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: 2K16R

Calculation Name: 2JEU-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JEU

Chain ID: A

ChEMBL ID:

UniProt ID: P03122

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 199
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2084687.382115
FMO2-HF: Nuclear repulsion 2004367.744308
FMO2-HF: Total energy -80319.637807
FMO2-MP2: Total energy -80549.954744


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:2:ACE )


Summations of interaction energy for fragment #1(A:2: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.
-1.763-0.721-0.004-0.484-0.5530
Interaction energy analysis for fragmet #1(A:2: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 : 0.004
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].
3A4ALA 0-0.045-0.0253.8550.7581.633-0.005-0.426-0.4450.000
4A5CYS 00.0260.0004.383-0.0100.0920.000-0.010-0.0910.000
5A6GLU -1-0.827-0.9044.320-3.262-3.1970.001-0.048-0.0170.000
6A7ARG 10.9670.9726.8080.9500.9500.0000.0000.0000.000
7A8LEU 0-0.041-0.0068.5840.1200.1200.0000.0000.0000.000
8A9HIS 00.0640.0279.6150.0560.0560.0000.0000.0000.000
9A10VAL 00.0300.02610.9980.0270.0270.0000.0000.0000.000
10A11ALA 0-0.050-0.00812.9170.0470.0470.0000.0000.0000.000
11A12GLN 0-0.052-0.06313.8810.0280.0280.0000.0000.0000.000
12A13GLU -1-0.871-0.93415.339-0.097-0.0970.0000.0000.0000.000
13A14THR 0-0.051-0.04016.7300.0100.0100.0000.0000.0000.000
14A15GLN 0-0.100-0.07317.8400.0300.0300.0000.0000.0000.000
15A16MET 0-0.003-0.00120.2120.0110.0110.0000.0000.0000.000
16A17GLN 00.0320.02919.566-0.007-0.0070.0000.0000.0000.000
17A18LEU 0-0.039-0.03022.6720.0070.0070.0000.0000.0000.000
18A19ILE 0-0.057-0.03423.8380.0070.0070.0000.0000.0000.000
19A20GLU -1-0.926-0.96425.018-0.050-0.0500.0000.0000.0000.000
20A21LYS 10.8210.93227.5140.0920.0920.0000.0000.0000.000
21A22SER 0-0.022-0.01629.2610.0050.0050.0000.0000.0000.000
22A23SER 0-0.088-0.05829.8630.0030.0030.0000.0000.0000.000
23A24ASP -1-0.796-0.89931.802-0.047-0.0470.0000.0000.0000.000
24A25LYS 10.9130.95731.1610.0830.0830.0000.0000.0000.000
25A26LEU 00.0910.04031.021-0.004-0.0040.0000.0000.0000.000
26A27GLN 0-0.020-0.02028.324-0.007-0.0070.0000.0000.0000.000
27A28ASP -1-0.778-0.87526.366-0.108-0.1080.0000.0000.0000.000
28A29HIS 0-0.008-0.00825.933-0.009-0.0090.0000.0000.0000.000
29A30ILE 00.0080.01225.0900.0000.0000.0000.0000.0000.000
30A31LEU 0-0.0160.01220.346-0.008-0.0080.0000.0000.0000.000
31A32TYR 00.0410.01521.569-0.012-0.0120.0000.0000.0000.000
32A33TRP 00.0070.00421.909-0.003-0.0030.0000.0000.0000.000
33A34THR 0-0.026-0.02518.9350.0000.0000.0000.0000.0000.000
34A35ALA 0-0.0140.01217.631-0.015-0.0150.0000.0000.0000.000
35A36VAL 00.0640.03917.471-0.002-0.0020.0000.0000.0000.000
36A37ARG 10.9260.96019.0520.1250.1250.0000.0000.0000.000
37A38THR 0-0.070-0.02813.406-0.004-0.0040.0000.0000.0000.000
38A39GLU -1-0.804-0.87714.184-0.047-0.0470.0000.0000.0000.000
39A40ASN 0-0.051-0.04414.8690.0450.0450.0000.0000.0000.000
40A41THR 0-0.013-0.01915.0770.0300.0300.0000.0000.0000.000
41A42LEU 0-0.058-0.0299.6670.0170.0170.0000.0000.0000.000
42A43LEU 00.0310.01812.5220.0730.0730.0000.0000.0000.000
43A44TYR 0-0.017-0.01114.3520.0410.0410.0000.0000.0000.000
44A45ALA 0-0.020-0.02512.4090.0220.0220.0000.0000.0000.000
45A46ALA 0-0.008-0.00111.4530.0410.0410.0000.0000.0000.000
46A47ARG 10.9440.98112.615-0.102-0.1020.0000.0000.0000.000
47A48LYS 10.8840.95816.109-0.065-0.0650.0000.0000.0000.000
48A49LYS 10.9360.9739.979-0.209-0.2090.0000.0000.0000.000
49A50GLY 0-0.0050.00514.6220.0290.0290.0000.0000.0000.000
50A51VAL 0-0.0140.00510.7680.0180.0180.0000.0000.0000.000
51A52THR 0-0.033-0.03514.059-0.038-0.0380.0000.0000.0000.000
52A53VAL 00.0040.00813.696-0.044-0.0440.0000.0000.0000.000
53A54LEU 00.0290.0237.7710.0900.0900.0000.0000.0000.000
54A55GLY 00.0510.0319.400-0.084-0.0840.0000.0000.0000.000
55A56HIS 0-0.007-0.01510.5840.0140.0140.0000.0000.0000.000
56A57CYS 0-0.028-0.01513.699-0.035-0.0350.0000.0000.0000.000
57A58ARG 10.9760.98114.810-0.098-0.0980.0000.0000.0000.000
58A59VAL 0-0.0060.00813.714-0.018-0.0180.0000.0000.0000.000
59A60PRO 00.0080.00416.703-0.002-0.0020.0000.0000.0000.000
60A61HIS 00.0990.02419.3270.0060.0060.0000.0000.0000.000
61A62SER 00.0390.01219.980-0.006-0.0060.0000.0000.0000.000
62A63VAL 00.0240.00920.943-0.011-0.0110.0000.0000.0000.000
63A64VAL 00.0150.01622.887-0.008-0.0080.0000.0000.0000.000
64A65CYS 0-0.066-0.02118.641-0.006-0.0060.0000.0000.0000.000
65A66GLN 00.009-0.00920.686-0.009-0.0090.0000.0000.0000.000
66A67GLU -1-0.880-0.94622.388-0.018-0.0180.0000.0000.0000.000
67A68ARG 10.9871.00721.671-0.010-0.0100.0000.0000.0000.000
68A69ALA 00.0000.00820.206-0.011-0.0110.0000.0000.0000.000
69A70LYS 10.9360.95921.9900.0050.0050.0000.0000.0000.000
70A71GLN 00.0040.01025.337-0.006-0.0060.0000.0000.0000.000
71A72ALA 00.0230.00722.655-0.004-0.0040.0000.0000.0000.000
72A73ILE 0-0.079-0.04222.089-0.009-0.0090.0000.0000.0000.000
73A74GLU -1-0.854-0.92425.007-0.039-0.0390.0000.0000.0000.000
74A75MET 0-0.0020.01127.1340.0000.0000.0000.0000.0000.000
75A76GLN 00.0330.03222.6720.0020.0020.0000.0000.0000.000
76A77LEU 0-0.050-0.04025.306-0.003-0.0030.0000.0000.0000.000
77A78SER 00.0200.02028.6060.0020.0020.0000.0000.0000.000
78A79LEU 00.0380.02028.8360.0010.0010.0000.0000.0000.000
79A80GLN 0-0.021-0.01425.461-0.013-0.0130.0000.0000.0000.000
80A81GLU -1-0.917-0.96130.238-0.054-0.0540.0000.0000.0000.000
81A82LEU 00.0210.01833.5340.0020.0020.0000.0000.0000.000
82A83SER 0-0.041-0.03332.001-0.001-0.0010.0000.0000.0000.000
83A84LYS 10.8820.95530.9180.0780.0780.0000.0000.0000.000
84A85THR 0-0.039-0.01635.9210.0040.0040.0000.0000.0000.000
85A86GLU -1-0.850-0.93839.130-0.041-0.0410.0000.0000.0000.000
86A87PHE 00.0080.00139.6730.0000.0000.0000.0000.0000.000
87A88GLY 0-0.094-0.02936.545-0.001-0.0010.0000.0000.0000.000
88A89ASP -1-0.894-0.94036.351-0.059-0.0590.0000.0000.0000.000
89A90GLU -1-0.925-0.96238.934-0.039-0.0390.0000.0000.0000.000
90A91PRO 00.0140.01837.713-0.003-0.0030.0000.0000.0000.000
91A92TRP 0-0.030-0.02134.4660.0040.0040.0000.0000.0000.000
92A93SER 00.0530.03534.124-0.003-0.0030.0000.0000.0000.000
93A94LEU 00.049-0.00127.819-0.001-0.0010.0000.0000.0000.000
94A95LEU 0-0.019-0.00331.7350.0020.0020.0000.0000.0000.000
95A96ASP -1-0.816-0.91634.525-0.035-0.0350.0000.0000.0000.000
96A97THR 0-0.0230.00329.594-0.001-0.0010.0000.0000.0000.000
97A98SER 00.0090.01330.654-0.002-0.0020.0000.0000.0000.000
98A99TRP 00.063-0.00329.6050.0000.0000.0000.0000.0000.000
99A100ASP -1-0.873-0.93631.631-0.016-0.0160.0000.0000.0000.000
100A101ARG 10.8110.91434.6410.0320.0320.0000.0000.0000.000
101A102TYR 0-0.036-0.01633.6220.0010.0010.0000.0000.0000.000
102A103MET 0-0.040-0.03633.9050.0010.0010.0000.0000.0000.000
103A104SER 0-0.053-0.00836.7400.0030.0030.0000.0000.0000.000
104A105GLU -1-0.842-0.91839.824-0.015-0.0150.0000.0000.0000.000
105A106PRO 0-0.053-0.03143.240-0.001-0.0010.0000.0000.0000.000
106A107LYS 10.9260.94539.0760.0110.0110.0000.0000.0000.000
107A108ARG 10.9090.95433.7030.0230.0230.0000.0000.0000.000
108A109CYS 0-0.0280.01837.574-0.002-0.0020.0000.0000.0000.000
109A110PHE 00.0410.01932.5890.0000.0000.0000.0000.0000.000
110A111LYS 10.8620.94838.1940.0260.0260.0000.0000.0000.000
111A112LYS 10.8520.92938.8830.0420.0420.0000.0000.0000.000
112A113GLY 00.0180.02041.8430.0010.0010.0000.0000.0000.000
113A114ALA 0-0.018-0.01143.5990.0010.0010.0000.0000.0000.000
114A115ARG 10.8610.90545.6450.0170.0170.0000.0000.0000.000
115A116VAL 0-0.009-0.00247.8720.0000.0000.0000.0000.0000.000
116A117VAL 0-0.0180.00550.1750.0000.0000.0000.0000.0000.000
117A118GLU -1-0.845-0.92452.612-0.007-0.0070.0000.0000.0000.000
118A119VAL 0-0.037-0.01754.8050.0000.0000.0000.0000.0000.000
119A120GLU -1-0.895-0.93556.737-0.005-0.0050.0000.0000.0000.000
120A121PHE 00.023-0.00555.2980.0000.0000.0000.0000.0000.000
121A122ASP -1-0.778-0.86360.884-0.002-0.0020.0000.0000.0000.000
122A123GLY 0-0.0120.01263.8010.0000.0000.0000.0000.0000.000
123A124ASN 0-0.032-0.02062.1020.0000.0000.0000.0000.0000.000
124A125ALA 00.0650.03861.2590.0000.0000.0000.0000.0000.000
125A126SER 0-0.062-0.04159.1290.0000.0000.0000.0000.0000.000
126A127ASN 0-0.088-0.04256.9450.0000.0000.0000.0000.0000.000
127A128THR 00.0400.02654.949-0.001-0.0010.0000.0000.0000.000
128A129ASN 0-0.018-0.00351.6980.0010.0010.0000.0000.0000.000
129A130TRP 0-0.053-0.03649.064-0.001-0.0010.0000.0000.0000.000
130A131TYR 0-0.061-0.05248.3590.0000.0000.0000.0000.0000.000
131A132THR 0-0.018-0.01744.195-0.001-0.0010.0000.0000.0000.000
132A133VAL 0-0.0160.01346.6480.0000.0000.0000.0000.0000.000
133A134TYR 00.014-0.01341.493-0.001-0.0010.0000.0000.0000.000
134A135SER 0-0.007-0.01146.1020.0000.0000.0000.0000.0000.000
135A136ASN 0-0.016-0.00544.6750.0020.0020.0000.0000.0000.000
136A137LEU 00.001-0.01242.9970.0000.0000.0000.0000.0000.000
137A138TYR 0-0.016-0.03239.6670.0010.0010.0000.0000.0000.000
138A139MET 00.010-0.00839.952-0.001-0.0010.0000.0000.0000.000
139A140ARG 10.9260.98633.1900.0460.0460.0000.0000.0000.000
140A141THR 0-0.004-0.00939.8030.0030.0030.0000.0000.0000.000
141A142GLU -1-0.936-0.97041.521-0.031-0.0310.0000.0000.0000.000
142A143ASP -1-0.972-0.96942.931-0.030-0.0300.0000.0000.0000.000
143A144GLY 0-0.021-0.00940.186-0.002-0.0020.0000.0000.0000.000
144A145TRP 0-0.061-0.06135.0840.0030.0030.0000.0000.0000.000
145A146GLN 0-0.003-0.00540.8780.0000.0000.0000.0000.0000.000
146A147LEU 0-0.0230.00344.0800.0010.0010.0000.0000.0000.000
147A148ALA 00.0140.01645.7390.0020.0020.0000.0000.0000.000
148A149LYS 10.9370.96347.2540.0250.0250.0000.0000.0000.000
149A150ALA 00.0240.01648.0250.0010.0010.0000.0000.0000.000
150A151GLY 0-0.043-0.02350.1490.0000.0000.0000.0000.0000.000
151A152ALA 00.0130.00952.7040.0000.0000.0000.0000.0000.000
152A153ASP -1-0.802-0.86554.987-0.012-0.0120.0000.0000.0000.000
153A154GLY 00.0670.01258.0490.0000.0000.0000.0000.0000.000
154A155THR 0-0.0320.03458.0970.0010.0010.0000.0000.0000.000
155A156GLY 00.029-0.01155.1830.0010.0010.0000.0000.0000.000
156A157LEU 0-0.0270.01149.030-0.001-0.0010.0000.0000.0000.000
157A158TYR 0-0.008-0.01751.8910.0000.0000.0000.0000.0000.000
158A159TYR 00.032-0.00347.565-0.001-0.0010.0000.0000.0000.000
159A160CYS 0-0.040-0.01650.9330.0010.0010.0000.0000.0000.000
160A161THR 00.0770.03848.600-0.001-0.0010.0000.0000.0000.000
161A162MET 0-0.020-0.02251.2570.0010.0010.0000.0000.0000.000
162A163ALA 00.0220.02250.9970.0000.0000.0000.0000.0000.000
163A164GLY 00.008-0.01053.1350.0010.0010.0000.0000.0000.000
164A165ALA 0-0.042-0.00256.1340.0000.0000.0000.0000.0000.000
165A166GLY 00.013-0.00157.1500.0010.0010.0000.0000.0000.000
166A167ARG 10.8670.93955.0600.0130.0130.0000.0000.0000.000
167A168ILE 00.0190.01450.2360.0010.0010.0000.0000.0000.000
168A169TYR 0-0.088-0.07951.547-0.001-0.0010.0000.0000.0000.000
169A170TYR 0-0.002-0.00247.3130.0000.0000.0000.0000.0000.000
170A171SER 0-0.0210.00149.1210.0010.0010.0000.0000.0000.000
171A172ARG 10.9870.99051.0310.0090.0090.0000.0000.0000.000
172A173PHE 00.0740.03253.0310.0010.0010.0000.0000.0000.000
173A174GLY 00.0460.02456.3790.0010.0010.0000.0000.0000.000
174A175ASP -1-0.859-0.95354.672-0.006-0.0060.0000.0000.0000.000
175A176GLU -1-0.907-0.94751.132-0.006-0.0060.0000.0000.0000.000
176A177ALA 00.0130.00854.8870.0010.0010.0000.0000.0000.000
177A178ALA 0-0.0350.02857.3820.0010.0010.0000.0000.0000.000
178A179ARG 10.8490.93948.4610.0060.0060.0000.0000.0000.000
179A180PHE 0-0.028-0.02050.2630.0010.0010.0000.0000.0000.000
180A181SER 0-0.076-0.05156.4190.0000.0000.0000.0000.0000.000
181A182THR 0-0.059-0.03760.1380.0000.0000.0000.0000.0000.000
182A183THR 0-0.066-0.07863.3510.0000.0000.0000.0000.0000.000
183A184GLY 0-0.0120.01162.7290.0000.0000.0000.0000.0000.000
184A185HIS 00.000-0.02863.012-0.001-0.0010.0000.0000.0000.000
185A186TYR 0-0.021-0.03359.9950.0000.0000.0000.0000.0000.000
186A187SER 0-0.052-0.01861.3300.0000.0000.0000.0000.0000.000
187A188VAL 00.010-0.00956.8330.0000.0000.0000.0000.0000.000
188A189ARG 10.9750.99758.2110.0080.0080.0000.0000.0000.000
189A190ASP -1-0.831-0.89955.021-0.015-0.0150.0000.0000.0000.000
190A191GLN 0-0.047-0.03555.466-0.001-0.0010.0000.0000.0000.000
191A192ASP -1-0.923-0.96458.018-0.012-0.0120.0000.0000.0000.000
192A193ARG 10.9230.96260.4060.0130.0130.0000.0000.0000.000
193A194VAL 00.0330.02560.7870.0000.0000.0000.0000.0000.000
194A195TYR 0-0.040-0.00959.3290.0000.0000.0000.0000.0000.000
195A196ALA 00.0470.00763.0080.0000.0000.0000.0000.0000.000
196A197GLY 0-0.0220.00163.1760.0000.0000.0000.0000.0000.000
197A198VAL 00.003-0.01064.1190.0000.0000.0000.0000.0000.000
198A199SER 0-0.0260.00660.9260.0000.0000.0000.0000.0000.000
199A200NME 0-0.0260.01262.9930.0000.0000.0000.0000.0000.000