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: VQ8Y1

Calculation Name: 2FBQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FBQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZJ9

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2353914.60454
FMO2-HF: Nuclear repulsion 2270486.029298
FMO2-HF: Total energy -83428.575241
FMO2-MP2: Total energy -83669.649244


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-9.344-6.2334.598-3.523-4.1860.014
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.019
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].
3A4SER00.0830.0243.275-2.089-0.0950.108-0.947-1.1550.004
4A5GLU-1-0.892-0.9402.127-4.193-3.7634.480-2.286-2.6240.009
5A6THR0-0.053-0.0383.806-2.146-1.4590.010-0.290-0.4070.001
6A7VAL0-0.016-0.0025.640-0.225-0.2250.0000.0000.0000.000
7A8GLU-1-0.788-0.8977.3970.6460.6460.0000.0000.0000.000
8A9ARG10.8680.9386.069-0.173-0.1730.0000.0000.0000.000
9A10ILE0-0.043-0.0219.299-0.163-0.1630.0000.0000.0000.000
10A11LEU0-0.021-0.00811.440-0.103-0.1030.0000.0000.0000.000
11A12ASP-1-0.786-0.87912.2990.4090.4090.0000.0000.0000.000
12A13ALA0-0.028-0.01213.401-0.064-0.0640.0000.0000.0000.000
13A14ALA0-0.013-0.01815.263-0.039-0.0390.0000.0000.0000.000
14A15GLU-1-0.792-0.86716.9020.3030.3030.0000.0000.0000.000
15A16GLN0-0.013-0.00717.999-0.016-0.0160.0000.0000.0000.000
16A17LEU00.012-0.00218.671-0.021-0.0210.0000.0000.0000.000
17A18PHE0-0.040-0.03019.760-0.016-0.0160.0000.0000.0000.000
18A19ALA00.0230.00722.566-0.011-0.0110.0000.0000.0000.000
19A20GLU-1-0.865-0.92322.1380.0810.0810.0000.0000.0000.000
20A21LYS10.8040.88125.378-0.058-0.0580.0000.0000.0000.000
21A22GLY00.0260.02926.348-0.006-0.0060.0000.0000.0000.000
22A23PHE00.006-0.00623.3080.0000.0000.0000.0000.0000.000
23A24ALA0-0.002-0.00226.139-0.002-0.0020.0000.0000.0000.000
24A25GLU-1-0.800-0.88827.8250.0390.0390.0000.0000.0000.000
25A26THR00.0180.03021.660-0.006-0.0060.0000.0000.0000.000
26A27SER00.004-0.00323.2220.0050.0050.0000.0000.0000.000
27A28LEU00.0930.02918.5290.0020.0020.0000.0000.0000.000
28A29ARG10.9590.99618.301-0.002-0.0020.0000.0000.0000.000
29A30LEU0-0.0230.00719.483-0.014-0.0140.0000.0000.0000.000
30A31ILE00.0610.03315.154-0.009-0.0090.0000.0000.0000.000
31A32THR0-0.029-0.03014.5020.0030.0030.0000.0000.0000.000
32A33SER0-0.052-0.03614.317-0.021-0.0210.0000.0000.0000.000
33A34LYS10.8160.91615.694-0.112-0.1120.0000.0000.0000.000
34A35ALA00.0520.03411.0030.0080.0080.0000.0000.0000.000
35A36GLY00.0140.03110.532-0.030-0.0300.0000.0000.0000.000
36A37VAL0-0.026-0.0168.614-0.091-0.0910.0000.0000.0000.000
37A38ASN00.0370.00911.2570.0600.0600.0000.0000.0000.000
38A39LEU00.0560.00613.3090.0150.0150.0000.0000.0000.000
39A40ALA00.0080.00814.2370.0290.0290.0000.0000.0000.000
40A41ALA00.0430.0299.8570.0170.0170.0000.0000.0000.000
41A42VAL00.000-0.00111.8410.0740.0740.0000.0000.0000.000
42A43ASN0-0.030-0.03814.1450.0440.0440.0000.0000.0000.000
43A44TYR0-0.020-0.00110.4290.0090.0090.0000.0000.0000.000
44A45HIS00.0030.0037.6100.1240.1240.0000.0000.0000.000
45A46PHE00.0070.00112.0300.0340.0340.0000.0000.0000.000
46A47GLY00.0270.03416.214-0.013-0.0130.0000.0000.0000.000
47A48SER0-0.052-0.03718.874-0.019-0.0190.0000.0000.0000.000
48A49LYS10.8600.91720.121-0.061-0.0610.0000.0000.0000.000
49A50LYS10.9420.97721.817-0.072-0.0720.0000.0000.0000.000
50A51ALA00.0760.04219.4980.0090.0090.0000.0000.0000.000
51A52LEU00.0080.01515.4050.0240.0240.0000.0000.0000.000
52A53ILE0-0.027-0.00918.4060.0270.0270.0000.0000.0000.000
53A54GLN0-0.004-0.01920.9880.0160.0160.0000.0000.0000.000
54A55ALA00.0030.02315.5140.0100.0100.0000.0000.0000.000
55A56VAL00.003-0.00216.8140.0330.0330.0000.0000.0000.000
56A57PHE0-0.006-0.01117.9600.0080.0080.0000.0000.0000.000
57A58SER00.0060.00318.643-0.014-0.0140.0000.0000.0000.000
58A59ARG10.7350.84911.953-0.597-0.5970.0000.0000.0000.000
59A60PHE0-0.022-0.00916.7830.0100.0100.0000.0000.0000.000
60A61LEU00.010-0.01119.990-0.012-0.0120.0000.0000.0000.000
61A62GLY00.0540.04519.407-0.019-0.0190.0000.0000.0000.000
62A63PRO0-0.016-0.02117.561-0.022-0.0220.0000.0000.0000.000
63A64PHE00.0190.01520.370-0.025-0.0250.0000.0000.0000.000
64A65CYS0-0.037-0.01423.774-0.024-0.0240.0000.0000.0000.000
65A66ALA00.0130.01022.236-0.016-0.0160.0000.0000.0000.000
66A67SER0-0.048-0.04623.928-0.015-0.0150.0000.0000.0000.000
67A68LEU0-0.002-0.00225.598-0.015-0.0150.0000.0000.0000.000
68A69GLU-1-0.837-0.92327.7050.1110.1110.0000.0000.0000.000
69A70LYS10.9851.00024.953-0.160-0.1600.0000.0000.0000.000
70A71GLU-1-0.774-0.84229.0950.0900.0900.0000.0000.0000.000
71A72LEU0-0.029-0.01331.355-0.010-0.0100.0000.0000.0000.000
72A73ASP-1-0.821-0.89331.3920.0970.0970.0000.0000.0000.000
73A74ARG10.8020.87231.833-0.100-0.1000.0000.0000.0000.000
74A75ARG10.8010.87233.941-0.095-0.0950.0000.0000.0000.000
75A76GLN00.0440.02236.987-0.001-0.0010.0000.0000.0000.000
76A77ALA00.0040.01336.953-0.004-0.0040.0000.0000.0000.000
77A78LYS10.9020.96038.487-0.069-0.0690.0000.0000.0000.000
78A79PRO00.005-0.01441.093-0.001-0.0010.0000.0000.0000.000
79A80GLU-1-0.888-0.91944.4640.0410.0410.0000.0000.0000.000
80A81ALA0-0.052-0.02142.0750.0010.0010.0000.0000.0000.000
81A82GLN0-0.045-0.02743.859-0.002-0.0020.0000.0000.0000.000
82A83HIS0-0.025-0.01743.9400.0020.0020.0000.0000.0000.000
83A84ALA0-0.0200.00340.683-0.001-0.0010.0000.0000.0000.000
84A85THR00.014-0.02242.683-0.001-0.0010.0000.0000.0000.000
85A86LEU00.019-0.00741.8110.0040.0040.0000.0000.0000.000
86A87GLU-1-0.738-0.83940.6400.0580.0580.0000.0000.0000.000
87A88ASP-1-0.847-0.88739.6340.0660.0660.0000.0000.0000.000
88A89LEU0-0.007-0.00437.3120.0070.0070.0000.0000.0000.000
89A90LEU0-0.0130.01036.0040.0070.0070.0000.0000.0000.000
90A91HIS00.0770.02635.2480.0090.0090.0000.0000.0000.000
91A92LEU0-0.063-0.00432.0550.0060.0060.0000.0000.0000.000
92A93LEU00.0030.01431.1610.0090.0090.0000.0000.0000.000
93A94VAL00.0210.01230.2580.0100.0100.0000.0000.0000.000
94A95SER0-0.046-0.03830.0610.0060.0060.0000.0000.0000.000
95A96GLN00.0340.02827.2230.0170.0170.0000.0000.0000.000
96A97ALA0-0.031-0.02325.8710.0160.0160.0000.0000.0000.000
97A98MET0-0.056-0.02825.3000.0130.0130.0000.0000.0000.000
98A99ALA0-0.0100.01424.8620.0020.0020.0000.0000.0000.000
99A100VAL0-0.067-0.02720.1760.0220.0220.0000.0000.0000.000
100A101LYS10.9550.98113.875-0.370-0.3700.0000.0000.0000.000
101A102PRO0-0.023-0.00518.1300.0300.0300.0000.0000.0000.000
102A103ARG10.7930.87713.492-0.388-0.3880.0000.0000.0000.000
103A104SER00.019-0.02515.973-0.031-0.0310.0000.0000.0000.000
104A105GLY00.0020.01718.269-0.031-0.0310.0000.0000.0000.000
105A106ASN0-0.039-0.03621.167-0.035-0.0350.0000.0000.0000.000
106A107ASP-1-0.729-0.84018.6310.2490.2490.0000.0000.0000.000
107A108LEU00.0770.03421.6220.0030.0030.0000.0000.0000.000
108A109SER0-0.034-0.02725.025-0.008-0.0080.0000.0000.0000.000
109A110ILE00.0100.00120.590-0.010-0.0100.0000.0000.0000.000
110A111PHE00.0140.00823.005-0.006-0.0060.0000.0000.0000.000
111A112MET00.0170.01524.238-0.009-0.0090.0000.0000.0000.000
112A113ARG10.8370.91826.180-0.103-0.1030.0000.0000.0000.000
113A114LEU0-0.024-0.01421.560-0.009-0.0090.0000.0000.0000.000
114A115LEU00.0090.00426.129-0.006-0.0060.0000.0000.0000.000
115A116GLY00.0470.01828.632-0.008-0.0080.0000.0000.0000.000
116A117LEU0-0.0120.00627.233-0.008-0.0080.0000.0000.0000.000
117A118ALA0-0.033-0.01827.874-0.005-0.0050.0000.0000.0000.000
118A119PHE0-0.0150.00029.742-0.005-0.0050.0000.0000.0000.000
119A120SER0-0.014-0.01833.043-0.005-0.0050.0000.0000.0000.000
120A121GLN00.0220.01429.722-0.002-0.0020.0000.0000.0000.000
121A122SER00.0200.01932.1450.0000.0000.0000.0000.0000.000
122A123GLN0-0.0090.00827.6140.0060.0060.0000.0000.0000.000
123A124GLY00.003-0.01230.0060.0070.0070.0000.0000.0000.000
124A125HIS0-0.057-0.04525.1550.0040.0040.0000.0000.0000.000
125A126LEU00.0370.03424.1210.0050.0050.0000.0000.0000.000
126A127ARG10.9750.98727.235-0.078-0.0780.0000.0000.0000.000
127A128LYS10.8020.88329.357-0.102-0.1020.0000.0000.0000.000
128A129TYR00.0380.01320.0250.0030.0030.0000.0000.0000.000
129A130LEU0-0.002-0.01324.0780.0080.0080.0000.0000.0000.000
130A131GLU-1-0.823-0.86927.0650.1010.1010.0000.0000.0000.000
131A132GLU-1-0.821-0.90627.6240.1130.1130.0000.0000.0000.000
132A133VAL0-0.047-0.00222.3660.0030.0030.0000.0000.0000.000
133A134TYR00.003-0.02921.0220.0100.0100.0000.0000.0000.000
134A135GLY00.0290.02127.589-0.007-0.0070.0000.0000.0000.000
135A136LYS10.8880.94730.100-0.104-0.1040.0000.0000.0000.000
136A137VAL00.0810.05028.058-0.007-0.0070.0000.0000.0000.000
137A138PHE0-0.003-0.01027.579-0.006-0.0060.0000.0000.0000.000
138A139ARG10.8100.86732.617-0.099-0.0990.0000.0000.0000.000
139A140ARG10.7630.85832.487-0.103-0.1030.0000.0000.0000.000
140A141TYR0-0.019-0.04033.785-0.004-0.0040.0000.0000.0000.000
141A142MET0-0.010-0.01335.829-0.006-0.0060.0000.0000.0000.000
142A143LEU0-0.036-0.00738.141-0.004-0.0040.0000.0000.0000.000
143A144LEU00.0620.03637.601-0.003-0.0030.0000.0000.0000.000
144A145VAL0-0.019-0.01738.309-0.003-0.0030.0000.0000.0000.000
145A146ASN0-0.087-0.04341.272-0.004-0.0040.0000.0000.0000.000
146A147GLU-1-0.899-0.96543.3270.0580.0580.0000.0000.0000.000
147A148ALA0-0.0240.00143.617-0.003-0.0030.0000.0000.0000.000
148A149ALA0-0.048-0.02445.564-0.001-0.0010.0000.0000.0000.000
149A150PRO00.0080.00547.467-0.001-0.0010.0000.0000.0000.000
150A151LYS10.9340.96649.724-0.038-0.0380.0000.0000.0000.000
151A152LEU00.0460.03548.016-0.001-0.0010.0000.0000.0000.000
152A153PRO00.0460.02350.3440.0010.0010.0000.0000.0000.000
153A154PRO00.0150.00146.6710.0020.0020.0000.0000.0000.000
154A155ILE00.0060.00145.6000.0030.0030.0000.0000.0000.000
155A156GLU-1-0.724-0.82946.2420.0430.0430.0000.0000.0000.000
156A157LEU00.0150.02243.2690.0020.0020.0000.0000.0000.000
157A158PHE0-0.006-0.00539.6820.0040.0040.0000.0000.0000.000
158A159TRP00.0120.00741.5200.0050.0050.0000.0000.0000.000
159A160ARG10.7960.87442.628-0.044-0.0440.0000.0000.0000.000
160A161VAL00.0140.00237.7390.0020.0020.0000.0000.0000.000
161A162HIS0-0.082-0.05637.0850.0080.0080.0000.0000.0000.000
162A163PHE0-0.0090.00138.7770.0020.0020.0000.0000.0000.000
163A164MET0-0.0010.01838.3510.0010.0010.0000.0000.0000.000
164A165LEU0-0.0020.00132.0360.0040.0040.0000.0000.0000.000
165A166GLY00.0110.00234.7040.0040.0040.0000.0000.0000.000
166A167ALA00.0210.01536.4420.0010.0010.0000.0000.0000.000
167A168ALA00.0400.01833.4700.0000.0000.0000.0000.0000.000
168A169ALA00.002-0.01131.7360.0040.0040.0000.0000.0000.000
169A170PHE0-0.015-0.01332.2900.0030.0030.0000.0000.0000.000
170A171SER00.006-0.01834.200-0.001-0.0010.0000.0000.0000.000
171A172MET0-0.010-0.00129.2640.0030.0030.0000.0000.0000.000
172A173SER0-0.0090.01929.5200.0040.0040.0000.0000.0000.000
173A174GLY00.0430.02230.602-0.001-0.0010.0000.0000.0000.000
174A175ILE0-0.0120.00329.310-0.005-0.0050.0000.0000.0000.000
175A176LYS10.8890.93125.534-0.097-0.0970.0000.0000.0000.000
176A177ALA00.0270.02532.280-0.004-0.0040.0000.0000.0000.000
177A178LEU00.0140.01135.584-0.003-0.0030.0000.0000.0000.000
178A179ARG10.8680.92430.142-0.073-0.0730.0000.0000.0000.000
179A180ALA00.0160.01835.903-0.003-0.0030.0000.0000.0000.000
180A181MET0-0.0060.00537.505-0.002-0.0020.0000.0000.0000.000
181A182ALA00.0200.01439.176-0.002-0.0020.0000.0000.0000.000
182A183GLU-1-0.911-0.96938.3320.0380.0380.0000.0000.0000.000
183A184THR0-0.066-0.04740.790-0.003-0.0030.0000.0000.0000.000
184A185ASP-1-0.940-0.97243.2700.0330.0330.0000.0000.0000.000
185A186PHE0-0.083-0.05044.277-0.001-0.0010.0000.0000.0000.000
186A187GLY0-0.0140.02443.595-0.001-0.0010.0000.0000.0000.000
187A188VAL0-0.022-0.01541.4140.0000.0000.0000.0000.0000.000
188A189ASN00.0420.03033.8300.0070.0070.0000.0000.0000.000
189A190THR0-0.0270.00737.0790.0010.0010.0000.0000.0000.000
190A191SER00.009-0.00432.5150.0040.0040.0000.0000.0000.000
191A192THR00.020-0.02529.080-0.003-0.0030.0000.0000.0000.000
192A193GLU-1-0.866-0.93430.9670.0860.0860.0000.0000.0000.000
193A194GLN00.0470.02732.488-0.002-0.0020.0000.0000.0000.000
194A195VAL00.0080.00334.533-0.002-0.0020.0000.0000.0000.000
195A196MET0-0.020-0.00629.3580.0010.0010.0000.0000.0000.000
196A197HIS0-0.019-0.02734.7460.0000.0000.0000.0000.0000.000
197A198LEU0-0.007-0.00537.391-0.003-0.0030.0000.0000.0000.000
198A199MET0-0.042-0.00534.428-0.001-0.0010.0000.0000.0000.000
199A200VAL0-0.0170.01537.818-0.002-0.0020.0000.0000.0000.000
200A201PRO00.0370.01840.267-0.001-0.0010.0000.0000.0000.000
201A202PHE00.0090.00942.178-0.002-0.0020.0000.0000.0000.000
202A203PHE0-0.001-0.02036.877-0.001-0.0010.0000.0000.0000.000
203A204ALA00.0260.01742.673-0.001-0.0010.0000.0000.0000.000
204A205ALA0-0.013-0.00644.568-0.002-0.0020.0000.0000.0000.000
205A206GLY00.004-0.00246.191-0.002-0.0020.0000.0000.0000.000
206A207MET0-0.053-0.03842.698-0.001-0.0010.0000.0000.0000.000
207A208ARG10.7990.85146.129-0.051-0.0510.0000.0000.0000.000
208A209ALA0-0.0050.02349.409-0.002-0.0020.0000.0000.0000.000
209A210GLU-1-0.896-0.93851.6140.0340.0340.0000.0000.0000.000
210A211SER0-0.075-0.06152.8030.0010.0010.0000.0000.0000.000
211A212GLY00.0380.01652.799-0.001-0.0010.0000.0000.0000.000
212A213ILE0-0.111-0.06450.9180.0000.0000.0000.0000.0000.000
213A214ASP-1-0.948-0.95655.4070.0300.0300.0000.0000.0000.000