FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 7KMYK

Calculation Name: 2B3A-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2B3A

Chain ID: A

ChEMBL ID:

UniProt ID: Q12967

Base Structure: SolutionNMR

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 87
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -623319.791855
FMO2-HF: Nuclear repulsion 587356.954063
FMO2-HF: Total energy -35962.837792
FMO2-MP2: Total energy -36065.116514


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:11:ASP)


Summations of interaction energy for fragment #1(A:11:ASP)
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.
-51.236-59.52731.738-13.473-9.9750.097
Interaction energy analysis for fragmet #1(A:11:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : 0.001
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].
3A13CYS00.0220.0253.823-2.321-0.232-0.024-1.012-1.053-0.001
23A33THR00.022-0.0092.961-4.296-1.4610.559-1.633-1.7610.015
24A34SER0-0.024-0.0461.689-28.004-43.09030.849-10.129-5.6340.080
25A35GLN0-0.072-0.0293.622-8.032-7.5550.047-0.144-0.3800.004
70A80PHE00.003-0.0153.1000.4661.8600.307-0.555-1.147-0.001
4A14ILE00.0150.0096.5480.2220.2220.0000.0000.0000.000
5A15ILE00.0010.00610.3260.1940.1940.0000.0000.0000.000
6A16ARG10.8480.92112.869-0.547-0.5470.0000.0000.0000.000
7A17VAL00.004-0.01015.8530.2240.2240.0000.0000.0000.000
8A18SER0-0.039-0.02918.451-0.167-0.1670.0000.0000.0000.000
9A19LEU00.0080.00122.2290.1220.1220.0000.0000.0000.000
10A20ASP-1-0.974-0.98725.0940.5730.5730.0000.0000.0000.000
11A21VAL00.009-0.00127.570-0.044-0.0440.0000.0000.0000.000
12A22ASP-1-0.861-0.89928.7810.2800.2800.0000.0000.0000.000
13A23ASN0-0.021-0.00627.893-0.043-0.0430.0000.0000.0000.000
14A24GLY00.0940.04525.5100.0480.0480.0000.0000.0000.000
15A25ASN0-0.009-0.00924.645-0.043-0.0430.0000.0000.0000.000
16A26MET0-0.060-0.06620.345-0.050-0.0500.0000.0000.0000.000
17A27TYR0-0.065-0.01621.733-0.029-0.0290.0000.0000.0000.000
18A28LYS10.8650.93118.664-0.531-0.5310.0000.0000.0000.000
19A29SER0-0.011-0.00415.1460.1290.1290.0000.0000.0000.000
20A30ILE0-0.015-0.00111.554-0.149-0.1490.0000.0000.0000.000
21A31LEU0-0.0160.0006.530-0.162-0.1620.0000.0000.0000.000
22A32VAL00.0160.0116.5330.3300.3300.0000.0000.0000.000
26A36ASP-1-0.813-0.8776.1611.6371.6370.0000.0000.0000.000
27A37LYS10.9520.9718.268-5.744-5.7440.0000.0000.0000.000
28A38ALA00.0700.03810.501-0.484-0.4840.0000.0000.0000.000
29A39PRO00.0360.02213.031-0.236-0.2360.0000.0000.0000.000
30A40ALA0-0.049-0.01512.268-0.368-0.3680.0000.0000.0000.000
31A41VAL0-0.004-0.00910.090-0.327-0.3270.0000.0000.0000.000
32A42ILE00.0060.00713.379-0.312-0.3120.0000.0000.0000.000
33A43ARG11.0171.01617.024-2.208-2.2080.0000.0000.0000.000
34A44LYS10.8030.87511.770-3.645-3.6450.0000.0000.0000.000
35A45ALA00.001-0.00415.851-0.258-0.2580.0000.0000.0000.000
36A46MET00.0130.03117.184-0.132-0.1320.0000.0000.0000.000
37A47ASP-1-0.737-0.83218.7701.0341.0340.0000.0000.0000.000
38A48LYS10.7830.86416.234-1.285-1.2850.0000.0000.0000.000
39A49HIS0-0.098-0.07619.729-0.232-0.2320.0000.0000.0000.000
40A50ASN0-0.036-0.02222.950-0.049-0.0490.0000.0000.0000.000
41A51LEU00.0130.02823.819-0.033-0.0330.0000.0000.0000.000
42A52GLU-1-1.002-1.00822.5500.7890.7890.0000.0000.0000.000
43A53GLU-1-0.967-0.98524.2500.6850.6850.0000.0000.0000.000
44A54GLU-1-0.813-0.88025.9250.6460.6460.0000.0000.0000.000
45A55GLU-1-0.887-0.94924.6730.9900.9900.0000.0000.0000.000
46A56PRO0-0.066-0.07120.8320.0080.0080.0000.0000.0000.000
47A57GLU-1-1.005-0.98823.2281.0001.0000.0000.0000.0000.000
48A58ASP-1-0.830-0.86326.4510.6750.6750.0000.0000.0000.000
49A59TYR0-0.037-0.05324.316-0.025-0.0250.0000.0000.0000.000
50A60GLU-1-0.764-0.86521.7431.2121.2120.0000.0000.0000.000
51A61LEU0-0.012-0.01115.547-0.058-0.0580.0000.0000.0000.000
52A62LEU0-0.049-0.03219.7400.0950.0950.0000.0000.0000.000
53A63GLN00.0270.03715.145-0.078-0.0780.0000.0000.0000.000
54A64ILE0-0.001-0.01518.989-0.080-0.0800.0000.0000.0000.000
55A65LEU0-0.0080.01918.903-0.025-0.0250.0000.0000.0000.000
56A66SER0-0.012-0.04621.450-0.109-0.1090.0000.0000.0000.000
57A67ASP-1-0.878-0.91525.0330.3850.3850.0000.0000.0000.000
58A68ASP-1-0.862-0.92527.5050.5450.5450.0000.0000.0000.000
59A69ARG10.9090.94423.119-0.758-0.7580.0000.0000.0000.000
60A70LYS10.9010.96622.840-0.570-0.5700.0000.0000.0000.000
61A71LEU0-0.031-0.01318.455-0.024-0.0240.0000.0000.0000.000
62A72LYS10.9490.96520.001-0.904-0.9040.0000.0000.0000.000
63A73ILE0-0.029-0.01014.7580.0780.0780.0000.0000.0000.000
64A74PRO00.0180.01817.570-0.006-0.0060.0000.0000.0000.000
65A75GLU-1-0.849-0.94516.6042.2132.2130.0000.0000.0000.000
66A76ASN0-0.048-0.02815.9830.3510.3510.0000.0000.0000.000
67A77ALA0-0.0020.01414.5940.0770.0770.0000.0000.0000.000
68A78ASN00.006-0.0069.1530.5440.5440.0000.0000.0000.000
69A79VAL00.0900.0348.148-0.393-0.3930.0000.0000.0000.000
71A81TYR0-0.043-0.0137.751-0.716-0.7160.0000.0000.0000.000
72A82ALA00.0000.00811.257-0.633-0.6330.0000.0000.0000.000
73A83MET0-0.0490.0019.587-0.686-0.6860.0000.0000.0000.000
74A84ASN0-0.016-0.05112.492-0.234-0.2340.0000.0000.0000.000
75A85SER00.0270.00310.938-0.227-0.2270.0000.0000.0000.000
76A86THR0-0.077-0.04013.309-0.280-0.2800.0000.0000.0000.000
77A87ALA0-0.023-0.00216.765-0.111-0.1110.0000.0000.0000.000
78A88ASN00.005-0.00518.176-0.203-0.2030.0000.0000.0000.000
79A89TYR00.0000.02613.7110.1450.1450.0000.0000.0000.000
80A90ASP-1-0.826-0.90215.7410.6630.6630.0000.0000.0000.000
81A91PHE0-0.018-0.02412.8840.2150.2150.0000.0000.0000.000
82A92VAL00.0360.02418.343-0.051-0.0510.0000.0000.0000.000
83A93LEU00.0150.00320.5340.1290.1290.0000.0000.0000.000
84A94LYS10.8180.89922.390-1.127-1.1270.0000.0000.0000.000
85A95LYS10.8500.92325.663-0.573-0.5730.0000.0000.0000.000
86A96ARG10.7180.83426.769-0.945-0.9450.0000.0000.0000.000
87A97THR-1-0.874-0.92029.6940.6070.6070.0000.0000.0000.000