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: QN1YY

Calculation Name: 2Q7F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Q7F

Chain ID: A

ChEMBL ID:

UniProt ID: O34452

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1968348.324117
FMO2-HF: Nuclear repulsion 1891316.834234
FMO2-HF: Total energy -77031.489883
FMO2-MP2: Total energy -77253.36686


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:43:ALA)


Summations of interaction energy for fragment #1(A:43: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.
-3.327-0.3310.133-1.387-1.742-0.002
Interaction energy analysis for fragmet #1(A:43:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.023
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].
3A45GLU-1-0.873-0.9033.802-0.3011.803-0.029-1.098-0.9770.000
4A46ALA00.0040.0286.2540.3000.3000.0000.0000.0000.000
5A47PHE0-0.014-0.0244.358-0.384-0.292-0.001-0.008-0.0820.000
6A48THR00.008-0.0239.080-0.146-0.1460.0000.0000.0000.000
7A49LYS10.7930.87211.156-0.202-0.2020.0000.0000.0000.000
8A50ALA0-0.019-0.00412.264-0.023-0.0230.0000.0000.0000.000
9A51ILE00.0320.01812.775-0.030-0.0300.0000.0000.0000.000
10A52GLU-1-0.858-0.90715.4860.1140.1140.0000.0000.0000.000
11A53GLU-1-1.011-1.02617.8990.0930.0930.0000.0000.0000.000
12A54ASN00.0050.01018.1280.0110.0110.0000.0000.0000.000
13A55LYN0-0.0520.00619.733-0.013-0.0130.0000.0000.0000.000
14A56GLU-1-0.842-0.92720.932-0.051-0.0510.0000.0000.0000.000
15A57ASP-1-0.897-0.94818.702-0.030-0.0300.0000.0000.0000.000
16A58ALA00.0610.02218.673-0.016-0.0160.0000.0000.0000.000
17A59ILE0-0.007-0.01114.931-0.039-0.0390.0000.0000.0000.000
18A60PRO0-0.021-0.00113.036-0.041-0.0410.0000.0000.0000.000
19A61TYR0-0.013-0.02812.305-0.081-0.0810.0000.0000.0000.000
20A62ILE0-0.0070.00313.319-0.087-0.0870.0000.0000.0000.000
21A63ASN0-0.042-0.0239.585-0.124-0.1240.0000.0000.0000.000
22A64PHE0-0.0020.0027.732-0.236-0.2360.0000.0000.0000.000
23A65ALA00.0390.0279.019-0.267-0.2670.0000.0000.0000.000
24A66ASN00.0160.0089.590-0.057-0.0570.0000.0000.0000.000
25A67LEU0-0.0410.0042.616-0.840-0.1500.164-0.262-0.592-0.002
26A68LEU00.0060.0016.549-0.244-0.2440.0000.0000.0000.000
27A69SER0-0.008-0.0068.8060.1240.1240.0000.0000.0000.000
28A70SER0-0.122-0.0546.388-0.036-0.0360.0000.0000.0000.000
29A71VAL0-0.014-0.0174.098-0.130-0.020-0.001-0.019-0.0910.000
30A72ASN0-0.054-0.0267.1950.2050.2050.0000.0000.0000.000
31A73GLU-1-0.845-0.9039.174-0.848-0.8480.0000.0000.0000.000
32A74LEU00.0520.01811.7410.0120.0120.0000.0000.0000.000
33A75GLU-1-0.847-0.91514.501-0.360-0.3600.0000.0000.0000.000
34A76ARG10.8560.91310.3860.7190.7190.0000.0000.0000.000
35A77ALA00.0290.01412.4660.0270.0270.0000.0000.0000.000
36A78LEU0-0.011-0.00913.9290.0520.0520.0000.0000.0000.000
37A79ALA0-0.0130.00717.2700.0400.0400.0000.0000.0000.000
38A80PHE0-0.036-0.02114.0940.0230.0230.0000.0000.0000.000
39A81TYR0-0.003-0.02713.1020.0240.0240.0000.0000.0000.000
40A82ASP-1-0.948-0.96417.591-0.147-0.1470.0000.0000.0000.000
41A83LYS10.8690.93518.4800.1320.1320.0000.0000.0000.000
42A84ALA0-0.005-0.01217.5550.0240.0240.0000.0000.0000.000
43A85LEU0-0.035-0.01519.6490.0230.0230.0000.0000.0000.000
44A86GLU-1-0.922-0.94222.818-0.083-0.0830.0000.0000.0000.000
45A87LEU0-0.077-0.01820.4570.0120.0120.0000.0000.0000.000
46A88ASP-1-0.819-0.91622.785-0.069-0.0690.0000.0000.0000.000
47A89SER0-0.0020.01223.693-0.011-0.0110.0000.0000.0000.000
48A90SER0-0.068-0.05225.816-0.001-0.0010.0000.0000.0000.000
49A91ALA00.0200.02220.3380.0010.0010.0000.0000.0000.000
50A92ALA00.0160.00321.500-0.021-0.0210.0000.0000.0000.000
51A93THR00.010-0.00916.685-0.012-0.0120.0000.0000.0000.000
52A94ALA00.0260.02517.516-0.041-0.0410.0000.0000.0000.000
53A95TYR0-0.032-0.02918.611-0.023-0.0230.0000.0000.0000.000
54A96TYR00.0350.00417.323-0.010-0.0100.0000.0000.0000.000
55A97GLY0-0.0030.00215.917-0.015-0.0150.0000.0000.0000.000
56A98ALA00.0400.00316.563-0.030-0.0300.0000.0000.0000.000
57A99GLY00.0110.00418.7220.0020.0020.0000.0000.0000.000
58A100ASN0-0.004-0.01916.8240.0150.0150.0000.0000.0000.000
59A101VAL0-0.0110.01215.344-0.006-0.0060.0000.0000.0000.000
60A102TYR0-0.009-0.01817.9430.0110.0110.0000.0000.0000.000
61A103VAL0-0.0030.00520.7620.0190.0190.0000.0000.0000.000
62A104VAL0-0.0240.00516.3940.0130.0130.0000.0000.0000.000
63A105LYS10.8250.90018.8950.3140.3140.0000.0000.0000.000
64A106GLU-1-0.871-0.89821.660-0.157-0.1570.0000.0000.0000.000
65A107MET0-0.077-0.01724.3870.0120.0120.0000.0000.0000.000
66A108TYR00.038-0.05025.959-0.004-0.0040.0000.0000.0000.000
67A109LYS10.9660.99127.8850.1140.1140.0000.0000.0000.000
68A110GLU-1-0.868-0.95226.122-0.142-0.1420.0000.0000.0000.000
69A111ALA00.0390.02124.341-0.005-0.0050.0000.0000.0000.000
70A112LYS10.9070.97025.2880.1010.1010.0000.0000.0000.000
71A113ASP-1-0.870-0.91228.094-0.124-0.1240.0000.0000.0000.000
72A114MET0-0.034-0.01022.6570.0030.0030.0000.0000.0000.000
73A115PHE00.0310.00820.7950.0030.0030.0000.0000.0000.000
74A116GLU-1-0.850-0.92825.372-0.088-0.0880.0000.0000.0000.000
75A117LYS10.7740.87426.5550.1380.1380.0000.0000.0000.000
76A118ALA00.0200.01523.2100.0060.0060.0000.0000.0000.000
77A119LEU00.0060.00324.9380.0090.0090.0000.0000.0000.000
78A120ARG10.7970.88627.7890.1040.1040.0000.0000.0000.000
79A121ALA0-0.052-0.01525.6490.0080.0080.0000.0000.0000.000
80A122GLY00.0000.00627.2720.0060.0060.0000.0000.0000.000
81A123MET0-0.095-0.02619.7960.0000.0000.0000.0000.0000.000
82A124GLU-1-0.878-0.95225.051-0.068-0.0680.0000.0000.0000.000
83A125ASN0-0.021-0.02321.3100.0050.0050.0000.0000.0000.000
84A126GLY00.0420.01925.622-0.005-0.0050.0000.0000.0000.000
85A127ASP-1-0.855-0.93019.861-0.164-0.1640.0000.0000.0000.000
86A128LEU0-0.037-0.00923.116-0.010-0.0100.0000.0000.0000.000
87A129PHE0-0.038-0.02924.231-0.001-0.0010.0000.0000.0000.000
88A130TYR0-0.011-0.02123.963-0.001-0.0010.0000.0000.0000.000
89A131MET0-0.021-0.00120.8760.0030.0030.0000.0000.0000.000
90A132LEU0-0.030-0.01224.9450.0000.0000.0000.0000.0000.000
91A133GLY00.0310.00327.7580.0050.0050.0000.0000.0000.000
92A134THR00.0570.00427.1660.0080.0080.0000.0000.0000.000
93A135VAL0-0.050-0.02025.6950.0010.0010.0000.0000.0000.000
94A136LEU0-0.083-0.05728.7860.0050.0050.0000.0000.0000.000
95A137VAL00.0260.02731.8830.0060.0060.0000.0000.0000.000
96A138LYS10.8630.93627.7630.1540.1540.0000.0000.0000.000
97A139LEU0-0.088-0.03230.6980.0020.0020.0000.0000.0000.000
98A140GLU-1-0.898-0.94334.086-0.077-0.0770.0000.0000.0000.000
99A141GLN0-0.088-0.05535.741-0.001-0.0010.0000.0000.0000.000
100A142PRO00.2060.10537.055-0.002-0.0020.0000.0000.0000.000
101A143LYS10.8930.96137.8760.0590.0590.0000.0000.0000.000
102A144LEU0-0.116-0.06236.1640.0030.0030.0000.0000.0000.000
103A145ALA00.0270.01433.651-0.002-0.0020.0000.0000.0000.000
104A146LEU00.0260.00834.222-0.001-0.0010.0000.0000.0000.000
105A147PRO00.0030.00336.0440.0010.0010.0000.0000.0000.000
106A148TYR0-0.007-0.00630.8940.0020.0020.0000.0000.0000.000
107A149LEU00.0330.00930.621-0.002-0.0020.0000.0000.0000.000
108A150GLN0-0.071-0.03232.7830.0010.0010.0000.0000.0000.000
109A151ARG10.8770.93631.5260.0610.0610.0000.0000.0000.000
110A152ALA00.010-0.00928.7070.0020.0020.0000.0000.0000.000
111A153VAL00.0080.02130.0580.0000.0000.0000.0000.0000.000
112A154GLU-1-0.842-0.89832.594-0.052-0.0520.0000.0000.0000.000
113A155LEU0-0.119-0.06528.5860.0040.0040.0000.0000.0000.000
114A156ASN0-0.025-0.02326.0120.0080.0080.0000.0000.0000.000
115A157GLU-1-0.778-0.84929.735-0.056-0.0560.0000.0000.0000.000
116A158ASN0-0.050-0.02829.0510.0060.0060.0000.0000.0000.000
117A159ASP-1-0.896-0.92726.199-0.117-0.1170.0000.0000.0000.000
118A160THR00.032-0.00828.8220.0000.0000.0000.0000.0000.000
119A161GLU-1-0.806-0.87626.835-0.118-0.1180.0000.0000.0000.000
120A162ALA00.0300.01428.4650.0010.0010.0000.0000.0000.000
121A163ARG10.7640.84730.0510.0620.0620.0000.0000.0000.000
122A164PHE0-0.016-0.01432.2330.0070.0070.0000.0000.0000.000
123A165GLN0-0.041-0.02830.0140.0050.0050.0000.0000.0000.000
124A166PHE00.005-0.00633.3810.0030.0030.0000.0000.0000.000
125A167GLY00.0340.01935.5520.0040.0040.0000.0000.0000.000
126A168MET0-0.021-0.01236.2990.0020.0020.0000.0000.0000.000
127A169CYS0-0.044-0.00236.3990.0010.0010.0000.0000.0000.000
128A170LEU0-0.022-0.01438.5090.0030.0030.0000.0000.0000.000
129A171ALA0-0.004-0.01041.2680.0030.0030.0000.0000.0000.000
130A172ASN0-0.089-0.03741.0390.0020.0020.0000.0000.0000.000
131A173GLU-1-0.878-0.95142.029-0.060-0.0600.0000.0000.0000.000
132A174GLY0-0.029-0.00544.1870.0020.0020.0000.0000.0000.000
133A175MET0-0.066-0.02344.1740.0020.0020.0000.0000.0000.000
134A176LEU00.0640.02044.805-0.002-0.0020.0000.0000.0000.000
135A177ASP-1-0.823-0.89346.281-0.038-0.0380.0000.0000.0000.000
136A178GLU-1-0.853-0.94043.319-0.043-0.0430.0000.0000.0000.000
137A179ALA00.0240.02041.623-0.002-0.0020.0000.0000.0000.000
138A180LEU0-0.027-0.00941.660-0.002-0.0020.0000.0000.0000.000
139A181SER0-0.072-0.03543.1590.0010.0010.0000.0000.0000.000
140A182GLN00.0370.03137.849-0.001-0.0010.0000.0000.0000.000
141A183PHE00.007-0.02338.066-0.002-0.0020.0000.0000.0000.000
142A184ALA0-0.0160.00239.663-0.001-0.0010.0000.0000.0000.000
143A185ALA00.0430.01837.8410.0010.0010.0000.0000.0000.000
144A186VAL0-0.023-0.01134.499-0.001-0.0010.0000.0000.0000.000
145A187THR0-0.038-0.01136.126-0.001-0.0010.0000.0000.0000.000
146A188GLU-1-1.015-1.00138.698-0.037-0.0370.0000.0000.0000.000
147A189GLN0-0.071-0.03133.044-0.003-0.0030.0000.0000.0000.000
148A190ASP-1-0.863-0.94232.463-0.073-0.0730.0000.0000.0000.000
149A191PRO0-0.006-0.00134.4820.0000.0000.0000.0000.0000.000
150A192GLY0-0.041-0.02135.2710.0020.0020.0000.0000.0000.000
151A193HIS00.0440.02732.2060.0010.0010.0000.0000.0000.000
152A194ALA00.014-0.00635.7860.0030.0030.0000.0000.0000.000
153A195ASP-1-0.835-0.91834.571-0.080-0.0800.0000.0000.0000.000
154A196ALA00.0170.03136.8780.0020.0020.0000.0000.0000.000
155A197PHE00.0150.00638.4860.0040.0040.0000.0000.0000.000
156A198TYR00.0140.00339.5770.0040.0040.0000.0000.0000.000
157A199ASN0-0.015-0.02738.0620.0020.0020.0000.0000.0000.000
158A200ALA00.0180.02841.6920.0020.0020.0000.0000.0000.000
159A201GLY0-0.018-0.01743.9390.0030.0030.0000.0000.0000.000
160A202VAL0-0.042-0.03144.0180.0020.0020.0000.0000.0000.000
161A203THR00.010-0.00444.0830.0010.0010.0000.0000.0000.000
162A204TYR00.006-0.02146.6940.0030.0030.0000.0000.0000.000
163A205ALA0-0.033-0.01449.5520.0020.0020.0000.0000.0000.000
164A206TYR0-0.0090.00247.8110.0010.0010.0000.0000.0000.000
165A207LYS10.7590.87849.5180.0380.0380.0000.0000.0000.000
166A208GLU-1-0.987-0.97552.822-0.032-0.0320.0000.0000.0000.000
167A209ASN0-0.005-0.01353.7690.0020.0020.0000.0000.0000.000
168A210ARG10.9380.95053.8860.0290.0290.0000.0000.0000.000
169A211GLU-1-0.922-0.95355.526-0.028-0.0280.0000.0000.0000.000
170A212LYS10.8600.91050.8540.0310.0310.0000.0000.0000.000
171A213ALA00.0030.01849.702-0.001-0.0010.0000.0000.0000.000
172A214LEU0-0.007-0.01349.282-0.002-0.0020.0000.0000.0000.000
173A215GLU-1-0.814-0.88249.661-0.034-0.0340.0000.0000.0000.000
174A216MET0-0.030-0.02345.621-0.001-0.0010.0000.0000.0000.000
175A217LEU00.0120.01445.014-0.002-0.0020.0000.0000.0000.000
176A218ASP-1-0.823-0.89845.850-0.038-0.0380.0000.0000.0000.000
177A219LYS10.7800.88343.6290.0390.0390.0000.0000.0000.000
178A220ALA00.0520.02741.633-0.001-0.0010.0000.0000.0000.000
179A221ILE0-0.040-0.02041.526-0.002-0.0020.0000.0000.0000.000
180A222ASP-1-0.924-0.94743.367-0.040-0.0400.0000.0000.0000.000
181A223ILE0-0.0170.01637.9510.0000.0000.0000.0000.0000.000
182A224GLN0-0.050-0.03535.700-0.002-0.0020.0000.0000.0000.000
183A225PRO0-0.007-0.01539.6250.0000.0000.0000.0000.0000.000
184A226ASP-1-0.918-0.94837.773-0.065-0.0650.0000.0000.0000.000
185A227HIS00.0470.02637.7380.0000.0000.0000.0000.0000.000
186A228MET00.003-0.02340.0890.0040.0040.0000.0000.0000.000
187A229LEU00.0010.01239.0950.0030.0030.0000.0000.0000.000
188A230ALA00.0550.03042.3700.0030.0030.0000.0000.0000.000
189A231LEU0-0.042-0.02144.0630.0030.0030.0000.0000.0000.000
190A232HIS0-0.051-0.04444.5980.0040.0040.0000.0000.0000.000
191A233ALA0-0.0100.00046.1110.0020.0020.0000.0000.0000.000
192A234LYS10.8410.90847.9860.0390.0390.0000.0000.0000.000
193A235LYS10.8320.93150.2660.0390.0390.0000.0000.0000.000
194A236LEU0-0.0080.00550.3760.0020.0020.0000.0000.0000.000