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: QV8GY

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 OptH
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 -2469683.204044
FMO2-HF: Nuclear repulsion 2386388.553044
FMO2-HF: Total energy -83294.651
FMO2-MP2: Total energy -83533.658078


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.
-17.303-10.8931.163-3.292-4.282-0.015
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 : -0.033 / q_NPA : -0.041
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].
3A4ILE0-0.0020.0183.286-1.3650.2900.041-0.798-0.898-0.002
4A5LEU0-0.012-0.0115.8411.0101.0100.0000.0000.0000.000
5A6GLY0-0.0020.0088.8810.0590.0590.0000.0000.0000.000
6A7TYR00.015-0.01111.8130.1850.1850.0000.0000.0000.000
7A8TRP00.0760.04315.046-0.050-0.0500.0000.0000.0000.000
8A9LYS10.9290.97716.5160.3410.3410.0000.0000.0000.000
9A10ILE0-0.012-0.00117.7510.0480.0480.0000.0000.0000.000
10A11LYS10.8000.90718.1050.0290.0290.0000.0000.0000.000
11A12GLY0-0.011-0.01118.895-0.030-0.0300.0000.0000.0000.000
12A13LEU0-0.032-0.04119.5590.0260.0260.0000.0000.0000.000
13A14VAL00.0040.01013.9380.0130.0130.0000.0000.0000.000
14A15GLN00.0830.06715.516-0.029-0.0290.0000.0000.0000.000
15A16PRO00.0170.00316.7450.0430.0430.0000.0000.0000.000
16A17THR00.000-0.00712.0980.0810.0810.0000.0000.0000.000
17A18ARG10.8520.92011.9990.3920.3920.0000.0000.0000.000
18A19LEU0-0.0180.00013.0890.1150.1150.0000.0000.0000.000
19A20LEU00.0040.00414.3260.0760.0760.0000.0000.0000.000
20A21LEU0-0.003-0.0128.1360.0860.0860.0000.0000.0000.000
21A22GLU-1-0.832-0.90710.8850.8450.8450.0000.0000.0000.000
22A23TYR0-0.040-0.02112.7520.0820.0820.0000.0000.0000.000
23A24LEU0-0.058-0.03712.4020.0090.0090.0000.0000.0000.000
24A25GLU-1-0.975-0.97811.4920.9220.9220.0000.0000.0000.000
25A26GLU-1-0.925-0.9567.0772.1042.1040.0000.0000.0000.000
26A27LYS10.9130.9523.107-7.089-5.6620.122-0.633-0.9160.005
27A28TYR0-0.099-0.0702.867-0.2190.3810.101-0.199-0.503-0.001
28A29GLU-1-0.960-0.9782.528-11.588-8.8620.900-1.659-1.966-0.017
29A30GLU-1-0.883-0.9704.677-0.753-0.751-0.001-0.0030.0010.000
30A31HIS00.0030.0358.2300.2550.2550.0000.0000.0000.000
31A32LEU00.001-0.00910.8880.1300.1300.0000.0000.0000.000
32A33TYR0-0.012-0.01813.8340.0690.0690.0000.0000.0000.000
33A34GLU-1-0.892-0.97117.265-0.342-0.3420.0000.0000.0000.000
34A35ARG10.8450.90720.2770.2000.2000.0000.0000.0000.000
35A36ASP-1-0.949-0.95022.828-0.278-0.2780.0000.0000.0000.000
36A60LEU0-0.029-0.03114.4720.0160.0160.0000.0000.0000.000
37A61GLU-1-0.920-0.96917.337-0.477-0.4770.0000.0000.0000.000
38A62PHE0-0.067-0.01420.4750.0340.0340.0000.0000.0000.000
39A63PRO00.0090.01916.5300.0160.0160.0000.0000.0000.000
40A64ASN0-0.026-0.03218.3710.0470.0470.0000.0000.0000.000
41A65LEU00.0010.03115.571-0.077-0.0770.0000.0000.0000.000
42A66PRO0-0.039-0.02214.5430.0820.0820.0000.0000.0000.000
43A67TYR0-0.018-0.04610.5020.2270.2270.0000.0000.0000.000
44A68TYR00.012-0.0037.537-0.221-0.2210.0000.0000.0000.000
45A69ILE0-0.0180.0006.4780.5150.5150.0000.0000.0000.000
46A70ASP-1-0.800-0.9035.158-1.875-1.8750.0000.0000.0000.000
47A71GLY0-0.044-0.0176.1760.1040.1040.0000.0000.0000.000
48A72ASP-1-0.938-0.9797.2790.1440.1440.0000.0000.0000.000
49A73VAL0-0.0270.01510.419-0.120-0.1200.0000.0000.0000.000
50A74LYS10.9700.9709.7070.9290.9290.0000.0000.0000.000
51A75LEU0-0.059-0.02312.2440.1730.1730.0000.0000.0000.000
52A76THR00.0500.01814.334-0.095-0.0950.0000.0000.0000.000
53A77GLN00.0240.00917.1410.0760.0760.0000.0000.0000.000
54A78SER00.0390.00817.130-0.010-0.0100.0000.0000.0000.000
55A79MET00.0440.02717.6830.0110.0110.0000.0000.0000.000
56A80ALA00.0120.00818.2410.0390.0390.0000.0000.0000.000
57A81ILE0-0.023-0.00212.4670.0300.0300.0000.0000.0000.000
58A82ILE00.0090.01114.1000.0390.0390.0000.0000.0000.000
59A83ARG10.8930.92716.0390.0950.0950.0000.0000.0000.000
60A84TYR00.0170.0209.8880.1010.1010.0000.0000.0000.000
61A85ILE00.0220.01310.3890.0970.0970.0000.0000.0000.000
62A86ALA00.022-0.00512.8350.1280.1280.0000.0000.0000.000
63A87ASP-1-0.945-0.98016.1110.1640.1640.0000.0000.0000.000
64A88LYS10.9170.96910.282-0.485-0.4850.0000.0000.0000.000
65A89HIS10.8380.93010.414-0.672-0.6720.0000.0000.0000.000
66A90ASN0-0.034-0.01015.424-0.030-0.0300.0000.0000.0000.000
67A91MET0-0.021-0.00717.622-0.006-0.0060.0000.0000.0000.000
68A92LEU0-0.0240.00019.371-0.028-0.0280.0000.0000.0000.000
69A93GLY00.0450.01721.901-0.024-0.0240.0000.0000.0000.000
70A94GLY00.0130.00024.9780.0000.0000.0000.0000.0000.000
71A95CYS0-0.074-0.03326.789-0.006-0.0060.0000.0000.0000.000
72A96PRO00.0330.00129.053-0.003-0.0030.0000.0000.0000.000
73A97LYS10.9950.99730.690-0.062-0.0620.0000.0000.0000.000
74A98GLU-1-0.792-0.89527.4790.1270.1270.0000.0000.0000.000
75A99ARG10.9090.95624.591-0.092-0.0920.0000.0000.0000.000
76A100ALA0-0.018-0.00327.304-0.011-0.0110.0000.0000.0000.000
77A101GLU-1-0.901-0.95030.0120.0410.0410.0000.0000.0000.000
78A102ILE00.0290.01123.740-0.007-0.0070.0000.0000.0000.000
79A103SER0-0.017-0.01926.376-0.014-0.0140.0000.0000.0000.000
80A104MET0-0.0310.00027.317-0.015-0.0150.0000.0000.0000.000
81A105LEU0-0.019-0.01127.857-0.006-0.0060.0000.0000.0000.000
82A106GLU-1-0.784-0.86323.108-0.041-0.0410.0000.0000.0000.000
83A107GLY0-0.016-0.00426.474-0.014-0.0140.0000.0000.0000.000
84A108ALA00.0440.02029.175-0.007-0.0070.0000.0000.0000.000
85A109VAL0-0.032-0.01425.679-0.002-0.0020.0000.0000.0000.000
86A110LEU0-0.035-0.02823.868-0.011-0.0110.0000.0000.0000.000
87A111ASP-1-0.883-0.92727.838-0.063-0.0630.0000.0000.0000.000
88A112ILE0-0.0020.00030.071-0.004-0.0040.0000.0000.0000.000
89A113ARG10.8470.93123.9150.1160.1160.0000.0000.0000.000
90A114TYR0-0.017-0.04123.727-0.013-0.0130.0000.0000.0000.000
91A115GLY0-0.0030.01229.141-0.005-0.0050.0000.0000.0000.000
92A116VAL00.0030.00529.484-0.002-0.0020.0000.0000.0000.000
93A117SER00.000-0.01026.445-0.004-0.0040.0000.0000.0000.000
94A118ARG10.9060.96429.5880.0840.0840.0000.0000.0000.000
95A119ILE00.0170.01232.586-0.001-0.0010.0000.0000.0000.000
96A120ALA00.0000.01330.6400.0020.0020.0000.0000.0000.000
97A121TYR00.0170.01026.444-0.008-0.0080.0000.0000.0000.000
98A122SER00.0000.01833.237-0.002-0.0020.0000.0000.0000.000
99A123LYS10.9900.97237.0620.0910.0910.0000.0000.0000.000
100A124ASP-1-0.908-0.94539.767-0.074-0.0740.0000.0000.0000.000
101A125PHE00.005-0.00435.2500.0040.0040.0000.0000.0000.000
102A126GLU-1-0.891-0.95938.752-0.057-0.0570.0000.0000.0000.000
103A127THR00.0000.00941.3080.0060.0060.0000.0000.0000.000
104A128LEU0-0.008-0.01438.8190.0030.0030.0000.0000.0000.000
105A129LYS10.9470.97537.9370.0510.0510.0000.0000.0000.000
106A130VAL0-0.0070.01439.2890.0050.0050.0000.0000.0000.000
107A131ASP-1-0.920-0.95741.615-0.044-0.0440.0000.0000.0000.000
108A132PHE0-0.058-0.04333.1100.0030.0030.0000.0000.0000.000
109A133LEU00.018-0.02036.8490.0030.0030.0000.0000.0000.000
110A134SER0-0.046-0.00839.6080.0050.0050.0000.0000.0000.000
111A135LYS10.9630.98339.5420.0440.0440.0000.0000.0000.000
112A136LEU00.0060.01834.0120.0030.0030.0000.0000.0000.000
113A137PRO00.0310.01237.5060.0050.0050.0000.0000.0000.000
114A138GLU-1-0.908-0.96139.572-0.010-0.0100.0000.0000.0000.000
115A139MET0-0.072-0.02634.4030.0020.0020.0000.0000.0000.000
116A140LEU0-0.010-0.00633.3760.0050.0050.0000.0000.0000.000
117A141LYS10.9410.97235.845-0.010-0.0100.0000.0000.0000.000
118A142MET0-0.0040.02432.5980.0090.0090.0000.0000.0000.000
119A143PHE00.031-0.01230.1570.0080.0080.0000.0000.0000.000
120A144GLU-1-0.758-0.89234.1730.0470.0470.0000.0000.0000.000
121A145ASP-1-0.876-0.94936.6370.0320.0320.0000.0000.0000.000
122A146ARG10.7680.87331.536-0.051-0.0510.0000.0000.0000.000
123A147LEU0-0.003-0.01330.7100.0080.0080.0000.0000.0000.000
124A148CYS0-0.140-0.06134.8110.0050.0050.0000.0000.0000.000
125A149HIS0-0.027-0.01037.3210.0070.0070.0000.0000.0000.000
126A150LYS10.9030.96732.385-0.079-0.0790.0000.0000.0000.000
127A151THR00.0030.01429.968-0.008-0.0080.0000.0000.0000.000
128A152TYR00.008-0.00426.002-0.004-0.0040.0000.0000.0000.000
129A153LEU00.0200.01026.845-0.006-0.0060.0000.0000.0000.000
130A154ASN0-0.018-0.00626.774-0.023-0.0230.0000.0000.0000.000
131A155GLY0-0.049-0.01929.0410.0040.0040.0000.0000.0000.000
132A156ASP-1-0.881-0.94629.5460.1440.1440.0000.0000.0000.000
133A157HIS0-0.032-0.01724.0670.0160.0160.0000.0000.0000.000
134A158VAL0-0.0100.00420.969-0.019-0.0190.0000.0000.0000.000
135A159THR0-0.038-0.01921.5240.0080.0080.0000.0000.0000.000
136A160HIS00.028-0.03218.8250.0190.0190.0000.0000.0000.000
137A161PRO00.029-0.00320.488-0.019-0.0190.0000.0000.0000.000
138A162ASP-1-0.719-0.85322.9860.1040.1040.0000.0000.0000.000
139A163PHE00.0320.00118.684-0.006-0.0060.0000.0000.0000.000
140A164MET0-0.0290.00121.227-0.020-0.0200.0000.0000.0000.000
141A165LEU0-0.0040.01122.726-0.013-0.0130.0000.0000.0000.000
142A166TYR0-0.071-0.06322.165-0.007-0.0070.0000.0000.0000.000
143A167ASP-1-0.854-0.94221.528-0.100-0.1000.0000.0000.0000.000
144A168ALA00.004-0.00123.638-0.011-0.0110.0000.0000.0000.000
145A169LEU0-0.027-0.02026.956-0.003-0.0030.0000.0000.0000.000
146A170ASP-1-0.863-0.91724.705-0.031-0.0310.0000.0000.0000.000
147A171VAL0-0.016-0.00725.521-0.007-0.0070.0000.0000.0000.000
148A172VAL00.005-0.01428.152-0.003-0.0030.0000.0000.0000.000
149A173LEU0-0.009-0.00530.4820.0020.0020.0000.0000.0000.000
150A174TYR0-0.005-0.00426.955-0.001-0.0010.0000.0000.0000.000
151A175MET0-0.095-0.03132.201-0.003-0.0030.0000.0000.0000.000
152A176ASP-1-0.864-0.94734.609-0.019-0.0190.0000.0000.0000.000
153A177PRO0-0.023-0.00135.4310.0050.0050.0000.0000.0000.000
154A178MET00.0360.01936.4880.0050.0050.0000.0000.0000.000
155A179CYS0-0.072-0.01535.1360.0040.0040.0000.0000.0000.000
156A180LEU0-0.010-0.02732.2400.0030.0030.0000.0000.0000.000
157A181ASP-1-0.898-0.93837.0250.0160.0160.0000.0000.0000.000
158A182ALA0-0.083-0.04240.2830.0040.0040.0000.0000.0000.000
159A183PHE0-0.036-0.01736.9950.0010.0010.0000.0000.0000.000
160A184PRO00.0490.02636.7890.0040.0040.0000.0000.0000.000
161A185LYS10.9270.95135.689-0.053-0.0530.0000.0000.0000.000
162A186LEU00.0430.02831.8080.0090.0090.0000.0000.0000.000
163A187VAL0-0.029-0.00231.9410.0060.0060.0000.0000.0000.000
164A188CYS0-0.089-0.05432.3660.0080.0080.0000.0000.0000.000
165A189PHE0-0.030-0.01626.0160.0130.0130.0000.0000.0000.000
166A190LYS10.8990.95427.336-0.024-0.0240.0000.0000.0000.000
167A191LYS10.9670.98127.157-0.054-0.0540.0000.0000.0000.000
168A192ARG10.9010.96727.406-0.102-0.1020.0000.0000.0000.000
169A193ILE00.0040.00522.2900.0220.0220.0000.0000.0000.000
170A194GLU-1-0.833-0.90023.0470.0920.0920.0000.0000.0000.000
171A195ALA0-0.021-0.00324.0240.0130.0130.0000.0000.0000.000
172A196ILE0-0.0330.00320.0700.0200.0200.0000.0000.0000.000
173A197PRO00.0270.01520.5110.0020.0020.0000.0000.0000.000
174A198GLN00.002-0.00815.866-0.070-0.0700.0000.0000.0000.000
175A199ILE0-0.016-0.00417.0800.0010.0010.0000.0000.0000.000
176A200ASP-1-0.817-0.90118.9850.1820.1820.0000.0000.0000.000
177A201LYS10.9500.97314.887-0.658-0.6580.0000.0000.0000.000
178A202TYR0-0.018-0.01212.948-0.025-0.0250.0000.0000.0000.000
179A203LEU0-0.0010.00616.732-0.048-0.0480.0000.0000.0000.000
180A204LYS10.8420.92319.845-0.198-0.1980.0000.0000.0000.000
181A205SER0-0.090-0.03315.7180.0020.0020.0000.0000.0000.000
182A206SER0-0.002-0.01715.564-0.017-0.0170.0000.0000.0000.000
183A207LYS10.9270.95010.072-0.528-0.5280.0000.0000.0000.000
184A208TYR00.0070.03714.299-0.071-0.0710.0000.0000.0000.000
185A209ILE00.0090.01115.125-0.021-0.0210.0000.0000.0000.000
186A210ALA00.006-0.00418.6200.0080.0080.0000.0000.0000.000
187A211TRP0-0.026-0.00222.1960.0140.0140.0000.0000.0000.000
188A212PRO00.0100.01422.337-0.012-0.0120.0000.0000.0000.000
189A213LEU0-0.002-0.01222.858-0.013-0.0130.0000.0000.0000.000
190A214GLN0-0.049-0.03023.888-0.004-0.0040.0000.0000.0000.000
191A215GLY00.0580.02124.407-0.014-0.0140.0000.0000.0000.000
192A216TRP00.0400.00720.6800.0220.0220.0000.0000.0000.000
193A217GLN00.0170.00627.0960.0140.0140.0000.0000.0000.000
194A218ALA0-0.061-0.01529.1930.0100.0100.0000.0000.0000.000
195A219THR0-0.029-0.01530.9670.0010.0010.0000.0000.0000.000
196A220PHE0-0.0100.00230.2460.0060.0060.0000.0000.0000.000
197A221GLY00.0410.00328.905-0.009-0.0090.0000.0000.0000.000
198A222GLY00.0070.02427.387-0.016-0.0160.0000.0000.0000.000
199A223GLY0-0.004-0.02228.9730.0120.0120.0000.0000.0000.000
200A224ASP-1-0.869-0.94327.028-0.183-0.1830.0000.0000.0000.000
201A225HIS0-0.0140.00726.7760.0020.0020.0000.0000.0000.000