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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: JL4Q9

Calculation Name: 5EE2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EE2

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H4

Base Structure: X-ray

Registration Date: 2023-06-22

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 122
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -949241.629923
FMO2-HF: Nuclear repulsion 904295.300579
FMO2-HF: Total energy -44946.329344
FMO2-MP2: Total energy -45080.663032


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:194:LEU)


Summations of interaction energy for fragment #1(A:194:LEU)
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.
-13.027-5.4547.851-4.464-10.96-0.033
Interaction energy analysis for fragmet #1(A:194:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.042
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].
3A196LYS10.8900.9553.592-3.259-0.913-0.017-1.086-1.243-0.001
4A197GLY00.0150.0164.410-0.0290.099-0.001-0.016-0.1120.000
5A198LYS10.7960.9126.804-0.089-0.0890.0000.0000.0000.000
6A199ILE0-0.046-0.0243.1970.0600.4830.054-0.085-0.3930.000
7A200THR00.0310.0226.893-0.175-0.1750.0000.0000.0000.000
8A201TYR0-0.003-0.0124.087-0.279-0.0670.000-0.020-0.1920.000
9A202GLN00.0320.01710.3920.0070.0070.0000.0000.0000.000
10A203VAL0-0.038-0.02912.3120.0060.0060.0000.0000.0000.000
11A204TRP00.0190.01214.9440.0160.0160.0000.0000.0000.000
12A205GLY00.0110.00117.164-0.016-0.0160.0000.0000.0000.000
13A206ILE00.0010.00019.2080.0210.0210.0000.0000.0000.000
14A207ARG10.7780.89721.7990.1540.1540.0000.0000.0000.000
15A208VAL00.0210.01624.7120.0090.0090.0000.0000.0000.000
16A209ARG10.8310.89727.8830.1120.1120.0000.0000.0000.000
17A210ASN0-0.001-0.00631.1440.0030.0030.0000.0000.0000.000
18A211GLY00.0060.00432.7120.0040.0040.0000.0000.0000.000
19A212GLN00.0110.01830.6420.0060.0060.0000.0000.0000.000
20A213PHE00.001-0.00424.904-0.006-0.0060.0000.0000.0000.000
21A214VAL00.0110.01226.3190.0060.0060.0000.0000.0000.000
22A215THR00.0610.01922.257-0.008-0.0080.0000.0000.0000.000
23A216SER0-0.0150.00220.7540.0040.0040.0000.0000.0000.000
24A217SER0-0.051-0.01421.6370.0240.0240.0000.0000.0000.000
25A235VAL0-0.031-0.02523.2430.0000.0000.0000.0000.0000.000
26A236LEU0-0.0020.00818.2100.0030.0030.0000.0000.0000.000
27A237SER00.0280.03217.695-0.005-0.0050.0000.0000.0000.000
28A238PHE0-0.0040.00014.156-0.001-0.0010.0000.0000.0000.000
29A239ILE0-0.005-0.00510.119-0.001-0.0010.0000.0000.0000.000
30A240THR0-0.0110.0009.617-0.018-0.0180.0000.0000.0000.000
31A241ALA00.0150.0065.5760.0510.0510.0000.0000.0000.000
32A242ASN0-0.048-0.0467.079-0.135-0.1350.0000.0000.0000.000
33A243PHE00.024-0.0192.748-5.066-2.1953.748-2.005-4.615-0.029
34A244ASN0-0.018-0.0025.5220.0880.0880.0000.0000.0000.000
35A245SER0-0.043-0.0348.925-0.003-0.0030.0000.0000.0000.000
36A246ASN0-0.067-0.0296.877-0.218-0.2180.0000.0000.0000.000
37A247THR00.0210.0178.6740.2180.2180.0000.0000.0000.000
38A248LEU00.006-0.0117.809-0.220-0.2200.0000.0000.0000.000
39A249ALA0-0.031-0.01210.9870.1180.1180.0000.0000.0000.000
40A250GLY00.011-0.00713.325-0.034-0.0340.0000.0000.0000.000
41A251LYS10.8600.93715.5980.2230.2230.0000.0000.0000.000
42A252ILE0-0.037-0.01316.2900.0040.0040.0000.0000.0000.000
43A253LEU00.0270.01419.2930.0120.0120.0000.0000.0000.000
44A254GLY00.0420.01222.6560.0040.0040.0000.0000.0000.000
45A255ASN0-0.028-0.02125.2870.0060.0060.0000.0000.0000.000
46A256SER0-0.008-0.00628.705-0.004-0.0040.0000.0000.0000.000
47A257ASP-1-0.906-0.93829.949-0.076-0.0760.0000.0000.0000.000
48A258TYR0-0.047-0.04720.761-0.007-0.0070.0000.0000.0000.000
49A259GLY00.0150.00826.915-0.007-0.0070.0000.0000.0000.000
50A260PRO0-0.016-0.02926.689-0.003-0.0030.0000.0000.0000.000
51A261ASP-1-0.739-0.84223.358-0.176-0.1760.0000.0000.0000.000
52A262VAL0-0.065-0.01819.0180.0030.0030.0000.0000.0000.000
53A263ASP-1-0.879-0.92619.623-0.298-0.2980.0000.0000.0000.000
54A264ILE00.0210.00013.933-0.003-0.0030.0000.0000.0000.000
55A265GLN0-0.011-0.01216.676-0.027-0.0270.0000.0000.0000.000
56A266ASN0-0.051-0.02115.739-0.016-0.0160.0000.0000.0000.000
57A267ALA00.0250.02212.2870.0290.0290.0000.0000.0000.000
58A268THR0-0.010-0.01711.574-0.103-0.1030.0000.0000.0000.000
59A269ILE0-0.027-0.0034.8530.0110.0110.0000.0000.0000.000
60A270THR00.009-0.0037.5610.1540.1540.0000.0000.0000.000
61A271GLY00.0360.0284.5470.1860.279-0.001-0.013-0.0780.000
62A272PRO0-0.034-0.0202.426-1.823-0.7950.805-0.639-1.1940.001
63A273THR0-0.030-0.0173.3320.4940.2570.0100.425-0.1970.000
64A274PHE00.0420.0056.348-0.320-0.3200.0000.0000.0000.000
65A275SER0-0.0130.0008.5790.1770.1770.0000.0000.0000.000
66A276GLY00.0490.02412.317-0.070-0.0700.0000.0000.0000.000
67A277ASP-1-0.813-0.87215.414-0.268-0.2680.0000.0000.0000.000
68A278ALA0-0.0020.00517.699-0.030-0.0300.0000.0000.0000.000
69A279THR0-0.005-0.00219.5510.0310.0310.0000.0000.0000.000
70A280SER00.003-0.02222.595-0.002-0.0020.0000.0000.0000.000
71A281GLY00.0360.01724.8130.0080.0080.0000.0000.0000.000
72A282GLY0-0.022-0.00828.0250.0090.0090.0000.0000.0000.000
73A283LYS10.8530.94526.9080.1290.1290.0000.0000.0000.000
74A284SER00.0440.01023.962-0.007-0.0070.0000.0000.0000.000
75A285GLY0-0.004-0.00821.4410.0170.0170.0000.0000.0000.000
76A286LYS10.8160.88618.8040.2650.2650.0000.0000.0000.000
77A287LEU0-0.014-0.01412.2990.0170.0170.0000.0000.0000.000
78A288GLU-1-0.849-0.92712.749-0.315-0.3150.0000.0000.0000.000
79A289GLY00.0150.00310.1170.0610.0610.0000.0000.0000.000
80A290LYS10.8280.9295.477-0.024-0.0240.0000.0000.0000.000
81A291PHE00.0470.0252.373-1.367-1.1823.251-0.976-2.459-0.004
82A292PHE00.0110.0004.0560.0090.2940.003-0.025-0.2620.000
83A302GLU-1-0.963-0.9889.6170.0900.0900.0000.0000.0000.000
84A303VAL0-0.033-0.0163.902-0.0610.0900.000-0.020-0.1320.000
85A304SER00.0540.0166.333-0.089-0.0890.0000.0000.0000.000
86A305ILE0-0.047-0.0045.967-0.101-0.1010.0000.0000.0000.000
87A306GLY00.0270.0067.9320.1070.1070.0000.0000.0000.000
88A307GLY0-0.003-0.00510.055-0.079-0.0790.0000.0000.0000.000
89A308LYS10.8310.92512.6300.3100.3100.0000.0000.0000.000
90A309ILE0-0.004-0.00915.819-0.037-0.0370.0000.0000.0000.000
91A310THR0-0.0240.00118.3250.0240.0240.0000.0000.0000.000
92A311PHE00.008-0.00621.435-0.017-0.0170.0000.0000.0000.000
93A312ASP-1-0.854-0.93024.598-0.156-0.1560.0000.0000.0000.000
94A313GLY0-0.0150.00027.1850.0100.0100.0000.0000.0000.000
95A314ASP-1-0.880-0.93628.304-0.110-0.1100.0000.0000.0000.000
96A315ARG10.9120.94824.3110.1500.1500.0000.0000.0000.000
97A316SER0-0.060-0.02926.848-0.002-0.0020.0000.0000.0000.000
98A317LEU00.0090.00825.2010.0010.0010.0000.0000.0000.000
99A318ASP-1-0.750-0.85622.590-0.186-0.1860.0000.0000.0000.000
100A319THR0-0.077-0.03818.6970.0090.0090.0000.0000.0000.000
101A320VAL00.0150.00816.178-0.021-0.0210.0000.0000.0000.000
102A321PHE0-0.009-0.01211.3080.0150.0150.0000.0000.0000.000
103A322GLY00.0400.01412.460-0.018-0.0180.0000.0000.0000.000
104A323GLY00.0260.00711.7090.0090.0090.0000.0000.0000.000
105A324VAL00.0100.0129.781-0.011-0.0110.0000.0000.0000.000
106A325SER0-0.058-0.0317.350-0.007-0.0070.0000.0000.0000.000
107A326TYR0-0.015-0.0139.3560.0640.0640.0000.0000.0000.000
108A327GLU-1-0.787-0.89411.0020.0780.0780.0000.0000.0000.000
109A328LYS10.9310.9715.543-0.889-0.8890.0000.0000.0000.000
110A329LYS10.8340.9058.9100.0540.0540.0000.0000.0000.000
111A330LEU00.0150.0124.576-0.173-0.085-0.001-0.004-0.0830.000
112A331ASP-1-0.815-0.9217.4320.8450.8450.0000.0000.0000.000
113A332ASP-1-0.839-0.8939.973-0.338-0.3380.0000.0000.0000.000
114A333THR00.0180.01310.116-0.075-0.0750.0000.0000.0000.000
115A334SER0-0.067-0.04112.678-0.043-0.0430.0000.0000.0000.000
116A335GLN00.0680.02112.316-0.128-0.1280.0000.0000.0000.000
117A336ASP-1-0.820-0.88413.420-0.474-0.4740.0000.0000.0000.000
118A337THR00.0190.00611.372-0.050-0.0500.0000.0000.0000.000
119A338ASN0-0.0140.00013.4100.0280.0280.0000.0000.0000.000
120A339HIS00.0200.02213.643-0.068-0.0680.0000.0000.0000.000
121A340LEU0-0.025-0.01010.4040.0540.0540.0000.0000.0000.000
122A341THR00.0110.00814.3460.0070.0070.0000.0000.0000.000