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: 63J6Z

Calculation Name: 3GKU-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKU

Chain ID: A

ChEMBL ID:

UniProt ID: D0VX24

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2086599.847851
FMO2-HF: Nuclear repulsion 2003046.998291
FMO2-HF: Total energy -83552.84956
FMO2-MP2: Total energy -83796.411489


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:0:ACE )


Summations of interaction energy for fragment #1(A:0: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.
0.8651.826-0.006-0.418-0.5370
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.009
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].
3A2ASP -1-0.853-0.9223.8130.3031.264-0.006-0.418-0.5370.000
4A3MET 0-0.066-0.0567.177-0.150-0.1500.0000.0000.0000.000
5A4VAL 00.0610.0599.8320.1380.1380.0000.0000.0000.000
6A5THR 0-0.042-0.02313.2260.0030.0030.0000.0000.0000.000
7A6VAL 00.0150.01715.6690.0230.0230.0000.0000.0000.000
8A7THR 0-0.014-0.01119.1570.0100.0100.0000.0000.0000.000
9A8ALA 0-0.031-0.03822.4880.0000.0000.0000.0000.0000.000
10A9LYS 10.9871.00925.9710.0530.0530.0000.0000.0000.000
11A10THR 00.0510.03728.1970.0010.0010.0000.0000.0000.000
12A11VAL 00.0460.00622.934-0.005-0.0050.0000.0000.0000.000
13A12GLU -1-0.922-0.96524.458-0.098-0.0980.0000.0000.0000.000
14A13GLU -1-0.854-0.94326.162-0.082-0.0820.0000.0000.0000.000
15A14ALA 0-0.027-0.00221.964-0.007-0.0070.0000.0000.0000.000
16A15VAL 00.0460.01921.210-0.015-0.0150.0000.0000.0000.000
17A16THR 00.0100.00921.829-0.012-0.0120.0000.0000.0000.000
18A17LYS 10.8940.94122.7090.0920.0920.0000.0000.0000.000
19A18ALA 00.0210.01217.979-0.004-0.0040.0000.0000.0000.000
20A19LEU 0-0.007-0.01018.910-0.021-0.0210.0000.0000.0000.000
21A20ILE 0-0.034-0.00620.712-0.004-0.0040.0000.0000.0000.000
22A21GLU -1-0.951-0.98717.268-0.172-0.1720.0000.0000.0000.000
23A22LEU 0-0.066-0.03313.361-0.015-0.0150.0000.0000.0000.000
24A23GLN 0-0.080-0.02916.845-0.028-0.0280.0000.0000.0000.000
25A24THR 0-0.0210.00016.966-0.009-0.0090.0000.0000.0000.000
26A25THR 0-0.021-0.03219.1000.0250.0250.0000.0000.0000.000
27A26SER 00.0570.01720.615-0.018-0.0180.0000.0000.0000.000
28A27ASP -1-0.878-0.92221.498-0.216-0.2160.0000.0000.0000.000
29A28LYS 10.8570.93217.5790.2300.2300.0000.0000.0000.000
30A29LEU 00.0260.03116.195-0.051-0.0510.0000.0000.0000.000
31A30THR 0-0.052-0.01813.2130.0020.0020.0000.0000.0000.000
32A31TYR 0-0.015-0.02714.933-0.014-0.0140.0000.0000.0000.000
33A32GLU -1-0.874-0.92513.156-0.248-0.2480.0000.0000.0000.000
34A33ILE 0-0.035-0.03616.6230.0080.0080.0000.0000.0000.000
35A34VAL 0-0.051-0.01616.9860.0070.0070.0000.0000.0000.000
36A35GLU -1-0.880-0.95919.566-0.041-0.0410.0000.0000.0000.000
37A36LYS 10.9390.98223.2730.0810.0810.0000.0000.0000.000
38A37GLY 00.0550.01826.0540.0050.0050.0000.0000.0000.000
39A38SER 0-0.006-0.01528.4710.0020.0020.0000.0000.0000.000
40A39ALA 0-0.001-0.00332.1930.0010.0010.0000.0000.0000.000
41A40GLY 00.0230.01335.3570.0000.0000.0000.0000.0000.000
42A41PHE 0-0.013-0.00938.7290.0020.0020.0000.0000.0000.000
43A42LEU 00.0600.02741.7230.0000.0000.0000.0000.0000.000
44A43GLY 00.0000.01542.0740.0000.0000.0000.0000.0000.000
45A44ILE 0-0.040-0.03337.338-0.001-0.0010.0000.0000.0000.000
46A45GLY 00.0400.02536.508-0.001-0.0010.0000.0000.0000.000
47A46SER 0-0.080-0.02833.407-0.003-0.0030.0000.0000.0000.000
48A47LYS 10.9260.93329.0520.0290.0290.0000.0000.0000.000
49A48PRO 0-0.0180.04625.537-0.003-0.0030.0000.0000.0000.000
50A49ALA 00.0460.01924.8720.0020.0020.0000.0000.0000.000
51A50ILE 0-0.064-0.03419.017-0.001-0.0010.0000.0000.0000.000
52A51ILE 0-0.033-0.01218.1390.0010.0010.0000.0000.0000.000
53A52ARG 10.9490.98212.2130.1580.1580.0000.0000.0000.000
54A53ALA 00.034-0.00214.026-0.003-0.0030.0000.0000.0000.000
55A54LYS 10.9360.9858.5321.0581.0580.0000.0000.0000.000
56A55ARG 11.0180.99911.6260.5490.5490.0000.0000.0000.000
57A56LYS 10.8860.93811.7770.2300.2300.0000.0000.0000.000
58A57GLU -1-0.946-0.9878.687-0.968-0.9680.0000.0000.0000.000
59A58THR 0-0.065-0.01711.8090.1560.1560.0000.0000.0000.000
60A59LEU 0-0.008-0.01612.848-0.042-0.0420.0000.0000.0000.000
61A60GLN 00.0780.01814.225-0.008-0.0080.0000.0000.0000.000
62A61ASP -1-0.799-0.9029.398-0.719-0.7190.0000.0000.0000.000
63A62LYS 10.9270.9679.6650.4270.4270.0000.0000.0000.000
64A63ALA 0-0.055-0.01911.3900.0570.0570.0000.0000.0000.000
65A64ILE 00.011-0.0059.3780.0540.0540.0000.0000.0000.000
66A65GLU -1-0.847-0.9055.492-0.620-0.6200.0000.0000.0000.000
67A66PHE 0-0.062-0.0348.2700.1570.1570.0000.0000.0000.000
68A67LEU 0-0.006-0.02611.3410.0680.0680.0000.0000.0000.000
69A68GLU -1-0.915-0.9467.7420.0890.0890.0000.0000.0000.000
70A69GLN 00.0260.0149.1300.1360.1360.0000.0000.0000.000
71A70VAL 0-0.048-0.02810.2780.0380.0380.0000.0000.0000.000
72A71PHE 00.001-0.04413.6450.0080.0080.0000.0000.0000.000
73A72ASP -1-0.913-0.92311.1190.4150.4150.0000.0000.0000.000
74A73ALA 00.0060.00113.1380.0060.0060.0000.0000.0000.000
75A74MET 0-0.172-0.09215.156-0.022-0.0220.0000.0000.0000.000
76A75ASN 0-0.055-0.01416.4340.0070.0070.0000.0000.0000.000
77A76MET 0-0.096-0.04616.573-0.021-0.0210.0000.0000.0000.000
78A77ALA 00.0490.04015.3530.0150.0150.0000.0000.0000.000
79A78VAL 0-0.090-0.06514.776-0.028-0.0280.0000.0000.0000.000
80A79ASP -1-0.857-0.91814.3840.0560.0560.0000.0000.0000.000
81A80ILE 0-0.037-0.02412.125-0.021-0.0210.0000.0000.0000.000
82A81SER 0-0.021-0.00314.794-0.011-0.0110.0000.0000.0000.000
83A82VAL 0-0.010-0.04415.2430.0060.0060.0000.0000.0000.000
84A83GLU -1-0.945-0.94017.911-0.104-0.1040.0000.0000.0000.000
85A84TYR 0-0.028-0.02419.2460.0060.0060.0000.0000.0000.000
86A85ASN 00.0040.01421.199-0.005-0.0050.0000.0000.0000.000
87A86GLU -1-0.856-0.95822.350-0.179-0.1790.0000.0000.0000.000
88A87THR 0-0.043-0.02524.6000.0030.0030.0000.0000.0000.000
89A88GLU -1-0.897-0.95227.915-0.078-0.0780.0000.0000.0000.000
90A89LYS 10.7820.92925.2200.1310.1310.0000.0000.0000.000
91A90GLU -1-0.947-0.99324.523-0.080-0.0800.0000.0000.0000.000
92A91MET 0-0.047-0.01216.731-0.007-0.0070.0000.0000.0000.000
93A92ASN 0-0.018-0.02821.4130.0200.0200.0000.0000.0000.000
94A93VAL 0-0.023-0.01116.577-0.005-0.0050.0000.0000.0000.000
95A94ASN 00.019-0.01219.4800.0210.0210.0000.0000.0000.000
96A95LEU 0-0.0060.00817.305-0.004-0.0040.0000.0000.0000.000
97A96LYS 10.9530.97019.3690.0170.0170.0000.0000.0000.000
98A97GLY 00.0690.01619.2070.0050.0050.0000.0000.0000.000
99A98ASP -1-0.911-0.96120.7690.0580.0580.0000.0000.0000.000
100A99ASP -1-0.797-0.90319.9440.0980.0980.0000.0000.0000.000
101A100MET 0-0.092-0.03319.656-0.011-0.0110.0000.0000.0000.000
102A101GLY 0-0.046-0.02022.650-0.010-0.0100.0000.0000.0000.000
103A102ILE 0-0.0060.00923.865-0.007-0.0070.0000.0000.0000.000
104A103LEU 00.0200.00823.064-0.007-0.0070.0000.0000.0000.000
105A104ILE 00.0300.00327.316-0.007-0.0070.0000.0000.0000.000
106A105GLY 0-0.023-0.01030.352-0.005-0.0050.0000.0000.0000.000
107A106LYS 10.9110.93828.063-0.027-0.0270.0000.0000.0000.000
108A107ARG 11.0331.03525.924-0.012-0.0120.0000.0000.0000.000
109A108GLY 0-0.0140.01726.663-0.005-0.0050.0000.0000.0000.000
110A109GLN 00.0620.00427.480-0.001-0.0010.0000.0000.0000.000
111A110THR 0-0.0420.00923.706-0.004-0.0040.0000.0000.0000.000
112A111LEU 00.0910.04222.713-0.005-0.0050.0000.0000.0000.000
113A112ASP -1-0.921-0.96523.633-0.037-0.0370.0000.0000.0000.000
114A113SER 0-0.077-0.04323.601-0.006-0.0060.0000.0000.0000.000
115A114LEU 00.0590.03317.785-0.008-0.0080.0000.0000.0000.000
116A115GLN 00.0430.03419.947-0.018-0.0180.0000.0000.0000.000
117A116TYR 0-0.069-0.03421.661-0.014-0.0140.0000.0000.0000.000
118A117LEU 00.005-0.00618.856-0.009-0.0090.0000.0000.0000.000
119A118VAL 00.0860.03415.753-0.016-0.0160.0000.0000.0000.000
120A119SER 00.0210.00217.939-0.027-0.0270.0000.0000.0000.000
121A120LEU 0-0.059-0.01420.373-0.010-0.0100.0000.0000.0000.000
122A121VAL 0-0.014-0.00714.117-0.011-0.0110.0000.0000.0000.000
123A122VAL 00.029-0.00616.240-0.021-0.0210.0000.0000.0000.000
124A123ASN 0-0.035-0.03517.623-0.011-0.0110.0000.0000.0000.000
125A124LYS 10.9231.00115.9100.1960.1960.0000.0000.0000.000
126A125SER 0-0.119-0.05916.023-0.024-0.0240.0000.0000.0000.000
127A126SER 0-0.007-0.01918.333-0.026-0.0260.0000.0000.0000.000
128A127SER 0-0.025-0.00421.2620.0100.0100.0000.0000.0000.000
129A128ASP -1-0.841-0.89124.447-0.116-0.1160.0000.0000.0000.000
130A129TYR 0-0.011-0.01624.557-0.006-0.0060.0000.0000.0000.000
131A130ILE 0-0.0030.00021.1690.0010.0010.0000.0000.0000.000
132A131ARG 10.9310.97124.2230.0810.0810.0000.0000.0000.000
133A132VAL 00.0120.02719.425-0.005-0.0050.0000.0000.0000.000
134A133LYS 10.8490.93022.5840.0830.0830.0000.0000.0000.000
135A134LEU 00.0240.01618.818-0.009-0.0090.0000.0000.0000.000
136A135ASP -1-0.862-0.94722.224-0.023-0.0230.0000.0000.0000.000
137A136THR 00.0460.02522.3570.0000.0000.0000.0000.0000.000
138A137GLU -1-0.821-0.88924.221-0.015-0.0150.0000.0000.0000.000
139A138ASN 00.0540.01826.4880.0020.0020.0000.0000.0000.000
140A139TYR 0-0.023-0.01527.7590.0050.0050.0000.0000.0000.000
141A140ARG 10.8190.90825.5690.0400.0400.0000.0000.0000.000
142A141GLU -1-0.880-0.92230.608-0.024-0.0240.0000.0000.0000.000
143A142ARG 10.8490.91828.7390.0110.0110.0000.0000.0000.000
144A143ARG 10.8390.89932.3390.0050.0050.0000.0000.0000.000
145A144LYS 10.9250.95134.4170.0230.0230.0000.0000.0000.000
146A145GLU -1-0.860-0.92036.718-0.010-0.0100.0000.0000.0000.000
147A146THR 0-0.051-0.01536.7500.0020.0020.0000.0000.0000.000
148A147LEU 00.005-0.00336.1740.0020.0020.0000.0000.0000.000
149A148GLU -1-0.835-0.93040.073-0.015-0.0150.0000.0000.0000.000
150A149THR 0-0.092-0.05142.2360.0010.0010.0000.0000.0000.000
151A150LEU 0-0.0110.00341.5630.0010.0010.0000.0000.0000.000
152A151ALA 00.0150.01144.0870.0010.0010.0000.0000.0000.000
153A152LYS 10.9590.97545.2780.0090.0090.0000.0000.0000.000
154A153ASN 0-0.022-0.00646.1350.0000.0000.0000.0000.0000.000
155A154ILE 0-0.028-0.03746.9010.0010.0010.0000.0000.0000.000
156A155ALA 00.0520.03249.5800.0000.0000.0000.0000.0000.000
157A156TYR 0-0.033-0.01051.8630.0000.0000.0000.0000.0000.000
158A157LYS 11.0451.01349.166-0.004-0.0040.0000.0000.0000.000
159A158VAL 0-0.0180.04552.4480.0000.0000.0000.0000.0000.000
160A159LYS 10.8940.94554.9320.0040.0040.0000.0000.0000.000
161A160ARG 10.9150.95357.001-0.001-0.0010.0000.0000.0000.000
162A161THR 0-0.037-0.04056.3700.0000.0000.0000.0000.0000.000
163A162LYS 10.9060.95658.8480.0010.0010.0000.0000.0000.000
164A163ARG 10.9731.00253.952-0.004-0.0040.0000.0000.0000.000
165A164SER 0-0.018-0.02453.2950.0000.0000.0000.0000.0000.000
166A165VAL 0-0.031-0.01948.4300.0010.0010.0000.0000.0000.000
167A166SER 0-0.0010.00646.927-0.001-0.0010.0000.0000.0000.000
168A167LEU 0-0.043-0.01542.7490.0010.0010.0000.0000.0000.000
169A168GLU -1-0.851-0.92838.8220.0060.0060.0000.0000.0000.000
170A169PRO 0-0.053-0.03537.987-0.002-0.0020.0000.0000.0000.000
171A170MET 00.0030.01136.3600.0000.0000.0000.0000.0000.000
172A171ASN 00.0880.06632.397-0.003-0.0030.0000.0000.0000.000
173A172PRO 00.044-0.00334.1670.0000.0000.0000.0000.0000.000
174A173TYR 00.0200.00931.482-0.001-0.0010.0000.0000.0000.000
175A174GLU -1-0.822-0.90334.027-0.005-0.0050.0000.0000.0000.000
176A175ARG 10.8790.94336.7010.0060.0060.0000.0000.0000.000
177A176ARG 10.9370.97738.8040.0220.0220.0000.0000.0000.000
178A177ILE 00.0050.00536.1100.0000.0000.0000.0000.0000.000
179A178ILE 00.0420.01940.3470.0000.0000.0000.0000.0000.000
180A179HIS 0-0.056-0.03343.0550.0000.0000.0000.0000.0000.000
181A180ALA 0-0.014-0.00343.2270.0000.0000.0000.0000.0000.000
182A181ALA 0-0.0260.00644.0680.0000.0000.0000.0000.0000.000
183A182LEU 0-0.035-0.02945.8040.0010.0010.0000.0000.0000.000
184A183GLN 0-0.037-0.00446.8960.0000.0000.0000.0000.0000.000
185A184ASN 0-0.027-0.02249.8690.0000.0000.0000.0000.0000.000
186A185ASP -1-0.814-0.89752.641-0.005-0.0050.0000.0000.0000.000
187A186LYS 10.9200.94854.3620.0090.0090.0000.0000.0000.000
188A187TYR 0-0.016-0.02156.9270.0000.0000.0000.0000.0000.000
189A188VAL 0-0.048-0.01252.3600.0010.0010.0000.0000.0000.000
190A189VAL 00.0000.00252.931-0.001-0.0010.0000.0000.0000.000
191A190THR 0-0.0010.00047.7750.0010.0010.0000.0000.0000.000
192A191ARG 10.9630.95748.3700.0010.0010.0000.0000.0000.000
193A192SER 0-0.054-0.01743.8220.0010.0010.0000.0000.0000.000
194A193ASP -1-0.859-0.91345.325-0.001-0.0010.0000.0000.0000.000
195A194GLY 00.0460.02043.8950.0000.0000.0000.0000.0000.000
196A195GLU -1-0.875-0.92941.439-0.002-0.0020.0000.0000.0000.000
197A196GLU -1-0.852-0.92135.826-0.003-0.0030.0000.0000.0000.000
198A197PRO 00.008-0.00934.5770.0010.0010.0000.0000.0000.000
199A198PHE 0-0.020-0.03436.6470.0010.0010.0000.0000.0000.000
200A199ARG 10.8780.95339.2920.0040.0040.0000.0000.0000.000
201A200HIS 00.010-0.00140.085-0.001-0.0010.0000.0000.0000.000
202A201VAL 00.0190.00542.632-0.001-0.0010.0000.0000.0000.000
203A202ILE 0-0.078-0.03544.9160.0010.0010.0000.0000.0000.000
204A203ILE 00.0210.00547.134-0.001-0.0010.0000.0000.0000.000
205A204SER 00.008-0.00350.5890.0010.0010.0000.0000.0000.000
206A205LEU 0-0.023-0.00554.394-0.001-0.0010.0000.0000.0000.000
207A206LYS 10.9430.98356.5830.0070.0070.0000.0000.0000.000
208A207ARG 10.9460.95658.6020.0030.0030.0000.0000.0000.000
209A208GLU -1-0.943-0.97061.847-0.006-0.0060.0000.0000.0000.000
210A209NME 00.0020.01864.8720.0000.0000.0000.0000.0000.000