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

tag_button

FMODB ID: K92L3

Calculation Name: 4GK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GK0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UI95

Base Structure: X-ray

Registration Date: 2023-06-22

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2415690.801182
FMO2-HF: Nuclear repulsion 2334102.608926
FMO2-HF: Total energy -81588.192256
FMO2-MP2: Total energy -81824.049502


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:9:LEU)


Summations of interaction energy for fragment #1(A:9:LEU)
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.
-9.555-2.7979.207-4.697-11.269-0.031
Interaction energy analysis for fragmet #1(A:9:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : 0.016
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].
3A11PHE0-0.0010.0112.734-3.0490.8211.422-1.692-3.600-0.009
4A12GLY00.0760.0314.260-0.030-0.001-0.001-0.012-0.0160.000
5A13GLN00.0300.0017.825-0.002-0.0020.0000.0000.0000.000
6A14VAL00.0570.03311.1890.0130.0130.0000.0000.0000.000
7A15VAL0-0.0010.0086.5710.0280.0280.0000.0000.0000.000
8A16ALA00.0240.0239.3800.0260.0260.0000.0000.0000.000
9A17ASP-1-0.808-0.90910.599-0.262-0.2620.0000.0000.0000.000
10A18VAL0-0.036-0.02112.1440.0320.0320.0000.0000.0000.000
11A19LEU0-0.006-0.0158.3380.0300.0300.0000.0000.0000.000
12A20CYS0-0.033-0.00112.8760.0200.0200.0000.0000.0000.000
13A21GLU-1-0.826-0.88915.814-0.142-0.1420.0000.0000.0000.000
14A22PHE0-0.033-0.02314.7680.0210.0210.0000.0000.0000.000
15A23LEU00.010-0.01514.0900.0190.0190.0000.0000.0000.000
16A24GLU-1-0.851-0.91917.917-0.129-0.1290.0000.0000.0000.000
17A25VAL0-0.042-0.04121.0950.0170.0170.0000.0000.0000.000
18A26ALA0-0.0020.01019.7860.0130.0130.0000.0000.0000.000
19A27VAL00.0200.01320.8210.0110.0110.0000.0000.0000.000
20A28HIS0-0.031-0.02423.2750.0170.0170.0000.0000.0000.000
21A29LEU0-0.030-0.01524.8490.0090.0090.0000.0000.0000.000
22A30ILE0-0.0030.00622.1720.0080.0080.0000.0000.0000.000
23A31LEU00.0020.00126.5510.0080.0080.0000.0000.0000.000
24A32TYR0-0.037-0.01629.1500.0080.0080.0000.0000.0000.000
25A33VAL0-0.024-0.02928.9930.0050.0050.0000.0000.0000.000
26A34ARG10.7380.84028.6780.0720.0720.0000.0000.0000.000
27A35GLU-1-0.916-0.94331.723-0.053-0.0530.0000.0000.0000.000
28A36VAL0-0.0340.00529.7830.0010.0010.0000.0000.0000.000
29A37TYR0-0.004-0.01130.3970.0000.0000.0000.0000.0000.000
30A38PRO00.0260.01734.7680.0010.0010.0000.0000.0000.000
31A39VAL00.0680.00136.075-0.002-0.0020.0000.0000.0000.000
32A40GLY0-0.032-0.01037.251-0.001-0.0010.0000.0000.0000.000
33A41ILE0-0.0120.00833.6190.0010.0010.0000.0000.0000.000
34A42PHE0-0.021-0.00429.972-0.004-0.0040.0000.0000.0000.000
35A43GLN0-0.019-0.00533.1770.0050.0050.0000.0000.0000.000
36A44LYS10.9470.98732.4030.0600.0600.0000.0000.0000.000
37A45ARG10.9810.98027.7070.1020.1020.0000.0000.0000.000
38A46LYS10.8560.90828.2470.0780.0780.0000.0000.0000.000
39A47LYS10.8570.93622.4700.1410.1410.0000.0000.0000.000
40A48TYR00.1080.04818.1330.0060.0060.0000.0000.0000.000
41A49ASN00.0210.01222.7040.0090.0090.0000.0000.0000.000
42A50VAL00.003-0.00624.1520.0090.0090.0000.0000.0000.000
43A51PRO0-0.097-0.04527.088-0.003-0.0030.0000.0000.0000.000
44A52VAL00.0690.04124.905-0.001-0.0010.0000.0000.0000.000
45A53GLN00.017-0.00228.3640.0040.0040.0000.0000.0000.000
46A54MET0-0.0320.00024.884-0.004-0.0040.0000.0000.0000.000
47A55SER00.0520.02429.5760.0080.0080.0000.0000.0000.000
48A56CYS0-0.059-0.02631.357-0.003-0.0030.0000.0000.0000.000
49A57HIS00.0120.02033.751-0.001-0.0010.0000.0000.0000.000
50A58PRO00.027-0.00332.837-0.005-0.0050.0000.0000.0000.000
51A59GLU-1-0.906-0.94132.062-0.088-0.0880.0000.0000.0000.000
52A60LEU00.0100.00829.381-0.006-0.0060.0000.0000.0000.000
53A61ASN0-0.031-0.04828.505-0.006-0.0060.0000.0000.0000.000
54A62GLN0-0.031-0.00527.212-0.003-0.0030.0000.0000.0000.000
55A63TYR00.0620.03825.719-0.009-0.0090.0000.0000.0000.000
56A64ILE0-0.0170.00323.210-0.013-0.0130.0000.0000.0000.000
57A65GLN0-0.025-0.01822.742-0.009-0.0090.0000.0000.0000.000
58A66ASP-1-0.833-0.91522.202-0.161-0.1610.0000.0000.0000.000
59A67THR0-0.027-0.02520.161-0.018-0.0180.0000.0000.0000.000
60A68LEU0-0.009-0.01017.391-0.024-0.0240.0000.0000.0000.000
61A69HIS0-0.039-0.01317.306-0.038-0.0380.0000.0000.0000.000
62A70CYS0-0.0240.00017.958-0.018-0.0180.0000.0000.0000.000
63A71VAL00.0030.00313.549-0.031-0.0310.0000.0000.0000.000
64A72LYS10.9090.94313.3780.2230.2230.0000.0000.0000.000
65A73PRO00.0180.00811.877-0.082-0.0820.0000.0000.0000.000
66A74LEU0-0.0030.00111.301-0.113-0.1130.0000.0000.0000.000
67A75LEU0-0.017-0.0068.719-0.145-0.1450.0000.0000.0000.000
68A76GLU-1-0.842-0.9007.007-0.817-0.8170.0000.0000.0000.000
69A77LYS10.7510.8666.5380.6820.6820.0000.0000.0000.000
70A78ASN0-0.055-0.0282.565-1.164-0.2771.530-0.654-1.764-0.008
71A79ASP-1-0.730-0.8545.429-1.247-1.2470.0000.0000.0000.000
72A80VAL0-0.043-0.0298.0830.1610.1610.0000.0000.0000.000
73A81GLU-1-0.891-0.9258.685-0.204-0.2040.0000.0000.0000.000
74A82LYS10.8170.88810.3760.1800.1800.0000.0000.0000.000
75A83VAL00.0010.02213.252-0.015-0.0150.0000.0000.0000.000
76A84VAL0-0.010-0.01515.5210.0140.0140.0000.0000.0000.000
77A85VAL00.0090.01719.015-0.001-0.0010.0000.0000.0000.000
78A86VAL0-0.004-0.00222.1650.0080.0080.0000.0000.0000.000
79A87ILE00.0060.00524.9460.0000.0000.0000.0000.0000.000
80A88LEU00.0090.00728.4680.0030.0030.0000.0000.0000.000
81A89ASP-1-0.713-0.85431.228-0.056-0.0560.0000.0000.0000.000
82A90LYS10.9710.98134.8400.0460.0460.0000.0000.0000.000
83A91GLU-1-0.946-0.96437.872-0.049-0.0490.0000.0000.0000.000
84A92HIS0-0.008-0.01033.640-0.002-0.0020.0000.0000.0000.000
85A93ARG10.8930.94732.8290.0480.0480.0000.0000.0000.000
86A94PRO00.0490.02427.9520.0000.0000.0000.0000.0000.000
87A95VAL0-0.032-0.00930.1300.0060.0060.0000.0000.0000.000
88A96GLU-1-0.719-0.84527.136-0.070-0.0700.0000.0000.0000.000
89A97LYS10.8550.93622.6400.0850.0850.0000.0000.0000.000
90A98PHE00.0370.00721.3780.0030.0030.0000.0000.0000.000
91A99VAL00.0030.00816.264-0.016-0.0160.0000.0000.0000.000
92A100PHE0-0.008-0.01714.2340.0070.0070.0000.0000.0000.000
93A101GLU-1-0.820-0.89511.868-0.147-0.1470.0000.0000.0000.000
94A102ILE00.002-0.0096.8380.0010.0010.0000.0000.0000.000
95A103THR00.0050.0006.6940.0040.0040.0000.0000.0000.000
96A104GLN00.0310.0102.277-3.146-2.2496.250-2.111-5.036-0.013
97A105PRO0-0.046-0.0094.1970.0030.2630.001-0.043-0.2180.000
98A106PRO00.0250.0044.417-0.486-0.286-0.001-0.013-0.1860.000
99A107LEU00.0140.0066.248-0.137-0.1370.0000.0000.0000.000
100A108LEU00.0090.0028.1040.1090.1090.0000.0000.0000.000
101A109SER0-0.008-0.00311.747-0.050-0.0500.0000.0000.0000.000
102A110ILE0-0.015-0.0057.6490.0140.0140.0000.0000.0000.000
103A111SER00.009-0.01111.5150.0090.0090.0000.0000.0000.000
104A112SER0-0.068-0.02210.6410.0180.0180.0000.0000.0000.000
105A113ASP-1-0.829-0.90712.992-0.084-0.0840.0000.0000.0000.000
106A114SER00.001-0.01911.576-0.038-0.0380.0000.0000.0000.000
107A115LEU0-0.012-0.0297.9840.0140.0140.0000.0000.0000.000
108A116LEU00.018-0.01811.1290.0180.0180.0000.0000.0000.000
109A117SER0-0.0210.00013.5940.0240.0240.0000.0000.0000.000
110A118HIS00.0080.00815.3660.0130.0130.0000.0000.0000.000
111A119VAL00.0100.03114.093-0.001-0.0010.0000.0000.0000.000
112A120GLU-1-0.880-0.95116.085-0.133-0.1330.0000.0000.0000.000
113A121GLN0-0.005-0.00719.2190.0000.0000.0000.0000.0000.000
114A122LEU0-0.028-0.01913.0760.0020.0020.0000.0000.0000.000
115A123LEU00.0010.00213.524-0.002-0.0020.0000.0000.0000.000
116A124ALA00.0360.02117.3010.0070.0070.0000.0000.0000.000
117A125ALA0-0.038-0.02219.1860.0090.0090.0000.0000.0000.000
118A126PHE0-0.006-0.01514.5870.0080.0080.0000.0000.0000.000
119A127ILE00.0160.01719.9770.0070.0070.0000.0000.0000.000
120A128LEU0-0.012-0.01022.6370.0080.0080.0000.0000.0000.000
121A129LYS10.8500.91322.6660.0780.0780.0000.0000.0000.000
122A130ILE00.0380.01820.9670.0040.0040.0000.0000.0000.000
123A131SER0-0.055-0.02925.0800.0040.0040.0000.0000.0000.000
124A132VAL0-0.030-0.01228.1010.0040.0040.0000.0000.0000.000
125A133CYS0-0.072-0.02226.6290.0030.0030.0000.0000.0000.000
126A134ASP-1-0.841-0.93528.701-0.057-0.0570.0000.0000.0000.000
127A135ALA0-0.052-0.01732.0470.0040.0040.0000.0000.0000.000
128A136VAL0-0.099-0.05628.4520.0030.0030.0000.0000.0000.000
129A137LEU0-0.058-0.00327.546-0.001-0.0010.0000.0000.0000.000
130A138ASP-1-0.862-0.92231.689-0.039-0.0390.0000.0000.0000.000
131A139HIS0-0.100-0.06533.780-0.004-0.0040.0000.0000.0000.000
132A140ASN0-0.011-0.01430.7970.0030.0030.0000.0000.0000.000
133A141PRO00.0140.00035.1800.0020.0020.0000.0000.0000.000
134A142PRO00.0310.01337.109-0.003-0.0030.0000.0000.0000.000
135A143GLY0-0.039-0.03638.2610.0010.0010.0000.0000.0000.000
136A144CYS0-0.051-0.01432.752-0.001-0.0010.0000.0000.0000.000
137A145THR00.0050.01432.276-0.002-0.0020.0000.0000.0000.000
138A146PHE0-0.002-0.02524.999-0.001-0.0010.0000.0000.0000.000
139A147THR00.0290.02725.213-0.003-0.0030.0000.0000.0000.000
140A148VAL0-0.004-0.00419.618-0.001-0.0010.0000.0000.0000.000
141A149LEU00.0120.01720.188-0.001-0.0010.0000.0000.0000.000
142A150VAL0-0.005-0.00914.305-0.012-0.0120.0000.0000.0000.000
143A151HIS00.0260.01714.7040.0100.0100.0000.0000.0000.000
144A152THR0-0.033-0.04212.358-0.026-0.0260.0000.0000.0000.000
145A153ARG10.8260.9155.7620.6070.6070.0000.0000.0000.000
146A154GLU-1-0.860-0.90910.427-0.402-0.4020.0000.0000.0000.000
147A155ALA00.0200.01412.341-0.011-0.0110.0000.0000.0000.000
148A156ALA0-0.020-0.01513.1760.0230.0230.0000.0000.0000.000
149A157THR00.008-0.01915.203-0.003-0.0030.0000.0000.0000.000
150A158ARG10.8290.8858.7550.8160.8160.0000.0000.0000.000
151A159ASN0-0.022-0.01112.829-0.083-0.0830.0000.0000.0000.000
152A160MET00.0460.01215.4250.0150.0150.0000.0000.0000.000
153A161GLU-1-0.872-0.92817.991-0.269-0.2690.0000.0000.0000.000
154A162LYS10.8220.90710.7450.8150.8150.0000.0000.0000.000
155A163ILE0-0.0260.00517.2340.0060.0060.0000.0000.0000.000
156A164GLN0-0.0110.02418.6360.0200.0200.0000.0000.0000.000
157A165VAL0-0.039-0.03719.4680.0150.0150.0000.0000.0000.000
158A166ILE0-0.0100.01022.4650.0100.0100.0000.0000.0000.000
159A167LYS10.9250.95525.4410.1190.1190.0000.0000.0000.000
160A168ASP-1-0.900-0.96328.592-0.110-0.1100.0000.0000.0000.000
161A169PHE0-0.050-0.01423.8640.0060.0060.0000.0000.0000.000
162A170PRO0-0.018-0.00625.072-0.014-0.0140.0000.0000.0000.000
163A171TRP00.012-0.00819.698-0.003-0.0030.0000.0000.0000.000
164A172ILE0-0.013-0.01424.0600.0040.0040.0000.0000.0000.000
165A173LEU0-0.050-0.03021.072-0.013-0.0130.0000.0000.0000.000
166A174ALA00.0200.01822.9520.0090.0090.0000.0000.0000.000
167A175ASP-1-0.880-0.95324.671-0.082-0.0820.0000.0000.0000.000
168A176GLU-1-0.901-0.95626.014-0.074-0.0740.0000.0000.0000.000
169A177GLN0-0.101-0.04427.9360.0070.0070.0000.0000.0000.000
170A178ASP-1-0.887-0.93925.959-0.101-0.1010.0000.0000.0000.000
171A179VAL0-0.041-0.03023.191-0.007-0.0070.0000.0000.0000.000
172A180HIS0-0.033-0.00825.6690.0000.0000.0000.0000.0000.000
173A181MET0-0.047-0.01526.9650.0000.0000.0000.0000.0000.000
174A182HIS0-0.013-0.00729.2540.0020.0020.0000.0000.0000.000
175A183ASP-1-0.869-0.92231.875-0.033-0.0330.0000.0000.0000.000
176A184PRO00.0440.01827.0950.0000.0000.0000.0000.0000.000
177A185ARG10.8150.88628.8700.0390.0390.0000.0000.0000.000
178A186LEU00.0030.00621.751-0.005-0.0050.0000.0000.0000.000
179A187ILE00.0220.01224.9640.0060.0060.0000.0000.0000.000
180A188PRO0-0.018-0.01321.325-0.010-0.0100.0000.0000.0000.000
181A189LEU0-0.0180.01221.1080.0040.0040.0000.0000.0000.000
182A190LYS10.9180.96117.6950.1080.1080.0000.0000.0000.000
183A191THR00.009-0.00114.583-0.011-0.0110.0000.0000.0000.000
184A192MET0-0.077-0.02410.5610.0230.0230.0000.0000.0000.000
185A193THR0-0.013-0.0199.820-0.022-0.0220.0000.0000.0000.000
186A194SER0-0.003-0.0298.6750.0050.0050.0000.0000.0000.000
187A195ASP-1-0.864-0.9217.766-0.235-0.2350.0000.0000.0000.000
188A196ILE0-0.029-0.0074.177-0.224-0.011-0.001-0.017-0.1950.000
189A197LEU0-0.0010.0093.670-0.873-0.4710.007-0.155-0.254-0.001
190A198LYS10.9500.9966.1310.2150.2150.0000.0000.0000.000
191A199MET0-0.0120.0158.707-0.017-0.0170.0000.0000.0000.000
192A200GLN0-0.013-0.01011.2400.0410.0410.0000.0000.0000.000
193A201LEU0-0.0040.01214.653-0.013-0.0130.0000.0000.0000.000
194A202TYR0-0.026-0.02516.7670.0110.0110.0000.0000.0000.000
195A203VAL00.0360.02720.501-0.009-0.0090.0000.0000.0000.000
196A204GLU-1-0.828-0.91121.836-0.081-0.0810.0000.0000.0000.000
197A205GLU-1-0.803-0.90825.213-0.060-0.0600.0000.0000.0000.000
198A206ARG10.7920.86928.9040.0580.0580.0000.0000.0000.000
199A207ALA00.0140.02131.7930.0010.0010.0000.0000.0000.000
200A208HIS0-0.067-0.03034.3060.0050.0050.0000.0000.0000.000
201A209LYS10.8460.93831.2130.0590.0590.0000.0000.0000.000