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: GN811

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 OptH
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 -3653659.839702
FMO2-HF: Nuclear repulsion 3532486.19245
FMO2-HF: Total energy -121173.647252
FMO2-MP2: Total energy -121525.455678


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.
-11.048-9.9566.433-3.361-4.164-0.029
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 : -0.035 / q_NPA : -0.024
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-1-0.870-0.9482.160-12.849-11.8666.434-3.353-4.065-0.029
4A5PRO0-0.015-0.0015.0300.9251.034-0.001-0.008-0.0990.000
5A6CYS0-0.046-0.0078.6450.0920.0920.0000.0000.0000.000
6A7GLY00.030-0.01111.4880.0680.0680.0000.0000.0000.000
7A8TYR0-0.0240.00112.239-0.104-0.1040.0000.0000.0000.000
8A9ILE00.0110.01714.2880.0850.0850.0000.0000.0000.000
9A10SER0-0.061-0.00416.757-0.050-0.0500.0000.0000.0000.000
10A11PRO00.014-0.01518.6670.0370.0370.0000.0000.0000.000
11A12GLU-1-0.781-0.83914.577-0.681-0.6810.0000.0000.0000.000
12A13SER00.0350.00317.4960.0050.0050.0000.0000.0000.000
13A14PRO0-0.103-0.02920.0180.0140.0140.0000.0000.0000.000
14A15VAL00.0610.02623.2780.0100.0100.0000.0000.0000.000
15A16VAL0-0.041-0.03326.5080.0000.0000.0000.0000.0000.000
16A17GLN00.0200.00529.3990.0010.0010.0000.0000.0000.000
17A18LEU0-0.060-0.01133.109-0.001-0.0010.0000.0000.0000.000
18A19HIS00.0380.00235.434-0.001-0.0010.0000.0000.0000.000
19A20SER0-0.076-0.02632.6520.0000.0000.0000.0000.0000.000
20A21ASN00.0300.00932.7990.0040.0040.0000.0000.0000.000
21A22PHE0-0.001-0.00723.231-0.008-0.0080.0000.0000.0000.000
22A23THR0-0.018-0.00825.8680.0100.0100.0000.0000.0000.000
23A24ALA0-0.0170.01322.707-0.019-0.0190.0000.0000.0000.000
24A25VAL00.011-0.01320.7200.0240.0240.0000.0000.0000.000
25A26CYS0-0.051-0.01318.512-0.019-0.0190.0000.0000.0000.000
26A27VAL0-0.040-0.01915.4340.0460.0460.0000.0000.0000.000
27A28LEU00.0310.00815.337-0.072-0.0720.0000.0000.0000.000
28A29LYS10.9140.9467.1631.5371.5370.0000.0000.0000.000
29A30GLU-1-0.797-0.91113.354-0.151-0.1510.0000.0000.0000.000
30A31LYS10.9800.9948.6330.1320.1320.0000.0000.0000.000
31A33MET0-0.024-0.00313.5490.0540.0540.0000.0000.0000.000
32A34ASP-1-0.876-0.93615.981-0.059-0.0590.0000.0000.0000.000
33A35TYR0-0.107-0.04713.8000.0590.0590.0000.0000.0000.000
34A36PHE0-0.018-0.02213.7630.0260.0260.0000.0000.0000.000
35A37HIS0-0.0110.01318.171-0.009-0.0090.0000.0000.0000.000
36A38VAL0-0.0160.00018.933-0.001-0.0010.0000.0000.0000.000
37A39ASN00.010-0.00120.664-0.014-0.0140.0000.0000.0000.000
38A40ALA00.0590.02621.8920.0030.0030.0000.0000.0000.000
39A41ASN0-0.031-0.02723.043-0.002-0.0020.0000.0000.0000.000
40A42TYR0-0.042-0.02622.4180.0100.0100.0000.0000.0000.000
41A43ILE0-0.0200.00219.729-0.002-0.0020.0000.0000.0000.000
42A44VAL0-0.035-0.01123.1000.0140.0140.0000.0000.0000.000
43A45TRP0-0.006-0.03221.943-0.030-0.0300.0000.0000.0000.000
44A46LYS10.9370.97224.6100.1380.1380.0000.0000.0000.000
45A47THR00.030-0.00125.256-0.020-0.0200.0000.0000.0000.000
46A48ASN00.0070.02026.9120.0070.0070.0000.0000.0000.000
47A49HIS0-0.002-0.01525.9270.0170.0170.0000.0000.0000.000
48A50PHE0-0.0120.01028.2560.0140.0140.0000.0000.0000.000
49A51THR0-0.022-0.02528.653-0.014-0.0140.0000.0000.0000.000
50A52ILE0-0.0200.00227.3230.0080.0080.0000.0000.0000.000
51A53PRO00.0270.03430.448-0.001-0.0010.0000.0000.0000.000
52A54LYS11.0200.99130.7130.0750.0750.0000.0000.0000.000
53A55GLU-1-0.919-0.95931.794-0.089-0.0890.0000.0000.0000.000
54A56GLN0-0.037-0.02132.2460.0060.0060.0000.0000.0000.000
55A57TYR0-0.067-0.03327.727-0.014-0.0140.0000.0000.0000.000
56A58THR0-0.0330.00128.6440.0090.0090.0000.0000.0000.000
57A59ILE00.006-0.00526.095-0.016-0.0160.0000.0000.0000.000
58A60ILE0-0.0110.00122.8290.0080.0080.0000.0000.0000.000
59A61ASN00.0400.02021.8310.0040.0040.0000.0000.0000.000
60A62ARG10.8910.92619.7340.1530.1530.0000.0000.0000.000
61A63THR00.0420.01118.0150.0150.0150.0000.0000.0000.000
62A64ALA0-0.028-0.01619.573-0.033-0.0330.0000.0000.0000.000
63A65SER00.0710.05321.7550.0290.0290.0000.0000.0000.000
64A66SER0-0.022-0.00423.189-0.027-0.0270.0000.0000.0000.000
65A67VAL00.0680.03725.5570.0210.0210.0000.0000.0000.000
66A68THR00.0270.00127.575-0.016-0.0160.0000.0000.0000.000
67A69PHE0-0.0170.00527.1390.0110.0110.0000.0000.0000.000
68A70THR0-0.007-0.03531.780-0.004-0.0040.0000.0000.0000.000
69A71ASP-1-0.905-0.96134.850-0.107-0.1070.0000.0000.0000.000
70A72ILE0-0.030-0.00430.3090.0020.0020.0000.0000.0000.000
71A73ALA00.0710.03534.4640.0020.0020.0000.0000.0000.000
72A74SER0-0.058-0.01532.0480.0060.0060.0000.0000.0000.000
73A75LEU00.0640.01832.599-0.008-0.0080.0000.0000.0000.000
74A76ASN0-0.049-0.02726.556-0.012-0.0120.0000.0000.0000.000
75A77ILE00.0090.02527.1940.0150.0150.0000.0000.0000.000
76A78GLN00.0310.03721.786-0.002-0.0020.0000.0000.0000.000
77A79LEU0-0.022-0.02022.7370.0240.0240.0000.0000.0000.000
78A80THR0-0.009-0.00420.361-0.043-0.0430.0000.0000.0000.000
79A82ASN00.0590.03018.832-0.051-0.0510.0000.0000.0000.000
80A83ILE00.0340.02516.966-0.001-0.0010.0000.0000.0000.000
81A84LEU0-0.015-0.01420.7580.0160.0160.0000.0000.0000.000
82A85THR0-0.033-0.02618.6060.0100.0100.0000.0000.0000.000
83A86PHE00.019-0.01721.9350.0100.0100.0000.0000.0000.000
84A87GLY00.0080.00823.9100.0110.0110.0000.0000.0000.000
85A88GLN0-0.082-0.04126.540-0.005-0.0050.0000.0000.0000.000
86A89LEU00.0200.03520.1550.0020.0020.0000.0000.0000.000
87A90GLU-1-0.901-0.94422.613-0.117-0.1170.0000.0000.0000.000
88A91GLN0-0.005-0.01215.6050.0200.0200.0000.0000.0000.000
89A92ASN0-0.030-0.03816.434-0.050-0.0500.0000.0000.0000.000
90A93VAL0-0.083-0.02314.661-0.020-0.0200.0000.0000.0000.000
91A94TYR0-0.045-0.10011.592-0.133-0.1330.0000.0000.0000.000
92A95GLY00.0030.00115.7040.0900.0900.0000.0000.0000.000
93A96ILE00.0060.02617.244-0.049-0.0490.0000.0000.0000.000
94A97THR0-0.011-0.01219.8030.0480.0480.0000.0000.0000.000
95A98ILE0-0.029-0.01622.865-0.015-0.0150.0000.0000.0000.000
96A99ILE00.0070.00425.5410.0200.0200.0000.0000.0000.000
97A100SER0-0.020-0.00827.701-0.003-0.0030.0000.0000.0000.000
98A101GLY00.0460.02330.9080.0040.0040.0000.0000.0000.000
99A102LEU0-0.044-0.02133.7400.0020.0020.0000.0000.0000.000
100A103PRO00.0490.04634.289-0.003-0.0030.0000.0000.0000.000
101A104PRO00.010-0.00234.3910.0090.0090.0000.0000.0000.000
102A105GLU-1-0.892-0.94637.438-0.091-0.0910.0000.0000.0000.000
103A106LYS10.9500.96840.7940.0920.0920.0000.0000.0000.000
104A107PRO0-0.024-0.00240.7730.0050.0050.0000.0000.0000.000
105A108LYS10.9750.98143.8020.0840.0840.0000.0000.0000.000
106A109ASN0-0.071-0.05147.5720.0020.0020.0000.0000.0000.000
107A110LEU0-0.0290.01645.9370.0000.0000.0000.0000.0000.000
108A111SER0-0.034-0.01148.9760.0030.0030.0000.0000.0000.000
109A112CYS0-0.057-0.02046.0220.0000.0000.0000.0000.0000.000
110A113ILE0-0.0040.00151.2740.0030.0030.0000.0000.0000.000
111A114VAL00.0300.01252.070-0.002-0.0020.0000.0000.0000.000
112A115ASN0-0.002-0.00153.5490.0000.0000.0000.0000.0000.000
113A116GLU-1-0.741-0.87854.721-0.036-0.0360.0000.0000.0000.000
114A117GLY0-0.026-0.01055.3840.0000.0000.0000.0000.0000.000
115A118LYS10.8890.94650.9430.0470.0470.0000.0000.0000.000
116A119LYS10.8950.97045.7760.0570.0570.0000.0000.0000.000
117A120MET0-0.0120.00347.3770.0010.0010.0000.0000.0000.000
118A121ARG10.9230.96647.3380.0570.0570.0000.0000.0000.000
119A123GLU-1-0.751-0.86446.450-0.070-0.0700.0000.0000.0000.000
120A124TRP0-0.021-0.01541.0940.0020.0020.0000.0000.0000.000
121A125ASP-1-0.801-0.87246.528-0.071-0.0710.0000.0000.0000.000
122A126GLY0-0.018-0.02043.132-0.003-0.0030.0000.0000.0000.000
123A127GLY0-0.065-0.04342.6840.0040.0040.0000.0000.0000.000
124A128ARG10.8760.94938.8290.1140.1140.0000.0000.0000.000
125A129GLU-1-0.783-0.87938.205-0.118-0.1180.0000.0000.0000.000
126A130THR0-0.073-0.04535.602-0.001-0.0010.0000.0000.0000.000
127A131HIS00.001-0.02135.022-0.009-0.0090.0000.0000.0000.000
128A132LEU0-0.017-0.00329.763-0.011-0.0110.0000.0000.0000.000
129A133GLU-1-0.948-0.96528.449-0.179-0.1790.0000.0000.0000.000
130A134THR0-0.032-0.02931.348-0.008-0.0080.0000.0000.0000.000
131A135ASN0-0.047-0.01929.6540.0120.0120.0000.0000.0000.000
132A136PHE00.0410.01033.9690.0010.0010.0000.0000.0000.000
133A137THR0-0.021-0.01834.9380.0010.0010.0000.0000.0000.000
134A138LEU0-0.0080.00537.6040.0010.0010.0000.0000.0000.000
135A139LYS10.8370.89335.9830.1140.1140.0000.0000.0000.000
136A140SER00.0320.01841.0250.0050.0050.0000.0000.0000.000
137A141GLU-1-0.878-0.93741.970-0.090-0.0900.0000.0000.0000.000
138A142TRP00.0870.04044.9800.0020.0020.0000.0000.0000.000
139A143ALA00.006-0.01346.468-0.002-0.0020.0000.0000.0000.000
140A144THR0-0.012-0.01446.717-0.001-0.0010.0000.0000.0000.000
141A145HIS0-0.0040.00042.4060.0000.0000.0000.0000.0000.000
142A146LYS10.8800.95238.1600.0950.0950.0000.0000.0000.000
143A147PHE0-0.047-0.01341.3760.0010.0010.0000.0000.0000.000
144A148ALA00.0150.01138.310-0.005-0.0050.0000.0000.0000.000
145A149ASP-1-0.813-0.87835.297-0.113-0.1130.0000.0000.0000.000
146A150CYS0-0.063-0.02337.758-0.003-0.0030.0000.0000.0000.000
147A151LYS10.9330.97030.3120.1560.1560.0000.0000.0000.000
148A152ALA00.0310.00836.7310.0040.0040.0000.0000.0000.000
149A153LYS10.8940.94536.6920.0790.0790.0000.0000.0000.000
150A154ARG10.9840.97832.4240.1210.1210.0000.0000.0000.000
151A155ASP-1-0.874-0.92637.050-0.086-0.0860.0000.0000.0000.000
152A156THR0-0.060-0.03040.5360.0030.0030.0000.0000.0000.000
153A157PRO00.0480.02139.149-0.001-0.0010.0000.0000.0000.000
154A158THR00.0110.00140.634-0.003-0.0030.0000.0000.0000.000
155A159SER0-0.038-0.04243.1380.0040.0040.0000.0000.0000.000
156A161THR0-0.052-0.02643.1110.0050.0050.0000.0000.0000.000
157A162VAL0-0.035-0.00242.862-0.003-0.0030.0000.0000.0000.000
158A163ASP-1-0.847-0.94040.307-0.073-0.0730.0000.0000.0000.000
159A164TYR00.034-0.02143.2630.0050.0050.0000.0000.0000.000
160A165SER0-0.066-0.05845.6020.0000.0000.0000.0000.0000.000
161A166THR00.0310.00849.382-0.002-0.0020.0000.0000.0000.000
162A167VAL0-0.0100.01250.6520.0020.0020.0000.0000.0000.000
163A168TYR0-0.016-0.02153.253-0.001-0.0010.0000.0000.0000.000
164A169PHE0-0.008-0.01756.4690.0010.0010.0000.0000.0000.000
165A170VAL00.0160.02552.3500.0010.0010.0000.0000.0000.000
166A171ASN0-0.081-0.05853.2880.0010.0010.0000.0000.0000.000
167A172ILE0-0.053-0.01947.033-0.001-0.0010.0000.0000.0000.000
168A173GLU-1-0.818-0.88845.913-0.072-0.0720.0000.0000.0000.000
169A174VAL0-0.012-0.02745.241-0.003-0.0030.0000.0000.0000.000
170A175TRP0-0.017-0.01539.4970.0020.0020.0000.0000.0000.000
171A176VAL00.0310.02340.373-0.002-0.0020.0000.0000.0000.000
172A177GLU-1-0.945-0.97235.230-0.134-0.1340.0000.0000.0000.000
173A178ALA00.004-0.00336.947-0.001-0.0010.0000.0000.0000.000
174A179GLU-1-0.921-0.98429.961-0.189-0.1890.0000.0000.0000.000
175A180ASN00.0210.01630.747-0.005-0.0050.0000.0000.0000.000
176A181ALA00.0330.01226.8530.0000.0000.0000.0000.0000.000
177A182LEU0-0.0340.01228.031-0.007-0.0070.0000.0000.0000.000
178A183GLY0-0.038-0.02730.6040.0080.0080.0000.0000.0000.000
179A184LYS10.9470.98930.6670.1680.1680.0000.0000.0000.000
180A185VAL0-0.051-0.02133.8690.0050.0050.0000.0000.0000.000
181A186THR00.0190.01037.568-0.001-0.0010.0000.0000.0000.000
182A187SER0-0.032-0.01240.3000.0010.0010.0000.0000.0000.000
183A188ASP-1-0.903-0.95243.853-0.080-0.0800.0000.0000.0000.000
184A189HIS10.8190.90342.2320.0870.0870.0000.0000.0000.000
185A190ILE0-0.0020.01147.0600.0030.0030.0000.0000.0000.000
186A191ASN00.011-0.00749.4250.0010.0010.0000.0000.0000.000
187A192PHE0-0.027-0.02450.2490.0030.0030.0000.0000.0000.000
188A193ASP-1-0.693-0.82853.503-0.047-0.0470.0000.0000.0000.000
189A194PRO00.019-0.01452.4440.0010.0010.0000.0000.0000.000
190A195VAL0-0.039-0.00454.9530.0010.0010.0000.0000.0000.000
191A196TYR0-0.057-0.03058.1460.0020.0020.0000.0000.0000.000
192A197LYS10.9000.95754.4400.0530.0530.0000.0000.0000.000
193A198VAL00.0510.02656.370-0.001-0.0010.0000.0000.0000.000
194A199LYS10.8650.97357.6630.0440.0440.0000.0000.0000.000
195A200PRO0-0.021-0.01359.0930.0000.0000.0000.0000.0000.000
196A201ASN00.0200.00059.208-0.001-0.0010.0000.0000.0000.000
197A202PRO0-0.0180.00262.1500.0000.0000.0000.0000.0000.000
198A203PRO0-0.049-0.03365.5590.0000.0000.0000.0000.0000.000
199A204HIS00.0370.01667.1180.0000.0000.0000.0000.0000.000
200A205ASN00.005-0.00769.2170.0000.0000.0000.0000.0000.000
201A206LEU0-0.035-0.01272.1450.0010.0010.0000.0000.0000.000
202A207SER0-0.017-0.00774.3770.0010.0010.0000.0000.0000.000
203A208VAL0-0.0050.00877.9790.0000.0000.0000.0000.0000.000
204A209ILE0-0.022-0.01881.1820.0000.0000.0000.0000.0000.000
205A210ASN0-0.011-0.01184.2770.0000.0000.0000.0000.0000.000
206A211SER0-0.031-0.01986.5350.0000.0000.0000.0000.0000.000
207A212GLU-1-0.904-0.96088.457-0.017-0.0170.0000.0000.0000.000
208A213GLU-1-0.902-0.95091.611-0.014-0.0140.0000.0000.0000.000
209A214LEU0-0.015-0.00593.3910.0000.0000.0000.0000.0000.000
210A215SER0-0.025-0.02893.2480.0000.0000.0000.0000.0000.000
211A216SER00.0140.00491.4390.0000.0000.0000.0000.0000.000
212A217ILE0-0.021-0.01387.839-0.001-0.0010.0000.0000.0000.000
213A218LEU0-0.031-0.00184.2600.0000.0000.0000.0000.0000.000
214A219LYS10.9110.97282.5020.0190.0190.0000.0000.0000.000
215A220LEU00.0230.00877.4300.0000.0000.0000.0000.0000.000
216A221THR0-0.070-0.03677.9960.0000.0000.0000.0000.0000.000
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