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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

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FMODB ID: K3333

Calculation Name: 5RS7-A-Xray89

Preferred Name:

Target Type:

Ligand Name: 1-{2-[(propan-2-yl)oxy]ethyl}-2-sulfanylidene-1,2,3,5-tetrahydro-4h-pyrrolo[3,2-d]pyrimidin-4-one

ligand 3-letter code: W4Y

PDB ID: 5RS7

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 212
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1827301.948544
FMO2-HF: Nuclear repulsion 1760293.923371
FMO2-HF: Total energy -67008.025173
FMO2-MP2: Total energy -67203.320529


3D Structure
Snapshot
 
Ligand structure

W4Y

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.
-69.371-50.31064.172-24.865-58.3720.079


Interactive mode: IFIE and PIEDA for fragment #212(A:201:W4Y )


Summations of interaction energy for fragment #212(A:201:W4Y )
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.
-69.371-50.3164.172-24.865-58.372-0.079
Interaction energy analysis for fragmet #212(A:201:W4Y )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.081 / q_NPA : 0.002
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 00.008-0.00821.8170.0070.0070.0000.0000.0000.000
2A4ASN 0-0.011-0.01316.7300.0210.0210.0000.0000.0000.000
3A5SER 00.0240.00116.793-0.033-0.0330.0000.0000.0000.000
4A6PHE 0-0.0440.00610.7070.0440.0440.0000.0000.0000.000
5A7SER 00.0240.00713.649-0.068-0.0680.0000.0000.0000.000
6A8GLY 00.011-0.01013.1380.1700.1700.0000.0000.0000.000
7A9TYR 0-0.035-0.0268.2800.1800.1800.0000.0000.0000.000
8A10LEU 0-0.0120.00012.381-0.212-0.2120.0000.0000.0000.000
9A11LYS 10.8160.90413.360-0.671-0.6710.0000.0000.0000.000
10A12LEU 0-0.053-0.01710.913-0.035-0.0350.0000.0000.0000.000
11A13THR 00.0300.00615.354-0.095-0.0950.0000.0000.0000.000
12A14ASP -1-0.860-0.90217.6900.6730.6730.0000.0000.0000.000
13A15ASN 0-0.006-0.00616.182-0.026-0.0260.0000.0000.0000.000
14A16VAL 00.0050.01511.2100.1290.1290.0000.0000.0000.000
15A17TYR 00.0320.01612.068-0.161-0.1610.0000.0000.0000.000
16A18ILE 00.0040.0027.1040.4230.4230.0000.0000.0000.000
17A19LYS 10.8380.9127.556-2.391-2.3910.0000.0000.0000.000
18A20ASN 0-0.0050.0066.5680.8750.8750.0000.0000.0000.000
19A21ALA 0-0.015-0.0205.868-0.850-0.8500.0000.0000.0000.000
20A22ASP -1-0.839-0.9062.913-1.8390.5930.327-1.162-1.5970.000
21A23ILE 00.0390.0051.815-8.183-11.12811.779-3.994-4.8400.028
22A24VAL 0-0.016-0.0133.674-2.895-2.5650.0500.007-0.3870.002
23A25GLU -1-0.820-0.9026.386-0.238-0.2380.0000.0000.0000.000
24A26GLU -1-0.751-0.8476.7251.4741.4740.0000.0000.0000.000
25A27ALA 0-0.015-0.0157.767-0.393-0.3930.0000.0000.0000.000
26A28LYS 10.8220.9019.730-0.219-0.2190.0000.0000.0000.000
27A29LYS 10.8190.92211.303-1.483-1.4830.0000.0000.0000.000
28A30VAL 0-0.045-0.03411.894-0.095-0.0950.0000.0000.0000.000
29A31LYS 10.8830.96613.243-0.537-0.5370.0000.0000.0000.000
30A32PRO 0-0.0030.01411.171-0.058-0.0580.0000.0000.0000.000
31A33THR 00.033-0.00414.498-0.093-0.0930.0000.0000.0000.000
32A34VAL 0-0.013-0.01113.001-0.096-0.0960.0000.0000.0000.000
33A35VAL 00.0070.0098.3580.2130.2130.0000.0000.0000.000
34A36VAL 00.0110.0036.799-0.275-0.2750.0000.0000.0000.000
35A37ASN 0-0.004-0.0236.2840.3290.3290.0000.0000.0000.000
36A38ALA 00.0100.0222.474-0.512-0.3231.850-0.593-1.4460.000
37A39ALA 00.0440.0494.456-0.569-0.3890.000-0.031-0.1490.000
38A40ASN 0-0.016-0.0206.813-0.118-0.1180.0000.0000.0000.000
39A41VAL 00.0480.0198.8510.1010.1010.0000.0000.0000.000
40A42TYR 00.0030.00312.1270.0570.0570.0000.0000.0000.000
41A43LEU 0-0.0010.01111.1510.0240.0240.0000.0000.0000.000
42A44LYS 10.9781.00111.1930.6500.6500.0000.0000.0000.000
43A45HIS 00.0220.0118.506-0.211-0.2110.0000.0000.0000.000
44A46GLY 00.0340.0288.460-0.045-0.0450.0000.0000.0000.000
45A47GLY 00.0640.0176.289-0.189-0.1890.0000.0000.0000.000
46A48GLY 00.0060.0092.311-0.1070.5751.776-1.141-1.3170.004
47A49VAL 00.0420.0272.022-8.213-4.3604.946-1.462-7.3360.014
48A50ALA 00.0330.0263.901-1.461-0.9190.023-0.054-0.5120.001
49A51GLY 0-0.038-0.0096.0530.0430.0430.0000.0000.0000.000
50A52ALA 00.0290.0243.9940.0930.2420.000-0.028-0.1220.000
51A53LEU 00.0570.0265.9700.5790.5790.0000.0000.0000.000
52A54ASN 00.0640.0137.9860.3120.3120.0000.0000.0000.000
53A55LYS 10.9640.9949.0191.7851.7850.0000.0000.0000.000
54A56ALA 0-0.038-0.0158.9990.1880.1880.0000.0000.0000.000
55A57THR 0-0.054-0.01210.9290.2040.2040.0000.0000.0000.000
56A58ASN 0-0.038-0.02513.7660.0290.0290.0000.0000.0000.000
57A59ASN 0-0.0030.00014.357-0.037-0.0370.0000.0000.0000.000
58A60ALA 00.0370.02915.6610.0260.0260.0000.0000.0000.000
59A61MET 00.0030.00911.122-0.020-0.0200.0000.0000.0000.000
60A62GLN 0-0.054-0.02813.023-0.077-0.0770.0000.0000.0000.000
61A63VAL 00.0230.02215.1950.0240.0240.0000.0000.0000.000
62A64GLU -1-0.719-0.83617.036-0.005-0.0050.0000.0000.0000.000
63A65SER 00.000-0.01014.2460.0270.0270.0000.0000.0000.000
64A66ASP -1-0.811-0.89216.456-0.419-0.4190.0000.0000.0000.000
65A67ASP -1-0.828-0.86618.753-0.112-0.1120.0000.0000.0000.000
66A68TYR 00.012-0.01217.4290.0280.0280.0000.0000.0000.000
67A69ILE 0-0.040-0.02415.5610.0100.0100.0000.0000.0000.000
68A70ALA 0-0.029-0.00419.4810.0070.0070.0000.0000.0000.000
69A71THR 0-0.039-0.00522.9230.0140.0140.0000.0000.0000.000
70A72ASN 0-0.080-0.04620.7520.0300.0300.0000.0000.0000.000
71A73GLY 00.0240.02520.9820.0040.0040.0000.0000.0000.000
72A74PRO 0-0.046-0.02516.6070.0030.0030.0000.0000.0000.000
73A75LEU 0-0.0080.00212.2320.0340.0340.0000.0000.0000.000
74A76LYS 10.9710.98015.3900.0640.0640.0000.0000.0000.000
75A77VAL 00.0260.00310.4910.0050.0050.0000.0000.0000.000
76A78GLY 00.0210.02211.0050.0580.0580.0000.0000.0000.000
77A79GLY 0-0.028-0.00712.3750.1150.1150.0000.0000.0000.000
78A80SER 0-0.014-0.04111.788-0.016-0.0160.0000.0000.0000.000
79A81CYS 0-0.0310.00913.495-0.021-0.0210.0000.0000.0000.000
80A82VAL 00.0100.01114.3550.0430.0430.0000.0000.0000.000
81A83LEU 00.0040.01014.862-0.048-0.0480.0000.0000.0000.000
82A84SER 00.0340.01417.1070.1060.1060.0000.0000.0000.000
83A85GLY 0-0.0150.00714.839-0.015-0.0150.0000.0000.0000.000
84A86HIS 0-0.033-0.03614.721-0.008-0.0080.0000.0000.0000.000
85A87ASN 0-0.015-0.01913.9980.0550.0550.0000.0000.0000.000
86A88LEU 0-0.022-0.0249.5370.0510.0510.0000.0000.0000.000
87A89ALA 0-0.013-0.00512.6310.1830.1830.0000.0000.0000.000
88A90LYS 10.8580.95014.609-0.401-0.4010.0000.0000.0000.000
89A91HIS 00.0260.01016.583-0.084-0.0840.0000.0000.0000.000
90A92CYS 0-0.011-0.00211.5730.1520.1520.0000.0000.0000.000
91A93LEU 0-0.0330.00311.956-0.115-0.1150.0000.0000.0000.000
92A94HIS 00.0530.0069.7580.0690.0690.0000.0000.0000.000
93A95VAL 00.009-0.0028.139-0.042-0.0420.0000.0000.0000.000
94A96VAL 0-0.0310.0157.152-0.220-0.2200.0000.0000.0000.000
95A97GLY 00.0480.0276.2200.2290.2290.0000.0000.0000.000
96A98PRO 0-0.0070.0067.168-0.247-0.2470.0000.0000.0000.000
97A99ASN 0-0.035-0.0207.134-0.405-0.4050.0000.0000.0000.000
98A100VAL 00.0600.0238.2090.2650.2650.0000.0000.0000.000
99A101ASN 0-0.057-0.0287.7620.3700.3700.0000.0000.0000.000
100A102LYS 10.8150.9079.1141.1531.1530.0000.0000.0000.000
101A103GLY 0-0.0030.00712.4860.0960.0960.0000.0000.0000.000
102A104GLU -1-0.795-0.84910.390-0.858-0.8580.0000.0000.0000.000
103A105ASP -1-0.813-0.91013.068-0.269-0.2690.0000.0000.0000.000
104A106ILE 00.0490.0119.952-0.031-0.0310.0000.0000.0000.000
105A107GLN 00.0020.00012.5580.0990.0990.0000.0000.0000.000
106A108LEU 0-0.044-0.02612.4220.0670.0670.0000.0000.0000.000
107A109LEU 0-0.032-0.0207.2800.0050.0050.0000.0000.0000.000
108A110LYS 10.8930.93910.885-0.244-0.2440.0000.0000.0000.000
109A111SER 00.014-0.00113.7110.0580.0580.0000.0000.0000.000
110A112ALA 00.0130.0079.1620.0330.0330.0000.0000.0000.000
111A113TYR 00.021-0.0077.1260.3520.3520.0000.0000.0000.000
112A114GLU -1-0.797-0.85311.7940.3360.3360.0000.0000.0000.000
113A115ASN 0-0.059-0.01912.536-0.014-0.0140.0000.0000.0000.000
114A116PHE 00.031-0.0087.9740.0070.0070.0000.0000.0000.000
115A117ASN 00.0040.01514.1420.0640.0640.0000.0000.0000.000
116A118GLN 0-0.0220.01917.291-0.051-0.0510.0000.0000.0000.000
117A119HIS 0-0.018-0.00616.003-0.003-0.0030.0000.0000.0000.000
118A120GLU -1-0.902-0.95017.6300.5460.5460.0000.0000.0000.000
119A121VAL 0-0.004-0.01314.4680.0610.0610.0000.0000.0000.000
120A122LEU 0-0.0320.02211.631-0.088-0.0880.0000.0000.0000.000
121A123LEU 0-0.0170.0156.8690.1060.1060.0000.0000.0000.000
122A124ALA 00.022-0.0016.761-0.381-0.3810.0000.0000.0000.000
123A125PRO 0-0.048-0.0172.752-2.015-0.6214.434-1.974-3.8540.006
124A126LEU 00.0570.0102.251-2.139-8.88412.0010.180-5.4360.004
125A127LEU 0-0.017-0.0022.717-4.904-2.8651.010-1.017-2.032-0.014
126A128SER 00.029-0.0223.394-0.0050.4490.026-0.099-0.3800.000
127A129ALA 00.0080.0262.890-0.7640.4650.165-0.338-1.057-0.001
128A130GLY 00.0490.0162.526-6.910-3.9981.929-1.947-2.895-0.022
129A131ILE 00.002-0.0232.366-0.2840.5031.2700.007-2.064-0.001
130A132PHE 0-0.064-0.0092.326-1.3900.1021.934-0.808-2.618-0.007
131A133GLY 00.0380.0215.0900.6950.736-0.001-0.003-0.0370.000
132A134ALA 0-0.0030.0106.6870.4600.4600.0000.0000.0000.000
133A135ASP -1-0.781-0.8937.187-0.096-0.0960.0000.0000.0000.000
134A136PRO 0-0.014-0.0245.3940.1510.1510.0000.0000.0000.000
135A137ILE 00.0220.0097.1300.5810.5810.0000.0000.0000.000
136A138HIS 00.0430.02410.4000.1860.1860.0000.0000.0000.000
137A139SER 0-0.010-0.0265.7820.4250.4250.0000.0000.0000.000
138A140LEU 0-0.0060.0038.2850.2300.2300.0000.0000.0000.000
139A141ARG 10.8420.9159.563-0.814-0.8140.0000.0000.0000.000
140A142VAL 00.0080.01211.081-0.052-0.0520.0000.0000.0000.000
141A143CYS 0-0.0200.0069.082-0.128-0.1280.0000.0000.0000.000
142A144VAL 00.0180.02011.871-0.092-0.0920.0000.0000.0000.000
143A145ASP -1-0.809-0.90014.2870.5280.5280.0000.0000.0000.000
144A146THR 0-0.123-0.06614.192-0.176-0.1760.0000.0000.0000.000
145A147VAL 0-0.046-0.01112.449-0.080-0.0800.0000.0000.0000.000
146A148ARG 10.9170.96315.764-0.433-0.4330.0000.0000.0000.000
147A149THR 0-0.0330.00616.955-0.001-0.0010.0000.0000.0000.000
148A150ASN 0-0.031-0.00415.9210.0940.0940.0000.0000.0000.000
149A151VAL 00.0120.0009.7280.0170.0170.0000.0000.0000.000
150A152TYR 00.0220.0229.819-0.045-0.0450.0000.0000.0000.000
151A153LEU 00.0300.0005.9060.1670.1670.0000.0000.0000.000
152A154ALA 0-0.004-0.0014.096-0.813-0.0840.000-0.355-0.374-0.001
153A155VAL 00.015-0.0031.817-15.993-16.57513.533-6.301-6.649-0.063
154A156PHE 0-0.061-0.0432.389-6.959-2.2684.869-0.887-8.6730.002
155A157ASP -1-0.821-0.8943.733-1.563-0.9390.099-0.057-0.6670.001
156A158LYS 10.9020.9057.562-0.314-0.3140.0000.0000.0000.000
157A159ASN 00.0100.0219.5140.2090.2090.0000.0000.0000.000
158A160LEU 0-0.025-0.0083.075-1.015-0.2390.697-0.230-1.243-0.001
159A161TYR 00.0280.0097.1960.1950.1950.0000.0000.0000.000
160A162ASP -1-0.832-0.9148.7570.7520.7520.0000.0000.0000.000
161A163LYS 10.8930.9669.489-0.538-0.5380.0000.0000.0000.000
162A164LEU 0-0.007-0.0035.708-0.132-0.058-0.001-0.003-0.0700.000
163A165VAL 00.0040.00510.324-0.161-0.1610.0000.0000.0000.000
164A166SER 0-0.021-0.01113.024-0.148-0.1480.0000.0000.0000.000
165A167SER 0-0.084-0.05013.295-0.098-0.0980.0000.0000.0000.000
166A168PHE 0-0.0130.00412.920-0.018-0.0180.0000.0000.0000.000
167A169LEU -1-0.825-0.87615.2230.6410.6410.0000.0000.0000.000
168A302HOH 0-0.036-0.0276.017-0.029-0.0290.0000.0000.0000.000
169A303HOH 0-0.054-0.04012.1430.0080.0080.0000.0000.0000.000
170A305HOH 0-0.065-0.05125.350-0.006-0.0060.0000.0000.0000.000
171A307HOH 00.0150.01111.4550.1240.1240.0000.0000.0000.000
172A315HOH 0-0.009-0.02119.3130.0260.0260.0000.0000.0000.000
173A325HOH 0-0.075-0.06120.2780.0120.0120.0000.0000.0000.000
174A332HOH 0-0.0020.0116.6410.0700.0700.0000.0000.0000.000
175A334HOH 0-0.026-0.0247.3670.0130.0130.0000.0000.0000.000
176A342HOH 0-0.043-0.03321.220-0.005-0.0050.0000.0000.0000.000
177A344HOH 0-0.026-0.02916.691-0.024-0.0240.0000.0000.0000.000
178A346HOH 0-0.022-0.02321.393-0.013-0.0130.0000.0000.0000.000
179A358HOH 0-0.016-0.0185.008-0.315-0.2880.000-0.001-0.0260.000
180A359HOH 0-0.013-0.03514.708-0.012-0.0120.0000.0000.0000.000
181A361HOH 00.019-0.0042.906-1.274-0.2950.224-0.597-0.606-0.006
182A363HOH 00.0160.01018.449-0.030-0.0300.0000.0000.0000.000
183A364HOH 0-0.045-0.0379.6390.0930.0930.0000.0000.0000.000
184A369HOH 0-0.059-0.03719.8870.0000.0000.0000.0000.0000.000
185A371HOH 0-0.049-0.0395.192-0.109-0.1090.0000.0000.0000.000
186A373HOH 0-0.027-0.01616.6870.0340.0340.0000.0000.0000.000
187A376HOH 0-0.031-0.0397.947-0.036-0.0360.0000.0000.0000.000
188A380HOH 00.0150.00215.8950.0160.0160.0000.0000.0000.000
189A387HOH 00.009-0.0118.236-0.027-0.0270.0000.0000.0000.000
190A388HOH 0-0.033-0.03116.875-0.011-0.0110.0000.0000.0000.000
191A389HOH 0-0.081-0.06818.903-0.018-0.0180.0000.0000.0000.000
192A390HOH 00.004-0.00217.1040.0300.0300.0000.0000.0000.000
193A393HOH 00.0130.0002.759-0.2180.4260.791-0.619-0.817-0.008
194A394HOH 0-0.003-0.00418.7400.0090.0090.0000.0000.0000.000
195A395HOH 0-0.009-0.01018.7510.0210.0210.0000.0000.0000.000
196A396HOH 0-0.022-0.02913.441-0.030-0.0300.0000.0000.0000.000
197A398HOH 0-0.021-0.02117.693-0.046-0.0460.0000.0000.0000.000
198A402HOH 0-0.023-0.04121.8530.0210.0210.0000.0000.0000.000
199A404HOH 00.002-0.01020.5950.0250.0250.0000.0000.0000.000
200A406HOH 0-0.029-0.01919.332-0.005-0.0050.0000.0000.0000.000
201A407HOH 00.0250.01216.063-0.013-0.0130.0000.0000.0000.000
202A411HOH 0-0.017-0.01612.3870.0220.0220.0000.0000.0000.000
203A413HOH 0-0.062-0.0579.9940.0130.0130.0000.0000.0000.000
204A414HOH 0-0.021-0.0222.652-1.9590.1250.441-1.358-1.168-0.017
205A423HOH 0-0.025-0.0109.7040.0150.0150.0000.0000.0000.000
206A427HOH 00.0630.03720.5210.0060.0060.0000.0000.0000.000
207A428HOH 0-0.005-0.0165.0430.0960.0960.0000.0000.0000.000
208A437HOH 00.001-0.00219.350-0.025-0.0250.0000.0000.0000.000
209A439HOH 0-0.033-0.02518.283-0.012-0.0120.0000.0000.0000.000
210A464HOH 00.0110.00810.943-0.012-0.0120.0000.0000.0000.000
211A492HOH 00.002-0.00220.034-0.003-0.0030.0000.0000.0000.000