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: LZ9M9

Calculation Name: 5XCK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XCK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BI08

Base Structure: X-ray

Registration Date: 2023-06-26

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1974295.541581
FMO2-HF: Nuclear repulsion 1903409.781896
FMO2-HF: Total energy -70885.759684
FMO2-MP2: Total energy -71091.833638


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-38.239-37.33327.039-13.763-14.181-0.016
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.012
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].
3A3VAL0-0.009-0.0043.8630.7022.027-0.011-0.581-0.7330.002
4A4LEU0-0.0090.0026.4290.1880.1880.0000.0000.0000.000
5A5VAL00.0190.00510.159-0.060-0.0600.0000.0000.0000.000
6A6ILE00.014-0.00813.0220.0760.0760.0000.0000.0000.000
7A7GLY00.0890.03616.426-0.023-0.0230.0000.0000.0000.000
8A8ASP-1-0.805-0.88519.904-0.174-0.1740.0000.0000.0000.000
9A9PHE00.0080.01118.2310.0170.0170.0000.0000.0000.000
10A10HIS0-0.020-0.01024.2280.0120.0120.0000.0000.0000.000
11A11VAL00.0260.00827.782-0.012-0.0120.0000.0000.0000.000
12A12PRO00.0040.00430.9720.0090.0090.0000.0000.0000.000
13A13HIS0-0.032-0.02134.0790.0010.0010.0000.0000.0000.000
14A14ARG10.9400.99333.4830.0670.0670.0000.0000.0000.000
15A15SER0-0.017-0.01232.1590.0010.0010.0000.0000.0000.000
16A16ALA00.0160.01528.554-0.002-0.0020.0000.0000.0000.000
17A17ALA00.0200.01026.9180.0020.0020.0000.0000.0000.000
18A18ILE00.0220.01520.393-0.008-0.0080.0000.0000.0000.000
19A19PRO00.0000.00822.4660.0160.0160.0000.0000.0000.000
20A20GLN0-0.012-0.01122.109-0.010-0.0100.0000.0000.0000.000
21A21VAL00.0500.01421.0190.0170.0170.0000.0000.0000.000
22A22PHE0-0.021-0.01417.9620.0150.0150.0000.0000.0000.000
23A23LEU00.0280.01817.0690.0270.0270.0000.0000.0000.000
24A24ASP-1-0.824-0.89617.5950.1930.1930.0000.0000.0000.000
25A25ARG10.8780.9539.381-0.232-0.2320.0000.0000.0000.000
26A26LEU0-0.0020.00112.8570.0780.0780.0000.0000.0000.000
27A27ASN0-0.016-0.02912.7190.1480.1480.0000.0000.0000.000
28A28THR0-0.065-0.04014.1610.0940.0940.0000.0000.0000.000
29A29GLY0-0.020-0.00310.6660.0690.0690.0000.0000.0000.000
30A30ARG10.8450.9031.956-23.364-26.47411.611-4.766-3.7350.056
31A31ILE00.0340.0256.6051.1171.1170.0000.0000.0000.000
32A32GLN0-0.078-0.0281.847-4.698-8.72811.376-4.132-3.214-0.034
33A33THR00.006-0.0275.085-0.855-0.773-0.001-0.003-0.0770.000
34A34VAL00.0050.0097.360-0.095-0.0950.0000.0000.0000.000
35A35LEU00.0010.0029.901-0.009-0.0090.0000.0000.0000.000
36A36CYS0-0.074-0.02712.7450.0310.0310.0000.0000.0000.000
37A37THR00.023-0.00216.2520.0060.0060.0000.0000.0000.000
38A38GLY00.0680.03419.4660.0160.0160.0000.0000.0000.000
39A39ASN0-0.088-0.07521.7690.0110.0110.0000.0000.0000.000
40A40LEU00.0200.00420.2430.0090.0090.0000.0000.0000.000
41A41CYS0-0.0140.00224.1080.0040.0040.0000.0000.0000.000
42A42GLY00.0090.00126.6010.0130.0130.0000.0000.0000.000
43A43LYS10.8000.87524.765-0.034-0.0340.0000.0000.0000.000
44A44GLU-1-0.802-0.90823.7310.0170.0170.0000.0000.0000.000
45A45THR0-0.0300.00020.6020.0090.0090.0000.0000.0000.000
46A46TYR00.0290.01818.2790.0020.0020.0000.0000.0000.000
47A47ASP-1-0.817-0.90318.9630.0530.0530.0000.0000.0000.000
48A48ILE0-0.013-0.00118.3500.0320.0320.0000.0000.0000.000
49A49LEU00.001-0.01414.6780.0340.0340.0000.0000.0000.000
50A50ARG10.8910.94314.0990.0480.0480.0000.0000.0000.000
51A51THR0-0.046-0.01115.6620.0360.0360.0000.0000.0000.000
52A52LEU0-0.0470.00012.2670.0560.0560.0000.0000.0000.000
53A53ALA00.0180.0039.6990.1640.1640.0000.0000.0000.000
54A54ARG10.8470.9166.992-0.029-0.0290.0000.0000.0000.000
55A55GLU-1-0.850-0.8777.856-0.868-0.8680.0000.0000.0000.000
56A56VAL0-0.014-0.01410.567-0.034-0.0340.0000.0000.0000.000
57A57HIS0-0.029-0.01210.7950.0780.0780.0000.0000.0000.000
58A58VAL0-0.026-0.03014.751-0.010-0.0100.0000.0000.0000.000
59A59VAL0-0.0350.01818.0090.0040.0040.0000.0000.0000.000
60A60LYS10.8190.89720.8540.1450.1450.0000.0000.0000.000
61A61GLY00.0780.02624.496-0.014-0.0140.0000.0000.0000.000
62A62ALA0-0.057-0.03225.4570.0130.0130.0000.0000.0000.000
63A63PHE0-0.007-0.02228.1870.0120.0120.0000.0000.0000.000
64A64ASP-1-0.745-0.83724.433-0.136-0.1360.0000.0000.0000.000
65A65GLU-1-0.890-0.93627.584-0.101-0.1010.0000.0000.0000.000
66A66MET0-0.056-0.02423.6680.0070.0070.0000.0000.0000.000
67A67GLN0-0.009-0.01626.813-0.012-0.0120.0000.0000.0000.000
68A68GLY0-0.004-0.00825.5330.0090.0090.0000.0000.0000.000
69A69LEU0-0.040-0.00421.037-0.010-0.0100.0000.0000.0000.000
70A70ASN00.002-0.00820.9210.0290.0290.0000.0000.0000.000
71A71GLU-1-0.807-0.89322.736-0.194-0.1940.0000.0000.0000.000
72A72THR0-0.091-0.06720.715-0.010-0.0100.0000.0000.0000.000
73A73GLU-1-0.843-0.89416.592-0.323-0.3230.0000.0000.0000.000
74A74VAL0-0.039-0.02715.839-0.038-0.0380.0000.0000.0000.000
75A75ILE0-0.0070.0139.8960.0160.0160.0000.0000.0000.000
76A76LYS10.8230.90410.8290.9850.9850.0000.0000.0000.000
77A77ILE00.0060.0054.477-0.215-0.138-0.001-0.008-0.0680.000
78A78GLY00.0420.0276.450-0.120-0.1200.0000.0000.0000.000
79A79ASN0-0.026-0.0467.2070.3390.3390.0000.0000.0000.000
80A80PHE00.0070.0277.8800.2950.2950.0000.0000.0000.000
81A81LYS10.7860.86510.4570.3580.3580.0000.0000.0000.000
82A82ILE00.001-0.0078.4860.0030.0030.0000.0000.0000.000
83A83GLY00.0400.02513.0260.0470.0470.0000.0000.0000.000
84A84LEU0-0.031-0.01314.169-0.030-0.0300.0000.0000.0000.000
85A85MET00.0360.01517.4030.0440.0440.0000.0000.0000.000
86A86ALA00.0660.04120.604-0.016-0.0160.0000.0000.0000.000
87A87GLY00.026-0.00123.094-0.012-0.0120.0000.0000.0000.000
88A88HIS0-0.042-0.01924.8700.0100.0100.0000.0000.0000.000
89A89GLN00.033-0.00425.2460.0050.0050.0000.0000.0000.000
90A90VAL0-0.050-0.00525.0580.0020.0020.0000.0000.0000.000
91A91ILE0-0.017-0.00228.4000.0110.0110.0000.0000.0000.000
92A92PRO00.024-0.01431.875-0.001-0.0010.0000.0000.0000.000
93A93TRP0-0.026-0.01529.492-0.004-0.0040.0000.0000.0000.000
94A94GLY00.0150.00726.2600.0060.0060.0000.0000.0000.000
95A95ASP-1-0.841-0.91427.055-0.192-0.1920.0000.0000.0000.000
96A96ARG10.9310.95826.1570.1750.1750.0000.0000.0000.000
97A97GLU-1-0.883-0.93826.276-0.231-0.2310.0000.0000.0000.000
98A98ALA0-0.022-0.01128.075-0.009-0.0090.0000.0000.0000.000
99A99LEU0-0.009-0.00822.206-0.013-0.0130.0000.0000.0000.000
100A100ALA00.0410.01623.719-0.027-0.0270.0000.0000.0000.000
101A101ILE0-0.038-0.02124.741-0.010-0.0100.0000.0000.0000.000
102A102TYR00.006-0.00823.319-0.004-0.0040.0000.0000.0000.000
103A103GLN0-0.033-0.02319.4830.0180.0180.0000.0000.0000.000
104A104ARG10.9150.95821.2540.2170.2170.0000.0000.0000.000
105A105GLN0-0.068-0.03523.9200.0030.0030.0000.0000.0000.000
106A106LEU0-0.0020.00920.0220.0090.0090.0000.0000.0000.000
107A107ASP-1-0.912-0.93220.199-0.458-0.4580.0000.0000.0000.000
108A108VAL0-0.0250.00315.925-0.049-0.0490.0000.0000.0000.000
109A109ASP-1-0.789-0.88813.451-0.664-0.6640.0000.0000.0000.000
110A110ILE0-0.007-0.00110.2120.0070.0070.0000.0000.0000.000
111A111LEU0-0.0130.00114.444-0.008-0.0080.0000.0000.0000.000
112A112ILE0-0.027-0.01212.0870.0000.0000.0000.0000.0000.000
113A113THR0-0.035-0.02716.7360.0540.0540.0000.0000.0000.000
114A114GLY0-0.018-0.02519.776-0.018-0.0180.0000.0000.0000.000
115A115HIS00.0850.05121.6250.0130.0130.0000.0000.0000.000
116A116THR00.001-0.01424.7010.0140.0140.0000.0000.0000.000
117A117HIS0-0.068-0.03424.7720.0090.0090.0000.0000.0000.000
118A118LYS10.8500.92824.4940.1430.1430.0000.0000.0000.000
119A119LEU0-0.0270.01017.078-0.013-0.0130.0000.0000.0000.000
120A120GLU-1-0.851-0.90319.642-0.257-0.2570.0000.0000.0000.000
121A121THR00.027-0.01415.513-0.080-0.0800.0000.0000.0000.000
122A122LYS10.7610.85118.1290.3350.3350.0000.0000.0000.000
123A123GLU-1-0.880-0.93818.056-0.390-0.3900.0000.0000.0000.000
124A124VAL0-0.045-0.02419.7330.0490.0490.0000.0000.0000.000
125A125GLY00.0050.00921.993-0.017-0.0170.0000.0000.0000.000
126A126GLY0-0.023-0.01019.6780.0030.0030.0000.0000.0000.000
127A127LYS10.8320.92217.5750.4470.4470.0000.0000.0000.000
128A128TYR00.0180.00414.1870.0360.0360.0000.0000.0000.000
129A129PHE0-0.040-0.02516.573-0.023-0.0230.0000.0000.0000.000
130A130LEU00.0070.00512.2310.0030.0030.0000.0000.0000.000
131A131ASN00.0500.01616.6800.0190.0190.0000.0000.0000.000
132A132PRO00.0390.02816.0610.0070.0070.0000.0000.0000.000
133A133GLY00.0470.03317.8080.0410.0410.0000.0000.0000.000
134A134SER0-0.004-0.01120.788-0.001-0.0010.0000.0000.0000.000
135A135ALA00.0280.01319.6860.0140.0140.0000.0000.0000.000
136A136THR0-0.078-0.07421.2880.0200.0200.0000.0000.0000.000
137A137GLY0-0.0040.00524.9030.0120.0120.0000.0000.0000.000
138A138ALA00.0080.01326.8460.0080.0080.0000.0000.0000.000
139A139TYR00.003-0.00628.863-0.008-0.0080.0000.0000.0000.000
140A140SER00.0900.03629.647-0.002-0.0020.0000.0000.0000.000
141A141PRO0-0.046-0.02831.6990.0030.0030.0000.0000.0000.000
142A142LEU0-0.0160.00529.5960.0020.0020.0000.0000.0000.000
143A143VAL0-0.056-0.03128.378-0.005-0.0050.0000.0000.0000.000
144A144ASP-1-0.922-0.95031.879-0.067-0.0670.0000.0000.0000.000
145A145ASN00.0110.01630.4750.0100.0100.0000.0000.0000.000
146A146PRO0-0.060-0.02928.034-0.009-0.0090.0000.0000.0000.000
147A147VAL0-0.003-0.01424.4080.0110.0110.0000.0000.0000.000
148A148PRO0-0.024-0.00123.720-0.014-0.0140.0000.0000.0000.000
149A149SER0-0.071-0.06320.1000.0150.0150.0000.0000.0000.000
150A150PHE0-0.034-0.00913.4720.0120.0120.0000.0000.0000.000
151A151MET00.0080.00812.587-0.021-0.0210.0000.0000.0000.000
152A152LEU0-0.033-0.0168.8740.0390.0390.0000.0000.0000.000
153A153LEU00.0150.0087.0170.1340.1340.0000.0000.0000.000
154A154GLU-1-0.891-0.9253.406-1.871-1.2040.019-0.176-0.5100.000
155A155ILE0-0.034-0.0132.9700.2191.5510.107-0.442-0.997-0.003
156A156ASN0-0.002-0.0122.445-9.435-4.9923.927-3.656-4.714-0.037
157A157ASP-1-0.870-0.9403.6740.0290.1490.0120.001-0.1330.000
158A158SER0-0.045-0.0086.556-0.202-0.2020.0000.0000.0000.000
159A159GLU-1-0.840-0.9087.2660.3880.3880.0000.0000.0000.000
160A160LEU00.0240.0096.695-0.671-0.6710.0000.0000.0000.000
161A161THR00.0240.0126.8550.3120.3120.0000.0000.0000.000
162A162ILE0-0.035-0.0177.757-0.345-0.3450.0000.0000.0000.000
163A163TYR0-0.050-0.0517.2770.2460.2460.0000.0000.0000.000
164A164GLU-1-0.811-0.88211.802-0.358-0.3580.0000.0000.0000.000
165A165TYR00.0020.00211.8850.1240.1240.0000.0000.0000.000
166A166THR00.023-0.00517.262-0.018-0.0180.0000.0000.0000.000
167A167LEU0-0.053-0.00721.0780.0180.0180.0000.0000.0000.000
168A168VAL00.011-0.01524.160-0.008-0.0080.0000.0000.0000.000
169A169ASP-1-0.895-0.93927.238-0.017-0.0170.0000.0000.0000.000
170A170GLY0-0.0070.00628.8050.0060.0060.0000.0000.0000.000
171A171SER0-0.055-0.02526.3540.0090.0090.0000.0000.0000.000
172A172VAL00.011-0.00919.597-0.011-0.0110.0000.0000.0000.000
173A173LYS10.8720.94121.0730.1460.1460.0000.0000.0000.000
174A174CYS0-0.046-0.02115.327-0.008-0.0080.0000.0000.0000.000
175A175GLU-1-0.846-0.90316.634-0.135-0.1350.0000.0000.0000.000
176A176ARG10.8360.87413.0290.1080.1080.0000.0000.0000.000
177A177VAL00.0140.02213.2010.0450.0450.0000.0000.0000.000
178A178ASP-1-0.852-0.90610.962-0.434-0.4340.0000.0000.0000.000
179A179PHE00.0300.01111.4980.0860.0860.0000.0000.0000.000
180A180ASN0-0.012-0.01511.025-0.057-0.0570.0000.0000.0000.000
181A181LYS10.7960.88911.4560.2480.2480.0000.0000.0000.000