Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: N228Q

Calculation Name: 4JKZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JKZ

Chain ID: A

ChEMBL ID:

UniProt ID: A0R6I8

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptAll
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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1699646.147037
FMO2-HF: Nuclear repulsion 1632300.295775
FMO2-HF: Total energy -67345.851262
FMO2-MP2: Total energy -67544.803312


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:11:SER)


Summations of interaction energy for fragment #1(A:11:SER)
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.
-21.005-17.2146.241-3.981-6.0490.024
Interaction energy analysis for fragmet #1(A:11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.001
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].
3A13LYS11.0110.9893.1870.0332.0590.051-0.914-1.1630.001
4A14SER0-0.025-0.0042.426-4.741-2.6860.964-1.227-1.7910.006
5A15ARG10.9941.0134.192-2.730-2.4490.001-0.080-0.2020.000
6A16VAL00.0030.0076.770-0.505-0.5050.0000.0000.0000.000
7A17ALA00.0810.0437.592-0.296-0.2960.0000.0000.0000.000
8A18ILE00.0010.0066.829-0.308-0.3080.0000.0000.0000.000
9A19VAL0-0.0090.01210.067-0.247-0.2470.0000.0000.0000.000
10A20GLU-1-0.921-0.96411.4810.4520.4520.0000.0000.0000.000
11A21ALA0-0.006-0.00312.826-0.127-0.1270.0000.0000.0000.000
12A22THR0-0.012-0.02913.736-0.111-0.1110.0000.0000.0000.000
13A23ARG10.7970.87316.122-0.572-0.5720.0000.0000.0000.000
14A24ALA00.0130.00417.487-0.063-0.0630.0000.0000.0000.000
15A25LEU0-0.031-0.02217.103-0.050-0.0500.0000.0000.0000.000
16A26LEU00.0370.02819.912-0.049-0.0490.0000.0000.0000.000
17A27LEU0-0.063-0.02022.041-0.038-0.0380.0000.0000.0000.000
18A28GLU-1-0.821-0.87821.8010.2380.2380.0000.0000.0000.000
19A29ARG10.9130.94623.821-0.229-0.2290.0000.0000.0000.000
20A30GLY0-0.0090.01425.357-0.004-0.0040.0000.0000.0000.000
21A31PHE00.0440.00223.9680.0220.0220.0000.0000.0000.000
22A32ASP-1-0.835-0.90024.8260.2290.2290.0000.0000.0000.000
23A33GLY0-0.0110.00024.335-0.004-0.0040.0000.0000.0000.000
24A34LEU0-0.0380.00918.8770.0160.0160.0000.0000.0000.000
25A35SER00.0360.01820.4440.0330.0330.0000.0000.0000.000
26A36ILE00.0670.01814.0600.0120.0120.0000.0000.0000.000
27A37GLU-1-0.791-0.87515.4940.5370.5370.0000.0000.0000.000
28A38ALA0-0.0050.00616.666-0.004-0.0040.0000.0000.0000.000
29A39VAL00.0110.00712.448-0.013-0.0130.0000.0000.0000.000
30A40ALA0-0.010-0.00611.8010.0690.0690.0000.0000.0000.000
31A41ALA0-0.007-0.00112.2020.0010.0010.0000.0000.0000.000
32A42LYS10.7790.88214.300-0.384-0.3840.0000.0000.0000.000
33A43ALA00.0030.0009.279-0.042-0.0420.0000.0000.0000.000
34A44GLY0-0.0200.0129.3700.0470.0470.0000.0000.0000.000
35A45VAL0-0.065-0.0356.326-0.021-0.0210.0000.0000.0000.000
36A46GLY00.0420.0179.049-0.133-0.1330.0000.0000.0000.000
37A47LYS10.8540.8879.587-0.199-0.1990.0000.0000.0000.000
38A48GLN00.0430.01410.1670.0910.0910.0000.0000.0000.000
39A49THR0-0.024-0.0114.6310.1470.233-0.001-0.006-0.0780.000
40A50ILE00.0120.0107.1640.5920.5920.0000.0000.0000.000
41A51TYR00.007-0.0059.748-0.007-0.0070.0000.0000.0000.000
42A52ARG10.8420.9412.217-13.504-15.0445.131-1.405-2.1850.014
43A53TRP0-0.044-0.0323.129-0.0930.7900.095-0.349-0.6300.003
44A54TRP0-0.013-0.0199.502-0.114-0.1140.0000.0000.0000.000
45A55PRO00.0120.01213.7830.0580.0580.0000.0000.0000.000
46A56SER0-0.026-0.05316.328-0.062-0.0620.0000.0000.0000.000
47A57ARG10.8400.91117.024-0.360-0.3600.0000.0000.0000.000
48A58HIS00.0200.01118.3880.0090.0090.0000.0000.0000.000
49A59ALA00.0380.02417.932-0.004-0.0040.0000.0000.0000.000
50A60LEU0-0.021-0.00613.023-0.008-0.0080.0000.0000.0000.000
51A61VAL0-0.019-0.01716.366-0.021-0.0210.0000.0000.0000.000
52A62ALA00.011-0.00219.144-0.037-0.0370.0000.0000.0000.000
53A63ASP-1-0.855-0.91015.9960.6850.6850.0000.0000.0000.000
54A64VAL0-0.008-0.01515.524-0.021-0.0210.0000.0000.0000.000
55A65LEU0-0.022-0.02918.082-0.055-0.0550.0000.0000.0000.000
56A66LEU0-0.0020.00520.877-0.041-0.0410.0000.0000.0000.000
57A67GLU-1-0.857-0.91815.4480.6680.6680.0000.0000.0000.000
58A68ASP-1-0.820-0.88520.5280.3120.3120.0000.0000.0000.000
59A69ALA00.0390.01923.560-0.031-0.0310.0000.0000.0000.000
60A70ASP-1-0.878-0.93726.4610.2020.2020.0000.0000.0000.000
61A71LYS10.7600.85924.481-0.261-0.2610.0000.0000.0000.000
62A72ILE0-0.080-0.03225.393-0.010-0.0100.0000.0000.0000.000
63A73LEU0-0.0020.01529.910-0.011-0.0110.0000.0000.0000.000
64A74ALA0-0.0200.00132.567-0.010-0.0100.0000.0000.0000.000
65A75ARG10.9170.93734.018-0.131-0.1310.0000.0000.0000.000
66A76MET00.0030.01738.831-0.003-0.0030.0000.0000.0000.000
67A77PRO0-0.053-0.02342.305-0.002-0.0020.0000.0000.0000.000
68A78LYS10.8290.88244.838-0.082-0.0820.0000.0000.0000.000
69A79THR0-0.074-0.05848.142-0.003-0.0030.0000.0000.0000.000
70A80ASP-1-0.883-0.94351.7670.0570.0570.0000.0000.0000.000
71A81ASP-1-0.798-0.88353.8270.0650.0650.0000.0000.0000.000
72A82VAL00.0580.03050.0770.0030.0030.0000.0000.0000.000
73A83THR0-0.074-0.05950.5440.0040.0040.0000.0000.0000.000
74A84ALA0-0.027-0.01750.9880.0040.0040.0000.0000.0000.000
75A85ASP-1-0.753-0.83147.5830.0800.0800.0000.0000.0000.000
76A86LEU00.0590.01146.1190.0060.0060.0000.0000.0000.000
77A87ALA0-0.020-0.00646.0420.0050.0050.0000.0000.0000.000
78A88SER0-0.023-0.00546.3130.0050.0050.0000.0000.0000.000
79A89TRP00.0430.02938.5480.0030.0030.0000.0000.0000.000
80A90ALA00.0310.02241.7960.0070.0070.0000.0000.0000.000
81A91GLY00.007-0.01142.3210.0050.0050.0000.0000.0000.000
82A92THR0-0.044-0.04339.3940.0010.0010.0000.0000.0000.000
83A93LEU00.0030.01535.7080.0070.0070.0000.0000.0000.000
84A94ALA00.0250.00437.8600.0080.0080.0000.0000.0000.000
85A95ALA0-0.0210.01439.5490.0030.0030.0000.0000.0000.000
86A96ALA00.0200.01034.9280.0040.0040.0000.0000.0000.000
87A97LEU0-0.0050.00033.3330.0100.0100.0000.0000.0000.000
88A98THR00.000-0.00435.6330.0030.0030.0000.0000.0000.000
89A99THR0-0.018-0.00534.120-0.001-0.0010.0000.0000.0000.000
90A100ARG10.8380.87431.162-0.171-0.1710.0000.0000.0000.000
91A101ARG10.8730.92325.541-0.232-0.2320.0000.0000.0000.000
92A102GLY00.0620.03629.6650.0170.0170.0000.0000.0000.000
93A103HIS00.0420.04331.5800.0100.0100.0000.0000.0000.000
94A104ALA0-0.026-0.02128.3130.0070.0070.0000.0000.0000.000
95A105MET0-0.0020.02426.0650.0190.0190.0000.0000.0000.000
96A106LEU00.0220.01427.6640.0180.0180.0000.0000.0000.000
97A107LYS10.9090.94929.810-0.202-0.2020.0000.0000.0000.000
98A108THR0-0.030-0.01423.0660.0160.0160.0000.0000.0000.000
99A109LEU00.0270.01024.5070.0270.0270.0000.0000.0000.000
100A110MET00.0060.02226.3690.0090.0090.0000.0000.0000.000
101A111ALA0-0.006-0.00925.7210.0020.0020.0000.0000.0000.000
102A112ALA00.004-0.00722.3720.0110.0110.0000.0000.0000.000
103A113SER0-0.042-0.04223.8740.0110.0110.0000.0000.0000.000
104A114LEU0-0.027-0.01826.638-0.007-0.0070.0000.0000.0000.000
105A115GLU-1-0.811-0.87021.5810.4940.4940.0000.0000.0000.000
106A116HIS00.0010.00021.3940.0010.0010.0000.0000.0000.000
107A117GLU-1-0.843-0.90124.9010.2390.2390.0000.0000.0000.000
108A118ASP-1-0.868-0.93722.8920.3350.3350.0000.0000.0000.000
109A119THR0-0.110-0.06421.7730.0400.0400.0000.0000.0000.000
110A120ALA00.0300.01023.741-0.011-0.0110.0000.0000.0000.000
111A121ALA0-0.016-0.00427.303-0.015-0.0150.0000.0000.0000.000
112A122ARG10.8630.93219.035-0.518-0.5180.0000.0000.0000.000
113A123LEU00.0130.00623.087-0.007-0.0070.0000.0000.0000.000
114A124ARG10.9550.97326.561-0.199-0.1990.0000.0000.0000.000
115A125GLU-1-0.832-0.88527.9760.1790.1790.0000.0000.0000.000
116A126GLY00.008-0.00226.662-0.010-0.0100.0000.0000.0000.000
117A127PHE0-0.030-0.03024.913-0.007-0.0070.0000.0000.0000.000
118A128SER0-0.058-0.01530.199-0.016-0.0160.0000.0000.0000.000
119A129ARG10.8520.88231.802-0.178-0.1780.0000.0000.0000.000
120A130PRO00.0470.01931.531-0.013-0.0130.0000.0000.0000.000
121A131LEU0-0.053-0.00733.972-0.012-0.0120.0000.0000.0000.000
122A132ILE00.0200.00936.855-0.008-0.0080.0000.0000.0000.000
123A133GLU-1-0.783-0.88237.2000.1270.1270.0000.0000.0000.000
124A134SER0-0.052-0.02938.071-0.009-0.0090.0000.0000.0000.000
125A135VAL0-0.041-0.01640.652-0.007-0.0070.0000.0000.0000.000
126A136ARG10.7700.85440.119-0.120-0.1200.0000.0000.0000.000
127A137ASP-1-0.791-0.89542.0530.0990.0990.0000.0000.0000.000
128A138ARG10.6640.82044.750-0.080-0.0800.0000.0000.0000.000
129A139LEU0-0.011-0.01446.579-0.005-0.0050.0000.0000.0000.000
130A140ARG10.8430.91146.958-0.080-0.0800.0000.0000.0000.000
131A141ASP-1-0.803-0.86348.3940.0760.0760.0000.0000.0000.000
132A142GLU-1-0.883-0.93150.7810.0640.0640.0000.0000.0000.000
133A143ASP-1-0.931-0.95653.0660.0620.0620.0000.0000.0000.000
134A144ILE0-0.0100.01751.383-0.001-0.0010.0000.0000.0000.000
135A145ASP-1-0.797-0.87851.5160.0770.0770.0000.0000.0000.000
136A146ALA00.016-0.02047.4830.0030.0030.0000.0000.0000.000
137A147ASP-1-0.898-0.93347.5440.0900.0900.0000.0000.0000.000
138A148HIS0-0.065-0.06648.6230.0040.0040.0000.0000.0000.000
139A149ALA0-0.0100.00547.5000.0030.0030.0000.0000.0000.000
140A150GLN0-0.046-0.04341.0330.0040.0040.0000.0000.0000.000
141A151ALA00.0260.01244.6140.0050.0050.0000.0000.0000.000
142A152ALA00.0040.00246.5580.0020.0020.0000.0000.0000.000
143A153ALA0-0.002-0.00542.2070.0020.0020.0000.0000.0000.000
144A154ASP-1-0.877-0.93541.1620.1330.1330.0000.0000.0000.000
145A155ALA0-0.037-0.01242.4930.0050.0050.0000.0000.0000.000
146A156LEU0-0.019-0.00443.8200.0020.0020.0000.0000.0000.000
147A157LEU00.002-0.00236.2480.0040.0040.0000.0000.0000.000
148A158GLY00.0190.01039.9190.0070.0070.0000.0000.0000.000
149A159ALA00.000-0.00541.2110.0030.0030.0000.0000.0000.000
150A160VAL0-0.0340.00238.800-0.002-0.0020.0000.0000.0000.000
151A161VAL00.010-0.00735.2140.0050.0050.0000.0000.0000.000
152A162ASN00.0270.01437.4580.0100.0100.0000.0000.0000.000
153A163ALA00.0230.03139.5500.0010.0010.0000.0000.0000.000
154A164VAL00.010-0.01035.5070.0020.0020.0000.0000.0000.000
155A165LEU0-0.029-0.03332.7990.0090.0090.0000.0000.0000.000
156A166SER0-0.046-0.01736.5360.0020.0020.0000.0000.0000.000
157A167GLU-1-0.804-0.84439.8450.1110.1110.0000.0000.0000.000
158A168GLY0-0.027-0.00737.7240.0000.0000.0000.0000.0000.000
159A169ARG10.8020.86536.095-0.141-0.1410.0000.0000.0000.000
160A170SER0-0.009-0.00939.727-0.003-0.0030.0000.0000.0000.000
161A171TYR0-0.014-0.01141.342-0.007-0.0070.0000.0000.0000.000
162A172SER00.011-0.01643.1240.0000.0000.0000.0000.0000.000
163A173ARG10.8780.94443.636-0.097-0.0970.0000.0000.0000.000
164A174GLN00.0770.03245.5210.0020.0020.0000.0000.0000.000
165A175ARG10.8150.89645.695-0.109-0.1090.0000.0000.0000.000
166A176ALA00.0630.04944.003-0.001-0.0010.0000.0000.0000.000
167A177GLU-1-0.830-0.90145.9540.0830.0830.0000.0000.0000.000
168A178THR0-0.044-0.03448.686-0.004-0.0040.0000.0000.0000.000
169A179SER0-0.011-0.01747.211-0.002-0.0020.0000.0000.0000.000
170A180ALA00.0060.00447.267-0.001-0.0010.0000.0000.0000.000
171A181ARG10.9020.93048.999-0.078-0.0780.0000.0000.0000.000
172A182ILE0-0.032-0.01152.534-0.003-0.0030.0000.0000.0000.000
173A183ILE00.0000.00247.588-0.002-0.0020.0000.0000.0000.000
174A184VAL00.0280.01250.693-0.002-0.0020.0000.0000.0000.000
175A185ALA0-0.067-0.03853.105-0.003-0.0030.0000.0000.0000.000
176A186GLY0-0.027-0.01655.120-0.003-0.0030.0000.0000.0000.000
177A187LEU00.0030.00750.7670.0000.0000.0000.0000.0000.000
178A188ARG10.8990.96555.471-0.062-0.0620.0000.0000.0000.000
179A189PRO00.0130.01957.6100.0000.0000.0000.0000.0000.000