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: 855MY

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 OptH
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 -2410276.589598
FMO2-HF: Nuclear repulsion 2323822.624619
FMO2-HF: Total energy -86453.964979
FMO2-MP2: Total energy -86703.765501


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.
-10.827-3.96900000000016.662-4.324-9.193-0.027
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 : 1.040 / q_NPA : 1.028
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].
3A76ARG10.9680.9772.05137.68440.8573.214-2.529-3.858-0.009
4A77ILE00.0500.0182.1452.1243.7553.188-0.888-3.930-0.011
5A78PHE00.032-0.0183.3102.6334.4890.262-0.899-1.218-0.007
6A79SER00.0130.0045.7075.0875.0870.0000.0000.0000.000
7A80LYS10.8750.9446.85830.68830.6880.0000.0000.0000.000
8A81LEU00.0260.0025.9872.3532.3530.0000.0000.0000.000
9A82THR0-0.012-0.0099.5772.7462.7460.0000.0000.0000.000
10A83LEU0-0.050-0.01611.5921.7771.7770.0000.0000.0000.000
11A84SER00.0250.01012.5741.4011.4010.0000.0000.0000.000
12A85ILE0-0.027-0.01111.9421.1811.1810.0000.0000.0000.000
13A86ARG10.9160.95515.20816.89416.8940.0000.0000.0000.000
14A87LEU00.0010.00317.3120.8410.8410.0000.0000.0000.000
15A88ALA00.0620.03318.0840.7500.7500.0000.0000.0000.000
16A89VAL0-0.030-0.02018.9720.8220.8220.0000.0000.0000.000
17A90LYS10.7740.86421.28413.49013.4900.0000.0000.0000.000
18A91GLU-1-0.921-0.94322.979-11.519-11.5190.0000.0000.0000.000
19A92GLY00.0120.01023.7920.4570.4570.0000.0000.0000.000
20A93GLY0-0.086-0.03724.5060.2930.2930.0000.0000.0000.000
21A94PRO00.015-0.00921.550-0.352-0.3520.0000.0000.0000.000
22A95ASN0-0.002-0.00121.637-0.438-0.4380.0000.0000.0000.000
23A96PRO00.015-0.00219.7610.1490.1490.0000.0000.0000.000
24A97GLU-1-0.915-0.95721.896-10.784-10.7840.0000.0000.0000.000
25A98ASN0-0.038-0.01725.2310.3330.3330.0000.0000.0000.000
26A99ASN0-0.036-0.00422.121-0.019-0.0190.0000.0000.0000.000
27A100SER00.0740.02221.908-0.561-0.5610.0000.0000.0000.000
28A101SER00.0360.02819.981-0.770-0.7700.0000.0000.0000.000
29A102LEU00.011-0.00116.883-0.926-0.9260.0000.0000.0000.000
30A103ALA00.001-0.00716.954-0.793-0.7930.0000.0000.0000.000
31A104ASN00.0110.00916.982-0.337-0.3370.0000.0000.0000.000
32A105ILE00.0080.01112.533-1.198-1.1980.0000.0000.0000.000
33A106LEU0-0.019-0.02012.216-1.422-1.4220.0000.0000.0000.000
34A107GLU-1-0.871-0.92812.577-16.342-16.3420.0000.0000.0000.000
35A108LEU00.0350.0289.228-1.163-1.1630.0000.0000.0000.000
36A109CYS0-0.062-0.0338.133-2.269-2.2690.0000.0000.0000.000
37A110ARG10.8990.9468.02114.62114.6210.0000.0000.0000.000
38A111SER0-0.036-0.0049.557-0.722-0.7220.0000.0000.0000.000
39A112LYS10.9040.9514.24229.73829.838-0.001-0.004-0.0940.000
40A113ASN0-0.011-0.0054.649-1.848-1.750-0.001-0.004-0.0930.000
41A114MET0-0.0610.0205.988-0.440-0.4400.0000.0000.0000.000
42A115PRO00.0130.0036.2792.3592.3590.0000.0000.0000.000
43A116LYS11.0231.0029.48714.08614.0860.0000.0000.0000.000
44A117SER00.0000.00512.6560.0110.0110.0000.0000.0000.000
45A118THR00.0240.0068.6870.4150.4150.0000.0000.0000.000
46A119ILE00.0370.01810.4750.2660.2660.0000.0000.0000.000
47A120GLU-1-0.913-0.97512.855-13.097-13.0970.0000.0000.0000.000
48A121SER0-0.035-0.00914.6260.8110.8110.0000.0000.0000.000
49A122ALA00.0090.01413.4630.4890.4890.0000.0000.0000.000
50A123LEU0-0.027-0.01615.5820.5060.5060.0000.0000.0000.000
51A124LYS10.9060.95818.06512.52512.5250.0000.0000.0000.000
52A125THR0-0.076-0.03618.3140.2470.2470.0000.0000.0000.000
53A126GLU-1-0.889-0.94120.703-10.712-10.7120.0000.0000.0000.000
54A127LYS10.9970.99523.32310.46910.4690.0000.0000.0000.000
55A128ASN00.0040.01624.707-0.171-0.1710.0000.0000.0000.000
56A129LYS10.9500.98920.25813.29913.2990.0000.0000.0000.000
57A130GLY0-0.023-0.01320.964-0.522-0.5220.0000.0000.0000.000
58A131ILE0-0.017-0.01321.9040.4570.4570.0000.0000.0000.000
59A132TYR0-0.034-0.05819.920-0.316-0.3160.0000.0000.0000.000
60A133LEU0-0.047-0.02820.8580.6560.6560.0000.0000.0000.000
61A134LEU00.0440.02321.155-0.680-0.6800.0000.0000.0000.000
62A135TYR0-0.011-0.00721.0760.8100.8100.0000.0000.0000.000
63A136GLU-1-0.722-0.87322.395-12.055-12.0550.0000.0000.0000.000
64A137GLY0-0.001-0.00923.5680.2340.2340.0000.0000.0000.000
65A138ARG10.8280.92524.40810.70210.7020.0000.0000.0000.000
66A139GLY00.0400.01822.117-0.302-0.3020.0000.0000.0000.000
67A140PRO0-0.011-0.00720.8330.4760.4760.0000.0000.0000.000
68A141GLY00.1010.05823.9700.4430.4430.0000.0000.0000.000
69A142GLY0-0.025-0.00926.3440.3110.3110.0000.0000.0000.000
70A143SER00.0100.01322.0780.3250.3250.0000.0000.0000.000
71A144SER0-0.045-0.04224.3240.4230.4230.0000.0000.0000.000
72A145LEU00.0120.00218.834-0.441-0.4410.0000.0000.0000.000
73A146LEU00.0150.02120.2540.6030.6030.0000.0000.0000.000
74A147ILE0-0.026-0.01216.891-0.986-0.9860.0000.0000.0000.000
75A148GLU-1-0.769-0.83817.334-15.365-15.3650.0000.0000.0000.000
76A149ALA00.0150.00116.539-1.303-1.3030.0000.0000.0000.000
77A150LEU0-0.041-0.01116.4051.0501.0500.0000.0000.0000.000
78A151SER00.0220.00116.769-0.340-0.3400.0000.0000.0000.000
79A152ASN0-0.045-0.03918.5330.7040.7040.0000.0000.0000.000
80A153SER0-0.012-0.01221.1510.7220.7220.0000.0000.0000.000
81A154GLY00.0800.05422.465-0.346-0.3460.0000.0000.0000.000
82A155PRO00.0290.00324.339-0.178-0.1780.0000.0000.0000.000
83A156LYS10.8900.93418.63915.11215.1120.0000.0000.0000.000
84A157CYS0-0.0260.02318.470-0.301-0.3010.0000.0000.0000.000
85A158HIS00.0160.01120.981-0.515-0.5150.0000.0000.0000.000
86A159LEU00.014-0.00923.596-0.028-0.0280.0000.0000.0000.000
87A160ASP-1-0.762-0.82218.660-14.927-14.9270.0000.0000.0000.000
88A161ILE00.001-0.00317.290-0.476-0.4760.0000.0000.0000.000
89A162LYS10.9680.99320.09910.99210.9920.0000.0000.0000.000
90A163TYR0-0.025-0.00919.698-0.056-0.0560.0000.0000.0000.000
91A164ILE0-0.039-0.02615.438-0.114-0.1140.0000.0000.0000.000
92A165LEU00.0270.00719.301-0.113-0.1130.0000.0000.0000.000
93A166ASN0-0.019-0.01321.3710.1720.1720.0000.0000.0000.000
94A167LYS10.8670.95515.68517.96717.9670.0000.0000.0000.000
95A168ASN0-0.060-0.03917.632-0.293-0.2930.0000.0000.0000.000
96A169GLY00.0240.01820.978-0.142-0.1420.0000.0000.0000.000
97A170GLY00.0130.01822.8560.3500.3500.0000.0000.0000.000
98A171MET0-0.038-0.02723.8980.4570.4570.0000.0000.0000.000
99A172MET0-0.018-0.00823.511-0.406-0.4060.0000.0000.0000.000
100A173ALA0-0.060-0.02826.1960.4260.4260.0000.0000.0000.000
101A174GLU-1-0.944-0.96328.572-9.135-9.1350.0000.0000.0000.000
102A175GLY0-0.014-0.01231.6010.1630.1630.0000.0000.0000.000
103A176ALA0-0.026-0.01731.398-0.288-0.2880.0000.0000.0000.000
104A177ARG10.9000.94928.28810.70410.7040.0000.0000.0000.000
105A178HIS00.0440.02629.155-0.493-0.4930.0000.0000.0000.000
106A179PHE0-0.082-0.04826.7160.3050.3050.0000.0000.0000.000
107A180PHE0-0.027-0.01922.293-0.012-0.0120.0000.0000.0000.000
108A181ASP-1-0.872-0.92926.773-9.918-9.9180.0000.0000.0000.000
109A182LYS10.8970.95023.25412.54712.5470.0000.0000.0000.000
110A183LYS10.9030.95926.48810.54110.5410.0000.0000.0000.000
111A184GLY00.004-0.01226.765-0.460-0.4600.0000.0000.0000.000
112A185VAL00.0030.00425.4030.2140.2140.0000.0000.0000.000
113A186VAL0-0.016-0.01427.199-0.226-0.2260.0000.0000.0000.000
114A187VAL00.0060.01224.8390.1540.1540.0000.0000.0000.000
115A188VAL00.004-0.00428.2880.0950.0950.0000.0000.0000.000
116A189GLY00.0450.03531.000-0.133-0.1330.0000.0000.0000.000
117A190VAL0-0.0030.00431.9920.2250.2250.0000.0000.0000.000
118A191GLU-1-0.949-0.98834.492-8.360-8.3600.0000.0000.0000.000
119A192ASP-1-0.837-0.92336.801-7.761-7.7610.0000.0000.0000.000
120A193ARG10.9110.94638.9457.9467.9460.0000.0000.0000.000
121A194GLU-1-1.043-1.01740.367-6.833-6.8330.0000.0000.0000.000
122A195LYS10.8570.92637.5618.3428.3420.0000.0000.0000.000
123A196LYS10.9640.98840.8226.8836.8830.0000.0000.0000.000
124A197ALA00.0360.01939.186-0.149-0.1490.0000.0000.0000.000
125A198VAL0-0.018-0.00437.1470.2270.2270.0000.0000.0000.000
126A199ASN00.0360.01937.402-0.267-0.2670.0000.0000.0000.000
127A200LEU00.0830.03435.3180.0420.0420.0000.0000.0000.000
128A201GLU-1-0.960-0.98038.100-7.012-7.0120.0000.0000.0000.000
129A202ARG10.9720.99941.1287.5977.5970.0000.0000.0000.000
130A203ALA0-0.028-0.01336.292-0.001-0.0010.0000.0000.0000.000
131A204LEU00.003-0.01437.122-0.074-0.0740.0000.0000.0000.000
132A205GLU-1-0.905-0.94739.618-7.007-7.0070.0000.0000.0000.000
133A206LEU00.010-0.00539.7380.0260.0260.0000.0000.0000.000
134A207ALA0-0.014-0.00437.196-0.053-0.0530.0000.0000.0000.000
135A208ILE00.0010.00538.759-0.005-0.0050.0000.0000.0000.000
136A209GLU-1-0.966-0.97441.892-6.971-6.9710.0000.0000.0000.000
137A210ALA0-0.097-0.05838.4370.0450.0450.0000.0000.0000.000
138A211GLY0-0.041-0.02139.211-0.100-0.1000.0000.0000.0000.000
139A212ALA0-0.117-0.05434.985-0.180-0.1800.0000.0000.0000.000
140A213GLU-1-0.919-0.96633.210-9.155-9.1550.0000.0000.0000.000
141A214ASP-1-0.888-0.95532.226-9.489-9.4890.0000.0000.0000.000
142A215VAL0-0.024-0.01032.745-0.139-0.1390.0000.0000.0000.000
143A216LYS10.8740.94328.17410.63710.6370.0000.0000.0000.000
144A217GLU-1-0.902-0.95730.215-9.299-9.2990.0000.0000.0000.000
145A218ALA0-0.068-0.03724.967-0.245-0.2450.0000.0000.0000.000
146A219GLU-1-0.879-0.94424.323-11.228-11.2280.0000.0000.0000.000
147A220ASP-1-0.926-0.97822.005-13.387-13.3870.0000.0000.0000.000
148A221GLU-1-0.927-0.98016.892-16.759-16.7590.0000.0000.0000.000
149A222GLU-1-1.056-0.98520.150-12.161-12.1610.0000.0000.0000.000
150A223GLU-1-1.008-0.99922.156-13.343-13.3430.0000.0000.0000.000
151A224LYS10.9460.95124.55010.91510.9150.0000.0000.0000.000
152A225ASN00.0200.02126.914-0.412-0.4120.0000.0000.0000.000
153A226LEU0-0.055-0.03325.3350.1060.1060.0000.0000.0000.000
154A227PHE00.0290.02429.2720.1010.1010.0000.0000.0000.000
155A228LYS10.9180.95822.49813.06713.0670.0000.0000.0000.000
156A229PHE00.0360.02229.1450.2270.2270.0000.0000.0000.000
157A230ILE0-0.013-0.01227.773-0.346-0.3460.0000.0000.0000.000
158A231CYS0-0.002-0.01230.7650.3480.3480.0000.0000.0000.000
159A232ASP-1-0.803-0.89131.341-9.192-9.1920.0000.0000.0000.000
160A233ALA0-0.008-0.02029.445-0.041-0.0410.0000.0000.0000.000
161A234SER0-0.023-0.02130.914-0.149-0.1490.0000.0000.0000.000
162A235SER00.0170.00833.8670.0910.0910.0000.0000.0000.000
163A236LEU00.0370.02627.6590.1040.1040.0000.0000.0000.000
164A237HIS0-0.025-0.02332.278-0.147-0.1470.0000.0000.0000.000
165A238GLN00.002-0.02033.8530.0660.0660.0000.0000.0000.000
166A239VAL00.0800.05434.3310.1420.1420.0000.0000.0000.000
167A240ARG10.9790.98828.43010.39210.3920.0000.0000.0000.000
168A241LYS10.8880.94733.0189.2469.2460.0000.0000.0000.000
169A242LYS10.9690.99637.1077.6497.6490.0000.0000.0000.000
170A243LEU00.0490.02034.2030.1260.1260.0000.0000.0000.000
171A244ASP-1-0.891-0.93235.945-8.498-8.4980.0000.0000.0000.000
172A245SER0-0.113-0.06437.9820.2020.2020.0000.0000.0000.000
173A246LEU0-0.025-0.00940.7080.1730.1730.0000.0000.0000.000
174A247GLY0-0.0040.02340.9010.0970.0970.0000.0000.0000.000
175A248LEU00.0060.00836.170-0.107-0.1070.0000.0000.0000.000
176A249CYS0-0.024-0.02334.0320.0570.0570.0000.0000.0000.000
177A250PRO0-0.041-0.04031.605-0.344-0.3440.0000.0000.0000.000
178A251VAL00.0060.01625.9050.0030.0030.0000.0000.0000.000
179A252SER0-0.042-0.02624.062-0.051-0.0510.0000.0000.0000.000
180A253CYS0-0.062-0.02425.6420.5380.5380.0000.0000.0000.000
181A254SER00.0030.00722.457-0.230-0.2300.0000.0000.0000.000
182A255MET0-0.064-0.02123.2150.5530.5530.0000.0000.0000.000
183A256GLU-1-0.857-0.92220.394-15.675-15.6750.0000.0000.0000.000
184A257PHE0-0.037-0.01620.6900.7950.7950.0000.0000.0000.000
185A258ILE00.0140.00522.965-0.424-0.4240.0000.0000.0000.000
186A259PRO0-0.0110.00224.0520.3230.3230.0000.0000.0000.000
187A260HIS10.8640.94326.77410.18210.1820.0000.0000.0000.000
188A261SER00.0320.01429.2990.2010.2010.0000.0000.0000.000
189A262LYS10.9730.98823.26312.22412.2240.0000.0000.0000.000
190A263VAL0-0.0230.00524.9960.4220.4220.0000.0000.0000.000
191A264GLN00.0150.00725.553-0.556-0.5560.0000.0000.0000.000
192A265LEU0-0.036-0.00921.6940.2170.2170.0000.0000.0000.000
193A266ALA00.0560.02624.660-0.053-0.0530.0000.0000.0000.000
194A267GLU-1-0.888-0.95322.365-12.777-12.7770.0000.0000.0000.000
195A268PRO00.0170.00421.636-0.595-0.5950.0000.0000.0000.000
196A269GLU-1-0.916-0.96422.195-12.186-12.1860.0000.0000.0000.000
197A270LEU0-0.025-0.01419.308-0.691-0.6910.0000.0000.0000.000
198A271GLU-1-0.930-0.96117.115-16.097-16.0970.0000.0000.0000.000
199A272GLN00.0230.01416.906-0.830-0.8300.0000.0000.0000.000
200A273ALA0-0.020-0.01317.978-0.609-0.6090.0000.0000.0000.000
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