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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: Q822Y

Calculation Name: 7LGO-A-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7LGO

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-02-22

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1125131.017881
FMO2-HF: Nuclear repulsion 1074815.810206
FMO2-HF: Total energy -50315.207675
FMO2-MP2: Total energy -50461.775345


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:PHE )


Summations of interaction energy for fragment #1(A:1:PHE )
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.
-1.2920.534-0.028-0.593-1.2040.002
Interaction energy analysis for fragmet #1(A:1:PHE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.026
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].
3A3GLU -1-0.940-0.9643.750-0.9260.797-0.027-0.591-1.1050.002
4A4GLN 00.0150.0045.1360.0030.106-0.001-0.002-0.0990.000
5A5PRO 0-0.025-0.0117.625-0.054-0.0540.0000.0000.0000.000
6A6ILE 00.0500.0299.3170.0770.0770.0000.0000.0000.000
7A7ASP -1-0.868-0.91711.308-0.076-0.0760.0000.0000.0000.000
8A8LEU 0-0.031-0.00714.535-0.028-0.0280.0000.0000.0000.000
9A9VAL 00.0340.03116.7600.0270.0270.0000.0000.0000.000
10A10PRO 00.0090.00220.309-0.008-0.0080.0000.0000.0000.000
11A11ASN 0-0.016-0.00123.534-0.015-0.0150.0000.0000.0000.000
12A12GLN 00.0270.00225.8950.0140.0140.0000.0000.0000.000
13A13PRO 0-0.0040.01729.493-0.005-0.0050.0000.0000.0000.000
14A14TYR 00.0500.02931.0510.0030.0030.0000.0000.0000.000
15A15PRO 0-0.027-0.02034.9570.0010.0010.0000.0000.0000.000
16A16ASN 00.005-0.00938.435-0.001-0.0010.0000.0000.0000.000
17A17ALA 0-0.0030.00636.754-0.002-0.0020.0000.0000.0000.000
18A18SER 00.0460.01938.2530.0020.0020.0000.0000.0000.000
19A19PHE 0-0.0060.00435.194-0.002-0.0020.0000.0000.0000.000
20A20ASP -1-0.737-0.84635.930-0.042-0.0420.0000.0000.0000.000
21A21ASN 00.0410.03836.8910.0020.0020.0000.0000.0000.000
22A22PHE 0-0.047-0.03130.523-0.003-0.0030.0000.0000.0000.000
23A23LYS 10.8420.92733.1640.0570.0570.0000.0000.0000.000
24A24PHE 0-0.006-0.02527.120-0.005-0.0050.0000.0000.0000.000
25A25VAL 0-0.033-0.01828.6610.0050.0050.0000.0000.0000.000
26A26CYS 0-0.044-0.01323.405-0.006-0.0060.0000.0000.0000.000
27A27ASP -1-0.780-0.86423.876-0.126-0.1260.0000.0000.0000.000
28A28ASN 0-0.014-0.00122.9620.0160.0160.0000.0000.0000.000
29A29ILE 00.0440.01325.7140.0050.0050.0000.0000.0000.000
30A30LYS 10.8860.93628.1980.0050.0050.0000.0000.0000.000
31A31PHE 00.0200.00122.6810.0080.0080.0000.0000.0000.000
32A32ALA 0-0.018-0.00126.8890.0030.0030.0000.0000.0000.000
33A33ASP -1-0.827-0.92028.757-0.028-0.0280.0000.0000.0000.000
34A34ASP -1-0.783-0.81829.1040.0070.0070.0000.0000.0000.000
35A35LEU 0-0.009-0.00825.2510.0060.0060.0000.0000.0000.000
36A36ASN 0-0.019-0.01229.9130.0010.0010.0000.0000.0000.000
37A37GLN 0-0.0050.01933.0830.0010.0010.0000.0000.0000.000
38A38LEU 0-0.033-0.01230.3850.0040.0040.0000.0000.0000.000
39A39THR 0-0.039-0.00332.5310.0020.0020.0000.0000.0000.000
40A40GLY 00.0240.02635.2070.0010.0010.0000.0000.0000.000
41A41TYR 0-0.016-0.00935.922-0.002-0.0020.0000.0000.0000.000
42A42LYS 10.9640.98738.0960.0200.0200.0000.0000.0000.000
43A43LYS 10.9270.98838.7210.0300.0300.0000.0000.0000.000
44A44PRO 0-0.014-0.01641.2210.0020.0020.0000.0000.0000.000
45A45ALA 00.005-0.00836.5350.0010.0010.0000.0000.0000.000
46A46SER 00.0000.00738.074-0.003-0.0030.0000.0000.0000.000
47A47ARG 10.8540.90131.4990.0480.0480.0000.0000.0000.000
48A48GLU -1-0.759-0.89031.505-0.065-0.0650.0000.0000.0000.000
49A49LEU 0-0.0270.00227.778-0.005-0.0050.0000.0000.0000.000
50A50LYS 10.9080.94825.5030.0980.0980.0000.0000.0000.000
51A51VAL 0-0.020-0.02122.206-0.005-0.0050.0000.0000.0000.000
52A52THR 00.0040.00518.5600.0080.0080.0000.0000.0000.000
53A53PHE 0-0.006-0.01116.9260.0240.0240.0000.0000.0000.000
54A54PHE 00.0420.0499.493-0.026-0.0260.0000.0000.0000.000
55A55PRO 00.018-0.0149.5220.0530.0530.0000.0000.0000.000
56A56ASP -1-0.815-0.88512.143-0.307-0.3070.0000.0000.0000.000
57A57LEU 0-0.034-0.00814.2660.0660.0660.0000.0000.0000.000
58A58ASN 00.003-0.02517.2700.0280.0280.0000.0000.0000.000
59A59GLY 00.0170.02220.2230.0180.0180.0000.0000.0000.000
60A60ASP -1-0.872-0.91821.892-0.114-0.1140.0000.0000.0000.000
61A61VAL 0-0.064-0.03422.7230.0100.0100.0000.0000.0000.000
62A62VAL 00.0520.03616.050-0.010-0.0100.0000.0000.0000.000
63A63ALA 0-0.008-0.00918.6910.0270.0270.0000.0000.0000.000
64A64ILE 00.003-0.00714.818-0.021-0.0210.0000.0000.0000.000
65A65ASP -1-0.735-0.83614.1780.1480.1480.0000.0000.0000.000
66A66TYR 00.022-0.01216.2180.0230.0230.0000.0000.0000.000
67A67LYS 10.8470.93911.112-0.184-0.1840.0000.0000.0000.000
68A68HIS 0-0.0040.00310.097-0.017-0.0170.0000.0000.0000.000
69A69TYR 00.008-0.00315.380-0.025-0.0250.0000.0000.0000.000
70A70THR 00.0280.02618.1330.0180.0180.0000.0000.0000.000
71A71PRO 00.0370.00920.808-0.020-0.0200.0000.0000.0000.000
72A72SER 00.0310.03422.384-0.011-0.0110.0000.0000.0000.000
73A73PHE 00.0000.02717.806-0.018-0.0180.0000.0000.0000.000
74A74LYS 10.9130.98423.704-0.066-0.0660.0000.0000.0000.000
75A75LYS 10.8170.88526.915-0.027-0.0270.0000.0000.0000.000
76A76GLY 00.0890.02125.432-0.009-0.0090.0000.0000.0000.000
77A77ALA 0-0.004-0.00520.4560.0100.0100.0000.0000.0000.000
78A78LYS 10.8540.92721.0680.0210.0210.0000.0000.0000.000
79A79LEU 00.0420.02713.2980.0180.0180.0000.0000.0000.000
80A80LEU 00.0120.01215.153-0.020-0.0200.0000.0000.0000.000
81A81HIS 0-0.032-0.04118.731-0.006-0.0060.0000.0000.0000.000
82A82LYS 10.8930.99119.0400.1660.1660.0000.0000.0000.000
83A83PRO 0-0.024-0.01220.7760.0060.0060.0000.0000.0000.000
84A84ILE 00.0300.02518.379-0.010-0.0100.0000.0000.0000.000
85A85VAL 0-0.016-0.00921.0910.0120.0120.0000.0000.0000.000
86A86TRP 00.031-0.00917.403-0.003-0.0030.0000.0000.0000.000
87A87HIS 0-0.018-0.00316.5220.0140.0140.0000.0000.0000.000
88A88VAL 00.0160.00019.0950.0160.0160.0000.0000.0000.000
89A89ASN 0-0.013-0.00418.6160.0010.0010.0000.0000.0000.000
90A90ASN 00.0370.03417.7200.0050.0050.0000.0000.0000.000
91A91ALA 00.0590.03620.864-0.010-0.0100.0000.0000.0000.000
92A92THR 0-0.0050.00423.4350.0090.0090.0000.0000.0000.000
93A93ASN 00.0350.02623.834-0.003-0.0030.0000.0000.0000.000
94A94LYS 11.0251.00827.206-0.059-0.0590.0000.0000.0000.000
95A95ALA 00.0080.02924.422-0.001-0.0010.0000.0000.0000.000
96A96THR 00.0710.03722.6080.0010.0010.0000.0000.0000.000
97A97TYR 0-0.0070.01625.314-0.008-0.0080.0000.0000.0000.000
98A98LYS 10.9220.95329.007-0.063-0.0630.0000.0000.0000.000
99A99PRO 0-0.011-0.00324.922-0.007-0.0070.0000.0000.0000.000
100A100ASN 00.0740.02724.764-0.008-0.0080.0000.0000.0000.000
101A101THR 0-0.053-0.02027.273-0.008-0.0080.0000.0000.0000.000
102A102TRP 0-0.050-0.02728.595-0.007-0.0070.0000.0000.0000.000
103A103CYS 0-0.0260.00824.799-0.005-0.0050.0000.0000.0000.000
104A104ILE 00.0440.02027.192-0.009-0.0090.0000.0000.0000.000
105A105ARG 10.8870.94429.937-0.013-0.0130.0000.0000.0000.000
106A106CYS 0-0.106-0.03227.778-0.001-0.0010.0000.0000.0000.000
107A107LEU 0-0.0210.00526.439-0.005-0.0050.0000.0000.0000.000
108A108TRP 0-0.048-0.01430.138-0.002-0.0020.0000.0000.0000.000
109A109SER 00.0350.00733.915-0.001-0.0010.0000.0000.0000.000
110A110THR 00.0670.04635.3890.0000.0000.0000.0000.0000.000
111A111LYS 10.8730.94830.1820.0560.0560.0000.0000.0000.000
112A112PRO 0-0.052-0.02135.2490.0000.0000.0000.0000.0000.000
113A113VAL -1-0.909-0.93338.300-0.032-0.0320.0000.0000.0000.000
114A201HOH 0-0.001-0.02722.2500.0000.0000.0000.0000.0000.000
115A202HOH 0-0.019-0.01414.2600.0070.0070.0000.0000.0000.000
116A203HOH 0-0.015-0.01725.166-0.004-0.0040.0000.0000.0000.000
117A204HOH 0-0.052-0.05024.9260.0040.0040.0000.0000.0000.000
118A205HOH 00.0330.02435.5420.0000.0000.0000.0000.0000.000
119A206HOH 0-0.035-0.03128.7330.0020.0020.0000.0000.0000.000
120A207HOH 0-0.020-0.01743.0860.0010.0010.0000.0000.0000.000
121A208HOH 00.0210.00738.6460.0010.0010.0000.0000.0000.000
122A210HOH 0-0.005-0.01116.218-0.002-0.0020.0000.0000.0000.000
123A212HOH 0-0.011-0.00831.499-0.002-0.0020.0000.0000.0000.000
124A213HOH 00.007-0.00234.8450.0020.0020.0000.0000.0000.000
125A214HOH 0-0.052-0.04024.681-0.001-0.0010.0000.0000.0000.000
126A215HOH 0-0.030-0.02330.7910.0000.0000.0000.0000.0000.000
127A216HOH 0-0.009-0.01718.632-0.004-0.0040.0000.0000.0000.000
128A217HOH 0-0.002-0.00535.1160.0000.0000.0000.0000.0000.000
129A219HOH 0-0.005-0.00815.8020.0080.0080.0000.0000.0000.000
130A220HOH 0-0.031-0.02827.782-0.003-0.0030.0000.0000.0000.000
131A221HOH 00.0290.02526.700-0.002-0.0020.0000.0000.0000.000
132A222HOH 0-0.014-0.01233.3190.0020.0020.0000.0000.0000.000
133A223HOH 0-0.046-0.04229.5380.0010.0010.0000.0000.0000.000
134A224HOH 0-0.059-0.04315.4650.0170.0170.0000.0000.0000.000
135A225HOH 0-0.038-0.03732.7180.0030.0030.0000.0000.0000.000
136A226HOH 0-0.028-0.01914.3060.0210.0210.0000.0000.0000.000
137A227HOH 0-0.005-0.01124.870-0.001-0.0010.0000.0000.0000.000
138A228HOH 0-0.008-0.01219.2370.0030.0030.0000.0000.0000.000
139A229HOH 0-0.010-0.01033.1550.0010.0010.0000.0000.0000.000
140A230HOH 00.0340.02335.8980.0000.0000.0000.0000.0000.000
141A233HOH 0-0.039-0.04126.2990.0010.0010.0000.0000.0000.000
142A234HOH 0-0.039-0.02529.2820.0030.0030.0000.0000.0000.000
143A235HOH 0-0.040-0.02741.0440.0010.0010.0000.0000.0000.000
144A236HOH 0-0.029-0.02127.6060.0000.0000.0000.0000.0000.000
145A237HOH 0-0.027-0.03027.5920.0010.0010.0000.0000.0000.000
146A238HOH 0-0.028-0.02039.7780.0000.0000.0000.0000.0000.000
147A239HOH 0-0.059-0.04125.9200.0030.0030.0000.0000.0000.000
148A241HOH 00.006-0.00218.744-0.005-0.0050.0000.0000.0000.000
149A244HOH 00.004-0.00621.526-0.007-0.0070.0000.0000.0000.000
150A245HOH 0-0.042-0.02837.6460.0010.0010.0000.0000.0000.000
151A246HOH 00.0070.00927.7870.0020.0020.0000.0000.0000.000
152A248HOH 0-0.019-0.02333.0880.0010.0010.0000.0000.0000.000
153A249HOH 0-0.054-0.05513.908-0.010-0.0100.0000.0000.0000.000
154A250HOH 0-0.055-0.04321.276-0.005-0.0050.0000.0000.0000.000
155A251HOH 0-0.002-0.00814.9980.0100.0100.0000.0000.0000.000
156A252HOH 00.0220.00830.2610.0010.0010.0000.0000.0000.000
157A253HOH 00.0300.01332.7840.0010.0010.0000.0000.0000.000
158A254HOH 00.0380.02433.2590.0000.0000.0000.0000.0000.000
159A255HOH 00.0250.01028.2950.0010.0010.0000.0000.0000.000
160A256HOH 00.0150.00633.0350.0000.0000.0000.0000.0000.000
161A257HOH 0-0.033-0.02122.801-0.002-0.0020.0000.0000.0000.000
162A259HOH 0-0.046-0.04420.703-0.005-0.0050.0000.0000.0000.000
163A260HOH 0-0.018-0.01329.0460.0040.0040.0000.0000.0000.000
164A262HOH 0-0.014-0.00734.2340.0020.0020.0000.0000.0000.000
165A263HOH 00.0170.01237.367-0.001-0.0010.0000.0000.0000.000
166A264HOH 00.006-0.01228.047-0.001-0.0010.0000.0000.0000.000
167A266HOH 0-0.011-0.00720.4490.0000.0000.0000.0000.0000.000
168A268HOH 00.0180.00528.7340.0020.0020.0000.0000.0000.000
169A269HOH 00.0310.02233.0480.0010.0010.0000.0000.0000.000
170A271HOH 0-0.027-0.02030.7040.0020.0020.0000.0000.0000.000
171A272HOH 00.0360.02331.838-0.001-0.0010.0000.0000.0000.000
172A273HOH 00.0080.00237.3730.0000.0000.0000.0000.0000.000
173A274HOH 00.0290.01216.298-0.008-0.0080.0000.0000.0000.000
174A275HOH 0-0.015-0.01830.8570.0020.0020.0000.0000.0000.000
175A276HOH 0-0.042-0.03133.5970.0010.0010.0000.0000.0000.000
176A277HOH 00.002-0.00319.685-0.010-0.0100.0000.0000.0000.000
177A278HOH 00.0380.02927.0800.0000.0000.0000.0000.0000.000
178A279HOH 00.0510.03427.5890.0010.0010.0000.0000.0000.000
179A281HOH 00.001-0.01139.1300.0010.0010.0000.0000.0000.000
180A282HOH 00.0070.00227.1830.0030.0030.0000.0000.0000.000