FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: JLLG9

Calculation Name: 5EKZ-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 5EKZ

Chain ID: A

ChEMBL ID:
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UniProt ID: Q8K0Z7

Base Structure: X-ray

Registration Date: 2023-06-21

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2414283.676748
FMO2-HF: Nuclear repulsion 2327827.834608
FMO2-HF: Total energy -86455.84214
FMO2-MP2: Total energy -86705.608154


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:74:ARG)


Summations of interaction energy for fragment #1(A:74: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.
-21.671-14.6523.748-3.636-7.128-0.019
Interaction energy analysis for fragmet #1(A:74:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.050 / q_NPA : 1.031
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].
3A76ARG10.8730.9272.81732.84535.5940.100-1.275-1.5730.001
4A77ILE00.0440.0192.3340.8672.9722.179-0.994-3.290-0.004
5A78PHE00.028-0.0022.8180.9332.8931.471-1.357-2.074-0.016
6A79SER0-0.0020.0055.6024.9024.9020.0000.0000.0000.000
7A80LYS10.8510.9267.57028.82728.8270.0000.0000.0000.000
8A81LEU00.0260.0145.8652.2732.2730.0000.0000.0000.000
9A82THR0-0.013-0.0199.5162.5602.5600.0000.0000.0000.000
10A83LEU0-0.071-0.02611.5171.7621.7620.0000.0000.0000.000
11A84SER00.0220.00012.2861.2841.2840.0000.0000.0000.000
12A85ILE0-0.009-0.00511.9831.1161.1160.0000.0000.0000.000
13A86ARG10.8490.92915.11216.77416.7740.0000.0000.0000.000
14A87LEU00.0150.01217.1390.7650.7650.0000.0000.0000.000
15A88ALA00.0420.02217.8410.7550.7550.0000.0000.0000.000
16A89VAL0-0.011-0.01618.6060.7280.7280.0000.0000.0000.000
17A90LYS10.7440.85821.01413.40713.4070.0000.0000.0000.000
18A91GLU-1-0.918-0.95822.514-11.494-11.4940.0000.0000.0000.000
19A92GLY00.0080.01023.5090.4190.4190.0000.0000.0000.000
20A93GLY0-0.056-0.01624.1090.2370.2370.0000.0000.0000.000
21A94PRO0-0.008-0.01720.937-0.351-0.3510.0000.0000.0000.000
22A95ASN0-0.0050.00121.144-0.482-0.4820.0000.0000.0000.000
23A96PRO00.0110.00319.5330.0790.0790.0000.0000.0000.000
24A97GLU-1-0.887-0.95221.615-11.271-11.2710.0000.0000.0000.000
25A98ASN0-0.066-0.03524.9670.2850.2850.0000.0000.0000.000
26A99ASN0-0.014-0.00321.681-0.050-0.0500.0000.0000.0000.000
27A100SER00.0810.03121.388-0.570-0.5700.0000.0000.0000.000
28A101SER00.0150.02019.966-0.782-0.7820.0000.0000.0000.000
29A102LEU00.0250.00816.317-0.964-0.9640.0000.0000.0000.000
30A103ALA0-0.005-0.00616.581-0.779-0.7790.0000.0000.0000.000
31A104ASN00.0130.01116.552-0.511-0.5110.0000.0000.0000.000
32A105ILE00.0160.01312.245-1.246-1.2460.0000.0000.0000.000
33A106LEU0-0.010-0.00811.922-1.496-1.4960.0000.0000.0000.000
34A107GLU-1-0.765-0.84312.364-16.753-16.7530.0000.0000.0000.000
35A108LEU00.0010.0139.176-1.154-1.1540.0000.0000.0000.000
36A109CYS0-0.053-0.0337.855-2.379-2.3790.0000.0000.0000.000
37A110ARG10.8250.8777.87014.28014.2800.0000.0000.0000.000
38A111SER0-0.017-0.0019.587-1.106-1.1060.0000.0000.0000.000
39A112LYS10.8530.9104.22726.41626.513-0.001-0.006-0.0890.000
40A113ASN0-0.015-0.0064.600-1.219-1.111-0.001-0.004-0.1020.000
41A114MET0-0.0230.0175.614-0.162-0.1620.0000.0000.0000.000
42A115PRO00.0200.0085.7772.3062.3060.0000.0000.0000.000
43A116LYS10.9450.9558.98314.22314.2230.0000.0000.0000.000
44A117SER00.0260.01112.3500.1730.1730.0000.0000.0000.000
45A118THR00.0200.0098.2600.3860.3860.0000.0000.0000.000
46A119ILE00.0530.02210.4980.4810.4810.0000.0000.0000.000
47A120GLU-1-0.851-0.90612.616-12.763-12.7630.0000.0000.0000.000
48A121SER00.005-0.00114.1200.6480.6480.0000.0000.0000.000
49A122ALA0-0.036-0.00512.9710.4200.4200.0000.0000.0000.000
50A123LEU0-0.010-0.01315.1290.5470.5470.0000.0000.0000.000
51A124LYS10.8530.92117.78812.94812.9480.0000.0000.0000.000
52A125THR0-0.064-0.02817.6500.2640.2640.0000.0000.0000.000
53A126GLU-1-0.870-0.93920.076-10.662-10.6620.0000.0000.0000.000
54A127LYS10.9510.98422.90910.54410.5440.0000.0000.0000.000
55A128ASN00.0150.01224.563-0.401-0.4010.0000.0000.0000.000
56A129LYS10.9550.99420.28713.39113.3910.0000.0000.0000.000
57A130GLY00.0090.00621.609-0.644-0.6440.0000.0000.0000.000
58A131ILE0-0.026-0.01622.5290.2350.2350.0000.0000.0000.000
59A132TYR0-0.017-0.03920.779-0.310-0.3100.0000.0000.0000.000
60A133LEU0-0.052-0.02721.4910.6150.6150.0000.0000.0000.000
61A134LEU00.0330.01721.668-0.636-0.6360.0000.0000.0000.000
62A135TYR0-0.026-0.02121.9670.7230.7230.0000.0000.0000.000
63A136GLU-1-0.671-0.82923.170-11.758-11.7580.0000.0000.0000.000
64A137GLY00.006-0.00824.2580.1190.1190.0000.0000.0000.000
65A138ARG10.8210.91525.12010.61810.6180.0000.0000.0000.000
66A139GLY00.0400.00922.638-0.391-0.3910.0000.0000.0000.000
67A140PRO00.0030.00121.8280.4530.4530.0000.0000.0000.000
68A141GLY00.0880.06424.8060.4550.4550.0000.0000.0000.000
69A142GLY0-0.042-0.02127.1260.2580.2580.0000.0000.0000.000
70A143SER00.0170.02622.6350.3170.3170.0000.0000.0000.000
71A144SER0-0.058-0.03225.4470.2770.2770.0000.0000.0000.000
72A145LEU00.006-0.00420.015-0.405-0.4050.0000.0000.0000.000
73A146LEU00.0090.00821.0460.6330.6330.0000.0000.0000.000
74A147ILE0-0.017-0.00517.539-0.962-0.9620.0000.0000.0000.000
75A148GLU-1-0.716-0.81917.953-14.189-14.1890.0000.0000.0000.000
76A149ALA00.0090.00316.940-1.286-1.2860.0000.0000.0000.000
77A150LEU0-0.033-0.01117.0460.8490.8490.0000.0000.0000.000
78A151SER00.017-0.01117.969-0.089-0.0890.0000.0000.0000.000
79A152ASN0-0.046-0.04117.8740.8850.8850.0000.0000.0000.000
80A153SER0-0.018-0.01421.2740.6820.6820.0000.0000.0000.000
81A154GLY00.0870.05123.133-0.229-0.2290.0000.0000.0000.000
82A155PRO00.0450.01324.406-0.179-0.1790.0000.0000.0000.000
83A156LYS10.8810.92119.65314.10814.1080.0000.0000.0000.000
84A157CYS0-0.030-0.00218.827-0.296-0.2960.0000.0000.0000.000
85A158HIS00.0030.00421.316-0.420-0.4200.0000.0000.0000.000
86A159LEU00.0240.00724.224-0.059-0.0590.0000.0000.0000.000
87A160ASP-1-0.788-0.84619.066-14.581-14.5810.0000.0000.0000.000
88A161ILE00.0150.01117.614-0.468-0.4680.0000.0000.0000.000
89A162LYS10.9420.97120.71010.83710.8370.0000.0000.0000.000
90A163TYR0-0.005-0.00819.829-0.185-0.1850.0000.0000.0000.000
91A164ILE0-0.052-0.03716.192-0.013-0.0130.0000.0000.0000.000
92A165LEU00.0270.01319.856-0.072-0.0720.0000.0000.0000.000
93A166ASN0-0.039-0.01422.0170.3360.3360.0000.0000.0000.000
94A167LYS10.8770.96417.08516.64916.6490.0000.0000.0000.000
95A168ASN0-0.043-0.02217.342-0.056-0.0560.0000.0000.0000.000
96A169GLY00.0350.02621.231-0.118-0.1180.0000.0000.0000.000
97A170GLY00.0420.04223.6260.2920.2920.0000.0000.0000.000
98A171MET0-0.064-0.05224.6300.4240.4240.0000.0000.0000.000
99A172MET0-0.0130.00523.992-0.461-0.4610.0000.0000.0000.000
100A173ALA0-0.034-0.01026.6030.3940.3940.0000.0000.0000.000
101A174GLU-1-0.946-0.97429.074-9.085-9.0850.0000.0000.0000.000
102A175GLY00.0200.00132.3100.1300.1300.0000.0000.0000.000
103A176ALA0-0.026-0.01532.412-0.302-0.3020.0000.0000.0000.000
104A177ARG10.8180.90128.00510.77710.7770.0000.0000.0000.000
105A178HIS00.0340.01830.002-0.550-0.5500.0000.0000.0000.000
106A179PHE0-0.055-0.03927.5410.3790.3790.0000.0000.0000.000
107A180PHE0-0.018-0.00823.0260.0150.0150.0000.0000.0000.000
108A181ASP-1-0.838-0.90927.399-9.879-9.8790.0000.0000.0000.000
109A182LYS10.8470.93622.53812.90612.9060.0000.0000.0000.000
110A183LYS10.7950.88326.78810.21610.2160.0000.0000.0000.000
111A184GLY00.0180.00126.985-0.475-0.4750.0000.0000.0000.000
112A185VAL0-0.016-0.00526.1230.2290.2290.0000.0000.0000.000
113A186VAL0-0.018-0.01927.891-0.161-0.1610.0000.0000.0000.000
114A187VAL00.0070.01725.2130.1210.1210.0000.0000.0000.000
115A188VAL0-0.016-0.01828.7020.1040.1040.0000.0000.0000.000
116A189GLY00.0610.04331.139-0.195-0.1950.0000.0000.0000.000
117A190VAL00.0130.00932.4480.2530.2530.0000.0000.0000.000
118A191GLU-1-0.862-0.92834.897-8.534-8.5340.0000.0000.0000.000
119A192ASP-1-0.778-0.86037.258-7.698-7.6980.0000.0000.0000.000
120A193ARG10.8770.91837.2878.0528.0520.0000.0000.0000.000
121A194GLU-1-0.887-0.93740.482-6.777-6.7770.0000.0000.0000.000
122A195LYS10.7840.87736.7468.6988.6980.0000.0000.0000.000
123A196LYS10.8040.90540.9246.8496.8490.0000.0000.0000.000
124A197ALA00.0330.01039.317-0.142-0.1420.0000.0000.0000.000
125A198VAL0-0.040-0.01437.6690.2260.2260.0000.0000.0000.000
126A199ASN00.007-0.00137.750-0.263-0.2630.0000.0000.0000.000
127A200LEU00.0530.02035.4900.0470.0470.0000.0000.0000.000
128A201GLU-1-0.927-0.95238.252-7.086-7.0860.0000.0000.0000.000
129A202ARG10.9270.94441.7007.5617.5610.0000.0000.0000.000
130A203ALA0-0.031-0.01536.7440.0010.0010.0000.0000.0000.000
131A204LEU00.013-0.00637.614-0.080-0.0800.0000.0000.0000.000
132A205GLU-1-0.934-0.96640.138-6.907-6.9070.0000.0000.0000.000
133A206LEU0-0.011-0.01540.4340.0270.0270.0000.0000.0000.000
134A207ALA0-0.0050.00438.031-0.084-0.0840.0000.0000.0000.000
135A208ILE00.0020.01139.396-0.015-0.0150.0000.0000.0000.000
136A209GLU-1-0.929-0.95642.584-6.954-6.9540.0000.0000.0000.000
137A210ALA0-0.065-0.05138.1540.0270.0270.0000.0000.0000.000
138A211GLY0-0.049-0.01939.140-0.109-0.1090.0000.0000.0000.000
139A212ALA0-0.082-0.03935.559-0.172-0.1720.0000.0000.0000.000
140A213GLU-1-0.852-0.90833.419-9.242-9.2420.0000.0000.0000.000
141A214ASP-1-0.818-0.90132.196-9.538-9.5380.0000.0000.0000.000
142A215VAL0-0.013-0.00733.030-0.128-0.1280.0000.0000.0000.000
143A216LYS10.7750.87628.9689.9299.9290.0000.0000.0000.000
144A217GLU-1-0.843-0.93730.552-9.255-9.2550.0000.0000.0000.000
145A218ALA0-0.053-0.02425.594-0.217-0.2170.0000.0000.0000.000
146A219GLU-1-0.814-0.89824.677-10.854-10.8540.0000.0000.0000.000
147A220ASP-1-0.885-0.94222.243-13.209-13.2090.0000.0000.0000.000
148A221GLU-1-0.916-0.99017.198-16.497-16.4970.0000.0000.0000.000
149A222GLU-1-0.924-0.90920.384-12.055-12.0550.0000.0000.0000.000
150A223GLU-1-1.009-0.99622.204-13.348-13.3480.0000.0000.0000.000
151A224LYS10.7650.85124.37611.87811.8780.0000.0000.0000.000
152A225ASN0-0.057-0.03626.890-0.053-0.0530.0000.0000.0000.000
153A226LEU0-0.072-0.03125.7740.2010.2010.0000.0000.0000.000
154A227PHE00.0070.00429.7380.1530.1530.0000.0000.0000.000
155A228LYS10.8760.94122.56713.19813.1980.0000.0000.0000.000
156A229PHE00.0330.01529.3930.2230.2230.0000.0000.0000.000
157A230ILE00.002-0.00328.470-0.415-0.4150.0000.0000.0000.000
158A231CYS0-0.010-0.00431.3560.3680.3680.0000.0000.0000.000
159A232ASP-1-0.783-0.87631.697-9.081-9.0810.0000.0000.0000.000
160A233ALA00.023-0.00329.506-0.055-0.0550.0000.0000.0000.000
161A234SER0-0.031-0.02730.905-0.122-0.1220.0000.0000.0000.000
162A235SER0-0.008-0.01733.9280.1640.1640.0000.0000.0000.000
163A236LEU00.0250.02127.8950.1750.1750.0000.0000.0000.000
164A237HIS00.0010.01032.526-0.196-0.1960.0000.0000.0000.000
165A238GLN0-0.008-0.01933.7190.1630.1630.0000.0000.0000.000
166A239VAL00.0610.03334.1900.0850.0850.0000.0000.0000.000
167A240ARG10.8540.92329.9239.8999.8990.0000.0000.0000.000
168A241LYS10.8790.93232.8969.2029.2020.0000.0000.0000.000
169A242LYS10.8890.96837.0377.7687.7680.0000.0000.0000.000
170A243LEU00.0610.03034.4480.1420.1420.0000.0000.0000.000
171A244ASP-1-0.807-0.88634.921-8.900-8.9000.0000.0000.0000.000
172A245SER0-0.104-0.06437.8350.1890.1890.0000.0000.0000.000
173A246LEU0-0.026-0.00140.9300.1690.1690.0000.0000.0000.000
174A247GLY00.0140.01141.3240.0660.0660.0000.0000.0000.000
175A248LEU00.0190.01936.623-0.078-0.0780.0000.0000.0000.000
176A249CYS0-0.008-0.01534.1390.0860.0860.0000.0000.0000.000
177A250PRO0-0.023-0.02631.836-0.323-0.3230.0000.0000.0000.000
178A251VAL00.0160.01926.1890.0290.0290.0000.0000.0000.000
179A252SER0-0.041-0.02324.047-0.143-0.1430.0000.0000.0000.000
180A253CYS0-0.049-0.02925.5450.5890.5890.0000.0000.0000.000
181A254SER0-0.027-0.02322.654-0.279-0.2790.0000.0000.0000.000
182A255MET0-0.041-0.02023.0930.6470.6470.0000.0000.0000.000
183A256GLU-1-0.789-0.85921.571-14.827-14.8270.0000.0000.0000.000
184A257PHE0-0.031-0.03721.3240.5400.5400.0000.0000.0000.000
185A258ILE00.0190.00723.820-0.377-0.3770.0000.0000.0000.000
186A259PRO0-0.0280.00024.7030.3330.3330.0000.0000.0000.000
187A260HIS10.8030.89427.48110.02710.0270.0000.0000.0000.000
188A261SER00.0140.01630.0470.2190.2190.0000.0000.0000.000
189A262LYS10.8660.91124.27212.02712.0270.0000.0000.0000.000
190A263VAL0-0.038-0.01325.8690.4110.4110.0000.0000.0000.000
191A264GLN00.0230.01126.129-0.653-0.6530.0000.0000.0000.000
192A265LEU0-0.039-0.01922.6670.1610.1610.0000.0000.0000.000
193A266ALA00.0430.02725.416-0.059-0.0590.0000.0000.0000.000
194A267GLU-1-0.884-0.95522.648-12.439-12.4390.0000.0000.0000.000
195A268PRO00.0360.02221.805-0.597-0.5970.0000.0000.0000.000
196A269GLU-1-0.895-0.96622.357-12.225-12.2250.0000.0000.0000.000
197A270LEU0-0.019-0.00719.690-0.592-0.5920.0000.0000.0000.000
198A271GLU-1-0.928-0.95817.553-15.775-15.7750.0000.0000.0000.000
199A272GLN0-0.022-0.01517.430-0.705-0.7050.0000.0000.0000.000
200A273ALA0-0.005-0.00518.784-0.447-0.4470.0000.0000.0000.000
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