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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: N9ZNQ

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 OptH
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 -948809.943997
FMO2-HF: Nuclear repulsion 903864.171311
FMO2-HF: Total energy -44945.772686
FMO2-MP2: Total energy -45080.111438


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.
-12.101-4.948.04-4.326-10.876-0.029
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 : -0.051 / 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].
3A196LYS10.9550.9923.577-3.347-0.964-0.015-1.108-1.260-0.002
4A197GLY00.0110.0144.3950.0270.147-0.001-0.016-0.1030.000
5A198LYS10.8010.9076.790-0.105-0.1050.0000.0000.0000.000
6A199ILE0-0.057-0.0323.2560.0250.4380.052-0.083-0.3820.000
7A200THR00.0320.0237.012-0.178-0.1780.0000.0000.0000.000
8A201TYR0-0.005-0.0143.4390.0650.3510.004-0.046-0.2440.000
9A202GLN00.0210.01310.2200.0180.0180.0000.0000.0000.000
10A203VAL0-0.025-0.02012.062-0.004-0.0040.0000.0000.0000.000
11A204TRP00.0170.01114.6730.0190.0190.0000.0000.0000.000
12A205GLY00.010-0.00417.262-0.021-0.0210.0000.0000.0000.000
13A206ILE0-0.0010.00119.2420.0230.0230.0000.0000.0000.000
14A207ARG10.7760.88421.8650.1600.1600.0000.0000.0000.000
15A208VAL00.0230.01624.6920.0080.0080.0000.0000.0000.000
16A209ARG10.8450.90627.9050.1190.1190.0000.0000.0000.000
17A210ASN0-0.008-0.00831.1250.0040.0040.0000.0000.0000.000
18A211GLY00.0060.00232.7270.0040.0040.0000.0000.0000.000
19A212GLN00.0130.01830.6670.0060.0060.0000.0000.0000.000
20A213PHE00.006-0.00324.902-0.006-0.0060.0000.0000.0000.000
21A214VAL00.0040.01226.3830.0060.0060.0000.0000.0000.000
22A215THR00.0560.01522.477-0.009-0.0090.0000.0000.0000.000
23A216SER00.0080.02020.7370.0010.0010.0000.0000.0000.000
24A217SER0-0.065-0.02621.7390.0090.0090.0000.0000.0000.000
25A235VAL0-0.025-0.02023.1560.0000.0000.0000.0000.0000.000
26A236LEU0-0.0090.00217.9050.0010.0010.0000.0000.0000.000
27A237SER00.0330.03417.543-0.002-0.0020.0000.0000.0000.000
28A238PHE00.0020.00414.035-0.005-0.0050.0000.0000.0000.000
29A239ILE0-0.006-0.0069.722-0.003-0.0030.0000.0000.0000.000
30A240THR0-0.014-0.0349.591-0.012-0.0120.0000.0000.0000.000
31A241ALA00.0110.0055.5540.0310.0310.0000.0000.0000.000
32A242ASN0-0.045-0.0517.227-0.093-0.0930.0000.0000.0000.000
33A243PHE00.000-0.0292.709-4.137-1.7783.728-1.760-4.327-0.024
34A244ASN0-0.0160.0015.5160.0470.0470.0000.0000.0000.000
35A245SER0-0.049-0.0478.935-0.003-0.0030.0000.0000.0000.000
36A246ASN0-0.042-0.0156.910-0.317-0.3170.0000.0000.0000.000
37A247THR00.0150.0138.7030.1920.1920.0000.0000.0000.000
38A248LEU00.004-0.0128.058-0.197-0.1970.0000.0000.0000.000
39A249ALA0-0.033-0.01411.1040.1070.1070.0000.0000.0000.000
40A250GLY00.008-0.00913.225-0.032-0.0320.0000.0000.0000.000
41A251LYS10.9550.99315.4540.2250.2250.0000.0000.0000.000
42A252ILE0-0.030-0.00816.3840.0020.0020.0000.0000.0000.000
43A253LEU00.0240.01119.1570.0120.0120.0000.0000.0000.000
44A254GLY00.0470.01922.4070.0020.0020.0000.0000.0000.000
45A255ASN0-0.022-0.01225.1480.0080.0080.0000.0000.0000.000
46A256SER00.0130.00028.484-0.003-0.0030.0000.0000.0000.000
47A257ASP-1-0.922-0.94129.798-0.082-0.0820.0000.0000.0000.000
48A258TYR0-0.072-0.06520.637-0.007-0.0070.0000.0000.0000.000
49A259GLY00.0130.01226.956-0.007-0.0070.0000.0000.0000.000
50A260PRO0-0.023-0.02926.686-0.003-0.0030.0000.0000.0000.000
51A261ASP-1-0.803-0.88923.272-0.172-0.1720.0000.0000.0000.000
52A262VAL0-0.064-0.03118.9750.0030.0030.0000.0000.0000.000
53A263ASP-1-0.908-0.95419.743-0.300-0.3000.0000.0000.0000.000
54A264ILE00.0230.00514.016-0.004-0.0040.0000.0000.0000.000
55A265GLN00.0020.00016.813-0.022-0.0220.0000.0000.0000.000
56A266ASN0-0.050-0.01615.767-0.020-0.0200.0000.0000.0000.000
57A267ALA00.0320.02412.2740.0250.0250.0000.0000.0000.000
58A268THR0-0.022-0.02111.585-0.095-0.0950.0000.0000.0000.000
59A269ILE0-0.0150.0044.897-0.008-0.0080.0000.0000.0000.000
60A270THR0-0.001-0.0097.4630.1460.1460.0000.0000.0000.000
61A271GLY00.0320.0304.5620.1550.250-0.001-0.013-0.0810.000
62A272PRO0-0.027-0.0172.481-1.821-0.7270.899-0.697-1.2950.001
63A273THR0-0.038-0.0223.3440.4080.1150.0140.483-0.2040.000
64A274PHE00.0350.0016.222-0.274-0.2740.0000.0000.0000.000
65A275SER0-0.020-0.0058.5210.1600.1600.0000.0000.0000.000
66A276GLY00.0540.02712.270-0.062-0.0620.0000.0000.0000.000
67A277ASP-1-0.874-0.91715.416-0.282-0.2820.0000.0000.0000.000
68A278ALA0-0.012-0.00917.759-0.028-0.0280.0000.0000.0000.000
69A279THR0-0.010-0.00619.6040.0300.0300.0000.0000.0000.000
70A280SER00.009-0.00622.677-0.003-0.0030.0000.0000.0000.000
71A281GLY00.0510.02324.8780.0080.0080.0000.0000.0000.000
72A282GLY0-0.026-0.01028.1040.0090.0090.0000.0000.0000.000
73A283LYS10.9120.97226.9500.1310.1310.0000.0000.0000.000
74A284SER00.0430.01123.960-0.008-0.0080.0000.0000.0000.000
75A285GLY0-0.011-0.01021.4320.0150.0150.0000.0000.0000.000
76A286LYS10.8940.94918.7780.2440.2440.0000.0000.0000.000
77A287LEU0-0.005-0.01012.3300.0150.0150.0000.0000.0000.000
78A288GLU-1-0.916-0.96812.637-0.334-0.3340.0000.0000.0000.000
79A289GLY00.0130.00110.0380.0580.0580.0000.0000.0000.000
80A290LYS10.8730.9565.9440.2170.2170.0000.0000.0000.000
81A291PHE00.0510.0202.369-1.358-1.2323.356-1.011-2.471-0.004
82A292PHE0-0.016-0.0143.997-0.0910.2640.005-0.052-0.3090.000
83A302GLU-1-0.963-0.9909.6350.0400.0400.0000.0000.0000.000
84A303VAL0-0.039-0.0223.931-0.0720.0830.000-0.020-0.1350.000
85A304SER00.0310.0066.131-0.060-0.0600.0000.0000.0000.000
86A305ILE0-0.0230.0095.907-0.184-0.1840.0000.0000.0000.000
87A306GLY00.0230.0048.0260.1300.1300.0000.0000.0000.000
88A307GLY0-0.003-0.0049.973-0.087-0.0870.0000.0000.0000.000
89A308LYS10.8890.96312.5520.3290.3290.0000.0000.0000.000
90A309ILE0-0.004-0.00715.751-0.034-0.0340.0000.0000.0000.000
91A310THR0-0.0050.01318.2800.0200.0200.0000.0000.0000.000
92A311PHE00.010-0.00821.446-0.015-0.0150.0000.0000.0000.000
93A312ASP-1-0.902-0.96624.555-0.159-0.1590.0000.0000.0000.000
94A313GLY0-0.054-0.01927.1140.0100.0100.0000.0000.0000.000
95A314ASP-1-0.883-0.93928.273-0.115-0.1150.0000.0000.0000.000
96A315ARG10.9160.94224.6710.1490.1490.0000.0000.0000.000
97A316SER0-0.059-0.02326.787-0.003-0.0030.0000.0000.0000.000
98A317LEU00.0030.00325.1070.0010.0010.0000.0000.0000.000
99A318ASP-1-0.754-0.84322.549-0.191-0.1910.0000.0000.0000.000
100A319THR0-0.075-0.03518.7200.0070.0070.0000.0000.0000.000
101A320VAL00.0100.00616.139-0.022-0.0220.0000.0000.0000.000
102A321PHE0-0.004-0.01211.3520.0180.0180.0000.0000.0000.000
103A322GLY00.0370.01212.536-0.027-0.0270.0000.0000.0000.000
104A323GLY00.0270.00711.6470.0230.0230.0000.0000.0000.000
105A324VAL00.0180.0209.711-0.034-0.0340.0000.0000.0000.000
106A325SER0-0.057-0.0307.405-0.002-0.0020.0000.0000.0000.000
107A326TYR0-0.024-0.0179.4010.0600.0600.0000.0000.0000.000
108A327GLU-1-0.820-0.88111.0170.0420.0420.0000.0000.0000.000
109A328LYS10.9410.9695.269-0.996-0.9960.0000.0000.0000.000
110A329LYS10.9360.9698.8860.0200.0200.0000.0000.0000.000
111A330LEU00.0120.0074.648-0.120-0.052-0.001-0.003-0.0650.000
112A331ASP-1-0.853-0.9327.4260.8360.8360.0000.0000.0000.000
113A332ASP-1-0.866-0.8779.932-0.295-0.2950.0000.0000.0000.000
114A333THR00.0150.01010.101-0.065-0.0650.0000.0000.0000.000
115A334SER0-0.059-0.07112.662-0.039-0.0390.0000.0000.0000.000
116A335GLN00.0660.02212.300-0.093-0.0930.0000.0000.0000.000
117A336ASP-1-0.822-0.88113.401-0.424-0.4240.0000.0000.0000.000
118A337THR00.0150.00811.511-0.042-0.0420.0000.0000.0000.000
119A338ASN00.0050.00813.5130.0060.0060.0000.0000.0000.000
120A339HIS00.0230.06213.703-0.056-0.0560.0000.0000.0000.000
121A340LEU0-0.035-0.01510.3870.0510.0510.0000.0000.0000.000
122A341THR0-0.051-0.05514.4760.0020.0020.0000.0000.0000.000