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: 5JMQZ

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2184821.880395
FMO2-HF: Nuclear repulsion 2102164.451614
FMO2-HF: Total energy -82657.428781
FMO2-MP2: Total energy -82896.114668


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.
-1.4371.2620.066-1.16-1.6050
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 : 0.030 / q_NPA : 0.014
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].
3A4PRO0-0.0090.0093.815-0.5801.205-0.014-0.803-0.9680.004
4A5SER00.0410.0025.5840.5010.5010.0000.0000.0000.000
5A6PRO0-0.049-0.0198.772-0.037-0.0370.0000.0000.0000.000
6A7THR00.0160.00711.8750.0410.0410.0000.0000.0000.000
7A8GLY00.0380.01913.8260.0440.0440.0000.0000.0000.000
8A9THR0-0.013-0.00416.1530.0230.0230.0000.0000.0000.000
9A10SER0-0.027-0.01418.7300.0370.0370.0000.0000.0000.000
10A11VAL00.0870.05322.514-0.008-0.0080.0000.0000.0000.000
11A12LYS10.8650.93625.4580.1840.1840.0000.0000.0000.000
12A13SER00.0470.02628.6570.0020.0020.0000.0000.0000.000
13A14LYS10.9270.95731.8610.1200.1200.0000.0000.0000.000
14A15ASN00.0790.04235.2240.0000.0000.0000.0000.0000.000
15A16PHE00.0500.03235.7990.0000.0000.0000.0000.0000.000
16A17ARG10.8990.97832.1300.1270.1270.0000.0000.0000.000
17A18THR0-0.002-0.01728.3700.0010.0010.0000.0000.0000.000
18A19VAL00.0070.01325.846-0.003-0.0030.0000.0000.0000.000
19A20LEU0-0.0180.01120.0110.0010.0010.0000.0000.0000.000
20A21TYR0-0.012-0.02721.794-0.003-0.0030.0000.0000.0000.000
21A22TRP00.0060.01115.4990.0190.0190.0000.0000.0000.000
22A23GLN0-0.025-0.00916.3920.0040.0040.0000.0000.0000.000
23A24TYR00.012-0.0258.167-0.054-0.0540.0000.0000.0000.000
24A25PRO00.0080.0109.0070.1250.1250.0000.0000.0000.000
25A26SER0-0.007-0.00411.9010.0450.0450.0000.0000.0000.000
26A27MET0-0.029-0.0127.282-0.114-0.1140.0000.0000.0000.000
27A28SER0-0.016-0.00311.9520.0650.0650.0000.0000.0000.000
28A29GLU-1-0.898-0.94012.096-0.411-0.4110.0000.0000.0000.000
29A30THR00.030-0.00713.450-0.075-0.0750.0000.0000.0000.000
30A31PRO0-0.020-0.00211.9730.0140.0140.0000.0000.0000.000
31A32HIS0-0.069-0.02112.9920.1440.1440.0000.0000.0000.000
32A33PHE0-0.006-0.00212.666-0.102-0.1020.0000.0000.0000.000
33A34VAL0-0.024-0.00914.9780.0650.0650.0000.0000.0000.000
34A35VAL00.0290.01116.031-0.036-0.0360.0000.0000.0000.000
35A36GLU-1-0.835-0.89518.076-0.187-0.1870.0000.0000.0000.000
36A37VAL00.0770.02220.310-0.011-0.0110.0000.0000.0000.000
37A38LYS10.8790.96222.7630.1230.1230.0000.0000.0000.000
38A39PRO00.0470.02524.9230.0020.0020.0000.0000.0000.000
39A40TYR00.032-0.00928.7040.0050.0050.0000.0000.0000.000
40A41LEU0-0.0060.00830.9660.0050.0050.0000.0000.0000.000
41A42SER00.0000.00728.3470.0040.0040.0000.0000.0000.000
42A43GLY00.0160.01727.6460.0050.0050.0000.0000.0000.000
43A44LYS10.8940.92324.5080.0580.0580.0000.0000.0000.000
44A45TYR0-0.090-0.09020.128-0.002-0.0020.0000.0000.0000.000
45A46GLN0-0.0040.00522.4910.0160.0160.0000.0000.0000.000
46A47THR0-0.011-0.01320.893-0.020-0.0200.0000.0000.0000.000
47A48VAL00.0560.03922.1640.0150.0150.0000.0000.0000.000
48A49SER00.002-0.00423.366-0.013-0.0130.0000.0000.0000.000
49A50THR00.0090.00224.889-0.012-0.0120.0000.0000.0000.000
50A51CYS0-0.117-0.05121.216-0.005-0.0050.0000.0000.0000.000
51A52VAL00.0490.01519.210-0.027-0.0270.0000.0000.0000.000
52A53ASN0-0.025-0.01516.768-0.015-0.0150.0000.0000.0000.000
53A54ILE00.0270.03218.2610.0160.0160.0000.0000.0000.000
54A55SER00.0560.01517.888-0.041-0.0410.0000.0000.0000.000
55A56ALA0-0.016-0.00318.785-0.031-0.0310.0000.0000.0000.000
56A57THR0-0.008-0.00917.334-0.022-0.0220.0000.0000.0000.000
57A58SER0-0.009-0.02719.6400.0150.0150.0000.0000.0000.000
58A60ASP-1-0.821-0.90223.805-0.150-0.1500.0000.0000.0000.000
59A61LEU00.0590.02323.803-0.002-0.0020.0000.0000.0000.000
60A62SER0-0.081-0.06727.8250.0120.0120.0000.0000.0000.000
61A63GLU-1-0.905-0.95929.166-0.143-0.1430.0000.0000.0000.000
62A64GLU-1-0.927-0.95426.554-0.136-0.1360.0000.0000.0000.000
63A65ILE0-0.091-0.03628.7390.0030.0030.0000.0000.0000.000
64A66ASN0-0.014-0.02631.8150.0050.0050.0000.0000.0000.000
65A67GLU-1-0.871-0.92033.936-0.067-0.0670.0000.0000.0000.000
66A68ILE00.032-0.00234.535-0.006-0.0060.0000.0000.0000.000
67A69PHE00.0540.01236.249-0.003-0.0030.0000.0000.0000.000
68A70HIS10.8030.91833.5250.0700.0700.0000.0000.0000.000
69A71SER0-0.043-0.05129.216-0.002-0.0020.0000.0000.0000.000
70A72TYR0-0.023-0.00926.9690.0020.0020.0000.0000.0000.000
71A73TRP00.0070.01422.2890.0050.0050.0000.0000.0000.000
72A74PHE00.0360.00621.3580.0050.0050.0000.0000.0000.000
73A75ARG10.8530.93015.8720.2040.2040.0000.0000.0000.000
74A76ILE00.0120.01014.4430.0130.0130.0000.0000.0000.000
75A77LYS10.8750.95910.6540.3040.3040.0000.0000.0000.000
76A78ALA00.023-0.0029.1200.0910.0910.0000.0000.0000.000
77A79ILE0-0.048-0.0299.056-0.108-0.1080.0000.0000.0000.000
78A80VAL00.016-0.0017.6890.0220.0220.0000.0000.0000.000
79A81GLY00.0750.0548.507-0.030-0.0300.0000.0000.0000.000
80A82SER0-0.057-0.0379.3270.0020.0020.0000.0000.0000.000
81A83GLN0-0.019-0.0053.111-1.140-0.2260.080-0.357-0.637-0.004
82A84GLN00.0400.0116.150-0.031-0.0310.0000.0000.0000.000
83A85SER00.0100.0305.3940.0090.0090.0000.0000.0000.000
84A86GLN0-0.005-0.0086.4470.2490.2490.0000.0000.0000.000
85A87TYR0-0.039-0.0418.691-0.135-0.1350.0000.0000.0000.000
86A88VAL0-0.0110.00912.1500.0160.0160.0000.0000.0000.000
87A89GLU-1-0.892-0.92113.640-0.157-0.1570.0000.0000.0000.000
88A90THR0-0.042-0.02117.336-0.010-0.0100.0000.0000.0000.000
89A91ASP-1-0.890-0.94620.416-0.172-0.1720.0000.0000.0000.000
90A92GLU-1-0.908-0.92723.289-0.098-0.0980.0000.0000.0000.000
91A93PHE0-0.008-0.01526.1880.0000.0000.0000.0000.0000.000
92A94VAL00.038-0.00128.2580.0060.0060.0000.0000.0000.000
93A95LEU0-0.0130.02332.0010.0000.0000.0000.0000.0000.000
94A96GLN00.010-0.01334.044-0.002-0.0020.0000.0000.0000.000
95A97LYS10.9220.98032.2200.0900.0900.0000.0000.0000.000
96A98HIS0-0.003-0.00729.881-0.002-0.0020.0000.0000.0000.000
97A99GLY0-0.0290.00232.729-0.007-0.0070.0000.0000.0000.000
98A100LYS10.9140.95133.2100.1240.1240.0000.0000.0000.000
99A101ILE00.0840.03936.682-0.003-0.0030.0000.0000.0000.000
100A102GLY0-0.074-0.04639.9540.0010.0010.0000.0000.0000.000
101A103PRO00.0060.02840.8960.0020.0020.0000.0000.0000.000
102A104PRO0-0.0100.01144.453-0.002-0.0020.0000.0000.0000.000
103A105LYS10.9200.96746.9940.0650.0650.0000.0000.0000.000
104A106LEU00.0150.00048.9120.0020.0020.0000.0000.0000.000
105A107ASN0-0.053-0.03552.316-0.002-0.0020.0000.0000.0000.000
106A108LEU00.0060.01655.4770.0010.0010.0000.0000.0000.000
107A109SER0-0.019-0.00658.5890.0010.0010.0000.0000.0000.000
108A110ARG10.9360.95662.1530.0340.0340.0000.0000.0000.000
109A111HIS0-0.0230.01865.6750.0010.0010.0000.0000.0000.000
110A112GLY00.001-0.00668.7940.0010.0010.0000.0000.0000.000
111A113ALA00.0580.01569.990-0.001-0.0010.0000.0000.0000.000
112A114GLU-1-0.903-0.95467.662-0.033-0.0330.0000.0000.0000.000
113A115ILE0-0.005-0.01161.780-0.001-0.0010.0000.0000.0000.000
114A116ILE00.0010.00761.0470.0000.0000.0000.0000.0000.000
115A117VAL0-0.049-0.03856.098-0.001-0.0010.0000.0000.0000.000
116A118ASP-1-0.815-0.88155.710-0.046-0.0460.0000.0000.0000.000
117A119VAL0-0.052-0.03750.650-0.002-0.0020.0000.0000.0000.000
118A120TYR00.0810.03648.9450.0000.0000.0000.0000.0000.000
119A121HIS10.8370.88543.0620.0730.0730.0000.0000.0000.000
120A122PRO0-0.0100.00444.769-0.001-0.0010.0000.0000.0000.000
121A123GLU-1-0.929-0.97639.907-0.087-0.0870.0000.0000.0000.000
122A124PHE0-0.038-0.01240.531-0.005-0.0050.0000.0000.0000.000
123A125PRO00.0020.00138.2790.0010.0010.0000.0000.0000.000
124A126SER00.0580.05841.0590.0030.0030.0000.0000.0000.000
125A127VAL00.0310.00942.699-0.003-0.0030.0000.0000.0000.000
126A128GLU-1-0.912-0.96844.212-0.061-0.0610.0000.0000.0000.000
127A129VAL0-0.062-0.02239.008-0.001-0.0010.0000.0000.0000.000
128A130ARG10.8880.95035.2510.1020.1020.0000.0000.0000.000
129A131PRO00.0780.03740.3460.0020.0020.0000.0000.0000.000
130A132TRP0-0.0010.00336.4320.0030.0030.0000.0000.0000.000
131A133MET00.0060.01039.829-0.001-0.0010.0000.0000.0000.000
132A134ARG10.9700.97542.1770.0550.0550.0000.0000.0000.000
133A135GLU-1-0.951-0.97043.594-0.055-0.0550.0000.0000.0000.000
134A136ILE0-0.025-0.00840.8380.0010.0010.0000.0000.0000.000
135A137TYR0-0.031-0.05242.7690.0000.0000.0000.0000.0000.000
136A138SER0-0.066-0.01846.7620.0020.0020.0000.0000.0000.000
137A139GLU-1-0.860-0.92446.674-0.046-0.0460.0000.0000.0000.000
138A140LEU0-0.103-0.04546.059-0.002-0.0020.0000.0000.0000.000
139A141SER0-0.0040.00748.4990.0030.0030.0000.0000.0000.000
140A142TYR00.0330.01147.697-0.005-0.0050.0000.0000.0000.000
141A143SER0-0.045-0.02250.3130.0030.0030.0000.0000.0000.000
142A144VAL00.0250.00052.338-0.002-0.0020.0000.0000.0000.000
143A145ILE0-0.064-0.03452.5560.0020.0020.0000.0000.0000.000
144A146PHE00.011-0.00156.038-0.001-0.0010.0000.0000.0000.000
145A147ARG10.9760.97856.4100.0440.0440.0000.0000.0000.000
146A148ASN0-0.0150.00060.1430.0010.0010.0000.0000.0000.000
147A149SER0-0.012-0.01061.1000.0000.0000.0000.0000.0000.000
148A150GLU-1-0.820-0.90162.567-0.034-0.0340.0000.0000.0000.000
149A151ASN0-0.004-0.01766.0700.0010.0010.0000.0000.0000.000
150A152GLU-1-0.890-0.93962.845-0.034-0.0340.0000.0000.0000.000
151A153SER0-0.150-0.05262.739-0.001-0.0010.0000.0000.0000.000
152A154ARG10.9740.97554.6320.0400.0400.0000.0000.0000.000
153A155LYS10.9150.95360.4190.0330.0330.0000.0000.0000.000
154A156ASN0-0.038-0.02556.072-0.003-0.0030.0000.0000.0000.000
155A157PHE00.0370.02557.5010.0020.0020.0000.0000.0000.000
156A158THR00.003-0.00554.424-0.002-0.0020.0000.0000.0000.000
157A159VAL0-0.0270.00054.5950.0020.0020.0000.0000.0000.000
158A160ALA00.050-0.00753.746-0.002-0.0020.0000.0000.0000.000
159A161ASP-1-0.888-0.92853.882-0.041-0.0410.0000.0000.0000.000
160A162CYS0-0.122-0.03052.8210.0030.0030.0000.0000.0000.000
161A163GLU-1-0.837-0.93053.255-0.045-0.0450.0000.0000.0000.000
162A164MET0-0.048-0.02051.100-0.001-0.0010.0000.0000.0000.000
163A165ASN0-0.053-0.02246.783-0.001-0.0010.0000.0000.0000.000
164A166GLU-1-0.990-1.00250.507-0.058-0.0580.0000.0000.0000.000
165A168ASN00.000-0.02854.8960.0010.0010.0000.0000.0000.000
166A169LEU00.0060.00058.2540.0010.0010.0000.0000.0000.000
167A170SER00.0190.02560.653-0.001-0.0010.0000.0000.0000.000
168A171ILE0-0.053-0.03460.4120.0010.0010.0000.0000.0000.000
169A172PRO0-0.0030.01264.8740.0000.0000.0000.0000.0000.000
170A173VAL00.003-0.00866.6080.0000.0000.0000.0000.0000.000
171A174PRO0-0.099-0.04467.3650.0010.0010.0000.0000.0000.000
172A175SER00.0270.00870.4330.0010.0010.0000.0000.0000.000
173A176GLU-1-0.902-0.97471.175-0.027-0.0270.0000.0000.0000.000
174A177GLY0-0.0170.01272.1610.0000.0000.0000.0000.0000.000
175A178SER0-0.071-0.04167.7390.0000.0000.0000.0000.0000.000
176A179THR00.008-0.00262.4470.0000.0000.0000.0000.0000.000
177A180TYR00.0110.00462.6310.0000.0000.0000.0000.0000.000
178A181CYS0-0.007-0.01155.6530.0000.0000.0000.0000.0000.000
179A182VAL00.005-0.00255.7400.0010.0010.0000.0000.0000.000
180A183SER00.0000.00651.243-0.002-0.0020.0000.0000.0000.000
181A184ALA00.0350.00350.8220.0020.0020.0000.0000.0000.000
182A185LYS10.9140.97546.3590.0550.0550.0000.0000.0000.000
183A186GLY00.0320.02146.2610.0020.0020.0000.0000.0000.000
184A187HIS0-0.011-0.00245.933-0.002-0.0020.0000.0000.0000.000
185A188PHE00.0220.00142.863-0.001-0.0010.0000.0000.0000.000
186A189PHE00.023-0.00442.712-0.002-0.0020.0000.0000.0000.000
187A190ASP-1-0.881-0.93247.176-0.044-0.0440.0000.0000.0000.000
188A191ASP-1-0.899-0.95646.737-0.052-0.0520.0000.0000.0000.000
189A192LEU0-0.093-0.03242.721-0.002-0.0020.0000.0000.0000.000
190A193ILE0-0.0100.00239.526-0.005-0.0050.0000.0000.0000.000
191A194VAL00.0050.01242.1970.0020.0020.0000.0000.0000.000
192A195GLY0-0.016-0.00941.967-0.004-0.0040.0000.0000.0000.000
193A196ALA0-0.072-0.04441.4900.0030.0030.0000.0000.0000.000
194A197SER00.008-0.01943.4530.0010.0010.0000.0000.0000.000
195A198SER0-0.013-0.00545.944-0.003-0.0030.0000.0000.0000.000
196A199GLU-1-0.965-0.97947.759-0.066-0.0660.0000.0000.0000.000
197A200GLU-1-0.943-0.98949.586-0.047-0.0470.0000.0000.0000.000
198A201SER0-0.0090.01753.372-0.001-0.0010.0000.0000.0000.000
199A203ILE0-0.006-0.00759.1950.0000.0000.0000.0000.0000.000
200A204TRP00.0090.01762.5470.0010.0010.0000.0000.0000.000
201A205VAL0-0.026-0.02066.1520.0000.0000.0000.0000.0000.000
202A206PRO0-0.070-0.02869.0040.0010.0010.0000.0000.0000.000
203A207ILE00.0470.04472.6920.0000.0000.0000.0000.0000.000