Manual

About

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: JLGV9

Calculation Name: 5EOV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EOV

Chain ID: A

ChEMBL ID:

UniProt ID: P9WJ62

Base Structure: X-ray

Registration Date: 2023-09-19

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134559.854233
FMO2-HF: Nuclear repulsion 2060935.334647
FMO2-HF: Total energy -73624.519586
FMO2-MP2: Total energy -73844.012209


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:64:SER)


Summations of interaction energy for fragment #1(A:64: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.
-22.082-18.7589.062-5.498-6.8840.017
Interaction energy analysis for fragmet #1(A:64:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.078 / q_NPA : 0.028
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].
3A66GLY00.0450.0142.940-4.951-2.3640.214-1.300-1.5000.009
4A67ALA00.0700.0182.041-5.239-6.3908.059-3.510-3.3980.006
5A68HIS00.0310.0123.492-0.798-0.3790.0160.014-0.4490.000
6A69LYS10.9030.9585.757-1.735-1.7350.0000.0000.0000.000
7A70LEU00.0340.0247.307-0.152-0.1520.0000.0000.0000.000
8A71VAL00.0220.0187.209-0.077-0.0770.0000.0000.0000.000
9A72GLY00.0390.0209.5190.0600.0600.0000.0000.0000.000
10A73ALA0-0.042-0.01911.7070.0120.0120.0000.0000.0000.000
11A74LEU0-0.025-0.02410.843-0.018-0.0180.0000.0000.0000.000
12A75GLU-1-0.902-0.95312.965-0.408-0.4080.0000.0000.0000.000
13A76ALA0-0.065-0.02415.5360.0300.0300.0000.0000.0000.000
14A77PHE0-0.054-0.03717.1020.0250.0250.0000.0000.0000.000
15A78ALA0-0.0030.01518.2890.0000.0000.0000.0000.0000.000
16A79ILE0-0.026-0.00116.889-0.001-0.0010.0000.0000.0000.000
17A80ALA00.0010.00516.852-0.050-0.0500.0000.0000.0000.000
18A81VAL00.019-0.00713.4100.0210.0210.0000.0000.0000.000
19A82ALA0-0.008-0.00716.586-0.007-0.0070.0000.0000.0000.000
20A83GLY0-0.012-0.01118.3550.0510.0510.0000.0000.0000.000
21A84ARG10.8220.92818.6020.3040.3040.0000.0000.0000.000
22A85ARG10.8980.95518.6430.2300.2300.0000.0000.0000.000
23A86CYS0-0.032-0.01914.8410.0300.0300.0000.0000.0000.000
24A87LEU00.0020.01215.939-0.010-0.0100.0000.0000.0000.000
25A88ASP-1-0.834-0.9409.320-0.380-0.3800.0000.0000.0000.000
26A89ALA0-0.019-0.03012.8740.0020.0020.0000.0000.0000.000
27A90GLY00.019-0.02212.6490.0420.0420.0000.0000.0000.000
28A91ALA0-0.0030.0419.4270.1240.1240.0000.0000.0000.000
29A92SER0-0.004-0.0028.832-0.028-0.0280.0000.0000.0000.000
30A93THR0-0.057-0.0193.494-1.592-1.0890.009-0.223-0.289-0.001
31A94GLY00.0670.0324.7470.2590.279-0.001-0.005-0.0130.000
32A95GLY0-0.030-0.0372.382-1.709-0.9180.717-0.813-0.6940.003
33A96PHE00.0180.0003.0010.9700.7650.0490.403-0.2470.000
34A97THR00.0450.0206.6070.0070.0070.0000.0000.0000.000
35A98GLU-1-0.920-0.9664.258-7.881-7.521-0.001-0.064-0.2940.000
36A99VAL00.0000.0234.8040.3350.3350.0000.0000.0000.000
37A100LEU0-0.032-0.0247.2590.3090.3090.0000.0000.0000.000
38A101LEU0-0.026-0.01610.2320.1710.1710.0000.0000.0000.000
39A102ASP-1-0.918-0.9517.947-2.236-2.2360.0000.0000.0000.000
40A103ARG10.7950.90010.5960.9770.9770.0000.0000.0000.000
41A104GLY00.0240.00112.8670.1420.1420.0000.0000.0000.000
42A105ALA0-0.0120.01214.3920.0980.0980.0000.0000.0000.000
43A106ALA0-0.038-0.01916.053-0.033-0.0330.0000.0000.0000.000
44A107HIS0-0.028-0.02017.5530.0070.0070.0000.0000.0000.000
45A108VAL00.0080.01111.7070.0160.0160.0000.0000.0000.000
46A109VAL0-0.0010.00915.090-0.007-0.0070.0000.0000.0000.000
47A110ALA00.0170.00211.8260.0130.0130.0000.0000.0000.000
48A111ALA0-0.018-0.01513.5610.0290.0290.0000.0000.0000.000
49A112ASP-1-0.888-0.94814.141-0.162-0.1620.0000.0000.0000.000
50A113VAL0-0.058-0.03714.9280.0300.0300.0000.0000.0000.000
51A114GLY0-0.046-0.03616.2490.0530.0530.0000.0000.0000.000
52A115TYR0-0.0120.00714.548-0.047-0.0470.0000.0000.0000.000
53A116GLY00.0070.01012.5300.0440.0440.0000.0000.0000.000
54A117GLN00.0020.00112.537-0.043-0.0430.0000.0000.0000.000
55A118LEU00.0510.0309.104-0.091-0.0910.0000.0000.0000.000
56A119ALA00.0270.0069.3270.1230.1230.0000.0000.0000.000
57A120TRP00.062-0.00611.041-0.051-0.0510.0000.0000.0000.000
58A121SER0-0.045-0.01510.4080.0390.0390.0000.0000.0000.000
59A122LEU00.0360.0227.790-0.024-0.0240.0000.0000.0000.000
60A123ARG10.9040.96811.7120.5480.5480.0000.0000.0000.000
61A124ASN0-0.002-0.01014.7210.0920.0920.0000.0000.0000.000
62A125ASP-1-0.805-0.87813.944-0.896-0.8960.0000.0000.0000.000
63A126PRO00.0190.00916.0140.0410.0410.0000.0000.0000.000
64A127ARG10.8130.90413.9080.9980.9980.0000.0000.0000.000
65A128VAL0-0.027-0.00712.444-0.011-0.0110.0000.0000.0000.000
66A129VAL00.0040.00615.4890.0580.0580.0000.0000.0000.000
67A130VAL0-0.006-0.00513.897-0.022-0.0220.0000.0000.0000.000
68A131LEU0-0.042-0.01816.4330.0480.0480.0000.0000.0000.000
69A132GLU-1-0.887-0.93617.540-0.201-0.2010.0000.0000.0000.000
70A133ARG10.8630.93719.2070.1220.1220.0000.0000.0000.000
71A134THR00.0220.02120.0660.0220.0220.0000.0000.0000.000
72A135ASN00.016-0.00221.0970.0130.0130.0000.0000.0000.000
73A136ALA00.1360.06617.942-0.021-0.0210.0000.0000.0000.000
74A137ARG10.8550.90319.895-0.072-0.0720.0000.0000.0000.000
75A138GLY00.0080.01622.972-0.002-0.0020.0000.0000.0000.000
76A139LEU0-0.043-0.00918.261-0.013-0.0130.0000.0000.0000.000
77A140THR00.0300.01622.8770.0090.0090.0000.0000.0000.000
78A141PRO00.0370.00824.451-0.017-0.0170.0000.0000.0000.000
79A142GLU-1-0.872-0.94525.811-0.117-0.1170.0000.0000.0000.000
80A143ALA0-0.066-0.02424.142-0.009-0.0090.0000.0000.0000.000
81A144ILE0-0.037-0.01320.471-0.015-0.0150.0000.0000.0000.000
82A145GLY00.0050.02022.152-0.028-0.0280.0000.0000.0000.000
83A146GLY0-0.023-0.01724.859-0.006-0.0060.0000.0000.0000.000
84A147ARG10.8620.92123.7710.0930.0930.0000.0000.0000.000
85A148VAL0-0.034-0.00719.209-0.014-0.0140.0000.0000.0000.000
86A149ASP-1-0.825-0.91720.733-0.233-0.2330.0000.0000.0000.000
87A150LEU0-0.010-0.00814.7090.0170.0170.0000.0000.0000.000
88A151VAL0-0.0010.00616.758-0.028-0.0280.0000.0000.0000.000
89A152VAL0-0.0160.00511.2270.0380.0380.0000.0000.0000.000
90A153ALA00.015-0.00913.717-0.023-0.0230.0000.0000.0000.000
91A154ASP-1-0.828-0.9059.1360.9930.9930.0000.0000.0000.000
92A155LEU00.0040.01812.1180.0040.0040.0000.0000.0000.000
93A156SER00.004-0.01813.6200.0510.0510.0000.0000.0000.000
94A157PHE0-0.031-0.01816.208-0.038-0.0380.0000.0000.0000.000
95A158ILE0-0.013-0.00118.871-0.038-0.0380.0000.0000.0000.000
96A159SER0-0.0120.00320.4320.0100.0100.0000.0000.0000.000
97A160LEU00.057-0.01518.099-0.027-0.0270.0000.0000.0000.000
98A161ALA00.0060.01321.946-0.026-0.0260.0000.0000.0000.000
99A162THR0-0.085-0.05523.924-0.022-0.0220.0000.0000.0000.000
100A163VAL00.0260.00219.906-0.013-0.0130.0000.0000.0000.000
101A164LEU00.0220.00922.013-0.020-0.0200.0000.0000.0000.000
102A165PRO0-0.0030.00323.821-0.016-0.0160.0000.0000.0000.000
103A166ALA00.0170.02323.138-0.012-0.0120.0000.0000.0000.000
104A167LEU0-0.012-0.01218.725-0.017-0.0170.0000.0000.0000.000
105A168VAL00.0220.01022.035-0.020-0.0200.0000.0000.0000.000
106A169GLY0-0.034-0.01524.994-0.011-0.0110.0000.0000.0000.000
107A170CYS0-0.043-0.01821.901-0.011-0.0110.0000.0000.0000.000
108A171ALA00.0240.03122.670-0.025-0.0250.0000.0000.0000.000
109A172SER00.0300.00323.9020.0210.0210.0000.0000.0000.000
110A173ARG10.9440.95526.1200.0730.0730.0000.0000.0000.000
111A174ASP-1-0.898-0.93627.106-0.146-0.1460.0000.0000.0000.000
112A175ALA0-0.0070.00122.082-0.012-0.0120.0000.0000.0000.000
113A176ASP-1-0.805-0.88119.629-0.149-0.1490.0000.0000.0000.000
114A177ILE0-0.0110.00019.161-0.019-0.0190.0000.0000.0000.000
115A178VAL0-0.004-0.01315.5910.0230.0230.0000.0000.0000.000
116A179PRO0-0.0180.00415.3890.0140.0140.0000.0000.0000.000
117A180LEU0-0.020-0.00611.2090.0060.0060.0000.0000.0000.000
118A181VAL00.008-0.01115.1090.0120.0120.0000.0000.0000.000
119A182LYS10.8550.92512.028-0.636-0.6360.0000.0000.0000.000
120A183PRO00.0560.01717.998-0.029-0.0290.0000.0000.0000.000
121A184GLN0-0.004-0.01016.036-0.071-0.0710.0000.0000.0000.000
122A185PHE0-0.065-0.03616.343-0.003-0.0030.0000.0000.0000.000
123A186GLU-1-0.797-0.88121.6220.1470.1470.0000.0000.0000.000
124A187VAL0-0.066-0.00624.119-0.023-0.0230.0000.0000.0000.000
125A188GLY00.0430.02226.774-0.001-0.0010.0000.0000.0000.000
126A189LYS10.9580.94929.279-0.122-0.1220.0000.0000.0000.000
127A190GLY0-0.016-0.00830.499-0.010-0.0100.0000.0000.0000.000
128A191GLN00.0150.01028.9660.0020.0020.0000.0000.0000.000
129A192VAL0-0.0240.01123.9330.0110.0110.0000.0000.0000.000
130A193GLY00.0020.00725.983-0.015-0.0150.0000.0000.0000.000
131A194PRO00.036-0.01226.1270.0170.0170.0000.0000.0000.000
132A195GLY00.0330.01723.3670.0140.0140.0000.0000.0000.000
133A196GLY0-0.0180.00721.6880.0380.0380.0000.0000.0000.000
134A197VAL00.0080.00519.9340.0310.0310.0000.0000.0000.000
135A198VAL00.0000.00922.056-0.037-0.0370.0000.0000.0000.000
136A199HIS00.002-0.01323.5740.0080.0080.0000.0000.0000.000
137A200ASP-1-0.844-0.93025.7670.1690.1690.0000.0000.0000.000
138A201PRO00.0370.01725.8170.0050.0050.0000.0000.0000.000
139A202GLN00.0410.01526.899-0.009-0.0090.0000.0000.0000.000
140A203LEU0-0.028-0.00727.491-0.010-0.0100.0000.0000.0000.000
141A204ARG10.8670.93821.363-0.292-0.2920.0000.0000.0000.000
142A205ALA00.0490.02324.265-0.004-0.0040.0000.0000.0000.000
143A206ARG10.9550.96626.346-0.137-0.1370.0000.0000.0000.000
144A207SER0-0.006-0.00623.513-0.008-0.0080.0000.0000.0000.000
145A208VAL00.0080.01121.467-0.007-0.0070.0000.0000.0000.000
146A209LEU00.0100.00323.965-0.018-0.0180.0000.0000.0000.000
147A210ALA0-0.028-0.00827.138-0.015-0.0150.0000.0000.0000.000
148A211VAL00.0200.01421.854-0.013-0.0130.0000.0000.0000.000
149A212ALA00.0090.00125.227-0.016-0.0160.0000.0000.0000.000
150A213ARG10.9570.98726.528-0.065-0.0650.0000.0000.0000.000
151A214ARG10.9050.97027.150-0.054-0.0540.0000.0000.0000.000
152A215ALA00.015-0.00225.262-0.010-0.0100.0000.0000.0000.000
153A216GLN0-0.0120.00127.305-0.005-0.0050.0000.0000.0000.000
154A217GLU-1-0.959-0.97830.5400.0290.0290.0000.0000.0000.000
155A218LEU0-0.074-0.02627.063-0.005-0.0050.0000.0000.0000.000
156A219GLY0-0.007-0.00130.687-0.010-0.0100.0000.0000.0000.000
157A220TRP0-0.054-0.02624.007-0.009-0.0090.0000.0000.0000.000
158A221HIS00.0470.01528.0210.0180.0180.0000.0000.0000.000
159A222SER00.0290.00525.353-0.007-0.0070.0000.0000.0000.000
160A223VAL0-0.021-0.00924.0320.0000.0000.0000.0000.0000.000
161A224GLY00.0340.00922.748-0.004-0.0040.0000.0000.0000.000
162A225VAL0-0.031-0.01920.8080.0060.0060.0000.0000.0000.000
163A226LYS10.9730.99915.995-0.120-0.1200.0000.0000.0000.000
164A227ALA00.0200.02017.0200.0260.0260.0000.0000.0000.000
165A228SER0-0.012-0.01811.449-0.021-0.0210.0000.0000.0000.000
166A229PRO0-0.009-0.00110.0400.0360.0360.0000.0000.0000.000
167A230LEU0-0.053-0.0277.0610.1370.1370.0000.0000.0000.000
168A231PRO00.0170.01611.209-0.006-0.0060.0000.0000.0000.000
169A232GLY00.0310.00711.7650.2090.2090.0000.0000.0000.000
170A233PRO0-0.008-0.01011.531-0.024-0.0240.0000.0000.0000.000
171A234SER00.002-0.00713.017-0.044-0.0440.0000.0000.0000.000
172A235GLY00.0070.00715.576-0.075-0.0750.0000.0000.0000.000
173A236ASN0-0.035-0.01316.855-0.097-0.0970.0000.0000.0000.000
174A237VAL00.0320.02915.9030.0840.0840.0000.0000.0000.000
175A238GLU-1-0.877-0.94312.9010.7420.7420.0000.0000.0000.000
176A239TYR00.0190.01116.1500.0080.0080.0000.0000.0000.000
177A240PHE00.0220.01910.475-0.005-0.0050.0000.0000.0000.000
178A241LEU0-0.007-0.00316.633-0.017-0.0170.0000.0000.0000.000
179A242TRP0-0.019-0.02019.407-0.008-0.0080.0000.0000.0000.000
180A243LEU0-0.006-0.01020.8070.0070.0070.0000.0000.0000.000
181A244ARG10.8430.90323.0380.1010.1010.0000.0000.0000.000
182A245THR0-0.036-0.01125.7780.0120.0120.0000.0000.0000.000
183A246GLN00.0080.00228.5660.0000.0000.0000.0000.0000.000
184A247THR0-0.033-0.02328.237-0.011-0.0110.0000.0000.0000.000
185A248ASP-1-0.812-0.89530.202-0.069-0.0690.0000.0000.0000.000
186A249ARG10.8820.93926.2590.0880.0880.0000.0000.0000.000
187A250ALA0-0.021-0.00229.3270.0050.0050.0000.0000.0000.000
188A251LEU0-0.0200.00226.7080.0030.0030.0000.0000.0000.000
189A252SER00.0130.01430.5970.0040.0040.0000.0000.0000.000
190A253ALA00.0560.01532.2250.0040.0040.0000.0000.0000.000
191A254LYS11.0110.99632.834-0.028-0.0280.0000.0000.0000.000
192A255GLY00.0130.01331.7970.0050.0050.0000.0000.0000.000
193A256LEU00.007-0.00125.9040.0040.0040.0000.0000.0000.000
194A257GLU-1-0.946-0.97628.2500.0740.0740.0000.0000.0000.000
195A258ASP-1-0.877-0.93829.6830.0650.0650.0000.0000.0000.000
196A259ALA0-0.014-0.00325.2780.0090.0090.0000.0000.0000.000
197A260VAL0-0.020-0.01524.8060.0160.0160.0000.0000.0000.000
198A261HIS00.0270.01325.4310.0230.0230.0000.0000.0000.000
199A262ARG10.8980.95525.137-0.044-0.0440.0000.0000.0000.000
200A263ALA00.0230.02621.1730.0160.0160.0000.0000.0000.000
201A264ILE0-0.098-0.06021.9010.0350.0350.0000.0000.0000.000
202A265SER0-0.069-0.05123.7250.0210.0210.0000.0000.0000.000
203A266GLU-1-0.985-0.97821.0010.1290.1290.0000.0000.0000.000
204A267GLY0-0.037-0.00220.0800.0220.0220.0000.0000.0000.000
205A268PRO0-0.036-0.02114.815-0.027-0.0270.0000.0000.0000.000