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: YYQJ2

Calculation Name: 5DAJ-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DAJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HY46

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 203
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2315426.28657
FMO2-HF: Nuclear repulsion 2232409.807874
FMO2-HF: Total energy -83016.478696
FMO2-MP2: Total energy -83255.626758


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:4:ACE )


Summations of interaction energy for fragment #1(A:4:ACE )
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.
-0.1520.811-0.005-0.404-0.555-0.001
Interaction energy analysis for fragmet #1(A:4:ACE )
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 : -0.002
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].
3A6GLU -1-0.818-0.9053.8530.0180.867-0.005-0.390-0.455-0.001
4A7ASP -1-0.911-0.9804.5960.5270.6410.000-0.014-0.1000.000
5A8SER 00.000-0.0105.057-0.064-0.0640.0000.0000.0000.000
6A9GLU -1-0.791-0.8896.661-0.639-0.6390.0000.0000.0000.000
7A10LYS 10.8840.9608.2620.1590.1590.0000.0000.0000.000
8A11THR 0-0.011-0.0079.4720.0670.0670.0000.0000.0000.000
9A12ARG 10.8980.9519.6470.2800.2800.0000.0000.0000.000
10A13THR 0-0.003-0.00412.3480.0160.0160.0000.0000.0000.000
11A14ALA 0-0.0040.00714.5220.0160.0160.0000.0000.0000.000
12A15ILE 0-0.005-0.00513.6390.0130.0130.0000.0000.0000.000
13A16LEU 0-0.007-0.00416.1880.0050.0050.0000.0000.0000.000
14A17LEU 00.0030.00018.6560.0030.0030.0000.0000.0000.000
15A18ALA 00.0320.02720.1460.0060.0060.0000.0000.0000.000
16A19ALA 0-0.004-0.01621.0980.0040.0040.0000.0000.0000.000
17A20GLU -1-0.836-0.89622.651-0.066-0.0660.0000.0000.0000.000
18A21GLU -1-0.950-0.98624.604-0.007-0.0070.0000.0000.0000.000
19A22LEU 00.016-0.00624.7130.0040.0040.0000.0000.0000.000
20A23PHE 0-0.023-0.02223.9570.0030.0030.0000.0000.0000.000
21A24LEU 0-0.023-0.00128.3790.0010.0010.0000.0000.0000.000
22A25GLU -1-0.902-0.94130.406-0.016-0.0160.0000.0000.0000.000
23A26LYS 10.8120.90529.406-0.004-0.0040.0000.0000.0000.000
24A27GLY 00.0300.03231.6460.0010.0010.0000.0000.0000.000
25A28VAL 0-0.015-0.00327.5400.0030.0030.0000.0000.0000.000
26A29SER 00.0010.00329.2030.0030.0030.0000.0000.0000.000
27A30HIS 0-0.0080.00531.2890.0050.0050.0000.0000.0000.000
28A31THR 0-0.027-0.02925.8440.0040.0040.0000.0000.0000.000
29A32SER 0-0.023-0.02126.5190.0010.0010.0000.0000.0000.000
30A33LEU 00.0800.00820.427-0.001-0.0010.0000.0000.0000.000
31A34GLU -1-0.984-0.99021.6800.0620.0620.0000.0000.0000.000
32A35GLN 0-0.021-0.01823.3840.0020.0020.0000.0000.0000.000
33A36ILE 00.0540.04419.7750.0010.0010.0000.0000.0000.000
34A37ALA 0-0.011-0.00419.0730.0000.0000.0000.0000.0000.000
35A38ARG 10.9350.96519.996-0.038-0.0380.0000.0000.0000.000
36A39ALA 0-0.0040.00122.6960.0030.0030.0000.0000.0000.000
37A40ALA 00.0110.01717.777-0.006-0.0060.0000.0000.0000.000
38A41GLY 0-0.0400.00618.2360.0040.0040.0000.0000.0000.000
39A42VAL 0-0.010-0.01314.4330.0250.0250.0000.0000.0000.000
40A43THR 00.0240.01215.313-0.015-0.0150.0000.0000.0000.000
41A44ARG 11.0150.97916.906-0.072-0.0720.0000.0000.0000.000
42A45GLY 00.0190.00716.626-0.011-0.0110.0000.0000.0000.000
43A46ALA 00.0510.02712.6600.0070.0070.0000.0000.0000.000
44A47VAL 00.0220.01313.271-0.018-0.0180.0000.0000.0000.000
45A48TYR 0-0.039-0.03115.647-0.020-0.0200.0000.0000.0000.000
46A49TRP 0-0.063-0.0158.269-0.041-0.0410.0000.0000.0000.000
47A50HIS 0-0.009-0.0038.724-0.008-0.0080.0000.0000.0000.000
48A51PHE 00.0360.01012.314-0.043-0.0430.0000.0000.0000.000
49A52GLN 00.0160.03414.7460.0010.0010.0000.0000.0000.000
50A53ASN 0-0.035-0.03617.8480.0080.0080.0000.0000.0000.000
51A54LYS 10.8940.94620.706-0.008-0.0080.0000.0000.0000.000
52A55ALA 00.0260.02823.101-0.008-0.0080.0000.0000.0000.000
53A56HIS 00.0040.00316.866-0.016-0.0160.0000.0000.0000.000
54A57LEU 0-0.020-0.00818.589-0.014-0.0140.0000.0000.0000.000
55A58PHE 00.005-0.00819.791-0.013-0.0130.0000.0000.0000.000
56A59ASN 00.002-0.00921.493-0.013-0.0130.0000.0000.0000.000
57A60GLU -1-0.868-0.93616.003-0.193-0.1930.0000.0000.0000.000
58A61MET 0-0.053-0.01219.174-0.012-0.0120.0000.0000.0000.000
59A62LEU 0-0.029-0.02021.084-0.006-0.0060.0000.0000.0000.000
60A63ASN 00.0110.00119.1260.0120.0120.0000.0000.0000.000
61A64GLN 0-0.045-0.01818.0900.0070.0070.0000.0000.0000.000
62A65VAL 0-0.016-0.00121.181-0.001-0.0010.0000.0000.0000.000
63A66ARG 10.8640.95423.8040.1020.1020.0000.0000.0000.000
64A67LEU 00.0190.01824.958-0.010-0.0100.0000.0000.0000.000
65A68PRO 0-0.0020.01023.6340.0050.0050.0000.0000.0000.000
66A69PRO 00.035-0.00425.4450.0070.0070.0000.0000.0000.000
67A70GLU -1-0.874-0.93725.368-0.129-0.1290.0000.0000.0000.000
68A71GLN 00.0520.01325.2580.0090.0090.0000.0000.0000.000
69A72LEU 0-0.0120.00129.3610.0080.0080.0000.0000.0000.000
70A73THR 0-0.008-0.02331.2440.0050.0050.0000.0000.0000.000
71A74GLU -1-0.964-0.94830.840-0.103-0.1030.0000.0000.0000.000
72A75ARG 10.7680.85833.4270.0770.0770.0000.0000.0000.000
73A76LEU 0-0.007-0.00835.1550.0060.0060.0000.0000.0000.000
74A77SER 0-0.065-0.06236.2730.0040.0040.0000.0000.0000.000
75A78GLY 0-0.033-0.01138.7650.0030.0030.0000.0000.0000.000
76A79CYS 0-0.063-0.01736.352-0.001-0.0010.0000.0000.0000.000
77A80ASP -1-0.766-0.84738.644-0.066-0.0660.0000.0000.0000.000
78A81GLY 00.0160.00240.6020.0020.0020.0000.0000.0000.000
79A82SER 0-0.082-0.03344.0030.0030.0030.0000.0000.0000.000
80A83ASP -1-0.789-0.90544.483-0.043-0.0430.0000.0000.0000.000
81A84PRO 00.0690.02942.529-0.002-0.0020.0000.0000.0000.000
82A85LEU 0-0.073-0.04742.966-0.001-0.0010.0000.0000.0000.000
83A86ARG 10.9290.97644.4780.0440.0440.0000.0000.0000.000
84A87SER 00.032-0.01139.4030.0010.0010.0000.0000.0000.000
85A88LEU 0-0.028-0.00639.543-0.002-0.0020.0000.0000.0000.000
86A89TYR 00.0040.00240.5350.0000.0000.0000.0000.0000.000
87A90ASP -1-0.850-0.92939.922-0.052-0.0520.0000.0000.0000.000
88A91LEU 0-0.024-0.01333.824-0.002-0.0020.0000.0000.0000.000
89A92CYS 0-0.089-0.05336.953-0.001-0.0010.0000.0000.0000.000
90A93LEU 00.0320.01439.1050.0010.0010.0000.0000.0000.000
91A94GLU -1-0.772-0.86935.424-0.070-0.0700.0000.0000.0000.000
92A95ALA 0-0.058-0.01834.608-0.002-0.0020.0000.0000.0000.000
93A96VAL 0-0.0070.01535.6410.0000.0000.0000.0000.0000.000
94A97GLN 00.0420.01638.093-0.002-0.0020.0000.0000.0000.000
95A98SER 0-0.118-0.09332.428-0.001-0.0010.0000.0000.0000.000
96A99LEU 0-0.039-0.01133.465-0.002-0.0020.0000.0000.0000.000
97A100LEU 00.0170.01535.1140.0010.0010.0000.0000.0000.000
98A101THR 00.0050.00233.936-0.001-0.0010.0000.0000.0000.000
99A102GLN 0-0.006-0.00229.123-0.007-0.0070.0000.0000.0000.000
100A103GLU -1-0.902-0.95229.559-0.046-0.0460.0000.0000.0000.000
101A104LYS 10.9170.96221.0650.1030.1030.0000.0000.0000.000
102A105LYS 10.9870.99227.0820.0750.0750.0000.0000.0000.000
103A106ARG 10.9140.97228.6970.0500.0500.0000.0000.0000.000
104A107ARG 10.8830.93426.6200.0470.0470.0000.0000.0000.000
105A108ILE 00.0390.00923.6120.0050.0050.0000.0000.0000.000
106A109LEU 0-0.003-0.00527.8730.0030.0030.0000.0000.0000.000
107A110THR 00.0130.00230.9380.0050.0050.0000.0000.0000.000
108A111ILE 0-0.030-0.02527.0210.0040.0040.0000.0000.0000.000
109A112LEU 0-0.058-0.02629.6430.0030.0030.0000.0000.0000.000
110A113MET 0-0.043-0.01131.0900.0030.0030.0000.0000.0000.000
111A114GLN 0-0.0040.01034.1980.0020.0020.0000.0000.0000.000
112A115ARG 10.8550.94331.8520.0250.0250.0000.0000.0000.000
113A116CYS 0-0.040-0.02230.7890.0010.0010.0000.0000.0000.000
114A117GLU -1-0.852-0.91232.740-0.009-0.0090.0000.0000.0000.000
115A118PHE 0-0.033-0.02630.0920.0010.0010.0000.0000.0000.000
116A119THR 00.0360.01832.9360.0010.0010.0000.0000.0000.000
117A120GLU -1-0.902-0.97232.085-0.011-0.0110.0000.0000.0000.000
118A121GLU -1-0.908-0.95128.821-0.001-0.0010.0000.0000.0000.000
119A122LEU 0-0.015-0.01027.627-0.002-0.0020.0000.0000.0000.000
120A123ARG 10.9720.99128.9910.0130.0130.0000.0000.0000.000
121A124GLU -1-0.858-0.94222.180-0.053-0.0530.0000.0000.0000.000
122A125ALA 0-0.032-0.02125.989-0.008-0.0080.0000.0000.0000.000
123A126GLN 00.0130.00526.967-0.003-0.0030.0000.0000.0000.000
124A127GLU -1-0.948-0.96828.861-0.037-0.0370.0000.0000.0000.000
125A128ARG 10.9780.97720.4630.0850.0850.0000.0000.0000.000
126A129ASN 0-0.0290.00127.719-0.010-0.0100.0000.0000.0000.000
127A130ASN 0-0.008-0.01829.768-0.001-0.0010.0000.0000.0000.000
128A131ALA 0-0.0060.00829.0550.0000.0000.0000.0000.0000.000
129A132PHE 00.0110.00528.319-0.001-0.0010.0000.0000.0000.000
130A133VAL 00.0040.00230.2920.0000.0000.0000.0000.0000.000
131A134GLN 0-0.055-0.02533.8860.0030.0030.0000.0000.0000.000
132A135MET 00.0370.01929.256-0.001-0.0010.0000.0000.0000.000
133A136PHE 00.0170.00833.7560.0000.0000.0000.0000.0000.000
134A137ILE 0-0.012-0.01735.0350.0030.0030.0000.0000.0000.000
135A138GLU -1-0.885-0.95036.325-0.051-0.0510.0000.0000.0000.000
136A139LEU 0-0.016-0.00233.6730.0010.0010.0000.0000.0000.000
137A140CYS 0-0.0210.00137.6970.0020.0020.0000.0000.0000.000
138A141GLU -1-0.917-0.95040.565-0.037-0.0370.0000.0000.0000.000
139A142GLN 0-0.006-0.02037.8070.0020.0020.0000.0000.0000.000
140A143LEU 00.0040.00841.0960.0010.0010.0000.0000.0000.000
141A144PHE 00.027-0.01842.8670.0020.0020.0000.0000.0000.000
142A145ALA 0-0.068-0.04545.2960.0020.0020.0000.0000.0000.000
143A146ARG 10.9230.98839.9730.0550.0550.0000.0000.0000.000
144A147ASP -1-0.902-0.94147.233-0.034-0.0340.0000.0000.0000.000
145A148GLU -1-0.914-0.97746.762-0.042-0.0420.0000.0000.0000.000
146A149CYS 0-0.072-0.02445.6910.0010.0010.0000.0000.0000.000
147A150ARG 10.9940.99949.3740.0340.0340.0000.0000.0000.000
148A151VAL 0-0.042-0.01751.1430.0020.0020.0000.0000.0000.000
149A152ARG 10.8810.94050.1540.0370.0370.0000.0000.0000.000
150A153LEU 0-0.0160.01449.3830.0000.0000.0000.0000.0000.000
151A154HIS 0-0.0040.00853.4660.0020.0020.0000.0000.0000.000
152A155PRO 0-0.021-0.03855.9770.0000.0000.0000.0000.0000.000
153A156GLY 0-0.0100.00457.0240.0000.0000.0000.0000.0000.000
154A157MET 0-0.0090.02350.5690.0000.0000.0000.0000.0000.000
155A158THR 0-0.028-0.02250.707-0.001-0.0010.0000.0000.0000.000
156A159PRO 00.0670.02346.4060.0000.0000.0000.0000.0000.000
157A160ARG 10.9941.01145.5070.0270.0270.0000.0000.0000.000
158A161ILE 0-0.033-0.02045.709-0.001-0.0010.0000.0000.0000.000
159A162ALA 00.0550.03347.1920.0000.0000.0000.0000.0000.000
160A163SER 00.0170.01141.7910.0000.0000.0000.0000.0000.000
161A164ARG 10.8270.91142.3710.0360.0360.0000.0000.0000.000
162A165ALA 0-0.0030.00443.9410.0000.0000.0000.0000.0000.000
163A166LEU 00.0370.01441.9410.0000.0000.0000.0000.0000.000
164A167HIS 00.0190.00436.0800.0010.0010.0000.0000.0000.000
165A168ALA 00.0110.00640.5160.0000.0000.0000.0000.0000.000
166A169LEU 00.0040.01542.8010.0010.0010.0000.0000.0000.000
167A170ILE 00.0150.00737.8220.0000.0000.0000.0000.0000.000
168A171LEU 0-0.031-0.01736.726-0.001-0.0010.0000.0000.0000.000
169A172GLY 00.017-0.00139.2460.0010.0010.0000.0000.0000.000
170A173LEU 00.0230.01841.3950.0010.0010.0000.0000.0000.000
171A174PHE 0-0.025-0.01633.601-0.001-0.0010.0000.0000.0000.000
172A175ASN 0-0.028-0.03038.2480.0030.0030.0000.0000.0000.000
173A176ASP -1-0.851-0.90439.664-0.024-0.0240.0000.0000.0000.000
174A177TRP 0-0.035-0.00436.6990.0000.0000.0000.0000.0000.000
175A178LEU 0-0.051-0.04134.8240.0000.0000.0000.0000.0000.000
176A179ARG 10.8230.90938.4450.0250.0250.0000.0000.0000.000
177A180ASP -1-0.912-0.96940.974-0.019-0.0190.0000.0000.0000.000
178A181PRO 00.0490.02340.3220.0000.0000.0000.0000.0000.000
179A182ARG 10.8200.90242.5670.0190.0190.0000.0000.0000.000
180A183LEU 0-0.089-0.02445.1870.0010.0010.0000.0000.0000.000
181A184PHE 0-0.010-0.01542.3250.0000.0000.0000.0000.0000.000
182A185ASP -1-0.749-0.85043.724-0.035-0.0350.0000.0000.0000.000
183A186PRO 0-0.093-0.05539.742-0.001-0.0010.0000.0000.0000.000
184A187ASP -1-0.958-0.96741.594-0.043-0.0430.0000.0000.0000.000
185A188THR 0-0.033-0.05742.4690.0000.0000.0000.0000.0000.000
186A189ASP -1-0.809-0.90645.756-0.028-0.0280.0000.0000.0000.000
187A190ALA 0-0.047-0.02042.5030.0000.0000.0000.0000.0000.000
188A191GLU -1-0.915-0.96844.474-0.037-0.0370.0000.0000.0000.000
189A192HIS 00.0110.00046.7720.0010.0010.0000.0000.0000.000
190A193LEU 0-0.043-0.01345.2740.0010.0010.0000.0000.0000.000
191A194LEU 0-0.030-0.01442.2410.0000.0000.0000.0000.0000.000
192A195GLU -1-0.832-0.91246.744-0.032-0.0320.0000.0000.0000.000
193A196PRO 0-0.027-0.00949.9670.0000.0000.0000.0000.0000.000
194A197MET 0-0.0120.00446.5650.0010.0010.0000.0000.0000.000
195A198PHE 00.024-0.00443.4220.0000.0000.0000.0000.0000.000
196A199ARG 10.8910.94949.4490.0280.0280.0000.0000.0000.000
197A200GLY 0-0.027-0.01352.6870.0010.0010.0000.0000.0000.000
198A201LEU 0-0.057-0.02347.5560.0010.0010.0000.0000.0000.000
199A202VAL 0-0.027-0.02649.5830.0000.0000.0000.0000.0000.000
200A203ARG 10.9160.95452.7660.0260.0260.0000.0000.0000.000
201A204ASP -1-0.931-0.95655.277-0.028-0.0280.0000.0000.0000.000
202A205TRP 0-0.094-0.04546.8290.0000.0000.0000.0000.0000.000
203A206NME 00.0100.02053.6310.0000.0000.0000.0000.0000.000