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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: GNNN1

Calculation Name: 5RUI-A-Xray89

Preferred Name:

Target Type:

Ligand Name: isoquinolin-1(2h)-one

ligand 3-letter code: 4YS

PDB ID: 5RUI

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 208
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1793138.378424
FMO2-HF: Nuclear repulsion 1727095.945958
FMO2-HF: Total energy -66042.432466
FMO2-MP2: Total energy -66235.998014


3D Structure
Snapshot
 
Ligand structure

4YS

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.
-34.610-17.11414.683-8.472-23.7080.022


Interactive mode: IFIE and PIEDA for fragment #208(A:201:4YS )


Summations of interaction energy for fragment #208(A:201:4YS )
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.
-34.61-17.11414.683-8.472-23.708-0.022
Interaction energy analysis for fragmet #208(A:201:4YS )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.011
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 00.014-0.00623.9140.0030.0030.0000.0000.0000.000
2A4ASN 0-0.015-0.01819.074-0.046-0.0460.0000.0000.0000.000
3A5SER 00.0290.00617.3960.0080.0080.0000.0000.0000.000
4A6PHE 0-0.0480.00312.275-0.091-0.0910.0000.0000.0000.000
5A7SER 00.0270.00915.1850.0850.0850.0000.0000.0000.000
6A8GLY 00.005-0.01114.919-0.128-0.1280.0000.0000.0000.000
7A9TYR 0-0.049-0.03211.367-0.065-0.0650.0000.0000.0000.000
8A10LEU 0-0.0030.01015.8340.0660.0660.0000.0000.0000.000
9A11LYS 10.8090.89517.1320.3210.3210.0000.0000.0000.000
10A12LEU 0-0.047-0.01315.5550.0250.0250.0000.0000.0000.000
11A13THR 00.0360.00819.8810.0300.0300.0000.0000.0000.000
12A14ASP -1-0.865-0.89522.010-0.300-0.3000.0000.0000.0000.000
13A15ASN 00.000-0.00519.9670.0010.0010.0000.0000.0000.000
14A16VAL 00.0040.01515.547-0.053-0.0530.0000.0000.0000.000
15A17TYR 00.0410.02615.6360.0380.0380.0000.0000.0000.000
16A18ILE 00.0230.01011.487-0.087-0.0870.0000.0000.0000.000
17A19LYS 10.8320.90610.9721.5461.5460.0000.0000.0000.000
18A20ASN 0-0.045-0.0258.760-0.088-0.0880.0000.0000.0000.000
19A21ALA 0-0.003-0.0117.5930.0380.0380.0000.0000.0000.000
20A22ASP -1-0.788-0.8972.534-24.171-20.2223.417-3.104-4.262-0.043
21A23ILE 00.0340.0002.273-1.1680.0741.482-0.611-2.113-0.001
22A24VAL 00.0010.0092.8431.1282.5710.278-0.482-1.2380.002
23A25GLU -1-0.830-0.9004.698-2.904-2.820-0.001-0.017-0.0670.000
24A26GLU -1-0.770-0.8696.437-0.745-0.7450.0000.0000.0000.000
25A27ALA 0-0.013-0.0137.4540.5530.5530.0000.0000.0000.000
26A28LYS 10.8240.9037.0903.6863.6860.0000.0000.0000.000
27A29LYS 10.8170.92110.7061.8671.8670.0000.0000.0000.000
28A30VAL 0-0.041-0.03212.1580.1880.1880.0000.0000.0000.000
29A31LYS 10.8760.96512.9971.1021.1020.0000.0000.0000.000
30A32PRO 00.0050.01911.8590.1280.1280.0000.0000.0000.000
31A33THR 00.027-0.00815.0420.0120.0120.0000.0000.0000.000
32A34VAL 0-0.016-0.01414.0960.0470.0470.0000.0000.0000.000
33A35VAL 00.0070.0088.511-0.109-0.1090.0000.0000.0000.000
34A36VAL 00.001-0.0039.8580.1630.1630.0000.0000.0000.000
35A37ASN 00.001-0.0198.110-0.066-0.0660.0000.0000.0000.000
36A38ALA 0-0.0070.0156.189-0.025-0.0250.0000.0000.0000.000
37A39ALA 00.0460.0428.0980.3710.3710.0000.0000.0000.000
38A40ASN 0-0.004-0.02011.203-0.117-0.1170.0000.0000.0000.000
39A41VAL 00.0420.02113.728-0.031-0.0310.0000.0000.0000.000
40A42TYR 00.0050.00316.727-0.031-0.0310.0000.0000.0000.000
41A43LEU 0-0.0040.01114.702-0.001-0.0010.0000.0000.0000.000
42A44LYS 10.9771.00614.667-0.637-0.6370.0000.0000.0000.000
43A45HIS 00.0270.01510.7650.2770.2770.0000.0000.0000.000
44A46GLY 00.0380.03110.3700.1170.1170.0000.0000.0000.000
45A47GLY 00.0320.0126.4020.3740.3740.0000.0000.0000.000
46A48GLY 00.0130.0092.754-1.974-1.2400.640-0.584-0.7900.005
47A49VAL 00.0220.0042.418-0.6471.3182.269-0.742-3.4920.005
48A50ALA 00.0130.0204.037-0.962-0.7900.0370.125-0.3350.001
49A51GLY 0-0.0120.0056.850-0.537-0.5370.0000.0000.0000.000
50A52ALA 00.0240.0192.919-2.757-1.1751.914-0.927-2.5700.007
51A53LEU 00.0380.0034.929-2.287-1.9610.000-0.024-0.3020.000
52A54ASN 00.0540.0066.965-0.522-0.5220.0000.0000.0000.000
53A55LYS 10.9660.9995.772-0.984-0.9840.0000.0000.0000.000
54A56ALA 0-0.037-0.0076.347-0.206-0.2060.0000.0000.0000.000
55A57THR 0-0.055-0.0188.3580.0300.0300.0000.0000.0000.000
56A58ASN 0-0.037-0.02511.3990.1320.1320.0000.0000.0000.000
57A59ASN 0-0.0040.00112.6720.1920.1920.0000.0000.0000.000
58A60ALA 00.0360.02914.4810.0490.0490.0000.0000.0000.000
59A61MET 00.0070.01310.6180.0860.0860.0000.0000.0000.000
60A62GLN 0-0.056-0.03114.7130.1820.1820.0000.0000.0000.000
61A63VAL 00.0290.02316.302-0.001-0.0010.0000.0000.0000.000
62A64GLU -1-0.726-0.84017.553-0.170-0.1700.0000.0000.0000.000
63A65SER 00.001-0.00916.432-0.001-0.0010.0000.0000.0000.000
64A66ASP -1-0.812-0.89518.8200.3630.3630.0000.0000.0000.000
65A67ASP -1-0.820-0.85921.4240.0260.0260.0000.0000.0000.000
66A68TYR 00.0420.01020.830-0.016-0.0160.0000.0000.0000.000
67A69ILE 0-0.044-0.02819.421-0.005-0.0050.0000.0000.0000.000
68A70ALA 0-0.028-0.00123.005-0.002-0.0020.0000.0000.0000.000
69A71THR 0-0.042-0.00826.152-0.009-0.0090.0000.0000.0000.000
70A72ASN 0-0.091-0.05424.405-0.020-0.0200.0000.0000.0000.000
71A73GLY 00.0170.02525.199-0.003-0.0030.0000.0000.0000.000
72A74PRO 0-0.064-0.03821.325-0.002-0.0020.0000.0000.0000.000
73A75LEU 0-0.008-0.00216.574-0.029-0.0290.0000.0000.0000.000
74A76LYS 10.9840.98620.423-0.024-0.0240.0000.0000.0000.000
75A77VAL 00.0270.00416.715-0.009-0.0090.0000.0000.0000.000
76A78GLY 00.0110.01716.959-0.016-0.0160.0000.0000.0000.000
77A79GLY 0-0.028-0.00618.242-0.040-0.0400.0000.0000.0000.000
78A80SER 0-0.016-0.04016.794-0.005-0.0050.0000.0000.0000.000
79A81CYS 0-0.0400.00717.2120.0160.0160.0000.0000.0000.000
80A82VAL 00.0110.00917.212-0.029-0.0290.0000.0000.0000.000
81A83LEU 00.0030.00916.8260.0360.0360.0000.0000.0000.000
82A84SER 00.0320.01517.638-0.098-0.0980.0000.0000.0000.000
83A85GLY 0-0.0110.00814.0460.0130.0130.0000.0000.0000.000
84A86HIS 0-0.029-0.03213.563-0.168-0.1680.0000.0000.0000.000
85A87ASN 0-0.024-0.02511.4900.0410.0410.0000.0000.0000.000
86A88LEU 0-0.015-0.0188.184-0.188-0.1880.0000.0000.0000.000
87A89ALA 0-0.013-0.00711.796-0.131-0.1310.0000.0000.0000.000
88A90LYS 10.8540.94814.1440.4360.4360.0000.0000.0000.000
89A91HIS 00.0310.01216.6580.0640.0640.0000.0000.0000.000
90A92CYS 0-0.018-0.00512.094-0.133-0.1330.0000.0000.0000.000
91A93LEU 0-0.0290.00613.4640.0970.0970.0000.0000.0000.000
92A94HIS 00.0520.00412.6870.0340.0340.0000.0000.0000.000
93A95VAL 00.0140.00212.1620.0250.0250.0000.0000.0000.000
94A96VAL 0-0.0350.01211.8860.0530.0530.0000.0000.0000.000
95A97GLY 00.0530.03012.106-0.044-0.0440.0000.0000.0000.000
96A98PRO 0-0.0100.00313.3070.0820.0820.0000.0000.0000.000
97A99ASN 0-0.020-0.00611.537-0.011-0.0110.0000.0000.0000.000
98A100VAL 00.0680.02613.399-0.010-0.0100.0000.0000.0000.000
99A101ASN 0-0.056-0.03010.945-0.067-0.0670.0000.0000.0000.000
100A102LYS 10.8090.90514.246-0.541-0.5410.0000.0000.0000.000
101A103GLY 00.0000.00917.171-0.031-0.0310.0000.0000.0000.000
102A104GLU -1-0.789-0.84216.3560.3110.3110.0000.0000.0000.000
103A105ASP -1-0.816-0.91118.8160.0970.0970.0000.0000.0000.000
104A106ILE 00.0510.01015.539-0.009-0.0090.0000.0000.0000.000
105A107GLN 00.0070.00518.454-0.043-0.0430.0000.0000.0000.000
106A108LEU 0-0.046-0.02618.684-0.023-0.0230.0000.0000.0000.000
107A109LEU 0-0.023-0.01712.867-0.016-0.0160.0000.0000.0000.000
108A110LYS 10.8920.93816.6090.0730.0730.0000.0000.0000.000
109A111SER 00.0330.01019.183-0.018-0.0180.0000.0000.0000.000
110A112ALA 00.0250.00914.675-0.015-0.0150.0000.0000.0000.000
111A113TYR 00.024-0.00311.667-0.071-0.0710.0000.0000.0000.000
112A114GLU -1-0.814-0.86316.380-0.124-0.1240.0000.0000.0000.000
113A115ASN 0-0.063-0.02216.926-0.004-0.0040.0000.0000.0000.000
114A116PHE 00.039-0.00711.425-0.029-0.0290.0000.0000.0000.000
115A117ASN 0-0.0120.00417.588-0.038-0.0380.0000.0000.0000.000
116A118GLN 0-0.0420.00420.7480.0090.0090.0000.0000.0000.000
117A119HIS 0-0.042-0.03018.294-0.034-0.0340.0000.0000.0000.000
118A120GLU -1-0.868-0.92819.976-0.325-0.3250.0000.0000.0000.000
119A121VAL 00.004-0.01316.831-0.014-0.0140.0000.0000.0000.000
120A122LEU 0-0.0370.02413.626-0.007-0.0070.0000.0000.0000.000
121A123LEU 0-0.0140.0168.410-0.009-0.0090.0000.0000.0000.000
122A124ALA 00.026-0.0048.8380.0390.0390.0000.0000.0000.000
123A125PRO 0-0.0380.0054.801-0.209-0.2090.0000.0000.0000.000
124A126LEU 00.0320.0086.5680.2600.2600.0000.0000.0000.000
125A127LEU 0-0.0020.0177.2830.0240.0240.0000.0000.0000.000
126A128SER 00.041-0.0069.296-0.009-0.0090.0000.0000.0000.000
127A129ALA 0-0.0050.0176.6230.1120.1120.0000.0000.0000.000
128A130GLY 00.0410.0294.6380.0090.044-0.001-0.010-0.0240.000
129A131ILE 00.017-0.0104.8950.1140.1140.0000.0000.0000.000
130A132PHE 0-0.068-0.0186.9580.0180.0180.0000.0000.0000.000
131A133GLY 00.0240.0189.121-0.066-0.0660.0000.0000.0000.000
132A134ALA 00.0010.00411.086-0.030-0.0300.0000.0000.0000.000
133A135ASP -1-0.793-0.89711.5120.0660.0660.0000.0000.0000.000
134A136PRO 0-0.018-0.0229.370-0.059-0.0590.0000.0000.0000.000
135A137ILE 00.0190.00811.373-0.073-0.0730.0000.0000.0000.000
136A138HIS 00.0450.02914.773-0.043-0.0430.0000.0000.0000.000
137A139SER 0-0.011-0.02510.964-0.052-0.0520.0000.0000.0000.000
138A140LEU 0-0.012-0.00512.944-0.046-0.0460.0000.0000.0000.000
139A141ARG 10.8440.91714.1260.1410.1410.0000.0000.0000.000
140A142VAL 00.0040.01016.154-0.005-0.0050.0000.0000.0000.000
141A143CYS 00.0020.01413.913-0.026-0.0260.0000.0000.0000.000
142A144VAL 0-0.0180.00216.056-0.007-0.0070.0000.0000.0000.000
143A145ASP -1-0.797-0.89118.812-0.142-0.1420.0000.0000.0000.000
144A146THR 0-0.122-0.06618.7200.0370.0370.0000.0000.0000.000
145A147VAL 0-0.050-0.01216.0520.0090.0090.0000.0000.0000.000
146A148ARG 10.9160.96419.5090.1730.1730.0000.0000.0000.000
147A149THR 0-0.0370.00619.5660.0000.0000.0000.0000.0000.000
148A150ASN 0-0.0130.00419.112-0.006-0.0060.0000.0000.0000.000
149A151VAL 00.0120.00013.147-0.045-0.0450.0000.0000.0000.000
150A152TYR 00.0220.02412.8610.0510.0510.0000.0000.0000.000
151A153LEU 00.022-0.0059.857-0.168-0.1680.0000.0000.0000.000
152A154ALA 0-0.001-0.0016.0280.0420.0420.0000.0000.0000.000
153A155VAL 0-0.032-0.0095.900-0.217-0.2170.0000.0000.0000.000
154A156PHE 00.0250.0122.909-5.740-0.0504.649-2.066-8.2730.002
155A157ASP -1-0.831-0.9105.2450.4250.523-0.001-0.011-0.0860.000
156A158LYS 10.8830.9238.2810.2290.2290.0000.0000.0000.000
157A159ASN 0-0.002-0.00311.758-0.019-0.0190.0000.0000.0000.000
158A160LEU 0-0.013-0.0157.758-0.034-0.0340.0000.0000.0000.000
159A161TYR 0-0.017-0.00810.663-0.051-0.0510.0000.0000.0000.000
160A162ASP -1-0.767-0.86011.921-0.311-0.3110.0000.0000.0000.000
161A163LYS 10.9470.99014.344-0.087-0.0870.0000.0000.0000.000
162A164LEU 0-0.045-0.01810.2590.0060.0060.0000.0000.0000.000
163A165VAL 00.0130.01114.7510.0000.0000.0000.0000.0000.000
164A166SER 0-0.046-0.03017.2350.0200.0200.0000.0000.0000.000
165A167SER 0-0.103-0.07117.4870.0190.0190.0000.0000.0000.000
166A168PHE 0-0.015-0.00317.7070.0070.0070.0000.0000.0000.000
167A169LEU -1-0.882-0.92619.869-0.169-0.1690.0000.0000.0000.000
168A304HOH 0-0.065-0.05127.2730.0050.0050.0000.0000.0000.000
169A316HOH 0-0.007-0.02124.054-0.009-0.0090.0000.0000.0000.000
170A325HOH 0-0.074-0.06122.214-0.011-0.0110.0000.0000.0000.000
171A338HOH 0-0.049-0.03612.3390.0000.0000.0000.0000.0000.000
172A340HOH 0-0.022-0.02324.5110.0060.0060.0000.0000.0000.000
173A343HOH 0-0.028-0.0254.1360.6960.7480.000-0.008-0.0430.000
174A344HOH 0-0.006-0.0104.3370.0730.1180.000-0.003-0.0420.000
175A346HOH 0-0.047-0.03821.7350.0050.0050.0000.0000.0000.000
176A347HOH 0-0.027-0.00811.9280.0290.0290.0000.0000.0000.000
177A350HOH 00.011-0.0058.490-0.076-0.0760.0000.0000.0000.000
178A357HOH 00.008-0.00623.3890.0030.0030.0000.0000.0000.000
179A360HOH 0-0.012-0.01510.535-0.013-0.0130.0000.0000.0000.000
180A365HOH 0-0.014-0.03515.3210.0190.0190.0000.0000.0000.000
181A371HOH 0-0.030-0.03714.0720.0370.0370.0000.0000.0000.000
182A372HOH 0-0.029-0.0229.043-0.023-0.0230.0000.0000.0000.000
183A374HOH 00.0160.00319.599-0.012-0.0120.0000.0000.0000.000
184A376HOH 0-0.027-0.01821.145-0.006-0.0060.0000.0000.0000.000
185A378HOH 0-0.008-0.0118.816-0.259-0.2590.0000.0000.0000.000
186A379HOH 0-0.065-0.0489.5010.0640.0640.0000.0000.0000.000
187A385HOH 0-0.059-0.03924.6550.0010.0010.0000.0000.0000.000
188A387HOH 0-0.007-0.01518.4900.0130.0130.0000.0000.0000.000
189A388HOH 0-0.017-0.02515.042-0.002-0.0020.0000.0000.0000.000
190A391HOH 0-0.003-0.0145.7040.0430.0430.0000.0000.0000.000
191A401HOH 0-0.008-0.0115.2980.1790.1790.0000.0000.0000.000
192A402HOH 0-0.013-0.0098.980-0.060-0.0600.0000.0000.0000.000
193A406HOH 00.0230.01313.891-0.048-0.0480.0000.0000.0000.000
194A407HOH 0-0.020-0.02121.8160.0110.0110.0000.0000.0000.000
195A408HOH 00.0250.0186.5390.1170.1170.0000.0000.0000.000
196A412HOH 0-0.019-0.01916.780-0.010-0.0100.0000.0000.0000.000
197A413HOH 0-0.022-0.04025.571-0.008-0.0080.0000.0000.0000.000
198A414HOH 00.004-0.00220.441-0.016-0.0160.0000.0000.0000.000
199A419HOH 00.013-0.01111.968-0.017-0.0170.0000.0000.0000.000
200A420HOH 00.0290.01220.5270.0080.0080.0000.0000.0000.000
201A422HOH 0-0.028-0.01824.0200.0050.0050.0000.0000.0000.000
202A428HOH 0-0.061-0.05815.5430.0220.0220.0000.0000.0000.000
203A433HOH 0-0.008-0.01224.773-0.008-0.0080.0000.0000.0000.000
204A453HOH 0-0.035-0.0374.4910.1580.2370.000-0.008-0.0710.000
205A456HOH 0-0.003-0.00523.3870.0040.0040.0000.0000.0000.000
206A458HOH 0-0.035-0.02618.7030.0080.0080.0000.0000.0000.000
207A492HOH 0-0.033-0.02710.158-0.025-0.0250.0000.0000.0000.000