Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: J3VJ9

Calculation Name: 4BSZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BSZ

Chain ID: A

ChEMBL ID:

UniProt ID: P05750

Base Structure: X-ray

Registration Date: 2023-03-14

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1569561.121638
FMO2-HF: Nuclear repulsion 1497290.983544
FMO2-HF: Total energy -72270.138094
FMO2-MP2: Total energy -72480.855382


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:12:VAL)


Summations of interaction energy for fragment #1(A:12:VAL)
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.
-4.903-0.1560.717-1.986-3.476-0.007
Interaction energy analysis for fragmet #1(A:12:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.031
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].
3A14ASP-1-0.813-0.9173.016-4.639-2.3090.149-1.092-1.387-0.005
4A15GLY0-0.006-0.0235.7420.5320.5320.0000.0000.0000.000
5A16VAL00.0260.0187.9920.2300.2300.0000.0000.0000.000
6A17PHE00.0390.0276.7070.2670.2670.0000.0000.0000.000
7A18TYR0-0.010-0.0103.4370.0640.3710.007-0.048-0.2660.000
8A19ALA0-0.018-0.0028.6740.1570.1570.0000.0000.0000.000
9A20GLU-1-0.881-0.95312.019-0.251-0.2510.0000.0000.0000.000
10A21LEU0-0.042-0.0228.8720.0970.0970.0000.0000.0000.000
11A22ASN0-0.016-0.00712.5900.0800.0800.0000.0000.0000.000
12A23GLU-1-0.962-0.95214.272-0.212-0.2120.0000.0000.0000.000
13A24PHE0-0.047-0.02616.0980.0310.0310.0000.0000.0000.000
14A25PHE00.0640.00913.1450.0300.0300.0000.0000.0000.000
15A26THR0-0.040-0.03117.7760.0150.0150.0000.0000.0000.000
16A27ARG10.9050.95219.8720.0730.0730.0000.0000.0000.000
17A28GLU-1-0.982-0.98520.5780.0050.0050.0000.0000.0000.000
18A29LEU0-0.082-0.04718.7080.0200.0200.0000.0000.0000.000
19A30ALA00.0170.02422.406-0.004-0.0040.0000.0000.0000.000
20A31GLU-1-0.888-0.94524.784-0.018-0.0180.0000.0000.0000.000
21A32GLU-1-0.883-0.94623.2020.0170.0170.0000.0000.0000.000
22A33GLY0-0.031-0.01223.4450.0060.0060.0000.0000.0000.000
23A34TYR00.0430.01214.3710.0160.0160.0000.0000.0000.000
24A35SER0-0.049-0.02417.279-0.008-0.0080.0000.0000.0000.000
25A36GLY00.004-0.01414.040-0.034-0.0340.0000.0000.0000.000
26A37VAL0-0.044-0.0159.5970.0410.0410.0000.0000.0000.000
27A38GLU-1-0.953-0.9627.1630.0710.0710.0000.0000.0000.000
28A39VAL0-0.009-0.0144.762-0.0770.018-0.001-0.011-0.0820.000
29A40ARG10.9170.9773.298-1.339-0.6330.034-0.235-0.505-0.001
30A41VAL00.0220.0092.523-1.574-0.4270.529-0.595-1.081-0.001
31A42THR0-0.031-0.0114.3250.3180.480-0.001-0.005-0.1550.000
32A43PRO00.031-0.0147.458-0.029-0.0290.0000.0000.0000.000
33A44THR0-0.026-0.00810.331-0.227-0.2270.0000.0000.0000.000
34A45LYS10.9530.9869.879-0.982-0.9820.0000.0000.0000.000
35A46THR0-0.0060.0096.6270.6720.6720.0000.0000.0000.000
36A47GLU-1-0.893-0.9527.5150.7340.7340.0000.0000.0000.000
37A48VAL00.0360.0087.7760.0510.0510.0000.0000.0000.000
38A49ILE0-0.0180.0019.656-0.032-0.0320.0000.0000.0000.000
39A50ILE00.0350.01711.650-0.071-0.0710.0000.0000.0000.000
40A51ARG10.9250.96712.4880.0490.0490.0000.0000.0000.000
41A52ALA00.0560.03216.159-0.026-0.0260.0000.0000.0000.000
42A53THR0-0.026-0.01619.8620.0120.0120.0000.0000.0000.000
43A54ARG10.7970.87923.149-0.008-0.0080.0000.0000.0000.000
44A55THR00.0190.00520.732-0.004-0.0040.0000.0000.0000.000
45A56GLN00.0220.00023.0180.0080.0080.0000.0000.0000.000
46A57ASP-1-0.810-0.90125.8780.0400.0400.0000.0000.0000.000
47A58VAL0-0.0010.00419.5820.0020.0020.0000.0000.0000.000
48A59LEU0-0.022-0.02220.4040.0100.0100.0000.0000.0000.000
49A60GLY00.0090.01023.4250.0040.0040.0000.0000.0000.000
50A61GLU-1-0.944-0.99126.9880.0740.0740.0000.0000.0000.000
51A62ASN0-0.032-0.01228.0030.0050.0050.0000.0000.0000.000
52A63GLY00.0420.02524.1610.0080.0080.0000.0000.0000.000
53A64ARG10.9390.98624.627-0.056-0.0560.0000.0000.0000.000
54A65ARG10.8900.96123.250-0.040-0.0400.0000.0000.0000.000
55A66ILE00.0640.03318.705-0.003-0.0030.0000.0000.0000.000
56A67ASN00.0180.00120.5920.0170.0170.0000.0000.0000.000
57A68GLU-1-0.908-0.94622.2370.0640.0640.0000.0000.0000.000
58A69LEU00.0120.00518.984-0.004-0.0040.0000.0000.0000.000
59A70THR00.004-0.01716.6210.0040.0040.0000.0000.0000.000
60A71LEU0-0.024-0.00818.0240.0140.0140.0000.0000.0000.000
61A72LEU0-0.017-0.00320.672-0.008-0.0080.0000.0000.0000.000
62A73VAL00.0180.00514.415-0.026-0.0260.0000.0000.0000.000
63A74GLN0-0.0050.00116.6730.0180.0180.0000.0000.0000.000
64A75LYS10.9350.96917.666-0.043-0.0430.0000.0000.0000.000
65A76ARG10.9070.96717.1420.1290.1290.0000.0000.0000.000
66A77PHE0-0.022-0.02513.668-0.027-0.0270.0000.0000.0000.000
67A78LYS10.8940.95814.888-0.005-0.0050.0000.0000.0000.000
68A79TYR00.0620.0468.8590.1050.1050.0000.0000.0000.000
69A80ALA00.0010.00415.266-0.035-0.0350.0000.0000.0000.000
70A81PRO00.0190.04016.4730.0540.0540.0000.0000.0000.000
71A82GLY00.0200.02017.2980.0030.0030.0000.0000.0000.000
72A83THR0-0.078-0.09412.5760.0380.0380.0000.0000.0000.000
73A84ILE0-0.019-0.00710.4550.1700.1700.0000.0000.0000.000
74A85VAL0-0.028-0.00612.328-0.082-0.0820.0000.0000.0000.000
75A86LEU0-0.0110.00012.8960.0390.0390.0000.0000.0000.000
76A87TYR0-0.016-0.00112.1620.0020.0020.0000.0000.0000.000
77A88ALA00.005-0.01215.204-0.035-0.0350.0000.0000.0000.000
78A89GLU-1-0.916-0.95413.8130.2270.2270.0000.0000.0000.000
79A90ARG10.9260.96717.418-0.071-0.0710.0000.0000.0000.000
80A91VAL0-0.009-0.00216.5400.0020.0020.0000.0000.0000.000
81A92GLN0-0.065-0.04119.863-0.010-0.0100.0000.0000.0000.000
82A93ASP-1-0.778-0.90020.872-0.067-0.0670.0000.0000.0000.000
83A94ARG10.9670.98118.0430.1380.1380.0000.0000.0000.000
84A95GLY00.003-0.00621.550-0.003-0.0030.0000.0000.0000.000
85A96LEU00.0110.00324.4740.0040.0040.0000.0000.0000.000
86A97SER0-0.0220.01023.7430.0060.0060.0000.0000.0000.000
87A98ALA00.0410.00325.784-0.008-0.0080.0000.0000.0000.000
88A99VAL00.0190.00624.060-0.005-0.0050.0000.0000.0000.000
89A100ALA00.0280.01521.434-0.007-0.0070.0000.0000.0000.000
90A101GLN00.010-0.00922.761-0.019-0.0190.0000.0000.0000.000
91A102ALA0-0.0010.01125.533-0.006-0.0060.0000.0000.0000.000
92A103GLU-1-0.914-0.95021.384-0.092-0.0920.0000.0000.0000.000
93A104SER0-0.034-0.01722.501-0.015-0.0150.0000.0000.0000.000
94A105MET0-0.026-0.02123.510-0.011-0.0110.0000.0000.0000.000
95A106LYS10.9770.99725.4600.0710.0710.0000.0000.0000.000
96A107PHE00.0140.00919.5330.0000.0000.0000.0000.0000.000
97A108LYS10.9050.94323.4230.1390.1390.0000.0000.0000.000
98A109LEU0-0.016-0.01025.961-0.001-0.0010.0000.0000.0000.000
99A110LEU0-0.040-0.01525.6340.0030.0030.0000.0000.0000.000
100A111ASN0-0.054-0.01622.882-0.012-0.0120.0000.0000.0000.000
101A112GLY00.0170.02426.431-0.005-0.0050.0000.0000.0000.000
102A113LEU0-0.0360.00126.9650.0020.0020.0000.0000.0000.000
103A114ALA00.003-0.00930.0170.0070.0070.0000.0000.0000.000
104A115ILE00.0930.02832.443-0.003-0.0030.0000.0000.0000.000
105A116ARG10.9590.98633.4120.0660.0660.0000.0000.0000.000
106A117ARG10.9590.98131.1560.1070.1070.0000.0000.0000.000
107A118ALA00.0120.01228.991-0.005-0.0050.0000.0000.0000.000
108A119ALA00.0380.00729.430-0.002-0.0020.0000.0000.0000.000
109A120TYR0-0.008-0.00631.5310.0010.0010.0000.0000.0000.000
110A121GLY00.0000.01127.761-0.001-0.0010.0000.0000.0000.000
111A122VAL00.007-0.00426.247-0.003-0.0030.0000.0000.0000.000
112A123VAL00.0400.00828.0170.0020.0020.0000.0000.0000.000
113A124ARG10.9440.97227.3730.1210.1210.0000.0000.0000.000
114A125TYR00.0080.01220.6310.0020.0020.0000.0000.0000.000
115A126VAL00.0050.02426.2660.0020.0020.0000.0000.0000.000
116A127MET0-0.041-0.01828.1530.0060.0060.0000.0000.0000.000
117A128GLU-1-0.963-0.96025.835-0.114-0.1140.0000.0000.0000.000
118A129SER0-0.052-0.06324.959-0.003-0.0030.0000.0000.0000.000
119A130GLY00.0120.01826.4640.0070.0070.0000.0000.0000.000
120A131ALA0-0.034-0.00829.8480.0070.0070.0000.0000.0000.000
121A132LYS10.9460.96831.6790.0280.0280.0000.0000.0000.000
122A133GLY00.025-0.00334.6130.0000.0000.0000.0000.0000.000
123A134CYS0-0.062-0.01231.477-0.002-0.0020.0000.0000.0000.000
124A135GLU-1-0.876-0.94434.223-0.039-0.0390.0000.0000.0000.000
125A136VAL0-0.032-0.01431.616-0.001-0.0010.0000.0000.0000.000
126A137VAL00.0290.00334.3620.0010.0010.0000.0000.0000.000
127A138VAL0-0.0170.00633.763-0.001-0.0010.0000.0000.0000.000
128A139SER00.016-0.00436.2930.0020.0020.0000.0000.0000.000
129A140GLY00.0180.00838.086-0.001-0.0010.0000.0000.0000.000
130A141LYS10.9050.95040.5440.0410.0410.0000.0000.0000.000
131A142LEU00.0220.01838.314-0.002-0.0020.0000.0000.0000.000
132A143ARG10.8710.94241.0710.0510.0510.0000.0000.0000.000
133A144ALA00.0200.01744.2260.0020.0020.0000.0000.0000.000
134A145ALA00.0280.00547.1580.0010.0010.0000.0000.0000.000
135A146ARG10.9850.98949.9810.0320.0320.0000.0000.0000.000
136A147ALA00.0370.03752.5040.0010.0010.0000.0000.0000.000
137A148LYS11.0050.98249.0020.0300.0300.0000.0000.0000.000
138A149ALA0-0.020-0.01947.848-0.001-0.0010.0000.0000.0000.000
139A150MET00.0000.01948.5340.0010.0010.0000.0000.0000.000
140A151LYS10.8900.94442.7800.0340.0340.0000.0000.0000.000
141A152PHE0-0.007-0.00843.0050.0010.0010.0000.0000.0000.000
142A153ALA00.049-0.00140.8570.0000.0000.0000.0000.0000.000
143A154ASP-1-0.867-0.90538.764-0.054-0.0540.0000.0000.0000.000
144A155GLY00.0290.00938.465-0.001-0.0010.0000.0000.0000.000
145A156PHE0-0.048-0.04135.848-0.002-0.0020.0000.0000.0000.000
146A157LEU00.0550.02036.844-0.001-0.0010.0000.0000.0000.000
147A158ILE0-0.0150.00335.427-0.001-0.0010.0000.0000.0000.000
148A159HIS0-0.019-0.01037.6950.0020.0020.0000.0000.0000.000
149A160SER00.0090.00138.7220.0010.0010.0000.0000.0000.000
150A161GLY00.0300.02941.2050.0000.0000.0000.0000.0000.000
151A162GLN0-0.055-0.03144.6850.0000.0000.0000.0000.0000.000
152A163PRO00.0900.02948.0890.0000.0000.0000.0000.0000.000
153A164VAL00.0230.00751.1160.0000.0000.0000.0000.0000.000
154A165ASN0-0.025-0.03147.2620.0000.0000.0000.0000.0000.000
155A166ASP-1-0.876-0.91150.618-0.025-0.0250.0000.0000.0000.000
156A167PHE0-0.074-0.05552.9330.0010.0010.0000.0000.0000.000
157A168ILE0-0.069-0.02551.0180.0020.0020.0000.0000.0000.000
158A169ASP-1-0.797-0.87454.509-0.017-0.0170.0000.0000.0000.000
159A170THR0-0.082-0.06652.3860.0010.0010.0000.0000.0000.000
160A171ALA00.0160.01555.588-0.001-0.0010.0000.0000.0000.000
161A172THR00.010-0.01453.4330.0000.0000.0000.0000.0000.000
162A173ARG10.8930.94756.7960.0080.0080.0000.0000.0000.000
163A174HIS00.0420.03055.6260.0000.0000.0000.0000.0000.000
164A175VAL00.0170.00659.0650.0000.0000.0000.0000.0000.000
165A176LEU00.0220.01460.8830.0000.0000.0000.0000.0000.000
166A177MET00.0020.00562.0570.0000.0000.0000.0000.0000.000
167A178ARG10.9790.97163.332-0.002-0.0020.0000.0000.0000.000
168A179GLN0-0.0010.00158.8290.0000.0000.0000.0000.0000.000
169A180GLY00.0570.03758.6750.0010.0010.0000.0000.0000.000
170A181VAL0-0.034-0.01857.1680.0000.0000.0000.0000.0000.000
171A182LEU00.0030.01256.6490.0000.0000.0000.0000.0000.000
172A183GLY00.0150.01454.754-0.001-0.0010.0000.0000.0000.000
173A184ILE0-0.002-0.00255.8260.0010.0010.0000.0000.0000.000
174A185LYS10.9540.96349.3030.0100.0100.0000.0000.0000.000
175A186VAL00.0100.01055.2820.0010.0010.0000.0000.0000.000
176A187LYS10.9410.96148.4350.0120.0120.0000.0000.0000.000
177A188ILE00.0370.02555.4880.0010.0010.0000.0000.0000.000
178A189MET00.0120.01052.135-0.001-0.0010.0000.0000.0000.000
179A190ARG10.8640.94956.7440.0170.0170.0000.0000.0000.000
180A191ASP-1-0.819-0.92958.605-0.013-0.0130.0000.0000.0000.000
181A192PRO00.0470.02357.2460.0000.0000.0000.0000.0000.000
182A193ALA0-0.055-0.03160.3620.0000.0000.0000.0000.0000.000
183A194LYS10.9020.95062.9160.0110.0110.0000.0000.0000.000
184A195SER0-0.046-0.01562.6090.0000.0000.0000.0000.0000.000
185A196ARG10.9280.97461.3850.0140.0140.0000.0000.0000.000
186A197THR00.0380.01664.6450.0010.0010.0000.0000.0000.000
187A198GLY00.0030.02167.3840.0000.0000.0000.0000.0000.000