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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: 1J1GZ

Calculation Name: 7KXB-A-Xray89

Preferred Name:

Target Type:

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

ligand 3-letter code: XB1

PDB ID: 7KXB

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 202
LigandCharge XB1=1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1787779.013365
FMO2-HF: Nuclear repulsion 1721292.549022
FMO2-HF: Total energy -66486.464343
FMO2-MP2: Total energy -66679.247351


3D Structure
Snapshot
 
Ligand structure

XB1

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.
-131.428-111.160103.985-34.157-90.1020.293


Interactive mode: IFIE and PIEDA for fragment #202(A:201:XB1 )


Summations of interaction energy for fragment #202(A:201:XB1 )
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.
-131.428-111.16103.985-34.157-90.102-0.293
Interaction energy analysis for fragmet #202(A:201:XB1 )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.706 / q_NPA : 0.934
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].
1A3VAL 0-0.016-0.02018.195-0.030-0.0300.0000.0000.0000.000
2A4ASN 0-0.009-0.01516.330-0.311-0.3110.0000.0000.0000.000
3A5SER 00.0490.03416.5910.2360.2360.0000.0000.0000.000
4A6PHE 0-0.0020.00211.611-0.072-0.0720.0000.0000.0000.000
5A7SER 00.0340.01114.2380.3990.3990.0000.0000.0000.000
6A8GLY 00.004-0.00713.865-0.403-0.4030.0000.0000.0000.000
7A9TYR 0-0.064-0.0499.952-0.374-0.3740.0000.0000.0000.000
8A10LEU 00.0150.01914.3560.4900.4900.0000.0000.0000.000
9A11LYS 10.8390.92015.64510.16110.1610.0000.0000.0000.000
10A12LEU 0-0.0090.00413.2260.2370.2370.0000.0000.0000.000
11A13THR 00.033-0.00517.6970.3540.3540.0000.0000.0000.000
12A14ASP -1-0.846-0.93219.682-10.364-10.3640.0000.0000.0000.000
13A15ASN 0-0.045-0.02317.5440.4790.4790.0000.0000.0000.000
14A16VAL 00.0180.02112.966-0.736-0.7360.0000.0000.0000.000
15A17TYR 0-0.012-0.00614.2450.8170.8170.0000.0000.0000.000
16A18ILE 00.0100.0109.469-0.885-0.8850.0000.0000.0000.000
17A19LYS 10.8040.8879.63914.09114.0910.0000.0000.0000.000
18A20ASN 00.0260.0248.176-0.871-0.8710.0000.0000.0000.000
19A21ALA 0-0.039-0.0376.3420.2980.2980.0000.0000.0000.000
20A22ASP -1-0.803-0.9082.448-28.000-25.1562.214-2.093-2.965-0.026
21A23ILE 00.0480.0141.915-0.869-0.1233.211-0.918-3.039-0.003
22A24VAL 00.0120.0053.199-0.567-0.0410.027-0.087-0.4660.000
23A25GLU -1-0.827-0.9035.303-15.292-15.2920.0000.0000.0000.000
24A26GLU -1-0.799-0.8636.355-13.143-13.1430.0000.0000.0000.000
25A27ALA 00.0230.0127.6360.6400.6400.0000.0000.0000.000
26A28LYS 10.8610.9188.75717.38717.3870.0000.0000.0000.000
27A29LYS 10.8130.9079.40014.90414.9040.0000.0000.0000.000
28A30VAL 0-0.050-0.01112.1720.5510.5510.0000.0000.0000.000
29A31LYS 10.8970.94513.22013.25513.2550.0000.0000.0000.000
30A32PRO 0-0.0110.00811.6520.5270.5270.0000.0000.0000.000
31A33THR 00.0390.01514.935-0.075-0.0750.0000.0000.0000.000
32A34VAL 0-0.011-0.00713.232-0.393-0.3930.0000.0000.0000.000
33A35VAL 0-0.0090.0058.3170.3850.3850.0000.0000.0000.000
34A36VAL 00.0060.0037.089-1.071-1.0710.0000.0000.0000.000
35A37ASN 0-0.005-0.0294.730-5.566-5.411-0.001-0.015-0.1390.000
36A38ALA 0-0.0080.0202.207-1.751-0.1043.615-1.703-3.5600.002
37A39ALA 00.0520.0212.230-33.864-33.6679.760-4.466-5.491-0.059
38A40ASN 00.0200.0052.345-8.548-6.3505.178-1.498-5.878-0.028
39A41VAL 00.0390.0223.3204.9365.0040.0510.167-0.286-0.001
40A42TYR 00.0080.0016.2154.0524.0520.0000.0000.0000.000
41A43LEU 0-0.0120.0075.4971.6801.6800.0000.0000.0000.000
42A44LYS 10.8710.9394.71831.86432.009-0.001-0.018-0.1260.000
43A45HIS 00.008-0.0112.610-25.474-23.5540.684-0.921-1.684-0.010
44A46GLY 00.0010.0012.8645.5846.1600.120-0.172-0.524-0.002
45A47GLY 00.0400.0123.1394.4845.4120.056-0.330-0.6540.002
46A48GLY 0-0.019-0.0012.467-7.601-6.1940.658-0.833-1.2320.001
47A49VAL 00.0510.0242.2770.0652.8318.339-2.108-8.9970.011
48A50ALA 00.0010.0162.2644.2235.6021.270-0.710-1.939-0.003
49A51GLY 00.0050.0064.3886.0816.394-0.001-0.031-0.2810.000
50A52ALA 0-0.0060.0013.3873.5954.3970.030-0.182-0.6500.000
51A53LEU 00.0600.0225.2772.8282.8280.0000.0000.0000.000
52A54ASN 00.0450.0116.8633.8013.8010.0000.0000.0000.000
53A55LYS 10.9380.9778.42722.00622.0060.0000.0000.0000.000
54A56ALA 0-0.0140.0027.8801.8011.8010.0000.0000.0000.000
55A57THR 0-0.028-0.0019.8051.1651.1650.0000.0000.0000.000
56A58ASN 0-0.040-0.02412.6690.8820.8820.0000.0000.0000.000
57A59ASN 0-0.0020.00411.274-0.993-0.9930.0000.0000.0000.000
58A60ALA 00.0480.03012.691-0.440-0.4400.0000.0000.0000.000
59A61MET 00.0180.0268.588-1.714-1.7140.0000.0000.0000.000
60A62GLN 0-0.034-0.0097.148-4.108-4.1080.0000.0000.0000.000
61A63VAL 00.0430.03010.0140.0080.0080.0000.0000.0000.000
62A64GLU -1-0.637-0.76813.286-19.652-19.6520.0000.0000.0000.000
63A65SER 0-0.012-0.0139.257-0.847-0.8470.0000.0000.0000.000
64A66ASP -1-0.791-0.87310.889-25.490-25.4900.0000.0000.0000.000
65A67ASP -1-0.799-0.83212.688-15.482-15.4820.0000.0000.0000.000
66A68TYR 00.0330.00412.2290.6920.6920.0000.0000.0000.000
67A69ILE 0-0.035-0.0189.7170.4600.4600.0000.0000.0000.000
68A70ALA 0-0.040-0.01113.6090.7720.7720.0000.0000.0000.000
69A71THR 0-0.032-0.00616.9661.1571.1570.0000.0000.0000.000
70A72ASN 0-0.057-0.02815.5591.3691.3690.0000.0000.0000.000
71A73GLY 00.0250.02414.9440.1520.1520.0000.0000.0000.000
72A74PRO 0-0.040-0.02010.899-1.070-1.0700.0000.0000.0000.000
73A75LEU 00.0140.0168.1831.3561.3560.0000.0000.0000.000
74A76LYS 10.9780.97811.01519.78319.7830.0000.0000.0000.000
75A77VAL 00.0200.0057.868-1.649-1.6490.0000.0000.0000.000
76A78GLY 00.0010.0078.7932.7582.7580.0000.0000.0000.000
77A79GLY 0-0.044-0.01510.3531.9531.9530.0000.0000.0000.000
78A80SER 0-0.033-0.0519.519-2.641-2.6410.0000.0000.0000.000
79A81CYS 0-0.0160.01310.9350.8700.8700.0000.0000.0000.000
80A82VAL 0-0.0030.00311.879-1.635-1.6350.0000.0000.0000.000
81A83LEU 0-0.0100.00210.7730.5130.5130.0000.0000.0000.000
82A84SER 00.0880.04514.2240.4490.4490.0000.0000.0000.000
83A85GLY 0-0.0260.00313.799-1.764-1.7640.0000.0000.0000.000
84A86HIS 0-0.016-0.03213.5890.7010.7010.0000.0000.0000.000
85A87ASN 0-0.017-0.01612.8230.0910.0910.0000.0000.0000.000
86A88LEU 0-0.050-0.0268.3150.4010.4010.0000.0000.0000.000
87A89ALA 00.0260.01012.0840.2520.2520.0000.0000.0000.000
88A90LYS 10.9321.00114.20513.08113.0810.0000.0000.0000.000
89A91HIS 00.0190.00116.075-0.226-0.2260.0000.0000.0000.000
90A92CYS 0-0.032-0.0199.601-0.898-0.8980.0000.0000.0000.000
91A93LEU 0-0.0100.01511.1640.1520.1520.0000.0000.0000.000
92A94HIS 00.0330.0017.225-7.461-7.4610.0000.0000.0000.000
93A95VAL 00.0320.0156.7142.5782.5780.0000.0000.0000.000
94A96VAL 0-0.0420.0084.704-9.543-9.430-0.001-0.011-0.1010.000
95A97GLY 00.0440.0254.3796.3406.451-0.001-0.007-0.1030.000
96A98PRO 00.0250.0135.151-5.089-4.932-0.001-0.008-0.1490.000
97A99ASN 0-0.015-0.0175.8431.4881.4880.0000.0000.0000.000
98A100VAL 00.0570.0296.6552.3422.3420.0000.0000.0000.000
99A101ASN 00.0250.0227.1063.1613.1610.0000.0000.0000.000
100A102LYS 10.8370.9168.77126.53126.5310.0000.0000.0000.000
101A103GLY 00.0330.03110.9600.7540.7540.0000.0000.0000.000
102A104GLU -1-0.833-0.8887.934-33.027-33.0270.0000.0000.0000.000
103A105ASP -1-0.796-0.90011.488-17.574-17.5740.0000.0000.0000.000
104A106ILE 00.0760.03110.530-1.388-1.3880.0000.0000.0000.000
105A107GLN 0-0.0030.01412.057-0.616-0.6160.0000.0000.0000.000
106A108LEU 0-0.014-0.02010.6440.0930.0930.0000.0000.0000.000
107A109LEU 0-0.034-0.0217.614-1.710-1.7100.0000.0000.0000.000
108A110LYS 10.8760.93310.32115.13515.1350.0000.0000.0000.000
109A111SER 00.001-0.00112.7900.5110.5110.0000.0000.0000.000
110A112ALA 0-0.047-0.0248.318-0.095-0.0950.0000.0000.0000.000
111A113TYR 00.0820.0167.545-0.829-0.8290.0000.0000.0000.000
112A114GLU -1-0.812-0.89011.794-14.875-14.8750.0000.0000.0000.000
113A115ASN 0-0.072-0.02311.7371.6061.6060.0000.0000.0000.000
114A116PHE 00.031-0.0108.0130.1740.1740.0000.0000.0000.000
115A117ASN 0-0.039-0.00814.1891.2381.2380.0000.0000.0000.000
116A118GLN 0-0.051-0.01317.3831.1871.1870.0000.0000.0000.000
117A119HIS 0-0.0150.00016.0720.8690.8690.0000.0000.0000.000
118A120GLU -1-0.879-0.93318.176-12.018-12.0180.0000.0000.0000.000
119A121VAL 0-0.004-0.01015.9550.1870.1870.0000.0000.0000.000
120A122LEU 0-0.0300.01212.411-0.644-0.6440.0000.0000.0000.000
121A123LEU 00.0070.0247.7700.5910.5910.0000.0000.0000.000
122A124ALA 00.007-0.0097.784-1.658-1.6580.0000.0000.0000.000
123A125PRO 0-0.0270.0002.5941.2542.6320.323-0.332-1.369-0.001
124A126LEU 00.0310.0143.539-1.971-1.3020.007-0.108-0.5690.000
125A127LEU 0-0.026-0.0092.852-14.057-11.4660.934-1.494-2.031-0.017
126A128SER 00.022-0.0313.3881.7632.5890.787-0.370-1.2430.002
127A129ALA 00.0010.0152.5523.3005.3161.425-0.628-2.813-0.011
128A130GLY 00.043-0.0112.296-2.716-11.39918.829-3.943-6.203-0.013
129A131ILE 0-0.020-0.0202.4995.877-0.3154.9016.720-5.429-0.011
130A132PHE 0-0.039-0.0352.318-16.253-17.06418.110-5.208-12.090-0.045
131A133GLY 00.0340.0183.9690.8400.2290.0150.787-0.1910.000
132A134ALA 0-0.0030.0225.5851.4851.530-0.001-0.006-0.0380.000
133A135ASP -1-0.769-0.8956.900-18.673-18.6730.0000.0000.0000.000
134A136PRO 0-0.017-0.0126.096-0.377-0.3770.0000.0000.0000.000
135A137ILE 00.0210.0087.5710.0510.0510.0000.0000.0000.000
136A138HIS 00.0090.00310.9740.8170.8170.0000.0000.0000.000
137A139SER 0-0.024-0.0376.1770.4830.4830.0000.0000.0000.000
138A140LEU 00.0040.0028.881-0.096-0.0960.0000.0000.0000.000
139A141ARG 10.8450.89510.21013.92813.9280.0000.0000.0000.000
140A142VAL 00.0120.00811.6230.4560.4560.0000.0000.0000.000
141A143CYS 0-0.055-0.00910.1370.5410.5410.0000.0000.0000.000
142A144VAL 00.0110.00212.2810.6270.6270.0000.0000.0000.000
143A145ASP -1-0.806-0.86215.172-13.060-13.0600.0000.0000.0000.000
144A146THR 0-0.088-0.04414.5940.5310.5310.0000.0000.0000.000
145A147VAL 0-0.072-0.04012.7560.1260.1260.0000.0000.0000.000
146A148ARG 10.9590.97616.07814.11314.1130.0000.0000.0000.000
147A149THR 0-0.0360.00417.3030.5080.5080.0000.0000.0000.000
148A150ASN 0-0.032-0.00717.5050.0250.0250.0000.0000.0000.000
149A151VAL 00.0250.00711.330-0.632-0.6320.0000.0000.0000.000
150A152TYR 0-0.017-0.00511.6040.6460.6460.0000.0000.0000.000
151A153LEU 00.015-0.0117.613-0.868-0.8680.0000.0000.0000.000
152A154ALA 0-0.0030.0004.7580.7410.831-0.001-0.007-0.0810.000
153A155VAL 0-0.0010.0014.4041.0281.3870.000-0.016-0.3420.000
154A156PHE 0-0.015-0.0052.466-6.913-2.2293.503-1.916-6.271-0.001
155A157ASP -1-0.806-0.9034.678-19.604-19.2250.001-0.056-0.3250.000
156A158LYS 10.8800.9267.60013.78213.7820.0000.0000.0000.000
157A159ASN 0-0.032-0.02410.7341.4561.4560.0000.0000.0000.000
158A160LEU 0-0.035-0.0186.3070.4540.4540.0000.0000.0000.000
159A161TYR 00.0190.0079.6000.5670.5670.0000.0000.0000.000
160A162ASP -1-0.789-0.88911.047-12.825-12.8250.0000.0000.0000.000
161A163LYS 10.9140.96511.64716.96916.9690.0000.0000.0000.000
162A164LEU 0-0.055-0.0277.9760.1390.1390.0000.0000.0000.000
163A165VAL 0-0.014-0.00912.6840.2810.2810.0000.0000.0000.000
164A166SER 0-0.095-0.04715.4140.6580.6580.0000.0000.0000.000
165A167SER -1-0.965-0.96216.037-12.020-12.0200.0000.0000.0000.000
166A322HOH 0-0.059-0.04718.866-0.058-0.0580.0000.0000.0000.000
167A325HOH 0-0.039-0.03317.3510.3550.3550.0000.0000.0000.000
168A329HOH 0-0.018-0.01812.290-0.028-0.0280.0000.0000.0000.000
169A331HOH 00.017-0.0072.0981.8903.6823.301-2.119-2.975-0.005
170A335HOH 0-0.025-0.0272.704-1.571-0.3530.185-0.671-0.732-0.005
171A336HOH 0-0.037-0.0295.453-2.343-2.3430.0000.0000.0000.000
172A343HOH 0-0.043-0.03312.0920.5990.5990.0000.0000.0000.000
173A345HOH 0-0.027-0.0266.2240.4140.4140.0000.0000.0000.000
174A346HOH 0-0.011-0.02415.824-0.211-0.2110.0000.0000.0000.000
175A347HOH 0-0.009-0.02911.837-1.094-1.0940.0000.0000.0000.000
176A348HOH 0-0.044-0.0399.4410.3770.3770.0000.0000.0000.000
177A349HOH 00.0380.02315.4010.0390.0390.0000.0000.0000.000
178A354HOH 0-0.025-0.01217.9220.0700.0700.0000.0000.0000.000
179A357HOH 0-0.019-0.0182.754-7.872-6.1120.426-0.831-1.3560.008
180A359HOH 0-0.017-0.02017.9470.2990.2990.0000.0000.0000.000
181A361HOH 0-0.059-0.04317.3440.2740.2740.0000.0000.0000.000
182A363HOH 00.001-0.01113.0830.1000.1000.0000.0000.0000.000
183A367HOH 0-0.013-0.01615.6370.4660.4660.0000.0000.0000.000
184A368HOH 0-0.050-0.03214.7640.3310.3310.0000.0000.0000.000
185A370HOH 00.0270.0221.935-18.703-20.93314.564-6.470-5.865-0.058
186A371HOH 0-0.017-0.02210.395-0.072-0.0720.0000.0000.0000.000
187A373HOH 0-0.048-0.03815.5690.1290.1290.0000.0000.0000.000
188A378HOH 0-0.019-0.02414.1950.4820.4820.0000.0000.0000.000
189A383HOH 0-0.001-0.00320.4450.2720.2720.0000.0000.0000.000
190A390HOH 0-0.016-0.0312.759-11.940-9.9501.469-1.545-1.915-0.020
191A397HOH 00.004-0.00618.8990.0760.0760.0000.0000.0000.000
192A404HOH 00.0250.01312.694-0.205-0.2050.0000.0000.0000.000
193A406HOH 0-0.003-0.00713.709-0.255-0.2550.0000.0000.0000.000
194A417HOH 00.007-0.0125.164-2.445-2.4450.0000.0000.0000.000
195A421HOH 0-0.030-0.0229.3940.1050.1050.0000.0000.0000.000
196A430HOH 0-0.006-0.00911.9400.5980.5980.0000.0000.0000.000
197A444HOH 00.0060.00515.807-0.112-0.1120.0000.0000.0000.000
198A449HOH 0-0.050-0.03417.5820.1590.1590.0000.0000.0000.000
199A455HOH 0-0.044-0.03616.9800.0700.0700.0000.0000.0000.000
200A470HOH 0-0.034-0.02218.0850.2970.2970.0000.0000.0000.000
201A478HOH 0-0.044-0.03018.9780.0810.0810.0000.0000.0000.000