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: 85Y5Y

Calculation Name: 2FYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FYI

Chain ID: A

ChEMBL ID:

UniProt ID: Q47083

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2645670.567378
FMO2-HF: Nuclear repulsion 2558867.371515
FMO2-HF: Total energy -86803.195863
FMO2-MP2: Total energy -87061.264794


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:85:SER)


Summations of interaction energy for fragment #1(A:85: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.
-16.776-11.3654.403-3.824-5.9890
Interaction energy analysis for fragmet #1(A:85:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.002
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].
3A87MET0-0.068-0.0332.668-6.631-3.8891.680-1.740-2.6820.014
4A88THR0-0.063-0.0532.718-2.910-0.8860.629-1.133-1.520-0.010
5A89ASN00.0240.0234.530-1.187-1.111-0.001-0.018-0.0560.000
6A90ASP-1-0.867-0.9336.509-0.097-0.0970.0000.0000.0000.000
7A91THR0-0.106-0.0417.5730.3230.3230.0000.0000.0000.000
8A92SER00.0550.0249.359-0.152-0.1520.0000.0000.0000.000
9A93GLY0-0.015-0.02312.6610.1100.1100.0000.0000.0000.000
10A94VAL0-0.0120.00615.361-0.064-0.0640.0000.0000.0000.000
11A95LEU0-0.0110.02113.1350.0230.0230.0000.0000.0000.000
12A96THR00.0420.02116.572-0.044-0.0440.0000.0000.0000.000
13A97ILE0-0.023-0.00716.2050.0290.0290.0000.0000.0000.000
14A98ALA00.0320.02220.7520.0030.0030.0000.0000.0000.000
15A99THR0-0.024-0.04022.912-0.002-0.0020.0000.0000.0000.000
16A100THR00.0280.00625.1980.0100.0100.0000.0000.0000.000
17A101HIS00.0210.00826.375-0.017-0.0170.0000.0000.0000.000
18A102THR00.017-0.00226.950-0.017-0.0170.0000.0000.0000.000
19A103GLN00.0240.01523.0020.0090.0090.0000.0000.0000.000
20A104ALA00.0220.01122.388-0.038-0.0380.0000.0000.0000.000
21A105ARG10.7530.85722.7880.2420.2420.0000.0000.0000.000
22A106TYR0-0.021-0.00824.026-0.008-0.0080.0000.0000.0000.000
23A107SER0-0.050-0.03120.6350.0210.0210.0000.0000.0000.000
24A108LEU00.0180.00817.819-0.045-0.0450.0000.0000.0000.000
25A109PRO00.0010.00316.757-0.081-0.0810.0000.0000.0000.000
26A110GLU-1-0.851-0.89214.730-0.750-0.7500.0000.0000.0000.000
27A111VAL00.0360.00612.446-0.128-0.1280.0000.0000.0000.000
28A112ILE0-0.012-0.01111.810-0.177-0.1770.0000.0000.0000.000
29A113LYS10.7980.89012.1630.7200.7200.0000.0000.0000.000
30A114ALA00.1050.0478.395-0.206-0.2060.0000.0000.0000.000
31A115PHE0-0.007-0.0127.209-0.569-0.5690.0000.0000.0000.000
32A116ARG10.9270.9547.9200.7090.7090.0000.0000.0000.000
33A117GLU-1-0.949-0.9636.076-2.151-2.1510.0000.0000.0000.000
34A118LEU0-0.060-0.0152.503-1.957-1.5922.096-0.900-1.561-0.004
35A119PHE0-0.014-0.0204.308-0.726-0.522-0.001-0.033-0.1700.000
36A120PRO00.0220.0285.9540.4770.4770.0000.0000.0000.000
37A121GLU-1-0.901-0.9438.950-0.472-0.4720.0000.0000.0000.000
38A122VAL0-0.074-0.02310.1470.2240.2240.0000.0000.0000.000
39A123ARG10.8450.90812.5860.3040.3040.0000.0000.0000.000
40A124LEU0-0.007-0.00414.2230.0540.0540.0000.0000.0000.000
41A125GLU-1-0.839-0.89616.104-0.292-0.2920.0000.0000.0000.000
42A126LEU0-0.011-0.01318.442-0.004-0.0040.0000.0000.0000.000
43A127ILE00.0140.01721.9540.0200.0200.0000.0000.0000.000
44A128GLN0-0.017-0.01725.606-0.011-0.0110.0000.0000.0000.000
45A129GLY00.0310.01627.9280.0120.0120.0000.0000.0000.000
46A130THR0-0.061-0.07530.435-0.003-0.0030.0000.0000.0000.000
47A131PRO00.027-0.00930.551-0.003-0.0030.0000.0000.0000.000
48A132GLN00.0230.02931.6000.0060.0060.0000.0000.0000.000
49A133GLU-1-0.799-0.84631.788-0.141-0.1410.0000.0000.0000.000
50A134ILE0-0.0230.00426.1420.0000.0000.0000.0000.0000.000
51A135ALA00.0160.01127.941-0.002-0.0020.0000.0000.0000.000
52A136THR0-0.014-0.02029.8620.0080.0080.0000.0000.0000.000
53A137LEU00.000-0.00426.9900.0040.0040.0000.0000.0000.000
54A138LEU0-0.0200.01023.1030.0010.0010.0000.0000.0000.000
55A139GLN0-0.108-0.07526.7630.0130.0130.0000.0000.0000.000
56A140ASN0-0.065-0.03429.9010.0180.0180.0000.0000.0000.000
57A141GLY00.0020.00725.5100.0100.0100.0000.0000.0000.000
58A142GLU-1-0.908-0.94325.075-0.140-0.1400.0000.0000.0000.000
59A143ALA0-0.048-0.03322.765-0.022-0.0220.0000.0000.0000.000
60A144ASP-1-0.838-0.89518.277-0.253-0.2530.0000.0000.0000.000
61A145ILE0-0.031-0.02415.8690.0180.0180.0000.0000.0000.000
62A146GLY00.0260.01820.602-0.010-0.0100.0000.0000.0000.000
63A147ILE0-0.021-0.01018.8680.0070.0070.0000.0000.0000.000
64A148ALA00.0290.01623.433-0.005-0.0050.0000.0000.0000.000
65A149SER00.0380.00226.5890.0020.0020.0000.0000.0000.000
66A150GLU-1-0.819-0.88328.918-0.100-0.1000.0000.0000.0000.000
67A151ARG10.9080.93630.8250.0910.0910.0000.0000.0000.000
68A152LEU00.0060.00525.7210.0080.0080.0000.0000.0000.000
69A153SER0-0.011-0.00629.1270.0020.0020.0000.0000.0000.000
70A154ASN0-0.056-0.02530.2670.0040.0040.0000.0000.0000.000
71A155ASP-1-0.776-0.86331.152-0.074-0.0740.0000.0000.0000.000
72A156PRO00.015-0.00231.5440.0010.0010.0000.0000.0000.000
73A157GLN0-0.032-0.01231.0640.0070.0070.0000.0000.0000.000
74A158LEU0-0.044-0.00426.955-0.004-0.0040.0000.0000.0000.000
75A159VAL00.0020.00324.3150.0130.0130.0000.0000.0000.000
76A160ALA0-0.009-0.00724.295-0.017-0.0170.0000.0000.0000.000
77A161PHE00.0320.02721.1150.0150.0150.0000.0000.0000.000
78A162PRO0-0.006-0.00122.947-0.022-0.0220.0000.0000.0000.000
79A163TRP00.003-0.00117.2890.0060.0060.0000.0000.0000.000
80A164PHE00.014-0.00420.8370.0020.0020.0000.0000.0000.000
81A165ARG10.8580.91823.3200.1160.1160.0000.0000.0000.000
82A166TRP0-0.0170.01226.875-0.008-0.0080.0000.0000.0000.000
83A167HIS00.026-0.00129.2170.0100.0100.0000.0000.0000.000
84A168HIS0-0.032-0.01432.708-0.008-0.0080.0000.0000.0000.000
85A169SER0-0.022-0.01034.6490.0030.0030.0000.0000.0000.000
86A170LEU00.0410.00436.613-0.001-0.0010.0000.0000.0000.000
87A171LEU0-0.0150.01337.0720.0000.0000.0000.0000.0000.000
88A172VAL0-0.006-0.01239.7890.0050.0050.0000.0000.0000.000
89A173PRO00.0580.01342.565-0.003-0.0030.0000.0000.0000.000
90A174HIS00.0060.01140.3100.0070.0070.0000.0000.0000.000
91A175ASP-1-0.898-0.93944.995-0.084-0.0840.0000.0000.0000.000
92A176HIS0-0.0230.00046.9390.0040.0040.0000.0000.0000.000
93A177PRO00.0260.00148.8080.0000.0000.0000.0000.0000.000
94A178LEU0-0.019-0.01446.7290.0020.0020.0000.0000.0000.000
95A179THR0-0.037-0.01744.8030.0010.0010.0000.0000.0000.000
96A180GLN0-0.034-0.01547.0290.0030.0030.0000.0000.0000.000
97A181ILE0-0.066-0.01649.3320.0040.0040.0000.0000.0000.000
98A182SER0-0.023-0.01247.932-0.004-0.0040.0000.0000.0000.000
99A183PRO0-0.012-0.02047.4880.0030.0030.0000.0000.0000.000
100A184LEU00.0480.04743.0070.0020.0020.0000.0000.0000.000
101A185THR00.0300.01346.0300.0000.0000.0000.0000.0000.000
102A186LEU00.0440.03143.944-0.001-0.0010.0000.0000.0000.000
103A187GLU-1-0.757-0.87847.436-0.057-0.0570.0000.0000.0000.000
104A188SER0-0.064-0.03349.2010.0030.0030.0000.0000.0000.000
105A189ILE00.0280.00643.617-0.001-0.0010.0000.0000.0000.000
106A190ALA00.006-0.01147.828-0.001-0.0010.0000.0000.0000.000
107A191LYS10.8210.91949.9680.0590.0590.0000.0000.0000.000
108A192TRP00.009-0.00148.8220.0010.0010.0000.0000.0000.000
109A193PRO00.0570.03549.304-0.001-0.0010.0000.0000.0000.000
110A194LEU0-0.044-0.01844.491-0.004-0.0040.0000.0000.0000.000
111A195ILE0-0.0110.00841.2670.0000.0000.0000.0000.0000.000
112A196THR0-0.004-0.03438.719-0.005-0.0050.0000.0000.0000.000
113A197TYR00.0050.00433.2170.0020.0020.0000.0000.0000.000
114A198ARG10.9440.96638.1020.1260.1260.0000.0000.0000.000
115A199GLN0-0.030-0.02938.639-0.003-0.0030.0000.0000.0000.000
116A200GLY0-0.002-0.00137.7820.0000.0000.0000.0000.0000.000
117A201ILE0-0.057-0.02233.823-0.006-0.0060.0000.0000.0000.000
118A202THR00.0110.00331.1400.0030.0030.0000.0000.0000.000
119A203GLY00.1090.06532.9950.0010.0010.0000.0000.0000.000
120A204ARG10.7900.87534.8220.0990.0990.0000.0000.0000.000
121A205SER0-0.029-0.03436.5880.0060.0060.0000.0000.0000.000
122A206ARG10.9070.93633.4610.1080.1080.0000.0000.0000.000
123A207ILE0-0.0070.01538.0720.0040.0040.0000.0000.0000.000
124A208ASP-1-0.777-0.86741.103-0.080-0.0800.0000.0000.0000.000
125A209ASP-1-0.840-0.90142.263-0.058-0.0580.0000.0000.0000.000
126A210ALA00.0160.01142.3490.0040.0040.0000.0000.0000.000
127A211PHE0-0.018-0.02044.3180.0030.0030.0000.0000.0000.000
128A212ALA00.0410.02747.0160.0040.0040.0000.0000.0000.000
129A213ARG10.6960.80040.9110.0700.0700.0000.0000.0000.000
130A214LYS10.7880.88248.6800.0570.0570.0000.0000.0000.000
131A215GLY0-0.0200.00351.0920.0020.0020.0000.0000.0000.000
132A216LEU0-0.074-0.03650.5960.0010.0010.0000.0000.0000.000
133A217LEU00.000-0.01249.542-0.001-0.0010.0000.0000.0000.000
134A218ALA00.0040.00646.2890.0000.0000.0000.0000.0000.000
135A219ASP-1-0.854-0.92648.299-0.071-0.0710.0000.0000.0000.000
136A220ILE0-0.081-0.03644.094-0.004-0.0040.0000.0000.0000.000
137A221VAL00.0220.02147.1280.0010.0010.0000.0000.0000.000
138A222LEU0-0.022-0.00841.853-0.002-0.0020.0000.0000.0000.000
139A223SER0-0.022-0.01942.1470.0000.0000.0000.0000.0000.000
140A224ALA00.0240.02637.9630.0000.0000.0000.0000.0000.000
141A225GLN0-0.008-0.02535.6120.0100.0100.0000.0000.0000.000
142A226ASP-1-0.829-0.92032.856-0.173-0.1730.0000.0000.0000.000
143A227SER00.0760.02631.7590.0110.0110.0000.0000.0000.000
144A228ASP-1-0.742-0.83831.239-0.216-0.2160.0000.0000.0000.000
145A229VAL00.0120.01234.5630.0080.0080.0000.0000.0000.000
146A230ILE0-0.026-0.00836.2690.0070.0070.0000.0000.0000.000
147A231LYS10.8590.94230.9450.2140.2140.0000.0000.0000.000
148A232THR0-0.023-0.01737.9540.0050.0050.0000.0000.0000.000
149A233TYR0-0.017-0.02340.2330.0080.0080.0000.0000.0000.000
150A234VAL0-0.0190.00041.1480.0060.0060.0000.0000.0000.000
151A235ALA00.0170.01241.2030.0050.0050.0000.0000.0000.000
152A236LEU0-0.084-0.03243.2150.0040.0040.0000.0000.0000.000
153A237GLY00.0170.01145.9230.0050.0050.0000.0000.0000.000
154A238LEU0-0.084-0.03446.1850.0040.0040.0000.0000.0000.000
155A239GLY00.015-0.00647.0920.0040.0040.0000.0000.0000.000
156A240ILE0-0.0340.00544.396-0.003-0.0030.0000.0000.0000.000
157A241GLY00.0480.01340.5840.0010.0010.0000.0000.0000.000
158A242LEU0-0.054-0.01339.0500.0010.0010.0000.0000.0000.000
159A243VAL00.0120.00934.151-0.002-0.0020.0000.0000.0000.000
160A244ALA00.0120.00430.1720.0040.0040.0000.0000.0000.000
161A245GLU-1-0.769-0.85029.167-0.165-0.1650.0000.0000.0000.000
162A246GLN00.0530.01225.2910.0090.0090.0000.0000.0000.000
163A247SER0-0.065-0.05427.454-0.011-0.0110.0000.0000.0000.000
164A248SER00.0310.01229.6970.0030.0030.0000.0000.0000.000
165A249GLY0-0.031-0.00326.2710.0010.0010.0000.0000.0000.000
166A250GLU-1-0.832-0.91625.778-0.279-0.2790.0000.0000.0000.000
167A251GLN0-0.071-0.04227.8170.0050.0050.0000.0000.0000.000
168A252GLU-1-0.929-0.95231.118-0.175-0.1750.0000.0000.0000.000
169A253GLU-1-0.763-0.87332.957-0.169-0.1690.0000.0000.0000.000
170A254GLU-1-0.833-0.90036.539-0.127-0.1270.0000.0000.0000.000
171A255ASN0-0.091-0.05638.8560.0090.0090.0000.0000.0000.000
172A256LEU0-0.045-0.01839.1870.0070.0070.0000.0000.0000.000
173A257ILE00.0470.02739.021-0.005-0.0050.0000.0000.0000.000
174A258ARG10.7500.84132.8520.1720.1720.0000.0000.0000.000
175A259LEU00.0060.01038.0390.0010.0010.0000.0000.0000.000
176A260ASP-1-0.835-0.92736.605-0.115-0.1150.0000.0000.0000.000
177A261THR00.006-0.02037.8880.0060.0060.0000.0000.0000.000
178A262ARG10.7980.88831.8390.1350.1350.0000.0000.0000.000
179A263HIS0-0.073-0.02937.3070.0010.0010.0000.0000.0000.000
180A264LEU0-0.073-0.03340.4230.0060.0060.0000.0000.0000.000
181A265PHE00.0260.00937.9700.0020.0020.0000.0000.0000.000
182A266ASP-1-0.801-0.86736.960-0.074-0.0740.0000.0000.0000.000
183A267ALA0-0.045-0.01331.591-0.006-0.0060.0000.0000.0000.000
184A268ASN00.003-0.00530.8430.0120.0120.0000.0000.0000.000
185A269THR0-0.016-0.02826.6060.0010.0010.0000.0000.0000.000
186A270VAL0-0.0470.01023.3130.0030.0030.0000.0000.0000.000
187A271TRP00.015-0.00924.2270.0050.0050.0000.0000.0000.000
188A272LEU00.0090.00017.806-0.023-0.0230.0000.0000.0000.000
189A273GLY0-0.018-0.00721.7930.0260.0260.0000.0000.0000.000
190A274LEU00.0630.01918.613-0.024-0.0240.0000.0000.0000.000
191A275LYS10.8970.94522.8700.0830.0830.0000.0000.0000.000
192A276ARG10.8720.91124.6120.0380.0380.0000.0000.0000.000
193A277GLY00.0080.00426.189-0.001-0.0010.0000.0000.0000.000
194A278GLN0-0.062-0.02422.2620.0100.0100.0000.0000.0000.000
195A279LEU00.029-0.00120.8530.0010.0010.0000.0000.0000.000
196A280GLN00.035-0.00617.021-0.022-0.0220.0000.0000.0000.000
197A281ARG10.8410.93212.0830.2640.2640.0000.0000.0000.000
198A282ASN00.013-0.0128.603-0.099-0.0990.0000.0000.0000.000
199A283TYR00.036-0.0089.4690.0220.0220.0000.0000.0000.000
200A284VAL0-0.0010.01010.444-0.086-0.0860.0000.0000.0000.000
201A285TRP0-0.011-0.02612.604-0.019-0.0190.0000.0000.0000.000
202A286ARG10.8630.9195.872-0.260-0.2600.0000.0000.0000.000
203A287PHE00.0430.01610.191-0.102-0.1020.0000.0000.0000.000
204A288LEU00.0100.00512.169-0.002-0.0020.0000.0000.0000.000
205A289GLU-1-0.855-0.9068.961-0.121-0.1210.0000.0000.0000.000
206A290LEU0-0.039-0.0207.967-0.007-0.0070.0000.0000.0000.000
207A291CYS0-0.080-0.02211.048-0.014-0.0140.0000.0000.0000.000
208A292ASN0-0.022-0.03114.7530.0320.0320.0000.0000.0000.000
209A293ALA00.0540.02814.1310.0350.0350.0000.0000.0000.000
210A294GLY0-0.029-0.00215.1180.0570.0570.0000.0000.0000.000
211A295LEU0-0.065-0.02716.8470.0360.0360.0000.0000.0000.000
212A296SER00.004-0.02514.5730.0000.0000.0000.0000.0000.000
213A297VAL00.0410.00610.906-0.032-0.0320.0000.0000.0000.000
214A298GLU-1-0.813-0.90714.0100.3400.3400.0000.0000.0000.000
215A299ASP-1-0.811-0.85816.8960.1090.1090.0000.0000.0000.000
216A300ILE0-0.0050.00715.582-0.017-0.0170.0000.0000.0000.000
217A301LYS10.8180.89913.545-0.287-0.2870.0000.0000.0000.000
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