736-0.595-0.5950.0000.0000.0000.000
92A92GLY00.0120.01720.373-0.458-0.4580.0000.0000.0000.000
93A93PHE0-0.016-0.03721.393-0.253-0.2530.0000.0000.0000.000
94A94SER0-0.005-0.02118.932-0.199-0.1990.0000.0000.0000.000
95A95LYS10.8680.94220.987-11.206-11.2060.0000.0000.0000.000
96A96TYR0-0.078-0.06122.179-0.250-0.2500.0000.0000.0000.000
97A97TRP00.0910.04821.754-0.455-0.4550.0000.0000.0000.000
98A98GLY0-0.028-0.00823.9090.0560.0560.0000.0000.0000.000
99A99ARG10.8070.90126.436-10.479-10.4790.0000.0000.0000.000
100A100ASP-1-0.819-0.91529.2089.3249.3240.0000.0000.0000.000
101A101GLU-1-0.831-0.92030.3659.5819.5810.0000.0000.0000.000
102A102TYR0-0.083-0.05323.3160.1370.1370.0000.0000.0000.000
103A103PHE0-0.027-0.03727.9160.1720.1720.0000.0000.0000.000
104A104GLU-1-0.900-0.95030.5468.6208.6200.0000.0000.0000.000
105A105LYS10.8370.93727.766-9.857-9.8570.0000.0000.0000.000
106A106ILE0-0.011-0.01428.5630.3610.3610.0000.0000.0000.000
107A107PRO0-0.047-0.02025.654-0.156-0.1560.0000.0000.0000.000
108A108GLU-1-0.913-0.94328.2248.6958.6950.0000.0000.0000.000
109A109ILE0-0.013-0.01825.3550.2120.2120.0000.0000.0000.000
110A110PRO00.0170.01528.187-0.154-0.1540.0000.0000.0000.000
111A111PHE00.0420.01323.854-0.152-0.1520.0000.0000.0000.000
112A112LEU00.0290.01028.0280.2360.2360.0000.0000.0000.000
113A113ASP-1-0.827-0.91229.5768.9388.9380.0000.0000.0000.000
114A114ASP-1-0.858-0.92628.6779.7149.7140.0000.0000.0000.000
115A115ILE0-0.019-0.00824.5780.2360.2360.0000.0000.0000.000
116A116ILE0-0.0180.00527.1560.1670.1670.0000.0000.0000.000
117A117LYS10.8430.92630.135-9.318-9.3180.0000.0000.0000.000
118A118SER0-0.074-0.02925.4960.2120.2120.0000.0000.0000.000
119A119ASN0-0.014-0.01825.109-0.346-0.3460.0000.0000.0000.000
120A120ILE0-0.017-0.01121.2940.5320.5320.0000.0000.0000.000
121A121LYS10.8700.92320.897-15.007-15.0070.0000.0000.0000.000
122A122CYS0-0.054-0.02319.891-0.245-0.2450.0000.0000.0000.000
123A123VAL00.0130.01820.4140.4920.4920.0000.0000.0000.000
124A124GLY00.0200.01318.404-0.144-0.1440.0000.0000.0000.000
125A125ILE0-0.009-0.00719.3330.0350.0350.0000.0000.0000.000
126A126ASP-1-0.726-0.80417.79614.31814.3180.0000.0000.0000.000
127A127ALA00.0250.01419.719-0.457-0.4570.0000.0000.0000.000
128A128CYS0-0.0200.00123.4590.1220.1220.0000.0000.0000.000
129A129THR0-0.0020.00026.153-0.105-0.1050.0000.0000.0000.000
130A130ILE00.0150.00724.5810.2130.2130.0000.0000.0000.000
131A131GLY00.0260.01627.134-0.186-0.1860.0000.0000.0000.000
132A132GLY00.0230.01330.9140.0820.0820.0000.0000.0000.000
133A133PHE00.000-0.00933.2850.2580.2580.0000.0000.0000.000
134A134GLU-1-0.848-0.93234.9788.2198.2190.0000.0000.0000.000
135A135GLU-1-0.856-0.92730.9879.0389.0380.0000.0000.0000.000
136A136HIS10.7890.89428.352-10.232-10.2320.0000.0000.0000.000
137A137LYS10.9550.97731.365-8.144-8.1440.0000.0000.0000.000
138A138ARG10.8720.94633.060-8.902-8.9020.0000.0000.0000.000
139A139LEU00.0330.02826.3730.0490.0490.0000.0000.0000.000
140A140LEU0-0.006-0.00328.2060.0680.0680.0000.0000.0000.000
141A141SER0-0.104-0.07430.772-0.044-0.0440.0000.0000.0000.000
142A142ASN0-0.083-0.05231.566-0.307-0.3070.0000.0000.0000.000
143A143ASN0-0.090-0.04827.5240.0680.0680.0000.0000.0000.000
144A144ILE00.0110.02124.7650.4280.4280.0000.0000.0000.000
145A145LEU0-0.036-0.02222.970-0.251-0.2510.0000.0000.0000.000
146A146ILE00.0500.01623.4850.2500.2500.0000.0000.0000.000
147A147ILE0-0.004-0.00318.1660.0370.0370.0000.0000.0000.000
148A148GLU-1-0.783-0.88421.21511.57711.5770.0000.0000.0000.000
149A149ASN0-0.005-0.00921.3100.1980.1980.0000.0000.0000.000
150A150LEU0-0.0020.01215.1850.6060.6060.0000.0000.0000.000
151A151ASN0-0.007-0.01913.023-0.492-0.4920.0000.0000.0000.000
152A152GLU-1-0.827-0.93114.90917.36017.3600.0000.0000.0000.000
153A153ASN0-0.045-0.03510.0390.0200.0200.0000.0000.0000.000
154A154LEU00.008-0.00411.0371.1121.1120.0000.0000.0000.000
155A155LYS10.9921.01513.282-15.489-15.4890.0000.0000.0000.000
156A156ASN0-0.063-0.0319.143-1.410-1.4100.0000.0000.0000.000
157A157LEU00.0090.0037.4821.2651.2650.0000.0000.0000.000
158A158VAL00.0310.02810.748-0.197-0.1970.0000.0000.0000.000
159A159GLY0-0.024-0.00513.6750.2090.2090.0000.0000.0000.000
160A160LYS10.8340.9218.566-22.856-22.8560.0000.0000.0000.000
161A161SER00.015-0.00111.113-1.256-1.2560.0000.0000.0000.000
162A162PHE00.0100.0107.7901.5101.5100.0000.0000.0000.000
163A163TYR00.0140.0098.248-3.476-3.4760.0000.0000.0000.000
164A164PHE00.0330.0129.0812.4632.4630.0000.0000.0000.000
165A165LEU0-0.004-0.0098.473-1.068-1.0680.0000.0000.0000.000
166A166GLY00.0470.01311.9520.3830.3830.0000.0000.0000.000
167A167LEU0-0.026-0.02312.169-0.865-0.8650.0000.0000.0000.000
168A168PRO00.0070.00716.0380.0260.0260.0000.0000.0000.000
169A169LEU00.0310.01719.6180.1790.1790.0000.0000.0000.000
170A170LYS10.9290.97721.380-14.465-14.4650.0000.0000.0000.000
171A171ILE00.007-0.00223.236-0.476-0.4760.0000.0000.0000.000
172A172PHE0-0.033-0.02724.1460.3160.3160.0000.0000.0000.000
173A173ASP-1-0.849-0.91828.4869.0519.0510.0000.0000.0000.000
174A174ILE00.0280.03527.860-0.324-0.3240.0000.0000.0000.000
175A175ASP-1-0.793-0.88830.06510.38410.3840.0000.0000.0000.000
176A176ALA00.0450.00826.9230.1640.1640.0000.0000.0000.000
177A177SER0-0.037-0.01023.576-0.168-0.1680.0000.0000.0000.000
178A178PRO00.0500.03421.3950.3710.3710.0000.0000.0000.000
179A179ILE0-0.032-0.01717.1240.2790.2790.0000.0000.0000.000
180A180ARG10.8500.92511.939-22.072-22.0720.0000.0000.0000.000
181A181CYS0-0.037-0.01513.3060.1740.1740.0000.0000.0000.000
182A182ILE00.0130.0096.7760.3530.3530.0000.0000.0000.000
183A183ALA0-0.010-0.0047.419-1.695-1.6950.0000.0000.0000.000
184A184ILE00.0120.0023.5680.9681.6920.017-0.378-0.3620.002
185A185LEU0-0.050-0.0322.403-7.708-6.4130.399-0.568-1.1260.001
186A186GLU-1-0.942-0.9613.63134.03334.6620.010-0.188-0.450-0.001