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: VQ7Z1

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2186056.411569
FMO2-HF: Nuclear repulsion 2103397.209587
FMO2-HF: Total energy -82659.201982
FMO2-MP2: Total energy -82897.895815


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.
-0.7291.6740.068-1.075-1.3960
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 : 0.033 / q_NPA : 0.015
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].
3A4PRO00.0010.0153.899-0.3641.182-0.004-0.732-0.8100.003
4A5SER00.0330.0055.9230.5260.5260.0000.0000.0000.000
5A6PRO0-0.031-0.0118.781-0.056-0.0560.0000.0000.0000.000
6A7THR00.0210.01312.3180.0360.0360.0000.0000.0000.000
7A8GLY00.0440.01414.2940.0420.0420.0000.0000.0000.000
8A9THR0-0.021-0.00116.2990.0230.0230.0000.0000.0000.000
9A10SER00.0160.00119.0520.0440.0440.0000.0000.0000.000
10A11VAL00.0610.04722.839-0.004-0.0040.0000.0000.0000.000
11A12LYS10.8070.89325.3500.2360.2360.0000.0000.0000.000
12A13SER00.027-0.00328.6970.0030.0030.0000.0000.0000.000
13A14LYS10.9200.95531.9250.1340.1340.0000.0000.0000.000
14A15ASN00.0230.00835.4910.0000.0000.0000.0000.0000.000
15A16PHE00.0600.03735.6810.0010.0010.0000.0000.0000.000
16A17ARG10.8910.96132.1620.1460.1460.0000.0000.0000.000
17A18THR0-0.008-0.01328.6440.0010.0010.0000.0000.0000.000
18A19VAL00.0150.01725.835-0.001-0.0010.0000.0000.0000.000
19A20LEU0-0.0110.00919.9320.0010.0010.0000.0000.0000.000
20A21TYR00.011-0.00521.860-0.002-0.0020.0000.0000.0000.000
21A22TRP00.0040.00815.5980.0210.0210.0000.0000.0000.000
22A23GLN0-0.024-0.00716.6020.0120.0120.0000.0000.0000.000
23A24TYR00.008-0.0407.973-0.050-0.0500.0000.0000.0000.000
24A25PRO00.0030.0058.9480.1390.1390.0000.0000.0000.000
25A26SER00.0070.00511.9360.0400.0400.0000.0000.0000.000
26A27MET0-0.0090.0037.534-0.073-0.0730.0000.0000.0000.000
27A28SER0-0.016-0.01611.8600.0690.0690.0000.0000.0000.000
28A29GLU-1-0.884-0.93211.419-0.384-0.3840.0000.0000.0000.000
29A30THR0-0.001-0.01312.803-0.086-0.0860.0000.0000.0000.000
30A31PRO00.0000.00211.8000.0190.0190.0000.0000.0000.000
31A32HIS0-0.048-0.01212.8410.1510.1510.0000.0000.0000.000
32A33PHE0-0.013-0.01412.910-0.128-0.1280.0000.0000.0000.000
33A34VAL0-0.041-0.01014.7920.0770.0770.0000.0000.0000.000
34A35VAL00.0120.01015.941-0.045-0.0450.0000.0000.0000.000
35A36GLU-1-0.789-0.84517.559-0.217-0.2170.0000.0000.0000.000
36A37VAL00.0320.00820.270-0.017-0.0170.0000.0000.0000.000
37A38LYS10.7980.90321.1570.1850.1850.0000.0000.0000.000
38A39PRO00.0670.02924.7670.0020.0020.0000.0000.0000.000
39A40TYR0-0.009-0.04028.6280.0070.0070.0000.0000.0000.000
40A41LEU0-0.0170.00730.7540.0060.0060.0000.0000.0000.000
41A42SER00.0120.02027.5730.0060.0060.0000.0000.0000.000
42A43GLY0-0.0010.00327.6730.0080.0080.0000.0000.0000.000
43A44LYS10.8420.90624.1940.0680.0680.0000.0000.0000.000
44A45TYR0-0.065-0.06819.839-0.004-0.0040.0000.0000.0000.000
45A46GLN0-0.050-0.01322.4810.0220.0220.0000.0000.0000.000
46A47THR0-0.018-0.02419.913-0.011-0.0110.0000.0000.0000.000
47A48VAL00.0210.01721.8220.0150.0150.0000.0000.0000.000
48A49SER0-0.0080.00223.075-0.012-0.0120.0000.0000.0000.000
49A50THR0-0.004-0.01825.034-0.007-0.0070.0000.0000.0000.000
50A51CYS0-0.089-0.03121.319-0.003-0.0030.0000.0000.0000.000
51A52VAL00.0490.01419.022-0.034-0.0340.0000.0000.0000.000
52A53ASN0-0.012-0.01616.466-0.010-0.0100.0000.0000.0000.000
53A54ILE00.0360.04017.8360.0120.0120.0000.0000.0000.000
54A55SER00.0560.01217.594-0.045-0.0450.0000.0000.0000.000
55A56ALA0-0.0190.00118.592-0.034-0.0340.0000.0000.0000.000
56A57THR0-0.019-0.01916.857-0.008-0.0080.0000.0000.0000.000
57A58SER0-0.047-0.03319.2760.0220.0220.0000.0000.0000.000
58A60ASP-1-0.794-0.85823.749-0.164-0.1640.0000.0000.0000.000
59A61LEU00.0470.01623.857-0.006-0.0060.0000.0000.0000.000
60A62SER0-0.083-0.07827.9060.0110.0110.0000.0000.0000.000
61A63GLU-1-0.819-0.89028.968-0.156-0.1560.0000.0000.0000.000
62A64GLU-1-0.827-0.93026.589-0.146-0.1460.0000.0000.0000.000
63A65ILE0-0.088-0.03028.0990.0050.0050.0000.0000.0000.000
64A66ASN0-0.054-0.04231.3610.0070.0070.0000.0000.0000.000
65A67GLU-1-0.768-0.85334.153-0.077-0.0770.0000.0000.0000.000
66A68ILE00.002-0.00634.539-0.008-0.0080.0000.0000.0000.000
67A69PHE00.0360.02036.405-0.004-0.0040.0000.0000.0000.000
68A70HIS10.8130.89433.8180.0820.0820.0000.0000.0000.000
69A71SER0-0.052-0.04729.204-0.001-0.0010.0000.0000.0000.000
70A72TYR0-0.017-0.01227.1130.0070.0070.0000.0000.0000.000
71A73TRP0-0.0020.00122.3540.0050.0050.0000.0000.0000.000
72A74PHE00.0410.00921.4110.0100.0100.0000.0000.0000.000
73A75ARG10.8310.91515.8260.2310.2310.0000.0000.0000.000
74A76ILE00.0080.00614.7780.0240.0240.0000.0000.0000.000
75A77LYS10.8800.95810.4760.3230.3230.0000.0000.0000.000
76A78ALA00.0350.0149.2860.1080.1080.0000.0000.0000.000
77A79ILE0-0.033-0.0179.063-0.074-0.0740.0000.0000.0000.000
78A80VAL00.009-0.0037.793-0.019-0.0190.0000.0000.0000.000
79A81GLY00.0920.0668.3810.0020.0020.0000.0000.0000.000
80A82SER0-0.091-0.0499.133-0.015-0.0150.0000.0000.0000.000
81A83GLN0-0.029-0.0113.185-0.7720.0850.072-0.343-0.586-0.003
82A84GLN00.0330.0066.036-0.104-0.1040.0000.0000.0000.000
83A85SER0-0.0090.0005.4550.0280.0280.0000.0000.0000.000
84A86GLN00.008-0.0046.3370.3170.3170.0000.0000.0000.000
85A87TYR0-0.056-0.0628.337-0.173-0.1730.0000.0000.0000.000
86A88VAL0-0.0040.01111.7100.0040.0040.0000.0000.0000.000
87A89GLU-1-0.787-0.87213.568-0.185-0.1850.0000.0000.0000.000
88A90THR0-0.045-0.03117.315-0.016-0.0160.0000.0000.0000.000
89A91ASP-1-0.894-0.95120.365-0.227-0.2270.0000.0000.0000.000
90A92GLU-1-0.807-0.86523.398-0.128-0.1280.0000.0000.0000.000
91A93PHE00.001-0.00926.203-0.001-0.0010.0000.0000.0000.000
92A94VAL00.0320.00628.4000.0060.0060.0000.0000.0000.000
93A95LEU00.0070.01032.116-0.001-0.0010.0000.0000.0000.000
94A96GLN0-0.004-0.01933.986-0.002-0.0020.0000.0000.0000.000
95A97LYS10.7990.90631.4700.1180.1180.0000.0000.0000.000
96A98HIS00.0000.00129.1160.0030.0030.0000.0000.0000.000
97A99GLY0-0.0210.00732.511-0.010-0.0100.0000.0000.0000.000
98A100LYS10.9250.96334.0730.1410.1410.0000.0000.0000.000
99A101ILE00.0640.03537.151-0.002-0.0020.0000.0000.0000.000
100A102GLY0-0.025-0.02140.3440.0000.0000.0000.0000.0000.000
101A103PRO00.0150.02641.3530.0030.0030.0000.0000.0000.000
102A104PRO0-0.004-0.00444.908-0.002-0.0020.0000.0000.0000.000
103A105LYS10.8380.93147.3540.0690.0690.0000.0000.0000.000
104A106LEU00.0060.01148.9540.0020.0020.0000.0000.0000.000
105A107ASN0-0.029-0.01652.375-0.004-0.0040.0000.0000.0000.000
106A108LEU00.0100.01755.4150.0010.0010.0000.0000.0000.000
107A109SER0-0.0090.00158.8370.0010.0010.0000.0000.0000.000
108A110ARG10.9010.93262.5070.0390.0390.0000.0000.0000.000
109A111HIS0-0.056-0.01665.9470.0010.0010.0000.0000.0000.000
110A112GLY00.015-0.00369.0920.0010.0010.0000.0000.0000.000
111A113ALA00.0270.01670.512-0.001-0.0010.0000.0000.0000.000
112A114GLU-1-0.824-0.87167.368-0.038-0.0380.0000.0000.0000.000
113A115ILE0-0.002-0.01762.0270.0000.0000.0000.0000.0000.000
114A116ILE0-0.0050.00161.3420.0000.0000.0000.0000.0000.000
115A117VAL0-0.035-0.02556.324-0.001-0.0010.0000.0000.0000.000
116A118ASP-1-0.820-0.89155.686-0.052-0.0520.0000.0000.0000.000
117A119VAL0-0.066-0.05250.881-0.002-0.0020.0000.0000.0000.000
118A120TYR00.0880.04649.1300.0000.0000.0000.0000.0000.000
119A121HIS10.8370.89943.8560.0840.0840.0000.0000.0000.000
120A122PRO00.0060.01544.936-0.001-0.0010.0000.0000.0000.000
121A123GLU-1-0.882-0.94039.963-0.099-0.0990.0000.0000.0000.000
122A124PHE0-0.017-0.01140.379-0.006-0.0060.0000.0000.0000.000
123A125PRO0-0.022-0.00138.4700.0020.0020.0000.0000.0000.000
124A126SER00.0430.03541.2150.0030.0030.0000.0000.0000.000
125A127VAL00.0330.01642.516-0.003-0.0030.0000.0000.0000.000
126A128GLU-1-0.856-0.93144.502-0.066-0.0660.0000.0000.0000.000
127A129VAL0-0.041-0.01939.073-0.001-0.0010.0000.0000.0000.000
128A130ARG10.8560.92735.4190.1110.1110.0000.0000.0000.000
129A131PRO00.0430.02040.5280.0010.0010.0000.0000.0000.000
130A132TRP00.0420.01835.9970.0030.0030.0000.0000.0000.000
131A133MET0-0.0300.00040.388-0.001-0.0010.0000.0000.0000.000
132A134ARG10.8950.94142.0710.0630.0630.0000.0000.0000.000
133A135GLU-1-0.924-0.94843.883-0.063-0.0630.0000.0000.0000.000
134A136ILE0-0.029-0.01640.6730.0000.0000.0000.0000.0000.000
135A137TYR0-0.017-0.05142.723-0.001-0.0010.0000.0000.0000.000
136A138SER0-0.026-0.00846.7340.0020.0020.0000.0000.0000.000
137A139GLU-1-0.893-0.94746.532-0.056-0.0560.0000.0000.0000.000
138A140LEU0-0.108-0.03546.169-0.002-0.0020.0000.0000.0000.000
139A141SER00.0040.00248.2620.0030.0030.0000.0000.0000.000
140A142TYR00.029-0.00447.854-0.006-0.0060.0000.0000.0000.000
141A143SER0-0.030-0.01750.5600.0030.0030.0000.0000.0000.000
142A144VAL00.007-0.00752.309-0.002-0.0020.0000.0000.0000.000
143A145ILE0-0.040-0.01652.7230.0020.0020.0000.0000.0000.000
144A146PHE00.0320.01056.314-0.001-0.0010.0000.0000.0000.000
145A147ARG10.9110.93555.6680.0550.0550.0000.0000.0000.000
146A148ASN00.0080.00461.0260.0010.0010.0000.0000.0000.000
147A149SER0-0.023-0.04261.6330.0000.0000.0000.0000.0000.000
148A150GLU-1-0.750-0.84063.229-0.041-0.0410.0000.0000.0000.000
149A151ASN0-0.056-0.03466.6840.0020.0020.0000.0000.0000.000
150A152GLU-1-0.916-0.95362.570-0.043-0.0430.0000.0000.0000.000
151A153SER0-0.096-0.02963.346-0.001-0.0010.0000.0000.0000.000
152A154ARG10.9230.94155.3010.0500.0500.0000.0000.0000.000
153A155LYS10.9170.95761.2210.0400.0400.0000.0000.0000.000
154A156ASN00.0180.00857.189-0.003-0.0030.0000.0000.0000.000
155A157PHE00.0280.01657.6370.0020.0020.0000.0000.0000.000
156A158THR0-0.021-0.02954.003-0.002-0.0020.0000.0000.0000.000
157A159VAL0-0.0180.00654.3810.0020.0020.0000.0000.0000.000
158A160ALA00.0730.01553.462-0.003-0.0030.0000.0000.0000.000
159A161ASP-1-0.894-0.94253.853-0.048-0.0480.0000.0000.0000.000
160A162CYS0-0.150-0.04352.6730.0030.0030.0000.0000.0000.000
161A163GLU-1-0.803-0.90853.006-0.053-0.0530.0000.0000.0000.000
162A164MET0-0.066-0.03351.408-0.001-0.0010.0000.0000.0000.000
163A165ASN0-0.046-0.01746.500-0.002-0.0020.0000.0000.0000.000
164A166GLU-1-0.985-1.00350.235-0.066-0.0660.0000.0000.0000.000
165A168ASN0-0.014-0.03454.8280.0000.0000.0000.0000.0000.000
166A169LEU0-0.002-0.00158.2010.0010.0010.0000.0000.0000.000
167A170SER00.012-0.00360.574-0.001-0.0010.0000.0000.0000.000
168A171ILE0-0.053-0.03160.1520.0000.0000.0000.0000.0000.000
169A172PRO0-0.022-0.00464.7900.0000.0000.0000.0000.0000.000
170A173VAL0-0.008-0.00467.4200.0000.0000.0000.0000.0000.000
171A174PRO0-0.085-0.04367.5780.0010.0010.0000.0000.0000.000
172A175SER0-0.001-0.03070.6840.0010.0010.0000.0000.0000.000
173A176GLU-1-0.843-0.91972.156-0.031-0.0310.0000.0000.0000.000
174A177GLY0-0.062-0.00971.676-0.001-0.0010.0000.0000.0000.000
175A178SER0-0.063-0.02568.7140.0000.0000.0000.0000.0000.000
176A179THR0-0.016-0.03263.2940.0000.0000.0000.0000.0000.000
177A180TYR0-0.031-0.01663.3000.0000.0000.0000.0000.0000.000
178A181CYS0-0.031-0.03055.8980.0000.0000.0000.0000.0000.000
179A182VAL00.008-0.00356.2610.0010.0010.0000.0000.0000.000
180A183SER0-0.003-0.01251.810-0.002-0.0020.0000.0000.0000.000
181A184ALA00.0100.00251.3340.0020.0020.0000.0000.0000.000
182A185LYS10.8750.94746.9940.0660.0660.0000.0000.0000.000
183A186GLY00.0490.02146.2820.0030.0030.0000.0000.0000.000
184A187HIS0-0.0330.00145.907-0.003-0.0030.0000.0000.0000.000
185A188PHE00.0310.00543.012-0.001-0.0010.0000.0000.0000.000
186A189PHE00.0310.01342.073-0.003-0.0030.0000.0000.0000.000
187A190ASP-1-0.873-0.92247.057-0.054-0.0540.0000.0000.0000.000
188A191ASP-1-0.896-0.96546.668-0.065-0.0650.0000.0000.0000.000
189A192LEU0-0.073-0.02342.519-0.003-0.0030.0000.0000.0000.000
190A193ILE0-0.0060.00839.376-0.006-0.0060.0000.0000.0000.000
191A194VAL0-0.0090.01042.0550.0030.0030.0000.0000.0000.000
192A195GLY0-0.032-0.01842.015-0.006-0.0060.0000.0000.0000.000
193A196ALA0-0.057-0.03641.9690.0030.0030.0000.0000.0000.000
194A197SER00.009-0.01043.8480.0020.0020.0000.0000.0000.000
195A198SER0-0.035-0.02146.451-0.003-0.0030.0000.0000.0000.000
196A199GLU-1-0.945-0.96948.261-0.077-0.0770.0000.0000.0000.000
197A200GLU-1-0.837-0.89850.143-0.056-0.0560.0000.0000.0000.000
198A201SER00.0050.02253.8740.0000.0000.0000.0000.0000.000
199A203ILE0-0.001-0.00159.5190.0000.0000.0000.0000.0000.000
200A204TRP00.0340.02462.9880.0010.0010.0000.0000.0000.000
201A205VAL0-0.016-0.00566.6240.0000.0000.0000.0000.0000.000
202A206PRO0-0.037-0.01469.5900.0010.0010.0000.0000.0000.000
203A207ILE00.0200.02673.2380.0000.0000.0000.0000.0000.000