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: YYLN2

Calculation Name: 3QK7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QK7

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 280
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3699081.980346
FMO2-HF: Nuclear repulsion 3592346.529012
FMO2-HF: Total energy -106735.451333
FMO2-MP2: Total energy -107049.275904


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:5:ARG)


Summations of interaction energy for fragment #1(A:5:ARG)
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.
-287.546-275.11217.5-14.177-15.758-0.146
Interaction energy analysis for fragmet #1(A:5:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.917
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].
3A7ASP-1-0.879-0.9422.794-70.204-63.0490.952-3.923-4.184-0.026
4A8ALA00.0020.0184.5326.0426.140-0.001-0.015-0.0820.000
5A9ILE0-0.007-0.0096.398-3.060-3.0600.0000.0000.0000.000
6A10ALA00.0110.0199.3592.7612.7610.0000.0000.0000.000
7A11LEU00.0100.00912.441-0.389-0.3890.0000.0000.0000.000
8A12ALA0-0.0030.00015.3730.8650.8650.0000.0000.0000.000
9A13TYR0-0.005-0.01017.9940.1750.1750.0000.0000.0000.000
10A14PRO00.0300.02921.5600.0830.0830.0000.0000.0000.000
11A15SER00.008-0.01324.8550.1920.1920.0000.0000.0000.000
12A16ARG10.7210.83127.57610.29410.2940.0000.0000.0000.000
13A17PRO00.0540.02328.875-0.217-0.2170.0000.0000.0000.000
14A18ARG11.0320.98230.9889.0109.0100.0000.0000.0000.000
15A19VAL0-0.0040.01231.458-0.222-0.2220.0000.0000.0000.000
16A20LEU00.0450.02328.9270.0470.0470.0000.0000.0000.000
17A21ASN0-0.095-0.03626.541-0.660-0.6600.0000.0000.0000.000
18A22ASN00.0400.02028.731-0.131-0.1310.0000.0000.0000.000
19A23SER00.0590.02028.552-0.433-0.4330.0000.0000.0000.000
20A24THR00.0810.03827.857-0.290-0.2900.0000.0000.0000.000
21A25PHE0-0.0040.00222.072-0.561-0.5610.0000.0000.0000.000
22A26LEU00.0180.00324.005-0.618-0.6180.0000.0000.0000.000
23A27GLU-1-0.838-0.91624.047-12.400-12.4000.0000.0000.0000.000
24A28MET0-0.012-0.01120.656-0.339-0.3390.0000.0000.0000.000
25A29ILE0-0.008-0.00319.278-0.832-0.8320.0000.0000.0000.000
26A30SER0-0.039-0.03319.218-0.715-0.7150.0000.0000.0000.000
27A31TRP0-0.032-0.03119.854-0.726-0.7260.0000.0000.0000.000
28A32ILE0-0.0190.00114.747-0.705-0.7050.0000.0000.0000.000
29A33GLY00.0190.00815.147-1.370-1.3700.0000.0000.0000.000
30A34ILE0-0.015-0.00315.105-0.912-0.9120.0000.0000.0000.000
31A35GLU-1-0.832-0.90515.897-17.602-17.6020.0000.0000.0000.000
32A36LEU00.0180.0119.891-0.816-0.8160.0000.0000.0000.000
33A37GLY00.0540.04211.243-1.624-1.6240.0000.0000.0000.000
34A38LYS10.7240.83313.43416.33916.3390.0000.0000.0000.000
35A39ARG10.6310.7119.10930.22030.2200.0000.0000.0000.000
36A40GLY0-0.013-0.0019.074-3.014-3.0140.0000.0000.0000.000
37A41LEU0-0.0080.0094.866-2.284-2.2840.0000.0000.0000.000
38A42ASP-1-0.895-0.9398.589-22.511-22.5110.0000.0000.0000.000
39A43LEU0-0.038-0.02710.398-1.371-1.3710.0000.0000.0000.000
40A44LEU0-0.050-0.02311.4511.8321.8320.0000.0000.0000.000
41A45LEU00.001-0.00414.081-0.130-0.1300.0000.0000.0000.000
42A46ILE0-0.015-0.02215.8000.4700.4700.0000.0000.0000.000
43A47PRO00.0070.01118.6840.0890.0890.0000.0000.0000.000
44A48ASP-1-0.851-0.93922.333-13.114-13.1140.0000.0000.0000.000
45A49GLU-1-0.923-0.95423.757-11.175-11.1750.0000.0000.0000.000
46A50PRO0-0.047-0.03326.7590.0320.0320.0000.0000.0000.000
47A51GLY0-0.011-0.02129.6100.2430.2430.0000.0000.0000.000
48A52GLU-1-0.806-0.85226.153-10.384-10.3840.0000.0000.0000.000
49A53LYS10.8970.94725.71211.33111.3310.0000.0000.0000.000
50A54TYR00.0310.02020.305-0.172-0.1720.0000.0000.0000.000
51A55GLN00.0860.03720.318-0.339-0.3390.0000.0000.0000.000
52A56SER00.0290.01718.388-0.540-0.5400.0000.0000.0000.000
53A57LEU00.0490.02615.968-0.929-0.9290.0000.0000.0000.000
54A58ILE0-0.0100.00615.295-1.194-1.1940.0000.0000.0000.000
55A59HIS00.0140.01715.405-0.396-0.3960.0000.0000.0000.000
56A60LEU00.002-0.01411.613-0.620-0.6200.0000.0000.0000.000
57A61VAL0-0.041-0.02011.229-1.546-1.5460.0000.0000.0000.000
58A62GLU-1-0.978-0.98911.789-16.417-16.4170.0000.0000.0000.000
59A63THR0-0.106-0.06311.180-0.104-0.1040.0000.0000.0000.000
60A64ARG10.9400.9705.54528.46628.4660.0000.0000.0000.000
61A65ARG10.9190.9626.72319.01219.0120.0000.0000.0000.000
62A66VAL00.0060.0017.0440.4880.4880.0000.0000.0000.000
63A67ASP-1-0.758-0.8371.789-101.320-99.90110.819-6.254-5.985-0.074
64A68ALA0-0.006-0.0025.0460.3860.460-0.001-0.002-0.0710.000
65A69LEU0-0.017-0.0217.4022.0782.0780.0000.0000.0000.000
66A70ILE00.0030.01211.0800.2990.2990.0000.0000.0000.000
67A71VAL0-0.008-0.00413.6990.9470.9470.0000.0000.0000.000
68A72ALA00.0300.01916.9550.4270.4270.0000.0000.0000.000
69A73HIS0-0.019-0.01620.2400.0820.0820.0000.0000.0000.000
70A74THR00.0090.01921.233-0.102-0.1020.0000.0000.0000.000
71A75GLN0-0.0020.00123.1150.7570.7570.0000.0000.0000.000
72A76PRO00.0530.01325.134-0.406-0.4060.0000.0000.0000.000
73A77GLU-1-0.843-0.92226.351-11.500-11.5000.0000.0000.0000.000
74A78ASP-1-0.820-0.89021.719-13.803-13.8030.0000.0000.0000.000
75A79PHE00.0460.00222.648-0.433-0.4330.0000.0000.0000.000
76A80ARG10.8020.88819.38814.12114.1210.0000.0000.0000.000
77A81LEU00.0180.00917.043-0.990-0.9900.0000.0000.0000.000
78A82GLN0-0.052-0.01717.900-0.647-0.6470.0000.0000.0000.000
79A83TYR0-0.032-0.01016.513-0.121-0.1210.0000.0000.0000.000
80A84LEU00.0200.01312.889-0.438-0.4380.0000.0000.0000.000
81A85GLN00.0150.00014.693-0.062-0.0620.0000.0000.0000.000
82A86LYS10.9110.95916.13013.55713.5570.0000.0000.0000.000
83A87GLN0-0.049-0.03314.9040.4000.4000.0000.0000.0000.000
84A88ASN0-0.102-0.04312.537-1.274-1.2740.0000.0000.0000.000
85A89PHE00.0090.0248.959-1.858-1.8580.0000.0000.0000.000
86A90PRO00.0300.0115.5712.3492.3490.0000.0000.0000.000
87A91PHE0-0.015-0.0228.6050.2590.2590.0000.0000.0000.000
88A92LEU00.0260.02411.1030.4000.4000.0000.0000.0000.000
89A93ALA0-0.032-0.03013.0060.4450.4450.0000.0000.0000.000
90A94LEU00.0110.00716.3670.2580.2580.0000.0000.0000.000
91A95GLY00.0240.01319.1240.8060.8060.0000.0000.0000.000
92A96ARG10.8430.90320.74511.70911.7090.0000.0000.0000.000
93A97SER00.0100.02022.0260.6340.6340.0000.0000.0000.000
94A98HIS0-0.033-0.00523.504-0.424-0.4240.0000.0000.0000.000
95A99LEU00.0300.00519.038-0.259-0.2590.0000.0000.0000.000
96A100PRO00.0020.01522.2060.2190.2190.0000.0000.0000.000
97A101LYS10.8640.92419.93113.07413.0740.0000.0000.0000.000
98A102PRO00.0290.00718.003-0.019-0.0190.0000.0000.0000.000
99A103TYR00.001-0.01515.489-0.615-0.6150.0000.0000.0000.000
100A104ALA00.0620.05112.6120.6580.6580.0000.0000.0000.000
101A105TRP0-0.013-0.00214.5630.1080.1080.0000.0000.0000.000
102A106PHE0-0.001-0.00717.151-0.120-0.1200.0000.0000.0000.000
103A107ASP-1-0.799-0.89218.855-12.343-12.3430.0000.0000.0000.000
104A108PHE00.0280.01522.597-0.117-0.1170.0000.0000.0000.000
105A109ASP-1-0.826-0.92025.959-10.304-10.3040.0000.0000.0000.000
106A110ASN0-0.002-0.00927.3020.5390.5390.0000.0000.0000.000
107A111HIS00.0180.01630.9060.1510.1510.0000.0000.0000.000
108A112ALA00.0190.00732.3000.3370.3370.0000.0000.0000.000
109A113GLY00.0430.01933.1520.2590.2590.0000.0000.0000.000
110A114ALA0-0.031-0.01634.6050.2600.2600.0000.0000.0000.000
111A115SER00.020-0.00236.8520.1800.1800.0000.0000.0000.000
112A116LEU0-0.039-0.01235.7820.2900.2900.0000.0000.0000.000
113A117ALA00.0250.01139.1200.2230.2230.0000.0000.0000.000
114A118VAL0-0.0060.00041.0390.2250.2250.0000.0000.0000.000
115A119LYS10.8460.90041.5457.5167.5160.0000.0000.0000.000
116A120ARG10.8980.95343.2137.1177.1170.0000.0000.0000.000
117A121LEU00.024-0.00144.9250.1880.1880.0000.0000.0000.000
118A122LEU0-0.021-0.01045.9190.1730.1730.0000.0000.0000.000
119A123GLU-1-0.907-0.93945.814-6.915-6.9150.0000.0000.0000.000
120A124LEU0-0.066-0.00848.1380.1340.1340.0000.0000.0000.000
121A125GLY00.004-0.00651.2650.1460.1460.0000.0000.0000.000
122A126HIS0-0.0410.00050.0370.1570.1570.0000.0000.0000.000
123A127GLN00.037-0.00351.056-0.036-0.0360.0000.0000.0000.000
124A128ARG10.9180.96951.2595.5695.5690.0000.0000.0000.000
125A129ILE00.0610.03945.518-0.001-0.0010.0000.0000.0000.000
126A130ALA00.0000.01347.170-0.034-0.0340.0000.0000.0000.000
127A131PHE0-0.011-0.02137.467-0.162-0.1620.0000.0000.0000.000
128A132VAL00.007-0.00541.7100.0690.0690.0000.0000.0000.000
129A133SER00.0080.01236.995-0.209-0.2090.0000.0000.0000.000
130A134THR00.001-0.02534.5390.0670.0670.0000.0000.0000.000
131A135ASP-1-0.875-0.92536.273-8.353-8.3530.0000.0000.0000.000
132A136ALA0-0.042-0.02132.067-0.073-0.0730.0000.0000.0000.000
133A137ARG10.8630.92631.5198.9218.9210.0000.0000.0000.000
134A138ILE00.0300.01526.713-0.329-0.3290.0000.0000.0000.000
135A139SER00.033-0.00625.7370.3250.3250.0000.0000.0000.000
136A140TYR00.0010.00227.3980.1500.1500.0000.0000.0000.000
137A141VAL0-0.021-0.01228.9760.2780.2780.0000.0000.0000.000
138A142ASP-1-0.886-0.94231.577-9.292-9.2920.0000.0000.0000.000
139A143GLN0-0.0030.00226.4570.2760.2760.0000.0000.0000.000
140A144ARG10.8340.92529.87810.29010.2900.0000.0000.0000.000
141A145LEU0-0.031-0.00934.4970.2860.2860.0000.0000.0000.000
142A146GLN00.000-0.01634.3660.4030.4030.0000.0000.0000.000
143A147GLY00.0620.03935.9120.1790.1790.0000.0000.0000.000
144A148TYR0-0.039-0.02337.2020.2120.2120.0000.0000.0000.000
145A149VAL0-0.013-0.01140.1360.1980.1980.0000.0000.0000.000
146A150GLN0-0.007-0.01936.3470.1690.1690.0000.0000.0000.000
147A151THR0-0.006-0.01440.1210.0790.0790.0000.0000.0000.000
148A152MET0-0.0120.00742.4020.1440.1440.0000.0000.0000.000
149A153SER0-0.0310.00044.1690.1790.1790.0000.0000.0000.000
150A154GLU-1-1.004-1.00642.224-7.372-7.3720.0000.0000.0000.000
151A155ALA0-0.030-0.02746.0490.0220.0220.0000.0000.0000.000
152A156GLY0-0.022-0.00249.0970.1070.1070.0000.0000.0000.000
153A157LEU0-0.0210.00349.2500.1700.1700.0000.0000.0000.000
154A158MET0-0.017-0.01049.039-0.090-0.0900.0000.0000.0000.000
155A159PRO00.0030.00346.4290.1110.1110.0000.0000.0000.000
156A160LEU00.0030.00649.5970.0270.0270.0000.0000.0000.000
157A161ALA00.013-0.00450.531-0.132-0.1320.0000.0000.0000.000
158A162GLY00.0050.00149.7860.0750.0750.0000.0000.0000.000
159A163TYR00.000-0.02348.261-0.071-0.0710.0000.0000.0000.000
160A164LEU0-0.0130.03041.250-0.139-0.1390.0000.0000.0000.000
161A165GLN0-0.030-0.02344.1020.0910.0910.0000.0000.0000.000
162A166LYS10.8710.92036.6598.3278.3270.0000.0000.0000.000
163A167ALA0-0.007-0.00540.6010.1960.1960.0000.0000.0000.000
164A168ASP-1-0.814-0.89838.580-8.470-8.4700.0000.0000.0000.000
165A169PRO0-0.0070.00034.8120.1640.1640.0000.0000.0000.000
166A170THR0-0.048-0.04537.155-0.090-0.0900.0000.0000.0000.000
167A171ARG10.9510.95439.7987.5747.5740.0000.0000.0000.000
168A172PRO0-0.001-0.01942.5700.1570.1570.0000.0000.0000.000
169A173GLY00.0240.02642.2360.1580.1580.0000.0000.0000.000
170A174GLY00.003-0.00842.9570.1160.1160.0000.0000.0000.000
171A175TYR00.0530.04344.1740.1700.1700.0000.0000.0000.000
172A176LEU0-0.031-0.00447.1130.1760.1760.0000.0000.0000.000
173A177ALA00.002-0.00645.0620.1280.1280.0000.0000.0000.000
174A178ALA00.0370.02047.1840.1000.1000.0000.0000.0000.000
175A179SER0-0.025-0.02549.3300.1660.1660.0000.0000.0000.000
176A180ARG10.8840.94747.0076.7366.7360.0000.0000.0000.000
177A181LEU0-0.014-0.00147.1460.0900.0900.0000.0000.0000.000
178A182LEU0-0.009-0.01851.6690.0930.0930.0000.0000.0000.000
179A183ALA0-0.042-0.00854.6620.1160.1160.0000.0000.0000.000
180A184LEU0-0.066-0.01551.9080.0750.0750.0000.0000.0000.000
181A185GLU-1-0.952-0.97156.458-5.167-5.1670.0000.0000.0000.000
182A186VAL0-0.015-0.01556.9750.0740.0740.0000.0000.0000.000
183A187PRO00.0030.03354.769-0.108-0.1080.0000.0000.0000.000
184A188PRO0-0.050-0.02150.3670.0490.0490.0000.0000.0000.000
185A189THR0-0.023-0.03452.5800.0600.0600.0000.0000.0000.000
186A190ALA00.0190.01248.322-0.008-0.0080.0000.0000.0000.000
187A191ILE0-0.040-0.02344.917-0.014-0.0140.0000.0000.0000.000
188A192ILE00.0410.03440.149-0.069-0.0690.0000.0000.0000.000
189A193THR0-0.020-0.00939.6530.0720.0720.0000.0000.0000.000
190A194ASP-1-0.758-0.88635.525-8.936-8.9360.0000.0000.0000.000
191A195CYS0-0.066-0.02434.425-0.321-0.3210.0000.0000.0000.000
192A196ASN00.1770.09134.4300.2280.2280.0000.0000.0000.000
193A197MET0-0.014-0.00535.7790.2680.2680.0000.0000.0000.000
194A198LEU0-0.030-0.02538.3660.2490.2490.0000.0000.0000.000
195A199GLY00.0500.03139.8690.2450.2450.0000.0000.0000.000
196A200ASP-1-0.701-0.82641.249-7.201-7.2010.0000.0000.0000.000
197A201GLY0-0.0310.00342.9940.2070.2070.0000.0000.0000.000
198A202VAL0-0.040-0.03844.3520.1880.1880.0000.0000.0000.000
199A203ALA00.0380.02045.5190.1820.1820.0000.0000.0000.000
200A204SER00.018-0.00146.7490.1760.1760.0000.0000.0000.000
201A205ALA0-0.092-0.04749.0610.1650.1650.0000.0000.0000.000
202A206LEU00.011-0.00348.9840.1450.1450.0000.0000.0000.000
203A207ASP-1-0.887-0.93151.220-6.034-6.0340.0000.0000.0000.000
204A208LYS10.8610.93153.0436.2016.2010.0000.0000.0000.000
205A209ALA0-0.061-0.03555.1110.1260.1260.0000.0000.0000.000
206A210GLY0-0.0010.00356.4040.1080.1080.0000.0000.0000.000
207A211LEU0-0.074-0.04354.6630.0410.0410.0000.0000.0000.000
208A212LEU00.0150.01248.650-0.086-0.0860.0000.0000.0000.000
209A213GLY00.0380.02351.5960.0870.0870.0000.0000.0000.000
210A214GLY00.021-0.00352.9250.0580.0580.0000.0000.0000.000
211A215GLU-1-0.960-0.99455.415-5.517-5.5170.0000.0000.0000.000
212A216GLY0-0.0570.00155.5560.0600.0600.0000.0000.0000.000
213A217ILE0-0.051-0.02350.428-0.037-0.0370.0000.0000.0000.000
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