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: 39RML

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 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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2136374.628843
FMO2-HF: Nuclear repulsion 2062749.55535
FMO2-HF: Total energy -73625.073493
FMO2-MP2: Total energy -73844.59345


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.
-25.985-20.6827.542-5.466-7.3780.02
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 : 0.024
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].
3A66GLY00.0560.0212.886-4.592-2.0520.337-1.295-1.5820.009
4A67ALA00.0460.0092.189-7.196-6.9336.068-2.882-3.4480.014
5A68HIS00.0240.0093.715-1.237-0.6360.018-0.166-0.4530.000
6A69LYS10.7950.9025.798-1.449-1.4490.0000.0000.0000.000
7A70LEU00.0330.0267.258-0.207-0.2070.0000.0000.0000.000
8A71VAL00.0190.0167.462-0.114-0.1140.0000.0000.0000.000
9A72GLY00.0310.0179.7330.0330.0330.0000.0000.0000.000
10A73ALA0-0.040-0.01811.944-0.010-0.0100.0000.0000.0000.000
11A74LEU0-0.018-0.02210.919-0.028-0.0280.0000.0000.0000.000
12A75GLU-1-0.839-0.90113.156-0.353-0.3530.0000.0000.0000.000
13A76ALA0-0.056-0.01615.7450.0200.0200.0000.0000.0000.000
14A77PHE0-0.069-0.04616.6770.0190.0190.0000.0000.0000.000
15A78ALA00.0010.01418.500-0.005-0.0050.0000.0000.0000.000
16A79ILE0-0.039-0.00217.044-0.007-0.0070.0000.0000.0000.000
17A80ALA00.0110.01117.012-0.046-0.0460.0000.0000.0000.000
18A81VAL00.027-0.00413.4790.0170.0170.0000.0000.0000.000
19A82ALA0-0.006-0.00516.688-0.013-0.0130.0000.0000.0000.000
20A83GLY0-0.014-0.01218.4190.0530.0530.0000.0000.0000.000
21A84ARG10.7890.90218.5270.3080.3080.0000.0000.0000.000
22A85ARG10.8750.93918.4880.2630.2630.0000.0000.0000.000
23A86CYS0-0.040-0.02514.6920.0360.0360.0000.0000.0000.000
24A87LEU00.0050.01015.799-0.013-0.0130.0000.0000.0000.000
25A88ASP-1-0.841-0.9339.132-0.671-0.6710.0000.0000.0000.000
26A89ALA0-0.003-0.02712.7190.0000.0000.0000.0000.0000.000
27A90GLY00.024-0.01612.5140.0560.0560.0000.0000.0000.000
28A91ALA00.0070.0449.3380.1130.1130.0000.0000.0000.000
29A92SER0-0.024-0.0128.673-0.003-0.0030.0000.0000.0000.000
30A93THR0-0.054-0.0263.605-1.211-0.8180.005-0.156-0.243-0.001
31A94GLY00.0690.0364.9050.3130.3130.0000.0000.0000.000
32A95GLY0-0.039-0.0302.262-2.122-1.3681.038-1.053-0.7380.003
33A96PHE00.011-0.0042.8561.9001.4020.0580.697-0.257-0.001
34A97THR00.0380.0096.4030.0710.0710.0000.0000.0000.000
35A98GLU-1-0.902-0.9553.622-10.954-9.7040.018-0.611-0.657-0.004
36A99VAL0-0.0050.0144.8520.4120.4120.0000.0000.0000.000
37A100LEU0-0.032-0.0217.3180.3550.3550.0000.0000.0000.000
38A101LEU0-0.031-0.01910.0510.1850.1850.0000.0000.0000.000
39A102ASP-1-0.920-0.9548.107-2.102-2.1020.0000.0000.0000.000
40A103ARG10.7340.85110.3360.9520.9520.0000.0000.0000.000
41A104GLY00.0220.00012.9240.1440.1440.0000.0000.0000.000
42A105ALA0-0.0130.01214.3100.0990.0990.0000.0000.0000.000
43A106ALA0-0.042-0.01716.078-0.034-0.0340.0000.0000.0000.000
44A107HIS0-0.019-0.01017.4840.0220.0220.0000.0000.0000.000
45A108VAL00.0040.00311.6120.0200.0200.0000.0000.0000.000
46A109VAL0-0.0140.00614.982-0.008-0.0080.0000.0000.0000.000
47A110ALA00.0270.00711.7460.0100.0100.0000.0000.0000.000
48A111ALA0-0.013-0.01313.4910.0390.0390.0000.0000.0000.000
49A112ASP-1-0.862-0.93814.094-0.352-0.3520.0000.0000.0000.000
50A113VAL0-0.068-0.04114.9130.0450.0450.0000.0000.0000.000
51A114GLY0-0.034-0.03116.2580.0600.0600.0000.0000.0000.000
52A115TYR0-0.026-0.00214.921-0.054-0.0540.0000.0000.0000.000
53A116GLY00.0110.01312.6180.0340.0340.0000.0000.0000.000
54A117GLN0-0.004-0.00212.698-0.039-0.0390.0000.0000.0000.000
55A118LEU00.0400.0268.993-0.119-0.1190.0000.0000.0000.000
56A119ALA00.0190.0119.4740.1410.1410.0000.0000.0000.000
57A120TRP00.0720.00911.206-0.046-0.0460.0000.0000.0000.000
58A121SER0-0.036-0.01310.4080.0610.0610.0000.0000.0000.000
59A122LEU00.0100.0077.968-0.023-0.0230.0000.0000.0000.000
60A123ARG10.8910.94911.7970.6170.6170.0000.0000.0000.000
61A124ASN0-0.009-0.01014.7910.0900.0900.0000.0000.0000.000
62A125ASP-1-0.784-0.84814.006-0.960-0.9600.0000.0000.0000.000
63A126PRO00.0210.00716.0610.0390.0390.0000.0000.0000.000
64A127ARG10.8130.88813.1841.0971.0970.0000.0000.0000.000
65A128VAL0-0.031-0.01412.396-0.012-0.0120.0000.0000.0000.000
66A129VAL00.0030.00715.4640.0640.0640.0000.0000.0000.000
67A130VAL00.0020.00113.887-0.027-0.0270.0000.0000.0000.000
68A131LEU0-0.038-0.01416.4300.0580.0580.0000.0000.0000.000
69A132GLU-1-0.895-0.93917.524-0.298-0.2980.0000.0000.0000.000
70A133ARG10.8750.92419.1950.1670.1670.0000.0000.0000.000
71A134THR00.0380.03320.0390.0190.0190.0000.0000.0000.000
72A135ASN0-0.008-0.01920.9780.0160.0160.0000.0000.0000.000
73A136ALA00.1440.07217.814-0.021-0.0210.0000.0000.0000.000
74A137ARG10.8540.90619.785-0.041-0.0410.0000.0000.0000.000
75A138GLY00.0180.02122.8750.0010.0010.0000.0000.0000.000
76A139LEU0-0.045-0.00318.128-0.012-0.0120.0000.0000.0000.000
77A140THR0-0.009-0.02822.7640.0120.0120.0000.0000.0000.000
78A141PRO00.0450.01524.333-0.020-0.0200.0000.0000.0000.000
79A142GLU-1-0.835-0.90325.678-0.140-0.1400.0000.0000.0000.000
80A143ALA0-0.069-0.02824.118-0.010-0.0100.0000.0000.0000.000
81A144ILE0-0.032-0.01020.286-0.018-0.0180.0000.0000.0000.000
82A145GLY00.0140.02122.055-0.030-0.0300.0000.0000.0000.000
83A146GLY0-0.022-0.01524.762-0.004-0.0040.0000.0000.0000.000
84A147ARG10.8350.90023.6320.1060.1060.0000.0000.0000.000
85A148VAL0-0.035-0.00818.997-0.013-0.0130.0000.0000.0000.000
86A149ASP-1-0.800-0.90420.618-0.254-0.2540.0000.0000.0000.000
87A150LEU0-0.007-0.00514.7060.0220.0220.0000.0000.0000.000
88A151VAL00.0020.00716.554-0.035-0.0350.0000.0000.0000.000
89A152VAL00.0040.01511.0120.0480.0480.0000.0000.0000.000
90A153ALA00.013-0.00913.534-0.035-0.0350.0000.0000.0000.000
91A154ASP-1-0.781-0.8819.4240.9730.9730.0000.0000.0000.000
92A155LEU00.0240.02411.981-0.003-0.0030.0000.0000.0000.000
93A156SER00.011-0.01113.6690.0660.0660.0000.0000.0000.000
94A157PHE0-0.028-0.01516.107-0.038-0.0380.0000.0000.0000.000
95A158ILE0-0.0110.00018.718-0.036-0.0360.0000.0000.0000.000
96A159SER0-0.012-0.01120.2940.0100.0100.0000.0000.0000.000
97A160LEU00.055-0.00817.701-0.030-0.0300.0000.0000.0000.000
98A161ALA0-0.0010.00321.765-0.026-0.0260.0000.0000.0000.000
99A162THR0-0.091-0.05823.883-0.020-0.0200.0000.0000.0000.000
100A163VAL00.016-0.00419.618-0.014-0.0140.0000.0000.0000.000
101A164LEU00.0190.01022.056-0.021-0.0210.0000.0000.0000.000
102A165PRO00.0030.00723.629-0.016-0.0160.0000.0000.0000.000
103A166ALA00.0140.02223.024-0.011-0.0110.0000.0000.0000.000
104A167LEU0-0.002-0.00318.466-0.019-0.0190.0000.0000.0000.000
105A168VAL00.0240.00921.851-0.019-0.0190.0000.0000.0000.000
106A169GLY0-0.034-0.01624.794-0.010-0.0100.0000.0000.0000.000
107A170CYS0-0.049-0.02221.734-0.011-0.0110.0000.0000.0000.000
108A171ALA00.0260.03122.485-0.026-0.0260.0000.0000.0000.000
109A172SER00.0370.02023.7060.0230.0230.0000.0000.0000.000
110A173ARG10.9450.95525.9050.0790.0790.0000.0000.0000.000
111A174ASP-1-0.893-0.93527.085-0.153-0.1530.0000.0000.0000.000
112A175ALA00.0060.01321.909-0.011-0.0110.0000.0000.0000.000
113A176ASP-1-0.790-0.86019.426-0.144-0.1440.0000.0000.0000.000
114A177ILE0-0.010-0.00418.925-0.024-0.0240.0000.0000.0000.000
115A178VAL00.005-0.00915.4790.0290.0290.0000.0000.0000.000
116A179PRO0-0.0220.00215.1460.0080.0080.0000.0000.0000.000
117A180LEU0-0.011-0.00211.1900.0280.0280.0000.0000.0000.000
118A181VAL00.003-0.01214.9810.0050.0050.0000.0000.0000.000
119A182LYS10.8360.91112.331-0.527-0.5270.0000.0000.0000.000
120A183PRO00.0570.01617.897-0.031-0.0310.0000.0000.0000.000
121A184GLN00.003-0.00215.946-0.067-0.0670.0000.0000.0000.000
122A185PHE0-0.064-0.03416.162-0.006-0.0060.0000.0000.0000.000
123A186GLU-1-0.782-0.85821.4990.1310.1310.0000.0000.0000.000
124A187VAL0-0.073-0.00924.029-0.022-0.0220.0000.0000.0000.000
125A188GLY00.0450.02226.687-0.003-0.0030.0000.0000.0000.000
126A189LYS10.9570.95229.210-0.110-0.1100.0000.0000.0000.000
127A190GLY0-0.008-0.00930.455-0.009-0.0090.0000.0000.0000.000
128A191GLN00.0150.01128.8410.0040.0040.0000.0000.0000.000
129A192VAL0-0.0190.01223.8410.0130.0130.0000.0000.0000.000
130A193GLY00.0080.01025.920-0.016-0.0160.0000.0000.0000.000
131A194PRO00.044-0.00826.0820.0150.0150.0000.0000.0000.000
132A195GLY00.0250.01423.3600.0160.0160.0000.0000.0000.000
133A196GLY0-0.0170.00821.6870.0360.0360.0000.0000.0000.000
134A197VAL00.0060.00519.8180.0280.0280.0000.0000.0000.000
135A198VAL00.0050.01621.978-0.037-0.0370.0000.0000.0000.000
136A199HIS00.0220.00123.4820.0110.0110.0000.0000.0000.000
137A200ASP-1-0.828-0.91725.6800.1800.1800.0000.0000.0000.000
138A201PRO00.0300.01325.7040.0050.0050.0000.0000.0000.000
139A202GLN00.0410.01026.777-0.011-0.0110.0000.0000.0000.000
140A203LEU0-0.0130.00027.228-0.011-0.0110.0000.0000.0000.000
141A204ARG10.8390.93521.200-0.314-0.3140.0000.0000.0000.000
142A205ALA00.0450.02224.139-0.004-0.0040.0000.0000.0000.000
143A206ARG10.9500.96126.215-0.148-0.1480.0000.0000.0000.000
144A207SER0-0.021-0.01623.421-0.009-0.0090.0000.0000.0000.000
145A208VAL00.0060.01021.289-0.009-0.0090.0000.0000.0000.000
146A209LEU00.0150.00523.833-0.019-0.0190.0000.0000.0000.000
147A210ALA0-0.026-0.00526.995-0.016-0.0160.0000.0000.0000.000
148A211VAL00.0180.00921.696-0.015-0.0150.0000.0000.0000.000
149A212ALA00.0140.01025.104-0.018-0.0180.0000.0000.0000.000
150A213ARG10.9270.97526.392-0.063-0.0630.0000.0000.0000.000
151A214ARG10.8210.91326.842-0.044-0.0440.0000.0000.0000.000
152A215ALA00.018-0.00125.043-0.012-0.0120.0000.0000.0000.000
153A216GLN0-0.014-0.01127.077-0.007-0.0070.0000.0000.0000.000
154A217GLU-1-0.870-0.92430.3150.0270.0270.0000.0000.0000.000
155A218LEU0-0.057-0.02027.080-0.005-0.0050.0000.0000.0000.000
156A219GLY0-0.012-0.00330.467-0.010-0.0100.0000.0000.0000.000
157A220TRP0-0.053-0.03023.906-0.008-0.0080.0000.0000.0000.000
158A221HIS00.0560.03227.7810.0200.0200.0000.0000.0000.000
159A222SER00.0270.00625.1970.0000.0000.0000.0000.0000.000
160A223VAL0-0.028-0.01424.0410.0000.0000.0000.0000.0000.000
161A224GLY00.0380.01522.781-0.002-0.0020.0000.0000.0000.000
162A225VAL0-0.033-0.02020.6630.0030.0030.0000.0000.0000.000
163A226LYS10.9110.96316.548-0.218-0.2180.0000.0000.0000.000
164A227ALA00.0020.01216.8640.0230.0230.0000.0000.0000.000
165A228SER0-0.011-0.01711.5480.0100.0100.0000.0000.0000.000
166A229PRO0-0.006-0.00210.0540.0280.0280.0000.0000.0000.000
167A230LEU0-0.041-0.0176.9830.1480.1480.0000.0000.0000.000
168A231PRO00.0090.01311.209-0.034-0.0340.0000.0000.0000.000
169A232GLY00.0390.00911.7560.2030.2030.0000.0000.0000.000
170A233PRO0-0.003-0.00811.499-0.020-0.0200.0000.0000.0000.000
171A234SER0-0.011-0.01013.012-0.044-0.0440.0000.0000.0000.000
172A235GLY00.0170.00815.574-0.074-0.0740.0000.0000.0000.000
173A236ASN0-0.046-0.02216.753-0.089-0.0890.0000.0000.0000.000
174A237VAL00.0360.03015.8120.0890.0890.0000.0000.0000.000
175A238GLU-1-0.847-0.93712.4590.7620.7620.0000.0000.0000.000
176A239TYR00.018-0.00316.0140.0190.0190.0000.0000.0000.000
177A240PHE00.0240.02110.225-0.013-0.0130.0000.0000.0000.000
178A241LEU00.0090.00316.481-0.013-0.0130.0000.0000.0000.000
179A242TRP0-0.008-0.01219.260-0.011-0.0110.0000.0000.0000.000
180A243LEU0-0.017-0.01620.6540.0070.0070.0000.0000.0000.000
181A244ARG10.8260.88922.7890.1010.1010.0000.0000.0000.000
182A245THR0-0.040-0.01225.5290.0120.0120.0000.0000.0000.000
183A246GLN0-0.001-0.00128.3250.0000.0000.0000.0000.0000.000
184A247THR0-0.022-0.02528.179-0.010-0.0100.0000.0000.0000.000
185A248ASP-1-0.783-0.84830.176-0.059-0.0590.0000.0000.0000.000
186A249ARG10.8330.88126.8330.0720.0720.0000.0000.0000.000
187A250ALA0-0.0130.00429.3320.0060.0060.0000.0000.0000.000
188A251LEU0-0.0120.00326.5790.0040.0040.0000.0000.0000.000
189A252SER00.0060.00730.4680.0020.0020.0000.0000.0000.000
190A253ALA00.0520.01532.0680.0050.0050.0000.0000.0000.000
191A254LYS11.0111.00032.680-0.038-0.0380.0000.0000.0000.000
192A255GLY00.0120.01231.6970.0060.0060.0000.0000.0000.000
193A256LEU00.010-0.00125.8040.0060.0060.0000.0000.0000.000
194A257GLU-1-0.928-0.96828.0950.0820.0820.0000.0000.0000.000
195A258ASP-1-0.857-0.92229.5310.0860.0860.0000.0000.0000.000
196A259ALA0-0.0040.00325.2050.0110.0110.0000.0000.0000.000
197A260VAL0-0.021-0.01624.6540.0190.0190.0000.0000.0000.000
198A261HIS00.0240.01325.2830.0240.0240.0000.0000.0000.000
199A262ARG10.8710.93125.456-0.070-0.0700.0000.0000.0000.000
200A263ALA00.0170.02321.0370.0200.0200.0000.0000.0000.000
201A264ILE0-0.082-0.05521.7560.0390.0390.0000.0000.0000.000
202A265SER0-0.074-0.05023.7130.0200.0200.0000.0000.0000.000
203A266GLU-1-0.933-0.95120.9880.1840.1840.0000.0000.0000.000
204A267GLY0-0.030-0.00220.0780.0240.0240.0000.0000.0000.000
205A268PRO0-0.032-0.01714.743-0.028-0.0280.0000.0000.0000.000