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: 9GGG2

Calculation Name: 5RSK-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-[(3-methoxy-1,2-oxazol-5-yl)methyl]-3h-purin-6-amine

ligand 3-letter code: W57

PDB ID: 5RSK

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

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 205
LigandCharge W57=1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1806539.543363
FMO2-HF: Nuclear repulsion 1740338.282352
FMO2-HF: Total energy -66201.261011
FMO2-MP2: Total energy -66395.417937


3D Structure
Snapshot
 
Ligand structure

W57

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.
-119.455-93.63457.529-29.766-53.5860.161


Interactive mode: IFIE and PIEDA for fragment #205(A:201:W57 )


Summations of interaction energy for fragment #205(A:201:W57 )
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.
-119.455-93.63457.529-29.766-53.586-0.161
Interaction energy analysis for fragmet #205(A:201:W57 )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.928
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 00.016-0.00421.235-0.029-0.0290.0000.0000.0000.000
2A4ASN 0-0.015-0.01616.031-0.431-0.4310.0000.0000.0000.000
3A5SER 00.014-0.01315.9390.3040.3040.0000.0000.0000.000
4A6PHE 0-0.0340.0169.833-0.547-0.5470.0000.0000.0000.000
5A7SER 00.0280.00912.7060.8860.8860.0000.0000.0000.000
6A8GLY 00.0240.00612.313-1.286-1.2860.0000.0000.0000.000
7A9TYR 0-0.055-0.0247.836-1.331-1.3310.0000.0000.0000.000
8A10LEU 00.0010.00712.2511.3881.3880.0000.0000.0000.000
9A11LYS 10.8140.90013.46513.21613.2160.0000.0000.0000.000
10A12LEU 0-0.052-0.01612.1870.3000.3000.0000.0000.0000.000
11A13THR 00.0360.00816.2710.6270.6270.0000.0000.0000.000
12A14ASP -1-0.860-0.89318.376-12.883-12.8830.0000.0000.0000.000
13A15ASN 0-0.002-0.00516.8510.3700.3700.0000.0000.0000.000
14A16VAL 00.0050.01512.143-1.075-1.0750.0000.0000.0000.000
15A17TYR 00.0450.03012.0241.2231.2230.0000.0000.0000.000
16A18ILE 0-0.001-0.0047.970-2.331-2.3310.0000.0000.0000.000
17A19LYS 10.8350.9047.40825.88425.8840.0000.0000.0000.000
18A20ASN 00.0100.0056.144-5.215-5.2150.0000.0000.0000.000
19A21ALA 0-0.011-0.0184.9813.0493.0490.0000.0000.0000.000
20A22ASP -1-0.777-0.8821.840-86.996-83.1799.462-6.443-6.836-0.073
21A23ILE 0-0.005-0.0271.938-2.659-7.03415.080-4.599-6.1060.010
22A24VAL 00.0170.0103.2465.0415.7550.059-0.084-0.6890.002
23A25GLU -1-0.824-0.9005.267-22.789-22.771-0.001-0.003-0.0140.000
24A26GLU -1-0.776-0.8576.472-21.571-21.5710.0000.0000.0000.000
25A27ALA 0-0.022-0.0177.7982.6872.6870.0000.0000.0000.000
26A28LYS 10.8280.9028.46127.22127.2210.0000.0000.0000.000
27A29LYS 10.9090.97911.25719.17319.1730.0000.0000.0000.000
28A30VAL 0-0.068-0.05511.2881.7091.7090.0000.0000.0000.000
29A31LYS 10.8720.96713.00518.80918.8090.0000.0000.0000.000
30A32PRO 0-0.0020.01510.5641.0471.0470.0000.0000.0000.000
31A33THR 00.039-0.00213.8800.0650.0650.0000.0000.0000.000
32A34VAL 0-0.024-0.01512.8900.2940.2940.0000.0000.0000.000
33A35VAL 00.0130.0117.904-0.801-0.8010.0000.0000.0000.000
34A36VAL 00.0150.0078.5961.1681.1680.0000.0000.0000.000
35A37ASN 00.000-0.0257.842-7.642-7.6420.0000.0000.0000.000
36A38ALA 0-0.0160.0085.1942.0912.0910.0000.0000.0000.000
37A39ALA 00.0410.0407.222-0.881-0.8810.0000.0000.0000.000
38A40ASN 0-0.015-0.02810.4421.4781.4780.0000.0000.0000.000
39A41VAL 00.0500.02212.5410.2370.2370.0000.0000.0000.000
40A42TYR 00.0120.00815.9020.6530.6530.0000.0000.0000.000
41A43LEU 0-0.0030.01014.3250.1750.1750.0000.0000.0000.000
42A44LYS 10.9761.00614.39817.48117.4810.0000.0000.0000.000
43A45HIS 00.0380.01910.247-3.727-3.7270.0000.0000.0000.000
44A46GLY 00.0340.03010.587-0.027-0.0270.0000.0000.0000.000
45A47GLY 00.0410.0117.2960.7290.7290.0000.0000.0000.000
46A48GLY 0-0.0160.0022.869-0.781-0.5450.137-0.218-0.1550.000
47A49VAL 00.0140.0082.705-4.025-1.2174.448-1.470-5.786-0.001
48A50ALA 00.0310.0303.9633.9564.3300.0400.072-0.4860.001
49A51GLY 0-0.0020.0086.8433.2313.2310.0000.0000.0000.000
50A52ALA 0-0.004-0.0012.7672.2143.0660.308-0.307-0.8530.001
51A53LEU 00.0270.0004.6833.3873.584-0.001-0.009-0.1880.000
52A54ASN 00.0520.0067.0853.8153.8150.0000.0000.0000.000
53A55LYS 10.9610.9887.75226.98926.9890.0000.0000.0000.000
54A56ALA 0-0.042-0.0077.8392.1632.1630.0000.0000.0000.000
55A57THR 0-0.047-0.0149.8351.9311.9310.0000.0000.0000.000
56A58ASN 0-0.035-0.02312.5851.2191.2190.0000.0000.0000.000
57A59ASN 0-0.002-0.00113.2210.2020.2020.0000.0000.0000.000
58A60ALA 00.0360.02814.7380.5400.5400.0000.0000.0000.000
59A61MET 00.0100.01610.696-0.349-0.3490.0000.0000.0000.000
60A62GLN 0-0.041-0.02814.257-1.232-1.2320.0000.0000.0000.000
61A63VAL 00.0190.01815.7030.5910.5910.0000.0000.0000.000
62A64GLU -1-0.721-0.83617.591-16.377-16.3770.0000.0000.0000.000
63A65SER 0-0.007-0.01116.160-0.012-0.0120.0000.0000.0000.000
64A66ASP -1-0.852-0.91718.492-15.656-15.6560.0000.0000.0000.000
65A67ASP -1-0.883-0.90920.867-11.950-11.9500.0000.0000.0000.000
66A68TYR 00.0430.00820.5720.3740.3740.0000.0000.0000.000
67A69ILE 0-0.043-0.02718.8650.3850.3850.0000.0000.0000.000
68A70ALA 0-0.028-0.00222.6880.4460.4460.0000.0000.0000.000
69A71THR 0-0.047-0.01225.9860.6510.6510.0000.0000.0000.000
70A72ASN 0-0.089-0.05623.9350.7090.7090.0000.0000.0000.000
71A73GLY 0-0.0140.01124.4320.1550.1550.0000.0000.0000.000
72A74PRO 0-0.071-0.04720.257-0.513-0.5130.0000.0000.0000.000
73A75LEU 0-0.016-0.00715.7020.3620.3620.0000.0000.0000.000
74A76LYS 10.9750.98119.29113.05813.0580.0000.0000.0000.000
75A77VAL 00.0220.00314.679-0.810-0.8100.0000.0000.0000.000
76A78GLY 00.0130.01515.1650.9230.9230.0000.0000.0000.000
77A79GLY 0-0.0180.00116.2900.3750.3750.0000.0000.0000.000
78A80SER 0-0.021-0.04315.259-1.255-1.2550.0000.0000.0000.000
79A81CYS 0-0.0290.01116.2900.8210.8210.0000.0000.0000.000
80A82VAL 00.0060.00916.661-1.315-1.3150.0000.0000.0000.000
81A83LEU 00.0080.01217.0770.8630.8630.0000.0000.0000.000
82A84SER 00.0380.01617.778-0.493-0.4930.0000.0000.0000.000
83A85GLY 0-0.0160.00414.273-1.198-1.1980.0000.0000.0000.000
84A86HIS 0-0.036-0.03713.916-0.683-0.6830.0000.0000.0000.000
85A87ASN 0-0.006-0.01612.9300.1050.1050.0000.0000.0000.000
86A88LEU 0-0.033-0.0288.603-0.155-0.1550.0000.0000.0000.000
87A89ALA 0-0.015-0.00812.341-0.590-0.5900.0000.0000.0000.000
88A90LYS 10.8610.95214.50214.30114.3010.0000.0000.0000.000
89A91HIS 00.0340.01616.2231.1621.1620.0000.0000.0000.000
90A92CYS 0-0.014-0.00512.351-2.065-2.0650.0000.0000.0000.000
91A93LEU 0-0.0310.00413.0771.2381.2380.0000.0000.0000.000
92A94HIS 00.0440.00212.089-3.965-3.9650.0000.0000.0000.000
93A95VAL 00.0180.00110.6802.0342.0340.0000.0000.0000.000
94A96VAL 0-0.0340.00710.515-2.644-2.6440.0000.0000.0000.000
95A97GLY 00.0390.02310.3731.5721.5720.0000.0000.0000.000
96A98PRO 00.0040.01511.315-0.395-0.3950.0000.0000.0000.000
97A99ASN 0-0.022-0.0029.944-1.401-1.4010.0000.0000.0000.000
98A100VAL 00.0790.03011.4301.7301.7300.0000.0000.0000.000
99A101ASN 0-0.069-0.0389.0842.7392.7390.0000.0000.0000.000
100A102LYS 10.8170.90912.94721.17421.1740.0000.0000.0000.000
101A103GLY 00.0040.01215.8560.9400.9400.0000.0000.0000.000
102A104GLU -1-0.792-0.84414.430-19.177-19.1770.0000.0000.0000.000
103A105ASP -1-0.806-0.90716.533-15.179-15.1790.0000.0000.0000.000
104A106ILE 00.0420.00712.962-0.785-0.7850.0000.0000.0000.000
105A107GLN 00.0170.00815.871-0.832-0.8320.0000.0000.0000.000
106A108LEU 0-0.052-0.03216.406-0.045-0.0450.0000.0000.0000.000
107A109LEU 0-0.027-0.01710.167-0.703-0.7030.0000.0000.0000.000
108A110LYS 10.8960.94013.97514.28314.2830.0000.0000.0000.000
109A111SER 00.0250.00816.4840.0020.0020.0000.0000.0000.000
110A112ALA 00.0100.00312.484-0.027-0.0270.0000.0000.0000.000
111A113TYR 00.033-0.0028.833-1.202-1.2020.0000.0000.0000.000
112A114GLU -1-0.802-0.85413.919-13.975-13.9750.0000.0000.0000.000
113A115ASN 0-0.054-0.01715.0441.3061.3060.0000.0000.0000.000
114A116PHE 00.031-0.0119.322-0.069-0.0690.0000.0000.0000.000
115A117ASN 0-0.018-0.00115.4990.4620.4620.0000.0000.0000.000
116A118GLN 0-0.0340.00918.8121.0751.0750.0000.0000.0000.000
117A119HIS 0-0.043-0.02816.4410.2380.2380.0000.0000.0000.000
118A120GLU -1-0.868-0.93017.746-13.240-13.2400.0000.0000.0000.000
119A121VAL 00.012-0.00714.117-0.143-0.1430.0000.0000.0000.000
120A122LEU 0-0.0460.01911.568-0.116-0.1160.0000.0000.0000.000
121A123LEU 0-0.0110.0185.9460.0340.0340.0000.0000.0000.000
122A124ALA 00.019-0.0086.8830.2200.2200.0000.0000.0000.000
123A125PRO 0-0.0290.0032.858-5.237-3.7530.294-0.423-1.355-0.001
124A126LEU 00.0180.0083.5736.6867.4780.002-0.142-0.6520.000
125A127LEU 00.0000.0084.528-5.537-5.372-0.001-0.011-0.1540.000
126A128SER 00.011-0.0236.9282.0602.0600.0000.0000.0000.000
127A129ALA 00.0130.0374.6091.8642.2350.000-0.025-0.3460.000
128A130GLY 00.013-0.0062.368-6.687-6.2462.609-1.494-1.5560.003
129A131ILE 0-0.027-0.0282.8888.7907.1640.1562.103-0.634-0.001
130A132PHE 0-0.070-0.0175.7954.3614.3610.0000.0000.0000.000
131A133GLY 00.0290.0177.1543.2483.2480.0000.0000.0000.000
132A134ALA 00.0120.0188.5362.2352.2350.0000.0000.0000.000
133A135ASP -1-0.821-0.9147.354-24.780-24.7800.0000.0000.0000.000
134A136PRO 0-0.014-0.0265.2390.1610.1610.0000.0000.0000.000
135A137ILE 00.0240.0107.7000.1430.1430.0000.0000.0000.000
136A138HIS 00.0460.03110.8000.9500.9500.0000.0000.0000.000
137A139SER 0-0.006-0.0248.1170.8210.8210.0000.0000.0000.000
138A140LEU 0-0.009-0.0039.6330.0620.0620.0000.0000.0000.000
139A141ARG 10.8440.91511.21816.56716.5670.0000.0000.0000.000
140A142VAL 00.0090.01213.2860.8090.8090.0000.0000.0000.000
141A143CYS 0-0.0430.00011.1140.7090.7090.0000.0000.0000.000
142A144VAL 00.0190.01613.2320.8490.8490.0000.0000.0000.000
143A145ASP -1-0.803-0.88915.678-14.270-14.2700.0000.0000.0000.000
144A146THR 0-0.111-0.06216.0221.1451.1450.0000.0000.0000.000
145A147VAL 0-0.076-0.03013.3110.5060.5060.0000.0000.0000.000
146A148ARG 10.9520.98516.69913.96413.9640.0000.0000.0000.000
147A149THR 0-0.0330.00617.2020.3730.3730.0000.0000.0000.000
148A150ASN 0-0.0180.00115.948-0.506-0.5060.0000.0000.0000.000
149A151VAL 00.0160.00310.041-0.606-0.6060.0000.0000.0000.000
150A152TYR 00.0260.0269.5150.9250.9250.0000.0000.0000.000
151A153LEU 00.019-0.0066.500-2.668-2.6680.0000.0000.0000.000
152A154ALA 00.0110.0122.8351.8902.6660.119-0.303-0.5920.000
153A155VAL 0-0.024-0.0162.430-28.380-23.1632.243-3.227-4.232-0.031
154A156PHE 0-0.031-0.0132.661-3.8723.1534.920-2.919-9.0250.005
155A157ASP -1-0.855-0.9292.524-38.054-34.9554.795-2.895-4.999-0.003
156A158LYS 10.9220.9454.20621.05621.3310.006-0.061-0.2200.000
157A159ASN 00.0170.0156.3902.5432.5430.0000.0000.0000.000
158A160LEU 0-0.033-0.0262.416-0.4100.3661.599-0.623-1.7520.002
159A161TYR 00.0220.0166.0491.1511.1510.0000.0000.0000.000
160A162ASP -1-0.811-0.9047.351-19.035-19.0350.0000.0000.0000.000
161A163LYS 10.9561.0038.56422.28622.2860.0000.0000.0000.000
162A164LEU 0-0.041-0.0035.9780.6260.6260.0000.0000.0000.000
163A165VAL 00.0010.00210.2230.7440.7440.0000.0000.0000.000
164A166SER 0-0.054-0.03712.9070.9340.9340.0000.0000.0000.000
165A167SER 0-0.065-0.05112.8370.6420.6420.0000.0000.0000.000
166A168PHE 0-0.010-0.00414.0220.0100.0100.0000.0000.0000.000
167A169LEU -1-0.835-0.88015.722-13.531-13.5310.0000.0000.0000.000
168A316HOH 00.0000.0004.881-1.079-1.0510.000-0.002-0.0260.000
169A319HOH 0-0.014-0.02621.548-0.086-0.0860.0000.0000.0000.000
170A327HOH 0-0.051-0.03712.5090.3720.3720.0000.0000.0000.000
171A328HOH 0-0.013-0.0089.784-0.136-0.1360.0000.0000.0000.000
172A333HOH 0-0.079-0.06521.984-0.089-0.0890.0000.0000.0000.000
173A337HOH 00.008-0.00612.244-0.519-0.5190.0000.0000.0000.000
174A347HOH 0-0.022-0.02423.2190.0050.0050.0000.0000.0000.000
175A351HOH 0-0.077-0.06419.5270.2080.2080.0000.0000.0000.000
176A357HOH 0-0.035-0.03319.5440.1620.1620.0000.0000.0000.000
177A361HOH 0-0.006-0.0098.886-1.064-1.0640.0000.0000.0000.000
178A362HOH 00.0170.0031.848-16.954-18.4488.769-3.820-3.455-0.040
179A363HOH 0-0.013-0.03515.377-0.548-0.5480.0000.0000.0000.000
180A364HOH 00.010-0.00319.9860.1840.1840.0000.0000.0000.000
181A365HOH 00.0150.00218.3290.0640.0640.0000.0000.0000.000
182A370HOH 0-0.026-0.01517.866-0.129-0.1290.0000.0000.0000.000
183A374HOH 0-0.067-0.06312.203-0.064-0.0640.0000.0000.0000.000
184A375HOH 0-0.005-0.0122.900-3.230-2.1710.205-0.623-0.641-0.005
185A378HOH 0-0.020-0.02812.9480.3120.3120.0000.0000.0000.000
186A384HOH 00.0300.0066.808-1.911-1.9110.0000.0000.0000.000
187A391HOH 0-0.064-0.0488.6610.2370.2370.0000.0000.0000.000
188A395HOH 0-0.008-0.0163.305-6.964-6.1830.037-0.396-0.422-0.003
189A396HOH 0-0.007-0.01516.4630.3750.3750.0000.0000.0000.000
190A401HOH 00.0320.0145.819-3.425-3.4250.0000.0000.0000.000
191A404HOH 00.001-0.00510.796-0.634-0.6340.0000.0000.0000.000
192A407HOH 0-0.026-0.04121.951-0.158-0.1580.0000.0000.0000.000
193A415HOH 0-0.018-0.0023.991-4.194-4.0260.001-0.055-0.1150.000
194A417HOH 0-0.054-0.04518.7800.2870.2870.0000.0000.0000.000
195A419HOH 0-0.015-0.01513.1890.2200.2200.0000.0000.0000.000
196A421HOH 0-0.008-0.0118.9670.9260.9260.0000.0000.0000.000
197A422HOH 00.012-0.01111.458-0.498-0.4980.0000.0000.0000.000
198A423HOH 0-0.003-0.00821.499-0.221-0.2210.0000.0000.0000.000
199A424HOH 0-0.009-0.01321.325-0.129-0.1290.0000.0000.0000.000
200A427HOH 00.004-0.00219.277-0.225-0.2250.0000.0000.0000.000
201A433HOH 0-0.039-0.04113.7660.0300.0300.0000.0000.0000.000
202A434HOH 00.0260.01119.510-0.082-0.0820.0000.0000.0000.000
203A475HOH 00.015-0.0122.412-11.705-9.8622.243-1.789-2.297-0.027
204A499HOH 0-0.032-0.02710.738-0.032-0.0320.0000.0000.0000.000