FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VV5L1

Calculation Name: 2B5I-D-Xray540

Preferred Name: Interleukin-2 receptor alpha chain

Target Type: SINGLE PROTEIN

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2B5I

Chain ID: D

ChEMBL ID: CHEMBL1778

UniProt ID: P01589

Base Structure: X-ray

Registration Date: 2025-07-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1049763.251327
FMO2-HF: Nuclear repulsion 995415.722672
FMO2-HF: Total energy -54347.528655
FMO2-MP2: Total energy -54493.992193


3D Structure Molmil
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(D:1:GLU)


Summations of interaction energy for fragment #1(D:1:GLU)
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.
-12.639-9.5743.166-2.488-3.7440.009
Interaction energy analysis for fragmet #1(D:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : -0.035
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].
4D2LEU0-0.1150.0562.3080.3100.6420.858-0.218-0.972-0.001
5D3CYS00.149-0.0583.824-2.045-0.576-0.018-0.758-0.6930.000
6D3CYS0-0.3390.1764.9210.3310.3310.0000.0000.0000.000
7D4ASP00.112-0.0566.221-0.618-0.6180.0000.0000.0000.000
8D4ASP-1-0.860-0.8489.5112.1312.1310.0000.0000.0000.000
9D5ASP00.162-0.0049.742-0.300-0.3000.0000.0000.0000.000
10D5ASP-1-0.964-0.88112.2281.4641.4640.0000.0000.0000.000
11D6ASP00.029-0.12411.0790.2260.2260.0000.0000.0000.000
12D6ASP-1-0.940-0.82413.5860.5140.5140.0000.0000.0000.000
13D7PRO0-0.067-0.14612.6230.0160.0160.0000.0000.0000.000
14D8PRO00.0340.01415.039-0.088-0.0880.0000.0000.0000.000
15D9GLU00.107-0.01518.5340.0030.0030.0000.0000.0000.000
16D9GLU-1-0.967-0.81520.9230.3320.3320.0000.0000.0000.000
17D10ILE00.044-0.09921.6570.0060.0060.0000.0000.0000.000
18D10ILE0-0.1000.10621.8730.0000.0000.0000.0000.0000.000
19D11PRO00.011-0.11624.101-0.027-0.0270.0000.0000.0000.000
20D12HIS00.0410.02627.6780.0050.0050.0000.0000.0000.000
21D12HIS0-0.0780.08330.431-0.008-0.0080.0000.0000.0000.000
22D13ALA00.189-0.11825.478-0.024-0.0240.0000.0000.0000.000
23D13ALA0-0.0370.09624.8590.0060.0060.0000.0000.0000.000
24D14THR0-0.023-0.03722.8360.0110.0110.0000.0000.0000.000
25D14THR0-0.0200.04922.859-0.001-0.0010.0000.0000.0000.000
26D15PHE00.076-0.09518.880-0.011-0.0110.0000.0000.0000.000
27D15PHE0-0.0230.11416.0180.0190.0190.0000.0000.0000.000
28D16LYS00.045-0.10618.059-0.028-0.0280.0000.0000.0000.000
29D16LYS10.8471.02619.484-0.225-0.2250.0000.0000.0000.000
30D17ALA00.113-0.10114.4640.0550.0550.0000.0000.0000.000
31D17ALA0-0.0230.15113.9690.0110.0110.0000.0000.0000.000
32D18MET00.075-0.09715.918-0.060-0.0600.0000.0000.0000.000
33D18MET0-0.1370.07317.9600.0030.0030.0000.0000.0000.000
34D19ALA00.088-0.11814.892-0.075-0.0750.0000.0000.0000.000
35D19ALA0-0.1110.09614.702-0.003-0.0030.0000.0000.0000.000
36D20TYR00.066-0.09011.3330.2000.2000.0000.0000.0000.000
37D20TYR0-0.1220.05711.1980.0040.0040.0000.0000.0000.000
38D21LYS00.126-0.0907.558-0.273-0.2730.0000.0000.0000.000
39D21LYS10.8501.0596.812-1.001-1.0010.0000.0000.0000.000
40D22GLU00.198-0.1337.8900.2170.2170.0000.0000.0000.000
41D22GLU-1-1.048-0.8206.028-2.035-2.0350.0000.0000.0000.000
42D23GLY0-0.039-0.0854.947-0.657-0.572-0.002-0.003-0.0800.000
43D24THR00.0210.0325.9950.1380.120-0.0020.0010.0190.000
44D24THR0-0.1290.0158.3530.1170.1170.0000.0000.0000.000
45D25MET00.069-0.1208.176-0.215-0.2150.0000.0000.0000.000
46D25MET0-0.1160.1008.750-0.065-0.0650.0000.0000.0000.000
47D26LEU00.129-0.09111.0370.1850.1850.0000.0000.0000.000
48D26LEU0-0.1320.10914.800-0.003-0.0030.0000.0000.0000.000
49D27ASN00.106-0.08014.584-0.099-0.0990.0000.0000.0000.000
50D27ASN0-0.0930.05515.504-0.041-0.0410.0000.0000.0000.000
51D28CYS00.071-0.08717.0740.0300.0300.0000.0000.0000.000
52D28CYS0-0.2590.22719.854-0.019-0.0190.0000.0000.0000.000
53D29GLU00.126-0.12520.492-0.010-0.0100.0000.0000.0000.000
54D29GLU-1-0.885-0.77920.077-0.126-0.1260.0000.0000.0000.000
55D30CYS00.080-0.09522.7670.0020.0020.0000.0000.0000.000
56D30CYS0-0.2430.20426.569-0.006-0.0060.0000.0000.0000.000
57D31LYS00.118-0.07026.4420.0130.0130.0000.0000.0000.000
58D31LYS10.7931.02829.4600.0510.0510.0000.0000.0000.000
59D32ARG00.076-0.11429.175-0.011-0.0110.0000.0000.0000.000
60D32ARG10.9121.10129.8630.0000.0000.0000.0000.0000.000
61D33GLY00.054-0.08331.9480.0020.0020.0000.0000.0000.000
62D34PHE0-0.003-0.02231.071-0.003-0.0030.0000.0000.0000.000
63D34PHE0-0.0450.09430.418-0.001-0.0010.0000.0000.0000.000
64D35ARG00.127-0.07928.6040.0070.0070.0000.0000.0000.000
65D35ARG10.7651.02528.7360.1680.1680.0000.0000.0000.000
66D36ARG00.151-0.07725.2880.0070.0070.0000.0000.0000.000
67D36ARG10.8731.07222.8960.2910.2910.0000.0000.0000.000
68D37ILE00.057-0.08626.7730.0120.0120.0000.0000.0000.000
69D37ILE0-0.0650.11127.7160.0000.0000.0000.0000.0000.000
70D38LYS00.016-0.10927.208-0.016-0.0160.0000.0000.0000.000
71D38LYS10.9001.06030.6180.1770.1770.0000.0000.0000.000
72D39SER0-0.058-0.11126.1190.0000.0000.0000.0000.0000.000
73D39SER0-0.0210.08126.6970.0070.0070.0000.0000.0000.000
74D40GLY00.078-0.06924.288-0.022-0.0220.0000.0000.0000.000
75D41SER00.0210.00519.7480.0020.0020.0000.0000.0000.000
76D41SER00.0320.09818.6770.0170.0170.0000.0000.0000.000
77D42LEU00.062-0.11018.6400.0550.0550.0000.0000.0000.000
78D42LEU0-0.0760.10117.7790.0020.0020.0000.0000.0000.000
79D43TYR00.088-0.07815.1260.0840.0840.0000.0000.0000.000
80D43TYR0-0.0760.09312.1900.0550.0550.0000.0000.0000.000
81D44MET00.101-0.13015.435-0.042-0.0420.0000.0000.0000.000
82D44MET0-0.1400.10415.9720.0370.0370.0000.0000.0000.000
83D45LEU00.121-0.09911.4650.1110.1110.0000.0000.0000.000
84D45LEU0-0.0810.1208.1570.0570.0570.0000.0000.0000.000
85D46CYS00.091-0.09210.6640.0630.0630.0000.0000.0000.000
86D46CYS0-0.2560.2269.8660.0270.0270.0000.0000.0000.000
87D47THR00.175-0.0309.295-0.416-0.4160.0000.0000.0000.000
88D47THR0-0.1460.04910.473-0.108-0.1080.0000.0000.0000.000
89D48GLY0-0.028-0.1679.8420.1220.1220.0000.0000.0000.000
90D49ASN00.1890.10510.6410.0940.0940.0000.0000.0000.000
91D49ASN0-0.1540.01912.150-0.149-0.1490.0000.0000.0000.000
92D50SER00.101-0.05111.7680.1630.1630.0000.0000.0000.000
93D50SER0-0.0470.07913.189-0.033-0.0330.0000.0000.0000.000
94D51SER0-0.050-0.13513.9430.0880.0880.0000.0000.0000.000
95D51SER0-0.0220.07716.8760.0120.0120.0000.0000.0000.000
96D52HIS0-0.008-0.07515.5000.1060.1060.0000.0000.0000.000
97D52HIS0-0.0690.06016.283-0.059-0.0590.0000.0000.0000.000
98D53SER00.108-0.15313.660-0.117-0.1170.0000.0000.0000.000
99D53SER00.0160.06412.960-0.022-0.0220.0000.0000.0000.000
100D54SER0-0.089-0.05814.2970.1320.1320.0000.0000.0000.000
101D54SER0-0.0210.07816.4610.0140.0140.0000.0000.0000.000
102D55TRP00.084-0.07713.917-0.156-0.1560.0000.0000.0000.000
103D55TRP0-0.1220.06812.596-0.009-0.0090.0000.0000.0000.000
104D56ASP00.139-0.09914.2860.1310.1310.0000.0000.0000.000
105D56ASP-1-0.951-0.78913.169-1.281-1.2810.0000.0000.0000.000
106D57ASN0-0.037-0.07915.8190.0310.0310.0000.0000.0000.000
107D57ASN0-0.0470.07915.8080.0670.0670.0000.0000.0000.000
108D58GLN00.143-0.13118.1390.0040.0040.0000.0000.0000.000
109D58GLN0-0.1070.11221.2020.0260.0260.0000.0000.0000.000
110D59CYS00.063-0.15621.049-0.007-0.0070.0000.0000.0000.000
111D60GLN00.142-0.07222.2930.0180.0180.0000.0000.0000.000
112D60GLN0-0.0720.10825.919-0.014-0.0140.0000.0000.0000.000
113D61CYS00.031-0.14026.045-0.012-0.0120.0000.0000.0000.000
114D62THR00.023-0.09328.5190.0040.0040.0000.0000.0000.000
115D62THR0-0.0100.08031.336-0.005-0.0050.0000.0000.0000.000
116D63SER00.101-0.05831.9890.0000.0000.0000.0000.0000.000
117D63SER00.0190.09836.1710.0040.0040.0000.0000.0000.000
118D64SER0-0.221-0.20034.031-0.008-0.0080.0000.0000.0000.000
119D64SER00.0730.08132.9780.0010.0010.0000.0000.0000.000
120D103HIS00.1750.09311.615-0.020-0.0200.0000.0000.0000.000
121D103HIS0-0.1180.05710.6860.2380.2380.0000.0000.0000.000
122D104CYS00.053-0.13012.560-0.022-0.0220.0000.0000.0000.000
123D105ARG00.115-0.08714.2960.1050.1050.0000.0000.0000.000
124D105ARG10.8601.06218.6720.0280.0280.0000.0000.0000.000
125D106GLU00.139-0.11116.921-0.056-0.0560.0000.0000.0000.000
126D106GLU-1-0.885-0.74818.059-0.007-0.0070.0000.0000.0000.000
127D107PRO0-0.055-0.10316.831-0.005-0.0050.0000.0000.0000.000
128D108PRO00.0240.00119.6550.0350.0350.0000.0000.0000.000
129D109PRO0-0.001-0.00723.158-0.018-0.0180.0000.0000.0000.000
130D110TRP00.1240.05024.6440.0060.0060.0000.0000.0000.000
131D110TRP0-0.0860.09719.693-0.018-0.0180.0000.0000.0000.000
132D111GLU00.142-0.03126.1920.0120.0120.0000.0000.0000.000
133D111GLU-1-1.104-0.93629.671-0.108-0.1080.0000.0000.0000.000
134D112ASN00.096-0.05028.9260.0140.0140.0000.0000.0000.000
135D112ASN0-0.1300.01930.0900.0120.0120.0000.0000.0000.000
136D113GLU00.080-0.14525.711-0.021-0.0210.0000.0000.0000.000
137D113GLU-1-0.773-0.69323.080-0.104-0.1040.0000.0000.0000.000
138D114ALA0-0.004-0.14324.6230.0150.0150.0000.0000.0000.000
139D114ALA0-0.0120.13323.6220.0010.0010.0000.0000.0000.000
140D115THR00.019-0.07324.752-0.009-0.0090.0000.0000.0000.000
141D115THR0-0.0750.02426.731-0.004-0.0040.0000.0000.0000.000
142D116GLU00.081-0.09322.731-0.003-0.0030.0000.0000.0000.000
143D116GLU-1-1.003-0.85021.8200.1170.1170.0000.0000.0000.000
144D117ARG00.082-0.10419.374-0.022-0.0220.0000.0000.0000.000
145D117ARG10.6650.93018.3750.0960.0960.0000.0000.0000.000
146D118ILE00.127-0.08017.0420.0600.0600.0000.0000.0000.000
147D118ILE0-0.1010.10115.602-0.004-0.0040.0000.0000.0000.000
148D119TYR00.013-0.11813.312-0.120-0.1200.0000.0000.0000.000
149D119TYR0-0.0870.05512.283-0.012-0.0120.0000.0000.0000.000
150D120HIS00.098-0.0839.8840.1770.1770.0000.0000.0000.000
151D120HIS0-0.1120.0909.180-0.031-0.0310.0000.0000.0000.000
152D121PHE00.085-0.0567.828-0.443-0.4430.0000.0000.0000.000
153D121PHE0-0.0540.0758.2790.0230.0230.0000.0000.0000.000
154D122VAL00.136-0.0973.3740.097-0.2320.0060.345-0.0230.000
155D122VAL0-0.0350.1612.375-0.0030.3601.100-0.840-0.6230.003
156D123VAL00.153-0.1083.179-2.830-2.4620.032-0.188-0.2120.001
157D123VAL0-0.0910.1182.479-1.180-0.4971.194-0.824-1.0530.006
158D124GLY0-0.098-0.1604.824-0.993-0.881-0.002-0.003-0.1070.000
159D125GLN00.055-0.0327.194-0.660-0.6600.0000.0000.0000.000
160D125GLN0-0.0930.1097.781-0.068-0.0680.0000.0000.0000.000
161D126MET00.115-0.0899.0220.1930.1930.0000.0000.0000.000
162D126MET0-0.1040.09713.084-0.054-0.0540.0000.0000.0000.000
163D127VAL0-0.010-0.13612.745-0.117-0.1170.0000.0000.0000.000
164D127VAL0-0.0650.14512.503-0.003-0.0030.0000.0000.0000.000
165D128TYR00.160-0.09415.0990.0400.0400.0000.0000.0000.000
166D128TYR0-0.1130.07817.535-0.009-0.0090.0000.0000.0000.000
167D129TYR00.115-0.07918.893-0.028-0.0280.0000.0000.0000.000
168D129TYR0-0.1190.06617.2130.0190.0190.0000.0000.0000.000
169D130GLN00.042-0.09721.534-0.004-0.0040.0000.0000.0000.000
170D130GLN0-0.0840.09324.067-0.003-0.0030.0000.0000.0000.000
171D131CYS00.093-0.10425.1700.0010.0010.0000.0000.0000.000
172D131CYS0-0.2640.24528.3150.0070.0070.0000.0000.0000.000
173D132VAL00.103-0.06928.293-0.008-0.0080.0000.0000.0000.000
174D132VAL0-0.0600.11628.467-0.001-0.0010.0000.0000.0000.000
175D133GLN00.057-0.12629.5210.0030.0030.0000.0000.0000.000
176D133GLN0-0.0560.12230.2280.0080.0080.0000.0000.0000.000
177D134GLY00.008-0.11332.714-0.008-0.0080.0000.0000.0000.000
178D135TYR00.013-0.02632.634-0.007-0.0070.0000.0000.0000.000
179D135TYR0-0.1120.10131.817-0.001-0.0010.0000.0000.0000.000
180D136ARG00.096-0.09132.8230.0040.0040.0000.0000.0000.000
181D136ARG10.8031.04235.310-0.139-0.1390.0000.0000.0000.000
182D137ALA00.180-0.09830.2140.0040.0040.0000.0000.0000.000
183D137ALA0-0.0840.09229.3110.0010.0010.0000.0000.0000.000
184D138LEU00.088-0.11130.714-0.011-0.0110.0000.0000.0000.000
185D138LEU0-0.1450.10431.689-0.002-0.0020.0000.0000.0000.000
186D139HIS00.081-0.09828.1870.0180.0180.0000.0000.0000.000
187D139HIS0-0.0370.10726.5110.0170.0170.0000.0000.0000.000
188D140ARG00.103-0.11327.670-0.023-0.0230.0000.0000.0000.000
189D140ARG10.8281.09626.684-0.363-0.3630.0000.0000.0000.000
190D141GLY0-0.017-0.10025.2220.0280.0280.0000.0000.0000.000
191D142PRO00.0350.02320.283-0.033-0.0330.0000.0000.0000.000
192D143ALA00.1370.04022.1470.0240.0240.0000.0000.0000.000
193D143ALA0-0.0740.10823.200-0.012-0.0120.0000.0000.0000.000
194D144GLU00.061-0.10317.940-0.046-0.0460.0000.0000.0000.000
195D144GLU-1-0.984-0.87516.9760.5700.5700.0000.0000.0000.000
196D145SER00.008-0.14315.586-0.002-0.0020.0000.0000.0000.000
197D145SER0-0.0310.08314.9640.0530.0530.0000.0000.0000.000
198D146VAL00.115-0.09712.002-0.054-0.0540.0000.0000.0000.000
199D146VAL0-0.1640.06010.923-0.014-0.0140.0000.0000.0000.000
200D147CYS00.164-0.0698.231-0.237-0.2370.0000.0000.0000.000
201D148LYS00.075-0.0668.2800.6000.6000.0000.0000.0000.000
202D148LYS10.8231.02011.063-1.696-1.6960.0000.0000.0000.000
203D149MET00.149-0.1056.896-0.044-0.0440.0000.0000.0000.000
204D149MET0-0.0870.1365.0660.0480.0480.0000.0000.0000.000
205D150THR0-0.021-0.0618.238-0.360-0.3600.0000.0000.0000.000
206D150THR0-0.142-0.01711.756-0.175-0.1750.0000.0000.0000.000
207D151HIS00.211-0.04210.0800.3430.3430.0000.0000.0000.000
208D151HIS0-0.1250.08813.596-0.100-0.1000.0000.0000.0000.000
209D152GLY0-0.015-0.1368.591-0.348-0.3480.0000.0000.0000.000
210D153LYS00.070-0.0059.2520.1600.1600.0000.0000.0000.000
211D153LYS10.7511.01510.580-1.714-1.7140.0000.0000.0000.000
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