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: YVL72

Calculation Name: 4EQ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQ2

Chain ID: A

ChEMBL ID:

UniProt ID: B4XN22

Base Structure: X-ray

Registration Date: 2023-09-24

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2185989.472272
FMO2-HF: Nuclear repulsion 2103330.876538
FMO2-HF: Total energy -82658.595734
FMO2-MP2: Total energy -82897.259822


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-1.2391.4620.049-1.176-1.5740.002
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.009
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].
3A4PRO0-0.0060.0093.815-0.6041.264-0.016-0.868-0.9840.005
4A5SER00.0450.0145.5850.4820.4820.0000.0000.0000.000
5A6PRO0-0.041-0.0208.826-0.037-0.0370.0000.0000.0000.000
6A7THR00.0120.00211.8760.0430.0430.0000.0000.0000.000
7A8GLY00.0390.02213.8270.0420.0420.0000.0000.0000.000
8A9THR0-0.0060.00216.1580.0180.0180.0000.0000.0000.000
9A10SER0-0.009-0.01118.7310.0390.0390.0000.0000.0000.000
10A11VAL00.0670.04922.515-0.007-0.0070.0000.0000.0000.000
11A12LYS10.8330.91725.4590.1920.1920.0000.0000.0000.000
12A13SER00.0380.00828.6580.0010.0010.0000.0000.0000.000
13A14LYS10.9350.96531.8610.1160.1160.0000.0000.0000.000
14A15ASN00.0260.01735.2250.0000.0000.0000.0000.0000.000
15A16PHE00.0550.03335.9300.0000.0000.0000.0000.0000.000
16A17ARG10.8620.95132.3730.1270.1270.0000.0000.0000.000
17A18THR00.0090.00028.5230.0000.0000.0000.0000.0000.000
18A19VAL00.0090.01325.975-0.003-0.0030.0000.0000.0000.000
19A20LEU0-0.0170.00620.1910.0010.0010.0000.0000.0000.000
20A21TYR0-0.002-0.02021.802-0.004-0.0040.0000.0000.0000.000
21A22TRP00.0140.01215.6390.0210.0210.0000.0000.0000.000
22A23GLN0-0.031-0.01316.3180.0020.0020.0000.0000.0000.000
23A24TYR00.018-0.0338.137-0.053-0.0530.0000.0000.0000.000
24A25PRO00.0020.0078.9840.1210.1210.0000.0000.0000.000
25A26SER00.001-0.00311.9010.0190.0190.0000.0000.0000.000
26A27MET0-0.025-0.0097.420-0.099-0.0990.0000.0000.0000.000
27A28SER0-0.023-0.00211.9370.0720.0720.0000.0000.0000.000
28A29GLU-1-0.889-0.93911.733-0.431-0.4310.0000.0000.0000.000
29A30THR00.038-0.00213.447-0.073-0.0730.0000.0000.0000.000
30A31PRO0-0.031-0.00911.7930.0180.0180.0000.0000.0000.000
31A32HIS0-0.044-0.01013.1480.1370.1370.0000.0000.0000.000
32A33PHE0-0.015-0.00312.937-0.099-0.0990.0000.0000.0000.000
33A34VAL0-0.020-0.00515.1470.0630.0630.0000.0000.0000.000
34A35VAL00.0240.01016.195-0.033-0.0330.0000.0000.0000.000
35A36GLU-1-0.812-0.85318.039-0.176-0.1760.0000.0000.0000.000
36A37VAL00.0670.01920.456-0.011-0.0110.0000.0000.0000.000
37A38LYS10.8100.91921.8060.1370.1370.0000.0000.0000.000
38A39PRO00.0490.02225.0470.0020.0020.0000.0000.0000.000
39A40TYR0-0.010-0.03728.8180.0050.0050.0000.0000.0000.000
40A41LEU0-0.0130.00931.0800.0050.0050.0000.0000.0000.000
41A42SER00.0080.01228.4310.0050.0050.0000.0000.0000.000
42A43GLY00.0110.00627.7390.0060.0060.0000.0000.0000.000
43A44LYS10.8630.92124.6000.0550.0550.0000.0000.0000.000
44A45TYR0-0.066-0.05820.002-0.002-0.0020.0000.0000.0000.000
45A46GLN0-0.027-0.00222.6040.0160.0160.0000.0000.0000.000
46A47THR0-0.022-0.02421.041-0.016-0.0160.0000.0000.0000.000
47A48VAL00.0470.04122.3230.0130.0130.0000.0000.0000.000
48A49SER0-0.007-0.00523.527-0.013-0.0130.0000.0000.0000.000
49A50THR0-0.010-0.00725.051-0.012-0.0120.0000.0000.0000.000
50A51CYS0-0.088-0.03721.440-0.006-0.0060.0000.0000.0000.000
51A52VAL00.0460.01419.404-0.026-0.0260.0000.0000.0000.000
52A53ASN0-0.017-0.01516.907-0.013-0.0130.0000.0000.0000.000
53A54ILE00.0250.03118.4090.0140.0140.0000.0000.0000.000
54A55SER00.0560.01718.045-0.039-0.0390.0000.0000.0000.000
55A56ALA0-0.020-0.00518.785-0.032-0.0320.0000.0000.0000.000
56A57THR0-0.004-0.00917.281-0.020-0.0200.0000.0000.0000.000
57A58SER0-0.041-0.03119.7180.0210.0210.0000.0000.0000.000
58A60ASP-1-0.784-0.85723.987-0.143-0.1430.0000.0000.0000.000
59A61LEU00.0530.01823.966-0.001-0.0010.0000.0000.0000.000
60A62SER0-0.076-0.08027.9960.0120.0120.0000.0000.0000.000
61A63GLU-1-0.875-0.93929.323-0.138-0.1380.0000.0000.0000.000
62A64GLU-1-0.888-0.94726.824-0.129-0.1290.0000.0000.0000.000
63A65ILE0-0.104-0.04428.6790.0030.0030.0000.0000.0000.000
64A66ASN0-0.022-0.03431.9710.0050.0050.0000.0000.0000.000
65A67GLU-1-0.797-0.86034.045-0.061-0.0610.0000.0000.0000.000
66A68ILE00.030-0.00234.681-0.006-0.0060.0000.0000.0000.000
67A69PHE00.0480.01336.389-0.003-0.0030.0000.0000.0000.000
68A70HIS10.7970.89533.6960.0660.0660.0000.0000.0000.000
69A71SER0-0.039-0.03829.411-0.002-0.0020.0000.0000.0000.000
70A72TYR00.0040.01327.0870.0040.0040.0000.0000.0000.000
71A73TRP0-0.004-0.00222.4400.0040.0040.0000.0000.0000.000
72A74PHE00.0480.01321.5030.0060.0060.0000.0000.0000.000
73A75ARG10.8410.91716.1600.1870.1870.0000.0000.0000.000
74A76ILE00.0070.01014.8450.0140.0140.0000.0000.0000.000
75A77LYS10.8820.95610.7320.2850.2850.0000.0000.0000.000
76A78ALA00.0140.0009.2830.0860.0860.0000.0000.0000.000
77A79ILE0-0.048-0.0319.227-0.104-0.1040.0000.0000.0000.000
78A80VAL00.005-0.0097.8600.0050.0050.0000.0000.0000.000
79A81GLY00.0840.0638.627-0.022-0.0220.0000.0000.0000.000
80A82SER0-0.069-0.0449.2990.0050.0050.0000.0000.0000.000
81A83GLN0-0.019-0.0043.164-0.902-0.0690.065-0.308-0.590-0.003
82A84GLN00.0370.0146.266-0.048-0.0480.0000.0000.0000.000
83A85SER00.0060.0205.5420.0250.0250.0000.0000.0000.000
84A86GLN0-0.009-0.0096.6040.2470.2470.0000.0000.0000.000
85A87TYR0-0.044-0.0658.806-0.139-0.1390.0000.0000.0000.000
86A88VAL0-0.0130.00812.2670.0190.0190.0000.0000.0000.000
87A89GLU-1-0.806-0.89613.775-0.146-0.1460.0000.0000.0000.000
88A90THR0-0.035-0.01817.463-0.010-0.0100.0000.0000.0000.000
89A91ASP-1-0.919-0.95920.452-0.170-0.1700.0000.0000.0000.000
90A92GLU-1-0.836-0.89623.289-0.096-0.0960.0000.0000.0000.000
91A93PHE00.001-0.00826.2810.0000.0000.0000.0000.0000.000
92A94VAL00.0380.00628.3950.0060.0060.0000.0000.0000.000
93A95LEU00.0010.02332.1380.0000.0000.0000.0000.0000.000
94A96GLN00.000-0.01334.192-0.001-0.0010.0000.0000.0000.000
95A97LYS10.8230.92931.4440.0890.0890.0000.0000.0000.000
96A98HIS00.001-0.01229.4690.0000.0000.0000.0000.0000.000
97A99GLY0-0.039-0.00432.730-0.007-0.0070.0000.0000.0000.000
98A100LYS10.9270.96233.3490.1170.1170.0000.0000.0000.000
99A101ILE00.0650.02636.683-0.003-0.0030.0000.0000.0000.000
100A102GLY0-0.030-0.02239.9540.0010.0010.0000.0000.0000.000
101A103PRO00.0150.03140.8970.0020.0020.0000.0000.0000.000
102A104PRO0-0.019-0.00244.454-0.002-0.0020.0000.0000.0000.000
103A105LYS10.8890.95846.9950.0600.0600.0000.0000.0000.000
104A106LEU00.011-0.00348.9130.0020.0020.0000.0000.0000.000
105A107ASN0-0.032-0.02652.317-0.002-0.0020.0000.0000.0000.000
106A108LEU00.0060.02255.4780.0010.0010.0000.0000.0000.000
107A109SER0-0.015-0.00758.5900.0010.0010.0000.0000.0000.000
108A110ARG10.9210.94562.1540.0330.0330.0000.0000.0000.000
109A111HIS0-0.053-0.00865.6760.0010.0010.0000.0000.0000.000
110A112GLY00.0140.00068.7950.0010.0010.0000.0000.0000.000
111A113ALA00.0460.01269.991-0.001-0.0010.0000.0000.0000.000
112A114GLU-1-0.850-0.88867.528-0.032-0.0320.0000.0000.0000.000
113A115ILE0-0.005-0.01561.816-0.001-0.0010.0000.0000.0000.000
114A116ILE00.0010.01061.1080.0000.0000.0000.0000.0000.000
115A117VAL0-0.053-0.03956.090-0.001-0.0010.0000.0000.0000.000
116A118ASP-1-0.820-0.88155.875-0.044-0.0440.0000.0000.0000.000
117A119VAL0-0.060-0.04250.671-0.002-0.0020.0000.0000.0000.000
118A120TYR00.0850.04049.1000.0000.0000.0000.0000.0000.000
119A121HIS10.8340.90243.5510.0710.0710.0000.0000.0000.000
120A122PRO0-0.0080.00044.954-0.001-0.0010.0000.0000.0000.000
121A123GLU-1-0.881-0.95040.066-0.085-0.0850.0000.0000.0000.000
122A124PHE0-0.033-0.01440.710-0.005-0.0050.0000.0000.0000.000
123A125PRO0-0.0030.00738.4940.0010.0010.0000.0000.0000.000
124A126SER00.0400.02241.2340.0030.0030.0000.0000.0000.000
125A127VAL00.0300.00742.871-0.002-0.0020.0000.0000.0000.000
126A128GLU-1-0.885-0.93444.378-0.060-0.0600.0000.0000.0000.000
127A129VAL0-0.052-0.01539.201-0.001-0.0010.0000.0000.0000.000
128A130ARG10.8830.93935.4850.0980.0980.0000.0000.0000.000
129A131PRO00.0670.02640.5120.0020.0020.0000.0000.0000.000
130A132TRP0-0.0110.00136.3680.0030.0030.0000.0000.0000.000
131A133MET0-0.0040.00540.3880.0000.0000.0000.0000.0000.000
132A134ARG10.9640.97542.3370.0530.0530.0000.0000.0000.000
133A135GLU-1-0.952-0.96644.018-0.052-0.0520.0000.0000.0000.000
134A136ILE0-0.028-0.01740.9230.0010.0010.0000.0000.0000.000
135A137TYR0-0.024-0.05242.7710.0000.0000.0000.0000.0000.000
136A138SER0-0.0100.00746.9240.0010.0010.0000.0000.0000.000
137A139GLU-1-0.915-0.95346.847-0.044-0.0440.0000.0000.0000.000
138A140LEU0-0.094-0.03546.350-0.002-0.0020.0000.0000.0000.000
139A141SER00.0080.00948.6590.0030.0030.0000.0000.0000.000
140A142TYR00.028-0.00347.881-0.005-0.0050.0000.0000.0000.000
141A143SER0-0.030-0.02350.4120.0020.0020.0000.0000.0000.000
142A144VAL00.003-0.01052.339-0.002-0.0020.0000.0000.0000.000
143A145ILE0-0.045-0.02352.3090.0020.0020.0000.0000.0000.000
144A146PHE00.006-0.00356.039-0.001-0.0010.0000.0000.0000.000
145A147ARG10.9250.94154.7190.0440.0440.0000.0000.0000.000
146A148ASN0-0.025-0.00860.1440.0010.0010.0000.0000.0000.000
147A149SER0-0.015-0.02461.1390.0000.0000.0000.0000.0000.000
148A150GLU-1-0.780-0.86662.568-0.033-0.0330.0000.0000.0000.000
149A151ASN0-0.047-0.03866.0710.0010.0010.0000.0000.0000.000
150A152GLU-1-0.893-0.94262.480-0.033-0.0330.0000.0000.0000.000
151A153SER0-0.137-0.04662.740-0.001-0.0010.0000.0000.0000.000
152A154ARG10.9660.96454.5680.0390.0390.0000.0000.0000.000
153A155LYS10.9210.95660.3910.0320.0320.0000.0000.0000.000
154A156ASN0-0.012-0.00256.606-0.003-0.0030.0000.0000.0000.000
155A157PHE00.0280.02057.5080.0020.0020.0000.0000.0000.000
156A158THR00.0220.00554.181-0.001-0.0010.0000.0000.0000.000
157A159VAL0-0.031-0.00454.6560.0020.0020.0000.0000.0000.000
158A160ALA00.047-0.00453.991-0.002-0.0020.0000.0000.0000.000
159A161ASP-1-0.886-0.93154.047-0.040-0.0400.0000.0000.0000.000
160A162CYS0-0.129-0.03452.9950.0030.0030.0000.0000.0000.000
161A163GLU-1-0.837-0.92653.424-0.044-0.0440.0000.0000.0000.000
162A164MET0-0.043-0.02351.275-0.001-0.0010.0000.0000.0000.000
163A165ASN0-0.054-0.02446.906-0.001-0.0010.0000.0000.0000.000
164A166GLU-1-0.985-0.99750.679-0.056-0.0560.0000.0000.0000.000
165A168ASN0-0.005-0.03255.0300.0010.0010.0000.0000.0000.000
166A169LEU00.0080.00158.3190.0010.0010.0000.0000.0000.000
167A170SER00.0230.00360.654-0.001-0.0010.0000.0000.0000.000
168A171ILE0-0.075-0.04260.2550.0010.0010.0000.0000.0000.000
169A172PRO00.0060.01064.8750.0000.0000.0000.0000.0000.000
170A173VAL0-0.009-0.00766.5180.0000.0000.0000.0000.0000.000
171A174PRO0-0.092-0.04767.3430.0010.0010.0000.0000.0000.000
172A175SER0-0.015-0.02870.4340.0010.0010.0000.0000.0000.000
173A176GLU-1-0.828-0.91571.216-0.026-0.0260.0000.0000.0000.000
174A177GLY0-0.043-0.00772.1760.0000.0000.0000.0000.0000.000
175A178SER0-0.075-0.02767.8080.0000.0000.0000.0000.0000.000
176A179THR0-0.008-0.02062.5490.0000.0000.0000.0000.0000.000
177A180TYR0-0.013-0.00762.6800.0000.0000.0000.0000.0000.000
178A181CYS0-0.015-0.02055.6540.0000.0000.0000.0000.0000.000
179A182VAL00.016-0.00155.9740.0010.0010.0000.0000.0000.000
180A183SER00.0070.00951.258-0.002-0.0020.0000.0000.0000.000
181A184ALA00.019-0.00150.8220.0020.0020.0000.0000.0000.000
182A185LYS10.8820.95546.6310.0530.0530.0000.0000.0000.000
183A186GLY00.0260.01946.2610.0020.0020.0000.0000.0000.000
184A187HIS0-0.0240.00645.934-0.002-0.0020.0000.0000.0000.000
185A188PHE00.0250.00343.041-0.001-0.0010.0000.0000.0000.000
186A189PHE00.0300.00142.508-0.002-0.0020.0000.0000.0000.000
187A190ASP-1-0.874-0.92847.321-0.043-0.0430.0000.0000.0000.000
188A191ASP-1-0.897-0.96146.742-0.051-0.0510.0000.0000.0000.000
189A192LEU0-0.078-0.02442.723-0.002-0.0020.0000.0000.0000.000
190A193ILE0-0.012-0.00139.501-0.005-0.0050.0000.0000.0000.000
191A194VAL0-0.0030.01242.1990.0020.0020.0000.0000.0000.000
192A195GLY0-0.016-0.00741.968-0.004-0.0040.0000.0000.0000.000
193A196ALA0-0.068-0.03741.4560.0020.0020.0000.0000.0000.000
194A197SER00.009-0.01843.4540.0010.0010.0000.0000.0000.000
195A198SER0-0.0100.00345.945-0.003-0.0030.0000.0000.0000.000
196A199GLU-1-0.977-0.98647.568-0.065-0.0650.0000.0000.0000.000
197A200GLU-1-0.869-0.94049.587-0.045-0.0450.0000.0000.0000.000
198A201SER0-0.0110.01853.373-0.001-0.0010.0000.0000.0000.000
199A203ILE0-0.002-0.00459.1960.0000.0000.0000.0000.0000.000
200A204TRP00.0200.01362.5480.0010.0010.0000.0000.0000.000
201A205VAL0-0.028-0.02366.1530.0000.0000.0000.0000.0000.000
202A206PRO0-0.060-0.02469.0050.0010.0010.0000.0000.0000.000
203A207ILE00.0470.04672.6930.0000.0000.0000.0000.0000.000