Manual

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

tag_button

FMODB ID: 8JMLY

Calculation Name: 7KR0-A-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7KR0

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-12-21

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 208
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1794906.579302
FMO2-HF: Nuclear repulsion 1728470.505701
FMO2-HF: Total energy -66436.073601
FMO2-MP2: Total energy -66630.634041


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:2:GLU )


Summations of interaction energy for fragment #1(A:2:GLU )
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.
-4.665-1.4930.101-1.356-1.9180.005
Interaction energy analysis for fragmet #1(A:2:GLU )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.947 / q_NPA : -0.976
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].
3A4ASN 0-0.023-0.0203.649-4.491-2.481-0.003-0.889-1.1190.005
4A5SER 00.0250.0172.860-3.554-2.6780.105-0.368-0.6140.000
5A6PHE 00.0000.0024.807-1.925-1.837-0.001-0.009-0.0780.000
6A7SER 00.016-0.0027.910-0.152-0.1520.0000.0000.0000.000
7A8GLY 0-0.008-0.01610.272-0.838-0.8380.0000.0000.0000.000
8A9TYR 0-0.072-0.05211.746-0.917-0.9170.0000.0000.0000.000
9A10LEU 00.0040.01515.2240.0410.0410.0000.0000.0000.000
10A11LYS 10.9060.94717.538-13.427-13.4270.0000.0000.0000.000
11A12LEU 0-0.056-0.01118.901-0.456-0.4560.0000.0000.0000.000
12A13THR 00.048-0.00121.345-0.255-0.2550.0000.0000.0000.000
13A14ASP -1-0.940-0.97720.28913.09413.0940.0000.0000.0000.000
14A15ASN 0-0.037-0.02018.0620.3000.3000.0000.0000.0000.000
15A16VAL 00.0180.02318.4560.4270.4270.0000.0000.0000.000
16A17TYR 00.0060.00615.600-0.111-0.1110.0000.0000.0000.000
17A18ILE 00.0120.00917.6040.0270.0270.0000.0000.0000.000
18A19LYS 10.8210.89212.335-19.325-19.3250.0000.0000.0000.000
19A20ASN 00.0180.01918.012-0.561-0.5610.0000.0000.0000.000
20A21ALA 0-0.016-0.02715.7580.3140.3140.0000.0000.0000.000
21A22ASP -1-0.804-0.90517.31714.60514.6050.0000.0000.0000.000
22A23ILE 00.0470.02115.8680.8890.8890.0000.0000.0000.000
23A24VAL 00.0060.00514.8181.0921.0920.0000.0000.0000.000
24A25GLU -1-0.872-0.94113.85319.37819.3780.0000.0000.0000.000
25A26GLU -1-0.815-0.87811.45021.82221.8220.0000.0000.0000.000
26A27ALA 00.0160.01410.0311.9771.9770.0000.0000.0000.000
27A28LYS 10.8510.9229.571-15.537-15.5370.0000.0000.0000.000
28A29LYS 10.8390.9187.672-17.278-17.2780.0000.0000.0000.000
29A30VAL 0-0.0100.0085.6403.2983.2980.0000.0000.0000.000
30A31LYS 10.9200.9674.294-34.214-34.0160.000-0.090-0.1070.000
31A32PRO 00.0160.0226.4362.6272.6270.0000.0000.0000.000
32A33THR 00.0140.0038.8770.1390.1390.0000.0000.0000.000
33A34VAL 0-0.016-0.01810.539-1.241-1.2410.0000.0000.0000.000
34A35VAL 00.0050.01413.7150.2820.2820.0000.0000.0000.000
35A36VAL 00.0100.00115.380-0.620-0.6200.0000.0000.0000.000
36A37ASN 0-0.020-0.03519.018-0.073-0.0730.0000.0000.0000.000
37A38ALA 0-0.0080.01421.690-0.253-0.2530.0000.0000.0000.000
38A39ALA 00.0350.02824.981-0.294-0.2940.0000.0000.0000.000
39A40ASN 00.004-0.00926.965-0.239-0.2390.0000.0000.0000.000
40A41VAL 00.0220.00530.1370.2210.2210.0000.0000.0000.000
41A42TYR 00.0040.00332.494-0.030-0.0300.0000.0000.0000.000
42A43LEU 0-0.0180.00126.5030.0740.0740.0000.0000.0000.000
43A44LYS 10.8620.93329.173-9.295-9.2950.0000.0000.0000.000
44A45HIS 00.0530.02225.894-0.219-0.2190.0000.0000.0000.000
45A46GLY 00.0370.02927.6170.2140.2140.0000.0000.0000.000
46A47GLY 0-0.007-0.01229.369-0.112-0.1120.0000.0000.0000.000
47A48GLY 00.0120.00827.5570.2340.2340.0000.0000.0000.000
48A49VAL 00.008-0.01121.3050.2250.2250.0000.0000.0000.000
49A50ALA 00.0170.02522.7650.4770.4770.0000.0000.0000.000
50A51GLY 0-0.0160.00124.0320.2500.2500.0000.0000.0000.000
51A52ALA 0-0.045-0.02221.5340.1570.1570.0000.0000.0000.000
52A53LEU 00.0250.00017.5830.4900.4900.0000.0000.0000.000
53A54ASN 00.039-0.00220.2160.6770.6770.0000.0000.0000.000
54A55LYS 10.9450.97722.577-11.429-11.4290.0000.0000.0000.000
55A56ALA 0-0.028-0.00517.4640.1040.1040.0000.0000.0000.000
56A57THR 0-0.0050.01017.9860.6240.6240.0000.0000.0000.000
57A58ASN 0-0.060-0.04219.7790.1980.1980.0000.0000.0000.000
58A59ASN 0-0.0030.00222.857-0.397-0.3970.0000.0000.0000.000
59A60ALA 00.0590.04521.295-0.394-0.3940.0000.0000.0000.000
60A61MET 00.0380.03719.831-0.416-0.4160.0000.0000.0000.000
61A62GLN 00.0020.00623.105-0.352-0.3520.0000.0000.0000.000
62A63VAL 0-0.0090.00026.480-0.355-0.3550.0000.0000.0000.000
63A64GLU -1-0.723-0.83422.02413.75113.7510.0000.0000.0000.000
64A65SER 0-0.026-0.02525.420-0.172-0.1720.0000.0000.0000.000
65A66ASP -1-0.818-0.88527.4559.4059.4050.0000.0000.0000.000
66A67ASP -1-0.890-0.93629.1249.8889.8880.0000.0000.0000.000
67A68TYR 0-0.0030.00527.646-0.142-0.1420.0000.0000.0000.000
68A69ILE 0-0.005-0.00729.779-0.296-0.2960.0000.0000.0000.000
69A70ALA 0-0.037-0.01332.489-0.293-0.2930.0000.0000.0000.000
70A71THR 0-0.0090.01633.077-0.314-0.3140.0000.0000.0000.000
71A72ASN 0-0.064-0.03530.913-0.150-0.1500.0000.0000.0000.000
72A73GLY 00.0220.03633.573-0.072-0.0720.0000.0000.0000.000
73A74PRO 0-0.045-0.02433.1340.2850.2850.0000.0000.0000.000
74A75LEU 00.0090.00827.475-0.008-0.0080.0000.0000.0000.000
75A76LYS 10.9690.98832.223-9.494-9.4940.0000.0000.0000.000
76A77VAL 00.0320.00432.1140.3070.3070.0000.0000.0000.000
77A78GLY 0-0.0010.00131.002-0.191-0.1910.0000.0000.0000.000
78A79GLY 0-0.055-0.02229.7620.1400.1400.0000.0000.0000.000
79A80SER 00.017-0.01024.5900.3310.3310.0000.0000.0000.000
80A81CYS 0-0.0560.00925.118-0.280-0.2800.0000.0000.0000.000
81A82VAL 00.0030.00719.2830.4140.4140.0000.0000.0000.000
82A83LEU 00.0080.02020.939-0.337-0.3370.0000.0000.0000.000
83A84SER 00.0560.03318.0101.3151.3150.0000.0000.0000.000
84A85GLY 0-0.0110.01015.042-0.624-0.6240.0000.0000.0000.000
85A86HIS 0-0.044-0.04215.5410.6740.6740.0000.0000.0000.000
86A87ASN 0-0.037-0.03413.7630.6560.6560.0000.0000.0000.000
87A88LEU 0-0.054-0.02612.2771.3921.3920.0000.0000.0000.000
88A89ALA 00.0250.01310.8720.9850.9850.0000.0000.0000.000
89A90LYS 10.9230.98610.748-23.140-23.1400.0000.0000.0000.000
90A91HIS 00.0090.00812.380-1.433-1.4330.0000.0000.0000.000
91A92CYS 0-0.006-0.00215.3640.5480.5480.0000.0000.0000.000
92A93LEU 0-0.0150.01518.082-0.645-0.6450.0000.0000.0000.000
93A94HIS 00.023-0.00820.323-0.412-0.4120.0000.0000.0000.000
94A95VAL 00.0260.00722.780-0.347-0.3470.0000.0000.0000.000
95A96VAL 0-0.0430.01025.379-0.035-0.0350.0000.0000.0000.000
96A97GLY 00.0360.02028.866-0.151-0.1510.0000.0000.0000.000
97A98PRO 0-0.0010.01130.125-0.102-0.1020.0000.0000.0000.000
98A99ASN 0-0.005-0.00233.354-0.023-0.0230.0000.0000.0000.000
99A100VAL 00.0340.02035.179-0.229-0.2290.0000.0000.0000.000
100A101ASN 0-0.026-0.00435.594-0.363-0.3630.0000.0000.0000.000
101A102LYS 10.8250.91138.028-7.634-7.6340.0000.0000.0000.000
102A103GLY 00.0110.01440.074-0.105-0.1050.0000.0000.0000.000
103A104GLU -1-0.770-0.83435.7228.4938.4930.0000.0000.0000.000
104A105ASP -1-0.779-0.88038.9617.7467.7460.0000.0000.0000.000
105A106ILE 00.0780.02933.9910.2520.2520.0000.0000.0000.000
106A107GLN 0-0.081-0.05134.9160.2780.2780.0000.0000.0000.000
107A108LEU 0-0.023-0.01334.2060.1710.1710.0000.0000.0000.000
108A109LEU 0-0.028-0.02128.9190.2960.2960.0000.0000.0000.000
109A110LYS 10.9270.96129.655-9.148-9.1480.0000.0000.0000.000
110A111SER 0-0.007-0.00629.3570.1920.1920.0000.0000.0000.000
111A112ALA 0-0.002-0.00428.1590.3090.3090.0000.0000.0000.000
112A113TYR 00.0670.01623.4530.6540.6540.0000.0000.0000.000
113A114GLU -1-0.829-0.89624.53310.20910.2090.0000.0000.0000.000
114A115ASN 0-0.071-0.02324.4310.2890.2890.0000.0000.0000.000
115A116PHE 00.0680.00720.2760.5080.5080.0000.0000.0000.000
116A117ASN 00.0080.01319.9361.0161.0160.0000.0000.0000.000
117A118GLN 0-0.0560.00621.253-0.032-0.0320.0000.0000.0000.000
118A119HIS 0-0.013-0.01016.2161.1791.1790.0000.0000.0000.000
119A120GLU -1-0.903-0.94712.96819.74219.7420.0000.0000.0000.000
120A121VAL 00.023-0.00310.076-0.154-0.1540.0000.0000.0000.000
121A122LEU 0-0.0430.01213.2570.5230.5230.0000.0000.0000.000
122A123LEU 00.0040.02211.986-0.092-0.0920.0000.0000.0000.000
123A124ALA 00.003-0.00614.504-0.444-0.4440.0000.0000.0000.000
124A125PRO 0-0.0030.00718.244-0.013-0.0130.0000.0000.0000.000
125A126LEU 00.0070.00721.108-0.036-0.0360.0000.0000.0000.000
126A127LEU 0-0.015-0.00223.975-0.302-0.3020.0000.0000.0000.000
127A128SER 00.019-0.01826.399-0.190-0.1900.0000.0000.0000.000
128A129ALA 00.0410.04027.183-0.363-0.3630.0000.0000.0000.000
129A130GLY 00.0240.00829.2670.0550.0550.0000.0000.0000.000
130A131ILE 0-0.016-0.02330.194-0.318-0.3180.0000.0000.0000.000
131A132PHE 0-0.073-0.02229.011-0.242-0.2420.0000.0000.0000.000
132A133GLY 00.0210.00132.787-0.195-0.1950.0000.0000.0000.000
133A134ALA 0-0.018-0.00232.318-0.227-0.2270.0000.0000.0000.000
134A135ASP -1-0.834-0.92632.8128.8768.8760.0000.0000.0000.000
135A136PRO 0-0.014-0.01329.0930.1820.1820.0000.0000.0000.000
136A137ILE 00.0410.00929.2190.3260.3260.0000.0000.0000.000
137A138HIS 00.0030.00430.8080.1270.1270.0000.0000.0000.000
138A139SER 0-0.018-0.02927.9090.2660.2660.0000.0000.0000.000
139A140LEU 0-0.005-0.00223.9570.3160.3160.0000.0000.0000.000
140A141ARG 10.9260.96526.764-8.710-8.7100.0000.0000.0000.000
141A142VAL 00.0270.02729.0600.0620.0620.0000.0000.0000.000
142A143CYS 0-0.068-0.02323.0300.3620.3620.0000.0000.0000.000
143A144VAL 00.002-0.00324.3210.3030.3030.0000.0000.0000.000
144A145ASP -1-0.893-0.93425.6629.7099.7090.0000.0000.0000.000
145A146THR 0-0.149-0.07126.938-0.272-0.2720.0000.0000.0000.000
146A147VAL 0-0.060-0.03020.5930.1020.1020.0000.0000.0000.000
147A148ARG 10.9410.96722.465-10.844-10.8440.0000.0000.0000.000
148A149THR 0-0.0280.00717.3960.0590.0590.0000.0000.0000.000
149A150ASN 0-0.020-0.00214.171-0.742-0.7420.0000.0000.0000.000
150A151VAL 00.0250.01015.3730.7780.7780.0000.0000.0000.000
151A152TYR 0-0.007-0.00112.147-0.182-0.1820.0000.0000.0000.000
152A153LEU 00.008-0.01015.3330.1740.1740.0000.0000.0000.000
153A154ALA 0-0.006-0.00216.2820.1500.1500.0000.0000.0000.000
154A155VAL 0-0.012-0.01618.275-0.529-0.5290.0000.0000.0000.000
155A156PHE 0-0.014-0.00420.7110.0350.0350.0000.0000.0000.000
156A157ASP -1-0.822-0.90822.0159.9199.9190.0000.0000.0000.000
157A158LYS 10.9020.92724.488-11.049-11.0490.0000.0000.0000.000
158A159ASN 0-0.064-0.04425.927-0.274-0.2740.0000.0000.0000.000
159A160LEU 0-0.011-0.00427.014-0.152-0.1520.0000.0000.0000.000
160A161TYR 00.0060.00220.295-0.123-0.1230.0000.0000.0000.000
161A162ASP -1-0.804-0.88725.51610.66910.6690.0000.0000.0000.000
162A163LYS 10.9110.95427.847-9.179-9.1790.0000.0000.0000.000
163A164LEU 00.0030.01325.378-0.139-0.1390.0000.0000.0000.000
164A165VAL 00.0200.02023.847-0.024-0.0240.0000.0000.0000.000
165A166SER 0-0.013-0.01226.589-0.152-0.1520.0000.0000.0000.000
166A167SER 0-0.055-0.02929.412-0.134-0.1340.0000.0000.0000.000
167A168PHE 0-0.027-0.03125.697-0.049-0.0490.0000.0000.0000.000
168A169LEU 0-0.073-0.04326.1920.0480.0480.0000.0000.0000.000
169A170GLU -2-1.865-1.90329.81616.99016.9900.0000.0000.0000.000
170A225HOH 0-0.057-0.04020.648-0.122-0.1220.0000.0000.0000.000
171A235HOH 0-0.023-0.02536.2000.1060.1060.0000.0000.0000.000
172A243HOH 00.0400.02334.7940.0540.0540.0000.0000.0000.000
173A259HOH 00.003-0.00826.5880.0640.0640.0000.0000.0000.000
174A260HOH 0-0.043-0.02935.782-0.100-0.1000.0000.0000.0000.000
175A266HOH 0-0.012-0.03620.252-0.165-0.1650.0000.0000.0000.000
176A270HOH 0-0.030-0.03318.042-0.305-0.3050.0000.0000.0000.000
177A275HOH 0-0.027-0.01123.4830.0170.0170.0000.0000.0000.000
178A280HOH 0-0.044-0.04322.804-0.042-0.0420.0000.0000.0000.000
179A281HOH 0-0.017-0.01527.2160.0800.0800.0000.0000.0000.000
180A282HOH 0-0.020-0.02136.130-0.099-0.0990.0000.0000.0000.000
181A284HOH 00.0250.00527.8760.0760.0760.0000.0000.0000.000
182A288HOH 00.0380.02128.2420.1560.1560.0000.0000.0000.000
183A292HOH 0-0.030-0.02428.643-0.181-0.1810.0000.0000.0000.000
184A306HOH 0-0.036-0.04032.8750.0330.0330.0000.0000.0000.000
185A309HOH 0-0.038-0.02920.468-0.141-0.1410.0000.0000.0000.000
186A317HOH 0-0.031-0.02236.825-0.039-0.0390.0000.0000.0000.000
187A319HOH 0-0.006-0.01027.186-0.037-0.0370.0000.0000.0000.000
188A323HOH 0-0.037-0.02634.446-0.117-0.1170.0000.0000.0000.000
189A324HOH 0-0.021-0.03210.490-0.089-0.0890.0000.0000.0000.000
190A326HOH 0-0.034-0.03130.344-0.125-0.1250.0000.0000.0000.000
191A327HOH 0-0.038-0.03123.303-0.231-0.2310.0000.0000.0000.000
192A328HOH 0-0.007-0.00730.1090.1030.1030.0000.0000.0000.000
193A332HOH 00.0310.01622.7680.1710.1710.0000.0000.0000.000
194A333HOH 00.0190.00624.7190.2310.2310.0000.0000.0000.000
195A338HOH 00.008-0.00533.6150.0860.0860.0000.0000.0000.000
196A342HOH 0-0.029-0.02923.9230.1370.1370.0000.0000.0000.000
197A343HOH 0-0.016-0.00830.633-0.059-0.0590.0000.0000.0000.000
198A359HOH 0-0.003-0.01128.023-0.172-0.1720.0000.0000.0000.000
199A362HOH 0-0.023-0.00427.4450.1180.1180.0000.0000.0000.000
200A366HOH 0-0.017-0.03027.656-0.008-0.0080.0000.0000.0000.000
201A372HOH 00.0260.01730.7500.1140.1140.0000.0000.0000.000
202A378HOH 00.007-0.00225.3820.1420.1420.0000.0000.0000.000
203A389HOH 00.009-0.01333.3850.0880.0880.0000.0000.0000.000
204A390HOH 0-0.003-0.01227.028-0.036-0.0360.0000.0000.0000.000
205A407HOH 00.0240.02028.379-0.064-0.0640.0000.0000.0000.000
206A441HOH 0-0.008-0.01730.801-0.039-0.0390.0000.0000.0000.000
207A465HOH 0-0.020-0.02134.0670.0510.0510.0000.0000.0000.000
208A471HOH 0-0.027-0.00734.1370.0280.0280.0000.0000.0000.000