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: 9MY62

Calculation Name: 2FI7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FI7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HXJ2

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 223
LigandCharge DLY=1,DAR=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2601763.008989
FMO2-HF: Nuclear repulsion 2513069.858054
FMO2-HF: Total energy -88693.150935
FMO2-MP2: Total energy -88956.350396


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:30:ASP)


Summations of interaction energy for fragment #1(A:30:ASP)
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.
-44.412-41.74218.533-8.86-12.3420.129
Interaction energy analysis for fragmet #1(A:30:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.766 / q_NPA : -0.901
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].
3A32GLY00.0520.0361.844-26.193-27.38316.426-8.475-6.7610.087
4A33ARG10.8240.9073.214-51.303-53.4380.2043.207-1.2760.012
5A34ASP-1-0.826-0.9172.58333.41137.2231.642-2.620-2.8340.020
6A35GLU-1-0.883-0.9212.84738.92140.9920.260-0.934-1.3970.010
7A36ALA0-0.007-0.0134.431-11.440-11.3280.001-0.038-0.0740.000
8A37ARG10.6890.8266.058-43.613-43.6130.0000.0000.0000.000
9A38ASP-1-0.789-0.8947.31130.04230.0420.0000.0000.0000.000
10A39ALA0-0.0030.0068.812-3.659-3.6590.0000.0000.0000.000
11A40TYR0-0.016-0.02810.735-3.889-3.8890.0000.0000.0000.000
12A41ILE0-0.0030.00611.666-2.433-2.4330.0000.0000.0000.000
13A42GLN00.0160.01712.952-3.083-3.0830.0000.0000.0000.000
14A43LEU00.0030.01314.995-1.478-1.4780.0000.0000.0000.000
15A44GLY00.001-0.00616.576-1.248-1.2480.0000.0000.0000.000
16A45LEU0-0.009-0.01816.896-1.163-1.1630.0000.0000.0000.000
17A46GLY00.0290.02519.156-0.820-0.8200.0000.0000.0000.000
18A47TYR0-0.064-0.04520.336-0.745-0.7450.0000.0000.0000.000
19A48LEU00.0120.00222.428-0.655-0.6550.0000.0000.0000.000
20A49GLN0-0.039-0.01323.491-0.626-0.6260.0000.0000.0000.000
21A50ARG10.8560.92524.028-12.627-12.6270.0000.0000.0000.000
22A51GLY00.0280.03027.047-0.455-0.4550.0000.0000.0000.000
23A52ASN0-0.078-0.02826.010-0.006-0.0060.0000.0000.0000.000
24A53THR00.0740.01425.7190.5460.5460.0000.0000.0000.000
25A54GLU-1-0.775-0.86425.39511.88011.8800.0000.0000.0000.000
26A55GLN0-0.060-0.02623.116-0.077-0.0770.0000.0000.0000.000
27A56ALA00.005-0.00121.4660.6920.6920.0000.0000.0000.000
28A57LYS10.7720.86220.275-10.536-10.5360.0000.0000.0000.000
29A58VAL00.0160.00619.5560.7440.7440.0000.0000.0000.000
30A59PRO0-0.025-0.01316.5260.8050.8050.0000.0000.0000.000
31A60LEU00.0590.02015.5171.3831.3830.0000.0000.0000.000
32A61ARG10.9410.97616.274-13.570-13.5700.0000.0000.0000.000
33A62LYS10.9670.99814.038-17.890-17.8900.0000.0000.0000.000
34A63ALA0-0.0040.00011.6051.6631.6630.0000.0000.0000.000
35A64LEU0-0.031-0.02211.9591.2331.2330.0000.0000.0000.000
36A65GLU-1-0.954-0.97414.14118.40518.4050.0000.0000.0000.000
37A66ILE0-0.106-0.0347.6780.9010.9010.0000.0000.0000.000
38A67ASP-1-0.713-0.8578.64128.62228.6220.0000.0000.0000.000
39A68PRO00.0120.01910.649-1.175-1.1750.0000.0000.0000.000
40A69SER0-0.063-0.03311.753-1.845-1.8450.0000.0000.0000.000
41A70SER0-0.0030.00811.443-0.725-0.7250.0000.0000.0000.000
42A71ALA00.0600.01312.797-1.354-1.3540.0000.0000.0000.000
43A72ASP-1-0.767-0.87413.42218.50918.5090.0000.0000.0000.000
44A73ALA00.0140.00913.613-0.884-0.8840.0000.0000.0000.000
45A74HIS10.7910.87415.511-17.740-17.7400.0000.0000.0000.000
46A75ALA00.0010.00718.259-0.958-0.9580.0000.0000.0000.000
47A76ALA00.0120.00118.004-0.822-0.8220.0000.0000.0000.000
48A77LEU0-0.025-0.01119.637-0.690-0.6900.0000.0000.0000.000
49A78ALA00.0080.00421.360-0.700-0.7000.0000.0000.0000.000
50A79VAL0-0.0020.00523.155-0.604-0.6040.0000.0000.0000.000
51A80VAL0-0.0170.01022.703-0.505-0.5050.0000.0000.0000.000
52A81PHE00.0350.00524.529-0.375-0.3750.0000.0000.0000.000
53A82GLN0-0.016-0.01427.622-0.008-0.0080.0000.0000.0000.000
54A83THR0-0.070-0.04427.810-0.401-0.4010.0000.0000.0000.000
55A84GLU-1-0.860-0.92628.27710.89110.8910.0000.0000.0000.000
56A85MET0-0.048-0.01731.639-0.395-0.3950.0000.0000.0000.000
57A86GLU-1-0.878-0.92830.6829.3099.3090.0000.0000.0000.000
58A87PRO00.002-0.01130.8840.3630.3630.0000.0000.0000.000
59A88LYS10.8970.93730.903-9.698-9.6980.0000.0000.0000.000
60A89LEU00.0400.01728.0760.2580.2580.0000.0000.0000.000
61A90ALA00.0260.00926.8410.4810.4810.0000.0000.0000.000
62A91ASP-1-0.761-0.84426.58010.52510.5250.0000.0000.0000.000
63A92GLU-1-0.859-0.92726.03611.19111.1910.0000.0000.0000.000
64A93GLU-1-0.823-0.88921.26114.59414.5940.0000.0000.0000.000
65A94TYR00.026-0.01222.0800.7960.7960.0000.0000.0000.000
66A95ARG10.7750.86923.208-10.015-10.0150.0000.0000.0000.000
67A96LYS10.8080.90420.088-12.521-12.5210.0000.0000.0000.000
68A97ALA0-0.023-0.01218.4890.6510.6510.0000.0000.0000.000
69A98LEU0-0.055-0.03518.7690.4580.4580.0000.0000.0000.000
70A99ALA0-0.042-0.00619.870-0.226-0.2260.0000.0000.0000.000
71A100SER0-0.071-0.00814.4840.2450.2450.0000.0000.0000.000
72A101ASP-1-0.769-0.90917.11815.07215.0720.0000.0000.0000.000
73A102SER0-0.031-0.01618.783-0.122-0.1220.0000.0000.0000.000
74A103ARG10.7890.85721.361-12.433-12.4330.0000.0000.0000.000
75A104ASN00.0560.03717.475-0.487-0.4870.0000.0000.0000.000
76A105ALA00.0690.03520.961-0.341-0.3410.0000.0000.0000.000
77A106ARG10.8310.89417.455-17.031-17.0310.0000.0000.0000.000
78A107VAL0-0.020-0.01319.497-0.358-0.3580.0000.0000.0000.000
79A108LEU00.0030.01122.707-0.520-0.5200.0000.0000.0000.000
80A109ASN00.000-0.01025.588-0.863-0.8630.0000.0000.0000.000
81A110ASN0-0.015-0.00423.429-0.656-0.6560.0000.0000.0000.000
82A111TYR0-0.021-0.02826.048-0.363-0.3630.0000.0000.0000.000
83A112GLY00.0150.00227.812-0.394-0.3940.0000.0000.0000.000
84A113GLY00.0060.00230.220-0.401-0.4010.0000.0000.0000.000
85A114PHE00.0220.02529.760-0.314-0.3140.0000.0000.0000.000
86A115LEU0-0.031-0.02530.951-0.363-0.3630.0000.0000.0000.000
87A116TYR0-0.035-0.01633.818-0.437-0.4370.0000.0000.0000.000
88A117GLU-1-0.853-0.91532.6359.4529.4520.0000.0000.0000.000
89A118GLN0-0.096-0.04434.498-0.142-0.1420.0000.0000.0000.000
90A119LYS10.9130.95037.250-7.735-7.7350.0000.0000.0000.000
91A120ARG10.8100.90232.255-9.453-9.4530.0000.0000.0000.000
92A121TYR00.000-0.03336.8030.2370.2370.0000.0000.0000.000
93A122GLU-1-0.912-0.95937.9607.6907.6900.0000.0000.0000.000
94A123GLU-1-0.778-0.87932.7939.4419.4410.0000.0000.0000.000
95A124ALA00.0100.00233.3020.2790.2790.0000.0000.0000.000
96A125TYR0-0.009-0.02033.4430.1940.1940.0000.0000.0000.000
97A126GLN00.0050.00633.2730.3370.3370.0000.0000.0000.000
98A127ARG10.9280.97127.684-10.247-10.2470.0000.0000.0000.000
99A128LEU00.0230.01329.5020.3180.3180.0000.0000.0000.000
100A129LEU00.0030.00431.4080.0980.0980.0000.0000.0000.000
101A130GLU-1-0.795-0.85427.20611.10011.1000.0000.0000.0000.000
102A131ALA0-0.008-0.00226.8160.2610.2610.0000.0000.0000.000
103A132SER0-0.108-0.05827.6950.1160.1160.0000.0000.0000.000
104A133GLN0-0.039-0.02028.253-0.167-0.1670.0000.0000.0000.000
105A134ASP-1-0.791-0.88122.79313.14613.1460.0000.0000.0000.000
106A135THR0-0.072-0.07426.050-0.125-0.1250.0000.0000.0000.000
107A136LEU0-0.023-0.01222.389-0.275-0.2750.0000.0000.0000.000
108A137TYR00.0150.02322.9330.2670.2670.0000.0000.0000.000
109A138PRO00.022-0.00222.154-0.506-0.5060.0000.0000.0000.000
110A139GLU-1-0.870-0.91025.31311.09211.0920.0000.0000.0000.000
111A140ARG10.8940.95127.400-10.396-10.3960.0000.0000.0000.000
112A141SER0-0.003-0.00629.120-0.164-0.1640.0000.0000.0000.000
113A142ARG10.9270.95726.256-11.658-11.6580.0000.0000.0000.000
114A143VAL0-0.0100.01228.704-0.137-0.1370.0000.0000.0000.000
115A144PHE0-0.025-0.02931.512-0.275-0.2750.0000.0000.0000.000
116A145GLU-1-0.864-0.93534.5228.7288.7280.0000.0000.0000.000
117A146ASN0-0.002-0.01531.415-0.452-0.4520.0000.0000.0000.000
118A147LEU0-0.036-0.00934.255-0.235-0.2350.0000.0000.0000.000
119A148GLY00.0210.02737.005-0.252-0.2520.0000.0000.0000.000
120A149LEU00.0410.01136.917-0.249-0.2490.0000.0000.0000.000
121A150VAL00.009-0.00336.377-0.188-0.1880.0000.0000.0000.000
122A151SER0-0.005-0.01839.716-0.193-0.1930.0000.0000.0000.000
123A152LEU0-0.025-0.00542.373-0.225-0.2250.0000.0000.0000.000
124A153GLN0-0.0150.01041.905-0.277-0.2770.0000.0000.0000.000
125A154MET0-0.0390.02140.077-0.139-0.1390.0000.0000.0000.000
126A155LYS10.9240.95644.981-6.555-6.5550.0000.0000.0000.000
127A156LYS10.8930.94643.418-7.275-7.2750.0000.0000.0000.000
128A157PRO00.0580.01746.1640.1430.1430.0000.0000.0000.000
129A158ALA00.0750.03847.1000.0940.0940.0000.0000.0000.000
130A159GLN0-0.006-0.01041.895-0.037-0.0370.0000.0000.0000.000
131A160ALA0-0.010-0.02142.6330.1720.1720.0000.0000.0000.000
132A161LYS10.8440.90742.736-6.160-6.1600.0000.0000.0000.000
133A162GLU-1-0.794-0.86941.1327.7907.7900.0000.0000.0000.000
134A163TYR00.008-0.00138.2710.1750.1750.0000.0000.0000.000
135A164PHE00.0470.01938.8000.2230.2230.0000.0000.0000.000
136A165GLU-1-0.901-0.95040.3307.0807.0800.0000.0000.0000.000
137A166LYS10.7290.85636.985-7.879-7.8790.0000.0000.0000.000
138A167SER00.006-0.01335.8020.2560.2560.0000.0000.0000.000
139A168LEU00.0160.00736.3970.1350.1350.0000.0000.0000.000
140A169ARG10.8630.92738.410-7.968-7.9680.0000.0000.0000.000
141A170LEU0-0.061-0.01932.3280.0610.0610.0000.0000.0000.000
142A171ASN0-0.002-0.00433.1280.0560.0560.0000.0000.0000.000
143A172ARG10.9950.99735.619-7.726-7.7260.0000.0000.0000.000
144A173ASN0-0.0160.01135.864-0.406-0.4060.0000.0000.0000.000
145A174GLN00.0350.02334.9940.1430.1430.0000.0000.0000.000
146A175PRO00.0820.03838.257-0.157-0.1570.0000.0000.0000.000
147A176SER00.0170.01037.812-0.201-0.2010.0000.0000.0000.000
148A177VAL00.0220.01137.702-0.135-0.1350.0000.0000.0000.000
149A178ALA0-0.001-0.00240.779-0.167-0.1670.0000.0000.0000.000
150A179LEU0-0.0100.00043.679-0.212-0.2120.0000.0000.0000.000
151A180GLU-1-0.796-0.85542.2467.0437.0430.0000.0000.0000.000
152A181MET0-0.0490.00144.059-0.123-0.1230.0000.0000.0000.000
153A182ALA00.0180.00846.513-0.170-0.1700.0000.0000.0000.000
154A183ASP-1-0.805-0.88548.5326.2216.2210.0000.0000.0000.000
155A184LEU0-0.069-0.03346.310-0.138-0.1380.0000.0000.0000.000
156A185LEU00.0490.02249.473-0.097-0.0970.0000.0000.0000.000
157A186TYR0-0.032-0.01652.139-0.166-0.1660.0000.0000.0000.000
158A187LYS10.8120.89350.323-6.453-6.4530.0000.0000.0000.000
159A188GLU-1-0.882-0.91251.9916.1346.1340.0000.0000.0000.000
160A189ARG10.8760.93655.995-5.323-5.3230.0000.0000.0000.000
161A190GLU-1-0.880-0.93353.7045.8715.8710.0000.0000.0000.000
162A191TYR00.041-0.00855.4130.0670.0670.0000.0000.0000.000
163A192VAL00.0290.02456.0430.0680.0680.0000.0000.0000.000
164A193PRO00.0470.02351.9060.0670.0670.0000.0000.0000.000
165A194ALA00.0150.01551.4290.1490.1490.0000.0000.0000.000
166A195ARG10.9150.94751.581-5.562-5.5620.0000.0000.0000.000
167A196GLN0-0.0040.01550.035-0.008-0.0080.0000.0000.0000.000
168A197TYR0-0.005-0.01544.6670.2080.2080.0000.0000.0000.000
169A198TYR0-0.011-0.00747.3740.1450.1450.0000.0000.0000.000
170A199ASP-1-0.860-0.93748.8476.1776.1770.0000.0000.0000.000
171A200LEU0-0.036-0.00643.1120.0790.0790.0000.0000.0000.000
172A201PHE0-0.056-0.03744.1050.1660.1660.0000.0000.0000.000
173A202ALA00.0140.00845.1040.1060.1060.0000.0000.0000.000
174A203GLN0-0.059-0.02645.0160.0570.0570.0000.0000.0000.000
175A204GLY0-0.026-0.01042.2010.1510.1510.0000.0000.0000.000
176A205GLY0-0.060-0.02242.4380.1080.1080.0000.0000.0000.000
177A206GLY00.030-0.00343.7010.1100.1100.0000.0000.0000.000
178A207GLN0-0.0050.02644.764-0.006-0.0060.0000.0000.0000.000
179A208ASN0-0.022-0.01644.883-0.036-0.0360.0000.0000.0000.000
180A209ALA00.0680.03248.099-0.089-0.0890.0000.0000.0000.000
181A210ARG10.8110.85044.906-7.015-7.0150.0000.0000.0000.000
182A211SER00.008-0.02047.619-0.058-0.0580.0000.0000.0000.000
183A212LEU0-0.0220.00449.740-0.099-0.0990.0000.0000.0000.000
184A213LEU0-0.0020.00752.818-0.105-0.1050.0000.0000.0000.000
185A214LEU0-0.0320.00050.273-0.106-0.1060.0000.0000.0000.000
186A215GLY00.0600.01453.234-0.073-0.0730.0000.0000.0000.000
187A216ILE0-0.041-0.01554.390-0.101-0.1010.0000.0000.0000.000
188A217ARG10.7110.81656.477-5.636-5.6360.0000.0000.0000.000
189A218LEU0-0.0170.00353.830-0.081-0.0810.0000.0000.0000.000
190A219ALA00.0320.01757.666-0.047-0.0470.0000.0000.0000.000
191A220LYS10.8360.92259.586-5.232-5.2320.0000.0000.0000.000
192A221VAL0-0.068-0.01960.469-0.096-0.0960.0000.0000.0000.000
193A222PHE00.0210.00758.272-0.026-0.0260.0000.0000.0000.000
194A223GLU-1-0.926-0.96562.9104.9004.9000.0000.0000.0000.000
195A224ASP-1-0.824-0.88759.5975.3945.3940.0000.0000.0000.000
196A225ARG10.8620.90962.236-4.856-4.8560.0000.0000.0000.000
197A226ASP-1-0.871-0.92462.5154.9904.9900.0000.0000.0000.000
198A227THR0-0.022-0.04356.5810.0620.0620.0000.0000.0000.000
199A228ALA0-0.053-0.02758.7340.0710.0710.0000.0000.0000.000
200A229ALA0-0.027-0.01160.3640.0240.0240.0000.0000.0000.000
201A230SER00.001-0.00257.8550.0380.0380.0000.0000.0000.000
202A231TYR00.0140.02653.0420.1430.1430.0000.0000.0000.000
203A232GLY00.0480.02257.145-0.027-0.0270.0000.0000.0000.000
204A233LEU0-0.029-0.03251.913-0.010-0.0100.0000.0000.0000.000
205A234GLN00.0590.02454.0840.1280.1280.0000.0000.0000.000
206A235LEU0-0.0190.00955.9800.0240.0240.0000.0000.0000.000
207A236DLY10.9630.95457.471-5.469-5.4690.0000.0000.0000.000
208A237DAR10.9500.98449.542-6.426-6.4260.0000.0000.0000.000
209A238LEU0-0.109-0.05751.8010.1100.1100.0000.0000.0000.000
210A239TYR0-0.0020.00548.7700.1510.1510.0000.0000.0000.000
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