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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: R12R8

Calculation Name: 7KG3-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 2-(n-morpholino)-ethanesulfonic acid

ligand 3-letter code: MES

PDB ID: 7KG3

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 181
LigandCharge MES=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1700828.821192
FMO2-HF: Nuclear repulsion 1636766.750108
FMO2-HF: Total energy -64062.071084
FMO2-MP2: Total energy -64249.342939


3D Structure
Snapshot
 
Ligand structure

MES

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.
-180.576-187.31086.551-28.592-51.230-0.109


Interactive mode: IFIE and PIEDA for fragment #181(A:203:MES )


Summations of interaction energy for fragment #181(A:203:MES )
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.
-180.576-187.3186.551-28.592-51.230.109
Interaction energy analysis for fragmet #181(A:203:MES )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.891 / q_NPA : -0.876
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].
1A2PRO 10.8110.88522.197-12.728-12.7280.0000.0000.0000.000
2A3VAL 00.0550.04023.984-0.398-0.3980.0000.0000.0000.000
3A4ASN 00.0210.01421.2090.5970.5970.0000.0000.0000.000
4A5SER 00.0510.03522.830-0.197-0.1970.0000.0000.0000.000
5A6PHE 0-0.016-0.00716.9560.1340.1340.0000.0000.0000.000
6A7SER 00.0270.00421.886-0.572-0.5720.0000.0000.0000.000
7A8GLY 00.006-0.00521.9490.5580.5580.0000.0000.0000.000
8A9TYR 0-0.066-0.04616.0440.6190.6190.0000.0000.0000.000
9A10LEU 00.0190.02420.311-0.838-0.8380.0000.0000.0000.000
10A11LYS 10.8350.92220.507-11.725-11.7250.0000.0000.0000.000
11A12LEU 0-0.0040.00017.140-0.260-0.2600.0000.0000.0000.000
12A13THR 00.0420.01420.667-0.400-0.4000.0000.0000.0000.000
13A14ASP -1-0.865-0.94822.86012.03312.0330.0000.0000.0000.000
14A15ASN 0-0.056-0.03719.217-0.608-0.6080.0000.0000.0000.000
15A16VAL 00.0170.02615.9740.9060.9060.0000.0000.0000.000
16A17TYR 00.0040.00317.759-1.150-1.1500.0000.0000.0000.000
17A18ILE 00.0120.01114.0041.4751.4750.0000.0000.0000.000
18A19LYS 10.8210.89615.556-17.165-17.1650.0000.0000.0000.000
19A20ASN 0-0.053-0.01615.0930.4430.4430.0000.0000.0000.000
20A21ALA 0-0.008-0.02214.616-1.392-1.3920.0000.0000.0000.000
21A22ASP -1-0.821-0.91012.90224.33724.3370.0000.0000.0000.000
22A23ILE 00.0580.0208.985-1.532-1.5320.0000.0000.0000.000
23A24VAL 00.0070.00711.658-1.196-1.1960.0000.0000.0000.000
24A25GLU -1-0.819-0.90414.05015.12715.1270.0000.0000.0000.000
25A26GLU -1-0.792-0.86015.20415.35615.3560.0000.0000.0000.000
26A27ALA 00.0400.02414.849-1.000-1.0000.0000.0000.0000.000
27A28LYS 10.7970.87116.897-17.442-17.4420.0000.0000.0000.000
28A29LYS 10.8490.92119.429-16.504-16.5040.0000.0000.0000.000
29A30VAL 0-0.030-0.00119.046-0.650-0.6500.0000.0000.0000.000
30A31LYS 10.8310.92319.313-15.574-15.5740.0000.0000.0000.000
31A32PRO 00.0520.03116.715-0.731-0.7310.0000.0000.0000.000
32A33THR 0-0.020-0.02319.322-0.390-0.3900.0000.0000.0000.000
33A34VAL 0-0.009-0.00714.529-0.168-0.1680.0000.0000.0000.000
34A35VAL 0-0.0140.00311.4180.0330.0330.0000.0000.0000.000
35A36VAL 00.0070.0098.347-0.256-0.2560.0000.0000.0000.000
36A37ASN 0-0.027-0.0404.8044.8224.963-0.001-0.004-0.1360.000
37A38ALA 0-0.0080.0202.676-3.924-2.3541.553-1.050-2.0730.013
38A39ALA 00.0510.0162.391-3.062-1.1964.057-2.133-3.791-0.033
39A40ASN 00.029-0.0081.903-9.687-10.52711.346-3.859-6.6470.021
40A41VAL 00.0250.0053.748-2.365-2.0140.015-0.040-0.3260.000
41A42TYR 0-0.012-0.0016.511-2.320-2.3200.0000.0000.0000.000
42A43LEU 0-0.0050.0125.520-1.645-1.6450.0000.0000.0000.000
43A44LYS 10.8530.9284.899-23.867-23.640-0.001-0.035-0.1920.000
44A45HIS 00.0360.0012.3368.81910.0921.756-1.194-1.835-0.012
45A46GLY 00.0060.0012.632-3.347-2.7030.296-0.057-0.884-0.001
46A47GLY 00.013-0.0012.869-3.482-2.8380.069-0.182-0.5300.000
47A48GLY 00.0100.0172.9831.5642.7600.182-0.557-0.821-0.006
48A49VAL 00.0470.0184.285-7.263-6.8870.000-0.039-0.3370.000
49A50ALA 00.0580.0452.463-7.278-6.8321.498-0.533-1.410-0.002
50A51GLY 00.0060.0054.177-4.195-4.0390.000-0.036-0.1200.000
51A52ALA 0-0.032-0.0115.818-3.230-3.2300.0000.0000.0000.000
52A53LEU 00.0470.0157.145-3.003-3.0030.0000.0000.0000.000
53A54ASN 00.0690.0217.198-3.062-3.0620.0000.0000.0000.000
54A55LYS 10.9480.9839.061-19.863-19.8630.0000.0000.0000.000
55A56ALA 0-0.0210.00211.502-1.515-1.5150.0000.0000.0000.000
56A57THR 0-0.058-0.02011.809-1.180-1.1800.0000.0000.0000.000
57A58ASN 0-0.048-0.03314.111-0.746-0.7460.0000.0000.0000.000
58A59ASN 00.0410.04010.9990.3200.3200.0000.0000.0000.000
59A60ALA 00.0170.01812.5420.0450.0450.0000.0000.0000.000
60A61MET 00.0070.0168.6140.7100.7100.0000.0000.0000.000
61A62GLN 0-0.015-0.0086.6672.0482.0480.0000.0000.0000.000
62A63VAL 00.0090.0099.749-0.241-0.2410.0000.0000.0000.000
63A64GLU -1-0.742-0.84613.10316.96616.9660.0000.0000.0000.000
64A65SER 0-0.012-0.0188.9870.4250.4250.0000.0000.0000.000
65A66ASP -1-0.857-0.91810.17219.54519.5450.0000.0000.0000.000
66A67ASP -1-0.937-0.95312.12213.17013.1700.0000.0000.0000.000
67A68TYR 00.0420.01012.443-0.491-0.4910.0000.0000.0000.000
68A69ILE 0-0.023-0.02110.088-0.255-0.2550.0000.0000.0000.000
69A70ALA 0-0.041-0.00913.554-0.421-0.4210.0000.0000.0000.000
70A71THR 0-0.034-0.00316.278-0.831-0.8310.0000.0000.0000.000
71A72ASN 0-0.103-0.06615.849-0.885-0.8850.0000.0000.0000.000
72A73GLY 0-0.0170.01015.353-0.063-0.0630.0000.0000.0000.000
73A74PRO 0-0.055-0.03611.3450.6230.6230.0000.0000.0000.000
74A75LEU 00.0140.0078.403-0.792-0.7920.0000.0000.0000.000
75A76LYS 10.9540.96411.429-16.825-16.8250.0000.0000.0000.000
76A77VAL 00.0180.0098.1371.1811.1810.0000.0000.0000.000
77A78GLY 00.0140.0149.059-2.065-2.0650.0000.0000.0000.000
78A79GLY 0-0.0150.00310.578-1.517-1.5170.0000.0000.0000.000
79A80SER 0-0.034-0.05210.2022.2752.2750.0000.0000.0000.000
80A81CYS 0-0.0280.00411.417-1.173-1.1730.0000.0000.0000.000
81A82VAL 0-0.0140.00212.2491.2511.2510.0000.0000.0000.000
82A83LEU 00.0060.01711.126-0.870-0.8700.0000.0000.0000.000
83A84SER 00.0410.01314.802-0.025-0.0250.0000.0000.0000.000
84A85GLY 0-0.0200.00914.1831.2561.2560.0000.0000.0000.000
85A86HIS 0-0.006-0.02913.622-0.426-0.4260.0000.0000.0000.000
86A87ASN 00.000-0.00616.408-0.010-0.0100.0000.0000.0000.000
87A88LEU 0-0.023-0.01612.462-0.335-0.3350.0000.0000.0000.000
88A89ALA 0-0.0020.00215.7170.0320.0320.0000.0000.0000.000
89A90LYS 10.8810.96617.608-13.572-13.5720.0000.0000.0000.000
90A91HIS 00.0050.00316.598-0.960-0.9600.0000.0000.0000.000
91A92CYS 00.0010.0049.9630.9230.9230.0000.0000.0000.000
92A93LEU 0-0.0180.00911.929-0.700-0.7000.0000.0000.0000.000
93A94HIS 00.034-0.0037.6084.9354.9350.0000.0000.0000.000
94A95VAL 00.007-0.0017.501-2.649-2.6490.0000.0000.0000.000
95A96VAL 0-0.0390.0005.2026.1276.1270.0000.0000.0000.000
96A97GLY 00.0580.0324.366-6.254-6.108-0.001-0.025-0.1200.000
97A98PRO 00.0090.0065.4410.7340.783-0.001-0.003-0.0460.000
98A99ASN 00.008-0.0055.5457.4757.4750.0000.0000.0000.000
99A100VAL 00.0510.0166.422-4.458-4.4580.0000.0000.0000.000
100A101ASN 00.0220.0247.203-5.316-5.3160.0000.0000.0000.000
101A102LYS 10.7840.8908.241-27.908-27.9080.0000.0000.0000.000
102A103GLY 00.0200.00810.343-1.683-1.6830.0000.0000.0000.000
103A104GLU -1-0.826-0.8758.29529.52829.5280.0000.0000.0000.000
104A105ASP -1-0.809-0.90911.60121.09021.0900.0000.0000.0000.000
105A106ILE 00.0490.0179.9551.8151.8150.0000.0000.0000.000
106A107GLN 00.0250.01811.5211.4311.4310.0000.0000.0000.000
107A108LEU 0-0.042-0.03310.515-0.317-0.3170.0000.0000.0000.000
108A109LEU 00.003-0.0156.4681.3771.3770.0000.0000.0000.000
109A110LYS 10.8630.9489.895-17.966-17.9660.0000.0000.0000.000
110A111SER 00.0290.01012.510-0.742-0.7420.0000.0000.0000.000
111A112ALA 0-0.037-0.0217.969-0.338-0.3380.0000.0000.0000.000
112A113TYR 00.057-0.0018.6930.4310.4310.0000.0000.0000.000
113A114GLU -1-0.891-0.95211.64616.47916.4790.0000.0000.0000.000
114A115ASN 0-0.053-0.01211.595-2.533-2.5330.0000.0000.0000.000
115A116PHE 00.022-0.0159.335-0.569-0.5690.0000.0000.0000.000
116A117ASN 0-0.027-0.01014.689-1.404-1.4040.0000.0000.0000.000
117A118GLN 0-0.067-0.01817.610-0.936-0.9360.0000.0000.0000.000
118A119HIS 0-0.048-0.03216.587-0.895-0.8950.0000.0000.0000.000
119A120GLU -1-0.845-0.91519.53613.74313.7430.0000.0000.0000.000
120A121VAL 00.0230.00819.5600.0870.0870.0000.0000.0000.000
121A122LEU 0-0.0330.02113.9330.2260.2260.0000.0000.0000.000
122A123LEU 0-0.0080.01813.090-0.372-0.3720.0000.0000.0000.000
123A124ALA 00.017-0.00210.1460.8820.8820.0000.0000.0000.000
124A125PRO 0-0.0260.0045.837-2.211-2.2110.0000.0000.0000.000
125A126LEU 00.0370.0207.154-0.934-0.9340.0000.0000.0000.000
126A127LEU 0-0.005-0.0024.23310.79211.1030.001-0.057-0.2560.000
127A128SER 00.011-0.0132.503-13.143-11.9434.235-2.553-2.8830.024
128A129ALA 00.0010.0123.313-7.890-9.3980.5292.096-1.1170.003
129A130GLY 00.0170.0171.956-16.183-19.4207.992-2.160-2.5960.022
130A131ILE 0-0.032-0.0352.360-8.373-8.3612.6691.266-3.9460.004
131A132PHE 0-0.046-0.0222.303-25.967-21.00310.194-3.765-11.3930.002
132A133GLY 00.0290.0163.965-9.170-8.8800.013-0.053-0.2500.001
133A134ALA 0-0.0150.0125.167-7.199-7.177-0.001-0.001-0.0210.000
134A135ASP -1-0.800-0.9116.95927.31527.3150.0000.0000.0000.000
135A136PRO 00.0010.0008.3490.4720.4720.0000.0000.0000.000
136A137ILE 00.0130.0009.361-0.695-0.6950.0000.0000.0000.000
137A138HIS 00.0180.01010.893-1.588-1.5880.0000.0000.0000.000
138A139SER 0-0.018-0.0297.107-2.257-2.2570.0000.0000.0000.000
139A140LEU 0-0.003-0.00710.112-0.643-0.6430.0000.0000.0000.000
140A141ARG 10.8990.93312.768-18.937-18.9370.0000.0000.0000.000
141A142VAL 00.0360.03211.804-1.035-1.0350.0000.0000.0000.000
142A143CYS 0-0.0070.01511.677-1.016-1.0160.0000.0000.0000.000
143A144VAL 0-0.041-0.02213.410-1.316-1.3160.0000.0000.0000.000
144A145ASP -1-0.899-0.93516.84116.15016.1500.0000.0000.0000.000
145A146THR 0-0.150-0.09214.594-1.172-1.1720.0000.0000.0000.000
146A147VAL 0-0.079-0.03113.903-0.538-0.5380.0000.0000.0000.000
147A148ARG 10.9670.98916.977-15.736-15.7360.0000.0000.0000.000
148A149THR 0-0.0290.00618.614-0.499-0.4990.0000.0000.0000.000
149A150ASN 0-0.020-0.00719.2640.5800.5800.0000.0000.0000.000
150A151VAL 00.015-0.00213.5310.6280.6280.0000.0000.0000.000
151A152TYR 0-0.019-0.00715.833-0.567-0.5670.0000.0000.0000.000
152A153LEU 00.019-0.00810.7111.2681.2680.0000.0000.0000.000
153A154ALA 0-0.026-0.01211.530-1.860-1.8600.0000.0000.0000.000
154A155VAL 0-0.006-0.00710.3163.3493.3490.0000.0000.0000.000
155A156PHE 00.0100.01010.558-1.949-1.9490.0000.0000.0000.000
156A157ASP -1-0.802-0.90511.88119.53219.5320.0000.0000.0000.000
157A158LYS 10.8730.92913.765-14.848-14.8480.0000.0000.0000.000
158A159ASN 0-0.019-0.01616.501-1.237-1.2370.0000.0000.0000.000
159A160LEU 0-0.025-0.0149.820-0.272-0.2720.0000.0000.0000.000
160A161TYR 00.0160.00414.334-0.045-0.0450.0000.0000.0000.000
161A162ASP -1-0.784-0.88615.62415.14015.1400.0000.0000.0000.000
162A163LYS 10.9130.96113.951-21.826-21.8260.0000.0000.0000.000
163A164LEU 0-0.030-0.01611.713-0.112-0.1120.0000.0000.0000.000
164A165VAL 0-0.034-0.01516.130-0.485-0.4850.0000.0000.0000.000
165A166SER 0-0.078-0.03719.412-1.028-1.0280.0000.0000.0000.000
166A167SER -1-0.907-0.92417.54615.79915.7990.0000.0000.0000.000
167A309HOH 0-0.026-0.0301.769-9.616-16.40913.562-4.053-2.7160.026
168A316HOH 0-0.018-0.0301.789-15.589-19.29211.394-4.348-3.3430.021
169A322HOH 0-0.036-0.0315.743-0.525-0.5250.0000.0000.0000.000
170A328HOH 0-0.008-0.03211.9940.7020.7020.0000.0000.0000.000
171A330HOH 0-0.010-0.03018.7760.1990.1990.0000.0000.0000.000
172A332HOH 0-0.048-0.0419.162-0.957-0.9570.0000.0000.0000.000
173A342HOH 0-0.032-0.02611.849-0.447-0.4470.0000.0000.0000.000
174A343HOH 0-0.029-0.03210.579-0.110-0.1100.0000.0000.0000.000
175A350HOH 0-0.014-0.02219.753-0.383-0.3830.0000.0000.0000.000
176A355HOH 0-0.027-0.0231.677-11.567-19.65514.566-4.135-2.3430.035
177A362HOH 00.0350.02116.105-0.078-0.0780.0000.0000.0000.000
178A363HOH 0-0.058-0.04219.147-0.272-0.2720.0000.0000.0000.000
179A394HOH 0-0.007-0.0282.430-1.5410.0100.629-1.082-1.098-0.009
180A400HOH 00.008-0.0095.3370.0680.0680.0000.0000.0000.000