FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZY5KN

Calculation Name: 4UF3-A-Xray372

Preferred Name: Bcl-2-like protein 11

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4UF3

Chain ID: A

ChEMBL ID: CHEMBL5777

UniProt ID: O43521

Base Structure: X-ray

Registration Date: 2023-06-19

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 136
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1186231.882823
FMO2-HF: Nuclear repulsion 1130986.463703
FMO2-HF: Total energy -55245.41912
FMO2-MP2: Total energy -55407.044572


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:3:ALA)


Summations of interaction energy for fragment #1(A:3: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.
-3.189-0.430.099-1.247-1.6110.002
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.001
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].
3A5ILE00.0470.0242.921-0.9971.6840.100-1.239-1.5420.002
4A6GLU-1-0.916-0.9515.221-2.253-2.175-0.001-0.008-0.0690.000
5A7PHE0-0.009-0.0178.3580.4650.4650.0000.0000.0000.000
6A8ASP-1-0.874-0.9426.750-1.366-1.3660.0000.0000.0000.000
7A9GLU-1-0.856-0.9309.812-0.441-0.4410.0000.0000.0000.000
8A10ILE0-0.0100.00113.0090.1280.1280.0000.0000.0000.000
9A11VAL00.0300.01211.8150.1060.1060.0000.0000.0000.000
10A12LYS10.8730.92111.9220.6620.6620.0000.0000.0000.000
11A13LYS10.9330.97015.7580.4140.4140.0000.0000.0000.000
12A14LEU00.013-0.00417.6610.0480.0480.0000.0000.0000.000
13A15LEU00.0080.01516.4820.0430.0430.0000.0000.0000.000
14A16ASN00.0040.00119.6830.0520.0520.0000.0000.0000.000
15A17ILE0-0.0110.00822.0050.0250.0250.0000.0000.0000.000
16A18TYR00.0230.01422.4770.0220.0220.0000.0000.0000.000
17A19ILE00.0480.01123.0750.0170.0170.0000.0000.0000.000
18A20ASN0-0.050-0.04325.4040.0240.0240.0000.0000.0000.000
19A21ASP-1-0.933-0.95027.546-0.121-0.1210.0000.0000.0000.000
20A22ILE0-0.0040.00227.0980.0130.0130.0000.0000.0000.000
21A23CYS0-0.059-0.03028.8310.0110.0110.0000.0000.0000.000
22A24THR00.0540.03631.6190.0080.0080.0000.0000.0000.000
23A25THR0-0.059-0.03732.5160.0080.0080.0000.0000.0000.000
24A26GLY0-0.053-0.03233.8540.0060.0060.0000.0000.0000.000
25A27GLU-1-0.913-0.96634.917-0.077-0.0770.0000.0000.0000.000
26A28LYS10.9160.94837.1690.0930.0930.0000.0000.0000.000
27A29ARG10.8540.93434.3620.0690.0690.0000.0000.0000.000
28A30LEU0-0.037-0.01439.5000.0040.0040.0000.0000.0000.000
29A31LEU00.0240.04742.0040.0020.0020.0000.0000.0000.000
30A32ASN00.0160.00944.446-0.001-0.0010.0000.0000.0000.000
31A33ASN00.019-0.02947.533-0.004-0.0040.0000.0000.0000.000
32A34TYR00.0310.02849.226-0.002-0.0020.0000.0000.0000.000
33A35GLU-1-0.784-0.90446.194-0.050-0.0500.0000.0000.0000.000
34A36LYS10.8920.95542.8650.0520.0520.0000.0000.0000.000
35A37SER0-0.065-0.03146.230-0.002-0.0020.0000.0000.0000.000
36A38ILE00.0660.03148.421-0.001-0.0010.0000.0000.0000.000
37A39LEU00.005-0.00240.798-0.002-0.0020.0000.0000.0000.000
38A40ASP-1-0.875-0.92844.673-0.070-0.0700.0000.0000.0000.000
39A41ARG10.9500.97845.9470.0490.0490.0000.0000.0000.000
40A42ILE00.0190.03643.973-0.001-0.0010.0000.0000.0000.000
41A43TYR00.0170.01437.923-0.002-0.0020.0000.0000.0000.000
42A44LYS10.8560.91043.8050.0660.0660.0000.0000.0000.000
43A45SER0-0.020-0.02446.5650.0010.0010.0000.0000.0000.000
44A46CYS0-0.016-0.01343.8630.0000.0000.0000.0000.0000.000
45A47GLU-1-0.871-0.92840.780-0.101-0.1010.0000.0000.0000.000
46A48TYR0-0.053-0.01544.569-0.001-0.0010.0000.0000.0000.000
47A49ILE0-0.009-0.01247.4150.0000.0000.0000.0000.0000.000
48A50LYS10.8360.90939.3970.1040.1040.0000.0000.0000.000
49A51LYS10.9430.99044.9700.0790.0790.0000.0000.0000.000
50A52ASN0-0.085-0.05046.2160.0010.0010.0000.0000.0000.000
51A53TYR0-0.0350.00448.2280.0030.0030.0000.0000.0000.000
52A54GLU-1-0.911-0.93843.043-0.100-0.1000.0000.0000.0000.000
53A55LEU0-0.022-0.03344.877-0.004-0.0040.0000.0000.0000.000
54A56ASP-1-0.866-0.94446.787-0.074-0.0740.0000.0000.0000.000
55A57PHE00.0430.00343.4900.0000.0000.0000.0000.0000.000
56A58ASN0-0.019-0.00241.519-0.007-0.0070.0000.0000.0000.000
57A59SER0-0.020-0.00942.939-0.003-0.0030.0000.0000.0000.000
58A60MET0-0.034-0.00745.2810.0020.0020.0000.0000.0000.000
59A61TYR00.004-0.00934.948-0.003-0.0030.0000.0000.0000.000
60A62ASN00.006-0.01240.140-0.009-0.0090.0000.0000.0000.000
61A63GLN0-0.063-0.01841.2800.0000.0000.0000.0000.0000.000
62A64ILE0-0.0100.00238.9410.0010.0010.0000.0000.0000.000
63A65ASN0-0.038-0.01835.066-0.007-0.0070.0000.0000.0000.000
64A66ILE0-0.0100.01536.235-0.007-0.0070.0000.0000.0000.000
65A67ASN0-0.030-0.05033.3290.0060.0060.0000.0000.0000.000
66A68ASP-1-0.953-0.96836.226-0.086-0.0860.0000.0000.0000.000
67A69ILE00.0120.02638.6200.0040.0040.0000.0000.0000.000
68A70THR0-0.024-0.00837.709-0.006-0.0060.0000.0000.0000.000
69A71THR00.035-0.00535.2530.0010.0010.0000.0000.0000.000
70A72SER0-0.005-0.01638.2410.0000.0000.0000.0000.0000.000
71A73ASP-1-0.843-0.88641.684-0.071-0.0710.0000.0000.0000.000
72A74ILE00.0130.00337.5490.0010.0010.0000.0000.0000.000
73A75LYS10.8850.95040.1110.0750.0750.0000.0000.0000.000
74A76SER0-0.019-0.02943.2060.0030.0030.0000.0000.0000.000
75A77LYS10.9861.00445.2900.0700.0700.0000.0000.0000.000
76A78ILE0-0.024-0.01341.9570.0020.0020.0000.0000.0000.000
77A79ILE0-0.037-0.02346.2320.0020.0020.0000.0000.0000.000
78A80GLU-1-0.894-0.95548.299-0.056-0.0560.0000.0000.0000.000
79A81ALA0-0.027-0.01050.5180.0030.0030.0000.0000.0000.000
80A82LEU0-0.001-0.01748.3390.0020.0020.0000.0000.0000.000
81A83LEU0-0.091-0.02451.9370.0030.0030.0000.0000.0000.000
82A84ILE0-0.015-0.00354.2300.0020.0020.0000.0000.0000.000
83A85ASP-1-0.782-0.85955.592-0.045-0.0450.0000.0000.0000.000
84A86SER0-0.001-0.00254.863-0.001-0.0010.0000.0000.0000.000
85A87ARG10.8300.87655.9660.0460.0460.0000.0000.0000.000
86A88PRO00.0600.03054.017-0.002-0.0020.0000.0000.0000.000
87A89SER00.0250.00952.816-0.002-0.0020.0000.0000.0000.000
88A90VAL00.0360.02952.319-0.003-0.0030.0000.0000.0000.000
89A91LYS10.8370.94750.0560.0460.0460.0000.0000.0000.000
90A92LEU00.0070.01247.863-0.003-0.0030.0000.0000.0000.000
91A93ALA00.0200.01947.733-0.004-0.0040.0000.0000.0000.000
92A94THR00.0190.01045.928-0.004-0.0040.0000.0000.0000.000
93A95LEU0-0.010-0.01042.705-0.004-0.0040.0000.0000.0000.000
94A96SER00.011-0.02342.921-0.005-0.0050.0000.0000.0000.000
95A97PHE00.0020.01642.693-0.005-0.0050.0000.0000.0000.000
96A98ILE00.010-0.00139.442-0.006-0.0060.0000.0000.0000.000
97A99SER0-0.067-0.03138.771-0.007-0.0070.0000.0000.0000.000
98A100LEU00.0410.00937.995-0.006-0.0060.0000.0000.0000.000
99A101ILE0-0.021-0.01236.035-0.008-0.0080.0000.0000.0000.000
100A102ALA0-0.042-0.03134.319-0.009-0.0090.0000.0000.0000.000
101A103GLU-1-0.907-0.95833.047-0.130-0.1300.0000.0000.0000.000
102A104LYS10.9110.97433.0690.1250.1250.0000.0000.0000.000
103A105TRP0-0.055-0.02730.808-0.011-0.0110.0000.0000.0000.000
104A106GLY00.0650.02828.556-0.001-0.0010.0000.0000.0000.000
105A107GLU-1-0.964-0.97923.926-0.301-0.3010.0000.0000.0000.000
106A108LYS10.8590.94924.7250.1540.1540.0000.0000.0000.000
107A109ASN00.0190.00025.4090.0020.0020.0000.0000.0000.000
108A110ARG11.0931.04226.8370.1570.1570.0000.0000.0000.000
109A111ALA0-0.002-0.01128.5040.0110.0110.0000.0000.0000.000
110A112LYS10.9450.97028.1580.1760.1760.0000.0000.0000.000
111A113ILE00.0100.02831.3140.0070.0070.0000.0000.0000.000
112A114MET0-0.032-0.02332.6530.0060.0060.0000.0000.0000.000
113A115GLU-1-0.914-0.95633.159-0.104-0.1040.0000.0000.0000.000
114A116ILE0-0.022-0.00736.1040.0050.0050.0000.0000.0000.000
115A117LEU00.0050.00138.1170.0050.0050.0000.0000.0000.000
116A118SER00.001-0.02137.8660.0060.0060.0000.0000.0000.000
117A119ASN0-0.039-0.00640.0360.0030.0030.0000.0000.0000.000
118A120GLU-1-0.808-0.92342.541-0.060-0.0600.0000.0000.0000.000
119A121ILE0-0.024-0.00342.9140.0030.0030.0000.0000.0000.000
120A122VAL00.0230.00342.5900.0010.0010.0000.0000.0000.000
121A123GLU-1-0.910-0.94744.904-0.048-0.0480.0000.0000.0000.000
122A124LYS10.9180.97647.6840.0480.0480.0000.0000.0000.000
123A125ILE0-0.034-0.03445.6280.0020.0020.0000.0000.0000.000
124A126SER00.0140.00247.1210.0020.0020.0000.0000.0000.000
125A127ASN0-0.053-0.02149.8510.0020.0020.0000.0000.0000.000
126A128ASN0-0.053-0.03653.1390.0000.0000.0000.0000.0000.000
127A129GLY00.0960.04752.682-0.001-0.0010.0000.0000.0000.000
128A130LYS10.9570.97753.3630.0320.0320.0000.0000.0000.000
129A131ASP-1-0.809-0.90456.228-0.038-0.0380.0000.0000.0000.000
130A132PHE0-0.080-0.03848.619-0.001-0.0010.0000.0000.0000.000
131A133ILE0-0.006-0.01651.209-0.002-0.0020.0000.0000.0000.000
132A134ASP-1-0.898-0.94853.657-0.040-0.0400.0000.0000.0000.000
133A135PHE0-0.082-0.04053.7420.0000.0000.0000.0000.0000.000
134A136ILE0-0.0080.00050.290-0.001-0.0010.0000.0000.0000.000
135A137ASP-1-0.942-0.97753.597-0.047-0.0470.0000.0000.0000.000
136A138ARG10.8800.95155.0460.0440.0440.0000.0000.0000.000