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: 4JNVN

Calculation Name: 4ECB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ECB

Chain ID: A

ChEMBL ID:

UniProt ID: P08515

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptAll
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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2479705.748532
FMO2-HF: Nuclear repulsion 2396409.718262
FMO2-HF: Total energy -83296.03027
FMO2-MP2: Total energy -83535.141284


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-32.417-32.72219.483-9.678-9.499-0.051
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.058
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].
3A4ILE0-0.0170.0033.014-2.958-0.9730.194-0.936-1.243-0.004
4A5LEU0-0.021-0.0095.3651.1001.123-0.001-0.001-0.0210.000
5A6GLY00.0350.0188.672-0.139-0.1390.0000.0000.0000.000
6A7TYR00.014-0.01811.5650.2510.2510.0000.0000.0000.000
7A8TRP00.0440.02714.746-0.084-0.0840.0000.0000.0000.000
8A9LYS10.8010.90116.3310.6580.6580.0000.0000.0000.000
9A10ILE0-0.025-0.00917.3600.0620.0620.0000.0000.0000.000
10A11LYS10.8220.91817.8960.1910.1910.0000.0000.0000.000
11A12GLY0-0.007-0.00918.845-0.030-0.0300.0000.0000.0000.000
12A13LEU0-0.029-0.03219.5690.0330.0330.0000.0000.0000.000
13A14VAL0-0.005-0.00613.9090.0090.0090.0000.0000.0000.000
14A15GLN00.0670.05915.281-0.071-0.0710.0000.0000.0000.000
15A16PRO00.019-0.00116.6420.0250.0250.0000.0000.0000.000
16A17THR00.006-0.00112.2820.0860.0860.0000.0000.0000.000
17A18ARG10.8200.89211.4850.7320.7320.0000.0000.0000.000
18A19LEU0-0.032-0.00613.0190.0890.0890.0000.0000.0000.000
19A20LEU00.0140.00514.2420.0720.0720.0000.0000.0000.000
20A21LEU00.0160.0048.3630.1030.1030.0000.0000.0000.000
21A22GLU-1-0.776-0.85911.3580.0450.0450.0000.0000.0000.000
22A23TYR0-0.017-0.01513.0240.1040.1040.0000.0000.0000.000
23A24LEU0-0.028-0.01712.1030.0340.0340.0000.0000.0000.000
24A25GLU-1-0.901-0.94011.7930.6700.6700.0000.0000.0000.000
25A26GLU-1-0.859-0.9067.2451.4931.4930.0000.0000.0000.000
26A27LYS10.8370.9212.081-4.440-2.9763.495-2.017-2.9420.025
27A28TYR0-0.046-0.0453.3920.1500.8920.030-0.302-0.470-0.002
28A29GLU-1-0.896-0.9361.702-27.361-31.89015.766-6.418-4.819-0.070
29A30GLU-1-0.809-0.9084.531-0.774-0.764-0.001-0.004-0.0040.000
30A31HIS0-0.036-0.0136.9980.3330.3330.0000.0000.0000.000
31A32LEU0-0.004-0.00810.5010.2200.2200.0000.0000.0000.000
32A33TYR00.0520.03713.4650.0090.0090.0000.0000.0000.000
33A34GLU-1-0.777-0.89916.720-0.620-0.6200.0000.0000.0000.000
34A35ARG10.8330.90819.8400.3470.3470.0000.0000.0000.000
35A36ASP-1-0.969-0.97322.551-0.401-0.4010.0000.0000.0000.000
36A60LEU0-0.035-0.03115.5590.0160.0160.0000.0000.0000.000
37A61GLU-1-0.920-0.96617.386-0.500-0.5000.0000.0000.0000.000
38A62PHE0-0.054-0.00419.7700.0440.0440.0000.0000.0000.000
39A63PRO0-0.0130.00415.5920.0000.0000.0000.0000.0000.000
40A64ASN00.018-0.01118.5640.0440.0440.0000.0000.0000.000
41A65LEU0-0.0050.02515.469-0.100-0.1000.0000.0000.0000.000
42A66PRO0-0.043-0.02314.7510.0800.0800.0000.0000.0000.000
43A67TYR0-0.006-0.03010.0530.0500.0500.0000.0000.0000.000
44A68TYR0-0.043-0.0477.751-0.265-0.2650.0000.0000.0000.000
45A69ILE0-0.0090.0016.8630.4440.4440.0000.0000.0000.000
46A70ASP-1-0.690-0.7975.608-0.785-0.7850.0000.0000.0000.000
47A71GLY00.0160.0116.237-0.039-0.0390.0000.0000.0000.000
48A72ASP-1-0.834-0.9117.2670.5220.5220.0000.0000.0000.000
49A73VAL0-0.0210.00110.626-0.223-0.2230.0000.0000.0000.000
50A74LYS10.8040.8779.5050.1780.1780.0000.0000.0000.000
51A75LEU0-0.0220.00212.7910.1410.1410.0000.0000.0000.000
52A76THR00.013-0.00314.418-0.120-0.1200.0000.0000.0000.000
53A77GLN00.0430.02116.9260.0710.0710.0000.0000.0000.000
54A78SER00.0490.02416.9590.0040.0040.0000.0000.0000.000
55A79MET00.0280.01517.4690.0040.0040.0000.0000.0000.000
56A80ALA00.0030.00618.2810.0460.0460.0000.0000.0000.000
57A81ILE0-0.0110.00212.3740.0460.0460.0000.0000.0000.000
58A82ILE0-0.0040.00014.1960.0580.0580.0000.0000.0000.000
59A83ARG10.8810.92715.9980.0840.0840.0000.0000.0000.000
60A84TYR0-0.005-0.0349.9980.1090.1090.0000.0000.0000.000
61A85ILE00.0110.00610.3830.1050.1050.0000.0000.0000.000
62A86ALA00.0220.01212.8560.1350.1350.0000.0000.0000.000
63A87ASP-1-0.926-0.96216.1440.2890.2890.0000.0000.0000.000
64A88LYS10.8480.93510.054-0.820-0.8200.0000.0000.0000.000
65A89HIS10.7600.86210.243-0.645-0.6450.0000.0000.0000.000
66A90ASN0-0.037-0.02015.330-0.039-0.0390.0000.0000.0000.000
67A91MET0-0.029-0.00517.275-0.030-0.0300.0000.0000.0000.000
68A92LEU0-0.033-0.00419.395-0.040-0.0400.0000.0000.0000.000
69A93GLY00.0410.03121.818-0.027-0.0270.0000.0000.0000.000
70A94GLY00.0220.01725.0050.0100.0100.0000.0000.0000.000
71A95CYS0-0.049-0.01026.758-0.003-0.0030.0000.0000.0000.000
72A96PRO00.041-0.00229.166-0.005-0.0050.0000.0000.0000.000
73A97LYS10.9130.95230.697-0.064-0.0640.0000.0000.0000.000
74A98GLU-1-0.798-0.90827.5330.1280.1280.0000.0000.0000.000
75A99ARG10.8890.93824.733-0.146-0.1460.0000.0000.0000.000
76A100ALA0-0.0140.00227.333-0.014-0.0140.0000.0000.0000.000
77A101GLU-1-0.832-0.88930.0690.0290.0290.0000.0000.0000.000
78A102ILE00.0410.01223.700-0.012-0.0120.0000.0000.0000.000
79A103SER0-0.011-0.03725.774-0.009-0.0090.0000.0000.0000.000
80A104MET0-0.056-0.01127.386-0.016-0.0160.0000.0000.0000.000
81A105LEU0-0.027-0.01427.729-0.009-0.0090.0000.0000.0000.000
82A106GLU-1-0.778-0.85822.863-0.057-0.0570.0000.0000.0000.000
83A107GLY00.0000.00126.359-0.019-0.0190.0000.0000.0000.000
84A108ALA00.0540.03029.090-0.011-0.0110.0000.0000.0000.000
85A109VAL0-0.024-0.00925.600-0.006-0.0060.0000.0000.0000.000
86A110LEU0-0.036-0.02723.679-0.018-0.0180.0000.0000.0000.000
87A111ASP-1-0.883-0.93227.573-0.098-0.0980.0000.0000.0000.000
88A112ILE00.0010.00129.948-0.006-0.0060.0000.0000.0000.000
89A113ARG10.8150.89622.9410.2330.2330.0000.0000.0000.000
90A114TYR0-0.014-0.02024.212-0.016-0.0160.0000.0000.0000.000
91A115GLY00.0030.01329.155-0.003-0.0030.0000.0000.0000.000
92A116VAL00.0310.01429.618-0.001-0.0010.0000.0000.0000.000
93A117SER0-0.048-0.04227.243-0.013-0.0130.0000.0000.0000.000
94A118ARG10.9010.95429.5040.1190.1190.0000.0000.0000.000
95A119ILE00.0000.00432.5690.0020.0020.0000.0000.0000.000
96A120ALA0-0.0030.00830.4140.0010.0010.0000.0000.0000.000
97A121TYR00.0100.00025.929-0.015-0.0150.0000.0000.0000.000
98A122SER00.0050.01932.7670.0030.0030.0000.0000.0000.000
99A123LYS10.9680.98936.5970.1310.1310.0000.0000.0000.000
100A124ASP-1-0.901-0.95639.163-0.119-0.1190.0000.0000.0000.000
101A125PHE00.0250.00934.6770.0060.0060.0000.0000.0000.000
102A126GLU-1-0.793-0.89438.409-0.112-0.1120.0000.0000.0000.000
103A127THR00.0040.00240.9620.0070.0070.0000.0000.0000.000
104A128LEU0-0.017-0.01738.6750.0050.0050.0000.0000.0000.000
105A129LYS10.8400.90337.8100.1130.1130.0000.0000.0000.000
106A130VAL0-0.0070.00639.0330.0040.0040.0000.0000.0000.000
107A131ASP-1-0.858-0.90641.461-0.073-0.0730.0000.0000.0000.000
108A132PHE00.015-0.00233.0600.0030.0030.0000.0000.0000.000
109A133LEU00.034-0.00536.8120.0040.0040.0000.0000.0000.000
110A134SER0-0.065-0.02239.5370.0070.0070.0000.0000.0000.000
111A135LYS10.8410.90839.7210.0750.0750.0000.0000.0000.000
112A136LEU0-0.0170.00433.9260.0030.0030.0000.0000.0000.000
113A137PRO00.0130.00437.3220.0040.0040.0000.0000.0000.000
114A138GLU-1-0.853-0.93939.404-0.044-0.0440.0000.0000.0000.000
115A139MET0-0.072-0.02533.8280.0030.0030.0000.0000.0000.000
116A140LEU0-0.0040.00233.3510.0040.0040.0000.0000.0000.000
117A141LYS10.8860.91435.7340.0180.0180.0000.0000.0000.000
118A142MET0-0.0310.00732.5260.0110.0110.0000.0000.0000.000
119A143PHE00.0480.00030.0190.0100.0100.0000.0000.0000.000
120A144GLU-1-0.752-0.86734.1410.0010.0010.0000.0000.0000.000
121A145ASP-1-0.817-0.89136.6830.0030.0030.0000.0000.0000.000
122A146ARG10.7670.86031.180-0.024-0.0240.0000.0000.0000.000
123A147LEU00.0030.00130.6230.0090.0090.0000.0000.0000.000
124A148CYS0-0.108-0.03734.7650.0030.0030.0000.0000.0000.000
125A149HIS0-0.0120.00736.9150.0090.0090.0000.0000.0000.000
126A150LYS10.8760.94631.998-0.051-0.0510.0000.0000.0000.000
127A151THR0-0.0110.00329.470-0.011-0.0110.0000.0000.0000.000
128A152TYR00.0010.00326.000-0.012-0.0120.0000.0000.0000.000
129A153LEU00.007-0.00326.7890.0020.0020.0000.0000.0000.000
130A154ASN0-0.019-0.01926.967-0.017-0.0170.0000.0000.0000.000
131A155GLY0-0.010-0.00828.9010.0040.0040.0000.0000.0000.000
132A156ASP-1-0.884-0.93629.2490.1020.1020.0000.0000.0000.000
133A157HIS0-0.016-0.00523.9540.0190.0190.0000.0000.0000.000
134A158VAL0-0.0200.00421.339-0.018-0.0180.0000.0000.0000.000
135A159THR0-0.034-0.03221.4690.0220.0220.0000.0000.0000.000
136A160HIS00.034-0.01418.5660.0100.0100.0000.0000.0000.000
137A161PRO00.025-0.01020.308-0.033-0.0330.0000.0000.0000.000
138A162ASP-1-0.750-0.85123.0660.0340.0340.0000.0000.0000.000
139A163PHE00.0490.01218.766-0.016-0.0160.0000.0000.0000.000
140A164MET0-0.039-0.00521.042-0.028-0.0280.0000.0000.0000.000
141A165LEU00.0040.01022.621-0.015-0.0150.0000.0000.0000.000
142A166TYR0-0.066-0.06122.021-0.011-0.0110.0000.0000.0000.000
143A167ASP-1-0.803-0.90621.443-0.251-0.2510.0000.0000.0000.000
144A168ALA0-0.018-0.01023.544-0.007-0.0070.0000.0000.0000.000
145A169LEU0-0.003-0.01026.8120.0020.0020.0000.0000.0000.000
146A170ASP-1-0.800-0.89825.267-0.156-0.1560.0000.0000.0000.000
147A171VAL0-0.028-0.02125.338-0.003-0.0030.0000.0000.0000.000
148A172VAL00.001-0.00828.0010.0000.0000.0000.0000.0000.000
149A173LEU00.0050.01030.2840.0050.0050.0000.0000.0000.000
150A174TYR0-0.067-0.03926.3990.0000.0000.0000.0000.0000.000
151A175MET0-0.094-0.03332.3190.0000.0000.0000.0000.0000.000
152A176ASP-1-0.828-0.93334.692-0.071-0.0710.0000.0000.0000.000
153A177PRO0-0.022-0.01035.5070.0040.0040.0000.0000.0000.000
154A178MET0-0.0070.01136.5750.0040.0040.0000.0000.0000.000
155A179CYS0-0.070-0.01435.2760.0060.0060.0000.0000.0000.000
156A180LEU0-0.005-0.02632.1810.0050.0050.0000.0000.0000.000
157A181ASP-1-0.878-0.93836.880-0.039-0.0390.0000.0000.0000.000
158A182ALA0-0.071-0.03140.2090.0060.0060.0000.0000.0000.000
159A183PHE0-0.049-0.01836.9030.0050.0050.0000.0000.0000.000
160A184PRO00.0630.02936.7730.0000.0000.0000.0000.0000.000
161A185LYS10.8590.89735.397-0.012-0.0120.0000.0000.0000.000
162A186LEU00.0320.01731.7160.0040.0040.0000.0000.0000.000
163A187VAL0-0.0030.00732.070-0.002-0.0020.0000.0000.0000.000
164A188CYS0-0.086-0.04833.0730.0010.0010.0000.0000.0000.000
165A189PHE0-0.015-0.00426.2760.0080.0080.0000.0000.0000.000
166A190LYS10.8480.92026.5410.0990.0990.0000.0000.0000.000
167A191LYS10.9390.96726.9600.0230.0230.0000.0000.0000.000
168A192ARG10.8710.94127.765-0.038-0.0380.0000.0000.0000.000
169A193ILE00.0120.00422.2900.0180.0180.0000.0000.0000.000
170A194GLU-1-0.815-0.89223.123-0.050-0.0500.0000.0000.0000.000
171A195ALA0-0.033-0.01323.9230.0060.0060.0000.0000.0000.000
172A196ILE0-0.0280.01020.2830.0250.0250.0000.0000.0000.000
173A197PRO00.0180.00520.921-0.017-0.0170.0000.0000.0000.000
174A198GLN0-0.015-0.01916.218-0.056-0.0560.0000.0000.0000.000
175A199ILE0-0.016-0.00317.160-0.040-0.0400.0000.0000.0000.000
176A200ASP-1-0.789-0.87219.234-0.006-0.0060.0000.0000.0000.000
177A201LYS10.8580.91614.890-0.365-0.3650.0000.0000.0000.000
178A202TYR0-0.023-0.00313.651-0.023-0.0230.0000.0000.0000.000
179A203LEU0-0.0020.00516.847-0.061-0.0610.0000.0000.0000.000
180A204LYS10.7950.89220.031-0.025-0.0250.0000.0000.0000.000
181A205SER0-0.055-0.03115.554-0.022-0.0220.0000.0000.0000.000
182A206SER0-0.011-0.02515.172-0.013-0.0130.0000.0000.0000.000
183A207LYS10.8440.91410.3250.1810.1810.0000.0000.0000.000
184A208TYR00.0120.02114.184-0.042-0.0420.0000.0000.0000.000
185A209ILE00.0050.01414.7300.0080.0080.0000.0000.0000.000
186A210ALA00.007-0.00118.3860.0250.0250.0000.0000.0000.000
187A211TRP0-0.046-0.00421.9680.0360.0360.0000.0000.0000.000
188A212PRO00.0000.00622.017-0.032-0.0320.0000.0000.0000.000
189A213LEU00.003-0.00122.556-0.025-0.0250.0000.0000.0000.000
190A214GLN0-0.0120.01323.837-0.009-0.0090.0000.0000.0000.000
191A215GLY00.0500.02223.986-0.027-0.0270.0000.0000.0000.000
192A216TRP00.0440.00220.0510.0300.0300.0000.0000.0000.000
193A217GLN00.0100.01126.6460.0080.0080.0000.0000.0000.000
194A218ALA0-0.057-0.02028.7870.0160.0160.0000.0000.0000.000
195A219THR0-0.042-0.03930.623-0.002-0.0020.0000.0000.0000.000
196A220PHE00.0000.00830.4040.0070.0070.0000.0000.0000.000
197A221GLY00.0440.00628.665-0.010-0.0100.0000.0000.0000.000
198A222GLY00.0160.02327.040-0.025-0.0250.0000.0000.0000.000
199A223GLY00.017-0.00528.5250.0120.0120.0000.0000.0000.000
200A224ASP-1-0.839-0.92726.254-0.339-0.3390.0000.0000.0000.000
201A225HIS0-0.0250.00526.2920.0060.0060.0000.0000.0000.000