FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: MNQ9Z

Calculation Name: 4YWK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YWK

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U3I4

Base Structure: X-ray

Registration Date: 2023-09-23

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

DOI:

Apendix: None


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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2282584.726048
FMO2-HF: Nuclear repulsion 2203077.102654
FMO2-HF: Total energy -79507.623394
FMO2-MP2: Total energy -79742.677115


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:1:VAL)


Summations of interaction energy for fragment #1(A:1: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.
-8.224-2.8673.261-2.854-5.7610
Interaction energy analysis for fragmet #1(A:1:VAL)
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 : -0.002
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].
3A3ARG10.9360.9403.7150.2681.755-0.003-0.818-0.6650.005
4A4GLU-1-0.999-1.0036.4620.7320.7320.0000.0000.0000.000
5A5GLU-1-0.793-0.8862.2041.7132.1742.248-0.824-1.885-0.001
6A6MET0-0.044-0.0192.444-1.505-0.5950.930-0.484-1.3560.000
7A7ILE0-0.043-0.0164.603-0.761-0.669-0.001-0.013-0.0770.000
8A8GLU-1-0.954-0.9668.2700.6470.6470.0000.0000.0000.000
9A9ARG10.7150.8073.378-1.587-1.0250.020-0.152-0.430-0.001
10A10PHE00.015-0.0086.765-0.323-0.3230.0000.0000.0000.000
11A11ALA0-0.030-0.0139.539-0.120-0.1200.0000.0000.0000.000
12A12ASN00.0070.00310.835-0.113-0.1130.0000.0000.0000.000
13A13PHE00.0040.01111.293-0.087-0.0870.0000.0000.0000.000
14A14LEU0-0.063-0.04012.997-0.046-0.0460.0000.0000.0000.000
15A15ARG10.7240.82915.406-0.253-0.2530.0000.0000.0000.000
16A16GLU-1-0.942-0.98515.3510.2190.2190.0000.0000.0000.000
17A17TYR0-0.0290.00115.801-0.019-0.0190.0000.0000.0000.000
18A18THR0-0.055-0.02917.5510.0070.0070.0000.0000.0000.000
19A19ASP-1-0.816-0.90220.856-0.035-0.0350.0000.0000.0000.000
20A20GLU-1-0.979-0.99523.099-0.047-0.0470.0000.0000.0000.000
21A21ASP-1-0.966-0.97225.731-0.020-0.0200.0000.0000.0000.000
22A22GLY0-0.074-0.04024.8540.0070.0070.0000.0000.0000.000
23A23ASN0-0.073-0.05825.5070.0170.0170.0000.0000.0000.000
24A24PRO00.0380.03421.674-0.008-0.0080.0000.0000.0000.000
25A25VAL00.006-0.01420.7110.0030.0030.0000.0000.0000.000
26A26TYR0-0.017-0.02917.737-0.011-0.0110.0000.0000.0000.000
27A27ARG10.9060.95119.714-0.081-0.0810.0000.0000.0000.000
28A28GLY00.0150.01321.8090.0000.0000.0000.0000.0000.000
29A29LYS10.8600.92620.2570.0720.0720.0000.0000.0000.000
30A30ILE00.0340.02617.930-0.005-0.0050.0000.0000.0000.000
31A31THR0-0.005-0.00922.0130.0020.0020.0000.0000.0000.000
32A32ASP-1-0.845-0.91425.178-0.025-0.0250.0000.0000.0000.000
33A33LEU0-0.074-0.03420.902-0.004-0.0040.0000.0000.0000.000
34A34LEU0-0.037-0.01625.4930.0020.0020.0000.0000.0000.000
35A35THR0-0.060-0.02128.2860.0000.0000.0000.0000.0000.000
36A36ILE00.011-0.00731.3660.0010.0010.0000.0000.0000.000
37A37THR0-0.062-0.03433.2750.0000.0000.0000.0000.0000.000
38A38PRO0-0.0280.02627.972-0.004-0.0040.0000.0000.0000.000
39A39LYS10.8680.91325.2360.0290.0290.0000.0000.0000.000
40A40ARG10.8670.89924.1600.0460.0460.0000.0000.0000.000
41A41SER0-0.013-0.03220.800-0.006-0.0060.0000.0000.0000.000
42A42VAL0-0.0050.01117.6910.0120.0120.0000.0000.0000.000
43A43ALA00.0070.01118.003-0.018-0.0180.0000.0000.0000.000
44A44ILE0-0.001-0.00713.4070.0250.0250.0000.0000.0000.000
45A45ASP-1-0.799-0.89116.731-0.193-0.1930.0000.0000.0000.000
46A46TRP00.000-0.03811.0880.0510.0510.0000.0000.0000.000
47A47MET0-0.0040.01214.253-0.037-0.0370.0000.0000.0000.000
48A48HIS00.0030.02316.1980.0110.0110.0000.0000.0000.000
49A49LEU00.0280.0288.9860.0220.0220.0000.0000.0000.000
50A50ASN0-0.011-0.01411.525-0.065-0.0650.0000.0000.0000.000
51A51SER0-0.129-0.06912.5830.0100.0100.0000.0000.0000.000
52A52PHE0-0.014-0.00411.0400.0110.0110.0000.0000.0000.000
53A53ASP-1-0.761-0.8646.569-0.135-0.1350.0000.0000.0000.000
54A54SER00.0320.0148.503-0.160-0.1600.0000.0000.0000.000
55A55GLU-1-0.910-0.9283.234-2.861-1.9800.020-0.314-0.586-0.002
56A56LEU00.0310.0183.959-0.855-0.6550.000-0.028-0.1720.000
57A57ALA00.002-0.0085.413-0.037-0.0370.0000.0000.0000.000
58A58HIS0-0.017-0.0117.1230.1720.1720.0000.0000.0000.000
59A59GLU-1-0.840-0.9263.024-3.400-2.6360.047-0.221-0.590-0.001
60A60VAL0-0.037-0.0116.0730.2380.2380.0000.0000.0000.000
61A61ILE0-0.063-0.0268.5500.1580.1580.0000.0000.0000.000
62A62GLU-1-0.797-0.8918.176-0.442-0.4420.0000.0000.0000.000
63A63ASN0-0.088-0.0475.4250.5760.5760.0000.0000.0000.000
64A64PRO00.0090.0188.517-0.068-0.0680.0000.0000.0000.000
65A65GLU-1-0.836-0.88410.990-0.267-0.2670.0000.0000.0000.000
66A66GLU-1-0.887-0.9407.241-0.951-0.9510.0000.0000.0000.000
67A67GLY00.0340.0216.7410.0680.0680.0000.0000.0000.000
68A68ILE0-0.029-0.0347.6740.2060.2060.0000.0000.0000.000
69A69SER0-0.0040.00310.7780.1000.1000.0000.0000.0000.000
70A70ALA00.0010.0067.2340.1220.1220.0000.0000.0000.000
71A71ALA00.0290.0169.0810.1540.1540.0000.0000.0000.000
72A72GLU-1-0.834-0.92210.832-0.086-0.0860.0000.0000.0000.000
73A73ASP-1-0.859-0.92211.6850.0570.0570.0000.0000.0000.000
74A74ALA00.0150.01110.7870.0400.0400.0000.0000.0000.000
75A75ILE0-0.019-0.01712.8390.0080.0080.0000.0000.0000.000
76A76GLN0-0.066-0.03616.0970.0120.0120.0000.0000.0000.000
77A77ILE00.0000.01314.066-0.006-0.0060.0000.0000.0000.000
78A78VAL00.0430.02615.686-0.005-0.0050.0000.0000.0000.000
79A79LEU0-0.041-0.01718.272-0.011-0.0110.0000.0000.0000.000
80A80ARG10.8660.93119.915-0.126-0.1260.0000.0000.0000.000
81A81GLU-1-0.905-0.94517.9690.2540.2540.0000.0000.0000.000
82A82ASP-1-0.792-0.86620.7680.1320.1320.0000.0000.0000.000
83A83PHE0-0.084-0.05621.980-0.014-0.0140.0000.0000.0000.000
84A84GLN0-0.043-0.00224.862-0.016-0.0160.0000.0000.0000.000
85A85ARG10.7830.86324.876-0.039-0.0390.0000.0000.0000.000
86A86GLU-1-0.825-0.91923.6220.1000.1000.0000.0000.0000.000
87A87ASP-1-0.877-0.90624.8470.0290.0290.0000.0000.0000.000
88A88VAL00.0160.01323.773-0.006-0.0060.0000.0000.0000.000
89A89GLY0-0.0090.00724.434-0.009-0.0090.0000.0000.0000.000
90A90LYS10.8500.90316.0400.0910.0910.0000.0000.0000.000
91A91ILE00.0010.01319.191-0.002-0.0020.0000.0000.0000.000
92A92HIS0-0.056-0.03218.014-0.017-0.0170.0000.0000.0000.000
93A93ALA00.0010.00814.0000.0180.0180.0000.0000.0000.000
94A94ARG10.7680.90015.8780.1050.1050.0000.0000.0000.000
95A95PHE00.0670.02910.8720.0090.0090.0000.0000.0000.000
96A96TYR00.0120.00816.1700.0050.0050.0000.0000.0000.000
97A97ASN0-0.038-0.03017.800-0.014-0.0140.0000.0000.0000.000
98A98LEU00.027-0.00314.884-0.016-0.0160.0000.0000.0000.000
99A99PRO0-0.0050.00315.4320.0310.0310.0000.0000.0000.000
100A100GLU-1-0.949-0.96718.531-0.235-0.2350.0000.0000.0000.000
101A101THR0-0.021-0.01720.556-0.013-0.0130.0000.0000.0000.000
102A102LEU0-0.050-0.00621.4080.0120.0120.0000.0000.0000.000
103A103MET0-0.010-0.02025.0600.0120.0120.0000.0000.0000.000
104A104VAL00.0130.00227.691-0.006-0.0060.0000.0000.0000.000
105A105LYS10.7380.85528.8670.0960.0960.0000.0000.0000.000
106A106ASP-1-0.839-0.91126.557-0.134-0.1340.0000.0000.0000.000
107A107ILE0-0.073-0.01723.704-0.010-0.0100.0000.0000.0000.000
108A108GLY00.013-0.00223.9210.0160.0160.0000.0000.0000.000
109A109ALA0-0.103-0.06222.901-0.012-0.0120.0000.0000.0000.000
110A110GLU-1-0.885-0.95219.948-0.201-0.2010.0000.0000.0000.000
111A111HIS00.0910.04418.395-0.019-0.0190.0000.0000.0000.000
112A112ILE0-0.091-0.04718.198-0.006-0.0060.0000.0000.0000.000
113A113ASN0-0.053-0.03313.9420.0080.0080.0000.0000.0000.000
114A114LYS10.8690.94113.2430.4160.4160.0000.0000.0000.000
115A115LEU0-0.0380.00013.4090.0620.0620.0000.0000.0000.000
116A116ILE0-0.032-0.02115.0770.0020.0020.0000.0000.0000.000
117A117GLN00.0570.01918.3990.0090.0090.0000.0000.0000.000
118A118VAL0-0.049-0.01620.8500.0070.0070.0000.0000.0000.000
119A119GLU-1-0.799-0.88624.528-0.118-0.1180.0000.0000.0000.000
120A120GLY0-0.012-0.02327.7790.0010.0010.0000.0000.0000.000
121A121ILE0-0.084-0.03330.9250.0040.0040.0000.0000.0000.000
122A122VAL00.0560.04631.881-0.002-0.0020.0000.0000.0000.000
123A123THR0-0.050-0.02934.3100.0050.0050.0000.0000.0000.000
124A124ARG10.8870.93135.8160.0700.0700.0000.0000.0000.000
125A125VAL00.0710.04133.670-0.005-0.0050.0000.0000.0000.000
126A126GLY0-0.029-0.00434.4800.0050.0050.0000.0000.0000.000
127A127GLU-1-0.904-0.94534.186-0.054-0.0540.0000.0000.0000.000
128A128ILE0-0.081-0.03433.8900.0040.0040.0000.0000.0000.000
129A129LYS10.9891.01532.9550.0350.0350.0000.0000.0000.000
130A130PRO0-0.042-0.02929.0870.0020.0020.0000.0000.0000.000
131A182PHE00.020-0.00125.426-0.001-0.0010.0000.0000.0000.000
132A183GLN00.0500.01429.3340.0040.0040.0000.0000.0000.000
133A184SER0-0.061-0.02129.401-0.007-0.0070.0000.0000.0000.000
134A185PHE00.0980.04428.8760.0040.0040.0000.0000.0000.000
135A186ARG10.7220.83130.9280.0760.0760.0000.0000.0000.000
136A187ILE00.0490.03427.4350.0060.0060.0000.0000.0000.000
137A188GLN0-0.027-0.02831.418-0.002-0.0020.0000.0000.0000.000
138A189ASP-1-0.714-0.86532.142-0.108-0.1080.0000.0000.0000.000
139A190ARG10.7880.87529.6290.1120.1120.0000.0000.0000.000
140A191PRO00.0220.01235.3720.0000.0000.0000.0000.0000.000
141A192GLU-1-0.766-0.86336.072-0.076-0.0760.0000.0000.0000.000
142A193THR0-0.041-0.02733.082-0.002-0.0020.0000.0000.0000.000
143A194LEU0-0.066-0.01636.235-0.003-0.0030.0000.0000.0000.000
144A195LYS10.8930.93736.6220.0880.0880.0000.0000.0000.000
145A196GLY00.0260.00041.2820.0000.0000.0000.0000.0000.000
146A197GLY0-0.003-0.01043.5540.0020.0020.0000.0000.0000.000
147A198GLU-1-0.851-0.90036.529-0.088-0.0880.0000.0000.0000.000
148A199MET00.004-0.00639.9470.0000.0000.0000.0000.0000.000
149A200PRO0-0.0170.00336.945-0.003-0.0030.0000.0000.0000.000
150A201ARG10.9290.97332.9150.0980.0980.0000.0000.0000.000
151A202PHE00.015-0.01132.6220.0000.0000.0000.0000.0000.000
152A203ILE0-0.0100.00425.9240.0000.0000.0000.0000.0000.000
153A204ASP-1-0.786-0.84830.169-0.087-0.0870.0000.0000.0000.000
154A205GLY00.0450.02726.638-0.010-0.0100.0000.0000.0000.000
155A206ILE0-0.052-0.03425.8020.0140.0140.0000.0000.0000.000
156A207LEU00.0450.02023.915-0.013-0.0130.0000.0000.0000.000
157A208LEU00.0340.02823.6450.0100.0100.0000.0000.0000.000
158A209ASP-1-0.841-0.94523.199-0.093-0.0930.0000.0000.0000.000
159A210ASP-1-0.761-0.83624.090-0.052-0.0520.0000.0000.0000.000
160A211ILE0-0.092-0.06624.9900.0100.0100.0000.0000.0000.000
161A212VAL0-0.048-0.01227.1880.0040.0040.0000.0000.0000.000
162A213ASP-1-0.876-0.93930.013-0.062-0.0620.0000.0000.0000.000
163A214VAL0-0.078-0.03427.9240.0020.0020.0000.0000.0000.000
164A215ALA0-0.013-0.00231.204-0.002-0.0020.0000.0000.0000.000
165A216LEU00.0280.01233.0240.0020.0020.0000.0000.0000.000
166A217PRO0-0.057-0.04736.169-0.003-0.0030.0000.0000.0000.000
167A218GLY0-0.037-0.01837.5610.0040.0040.0000.0000.0000.000
168A219ASP-1-0.815-0.88133.972-0.066-0.0660.0000.0000.0000.000
169A220ARG10.7420.82333.0710.0690.0690.0000.0000.0000.000
170A221VAL00.0070.00328.5480.0020.0020.0000.0000.0000.000
171A222ILE00.0370.02523.778-0.002-0.0020.0000.0000.0000.000
172A223VAL0-0.018-0.01323.6320.0040.0040.0000.0000.0000.000
173A224THR00.0520.01418.112-0.007-0.0070.0000.0000.0000.000
174A225GLY00.012-0.00518.7500.0220.0220.0000.0000.0000.000
175A226ILE00.0500.05114.947-0.019-0.0190.0000.0000.0000.000
176A227LEU0-0.053-0.02718.5420.0390.0390.0000.0000.0000.000
177A228ARG10.7500.83417.1260.2430.2430.0000.0000.0000.000
178A229VAL0-0.017-0.02423.0350.0080.0080.0000.0000.0000.000
179A230VAL00.0200.01926.5010.0040.0040.0000.0000.0000.000
180A231LEU0-0.044-0.01429.9420.0020.0020.0000.0000.0000.000
181A232GLU-1-0.868-0.93032.720-0.074-0.0740.0000.0000.0000.000
182A233LYS10.9920.97035.4600.0570.0570.0000.0000.0000.000
183A234ARG10.8050.85838.9010.0550.0550.0000.0000.0000.000
184A235GLU-1-0.829-0.87140.605-0.051-0.0510.0000.0000.0000.000
185A236LYS10.8870.94537.1080.0730.0730.0000.0000.0000.000
186A237THR00.0090.00139.4590.0010.0010.0000.0000.0000.000
187A238PRO0-0.030-0.02337.097-0.003-0.0030.0000.0000.0000.000
188A239ILE0-0.0070.01433.1880.0000.0000.0000.0000.0000.000
189A240PHE00.0360.00428.5180.0030.0030.0000.0000.0000.000
190A241ARG10.8110.92029.4500.1010.1010.0000.0000.0000.000
191A242LYS10.9960.98923.6350.1760.1760.0000.0000.0000.000
192A243ILE0-0.030-0.00825.7710.0110.0110.0000.0000.0000.000
193A244LEU00.0200.01321.191-0.011-0.0110.0000.0000.0000.000
194A245GLU-1-0.848-0.90420.205-0.174-0.1740.0000.0000.0000.000
195A246VAL0-0.045-0.02720.621-0.022-0.0220.0000.0000.0000.000
196A247ASN0-0.003-0.01416.214-0.004-0.0040.0000.0000.0000.000
197A248HIS00.0180.00019.2790.0110.0110.0000.0000.0000.000
198A249ILE0-0.016-0.01221.343-0.007-0.0070.0000.0000.0000.000
199A250GLU-1-0.864-0.90424.575-0.116-0.1160.0000.0000.0000.000