FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LL419

Calculation Name: 7KQO-A-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7KQO

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 211
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1798289.110962
FMO2-HF: Nuclear repulsion 1731526.426533
FMO2-HF: Total energy -66762.68443
FMO2-MP2: Total energy -66957.045605


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:SER )


Summations of interaction energy for fragment #1(A:1:SER )
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.
1.2153.4590.002-1.036-1.210.002
Interaction energy analysis for fragmet #1(A:1:SER )
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 : 0.014
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].
3A3VAL 00.0110.0083.650-1.7370.1000.002-0.963-0.8760.002
4A4ASN 00.003-0.0154.6571.1941.303-0.001-0.005-0.1020.000
5A5SER 00.0320.0067.6750.0550.0550.0000.0000.0000.000
6A6PHE 0-0.0170.0168.6810.2290.2290.0000.0000.0000.000
7A7SER 00.008-0.00210.311-0.078-0.0780.0000.0000.0000.000
8A8GLY 00.014-0.00612.9760.0850.0850.0000.0000.0000.000
9A9TYR 0-0.078-0.05911.0990.0630.0630.0000.0000.0000.000
10A10LEU 00.0040.01612.476-0.038-0.0380.0000.0000.0000.000
11A11LYS 10.7920.8876.113-1.694-1.6940.0000.0000.0000.000
12A12LEU 0-0.036-0.00311.188-0.038-0.0380.0000.0000.0000.000
13A13THR 00.0410.01011.0780.0050.0050.0000.0000.0000.000
14A14ASP -1-0.828-0.8596.5372.4232.4230.0000.0000.0000.000
15A15ASN 0-0.016-0.0156.1290.6930.6930.0000.0000.0000.000
16A16VAL 00.0070.0177.417-0.207-0.2070.0000.0000.0000.000
17A17TYR 00.0350.0234.419-0.686-0.651-0.001-0.008-0.0260.000
18A18ILE 00.0150.00711.139-0.051-0.0510.0000.0000.0000.000
19A19LYS 10.8280.90314.7330.2590.2590.0000.0000.0000.000
20A20ASN 00.0210.02217.0060.0270.0270.0000.0000.0000.000
21A21ALA 0-0.031-0.03019.121-0.028-0.0280.0000.0000.0000.000
22A22ASP -1-0.811-0.90121.051-0.082-0.0820.0000.0000.0000.000
23A23ILE 00.0320.00618.433-0.022-0.0220.0000.0000.0000.000
24A24VAL 00.0240.01320.345-0.022-0.0220.0000.0000.0000.000
25A25GLU -1-0.830-0.90422.268-0.182-0.1820.0000.0000.0000.000
26A26GLU -1-0.811-0.87816.275-0.319-0.3190.0000.0000.0000.000
27A27ALA 0-0.009-0.00617.637-0.048-0.0480.0000.0000.0000.000
28A28LYS 10.8120.88918.7020.1320.1320.0000.0000.0000.000
29A29LYS 10.8980.96117.9980.3490.3490.0000.0000.0000.000
30A30VAL 0-0.029-0.02212.771-0.034-0.0340.0000.0000.0000.000
31A31LYS 10.8170.91715.3060.2170.2170.0000.0000.0000.000
32A32PRO 0-0.0020.01513.075-0.048-0.0480.0000.0000.0000.000
33A33THR 00.0430.00511.4300.0420.0420.0000.0000.0000.000
34A34VAL 0-0.012-0.01613.3290.0550.0550.0000.0000.0000.000
35A35VAL 0-0.0110.00614.330-0.014-0.0140.0000.0000.0000.000
36A36VAL 00.0120.00616.0430.0160.0160.0000.0000.0000.000
37A37ASN 0-0.014-0.03418.643-0.009-0.0090.0000.0000.0000.000
38A38ALA 0-0.0020.02422.3900.0160.0160.0000.0000.0000.000
39A39ALA 00.0310.03424.445-0.007-0.0070.0000.0000.0000.000
40A40ASN 00.012-0.00926.9130.0100.0100.0000.0000.0000.000
41A41VAL 00.0510.02030.033-0.004-0.0040.0000.0000.0000.000
42A42TYR 00.0020.00331.6670.0000.0000.0000.0000.0000.000
43A43LEU 0-0.0100.00727.762-0.005-0.0050.0000.0000.0000.000
44A44LYS 10.8730.94731.0510.0050.0050.0000.0000.0000.000
45A45HIS 00.0190.00827.9700.0070.0070.0000.0000.0000.000
46A46GLY 00.0510.04131.370-0.006-0.0060.0000.0000.0000.000
47A47GLY 00.0280.00432.193-0.004-0.0040.0000.0000.0000.000
48A48GLY 00.0280.02729.4680.0030.0030.0000.0000.0000.000
49A49VAL 00.0400.00722.767-0.009-0.0090.0000.0000.0000.000
50A50ALA 00.0180.02526.192-0.011-0.0110.0000.0000.0000.000
51A51GLY 0-0.0190.00027.500-0.007-0.0070.0000.0000.0000.000
52A52ALA 0-0.005-0.00126.968-0.006-0.0060.0000.0000.0000.000
53A53LEU 00.0220.00021.992-0.011-0.0110.0000.0000.0000.000
54A54ASN 00.0540.00226.026-0.011-0.0110.0000.0000.0000.000
55A55LYS 10.9630.99229.0130.0610.0610.0000.0000.0000.000
56A56ALA 0-0.0230.00126.451-0.004-0.0040.0000.0000.0000.000
57A57THR 0-0.050-0.01726.151-0.008-0.0080.0000.0000.0000.000
58A58ASN 0-0.041-0.02628.7660.0040.0040.0000.0000.0000.000
59A59ASN 00.0140.00931.8020.0060.0060.0000.0000.0000.000
60A60ALA 00.0360.02629.8610.0060.0060.0000.0000.0000.000
61A61MET 00.0110.01724.1850.0080.0080.0000.0000.0000.000
62A62GLN 0-0.005-0.00729.1190.0080.0080.0000.0000.0000.000
63A63VAL 00.0200.01832.2670.0060.0060.0000.0000.0000.000
64A64GLU -1-0.692-0.80827.081-0.060-0.0600.0000.0000.0000.000
65A65SER 00.012-0.00229.5320.0080.0080.0000.0000.0000.000
66A66ASP -1-0.817-0.89131.190-0.012-0.0120.0000.0000.0000.000
67A67ASP -1-0.871-0.89633.590-0.019-0.0190.0000.0000.0000.000
68A68TYR 00.0580.03328.3970.0050.0050.0000.0000.0000.000
69A69ILE 0-0.047-0.02432.1430.0070.0070.0000.0000.0000.000
70A70ALA 0-0.0150.00934.4620.0040.0040.0000.0000.0000.000
71A71THR 0-0.0020.00934.3830.0020.0020.0000.0000.0000.000
72A72ASN 0-0.079-0.04631.8970.0070.0070.0000.0000.0000.000
73A73GLY 0-0.0120.01134.3940.0060.0060.0000.0000.0000.000
74A74PRO 0-0.055-0.04933.378-0.001-0.0010.0000.0000.0000.000
75A75LEU 00.0050.01726.7020.0050.0050.0000.0000.0000.000
76A76LYS 10.9570.96829.332-0.076-0.0760.0000.0000.0000.000
77A77VAL 00.0370.01228.7450.0000.0000.0000.0000.0000.000
78A78GLY 00.0030.00925.6520.0060.0060.0000.0000.0000.000
79A79GLY 0-0.028-0.00724.5660.0130.0130.0000.0000.0000.000
80A80SER 0-0.020-0.04022.034-0.006-0.0060.0000.0000.0000.000
81A81CYS 0-0.0380.01023.7440.0010.0010.0000.0000.0000.000
82A82VAL 00.0160.01219.575-0.006-0.0060.0000.0000.0000.000
83A83LEU 0-0.0050.00722.2070.0010.0010.0000.0000.0000.000
84A84SER 00.0430.01822.219-0.021-0.0210.0000.0000.0000.000
85A85GLY 00.0020.01420.8430.0120.0120.0000.0000.0000.000
86A86HIS 0-0.031-0.03321.863-0.016-0.0160.0000.0000.0000.000
87A87ASN 0-0.036-0.03223.473-0.014-0.0140.0000.0000.0000.000
88A88LEU 0-0.027-0.01121.267-0.020-0.0200.0000.0000.0000.000
89A89ALA 00.0280.01417.371-0.027-0.0270.0000.0000.0000.000
90A90LYS 10.8570.94716.6170.2200.2200.0000.0000.0000.000
91A91HIS 00.0290.01516.6750.0120.0120.0000.0000.0000.000
92A92CYS 0-0.009-0.00118.351-0.015-0.0150.0000.0000.0000.000
93A93LEU 0-0.0320.00816.8320.0120.0120.0000.0000.0000.000
94A94HIS 00.0430.00019.8990.0110.0110.0000.0000.0000.000
95A95VAL 00.0200.00619.6170.0110.0110.0000.0000.0000.000
96A96VAL 0-0.0350.01022.991-0.008-0.0080.0000.0000.0000.000
97A97GLY 00.0390.02525.7060.0140.0140.0000.0000.0000.000
98A98PRO 00.0040.01326.144-0.012-0.0120.0000.0000.0000.000
99A99ASN 0-0.0120.00029.3630.0000.0000.0000.0000.0000.000
100A100VAL 00.0760.03231.1940.0000.0000.0000.0000.0000.000
101A101ASN 0-0.055-0.02033.7890.0000.0000.0000.0000.0000.000
102A102LYS 10.8250.90634.140-0.034-0.0340.0000.0000.0000.000
103A103GLY 0-0.0090.00536.6630.0000.0000.0000.0000.0000.000
104A104GLU -1-0.791-0.84932.2240.0550.0550.0000.0000.0000.000
105A105ASP -1-0.785-0.89432.2700.1030.1030.0000.0000.0000.000
106A106ILE 00.0440.01327.6960.0040.0040.0000.0000.0000.000
107A107GLN 0-0.036-0.02227.5320.0190.0190.0000.0000.0000.000
108A108LEU 00.0090.00026.5190.0130.0130.0000.0000.0000.000
109A109LEU 0-0.039-0.02223.0150.0010.0010.0000.0000.0000.000
110A110LYS 10.8760.93619.309-0.285-0.2850.0000.0000.0000.000
111A111SER 00.011-0.01321.2240.0160.0160.0000.0000.0000.000
112A112ALA 00.0160.00222.0820.0020.0020.0000.0000.0000.000
113A113TYR 00.0450.00017.279-0.005-0.0050.0000.0000.0000.000
114A114GLU -1-0.863-0.91717.1780.2560.2560.0000.0000.0000.000
115A115ASN 0-0.0250.00617.4440.0060.0060.0000.0000.0000.000
116A116PHE 00.042-0.00113.796-0.025-0.0250.0000.0000.0000.000
117A117ASN 0-0.028-0.00812.7980.0670.0670.0000.0000.0000.000
118A118GLN 0-0.0250.01413.3750.0330.0330.0000.0000.0000.000
119A119HIS 0-0.046-0.02612.473-0.072-0.0720.0000.0000.0000.000
120A120GLU -1-0.856-0.9277.1540.1750.1750.0000.0000.0000.000
121A121VAL 0-0.002-0.0175.6260.0570.0570.0000.0000.0000.000
122A122LEU 0-0.0490.0178.393-0.064-0.0640.0000.0000.0000.000
123A123LEU 0-0.0080.01911.3930.0240.0240.0000.0000.0000.000
124A124ALA 00.018-0.00513.8680.0090.0090.0000.0000.0000.000
125A125PRO 0-0.0100.01216.5480.0000.0000.0000.0000.0000.000
126A126LEU 00.0330.01818.9490.0180.0180.0000.0000.0000.000
127A127LEU 00.0180.02820.051-0.021-0.0210.0000.0000.0000.000
128A128SER 00.024-0.01922.6190.0130.0130.0000.0000.0000.000
129A129ALA 00.0080.02524.757-0.002-0.0020.0000.0000.0000.000
130A130GLY 00.0460.02926.521-0.008-0.0080.0000.0000.0000.000
131A131ILE 00.005-0.01728.9030.0040.0040.0000.0000.0000.000
132A132PHE 0-0.073-0.02728.453-0.001-0.0010.0000.0000.0000.000
133A133GLY 00.0050.00930.6020.0060.0060.0000.0000.0000.000
134A134ALA 00.0210.02027.6290.0030.0030.0000.0000.0000.000
135A135ASP -1-0.817-0.91627.9300.0800.0800.0000.0000.0000.000
136A136PRO 0-0.013-0.01324.5160.0120.0120.0000.0000.0000.000
137A137ILE 00.0260.00223.3540.0100.0100.0000.0000.0000.000
138A138HIS 00.0290.01723.2740.0220.0220.0000.0000.0000.000
139A139SER 0-0.014-0.02722.2870.0250.0250.0000.0000.0000.000
140A140LEU 0-0.003-0.00316.7630.0170.0170.0000.0000.0000.000
141A141ARG 10.7880.85918.406-0.255-0.2550.0000.0000.0000.000
142A142VAL 00.0210.01219.2280.0330.0330.0000.0000.0000.000
143A143CYS 0-0.053-0.00615.7130.0380.0380.0000.0000.0000.000
144A144VAL 00.0360.02214.2090.0500.0500.0000.0000.0000.000
145A145ASP -1-0.781-0.84714.6770.4060.4060.0000.0000.0000.000
146A146THR 0-0.113-0.06416.428-0.007-0.0070.0000.0000.0000.000
147A147VAL 0-0.059-0.02111.3830.0040.0040.0000.0000.0000.000
148A148ARG 10.9230.97110.528-0.482-0.4820.0000.0000.0000.000
149A149THR 0-0.0180.0177.8040.2170.2170.0000.0000.0000.000
150A150ASN 0-0.032-0.0023.6610.5520.7940.003-0.057-0.1890.000
151A151VAL 00.0170.0037.142-0.280-0.2800.0000.0000.0000.000
152A152TYR 00.0180.0186.2020.1230.1230.0000.0000.0000.000
153A153LEU 00.010-0.01011.762-0.051-0.0510.0000.0000.0000.000
154A154ALA 00.0070.00215.414-0.023-0.0230.0000.0000.0000.000
155A155VAL 0-0.047-0.02918.2460.0190.0190.0000.0000.0000.000
156A156PHE 0-0.016-0.01121.309-0.012-0.0120.0000.0000.0000.000
157A157ASP -1-0.821-0.91424.557-0.020-0.0200.0000.0000.0000.000
158A158LYS 10.8960.92823.6710.0560.0560.0000.0000.0000.000
159A159ASN 00.009-0.00225.7360.0030.0030.0000.0000.0000.000
160A160LEU 0-0.026-0.01124.5150.0100.0100.0000.0000.0000.000
161A161TYR 0-0.025-0.01217.1220.0070.0070.0000.0000.0000.000
162A162ASP -1-0.769-0.86722.245-0.013-0.0130.0000.0000.0000.000
163A163LYS 10.9310.99724.329-0.045-0.0450.0000.0000.0000.000
164A164LEU 0-0.024-0.00220.8500.0130.0130.0000.0000.0000.000
165A165VAL 0-0.0020.00318.5510.0220.0220.0000.0000.0000.000
166A166SER 0-0.077-0.05720.8080.0160.0160.0000.0000.0000.000
167A167SER 0-0.082-0.05923.7190.0040.0040.0000.0000.0000.000
168A168PHE 0-0.024-0.01116.2210.0110.0110.0000.0000.0000.000
169A169LEU -1-0.869-0.91218.8780.2850.2850.0000.0000.0000.000
170A218HOH 0-0.063-0.05929.904-0.004-0.0040.0000.0000.0000.000
171A253HOH 0-0.068-0.05631.1150.0000.0000.0000.0000.0000.000
172A255HOH 00.0190.00121.863-0.005-0.0050.0000.0000.0000.000
173A256HOH 00.0270.02626.962-0.001-0.0010.0000.0000.0000.000
174A261HOH 00.006-0.00525.2690.0040.0040.0000.0000.0000.000
175A262HOH 0-0.016-0.01235.813-0.001-0.0010.0000.0000.0000.000
176A265HOH 0-0.053-0.04133.6440.0010.0010.0000.0000.0000.000
177A266HOH 0-0.012-0.01534.384-0.002-0.0020.0000.0000.0000.000
178A267HOH 0-0.023-0.02118.214-0.007-0.0070.0000.0000.0000.000
179A269HOH 00.002-0.01811.061-0.018-0.0180.0000.0000.0000.000
180A270HOH 0-0.006-0.00623.635-0.003-0.0030.0000.0000.0000.000
181A276HOH 0-0.007-0.01025.1710.0020.0020.0000.0000.0000.000
182A279HOH 0-0.013-0.03524.6780.0040.0040.0000.0000.0000.000
183A282HOH 0-0.016-0.01125.4230.0040.0040.0000.0000.0000.000
184A284HOH 0-0.038-0.02722.433-0.005-0.0050.0000.0000.0000.000
185A286HOH 00.014-0.00214.1500.0340.0340.0000.0000.0000.000
186A292HOH 0-0.027-0.01611.412-0.016-0.0160.0000.0000.0000.000
187A300HOH 0-0.005-0.01611.035-0.011-0.0110.0000.0000.0000.000
188A308HOH 0-0.056-0.03940.0220.0000.0000.0000.0000.0000.000
189A318HOH 0-0.012-0.00734.395-0.003-0.0030.0000.0000.0000.000
190A319HOH 0-0.028-0.02129.406-0.002-0.0020.0000.0000.0000.000
191A324HOH 0-0.056-0.04637.0130.0010.0010.0000.0000.0000.000
192A325HOH 0-0.060-0.04728.5910.0010.0010.0000.0000.0000.000
193A328HOH 0-0.019-0.02113.224-0.005-0.0050.0000.0000.0000.000
194A331HOH 0-0.009-0.01925.672-0.002-0.0020.0000.0000.0000.000
195A336HOH 0-0.057-0.0567.966-0.126-0.1260.0000.0000.0000.000
196A343HOH 00.0230.01527.563-0.001-0.0010.0000.0000.0000.000
197A350HOH 0-0.039-0.03231.854-0.001-0.0010.0000.0000.0000.000
198A353HOH 00.013-0.00929.3150.0030.0030.0000.0000.0000.000
199A354HOH 0-0.013-0.01619.266-0.002-0.0020.0000.0000.0000.000
200A355HOH 00.000-0.0224.541-0.463-0.442-0.001-0.003-0.0170.000
201A358HOH 0-0.001-0.00820.506-0.004-0.0040.0000.0000.0000.000
202A359HOH 0-0.0020.00117.143-0.020-0.0200.0000.0000.0000.000
203A370HOH 0-0.007-0.01112.5680.0520.0520.0000.0000.0000.000
204A375HOH 0-0.041-0.04232.136-0.003-0.0030.0000.0000.0000.000
205A388HOH 0-0.030-0.02312.2160.0090.0090.0000.0000.0000.000
206A389HOH 0-0.029-0.02029.0470.0030.0030.0000.0000.0000.000
207A393HOH 0-0.033-0.02321.4770.0030.0030.0000.0000.0000.000
208A399HOH 00.0190.00914.876-0.009-0.0090.0000.0000.0000.000
209A401HOH 0-0.035-0.03627.176-0.003-0.0030.0000.0000.0000.000
210A491HOH 00.0100.00336.9080.0000.0000.0000.0000.0000.000
211A536HOH 0-0.023-0.02037.729-0.001-0.0010.0000.0000.0000.000