Manual

About

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

tag_button

FMODB ID: KR413

Calculation Name: 7LG7-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1h-purin-8-yl)sulfanyl]-n-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide

ligand 3-letter code: XYJ

PDB ID: 7LG7

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-03-24

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 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1770731.407724
FMO2-HF: Nuclear repulsion 1704801.733368
FMO2-HF: Total energy -65929.674356
FMO2-MP2: Total energy -66121.176041


3D Structure
Snapshot
 
Ligand structure

XYJ

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.
-144.803-118.888101.926-38.467-89.3760.063


Interactive mode: IFIE and PIEDA for fragment #188(A:201:XYJ )


Summations of interaction energy for fragment #188(A:201:XYJ )
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.
-144.803-118.888101.926-38.467-89.376-0.063
Interaction energy analysis for fragmet #188(A:201:XYJ )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : 0.049
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].
1A1GLY 00.003-0.01622.599-0.004-0.0040.0000.0000.0000.000
2A2PRO 0-0.046-0.00118.0810.0260.0260.0000.0000.0000.000
3A3VAL 00.0140.00018.2850.0500.0500.0000.0000.0000.000
4A4ASN 0-0.031-0.01315.538-0.227-0.2270.0000.0000.0000.000
5A5SER 00.0540.03516.432-0.007-0.0070.0000.0000.0000.000
6A6PHE 0-0.007-0.00710.3140.0490.0490.0000.0000.0000.000
7A7SER 00.0200.00013.3810.1420.1420.0000.0000.0000.000
8A8GLY 0-0.001-0.00412.932-0.063-0.0630.0000.0000.0000.000
9A9TYR 0-0.067-0.0498.432-0.207-0.2070.0000.0000.0000.000
10A10LEU 00.0180.01512.4230.2750.2750.0000.0000.0000.000
11A11LYS 10.8480.92313.8191.1031.1030.0000.0000.0000.000
12A12LEU 0-0.0140.00512.0860.1070.1070.0000.0000.0000.000
13A13THR 00.0510.01516.3870.1530.1530.0000.0000.0000.000
14A14ASP -1-0.852-0.93718.523-1.303-1.3030.0000.0000.0000.000
15A15ASN 0-0.074-0.04316.9280.1500.1500.0000.0000.0000.000
16A16VAL 00.0230.02212.303-0.331-0.3310.0000.0000.0000.000
17A17TYR 00.004-0.00312.7200.3750.3750.0000.0000.0000.000
18A18ILE 00.0070.0087.979-0.810-0.8100.0000.0000.0000.000
19A19LYS 10.8310.9057.7722.5212.5210.0000.0000.0000.000
20A20ASN 0-0.048-0.0146.288-0.657-0.6570.0000.0000.0000.000
21A21ALA 0-0.015-0.0224.8430.8860.8860.0000.0000.0000.000
22A22ASP -1-0.802-0.9072.549-6.725-2.1302.443-2.859-4.179-0.020
23A23ILE 00.0510.0121.836-9.288-11.52710.370-3.222-4.9090.023
24A24VAL 00.0100.0043.216-3.027-2.2520.041-0.186-0.6300.001
25A25GLU -1-0.835-0.9085.110-0.394-0.323-0.001-0.002-0.0680.000
26A26GLU -1-0.806-0.8736.451-1.829-1.8290.0000.0000.0000.000
27A27ALA 00.0250.0167.729-0.169-0.1690.0000.0000.0000.000
28A28LYS 10.8500.9128.5070.0280.0280.0000.0000.0000.000
29A29LYS 10.8210.9129.4460.6540.6540.0000.0000.0000.000
30A30VAL 0-0.038-0.01011.4330.0340.0340.0000.0000.0000.000
31A31LYS 10.9260.96413.3490.7630.7630.0000.0000.0000.000
32A32PRO 00.0190.01311.0280.0720.0720.0000.0000.0000.000
33A33THR 00.0330.00014.3230.1760.1760.0000.0000.0000.000
34A34VAL 0-0.038-0.02012.6350.1180.1180.0000.0000.0000.000
35A35VAL 0-0.0020.0097.914-0.163-0.1630.0000.0000.0000.000
36A36VAL 0-0.014-0.0096.9420.2110.2110.0000.0000.0000.000
37A37ASN 0-0.001-0.0255.053-2.560-2.5600.0000.0000.0000.000
38A38ALA 0-0.0370.0021.888-2.425-2.7595.845-2.310-3.202-0.006
39A39ALA 00.0690.0312.320-10.876-7.8654.179-2.941-4.250-0.046
40A40ASN 00.013-0.0151.902-9.994-10.80710.374-3.447-6.1150.018
41A41VAL 00.0330.0123.604-0.1280.1100.0190.013-0.2700.000
42A42TYR 00.0070.0016.650-0.121-0.1210.0000.0000.0000.000
43A43LEU 0-0.0050.0165.4250.0950.0950.0000.0000.0000.000
44A44LYS 10.8470.9245.083-1.237-1.080-0.001-0.016-0.1410.000
45A45HIS 00.0440.0112.8090.7852.4070.363-0.852-1.134-0.006
46A46GLY 00.0160.0133.214-1.072-0.3410.030-0.220-0.5420.001
47A47GLY 00.013-0.0102.865-0.813-0.2060.051-0.139-0.5180.000
48A48GLY 00.0070.0133.056-5.225-2.9110.190-1.057-1.447-0.003
49A49VAL 00.0460.0182.160-7.914-4.1967.607-2.493-8.8320.005
50A50ALA 00.0250.0252.700-1.562-0.3220.577-0.410-1.4070.000
51A51GLY 0-0.025-0.0044.2620.3250.487-0.001-0.013-0.1480.000
52A52ALA 0-0.018-0.0113.055-1.717-0.9520.126-0.166-0.7250.000
53A53LEU 00.021-0.0054.902-0.899-0.768-0.001-0.007-0.1240.000
54A54ASN 00.0430.0017.296-0.306-0.3060.0000.0000.0000.000
55A55LYS 10.9390.9797.691-2.094-2.0940.0000.0000.0000.000
56A56ALA 0-0.023-0.0027.603-0.131-0.1310.0000.0000.0000.000
57A57THR 0-0.039-0.0069.657-0.154-0.1540.0000.0000.0000.000
58A58ASN 0-0.017-0.01012.4640.0680.0680.0000.0000.0000.000
59A59ASN 00.0120.01911.6480.1790.1790.0000.0000.0000.000
60A60ALA 00.0460.03213.036-0.018-0.0180.0000.0000.0000.000
61A61MET 00.0020.0178.776-0.167-0.1670.0000.0000.0000.000
62A62GLN 0-0.0270.0027.1780.2460.2460.0000.0000.0000.000
63A63VAL 00.0230.02210.0620.0300.0300.0000.0000.0000.000
64A64GLU -1-0.715-0.83513.322-0.980-0.9800.0000.0000.0000.000
65A65SER 0-0.028-0.0258.987-0.227-0.2270.0000.0000.0000.000
66A66ASP -1-0.825-0.92511.0170.7180.7180.0000.0000.0000.000
67A67ASP -1-0.954-0.96212.246-0.138-0.1380.0000.0000.0000.000
68A68TYR 00.0300.01012.487-0.040-0.0400.0000.0000.0000.000
69A69ILE 0-0.048-0.0279.912-0.001-0.0010.0000.0000.0000.000
70A70ALA 0-0.044-0.01813.3500.0500.0500.0000.0000.0000.000
71A71THR 0-0.038-0.00516.2000.0300.0300.0000.0000.0000.000
72A72ASN 0-0.075-0.05516.3420.0030.0030.0000.0000.0000.000
73A73GLY 00.0010.02415.538-0.026-0.0260.0000.0000.0000.000
74A74PRO 0-0.044-0.03111.156-0.090-0.0900.0000.0000.0000.000
75A75LEU 00.0090.0098.440-0.081-0.0810.0000.0000.0000.000
76A76LYS 10.9560.96411.2730.8610.8610.0000.0000.0000.000
77A77VAL 00.0230.0078.203-0.289-0.2890.0000.0000.0000.000
78A78GLY 0-0.017-0.0018.9050.0800.0800.0000.0000.0000.000
79A79GLY 0-0.054-0.01910.436-0.196-0.1960.0000.0000.0000.000
80A80SER 0-0.029-0.04410.339-0.346-0.3460.0000.0000.0000.000
81A81CYS 00.0220.01511.6330.3430.3430.0000.0000.0000.000
82A82VAL 0-0.041-0.00712.467-0.376-0.3760.0000.0000.0000.000
83A83LEU 00.0060.01910.9670.2290.2290.0000.0000.0000.000
84A84SER 00.0450.01714.694-0.188-0.1880.0000.0000.0000.000
85A85GLY 0-0.0190.00714.226-0.175-0.1750.0000.0000.0000.000
86A86HIS 0-0.003-0.01013.8760.1750.1750.0000.0000.0000.000
87A87ASN 0-0.002-0.01012.557-0.031-0.0310.0000.0000.0000.000
88A88LEU 0-0.061-0.0238.5450.0440.0440.0000.0000.0000.000
89A89ALA 00.0270.01312.224-0.130-0.1300.0000.0000.0000.000
90A90LYS 10.8910.97814.5771.2321.2320.0000.0000.0000.000
91A91HIS 00.007-0.00516.2270.2080.2080.0000.0000.0000.000
92A92CYS 00.0080.00210.310-0.363-0.3630.0000.0000.0000.000
93A93LEU 0-0.0220.00911.5010.2780.2780.0000.0000.0000.000
94A94HIS 00.037-0.0037.876-1.697-1.6970.0000.0000.0000.000
95A95VAL 00.006-0.0057.2820.9010.9010.0000.0000.0000.000
96A96VAL 0-0.0290.0145.319-1.457-1.4570.0000.0000.0000.000
97A97GLY 00.0270.0134.265-0.271-0.1160.000-0.030-0.1240.000
98A98PRO 00.0220.0135.1360.1930.260-0.001-0.005-0.0620.000
99A99ASN 0-0.010-0.0265.3272.5822.5820.0000.0000.0000.000
100A100VAL 00.0480.0176.521-0.679-0.6790.0000.0000.0000.000
101A101ASN 0-0.029-0.0107.041-1.129-1.1290.0000.0000.0000.000
102A102LYS 10.8450.9207.765-2.676-2.6760.0000.0000.0000.000
103A103GLY 00.0250.02310.187-0.232-0.2320.0000.0000.0000.000
104A104GLU -1-0.784-0.8388.2100.6180.6180.0000.0000.0000.000
105A105ASP -1-0.828-0.91811.4580.1800.1800.0000.0000.0000.000
106A106ILE 00.0450.0119.7950.0090.0090.0000.0000.0000.000
107A107GLN 00.0260.01711.349-0.295-0.2950.0000.0000.0000.000
108A108LEU 0-0.048-0.03410.426-0.243-0.2430.0000.0000.0000.000
109A109LEU 0-0.023-0.0136.820-0.175-0.1750.0000.0000.0000.000
110A110LYS 10.8800.9359.7690.5640.5640.0000.0000.0000.000
111A111SER 00.006-0.00212.591-0.112-0.1120.0000.0000.0000.000
112A112ALA 0-0.030-0.0187.863-0.149-0.1490.0000.0000.0000.000
113A113TYR 00.0580.0127.452-1.328-1.3280.0000.0000.0000.000
114A114GLU -1-0.830-0.90311.448-1.249-1.2490.0000.0000.0000.000
115A115ASN 0-0.069-0.02411.2270.3180.3180.0000.0000.0000.000
116A116PHE 00.031-0.0097.851-0.086-0.0860.0000.0000.0000.000
117A117ASN 0-0.0140.00213.9490.1030.1030.0000.0000.0000.000
118A118GLN 0-0.055-0.01317.0890.1810.1810.0000.0000.0000.000
119A119HIS 0-0.021-0.01215.7840.1370.1370.0000.0000.0000.000
120A120GLU -1-0.899-0.93517.877-1.441-1.4410.0000.0000.0000.000
121A121VAL 00.0270.00314.541-0.088-0.0880.0000.0000.0000.000
122A122LEU 0-0.0270.02311.5120.0050.0050.0000.0000.0000.000
123A123LEU 00.0060.0276.654-0.022-0.0220.0000.0000.0000.000
124A124ALA 00.0290.0086.7650.1250.1250.0000.0000.0000.000
125A125PRO 0-0.0200.0012.773-2.785-1.1400.353-0.379-1.619-0.001
126A126LEU 00.0210.0093.3051.4762.6330.020-0.192-0.985-0.001
127A127LEU 00.0040.0022.823-12.172-9.5260.753-1.477-1.921-0.015
128A128SER 00.026-0.0192.338-0.893-0.2435.795-2.959-3.4860.012
129A129ALA 0-0.0200.0022.4003.3902.2730.7432.794-2.420-0.006
130A130GLY 0-0.006-0.0032.239-7.005-5.3389.273-4.702-6.2380.013
131A131ILE 0-0.013-0.0222.283-1.997-4.9812.3194.993-4.328-0.001
132A132PHE 0-0.037-0.0222.302-15.759-12.03311.473-3.456-11.743-0.018
133A133GLY 00.0270.0233.951-3.283-3.0250.014-0.024-0.2480.000
134A134ALA 0-0.0040.0085.505-1.550-1.5500.0000.0000.0000.000
135A135ASP -1-0.794-0.9126.931-1.266-1.2660.0000.0000.0000.000
136A136PRO 0-0.007-0.0025.764-0.766-0.7660.0000.0000.0000.000
137A137ILE 00.015-0.0027.256-0.800-0.8000.0000.0000.0000.000
138A138HIS 00.0270.01710.814-0.219-0.2190.0000.0000.0000.000
139A139SER 0-0.035-0.0436.086-0.457-0.4570.0000.0000.0000.000
140A140LEU 0-0.004-0.0078.690-0.457-0.4570.0000.0000.0000.000
141A141ARG 10.9060.93810.2591.6741.6740.0000.0000.0000.000
142A142VAL 00.0350.03111.6160.1440.1440.0000.0000.0000.000
143A143CYS 0-0.029-0.00710.192-0.090-0.0900.0000.0000.0000.000
144A144VAL 0-0.042-0.02212.3470.1690.1690.0000.0000.0000.000
145A145ASP -1-0.916-0.94515.251-1.342-1.3420.0000.0000.0000.000
146A146THR 0-0.117-0.05514.3560.3070.3070.0000.0000.0000.000
147A147VAL 0-0.081-0.04612.6380.1000.1000.0000.0000.0000.000
148A148ARG 10.9710.98816.0171.5171.5170.0000.0000.0000.000
149A149THR 0-0.042-0.00517.2050.0600.0600.0000.0000.0000.000
150A150ASN 0-0.023-0.00216.197-0.121-0.1210.0000.0000.0000.000
151A151VAL 00.0180.00410.108-0.180-0.1800.0000.0000.0000.000
152A152TYR 0-0.022-0.00810.2030.1790.1790.0000.0000.0000.000
153A153LEU 00.008-0.0096.673-0.669-0.6690.0000.0000.0000.000
154A154ALA 00.0030.0053.3551.0501.6190.029-0.098-0.5000.000
155A155VAL 0-0.018-0.0172.699-11.540-9.3671.834-1.649-2.358-0.022
156A156PHE 00.0070.0042.589-1.5552.7253.372-1.880-5.771-0.002
157A157ASP -1-0.783-0.8963.7070.5781.0950.018-0.058-0.4760.000
158A158LYS 10.8710.9287.1880.1640.1640.0000.0000.0000.000
159A159ASN 0-0.023-0.0179.755-0.211-0.2110.0000.0000.0000.000
160A160LEU 0-0.020-0.0175.833-0.075-0.0750.0000.0000.0000.000
161A161TYR 00.0150.0077.745-0.348-0.3480.0000.0000.0000.000
162A162ASP -1-0.789-0.8919.316-1.146-1.1460.0000.0000.0000.000
163A163LYS 10.9180.96412.1510.8470.8470.0000.0000.0000.000
164A164LEU 0-0.035-0.0147.695-0.084-0.0840.0000.0000.0000.000
165A165VAL 0-0.026-0.00811.6950.1110.1110.0000.0000.0000.000
166A166SER 0-0.076-0.04113.9140.2230.2230.0000.0000.0000.000
167A167SER -1-0.923-0.93514.779-1.351-1.3510.0000.0000.0000.000
168A305HOH 0-0.012-0.02011.244-0.023-0.0230.0000.0000.0000.000
169A307HOH 0-0.016-0.0181.864-3.959-7.7318.111-2.247-2.0910.011
170A308HOH 00.0080.00710.084-0.149-0.1490.0000.0000.0000.000
171A309HOH 00.003-0.0072.325-0.2851.5042.804-2.005-2.588-0.014
172A312HOH 0-0.009-0.03211.975-0.127-0.1270.0000.0000.0000.000
173A314HOH 0-0.051-0.04517.5110.0040.0040.0000.0000.0000.000
174A317HOH 0-0.035-0.0365.725-0.354-0.3540.0000.0000.0000.000
175A318HOH 0-0.018-0.0227.431-0.053-0.0530.0000.0000.0000.000
176A319HOH 0-0.004-0.02514.389-0.035-0.0350.0000.0000.0000.000
177A320HOH 0-0.061-0.04617.6080.0220.0220.0000.0000.0000.000
178A322HOH 0-0.024-0.01915.514-0.020-0.0200.0000.0000.0000.000
179A323HOH 0-0.041-0.0235.8180.2390.2390.0000.0000.0000.000
180A327HOH 0-0.007-0.0242.350-3.546-1.9900.879-1.222-1.213-0.014
181A330HOH 00.0150.0011.721-8.221-14.08011.926-3.542-2.5250.028
182A332HOH 0-0.007-0.01816.4960.0910.0910.0000.0000.0000.000
183A339HOH 0-0.008-0.0305.517-0.208-0.2080.0000.0000.0000.000
184A342HOH 00.0040.00112.266-0.055-0.0550.0000.0000.0000.000
185A343HOH 0-0.008-0.0067.195-0.218-0.2180.0000.0000.0000.000
186A344HOH 00.0330.02212.877-0.062-0.0620.0000.0000.0000.000
187A349HOH 0-0.024-0.0044.6200.1230.1640.000-0.002-0.0390.000