FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: GNQ11

Calculation Name: 5RU6-A-Xray89

Preferred Name:

Target Type:

Ligand Name: naphthalene-2-carboximidamide

ligand 3-letter code: 2UP

PDB ID: 5RU6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-27

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 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1778495.041013
FMO2-HF: Nuclear repulsion 1712698.735576
FMO2-HF: Total energy -65796.305438
FMO2-MP2: Total energy -65988.958221


3D Structure
Snapshot
 
Ligand structure

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.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:3:VAL )


Summations of interaction energy for fragment #1(A:3:VAL )
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.
0.0322.3250.233-1.163-1.364-0.002
Interaction energy analysis for fragmet #1(A:3:VAL )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.007
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].
3A5SER 00.0280.0043.032-1.3320.9610.233-1.163-1.364-0.002
4A6PHE 0-0.0390.0075.4640.1750.1750.0000.0000.0000.000
5A7SER 00.0270.0106.7230.1020.1020.0000.0000.0000.000
6A8GLY 00.007-0.0099.0000.0140.0140.0000.0000.0000.000
7A9TYR 0-0.055-0.03710.2390.0070.0070.0000.0000.0000.000
8A10LEU 00.0000.01211.7540.0390.0390.0000.0000.0000.000
9A11LYS 10.8060.8949.622-1.099-1.0990.0000.0000.0000.000
10A12LEU 0-0.060-0.02413.040-0.050-0.0500.0000.0000.0000.000
11A13THR 00.0270.00114.526-0.008-0.0080.0000.0000.0000.000
12A14ASP -1-0.872-0.91312.4031.1071.1070.0000.0000.0000.000
13A15ASN 0-0.002-0.00410.9220.1840.1840.0000.0000.0000.000
14A16VAL 00.0100.01912.072-0.016-0.0160.0000.0000.0000.000
15A17TYR 00.0320.0248.039-0.012-0.0120.0000.0000.0000.000
16A18ILE 00.0240.01012.817-0.062-0.0620.0000.0000.0000.000
17A19LYS 10.8320.90212.6290.0270.0270.0000.0000.0000.000
18A20ASN 0-0.054-0.02516.396-0.013-0.0130.0000.0000.0000.000
19A21ALA 0-0.009-0.01717.194-0.016-0.0160.0000.0000.0000.000
20A22ASP -1-0.817-0.90819.265-0.006-0.0060.0000.0000.0000.000
21A23ILE 00.001-0.00918.208-0.016-0.0160.0000.0000.0000.000
22A24VAL 00.0240.01918.733-0.018-0.0180.0000.0000.0000.000
23A25GLU -1-0.817-0.89319.390-0.106-0.1060.0000.0000.0000.000
24A26GLU -1-0.779-0.85812.749-0.110-0.1100.0000.0000.0000.000
25A27ALA 0-0.022-0.02114.496-0.043-0.0430.0000.0000.0000.000
26A28LYS 10.8260.90315.6360.0570.0570.0000.0000.0000.000
27A29LYS 10.8230.91312.0050.1650.1650.0000.0000.0000.000
28A30VAL 0-0.041-0.0299.246-0.047-0.0470.0000.0000.0000.000
29A31LYS 10.8730.96211.2620.1640.1640.0000.0000.0000.000
30A32PRO 00.0070.02011.506-0.059-0.0590.0000.0000.0000.000
31A33THR 00.026-0.00810.937-0.017-0.0170.0000.0000.0000.000
32A34VAL 0-0.014-0.01313.5650.0220.0220.0000.0000.0000.000
33A35VAL 00.0050.00815.3010.0190.0190.0000.0000.0000.000
34A36VAL 00.0060.00217.888-0.002-0.0020.0000.0000.0000.000
35A37ASN 0-0.007-0.02720.275-0.004-0.0040.0000.0000.0000.000
36A38ALA 0-0.0030.02023.8150.0110.0110.0000.0000.0000.000
37A39ALA 00.0410.04026.189-0.009-0.0090.0000.0000.0000.000
38A40ASN 0-0.002-0.01928.8640.0050.0050.0000.0000.0000.000
39A41VAL 00.0470.02432.271-0.003-0.0030.0000.0000.0000.000
40A42TYR 0-0.002-0.00234.226-0.001-0.0010.0000.0000.0000.000
41A43LEU 0-0.0060.00829.626-0.004-0.0040.0000.0000.0000.000
42A44LYS 10.9811.00932.762-0.009-0.0090.0000.0000.0000.000
43A45HIS 00.0220.01429.4220.0100.0100.0000.0000.0000.000
44A46GLY 00.0490.03932.127-0.004-0.0040.0000.0000.0000.000
45A47GLY 00.0510.01932.665-0.004-0.0040.0000.0000.0000.000
46A48GLY 00.0200.02230.2080.0030.0030.0000.0000.0000.000
47A49VAL 00.031-0.00123.506-0.008-0.0080.0000.0000.0000.000
48A50ALA 00.0190.02626.322-0.009-0.0090.0000.0000.0000.000
49A51GLY 0-0.0120.00828.135-0.008-0.0080.0000.0000.0000.000
50A52ALA 00.0050.00526.266-0.008-0.0080.0000.0000.0000.000
51A53LEU 00.0360.01021.487-0.011-0.0110.0000.0000.0000.000
52A54ASN 00.0610.00625.210-0.014-0.0140.0000.0000.0000.000
53A55LYS 10.9721.00328.2560.0240.0240.0000.0000.0000.000
54A56ALA 0-0.039-0.01024.048-0.006-0.0060.0000.0000.0000.000
55A57THR 0-0.052-0.01424.482-0.010-0.0100.0000.0000.0000.000
56A58ASN 0-0.037-0.02626.7430.0010.0010.0000.0000.0000.000
57A59ASN 00.0010.00430.1800.0040.0040.0000.0000.0000.000
58A60ALA 00.0350.02828.4200.0040.0040.0000.0000.0000.000
59A61MET 00.0010.00824.2360.0060.0060.0000.0000.0000.000
60A62GLN 0-0.056-0.03028.8050.0080.0080.0000.0000.0000.000
61A63VAL 00.0300.02732.3800.0030.0030.0000.0000.0000.000
62A64GLU -1-0.727-0.84227.276-0.042-0.0420.0000.0000.0000.000
63A65SER 00.009-0.00730.3200.0060.0060.0000.0000.0000.000
64A66ASP -1-0.816-0.89532.130-0.007-0.0070.0000.0000.0000.000
65A67ASP -1-0.822-0.86134.154-0.019-0.0190.0000.0000.0000.000
66A68TYR 00.004-0.01730.2940.0040.0040.0000.0000.0000.000
67A69ILE 0-0.039-0.02533.5510.0050.0050.0000.0000.0000.000
68A70ALA 0-0.0260.00136.0840.0030.0030.0000.0000.0000.000
69A71THR 0-0.036-0.00535.7200.0000.0000.0000.0000.0000.000
70A72ASN 0-0.084-0.04833.3710.0030.0030.0000.0000.0000.000
71A73GLY 00.0230.02436.3500.0040.0040.0000.0000.0000.000
72A74PRO 0-0.040-0.02235.6600.0000.0000.0000.0000.0000.000
73A75LEU 0-0.015-0.00129.4400.0030.0030.0000.0000.0000.000
74A76LYS 10.9740.98132.708-0.053-0.0530.0000.0000.0000.000
75A77VAL 00.0310.00732.1260.0020.0020.0000.0000.0000.000
76A78GLY 00.0150.01929.4150.0020.0020.0000.0000.0000.000
77A79GLY 0-0.028-0.00728.5130.0100.0100.0000.0000.0000.000
78A80SER 0-0.010-0.03824.7860.0000.0000.0000.0000.0000.000
79A81CYS 0-0.0310.01026.145-0.002-0.0020.0000.0000.0000.000
80A82VAL 00.0080.00821.1610.0020.0020.0000.0000.0000.000
81A83LEU 00.0020.00823.708-0.004-0.0040.0000.0000.0000.000
82A84SER 00.0290.01222.810-0.011-0.0110.0000.0000.0000.000
83A85GLY 0-0.0090.01020.3670.0140.0140.0000.0000.0000.000
84A86HIS 0-0.027-0.03121.437-0.013-0.0130.0000.0000.0000.000
85A87ASN 0-0.028-0.02821.379-0.013-0.0130.0000.0000.0000.000
86A88LEU 0-0.020-0.02019.051-0.018-0.0180.0000.0000.0000.000
87A89ALA 0-0.001-0.00216.262-0.017-0.0170.0000.0000.0000.000
88A90LYS 10.8480.94515.6140.1690.1690.0000.0000.0000.000
89A91HIS 00.0290.01216.955-0.002-0.0020.0000.0000.0000.000
90A92CYS 0-0.019-0.00618.8700.0030.0030.0000.0000.0000.000
91A93LEU 0-0.0280.00819.5660.0020.0020.0000.0000.0000.000
92A94HIS 00.0570.00621.8510.0160.0160.0000.0000.0000.000
93A95VAL 00.0120.00222.6110.0040.0040.0000.0000.0000.000
94A96VAL 0-0.0380.00925.731-0.004-0.0040.0000.0000.0000.000
95A97GLY 00.0510.03128.5470.0070.0070.0000.0000.0000.000
96A98PRO 0-0.0080.00229.107-0.010-0.0100.0000.0000.0000.000
97A99ASN 0-0.021-0.00832.1000.0030.0030.0000.0000.0000.000
98A100VAL 00.0610.02133.861-0.002-0.0020.0000.0000.0000.000
99A101ASN 0-0.050-0.02335.973-0.002-0.0020.0000.0000.0000.000
100A102LYS 10.8090.90435.832-0.039-0.0390.0000.0000.0000.000
101A103GLY 00.0020.01039.434-0.001-0.0010.0000.0000.0000.000
102A104GLU -1-0.789-0.84635.0910.0510.0510.0000.0000.0000.000
103A105ASP -1-0.813-0.91036.6550.0790.0790.0000.0000.0000.000
104A106ILE 00.0500.01231.3320.0030.0030.0000.0000.0000.000
105A107GLN 00.0040.00431.8450.0150.0150.0000.0000.0000.000
106A108LEU 0-0.045-0.02831.4630.0080.0080.0000.0000.0000.000
107A109LEU 0-0.030-0.02226.5430.0030.0030.0000.0000.0000.000
108A110LYS 10.8980.94225.219-0.184-0.1840.0000.0000.0000.000
109A111SER 00.0260.00526.0060.0090.0090.0000.0000.0000.000
110A112ALA 00.0230.01126.4900.0020.0020.0000.0000.0000.000
111A113TYR 00.024-0.00520.7020.0050.0050.0000.0000.0000.000
112A114GLU -1-0.814-0.86321.5720.1820.1820.0000.0000.0000.000
113A115ASN 0-0.066-0.02422.0380.0010.0010.0000.0000.0000.000
114A116PHE 00.038-0.00817.583-0.012-0.0120.0000.0000.0000.000
115A117ASN 0-0.0140.00217.2250.0650.0650.0000.0000.0000.000
116A118GLN 0-0.0420.00417.7320.0090.0090.0000.0000.0000.000
117A119HIS 0-0.036-0.02515.078-0.042-0.0420.0000.0000.0000.000
118A120GLU -1-0.872-0.9309.9440.4020.4020.0000.0000.0000.000
119A121VAL 00.007-0.0117.5530.2060.2060.0000.0000.0000.000
120A122LEU 0-0.0370.02410.999-0.170-0.1700.0000.0000.0000.000
121A123LEU 0-0.0160.01512.9940.0580.0580.0000.0000.0000.000
122A124ALA 00.026-0.00414.633-0.025-0.0250.0000.0000.0000.000
123A125PRO 0-0.0390.00017.9200.0090.0090.0000.0000.0000.000
124A126LEU 00.0400.01520.9110.0140.0140.0000.0000.0000.000
125A127LEU 00.0020.01922.679-0.022-0.0220.0000.0000.0000.000
126A128SER 00.029-0.01525.0680.0080.0080.0000.0000.0000.000
127A129ALA 0-0.0040.02026.281-0.004-0.0040.0000.0000.0000.000
128A130GLY 00.0300.02328.273-0.007-0.0070.0000.0000.0000.000
129A131ILE 00.016-0.01430.0390.0010.0010.0000.0000.0000.000
130A132PHE 0-0.070-0.02230.420-0.004-0.0040.0000.0000.0000.000
131A133GLY 00.0250.02032.5250.0020.0020.0000.0000.0000.000
132A134ALA 00.0000.00330.1480.0010.0010.0000.0000.0000.000
133A135ASP -1-0.796-0.89930.7410.1000.1000.0000.0000.0000.000
134A136PRO 0-0.012-0.01726.3050.0090.0090.0000.0000.0000.000
135A137ILE 00.0250.00925.7520.0130.0130.0000.0000.0000.000
136A138HIS 00.0360.02326.3310.0180.0180.0000.0000.0000.000
137A139SER 0-0.011-0.02425.0320.0170.0170.0000.0000.0000.000
138A140LEU 0-0.016-0.00419.4650.0130.0130.0000.0000.0000.000
139A141ARG 10.8510.92222.012-0.201-0.2010.0000.0000.0000.000
140A142VAL 00.0110.01223.6630.0160.0160.0000.0000.0000.000
141A143CYS 0-0.0310.00218.9630.0240.0240.0000.0000.0000.000
142A144VAL 00.0150.01618.1690.0300.0300.0000.0000.0000.000
143A145ASP -1-0.802-0.89319.9150.2630.2630.0000.0000.0000.000
144A146THR 0-0.121-0.06621.536-0.019-0.0190.0000.0000.0000.000
145A147VAL 0-0.054-0.01316.110-0.005-0.0050.0000.0000.0000.000
146A148ARG 10.9180.96516.643-0.275-0.2750.0000.0000.0000.000
147A149THR 0-0.0440.00013.2530.0990.0990.0000.0000.0000.000
148A150ASN 0-0.0060.0079.0330.1000.1000.0000.0000.0000.000
149A151VAL 00.0120.00111.094-0.123-0.1230.0000.0000.0000.000
150A152TYR 00.0230.0256.3730.1370.1370.0000.0000.0000.000
151A153LEU 00.020-0.00712.709-0.079-0.0790.0000.0000.0000.000
152A154ALA 00.0060.00316.363-0.003-0.0030.0000.0000.0000.000
153A155VAL 00.0020.00518.197-0.005-0.0050.0000.0000.0000.000
154A156PHE 00.009-0.00321.483-0.006-0.0060.0000.0000.0000.000
155A157ASP -1-0.811-0.91223.7230.0440.0440.0000.0000.0000.000
156A158LYS 10.8640.91822.339-0.058-0.0580.0000.0000.0000.000
157A159ASN 0-0.027-0.01625.2230.0120.0120.0000.0000.0000.000
158A160LEU 00.008-0.00225.5610.0070.0070.0000.0000.0000.000
159A161TYR 0-0.015-0.00417.0250.0040.0040.0000.0000.0000.000
160A162ASP -1-0.766-0.86023.2370.0970.0970.0000.0000.0000.000
161A163LYS 10.9470.99024.848-0.076-0.0760.0000.0000.0000.000
162A164LEU 0-0.042-0.01622.5980.0050.0050.0000.0000.0000.000
163A165VAL 00.0090.01019.9240.0150.0150.0000.0000.0000.000
164A166SER 0-0.046-0.03222.4930.0060.0060.0000.0000.0000.000
165A167SER 0-0.105-0.07225.7750.0010.0010.0000.0000.0000.000
166A168PHE 0-0.012-0.00320.0630.0000.0000.0000.0000.0000.000
167A169LEU -1-0.880-0.92523.2980.2430.2430.0000.0000.0000.000
168A204HOH 0-0.065-0.05137.6760.0000.0000.0000.0000.0000.000
169A215HOH 0-0.009-0.02224.5980.0110.0110.0000.0000.0000.000
170A223HOH 0-0.074-0.06131.7540.0000.0000.0000.0000.0000.000
171A232HOH 00.007-0.00527.3470.0050.0050.0000.0000.0000.000
172A234HOH 0-0.008-0.01225.170-0.005-0.0050.0000.0000.0000.000
173A237HOH 0-0.040-0.03527.423-0.005-0.0050.0000.0000.0000.000
174A240HOH 0-0.048-0.03533.9280.0010.0010.0000.0000.0000.000
175A241HOH 0-0.030-0.01033.198-0.002-0.0020.0000.0000.0000.000
176A243HOH 0-0.021-0.02321.097-0.007-0.0070.0000.0000.0000.000
177A244HOH 0-0.028-0.02426.4660.0000.0000.0000.0000.0000.000
178A246HOH 0-0.015-0.03625.1800.0050.0050.0000.0000.0000.000
179A250HOH 0-0.063-0.04830.1650.0000.0000.0000.0000.0000.000
180A256HOH 0-0.028-0.03532.627-0.003-0.0030.0000.0000.0000.000
181A258HOH 0-0.060-0.03836.7400.0000.0000.0000.0000.0000.000
182A259HOH 0-0.009-0.01327.5130.0030.0030.0000.0000.0000.000
183A262HOH 00.0150.00224.527-0.002-0.0020.0000.0000.0000.000
184A269HOH 0-0.017-0.01033.847-0.001-0.0010.0000.0000.0000.000
185A275HOH 0-0.029-0.01916.698-0.001-0.0010.0000.0000.0000.000
186A276HOH 0-0.028-0.02230.9910.0000.0000.0000.0000.0000.000
187A277HOH 0-0.007-0.01512.7980.0060.0060.0000.0000.0000.000
188A285HOH 0-0.019-0.02021.5410.0040.0040.0000.0000.0000.000
189A288HOH 0-0.010-0.01131.086-0.002-0.0020.0000.0000.0000.000
190A292HOH 00.007-0.00527.024-0.003-0.0030.0000.0000.0000.000
191A293HOH 0-0.017-0.02612.408-0.042-0.0420.0000.0000.0000.000
192A296HOH 0-0.019-0.02018.980-0.010-0.0100.0000.0000.0000.000
193A300HOH 00.004-0.00122.0020.0040.0040.0000.0000.0000.000
194A301HOH 0-0.003-0.00533.6900.0010.0010.0000.0000.0000.000
195A304HOH 00.0270.01928.8390.0010.0010.0000.0000.0000.000
196A305HOH 0-0.023-0.0409.745-0.035-0.0350.0000.0000.0000.000
197A316HOH 0-0.029-0.01923.532-0.007-0.0070.0000.0000.0000.000
198A317HOH 00.013-0.01030.7120.0030.0030.0000.0000.0000.000
199A318HOH 00.0250.01130.4220.0010.0010.0000.0000.0000.000
200A319HOH 0-0.060-0.05634.822-0.002-0.0020.0000.0000.0000.000
201A322HOH 0-0.034-0.02328.6270.0020.0020.0000.0000.0000.000
202A329HOH 00.0330.01916.7150.0140.0140.0000.0000.0000.000
203A330HOH 0-0.019-0.01924.8460.0070.0070.0000.0000.0000.000
204A331HOH 00.0230.01216.360-0.007-0.0070.0000.0000.0000.000
205A347HOH 0-0.002-0.00929.0320.0000.0000.0000.0000.0000.000
206A353HOH 0-0.013-0.01728.289-0.002-0.0020.0000.0000.0000.000
207A360HOH 0-0.035-0.02636.715-0.001-0.0010.0000.0000.0000.000
208A362HOH 0-0.003-0.00421.088-0.006-0.0060.0000.0000.0000.000
209A366HOH 00.0070.01022.2260.0020.0020.0000.0000.0000.000
210A394HOH 0-0.034-0.02832.430-0.001-0.0010.0000.0000.0000.000