FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YV352

Calculation Name: 3EQ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EQ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I045

Base Structure: X-ray

Registration Date: 2023-09-24

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 387
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5131055.630086
FMO2-HF: Nuclear repulsion 4982568.193446
FMO2-HF: Total energy -148487.436639
FMO2-MP2: Total energy -148923.90209


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:4:VAL)


Summations of interaction energy for fragment #1(A:4:VAL)
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.
0.0119999999999993.5670.305-1.823-2.037-0.003
Interaction energy analysis for fragmet #1(A:4:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.036
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].
3A6ALA0-0.0020.0053.8690.0121.650-0.021-0.837-0.7810.001
4A7THR0-0.043-0.0306.9190.4070.4070.0000.0000.0000.000
5A8LEU0-0.016-0.0198.078-0.209-0.2090.0000.0000.0000.000
6A9LEU0-0.0120.00511.4450.0850.0850.0000.0000.0000.000
7A10ILE0-0.025-0.01314.569-0.055-0.0550.0000.0000.0000.000
8A11ILE00.008-0.00717.0230.0020.0020.0000.0000.0000.000
9A12ASP-1-0.798-0.90620.6760.1320.1320.0000.0000.0000.000
10A13ASP-1-0.792-0.88322.9450.1290.1290.0000.0000.0000.000
11A14ASP-1-0.796-0.86525.1420.1180.1180.0000.0000.0000.000
12A15GLU-1-0.843-0.91323.6140.2100.2100.0000.0000.0000.000
13A16VAL0-0.017-0.01222.4160.0190.0190.0000.0000.0000.000
14A17VAL00.002-0.00122.0870.0110.0110.0000.0000.0000.000
15A18ARG10.7910.87518.710-0.228-0.2280.0000.0000.0000.000
16A19GLU-1-0.854-0.91317.9810.3790.3790.0000.0000.0000.000
17A20SER0-0.068-0.03117.1570.0450.0450.0000.0000.0000.000
18A21LEU00.013-0.01316.7800.0220.0220.0000.0000.0000.000
19A22ALA0-0.0110.00013.9450.0520.0520.0000.0000.0000.000
20A23ALA0-0.0030.00012.3450.1400.1400.0000.0000.0000.000
21A24TYR0-0.009-0.00712.0580.0710.0710.0000.0000.0000.000
22A25LEU0-0.001-0.00210.9590.0090.0090.0000.0000.0000.000
23A26GLU-1-0.788-0.8737.4971.8991.8990.0000.0000.0000.000
24A27ASP-1-0.950-0.9607.0390.9490.9490.0000.0000.0000.000
25A28SER0-0.069-0.0577.708-0.096-0.0960.0000.0000.0000.000
26A29ASN0-0.131-0.0752.861-3.926-2.1290.317-0.909-1.204-0.004
27A30PHE0-0.051-0.0194.1381.9442.0640.009-0.077-0.0520.000
28A31LYS10.8180.8964.823-1.499-1.4990.0000.0000.0000.000
29A32VAL00.0080.0296.553-0.549-0.5490.0000.0000.0000.000
30A33LEU00.0130.01310.3830.0270.0270.0000.0000.0000.000
31A34GLN00.016-0.00213.122-0.091-0.0910.0000.0000.0000.000
32A35ALA0-0.032-0.01416.680-0.014-0.0140.0000.0000.0000.000
33A36LEU0-0.0060.00420.148-0.006-0.0060.0000.0000.0000.000
34A37ASN0-0.037-0.03123.424-0.010-0.0100.0000.0000.0000.000
35A38GLY00.0410.00223.8930.0110.0110.0000.0000.0000.000
36A39LEU00.0250.01323.9750.0080.0080.0000.0000.0000.000
37A40GLN00.0060.00520.782-0.006-0.0060.0000.0000.0000.000
38A41GLY00.0450.01919.8030.0150.0150.0000.0000.0000.000
39A42LEU0-0.004-0.00619.9970.0030.0030.0000.0000.0000.000
40A43GLN0-0.075-0.04221.885-0.002-0.0020.0000.0000.0000.000
41A44ILE00.0040.00516.077-0.003-0.0030.0000.0000.0000.000
42A45PHE0-0.001-0.00116.6970.0070.0070.0000.0000.0000.000
43A46GLU-1-0.863-0.91118.7520.0790.0790.0000.0000.0000.000
44A47SER0-0.087-0.06517.739-0.016-0.0160.0000.0000.0000.000
45A48GLU-1-0.905-0.92513.4260.2890.2890.0000.0000.0000.000
46A49GLN0-0.052-0.04114.616-0.008-0.0080.0000.0000.0000.000
47A50PRO0-0.027-0.01211.813-0.019-0.0190.0000.0000.0000.000
48A51ASP-1-0.845-0.9179.186-0.067-0.0670.0000.0000.0000.000
49A52LEU0-0.056-0.03712.475-0.049-0.0490.0000.0000.0000.000
50A53VAL00.0130.02014.3060.0580.0580.0000.0000.0000.000
51A54ILE00.0090.00214.817-0.034-0.0340.0000.0000.0000.000
52A55CYS0-0.028-0.00918.5570.0130.0130.0000.0000.0000.000
53A56ASP-1-0.728-0.84921.8800.0920.0920.0000.0000.0000.000
54A57LEU0-0.031-0.00925.1740.0010.0010.0000.0000.0000.000
55A58ARG10.8030.85927.845-0.118-0.1180.0000.0000.0000.000
56A59MET0-0.0030.02030.5530.0020.0020.0000.0000.0000.000
57A60PRO0-0.018-0.03933.3390.0000.0000.0000.0000.0000.000
58A61GLN0-0.027-0.01828.800-0.004-0.0040.0000.0000.0000.000
59A62ILE0-0.0160.01225.0510.0080.0080.0000.0000.0000.000
60A63ASP-1-0.806-0.92327.0310.1030.1030.0000.0000.0000.000
61A64GLY00.0160.00827.100-0.008-0.0080.0000.0000.0000.000
62A65LEU0-0.003-0.00827.5270.0000.0000.0000.0000.0000.000
63A66GLU-1-0.923-0.96829.6730.0570.0570.0000.0000.0000.000
64A67LEU0-0.0150.00722.044-0.003-0.0030.0000.0000.0000.000
65A68ILE00.0130.00124.8450.0000.0000.0000.0000.0000.000
66A69ARG10.9250.97125.891-0.050-0.0500.0000.0000.0000.000
67A70ARG10.8260.91226.474-0.083-0.0830.0000.0000.0000.000
68A71ILE00.0050.01221.077-0.004-0.0040.0000.0000.0000.000
69A72ARG10.7780.88121.574-0.042-0.0420.0000.0000.0000.000
70A73GLN0-0.059-0.04426.361-0.006-0.0060.0000.0000.0000.000
71A74THR0-0.056-0.01123.885-0.003-0.0030.0000.0000.0000.000
72A75ALA0-0.025-0.01424.8740.0010.0010.0000.0000.0000.000
73A76SER0-0.0180.00320.462-0.005-0.0050.0000.0000.0000.000
74A77GLU-1-0.885-0.94620.8180.0280.0280.0000.0000.0000.000
75A78THR00.0020.02415.875-0.019-0.0190.0000.0000.0000.000
76A79PRO0-0.002-0.01116.4160.0070.0070.0000.0000.0000.000
77A80ILE00.0450.02818.0440.0210.0210.0000.0000.0000.000
78A81ILE0-0.017-0.00117.797-0.019-0.0190.0000.0000.0000.000
79A82VAL00.000-0.00921.0460.0170.0170.0000.0000.0000.000
80A83LEU00.010-0.00921.048-0.011-0.0110.0000.0000.0000.000
81A84SER0-0.029-0.02024.903-0.007-0.0070.0000.0000.0000.000
82A85GLY00.0470.03027.991-0.008-0.0080.0000.0000.0000.000
83A86ALA0-0.078-0.05129.6350.0010.0010.0000.0000.0000.000
84A87GLY00.0240.01731.571-0.005-0.0050.0000.0000.0000.000
85A88VAL0-0.020-0.00632.364-0.006-0.0060.0000.0000.0000.000
86A89MET00.027-0.00332.6680.0000.0000.0000.0000.0000.000
87A90SER0-0.040-0.02734.558-0.003-0.0030.0000.0000.0000.000
88A91ASP-1-0.851-0.91731.9000.0490.0490.0000.0000.0000.000
89A92ALA00.0190.02229.7520.0020.0020.0000.0000.0000.000
90A93VAL0-0.039-0.02530.411-0.003-0.0030.0000.0000.0000.000
91A94GLU-1-0.825-0.89532.6400.0290.0290.0000.0000.0000.000
92A95ALA00.0110.00727.128-0.001-0.0010.0000.0000.0000.000
93A96LEU00.0130.00027.370-0.002-0.0020.0000.0000.0000.000
94A97ARG10.8020.89529.103-0.028-0.0280.0000.0000.0000.000
95A98LEU0-0.070-0.03629.056-0.003-0.0030.0000.0000.0000.000
96A99GLY00.0200.01926.7640.0020.0020.0000.0000.0000.000
97A100ALA0-0.028-0.01023.8150.0030.0030.0000.0000.0000.000
98A101ALA0-0.089-0.04320.864-0.010-0.0100.0000.0000.0000.000
99A102ASP-1-0.905-0.96222.6000.0030.0030.0000.0000.0000.000
100A103TYR0-0.067-0.04323.8410.0130.0130.0000.0000.0000.000
101A104LEU00.0050.01021.074-0.006-0.0060.0000.0000.0000.000
102A105ILE0-0.026-0.00125.6520.0000.0000.0000.0000.0000.000
103A106LYS10.7610.85924.889-0.122-0.1220.0000.0000.0000.000
104A107PRO0-0.010-0.01227.182-0.005-0.0050.0000.0000.0000.000
105A108LEU0-0.029-0.03121.339-0.009-0.0090.0000.0000.0000.000
106A109GLU-1-0.909-0.95223.9970.0890.0890.0000.0000.0000.000
107A110ASP-1-0.893-0.94021.4140.0440.0440.0000.0000.0000.000
108A111LEU00.0340.01017.799-0.001-0.0010.0000.0000.0000.000
109A112ALA0-0.002-0.00917.4860.0140.0140.0000.0000.0000.000
110A113VAL0-0.019-0.01418.565-0.016-0.0160.0000.0000.0000.000
111A114LEU00.0170.02416.589-0.014-0.0140.0000.0000.0000.000
112A115GLU-1-0.717-0.81112.3470.1780.1780.0000.0000.0000.000
113A116HIS00.0060.01515.258-0.037-0.0370.0000.0000.0000.000
114A117SER0-0.021-0.02217.853-0.017-0.0170.0000.0000.0000.000
115A118VAL00.0510.01712.759-0.019-0.0190.0000.0000.0000.000
116A119ARG10.8440.90610.2060.0750.0750.0000.0000.0000.000
117A120ARG10.8940.94014.9690.0220.0220.0000.0000.0000.000
118A121ALA0-0.032-0.01716.778-0.012-0.0120.0000.0000.0000.000
119A122LEU00.0390.03110.798-0.013-0.0130.0000.0000.0000.000
120A123ASP-1-0.885-0.94514.367-0.263-0.2630.0000.0000.0000.000
121A124ARG10.8620.92215.6900.0670.0670.0000.0000.0000.000
122A125ALA00.0130.01715.6420.0220.0220.0000.0000.0000.000
123A126TYR00.005-0.03111.836-0.018-0.0180.0000.0000.0000.000
124A127LEU00.0150.01014.5910.0040.0040.0000.0000.0000.000
125A128ARG10.8700.92317.6710.0660.0660.0000.0000.0000.000
126A129VAL00.0210.02214.8740.0110.0110.0000.0000.0000.000
127A130GLU-1-0.743-0.84413.482-0.238-0.2380.0000.0000.0000.000
128A131ASN0-0.020-0.00417.4440.0090.0090.0000.0000.0000.000
129A132GLN00.0020.00020.9930.0120.0120.0000.0000.0000.000
130A133ARG10.8640.91114.1070.1850.1850.0000.0000.0000.000
131A134TYR00.000-0.00117.3160.0040.0040.0000.0000.0000.000
132A135ARG10.8720.93622.4710.0680.0680.0000.0000.0000.000
133A136ASP-1-0.878-0.93922.377-0.074-0.0740.0000.0000.0000.000
134A137LYN00.0470.03019.361-0.001-0.0010.0000.0000.0000.000
135A138LEU0-0.0140.00324.0410.0030.0030.0000.0000.0000.000
136A139GLU-1-0.853-0.91426.858-0.043-0.0430.0000.0000.0000.000
137A140ALA0-0.018-0.00326.2570.0050.0050.0000.0000.0000.000
138A141ALA00.0510.02226.7870.0040.0040.0000.0000.0000.000
139A142ASN0-0.035-0.03128.7020.0050.0050.0000.0000.0000.000
140A143ARG10.7940.88730.7710.0510.0510.0000.0000.0000.000
141A144GLU-1-0.940-0.96528.610-0.061-0.0610.0000.0000.0000.000
142A145LEU0-0.0060.00932.4860.0020.0020.0000.0000.0000.000
143A146GLN00.013-0.00134.1510.0010.0010.0000.0000.0000.000
144A147ALA0-0.0100.00335.9510.0030.0030.0000.0000.0000.000
145A148SER0-0.060-0.04335.9450.0020.0020.0000.0000.0000.000
146A149LEU00.0160.00237.8760.0020.0020.0000.0000.0000.000
147A150ASN00.0030.00140.2200.0010.0010.0000.0000.0000.000
148A151LEU0-0.022-0.00139.6910.0020.0020.0000.0000.0000.000
149A152LEU00.0220.00240.0490.0010.0010.0000.0000.0000.000
150A153GLN00.0260.02343.5850.0000.0000.0000.0000.0000.000
151A154GLU-1-0.890-0.93545.986-0.024-0.0240.0000.0000.0000.000
152A155ASP-1-0.903-0.95245.673-0.032-0.0320.0000.0000.0000.000
153A156GLN0-0.013-0.02046.1960.0010.0010.0000.0000.0000.000
154A157ASN0-0.041-0.02849.6540.0010.0010.0000.0000.0000.000
155A158ALA0-0.030-0.01250.5870.0010.0010.0000.0000.0000.000
156A159GLY00.0210.00151.4260.0010.0010.0000.0000.0000.000
157A160ARG10.8110.89952.8570.0270.0270.0000.0000.0000.000
158A161GLN0-0.018-0.00155.4080.0020.0020.0000.0000.0000.000
159A162VAL0-0.019-0.02154.9290.0010.0010.0000.0000.0000.000
160A163GLN0-0.009-0.01756.7290.0010.0010.0000.0000.0000.000
161A164MET00.0330.01058.5900.0010.0010.0000.0000.0000.000
162A165ASN0-0.061-0.04060.5300.0010.0010.0000.0000.0000.000
163A166MET0-0.063-0.00258.5760.0010.0010.0000.0000.0000.000
164A167LEU0-0.0120.01363.3220.0000.0000.0000.0000.0000.000
165A168PRO0-0.0360.00365.8390.0010.0010.0000.0000.0000.000
166A169VAL0-0.034-0.01969.5080.0000.0000.0000.0000.0000.000
167A170THR0-0.0110.01671.0820.0000.0000.0000.0000.0000.000
168A171PRO0-0.0040.00373.0670.0000.0000.0000.0000.0000.000
169A172TRP0-0.026-0.02075.2010.0000.0000.0000.0000.0000.000
170A173SER00.004-0.00576.9190.0000.0000.0000.0000.0000.000
171A174ILE0-0.027-0.00879.7360.0000.0000.0000.0000.0000.000
172A175GLU-1-0.834-0.89082.005-0.012-0.0120.0000.0000.0000.000
173A176GLY00.0110.01184.5200.0000.0000.0000.0000.0000.000
174A177LEU0-0.0260.00380.5530.0000.0000.0000.0000.0000.000
175A178GLU-1-0.922-0.97977.801-0.014-0.0140.0000.0000.0000.000
176A179PHE00.0110.00874.2970.0000.0000.0000.0000.0000.000
177A180SER00.0290.01173.5280.0000.0000.0000.0000.0000.000
178A181HIS00.0690.04267.6940.0000.0000.0000.0000.0000.000
179A182ARG10.8450.90967.3650.0180.0180.0000.0000.0000.000
180A183ILE00.0340.02761.0000.0000.0000.0000.0000.0000.000
181A184ILE0-0.071-0.03561.9140.0010.0010.0000.0000.0000.000
182A185PRO0-0.010-0.00858.323-0.001-0.0010.0000.0000.0000.000
183A186SER00.032-0.00455.4890.0000.0000.0000.0000.0000.000
184A187LEU00.0210.04750.599-0.001-0.0010.0000.0000.0000.000
185A188TYR0-0.061-0.03545.8710.0000.0000.0000.0000.0000.000
186A189LEU0-0.076-0.02250.1570.0010.0010.0000.0000.0000.000
187A190SER00.0350.03852.462-0.001-0.0010.0000.0000.0000.000
188A191GLY00.0320.00255.0700.0000.0000.0000.0000.0000.000
189A192ASP-1-0.863-0.93055.620-0.025-0.0250.0000.0000.0000.000
190A193PHE0-0.026-0.02259.3320.0000.0000.0000.0000.0000.000
191A194VAL0-0.003-0.00161.8510.0000.0000.0000.0000.0000.000
192A195ASP-1-0.739-0.85965.674-0.018-0.0180.0000.0000.0000.000
193A196TYR00.006-0.02967.8950.0000.0000.0000.0000.0000.000
194A197PHE0-0.045-0.00368.0910.0000.0000.0000.0000.0000.000
195A198ARG10.8150.88173.2980.0120.0120.0000.0000.0000.000
196A199VAL00.0100.00474.7210.0000.0000.0000.0000.0000.000
197A200ASP-1-0.827-0.91177.353-0.013-0.0130.0000.0000.0000.000
198A201GLU-1-0.855-0.89780.313-0.012-0.0120.0000.0000.0000.000
199A202ARG10.7400.83082.1080.0120.0120.0000.0000.0000.000
200A203ARG10.7850.87178.8080.0130.0130.0000.0000.0000.000
201A204VAL00.009-0.00376.3220.0000.0000.0000.0000.0000.000
202A205ALA00.0020.01272.5990.0000.0000.0000.0000.0000.000
203A206PHE0-0.016-0.02171.4690.0000.0000.0000.0000.0000.000
204A207TYR0-0.031-0.04364.0070.0000.0000.0000.0000.0000.000
205A208LEU00.0010.01264.3270.0000.0000.0000.0000.0000.000
206A209ALA0-0.044-0.03161.4820.0000.0000.0000.0000.0000.000
207A210ASP-1-0.695-0.81658.990-0.025-0.0250.0000.0000.0000.000
208A211VAL0-0.074-0.03853.605-0.001-0.0010.0000.0000.0000.000
209A212SER0-0.035-0.02053.152-0.001-0.0010.0000.0000.0000.000
210A213GLY00.0230.01450.635-0.001-0.0010.0000.0000.0000.000
211A214HIS00.0330.04847.0130.0010.0010.0000.0000.0000.000
212A215GLY00.012-0.00148.176-0.002-0.0020.0000.0000.0000.000
213A216ALA00.0390.00147.6110.0010.0010.0000.0000.0000.000
214A217SER0-0.046-0.01146.6200.0010.0010.0000.0000.0000.000
215A218SER00.003-0.02048.6860.0000.0000.0000.0000.0000.000
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