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: N639Q

Calculation Name: 2B5I-B-Xray547

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: B

ChEMBL ID: CHEMBL1778

UniProt ID: P01589

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2295603.391597
FMO2-HF: Nuclear repulsion 2212001.656969
FMO2-HF: Total energy -83601.734628
FMO2-MP2: Total energy -83843.140191


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(B:6:SER)


Summations of interaction energy for fragment #1(B:6: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.
-169.037-177.09445.524-21.219-16.246-0.194
Interaction energy analysis for fragmet #1(B:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.775 / q_NPA : 0.852
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].
3B8PHE00.011-0.0123.750-1.2370.282-0.022-0.753-0.7430.000
16B22TRP00.0400.0084.613-2.787-2.662-0.001-0.010-0.1140.000
17B23SER00.0540.0342.571-9.512-6.0460.417-2.079-1.804-0.024
18B24GLN00.0220.0052.205-24.281-23.7725.029-2.967-2.571-0.034
19B25ASP-1-0.803-0.8961.595-155.558-169.39240.064-15.348-10.881-0.135
20B26GLY0-0.0170.0143.25710.51610.6740.037-0.062-0.133-0.001
4B9THR0-0.016-0.0116.7102.2352.2350.0000.0000.0000.000
5B10CYS0-0.065-0.0229.927-0.234-0.2340.0000.0000.0000.000
6B11PHE00.0700.02513.2840.1460.1460.0000.0000.0000.000
7B12TYR0-0.073-0.04716.8960.2800.2800.0000.0000.0000.000
8B13ASN00.0700.03120.3310.1830.1830.0000.0000.0000.000
9B14SER0-0.0040.00523.0860.8290.8290.0000.0000.0000.000
10B15ARG10.8440.92725.57410.56410.5640.0000.0000.0000.000
11B16ALA00.0050.02325.936-0.126-0.1260.0000.0000.0000.000
12B17GLN0-0.001-0.00120.1560.4380.4380.0000.0000.0000.000
13B18ILE00.0100.01316.3370.1050.1050.0000.0000.0000.000
14B19SER0-0.027-0.00815.9510.0200.0200.0000.0000.0000.000
15B21VAL00.0270.0117.9141.0291.0290.0000.0000.0000.000
21B27ALA0-0.011-0.0066.8234.2594.2590.0000.0000.0000.000
22B28LEU0-0.0190.0158.246-2.479-2.4790.0000.0000.0000.000
23B29GLN0-0.020-0.0349.2503.1553.1550.0000.0000.0000.000
24B30ASP-1-0.773-0.86711.483-18.522-18.5220.0000.0000.0000.000
25B31THR0-0.044-0.02713.180-0.459-0.4590.0000.0000.0000.000
26B32SER0-0.058-0.02514.5620.3100.3100.0000.0000.0000.000
27B33CYS00.054-0.0039.849-3.411-3.4110.0000.0000.0000.000
28B34GLN00.0230.01712.5811.5901.5900.0000.0000.0000.000
29B35VAL00.0220.00811.489-1.643-1.6430.0000.0000.0000.000
30B36HIS0-0.036-0.03713.6802.0462.0460.0000.0000.0000.000
31B37ALA0-0.009-0.00715.927-0.772-0.7720.0000.0000.0000.000
32B38TRP00.0370.00218.0921.4661.4660.0000.0000.0000.000
33B39PRO0-0.018-0.01220.656-0.338-0.3380.0000.0000.0000.000
34B40ASP-1-0.749-0.84522.969-12.270-12.2700.0000.0000.0000.000
35B41ARG10.8160.89024.46112.21012.2100.0000.0000.0000.000
36B42ARG10.7860.87026.63511.64811.6480.0000.0000.0000.000
37B43ARG10.9260.95527.9339.8909.8900.0000.0000.0000.000
38B44TRP00.0180.01423.0170.1630.1630.0000.0000.0000.000
39B45GLN0-0.008-0.00322.1050.1100.1100.0000.0000.0000.000
40B46GLN0-0.021-0.00921.1270.3110.3110.0000.0000.0000.000
41B47THR0-0.015-0.00918.300-0.693-0.6930.0000.0000.0000.000
42B48CYS0-0.031-0.00912.3301.2721.2720.0000.0000.0000.000
43B49GLU-1-0.904-0.95116.027-17.171-17.1710.0000.0000.0000.000
44B50LEU0-0.048-0.0259.589-0.237-0.2370.0000.0000.0000.000
45B51LEU00.0270.01813.2070.1250.1250.0000.0000.0000.000
46B52PRO0-0.016-0.00511.937-1.557-1.5570.0000.0000.0000.000
47B53VAL0-0.007-0.00511.8801.6001.6000.0000.0000.0000.000
48B54SER00.002-0.00310.3831.2911.2910.0000.0000.0000.000
49B55GLN00.009-0.00310.896-2.245-2.2450.0000.0000.0000.000
50B56ALA0-0.0010.0076.305-0.186-0.1860.0000.0000.0000.000
51B57SER0-0.031-0.0235.832-8.057-8.0570.0000.0000.0000.000
52B58TRP00.0270.0166.3831.9971.9970.0000.0000.0000.000
53B59ALA00.0240.0149.511-1.780-1.7800.0000.0000.0000.000
54B61ASN00.0220.02014.624-0.016-0.0160.0000.0000.0000.000
55B62LEU00.0330.02516.2060.6380.6380.0000.0000.0000.000
56B63ILE00.0350.01419.4440.3380.3380.0000.0000.0000.000
57B64LEU00.0070.00121.3970.2910.2910.0000.0000.0000.000
58B65GLY0-0.021-0.02525.0380.5100.5100.0000.0000.0000.000
59B66ALA00.0400.03328.133-0.174-0.1740.0000.0000.0000.000
60B67PRO00.0580.02528.349-0.086-0.0860.0000.0000.0000.000
61B68ASP-1-0.768-0.88528.777-10.369-10.3690.0000.0000.0000.000
62B69SER0-0.101-0.04730.2280.1580.1580.0000.0000.0000.000
63B70GLN00.0150.00028.421-0.104-0.1040.0000.0000.0000.000
64B71LYS10.8720.94326.64210.84010.8400.0000.0000.0000.000
65B72LEU0-0.034-0.00322.500-0.112-0.1120.0000.0000.0000.000
66B73THR00.0250.00226.7520.3910.3910.0000.0000.0000.000
67B74THR00.0300.00926.755-0.424-0.4240.0000.0000.0000.000
68B75VAL0-0.0110.00227.166-0.085-0.0850.0000.0000.0000.000
69B76ASP-1-0.781-0.85924.771-11.692-11.6920.0000.0000.0000.000
70B77ILE0-0.015-0.00920.044-0.402-0.4020.0000.0000.0000.000
71B78VAL0-0.022-0.01518.4640.3990.3990.0000.0000.0000.000
72B79THR00.0080.00116.283-0.674-0.6740.0000.0000.0000.000
73B80LEU0-0.056-0.02613.4130.4770.4770.0000.0000.0000.000
74B81ARG10.9220.95012.15618.23718.2370.0000.0000.0000.000
75B82VAL00.0250.0257.9840.9260.9260.0000.0000.0000.000
76B83LEU0-0.028-0.00910.395-0.389-0.3890.0000.0000.0000.000
77B85ARG10.9130.96212.51816.46716.4670.0000.0000.0000.000
78B86GLU-1-0.777-0.86114.442-18.781-18.7810.0000.0000.0000.000
79B87GLY0-0.013-0.00816.1140.9690.9690.0000.0000.0000.000
80B88VAL0-0.026-0.01719.7770.1760.1760.0000.0000.0000.000
81B89ARG10.8620.92218.22016.65116.6510.0000.0000.0000.000
82B90TRP00.0500.02615.005-0.230-0.2300.0000.0000.0000.000
83B91ARG10.8580.93211.26724.48224.4820.0000.0000.0000.000
84B92VAL0-0.012-0.01810.741-0.926-0.9260.0000.0000.0000.000
85B93MET0-0.012-0.0076.1540.5560.5560.0000.0000.0000.000
86B94ALA0-0.0030.0015.943-6.084-6.0840.0000.0000.0000.000
87B95ILE00.005-0.0097.7753.7973.7970.0000.0000.0000.000
88B96GLN00.0070.00110.2070.0860.0860.0000.0000.0000.000
89B97ASP-1-0.844-0.89912.779-17.354-17.3540.0000.0000.0000.000
90B98PHE0-0.015-0.01115.3000.6290.6290.0000.0000.0000.000
91B99LYS11.0341.01817.12215.23415.2340.0000.0000.0000.000
92B100PRO00.0060.00420.095-0.236-0.2360.0000.0000.0000.000
93B101PHE0-0.013-0.02821.493-0.116-0.1160.0000.0000.0000.000
94B102GLU-1-0.853-0.91820.116-13.149-13.1490.0000.0000.0000.000
95B103ASN0-0.0270.00015.730-1.391-1.3910.0000.0000.0000.000
96B104LEU0-0.0150.00318.436-0.296-0.2960.0000.0000.0000.000
97B105ARG10.9320.97116.01717.30117.3010.0000.0000.0000.000
98B106LEU00.0010.00820.704-0.072-0.0720.0000.0000.0000.000
99B107MET0-0.011-0.01523.262-0.685-0.6850.0000.0000.0000.000
100B108ALA00.0090.00725.1330.2250.2250.0000.0000.0000.000
101B109PRO0-0.061-0.01926.8420.1730.1730.0000.0000.0000.000
102B110ILE0-0.006-0.00830.558-0.174-0.1740.0000.0000.0000.000
103B111SER0-0.019-0.04932.9450.0990.0990.0000.0000.0000.000
104B112LEU0-0.049-0.01133.0320.2130.2130.0000.0000.0000.000
105B113GLN0-0.021-0.00636.9010.2430.2430.0000.0000.0000.000
106B114VAL00.0210.00640.567-0.019-0.0190.0000.0000.0000.000
107B115VAL0-0.045-0.00943.1760.0870.0870.0000.0000.0000.000
108B116HIS0-0.046-0.04645.5540.1430.1430.0000.0000.0000.000
109B117VAL0-0.009-0.00246.099-0.133-0.1330.0000.0000.0000.000
110B118GLU-1-0.862-0.92448.306-6.037-6.0370.0000.0000.0000.000
111B119THR00.024-0.00549.611-0.094-0.0940.0000.0000.0000.000
112B120HIS00.0340.02248.851-0.056-0.0560.0000.0000.0000.000
113B121ARG10.7660.85346.5396.4086.4080.0000.0000.0000.000
114B122CYS0-0.047-0.01642.7730.0670.0670.0000.0000.0000.000
115B123ASN00.0340.03243.188-0.291-0.2910.0000.0000.0000.000
116B124ILE00.0130.01037.9910.0290.0290.0000.0000.0000.000
117B125SER0-0.005-0.00539.441-0.040-0.0400.0000.0000.0000.000
118B126TRP0-0.004-0.01333.910-0.104-0.1040.0000.0000.0000.000
119B127GLU-1-0.831-0.87535.474-8.350-8.3500.0000.0000.0000.000
120B128ILE0-0.058-0.03931.318-0.386-0.3860.0000.0000.0000.000
121B129SER00.0280.01829.0670.1420.1420.0000.0000.0000.000
122B130GLN00.025-0.00126.611-0.260-0.2600.0000.0000.0000.000
123B131ALA0-0.0060.00028.008-0.469-0.4690.0000.0000.0000.000
124B132SER0-0.019-0.02629.0790.4410.4410.0000.0000.0000.000
125B133HIS00.0550.02030.9150.0630.0630.0000.0000.0000.000
126B134TYR0-0.063-0.03630.3770.3830.3830.0000.0000.0000.000
127B135PHE00.0300.00926.392-0.012-0.0120.0000.0000.0000.000
128B136GLU-1-0.815-0.88732.101-8.152-8.1520.0000.0000.0000.000
129B137ARG10.8610.89835.4397.7717.7710.0000.0000.0000.000
130B138HIS10.8520.93632.0519.0769.0760.0000.0000.0000.000
131B139LEU00.000-0.00429.236-0.407-0.4070.0000.0000.0000.000
132B140GLU-1-0.872-0.92528.088-10.393-10.3930.0000.0000.0000.000
133B141PHE0-0.022-0.01929.586-0.300-0.3000.0000.0000.0000.000
134B142GLU-1-0.798-0.88026.505-11.398-11.3980.0000.0000.0000.000
135B143ALA0-0.011-0.00529.876-0.163-0.1630.0000.0000.0000.000
136B144ARG10.8880.96526.39611.08511.0850.0000.0000.0000.000
137B145THR00.009-0.00832.3650.0600.0600.0000.0000.0000.000
138B146LEU0-0.0070.02432.8140.0120.0120.0000.0000.0000.000
139B147SER00.009-0.00835.4430.2620.2620.0000.0000.0000.000
140B148PRO00.033-0.00137.843-0.143-0.1430.0000.0000.0000.000
141B149GLY0-0.0230.00339.138-0.032-0.0320.0000.0000.0000.000
142B150HIS10.8350.92335.0338.2668.2660.0000.0000.0000.000
143B151THR00.018-0.01430.294-0.110-0.1100.0000.0000.0000.000
144B152TRP00.041-0.00528.6090.1270.1270.0000.0000.0000.000
145B153GLU-1-0.948-0.98725.477-11.530-11.5300.0000.0000.0000.000
146B154GLU-1-0.840-0.89228.184-9.146-9.1460.0000.0000.0000.000
147B155ALA0-0.0240.00531.0720.3040.3040.0000.0000.0000.000
148B156PRO0-0.035-0.02230.980-0.270-0.2700.0000.0000.0000.000
149B157LEU0-0.0120.00026.646-0.002-0.0020.0000.0000.0000.000
150B158LEU0-0.013-0.00631.1020.2100.2100.0000.0000.0000.000
151B159THR0-0.022-0.02031.374-0.263-0.2630.0000.0000.0000.000
152B160LEU00.0060.00932.7130.3090.3090.0000.0000.0000.000
153B161LYS10.9690.98332.1688.9448.9440.0000.0000.0000.000
154B162GLN0-0.002-0.01533.9860.0240.0240.0000.0000.0000.000
155B163LYS10.9030.96234.7278.6738.6730.0000.0000.0000.000
156B164GLN0-0.046-0.02135.6370.2930.2930.0000.0000.0000.000
157B165GLU-1-0.880-0.95535.388-8.985-8.9850.0000.0000.0000.000
158B166TRP00.0280.01237.3440.0800.0800.0000.0000.0000.000
159B167ILE0-0.018-0.01236.911-0.100-0.1000.0000.0000.0000.000
160B168CYS-1-0.785-0.84639.999-6.904-6.9040.0000.0000.0000.000
161B169LEU0-0.054-0.01838.293-0.107-0.1070.0000.0000.0000.000
162B170GLU-1-0.777-0.90542.349-6.496-6.4960.0000.0000.0000.000
163B171THR0-0.082-0.04044.013-0.070-0.0700.0000.0000.0000.000
164B172LEU0-0.0300.00242.207-0.100-0.1000.0000.0000.0000.000
165B173THR0-0.026-0.02145.7040.1900.1900.0000.0000.0000.000
166B174PRO00.0590.04047.453-0.105-0.1050.0000.0000.0000.000
167B175ASP-1-0.849-0.89549.182-6.406-6.4060.0000.0000.0000.000
168B176THR0-0.037-0.01943.509-0.075-0.0750.0000.0000.0000.000
169B177GLN0-0.040-0.02841.621-0.077-0.0770.0000.0000.0000.000
170B178TYR00.0350.01039.568-0.004-0.0040.0000.0000.0000.000
171B179GLU-1-0.885-0.94234.116-9.258-9.2580.0000.0000.0000.000
172B180PHE00.000-0.00234.966-0.067-0.0670.0000.0000.0000.000
173B181GLN0-0.015-0.00127.415-0.195-0.1950.0000.0000.0000.000
174B182VAL00.0160.00730.5670.0630.0630.0000.0000.0000.000
175B183ARG10.8260.90121.95512.30012.3000.0000.0000.0000.000
176B184VAL00.0450.01426.6600.3560.3560.0000.0000.0000.000
177B185LYS10.8520.93022.60211.39111.3910.0000.0000.0000.000
178B186PRO00.0190.01024.4540.4850.4850.0000.0000.0000.000
179B187LEU0-0.022-0.00925.765-0.282-0.2820.0000.0000.0000.000
180B188GLN0-0.052-0.01625.3800.2530.2530.0000.0000.0000.000
181B189GLY00.0400.02922.416-0.283-0.2830.0000.0000.0000.000
182B190GLU-1-0.950-0.97718.566-15.649-15.6490.0000.0000.0000.000
183B191PHE0-0.023-0.01114.953-0.570-0.5700.0000.0000.0000.000
184B192THR0-0.079-0.05117.260-0.873-0.8730.0000.0000.0000.000
185B193THR0-0.041-0.02316.2720.0560.0560.0000.0000.0000.000
186B194TRP00.002-0.01219.6770.3660.3660.0000.0000.0000.000
187B195SER0-0.025-0.00820.862-0.537-0.5370.0000.0000.0000.000
188B196PRO0-0.035-0.02920.7400.0110.0110.0000.0000.0000.000
189B197TRP00.0290.01622.8560.4570.4570.0000.0000.0000.000
190B198SER00.0230.01926.090-0.240-0.2400.0000.0000.0000.000
191B199GLN00.002-0.00628.105-0.446-0.4460.0000.0000.0000.000
192B200PRO0-0.0060.00630.1700.1320.1320.0000.0000.0000.000
193B201LEU0-0.0140.00032.7830.1290.1290.0000.0000.0000.000
194B202ALA00.0140.00636.4120.0640.0640.0000.0000.0000.000
195B203PHE0-0.022-0.01938.6580.1410.1410.0000.0000.0000.000
196B204ARG10.8330.89742.1126.6016.6010.0000.0000.0000.000
197B205THR0-0.025-0.02345.1760.0250.0250.0000.0000.0000.000
198B206LYS10.8590.92747.4776.2566.2560.0000.0000.0000.000
199B207PRO-1-0.874-0.92951.223-5.901-5.9010.0000.0000.0000.000