FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: N1Z4Q

Calculation Name: 1I1R-A-Xray372

Preferred Name: Interleukin-6 receptor subunit beta

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1I1R

Chain ID: A

ChEMBL ID: CHEMBL3124734

UniProt ID: P40189

Base Structure: X-ray

Registration Date: 2023-03-13

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 297
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3647074.146716
FMO2-HF: Nuclear repulsion 3525897.518121
FMO2-HF: Total energy -121176.628595
FMO2-MP2: Total energy -121528.132071


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-3.265-0.9040.411-0.834-1.939-0.001
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / 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].
3A4ASP-1-0.821-0.8952.602-4.727-2.5260.412-0.814-1.800-0.001
4A5PRO00.0360.0254.5230.5270.687-0.001-0.020-0.1390.000
5A6CYS0-0.058-0.0168.253-0.014-0.0140.0000.0000.0000.000
6A7GLY00.037-0.00410.9420.0120.0120.0000.0000.0000.000
7A8TYR0-0.030-0.00111.632-0.074-0.0740.0000.0000.0000.000
8A9ILE00.0030.00613.8630.0540.0540.0000.0000.0000.000
9A10SER0-0.0330.00516.941-0.039-0.0390.0000.0000.0000.000
10A11PRO00.029-0.00919.2410.0240.0240.0000.0000.0000.000
11A12GLU-1-0.830-0.87814.787-0.385-0.3850.0000.0000.0000.000
12A13SER00.025-0.01817.7170.0240.0240.0000.0000.0000.000
13A14PRO0-0.091-0.02420.1380.0100.0100.0000.0000.0000.000
14A15VAL00.0420.01423.6450.0120.0120.0000.0000.0000.000
15A16VAL0-0.017-0.01726.830-0.003-0.0030.0000.0000.0000.000
16A17GLN0-0.028-0.02229.8480.0040.0040.0000.0000.0000.000
17A18LEU0-0.0010.01833.6150.0000.0000.0000.0000.0000.000
18A19HIS0-0.023-0.01135.941-0.002-0.0020.0000.0000.0000.000
19A20SER0-0.063-0.03433.550-0.002-0.0020.0000.0000.0000.000
20A21ASN00.012-0.00633.5990.0040.0040.0000.0000.0000.000
21A22PHE00.0130.00523.930-0.006-0.0060.0000.0000.0000.000
22A23THR0-0.012-0.01826.2970.0090.0090.0000.0000.0000.000
23A24ALA0-0.0010.02622.757-0.013-0.0130.0000.0000.0000.000
24A25VAL00.010-0.02020.8940.0160.0160.0000.0000.0000.000
25A26CYS0-0.090-0.00318.340-0.016-0.0160.0000.0000.0000.000
26A27VAL0-0.016-0.01214.9630.0250.0250.0000.0000.0000.000
27A28LEU00.0460.01714.747-0.034-0.0340.0000.0000.0000.000
28A29LYS10.7930.8796.2101.2301.2300.0000.0000.0000.000
29A30GLU-1-0.776-0.87112.721-0.122-0.1220.0000.0000.0000.000
30A31LYS10.9980.9939.0490.2230.2230.0000.0000.0000.000
31A33MET0-0.044-0.00713.4570.0450.0450.0000.0000.0000.000
32A34ASP-1-0.887-0.94615.321-0.071-0.0710.0000.0000.0000.000
33A35TYR0-0.084-0.03113.3150.0510.0510.0000.0000.0000.000
34A36PHE0-0.013-0.02412.9330.0290.0290.0000.0000.0000.000
35A37HIS0-0.0170.00217.841-0.011-0.0110.0000.0000.0000.000
36A38VAL0-0.0010.01818.231-0.003-0.0030.0000.0000.0000.000
37A39ASN00.019-0.01020.482-0.014-0.0140.0000.0000.0000.000
38A40ALA00.0430.01921.6250.0060.0060.0000.0000.0000.000
39A41ASN0-0.062-0.05022.7610.0030.0030.0000.0000.0000.000
40A42TYR0-0.029-0.00222.4710.0050.0050.0000.0000.0000.000
41A43ILE0-0.029-0.01119.3820.0050.0050.0000.0000.0000.000
42A44VAL0-0.029-0.01622.8410.0080.0080.0000.0000.0000.000
43A45TRP00.0060.00021.839-0.013-0.0130.0000.0000.0000.000
44A46LYS10.8350.90224.3440.0350.0350.0000.0000.0000.000
45A47THR00.0090.00225.004-0.015-0.0150.0000.0000.0000.000
46A48ASN00.012-0.00327.1490.0040.0040.0000.0000.0000.000
47A49HIS0-0.003-0.00624.9910.0100.0100.0000.0000.0000.000
48A50PHE0-0.0180.01227.9820.0070.0070.0000.0000.0000.000
49A51THR0-0.025-0.02827.988-0.008-0.0080.0000.0000.0000.000
50A52ILE00.0080.02627.5770.0030.0030.0000.0000.0000.000
51A53PRO00.0190.02030.0750.0010.0010.0000.0000.0000.000
52A54LYS10.9450.93630.3830.0310.0310.0000.0000.0000.000
53A55GLU-1-0.865-0.92531.382-0.042-0.0420.0000.0000.0000.000
54A56GLN0-0.024-0.01231.9840.0030.0030.0000.0000.0000.000
55A57TYR0-0.053-0.02327.411-0.008-0.0080.0000.0000.0000.000
56A58THR0-0.024-0.00928.1390.0060.0060.0000.0000.0000.000
57A59ILE0-0.0040.00625.622-0.012-0.0120.0000.0000.0000.000
58A60ILE00.0120.01523.1150.0040.0040.0000.0000.0000.000
59A61ASN00.006-0.00922.138-0.004-0.0040.0000.0000.0000.000
60A62ARG10.8710.89619.4090.1230.1230.0000.0000.0000.000
61A63THR00.0400.02217.4020.0180.0180.0000.0000.0000.000
62A64ALA0-0.0120.00119.018-0.023-0.0230.0000.0000.0000.000
63A65SER00.0350.01721.2990.0200.0200.0000.0000.0000.000
64A66SER0-0.022-0.02522.690-0.016-0.0160.0000.0000.0000.000
65A67VAL00.0490.03025.2150.0140.0140.0000.0000.0000.000
66A68THR00.0110.00827.456-0.013-0.0130.0000.0000.0000.000
67A69PHE0-0.0110.00626.9710.0080.0080.0000.0000.0000.000
68A70THR0-0.009-0.02632.131-0.004-0.0040.0000.0000.0000.000
69A71ASP-1-0.878-0.94335.423-0.060-0.0600.0000.0000.0000.000
70A72ILE0-0.021-0.00530.6090.0030.0030.0000.0000.0000.000
71A73ALA00.0640.02834.8790.0000.0000.0000.0000.0000.000
72A74SER0-0.046-0.02232.3180.0050.0050.0000.0000.0000.000
73A75LEU00.0440.03132.633-0.006-0.0060.0000.0000.0000.000
74A76ASN0-0.048-0.02526.503-0.006-0.0060.0000.0000.0000.000
75A77ILE00.0070.01427.1030.0110.0110.0000.0000.0000.000
76A78GLN00.0660.05122.650-0.002-0.0020.0000.0000.0000.000
77A79LEU0-0.021-0.02023.1480.0130.0130.0000.0000.0000.000
78A80THR00.001-0.00120.002-0.022-0.0220.0000.0000.0000.000
79A82ASN00.0410.00218.425-0.027-0.0270.0000.0000.0000.000
80A83ILE00.0330.01416.484-0.011-0.0110.0000.0000.0000.000
81A84LEU0-0.0050.00520.6250.0180.0180.0000.0000.0000.000
82A85THR0-0.041-0.02718.4210.0020.0020.0000.0000.0000.000
83A86PHE00.030-0.00721.8060.0020.0020.0000.0000.0000.000
84A87GLY0-0.0020.00223.7440.0120.0120.0000.0000.0000.000
85A88GLN0-0.065-0.03225.829-0.004-0.0040.0000.0000.0000.000
86A89LEU00.0310.03320.169-0.001-0.0010.0000.0000.0000.000
87A90GLU-1-0.789-0.85721.695-0.025-0.0250.0000.0000.0000.000
88A91GLN0-0.025-0.01215.2610.0230.0230.0000.0000.0000.000
89A92ASN0-0.065-0.05116.111-0.035-0.0350.0000.0000.0000.000
90A93VAL0-0.053-0.01314.3250.0080.0080.0000.0000.0000.000
91A94TYR0-0.018-0.04611.410-0.083-0.0830.0000.0000.0000.000
92A95GLY0-0.024-0.01015.3640.0560.0560.0000.0000.0000.000
93A96ILE00.0390.03517.147-0.032-0.0320.0000.0000.0000.000
94A97THR0-0.041-0.03519.7210.0320.0320.0000.0000.0000.000
95A98ILE00.0010.02122.932-0.010-0.0100.0000.0000.0000.000
96A99ILE0-0.013-0.00324.8400.0120.0120.0000.0000.0000.000
97A100SER0-0.046-0.04527.876-0.003-0.0030.0000.0000.0000.000
98A101GLY00.0660.03031.3110.0050.0050.0000.0000.0000.000
99A102LEU0-0.047-0.02434.1700.0000.0000.0000.0000.0000.000
100A103PRO00.0640.03834.671-0.001-0.0010.0000.0000.0000.000
101A104PRO0-0.0050.01034.7940.0070.0070.0000.0000.0000.000
102A105GLU-1-0.813-0.89137.793-0.056-0.0560.0000.0000.0000.000
103A106LYS10.8260.89141.2770.0560.0560.0000.0000.0000.000
104A107PRO0-0.027-0.00341.3160.0030.0030.0000.0000.0000.000
105A108LYS10.8400.90544.2820.0510.0510.0000.0000.0000.000
106A109ASN0-0.043-0.04748.1050.0000.0000.0000.0000.0000.000
107A110LEU0-0.0390.01446.5620.0010.0010.0000.0000.0000.000
108A111SER0-0.0170.00049.6480.0020.0020.0000.0000.0000.000
109A112CYS0-0.028-0.01147.095-0.001-0.0010.0000.0000.0000.000
110A113ILE0-0.0100.00152.1860.0020.0020.0000.0000.0000.000
111A114VAL00.0370.01452.907-0.001-0.0010.0000.0000.0000.000
112A115ASN00.0210.02054.4920.0000.0000.0000.0000.0000.000
113A116GLU-1-0.725-0.85755.662-0.022-0.0220.0000.0000.0000.000
114A117GLY0-0.0030.00156.5730.0010.0010.0000.0000.0000.000
115A118LYS10.8780.94052.0290.0250.0250.0000.0000.0000.000
116A119LYS10.8600.93247.0900.0360.0360.0000.0000.0000.000
117A120MET0-0.0110.00648.4320.0010.0010.0000.0000.0000.000
118A121ARG10.8310.90448.3470.0330.0330.0000.0000.0000.000
119A123GLU-1-0.735-0.83747.170-0.039-0.0390.0000.0000.0000.000
120A124TRP0-0.014-0.01541.6010.0000.0000.0000.0000.0000.000
121A125ASP-1-0.828-0.89246.745-0.042-0.0420.0000.0000.0000.000
122A126GLY0-0.003-0.01343.796-0.003-0.0030.0000.0000.0000.000
123A127GLY0-0.037-0.02742.9970.0020.0020.0000.0000.0000.000
124A128ARG10.8480.92339.0840.0720.0720.0000.0000.0000.000
125A129GLU-1-0.829-0.90338.499-0.065-0.0650.0000.0000.0000.000
126A130THR0-0.075-0.05535.6920.0000.0000.0000.0000.0000.000
127A131HIS00.016-0.01135.126-0.005-0.0050.0000.0000.0000.000
128A132LEU00.0060.01329.725-0.005-0.0050.0000.0000.0000.000
129A133GLU-1-0.942-0.95829.308-0.096-0.0960.0000.0000.0000.000
130A134THR0-0.038-0.01831.619-0.007-0.0070.0000.0000.0000.000
131A135ASN0-0.024-0.00930.3700.0080.0080.0000.0000.0000.000
132A136PHE00.0600.01934.4850.0000.0000.0000.0000.0000.000
133A137THR0-0.012-0.01635.9440.0010.0010.0000.0000.0000.000
134A138LEU0-0.0070.01238.536-0.001-0.0010.0000.0000.0000.000
135A139LYS10.8200.91136.1820.0830.0830.0000.0000.0000.000
136A140SER00.001-0.00141.6780.0040.0040.0000.0000.0000.000
137A141GLU-1-0.862-0.93442.191-0.066-0.0660.0000.0000.0000.000
138A142TRP00.0640.02445.5290.0020.0020.0000.0000.0000.000
139A143ALA0-0.003-0.00946.863-0.002-0.0020.0000.0000.0000.000
140A144THR0-0.028-0.01647.388-0.001-0.0010.0000.0000.0000.000
141A145HIS0-0.007-0.00143.126-0.001-0.0010.0000.0000.0000.000
142A146LYS10.8570.93738.4360.0680.0680.0000.0000.0000.000
143A147PHE0-0.027-0.00341.8710.0010.0010.0000.0000.0000.000
144A148ALA00.0180.00738.999-0.004-0.0040.0000.0000.0000.000
145A149ASP-1-0.820-0.90836.675-0.074-0.0740.0000.0000.0000.000
146A150CYS0-0.074-0.02937.991-0.003-0.0030.0000.0000.0000.000
147A151LYS10.9080.95031.3320.0950.0950.0000.0000.0000.000
148A152ALA00.0300.01037.6670.0030.0030.0000.0000.0000.000
149A153LYS10.9010.95437.4120.0440.0440.0000.0000.0000.000
150A154ARG10.8970.91633.2950.0560.0560.0000.0000.0000.000
151A155ASP-1-0.804-0.88337.422-0.046-0.0460.0000.0000.0000.000
152A156THR0-0.040-0.02540.8080.0030.0030.0000.0000.0000.000
153A157PRO00.0260.02239.220-0.001-0.0010.0000.0000.0000.000
154A158THR00.0150.00240.992-0.002-0.0020.0000.0000.0000.000
155A159SER0-0.005-0.02643.7510.0020.0020.0000.0000.0000.000
156A161THR0-0.036-0.02344.1500.0030.0030.0000.0000.0000.000
157A162VAL0-0.032-0.00843.866-0.001-0.0010.0000.0000.0000.000
158A163ASP-1-0.808-0.90941.321-0.047-0.0470.0000.0000.0000.000
159A164TYR00.0390.01243.9210.0040.0040.0000.0000.0000.000
160A165SER0-0.054-0.04646.1780.0010.0010.0000.0000.0000.000
161A166THR00.0190.00249.999-0.001-0.0010.0000.0000.0000.000
162A167VAL0-0.0030.01051.7370.0010.0010.0000.0000.0000.000
163A168TYR00.002-0.00754.058-0.001-0.0010.0000.0000.0000.000
164A169PHE0-0.007-0.01657.2080.0000.0000.0000.0000.0000.000
165A170VAL0-0.013-0.00153.2500.0000.0000.0000.0000.0000.000
166A171ASN0-0.080-0.04354.1510.0010.0010.0000.0000.0000.000
167A172ILE0-0.065-0.02047.500-0.001-0.0010.0000.0000.0000.000
168A173GLU-1-0.767-0.85446.642-0.050-0.0500.0000.0000.0000.000
169A174VAL0-0.016-0.03346.246-0.001-0.0010.0000.0000.0000.000
170A175TRP0-0.012-0.01140.2490.0010.0010.0000.0000.0000.000
171A176VAL00.0370.01841.159-0.001-0.0010.0000.0000.0000.000
172A177GLU-1-0.821-0.88734.798-0.095-0.0950.0000.0000.0000.000
173A178ALA00.005-0.01037.1170.0020.0020.0000.0000.0000.000
174A179GLU-1-0.857-0.92930.740-0.123-0.1230.0000.0000.0000.000
175A180ASN00.011-0.00130.946-0.003-0.0030.0000.0000.0000.000
176A181ALA00.0360.01426.848-0.002-0.0020.0000.0000.0000.000
177A182LEU0-0.0150.02328.424-0.006-0.0060.0000.0000.0000.000
178A183GLY0-0.024-0.01531.1500.0030.0030.0000.0000.0000.000
179A184LYS10.8070.89331.5400.1150.1150.0000.0000.0000.000
180A185VAL0-0.031-0.00734.3950.0020.0020.0000.0000.0000.000
181A186THR0-0.006-0.01438.191-0.001-0.0010.0000.0000.0000.000
182A187SER0-0.005-0.01140.8840.0010.0010.0000.0000.0000.000
183A188ASP-1-0.825-0.89444.502-0.055-0.0550.0000.0000.0000.000
184A189HIS10.8130.90143.1330.0600.0600.0000.0000.0000.000
185A190ILE00.0020.01248.0220.0020.0020.0000.0000.0000.000
186A191ASN00.004-0.01050.1660.0010.0010.0000.0000.0000.000
187A192PHE00.001-0.00851.1470.0020.0020.0000.0000.0000.000
188A193ASP-1-0.726-0.85054.207-0.032-0.0320.0000.0000.0000.000
189A194PRO00.011-0.01253.0060.0010.0010.0000.0000.0000.000
190A195VAL0-0.0050.00555.6640.0010.0010.0000.0000.0000.000
191A196TYR0-0.026-0.01058.9820.0010.0010.0000.0000.0000.000
192A197LYS10.8470.92554.8840.0330.0330.0000.0000.0000.000
193A198VAL00.0240.02157.3290.0000.0000.0000.0000.0000.000
194A199LYS10.7720.88758.5490.0240.0240.0000.0000.0000.000
195A200PRO0-0.025-0.01659.8270.0000.0000.0000.0000.0000.000
196A201ASN0-0.036-0.03459.7650.0000.0000.0000.0000.0000.000
197A202PRO00.0070.00963.0710.0000.0000.0000.0000.0000.000
198A203PRO0-0.036-0.02766.6430.0000.0000.0000.0000.0000.000
199A204HIS00.0330.01366.9770.0010.0010.0000.0000.0000.000
200A205ASN0-0.005-0.02270.3320.0000.0000.0000.0000.0000.000
201A206LEU0-0.0280.00773.0910.0000.0000.0000.0000.0000.000
202A207SER0-0.015-0.00675.2070.0000.0000.0000.0000.0000.000
203A208VAL0-0.011-0.01578.7770.0000.0000.0000.0000.0000.000
204A209ILE0-0.009-0.00582.2020.0000.0000.0000.0000.0000.000
205A210ASN00.0160.01085.4480.0000.0000.0000.0000.0000.000
206A211SER0-0.038-0.02887.3000.0000.0000.0000.0000.0000.000
207A212GLU-1-0.903-0.96189.363-0.010-0.0100.0000.0000.0000.000
208A213GLU-1-0.873-0.91192.679-0.008-0.0080.0000.0000.0000.000
209A214LEU0-0.023-0.02594.2460.0000.0000.0000.0000.0000.000
210A215SER0-0.039-0.04093.9100.0000.0000.0000.0000.0000.000
211A216SER00.0150.00892.4950.0000.0000.0000.0000.0000.000
212A217ILE0-0.019-0.00388.8190.0000.0000.0000.0000.0000.000
213A218LEU0-0.026-0.00985.4240.0000.0000.0000.0000.0000.000
214A219LYS10.9150.97983.3580.0110.0110.0000.0000.0000.000
215A220LEU00.0250.01978.4430.0000.0000.0000.0000.0000.000
216A221THR0-0.013-0.02979.0900.0000.0000.0000.0000.0000.000
217A222TRP0-0.007-0.00172.7960.0000.0000.0000.0000.0000.000
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