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: KRN43

Calculation Name: 3GKU-A-Xray307

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 MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2086648.249001
FMO2-HF: Nuclear repulsion 2003095.232335
FMO2-HF: Total energy -83553.016666
FMO2-MP2: Total energy -83796.601046


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.
0.8221.715-0.014-0.38-0.4990
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 : 0.037 / q_NPA : 0.010
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 -1-0.854-0.9253.8090.2911.184-0.014-0.380-0.4990.000
4A3MET 0-0.061-0.0507.246-0.148-0.1480.0000.0000.0000.000
5A4VAL 00.0540.0579.8540.1340.1340.0000.0000.0000.000
6A5THR 0-0.039-0.02213.2610.0040.0040.0000.0000.0000.000
7A6VAL 00.0080.01515.6980.0220.0220.0000.0000.0000.000
8A7THR 0-0.017-0.01219.1840.0100.0100.0000.0000.0000.000
9A8ALA 0-0.031-0.03822.512-0.001-0.0010.0000.0000.0000.000
10A9LYS 10.9951.01125.9920.0530.0530.0000.0000.0000.000
11A10THR 00.0480.03828.1990.0010.0010.0000.0000.0000.000
12A11VAL 00.0500.00822.922-0.005-0.0050.0000.0000.0000.000
13A12GLU -1-0.926-0.96824.455-0.098-0.0980.0000.0000.0000.000
14A13GLU -1-0.855-0.94226.177-0.083-0.0830.0000.0000.0000.000
15A14ALA 0-0.023-0.00121.973-0.007-0.0070.0000.0000.0000.000
16A15VAL 00.0450.01621.251-0.015-0.0150.0000.0000.0000.000
17A16THR 00.0020.00421.874-0.013-0.0130.0000.0000.0000.000
18A17LYS 10.8970.94222.7490.0930.0930.0000.0000.0000.000
19A18ALA 00.0240.01318.027-0.003-0.0030.0000.0000.0000.000
20A19LEU 0-0.002-0.00618.960-0.022-0.0220.0000.0000.0000.000
21A20ILE 0-0.040-0.00920.763-0.005-0.0050.0000.0000.0000.000
22A21GLU -1-0.951-0.98717.340-0.177-0.1770.0000.0000.0000.000
23A22LEU 0-0.064-0.03013.421-0.015-0.0150.0000.0000.0000.000
24A23GLN 0-0.082-0.03016.930-0.029-0.0290.0000.0000.0000.000
25A24THR 0-0.0170.00117.009-0.009-0.0090.0000.0000.0000.000
26A25THR 0-0.018-0.02919.1420.0250.0250.0000.0000.0000.000
27A26SER 00.0540.01420.649-0.018-0.0180.0000.0000.0000.000
28A27ASP -1-0.883-0.92521.527-0.219-0.2190.0000.0000.0000.000
29A28LYS 10.8570.93217.6090.2380.2380.0000.0000.0000.000
30A29LEU 00.0290.03316.228-0.050-0.0500.0000.0000.0000.000
31A30THR 0-0.046-0.01713.2370.0050.0050.0000.0000.0000.000
32A31TYR 0-0.021-0.02614.966-0.014-0.0140.0000.0000.0000.000
33A32GLU -1-0.878-0.92713.121-0.235-0.2350.0000.0000.0000.000
34A33ILE 0-0.031-0.03616.5950.0060.0060.0000.0000.0000.000
35A34VAL 0-0.049-0.01516.9800.0070.0070.0000.0000.0000.000
36A35GLU -1-0.879-0.95919.557-0.039-0.0390.0000.0000.0000.000
37A36LYS 10.9400.98323.2670.0780.0780.0000.0000.0000.000
38A37GLY 00.0460.01626.0460.0050.0050.0000.0000.0000.000
39A38SER 0-0.004-0.01528.4730.0020.0020.0000.0000.0000.000
40A39ALA 0-0.002-0.00632.1940.0000.0000.0000.0000.0000.000
41A40GLY 00.0270.01435.3650.0000.0000.0000.0000.0000.000
42A41PHE 0-0.0150.01638.7370.0020.0020.0000.0000.0000.000
43A42LEU 00.0330.00341.7370.0000.0000.0000.0000.0000.000
44A43GLY 00.0180.00341.8120.0000.0000.0000.0000.0000.000
45A44ILE 0-0.022-0.03637.4400.0000.0000.0000.0000.0000.000
46A45GLY 00.0550.05336.528-0.001-0.0010.0000.0000.0000.000
47A46SER 0-0.099-0.03333.428-0.003-0.0030.0000.0000.0000.000
48A47LYS 10.9260.93229.0620.0270.0270.0000.0000.0000.000
49A48PRO 0-0.0240.04425.558-0.003-0.0030.0000.0000.0000.000
50A49ALA 00.0550.02024.8720.0020.0020.0000.0000.0000.000
51A50ILE 0-0.065-0.03419.031-0.001-0.0010.0000.0000.0000.000
52A51ILE 0-0.036-0.01318.1440.0020.0020.0000.0000.0000.000
53A52ARG 10.9470.98012.2190.1490.1490.0000.0000.0000.000
54A53ALA 00.036-0.00114.034-0.001-0.0010.0000.0000.0000.000
55A54LYS 10.9280.9868.5711.0691.0690.0000.0000.0000.000
56A55ARG 11.0181.00211.6660.5650.5650.0000.0000.0000.000
57A56LYS 10.8890.93811.8060.2350.2350.0000.0000.0000.000
58A57GLU -1-0.947-0.9888.692-0.984-0.9840.0000.0000.0000.000
59A58THR 0-0.071-0.01711.8370.1600.1600.0000.0000.0000.000
60A59LEU 0-0.003-0.01612.858-0.042-0.0420.0000.0000.0000.000
61A60GLN 00.0800.01814.222-0.007-0.0070.0000.0000.0000.000
62A61ASP -1-0.792-0.9009.409-0.743-0.7430.0000.0000.0000.000
63A62LYS 10.9300.9689.6570.4300.4300.0000.0000.0000.000
64A63ALA 0-0.055-0.01911.3800.0600.0600.0000.0000.0000.000
65A64ILE 00.001-0.0099.3530.0550.0550.0000.0000.0000.000
66A65GLU -1-0.846-0.9045.452-0.618-0.6180.0000.0000.0000.000
67A66PHE 0-0.058-0.0308.2400.1600.1600.0000.0000.0000.000
68A67LEU 0-0.008-0.02611.3010.0710.0710.0000.0000.0000.000
69A68GLU -1-0.919-0.9487.7110.0520.0520.0000.0000.0000.000
70A69GLN 00.0230.0109.0750.1400.1400.0000.0000.0000.000
71A70VAL 0-0.041-0.02610.2210.0390.0390.0000.0000.0000.000
72A71PHE 00.002-0.04413.5940.0080.0080.0000.0000.0000.000
73A72ASP -1-0.917-0.92411.0600.4190.4190.0000.0000.0000.000
74A73ALA 00.0080.00213.0790.0080.0080.0000.0000.0000.000
75A74MET 0-0.181-0.09415.095-0.022-0.0220.0000.0000.0000.000
76A75ASN 0-0.057-0.01516.3710.0070.0070.0000.0000.0000.000
77A76MET 0-0.095-0.04716.510-0.021-0.0210.0000.0000.0000.000
78A77ALA 00.0510.04115.3080.0120.0120.0000.0000.0000.000
79A78VAL 0-0.090-0.06214.734-0.027-0.0270.0000.0000.0000.000
80A79ASP -1-0.856-0.91714.3490.0420.0420.0000.0000.0000.000
81A80ILE 0-0.037-0.02312.092-0.017-0.0170.0000.0000.0000.000
82A81SER 0-0.024-0.00514.778-0.012-0.0120.0000.0000.0000.000
83A82VAL 0-0.010-0.04315.2350.0080.0080.0000.0000.0000.000
84A83GLU -1-0.949-0.94217.904-0.112-0.1120.0000.0000.0000.000
85A84TYR 0-0.021-0.02219.2480.0070.0070.0000.0000.0000.000
86A85ASN 00.0050.01521.202-0.005-0.0050.0000.0000.0000.000
87A86GLU -1-0.857-0.95722.364-0.185-0.1850.0000.0000.0000.000
88A87THR 0-0.043-0.02724.6110.0030.0030.0000.0000.0000.000
89A88GLU -1-0.902-0.95327.922-0.081-0.0810.0000.0000.0000.000
90A89LYS 10.7830.92925.2240.1350.1350.0000.0000.0000.000
91A90GLU -1-0.950-0.99424.517-0.084-0.0840.0000.0000.0000.000
92A91MET 0-0.043-0.01216.747-0.008-0.0080.0000.0000.0000.000
93A92ASN 0-0.032-0.03221.4000.0210.0210.0000.0000.0000.000
94A93VAL 0-0.010-0.00616.554-0.006-0.0060.0000.0000.0000.000
95A94ASN 00.010-0.01519.4630.0220.0220.0000.0000.0000.000
96A95LEU 00.0020.01117.271-0.006-0.0060.0000.0000.0000.000
97A96LYS 10.9590.97319.3410.0250.0250.0000.0000.0000.000
98A97GLY 00.0660.01419.1750.0040.0040.0000.0000.0000.000
99A98ASP -1-0.912-0.96020.7350.0550.0550.0000.0000.0000.000
100A99ASP -1-0.788-0.89919.8970.0950.0950.0000.0000.0000.000
101A100MET 0-0.095-0.03719.398-0.010-0.0100.0000.0000.0000.000
102A101GLY 0-0.044-0.02122.611-0.010-0.0100.0000.0000.0000.000
103A102ILE 0-0.0040.00623.824-0.007-0.0070.0000.0000.0000.000
104A103LEU 00.0260.00923.018-0.006-0.0060.0000.0000.0000.000
105A104ILE 00.0160.00027.266-0.007-0.0070.0000.0000.0000.000
106A105GLY 0-0.011-0.00630.305-0.004-0.0040.0000.0000.0000.000
107A106LYS 10.9090.93828.011-0.026-0.0260.0000.0000.0000.000
108A107ARG 11.0281.03325.880-0.009-0.0090.0000.0000.0000.000
109A108GLY 0-0.0180.01526.618-0.005-0.0050.0000.0000.0000.000
110A109GLN 00.0650.00627.437-0.001-0.0010.0000.0000.0000.000
111A110THR 0-0.0420.00823.654-0.004-0.0040.0000.0000.0000.000
112A111LEU 00.0940.04522.672-0.004-0.0040.0000.0000.0000.000
113A112ASP -1-0.927-0.96523.592-0.039-0.0390.0000.0000.0000.000
114A113SER 0-0.072-0.04323.552-0.006-0.0060.0000.0000.0000.000
115A114LEU 00.0530.03017.739-0.008-0.0080.0000.0000.0000.000
116A115GLN 00.0410.03219.907-0.017-0.0170.0000.0000.0000.000
117A116TYR 0-0.064-0.03221.627-0.014-0.0140.0000.0000.0000.000
118A117LEU 00.012-0.00418.813-0.008-0.0080.0000.0000.0000.000
119A118VAL 00.0830.03415.719-0.015-0.0150.0000.0000.0000.000
120A119SER 00.010-0.00317.905-0.027-0.0270.0000.0000.0000.000
121A120LEU 0-0.056-0.01220.339-0.010-0.0100.0000.0000.0000.000
122A121VAL 0-0.008-0.00414.088-0.010-0.0100.0000.0000.0000.000
123A122VAL 00.032-0.00416.226-0.020-0.0200.0000.0000.0000.000
124A123ASN 0-0.045-0.03917.608-0.011-0.0110.0000.0000.0000.000
125A124LYS 10.9291.00315.8860.1940.1940.0000.0000.0000.000
126A125SER 0-0.119-0.05916.016-0.023-0.0230.0000.0000.0000.000
127A126SER 0-0.014-0.02418.329-0.027-0.0270.0000.0000.0000.000
128A127SER 0-0.018-0.00121.2610.0100.0100.0000.0000.0000.000
129A128ASP -1-0.840-0.88824.449-0.119-0.1190.0000.0000.0000.000
130A129TYR 0-0.014-0.01824.555-0.006-0.0060.0000.0000.0000.000
131A130ILE 0-0.0010.00021.1690.0010.0010.0000.0000.0000.000
132A131ARG 10.9310.97224.2140.0840.0840.0000.0000.0000.000
133A132VAL 00.0140.02719.407-0.006-0.0060.0000.0000.0000.000
134A133LYS 10.8500.93022.5650.0870.0870.0000.0000.0000.000
135A134LEU 00.0270.01718.787-0.009-0.0090.0000.0000.0000.000
136A135ASP -1-0.865-0.95022.195-0.027-0.0270.0000.0000.0000.000
137A136THR 00.0430.02622.327-0.001-0.0010.0000.0000.0000.000
138A137GLU -1-0.823-0.89124.199-0.021-0.0210.0000.0000.0000.000
139A138ASN 00.0550.01926.4630.0030.0030.0000.0000.0000.000
140A139TYR 0-0.024-0.01527.7250.0050.0050.0000.0000.0000.000
141A140ARG 10.8140.90525.5360.0430.0430.0000.0000.0000.000
142A141GLU -1-0.877-0.92130.576-0.027-0.0270.0000.0000.0000.000
143A142ARG 10.8550.92228.7090.0150.0150.0000.0000.0000.000
144A143ARG 10.8420.90232.3020.0070.0070.0000.0000.0000.000
145A144LYS 10.9190.94934.3800.0250.0250.0000.0000.0000.000
146A145GLU -1-0.864-0.92336.683-0.012-0.0120.0000.0000.0000.000
147A146THR 0-0.052-0.01736.7140.0030.0030.0000.0000.0000.000
148A147LEU 00.012-0.00136.1320.0020.0020.0000.0000.0000.000
149A148GLU -1-0.832-0.92740.033-0.016-0.0160.0000.0000.0000.000
150A149THR 0-0.086-0.04842.1990.0010.0010.0000.0000.0000.000
151A150LEU 0-0.0170.00341.5190.0010.0010.0000.0000.0000.000
152A151ALA 00.0030.00544.0460.0010.0010.0000.0000.0000.000
153A152LYS 10.9590.97445.2450.0100.0100.0000.0000.0000.000
154A153ASN 0-0.018-0.00346.0950.0000.0000.0000.0000.0000.000
155A154ILE 0-0.021-0.03646.8570.0010.0010.0000.0000.0000.000
156A155ALA 00.0490.03049.5360.0000.0000.0000.0000.0000.000
157A156TYR 0-0.036-0.01151.8200.0000.0000.0000.0000.0000.000
158A157LYS 11.0411.00949.122-0.003-0.0030.0000.0000.0000.000
159A158VAL 0-0.0190.04552.4030.0000.0000.0000.0000.0000.000
160A159LYS 10.9030.94854.8920.0050.0050.0000.0000.0000.000
161A160ARG 10.9280.95756.9580.0000.0000.0000.0000.0000.000
162A161THR 0-0.043-0.03756.3240.0000.0000.0000.0000.0000.000
163A162LYS 10.8990.95358.8020.0020.0020.0000.0000.0000.000
164A163ARG 10.9711.00053.900-0.004-0.0040.0000.0000.0000.000
165A164SER 0-0.024-0.02653.2450.0000.0000.0000.0000.0000.000
166A165VAL 0-0.026-0.01748.3810.0010.0010.0000.0000.0000.000
167A166SER 0-0.0030.00746.876-0.001-0.0010.0000.0000.0000.000
168A167LEU 0-0.037-0.01542.7020.0010.0010.0000.0000.0000.000
169A168GLU -1-0.857-0.93038.7720.0050.0050.0000.0000.0000.000
170A169PRO 0-0.050-0.03537.934-0.002-0.0020.0000.0000.0000.000
171A170MET 00.0010.01136.314-0.001-0.0010.0000.0000.0000.000
172A171ASN 00.0900.06932.349-0.003-0.0030.0000.0000.0000.000
173A172PRO 00.049-0.00334.1210.0000.0000.0000.0000.0000.000
174A173TYR 00.0180.00831.441-0.001-0.0010.0000.0000.0000.000
175A174GLU -1-0.828-0.90333.983-0.007-0.0070.0000.0000.0000.000
176A175ARG 10.8770.94036.6590.0070.0070.0000.0000.0000.000
177A176ARG 10.9400.97938.7650.0230.0230.0000.0000.0000.000
178A177ILE 0-0.0030.00136.0740.0000.0000.0000.0000.0000.000
179A178ILE 00.0410.02040.3100.0000.0000.0000.0000.0000.000
180A179HIS 0-0.046-0.03043.0130.0000.0000.0000.0000.0000.000
181A180ALA 0-0.017-0.00343.1910.0000.0000.0000.0000.0000.000
182A181ALA 0-0.0280.00144.0310.0000.0000.0000.0000.0000.000
183A182LEU 0-0.037-0.02845.7680.0010.0010.0000.0000.0000.000
184A183GLN 0-0.035-0.00546.8630.0000.0000.0000.0000.0000.000
185A184ASN 0-0.028-0.02249.8330.0000.0000.0000.0000.0000.000
186A185ASP -1-0.814-0.89552.603-0.006-0.0060.0000.0000.0000.000
187A186LYS 10.9210.94854.3250.0100.0100.0000.0000.0000.000
188A187TYR 0-0.011-0.02056.8880.0000.0000.0000.0000.0000.000
189A188VAL 0-0.051-0.01452.3170.0010.0010.0000.0000.0000.000
190A189VAL 0-0.0040.00152.890-0.001-0.0010.0000.0000.0000.000
191A190THR 0-0.0060.00047.7310.0010.0010.0000.0000.0000.000
192A191ARG 10.9660.95648.3250.0010.0010.0000.0000.0000.000
193A192SER 0-0.053-0.01543.7740.0010.0010.0000.0000.0000.000
194A193ASP -1-0.857-0.91345.275-0.001-0.0010.0000.0000.0000.000
195A194GLY 00.0550.02443.8420.0000.0000.0000.0000.0000.000
196A195GLU -1-0.878-0.92941.385-0.002-0.0020.0000.0000.0000.000
197A196GLU -1-0.851-0.92235.775-0.004-0.0040.0000.0000.0000.000
198A197PRO 00.006-0.00934.5220.0010.0010.0000.0000.0000.000
199A198PHE 0-0.016-0.03436.5920.0010.0010.0000.0000.0000.000
200A199ARG 10.8750.95339.2390.0040.0040.0000.0000.0000.000
201A200HIS 00.009-0.00240.034-0.001-0.0010.0000.0000.0000.000
202A201VAL 00.0270.01142.582-0.001-0.0010.0000.0000.0000.000
203A202ILE 0-0.083-0.03744.8690.0010.0010.0000.0000.0000.000
204A203ILE 00.0230.00647.090-0.001-0.0010.0000.0000.0000.000
205A204SER 0-0.001-0.00850.5430.0010.0010.0000.0000.0000.000
206A205LEU 0-0.022-0.00554.347-0.001-0.0010.0000.0000.0000.000
207A206LYS 10.9500.98556.5440.0080.0080.0000.0000.0000.000
208A207ARG 10.9450.95758.5580.0030.0030.0000.0000.0000.000
209A208GLU -1-0.943-0.97161.803-0.006-0.0060.0000.0000.0000.000
210A209NME 00.0020.01964.8290.0000.0000.0000.0000.0000.000