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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: 39KJL

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 OptAll
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 -948081.040025
FMO2-HF: Nuclear repulsion 903134.477937
FMO2-HF: Total energy -44946.562088
FMO2-MP2: Total energy -45080.850505


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.
-12.551-3.3797.906-5.134-11.946-0.032
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 : -0.037 / q_NPA : -0.031
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].
3A196LYS10.8510.9203.792-5.398-2.111-0.028-1.667-1.592-0.005
4A197GLY00.0060.0164.5850.9841.129-0.001-0.008-0.1360.000
5A198LYS10.7950.9016.411-0.435-0.4350.0000.0000.0000.000
6A199ILE0-0.045-0.0253.131-0.1670.3040.094-0.098-0.4670.000
7A200THR00.0160.0067.205-0.184-0.1840.0000.0000.0000.000
8A201TYR0-0.016-0.0233.998-0.1990.0070.000-0.023-0.1840.000
9A202GLN00.0440.03210.575-0.004-0.0040.0000.0000.0000.000
10A203VAL0-0.068-0.04312.101-0.011-0.0110.0000.0000.0000.000
11A204TRP00.0310.01314.7150.0150.0150.0000.0000.0000.000
12A205GLY00.0230.00816.913-0.019-0.0190.0000.0000.0000.000
13A206ILE0-0.010-0.00619.1540.0170.0170.0000.0000.0000.000
14A207ARG10.7850.89421.8600.1030.1030.0000.0000.0000.000
15A208VAL00.0150.01424.9030.0070.0070.0000.0000.0000.000
16A209ARG10.8100.89128.1710.0790.0790.0000.0000.0000.000
17A210ASN0-0.001-0.00431.5340.0010.0010.0000.0000.0000.000
18A211GLY00.0170.01433.7530.0030.0030.0000.0000.0000.000
19A212GLN0-0.019-0.00130.9220.0030.0030.0000.0000.0000.000
20A213PHE00.0130.00325.185-0.004-0.0040.0000.0000.0000.000
21A214VAL00.0180.01126.4460.0050.0050.0000.0000.0000.000
22A215THR00.0510.01722.128-0.008-0.0080.0000.0000.0000.000
23A216SER00.0190.02120.5410.0030.0030.0000.0000.0000.000
24A217SER0-0.081-0.02321.9410.0140.0140.0000.0000.0000.000
25A235VAL0-0.026-0.02223.4680.0020.0020.0000.0000.0000.000
26A236LEU00.0040.00618.1240.0000.0000.0000.0000.0000.000
27A237SER00.0070.02117.583-0.005-0.0050.0000.0000.0000.000
28A238PHE00.0000.00214.5010.0050.0050.0000.0000.0000.000
29A239ILE0-0.010-0.0049.913-0.011-0.0110.0000.0000.0000.000
30A240THR0-0.008-0.0099.5210.0200.0200.0000.0000.0000.000
31A241ALA00.0230.0135.506-0.034-0.0340.0000.0000.0000.000
32A242ASN0-0.035-0.0327.4040.1380.1380.0000.0000.0000.000
33A243PHE00.025-0.0092.594-4.596-1.7303.758-1.915-4.708-0.026
34A244ASN0-0.0220.0015.3800.2300.207-0.001-0.0020.0260.000
35A245SER0-0.037-0.0358.617-0.082-0.0820.0000.0000.0000.000
36A246ASN0-0.066-0.0266.750-0.338-0.3380.0000.0000.0000.000
37A247THR00.0060.0108.6830.1130.1130.0000.0000.0000.000
38A248LEU00.004-0.0157.951-0.115-0.1150.0000.0000.0000.000
39A249ALA0-0.030-0.00810.8420.0730.0730.0000.0000.0000.000
40A250GLY00.008-0.02012.909-0.016-0.0160.0000.0000.0000.000
41A251LYS10.8270.92015.3000.1200.1200.0000.0000.0000.000
42A252ILE0-0.0050.00116.0940.0090.0090.0000.0000.0000.000
43A253LEU00.0150.00318.9720.0060.0060.0000.0000.0000.000
44A254GLY00.0590.01322.3240.0000.0000.0000.0000.0000.000
45A255ASN0-0.048-0.03825.3660.0040.0040.0000.0000.0000.000
46A256SER0-0.022-0.03528.496-0.003-0.0030.0000.0000.0000.000
47A257ASP-1-0.880-0.89729.917-0.049-0.0490.0000.0000.0000.000
48A258TYR0-0.030-0.04120.928-0.005-0.0050.0000.0000.0000.000
49A259GLY00.0270.02127.112-0.007-0.0070.0000.0000.0000.000
50A260PRO0-0.008-0.02627.188-0.001-0.0010.0000.0000.0000.000
51A261ASP-1-0.757-0.85622.962-0.100-0.1000.0000.0000.0000.000
52A262VAL0-0.0400.00519.1430.0000.0000.0000.0000.0000.000
53A263ASP-1-0.877-0.92519.613-0.169-0.1690.0000.0000.0000.000
54A264ILE00.0320.00914.206-0.008-0.0080.0000.0000.0000.000
55A265GLN0-0.026-0.02716.650-0.005-0.0050.0000.0000.0000.000
56A266ASN0-0.028-0.01815.982-0.008-0.0080.0000.0000.0000.000
57A267ALA00.0200.03412.8820.0030.0030.0000.0000.0000.000
58A268THR00.0290.00811.393-0.023-0.0230.0000.0000.0000.000
59A269ILE0-0.059-0.0234.8350.0150.0150.0000.0000.0000.000
60A270THR0-0.015-0.0217.0960.2040.2040.0000.0000.0000.000
61A271GLY00.0640.0434.2350.1310.2570.000-0.024-0.1020.000
62A272PRO0-0.034-0.0182.342-2.172-0.8771.530-1.156-1.6690.000
63A273THR0-0.042-0.0283.4250.5860.1020.0090.702-0.2280.000
64A274PHE00.0440.0076.318-0.291-0.2910.0000.0000.0000.000
65A275SER0-0.0110.0038.6190.1430.1430.0000.0000.0000.000
66A276GLY00.0400.01612.448-0.041-0.0410.0000.0000.0000.000
67A277ASP-1-0.804-0.87215.713-0.198-0.1980.0000.0000.0000.000
68A278ALA00.0020.00718.035-0.019-0.0190.0000.0000.0000.000
69A279THR0-0.031-0.01919.9750.0200.0200.0000.0000.0000.000
70A280SER00.018-0.01222.8690.0000.0000.0000.0000.0000.000
71A281GLY00.0240.00925.3030.0030.0030.0000.0000.0000.000
72A282GLY0-0.0190.00028.6010.0050.0050.0000.0000.0000.000
73A283LYS10.7880.88227.4000.0900.0900.0000.0000.0000.000
74A284SER00.0350.00724.372-0.003-0.0030.0000.0000.0000.000
75A285GLY00.014-0.00322.3680.0120.0120.0000.0000.0000.000
76A286LYS10.8010.89218.7020.1990.1990.0000.0000.0000.000
77A287LEU0-0.010-0.00212.8500.0130.0130.0000.0000.0000.000
78A288GLU-1-0.836-0.92112.795-0.272-0.2720.0000.0000.0000.000
79A289GLY00.0140.00110.0540.0540.0540.0000.0000.0000.000
80A290LYS10.8400.9295.1980.0000.0000.0000.0000.0000.000
81A291PHE00.0420.0272.304-1.465-0.8472.539-0.857-2.300-0.001
82A292PHE00.0090.0033.980-0.0240.3200.006-0.047-0.3040.000
83A302GLU-1-0.923-0.9609.4650.1160.1160.0000.0000.0000.000
84A303VAL0-0.035-0.0183.860-0.1290.0540.001-0.023-0.1600.000
85A304SER00.0490.0196.359-0.021-0.0210.0000.0000.0000.000
86A305ILE0-0.051-0.0135.885-0.111-0.1110.0000.0000.0000.000
87A306GLY00.0310.0068.1270.0850.0850.0000.0000.0000.000
88A307GLY0-0.001-0.00110.060-0.065-0.0650.0000.0000.0000.000
89A308LYS10.8380.92712.6770.2560.2560.0000.0000.0000.000
90A309ILE00.003-0.00715.760-0.031-0.0310.0000.0000.0000.000
91A310THR0-0.037-0.01918.3860.0170.0170.0000.0000.0000.000
92A311PHE00.014-0.00421.607-0.010-0.0100.0000.0000.0000.000
93A312ASP-1-0.839-0.91924.798-0.123-0.1230.0000.0000.0000.000
94A313GLY0-0.0080.01127.3960.0080.0080.0000.0000.0000.000
95A314ASP-1-0.844-0.90428.596-0.077-0.0770.0000.0000.0000.000
96A315ARG10.8580.90824.2260.1220.1220.0000.0000.0000.000
97A316SER0-0.050-0.02627.5160.0000.0000.0000.0000.0000.000
98A317LEU00.0140.00125.6230.0020.0020.0000.0000.0000.000
99A318ASP-1-0.753-0.83422.844-0.148-0.1480.0000.0000.0000.000
100A319THR0-0.061-0.03019.0370.0080.0080.0000.0000.0000.000
101A320VAL00.0220.01316.641-0.018-0.0180.0000.0000.0000.000
102A321PHE0-0.014-0.01311.6990.0170.0170.0000.0000.0000.000
103A322GLY00.0390.01512.466-0.023-0.0230.0000.0000.0000.000
104A323GLY00.0070.00611.5190.0180.0180.0000.0000.0000.000
105A324VAL00.0170.0119.635-0.032-0.0320.0000.0000.0000.000
106A325SER0-0.033-0.0327.0290.0100.0100.0000.0000.0000.000
107A326TYR0-0.0070.0089.1220.0530.0530.0000.0000.0000.000
108A327GLU-1-0.762-0.85811.0930.3090.3090.0000.0000.0000.000
109A328LYS10.8680.9186.584-0.578-0.5780.0000.0000.0000.000
110A329LYS10.8270.9038.685-0.313-0.3130.0000.0000.0000.000
111A330LEU00.0280.0164.606-0.168-0.030-0.001-0.016-0.1220.000
112A331ASP-1-0.807-0.9047.6301.5441.5440.0000.0000.0000.000
113A332ASP-1-0.808-0.8789.784-0.003-0.0030.0000.0000.0000.000
114A333THR0-0.002-0.00110.2700.0430.0430.0000.0000.0000.000
115A334SER0-0.057-0.03112.757-0.084-0.0840.0000.0000.0000.000
116A335GLN00.0720.01711.920-0.027-0.0270.0000.0000.0000.000
117A336ASP-1-0.817-0.87713.455-0.168-0.1680.0000.0000.0000.000
118A337THR00.0260.00811.5100.0020.0020.0000.0000.0000.000
119A338ASN0-0.037-0.01613.324-0.002-0.0020.0000.0000.0000.000
120A339HIS00.0270.03213.6770.0020.0020.0000.0000.0000.000
121A340LEU0-0.017-0.00110.4320.0330.0330.0000.0000.0000.000
122A341THR00.0290.01314.440-0.008-0.0080.0000.0000.0000.000