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: 82GLY

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 OptHSide
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 -3652699.757027
FMO2-HF: Nuclear repulsion 3531524.100158
FMO2-HF: Total energy -121175.656869
FMO2-MP2: Total energy -121527.285155


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.
-4.361-2.0360.118-0.735-1.7090
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 : -0.006 / q_NPA : -0.021
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-1-0.887-0.9492.873-5.643-3.4370.119-0.725-1.6010.000
4A5PRO00.0520.0294.9750.5480.667-0.001-0.010-0.1080.000
5A6CYS0-0.0540.0038.6030.0520.0520.0000.0000.0000.000
6A7GLY00.046-0.00211.4620.0320.0320.0000.0000.0000.000
7A8TYR0-0.0240.00412.453-0.076-0.0760.0000.0000.0000.000
8A9ILE00.0000.01314.4230.0570.0570.0000.0000.0000.000
9A10SER0-0.0500.00117.182-0.041-0.0410.0000.0000.0000.000
10A11PRO00.019-0.01519.1670.0280.0280.0000.0000.0000.000
11A12GLU-1-0.841-0.91514.892-0.474-0.4740.0000.0000.0000.000
12A13SER00.0450.01717.8630.0140.0140.0000.0000.0000.000
13A14PRO0-0.098-0.02820.3560.0080.0080.0000.0000.0000.000
14A15VAL00.0510.02023.7700.0090.0090.0000.0000.0000.000
15A16VAL0-0.026-0.02826.985-0.002-0.0020.0000.0000.0000.000
16A17GLN00.0070.00129.9430.0030.0030.0000.0000.0000.000
17A18LEU0-0.031-0.00533.6650.0000.0000.0000.0000.0000.000
18A19HIS00.001-0.01235.813-0.001-0.0010.0000.0000.0000.000
19A20SER0-0.075-0.02633.237-0.001-0.0010.0000.0000.0000.000
20A21ASN00.013-0.00933.3350.0050.0050.0000.0000.0000.000
21A22PHE00.002-0.00523.724-0.006-0.0060.0000.0000.0000.000
22A23THR0-0.017-0.01426.5100.0080.0080.0000.0000.0000.000
23A24ALA0-0.0120.01822.970-0.015-0.0150.0000.0000.0000.000
24A25VAL00.006-0.02021.3070.0180.0180.0000.0000.0000.000
25A26CYS0-0.072-0.01318.685-0.017-0.0170.0000.0000.0000.000
26A27VAL0-0.033-0.01815.5260.0310.0310.0000.0000.0000.000
27A28LEU00.0350.01315.323-0.046-0.0460.0000.0000.0000.000
28A29LYS10.8330.9006.9651.1391.1390.0000.0000.0000.000
29A30GLU-1-0.766-0.86713.356-0.120-0.1200.0000.0000.0000.000
30A31LYS10.9970.9998.7600.1450.1450.0000.0000.0000.000
31A33MET0-0.028-0.00213.5490.0430.0430.0000.0000.0000.000
32A34ASP-1-0.887-0.94015.952-0.050-0.0500.0000.0000.0000.000
33A35TYR0-0.089-0.04213.7190.0480.0480.0000.0000.0000.000
34A36PHE0-0.010-0.02313.5160.0250.0250.0000.0000.0000.000
35A37HIS0-0.0300.00818.150-0.010-0.0100.0000.0000.0000.000
36A38VAL0-0.026-0.00618.8460.0000.0000.0000.0000.0000.000
37A39ASN00.022-0.00420.663-0.013-0.0130.0000.0000.0000.000
38A40ALA00.0700.04121.8860.0060.0060.0000.0000.0000.000
39A41ASN0-0.054-0.04323.0290.0010.0010.0000.0000.0000.000
40A42TYR0-0.055-0.02722.4630.0060.0060.0000.0000.0000.000
41A43ILE0-0.0210.00119.4430.0030.0030.0000.0000.0000.000
42A44VAL0-0.023-0.01323.0710.0090.0090.0000.0000.0000.000
43A45TRP00.005-0.01222.040-0.019-0.0190.0000.0000.0000.000
44A46LYS10.8620.92724.7120.0660.0660.0000.0000.0000.000
45A47THR00.0410.01425.360-0.016-0.0160.0000.0000.0000.000
46A48ASN00.0020.00927.0020.0040.0040.0000.0000.0000.000
47A49HIS0-0.012-0.01525.4380.0120.0120.0000.0000.0000.000
48A50PHE0-0.0040.01628.3830.0100.0100.0000.0000.0000.000
49A51THR0-0.029-0.03228.375-0.009-0.0090.0000.0000.0000.000
50A52ILE00.0010.00627.7800.0040.0040.0000.0000.0000.000
51A53PRO00.0120.01930.4340.0010.0010.0000.0000.0000.000
52A54LYS10.9570.94330.7190.0430.0430.0000.0000.0000.000
53A55GLU-1-0.861-0.91831.761-0.055-0.0550.0000.0000.0000.000
54A56GLN0-0.035-0.01832.3510.0030.0030.0000.0000.0000.000
55A57TYR0-0.067-0.02927.732-0.010-0.0100.0000.0000.0000.000
56A58THR0-0.0090.00728.6490.0090.0090.0000.0000.0000.000
57A59ILE0-0.022-0.01526.093-0.012-0.0120.0000.0000.0000.000
58A60ILE00.0010.00923.1950.0050.0050.0000.0000.0000.000
59A61ASN00.0260.00222.3230.0000.0000.0000.0000.0000.000
60A62ARG10.8590.89119.6500.1210.1210.0000.0000.0000.000
61A63THR00.0280.01117.8500.0150.0150.0000.0000.0000.000
62A64ALA0-0.011-0.00619.672-0.021-0.0210.0000.0000.0000.000
63A65SER00.0640.04521.8990.0200.0200.0000.0000.0000.000
64A66SER0-0.014-0.00823.347-0.019-0.0190.0000.0000.0000.000
65A67VAL00.0480.03025.7980.0150.0150.0000.0000.0000.000
66A68THR00.0290.00427.871-0.015-0.0150.0000.0000.0000.000
67A69PHE0-0.0150.01027.0350.0090.0090.0000.0000.0000.000
68A70THR0-0.003-0.02331.984-0.005-0.0050.0000.0000.0000.000
69A71ASP-1-0.885-0.94935.175-0.074-0.0740.0000.0000.0000.000
70A72ILE0-0.024-0.00230.3270.0030.0030.0000.0000.0000.000
71A73ALA00.0730.03334.6700.0010.0010.0000.0000.0000.000
72A74SER0-0.052-0.01032.1730.0050.0050.0000.0000.0000.000
73A75LEU00.0510.01232.656-0.006-0.0060.0000.0000.0000.000
74A76ASN0-0.036-0.02426.525-0.010-0.0100.0000.0000.0000.000
75A77ILE0-0.0080.00726.9820.0120.0120.0000.0000.0000.000
76A78GLN00.0370.04122.427-0.002-0.0020.0000.0000.0000.000
77A79LEU0-0.020-0.01622.8590.0170.0170.0000.0000.0000.000
78A80THR0-0.001-0.00520.297-0.021-0.0210.0000.0000.0000.000
79A82ASN00.0390.00118.865-0.032-0.0320.0000.0000.0000.000
80A83ILE00.0420.02916.702-0.006-0.0060.0000.0000.0000.000
81A84LEU0-0.034-0.02120.7260.0160.0160.0000.0000.0000.000
82A85THR0-0.039-0.02418.5210.0060.0060.0000.0000.0000.000
83A86PHE00.040-0.00721.9090.0060.0060.0000.0000.0000.000
84A87GLY00.0080.00923.8780.0110.0110.0000.0000.0000.000
85A88GLN0-0.081-0.04026.538-0.003-0.0030.0000.0000.0000.000
86A89LEU00.0300.03820.3450.0010.0010.0000.0000.0000.000
87A90GLU-1-0.794-0.86622.577-0.058-0.0580.0000.0000.0000.000
88A91GLN0-0.010-0.01115.4060.0230.0230.0000.0000.0000.000
89A92ASN0-0.053-0.04216.816-0.034-0.0340.0000.0000.0000.000
90A93VAL0-0.063-0.01614.642-0.005-0.0050.0000.0000.0000.000
91A94TYR0-0.009-0.04311.449-0.088-0.0880.0000.0000.0000.000
92A95GLY00.000-0.00515.8060.0630.0630.0000.0000.0000.000
93A96ILE00.0130.02517.322-0.036-0.0360.0000.0000.0000.000
94A97THR0-0.010-0.00919.8730.0360.0360.0000.0000.0000.000
95A98ILE0-0.031-0.01822.933-0.013-0.0130.0000.0000.0000.000
96A99ILE0-0.0010.00425.0840.0160.0160.0000.0000.0000.000
97A100SER0-0.020-0.00727.828-0.003-0.0030.0000.0000.0000.000
98A101GLY00.0540.02831.1680.0040.0040.0000.0000.0000.000
99A102LEU0-0.048-0.01834.0740.0010.0010.0000.0000.0000.000
100A103PRO00.0620.04334.908-0.002-0.0020.0000.0000.0000.000
101A104PRO00.0060.00934.9830.0080.0080.0000.0000.0000.000
102A105GLU-1-0.841-0.91038.068-0.067-0.0670.0000.0000.0000.000
103A106LYS10.8440.91041.4110.0660.0660.0000.0000.0000.000
104A107PRO0-0.021-0.00141.3990.0040.0040.0000.0000.0000.000
105A108LYS10.8980.93644.4010.0610.0610.0000.0000.0000.000
106A109ASN0-0.042-0.03748.1750.0010.0010.0000.0000.0000.000
107A110LEU0-0.0230.01846.0710.0010.0010.0000.0000.0000.000
108A111SER0-0.032-0.00949.3420.0020.0020.0000.0000.0000.000
109A112CYS0-0.047-0.00946.4190.0000.0000.0000.0000.0000.000
110A113ILE0-0.0050.00751.6360.0020.0020.0000.0000.0000.000
111A114VAL00.0370.01252.448-0.001-0.0010.0000.0000.0000.000
112A115ASN0-0.0030.00853.9410.0000.0000.0000.0000.0000.000
113A116GLU-1-0.718-0.86955.111-0.027-0.0270.0000.0000.0000.000
114A117GLY0-0.019-0.00955.7680.0010.0010.0000.0000.0000.000
115A118LYS10.8890.94751.3360.0330.0330.0000.0000.0000.000
116A119LYS10.8530.92546.3560.0450.0450.0000.0000.0000.000
117A120MET0-0.013-0.00147.7460.0010.0010.0000.0000.0000.000
118A121ARG10.8660.92247.7310.0410.0410.0000.0000.0000.000
119A123GLU-1-0.748-0.85346.868-0.049-0.0490.0000.0000.0000.000
120A124TRP0-0.019-0.01141.4540.0000.0000.0000.0000.0000.000
121A125ASP-1-0.831-0.89046.987-0.052-0.0520.0000.0000.0000.000
122A126GLY0-0.017-0.02143.591-0.003-0.0030.0000.0000.0000.000
123A127GLY0-0.056-0.03743.2410.0030.0030.0000.0000.0000.000
124A128ARG10.8510.92539.2580.0850.0850.0000.0000.0000.000
125A129GLU-1-0.804-0.88938.630-0.082-0.0820.0000.0000.0000.000
126A130THR0-0.070-0.04535.979-0.001-0.0010.0000.0000.0000.000
127A131HIS0-0.009-0.02435.313-0.006-0.0060.0000.0000.0000.000
128A132LEU00.0000.01230.018-0.007-0.0070.0000.0000.0000.000
129A133GLU-1-0.948-0.96529.327-0.123-0.1230.0000.0000.0000.000
130A134THR0-0.032-0.03231.733-0.007-0.0070.0000.0000.0000.000
131A135ASN0-0.035-0.00630.3500.0070.0070.0000.0000.0000.000
132A136PHE00.0590.01634.4200.0000.0000.0000.0000.0000.000
133A137THR0-0.027-0.01935.4370.0010.0010.0000.0000.0000.000
134A138LEU0-0.0110.00437.9630.0010.0010.0000.0000.0000.000
135A139LYS10.8280.90535.6440.0960.0960.0000.0000.0000.000
136A140SER00.0230.00541.2860.0040.0040.0000.0000.0000.000
137A141GLU-1-0.885-0.93941.951-0.075-0.0750.0000.0000.0000.000
138A142TRP00.0790.03445.1460.0020.0020.0000.0000.0000.000
139A143ALA00.002-0.01346.570-0.002-0.0020.0000.0000.0000.000
140A144THR0-0.010-0.01446.838-0.001-0.0010.0000.0000.0000.000
141A145HIS00.0000.00642.409-0.001-0.0010.0000.0000.0000.000
142A146LYS10.8890.95238.2220.0790.0790.0000.0000.0000.000
143A147PHE0-0.055-0.02141.5210.0010.0010.0000.0000.0000.000
144A148ALA00.0050.00738.543-0.004-0.0040.0000.0000.0000.000
145A149ASP-1-0.820-0.90135.763-0.090-0.0900.0000.0000.0000.000
146A150CYS0-0.068-0.02638.069-0.002-0.0020.0000.0000.0000.000
147A151LYS10.8870.94230.8280.1170.1170.0000.0000.0000.000
148A152ALA00.0300.00837.1310.0030.0030.0000.0000.0000.000
149A153LYS10.8980.94837.1720.0560.0560.0000.0000.0000.000
150A154ARG10.9810.98133.1950.0800.0800.0000.0000.0000.000
151A155ASP-1-0.891-0.93937.616-0.059-0.0590.0000.0000.0000.000
152A156THR0-0.038-0.02341.1220.0020.0020.0000.0000.0000.000
153A157PRO00.0480.02639.603-0.001-0.0010.0000.0000.0000.000
154A158THR00.003-0.00441.146-0.003-0.0030.0000.0000.0000.000
155A159SER0-0.006-0.03243.6170.0020.0020.0000.0000.0000.000
156A161THR0-0.056-0.02543.5330.0040.0040.0000.0000.0000.000
157A162VAL0-0.026-0.00343.206-0.002-0.0020.0000.0000.0000.000
158A163ASP-1-0.810-0.91940.789-0.057-0.0570.0000.0000.0000.000
159A164TYR00.0250.00743.5340.0040.0040.0000.0000.0000.000
160A165SER0-0.051-0.04645.8830.0000.0000.0000.0000.0000.000
161A166THR00.0330.01249.665-0.002-0.0020.0000.0000.0000.000
162A167VAL0-0.0100.00950.9790.0020.0020.0000.0000.0000.000
163A168TYR0-0.011-0.02053.474-0.001-0.0010.0000.0000.0000.000
164A169PHE00.000-0.00756.6950.0000.0000.0000.0000.0000.000
165A170VAL00.0000.01552.5820.0000.0000.0000.0000.0000.000
166A171ASN0-0.078-0.04253.5350.0010.0010.0000.0000.0000.000
167A172ILE0-0.050-0.02247.135-0.001-0.0010.0000.0000.0000.000
168A173GLU-1-0.787-0.85946.282-0.058-0.0580.0000.0000.0000.000
169A174VAL0-0.019-0.03345.657-0.002-0.0020.0000.0000.0000.000
170A175TRP00.000-0.00639.9500.0020.0020.0000.0000.0000.000
171A176VAL00.0280.02441.023-0.002-0.0020.0000.0000.0000.000
172A177GLU-1-0.834-0.90734.784-0.109-0.1090.0000.0000.0000.000
173A178ALA00.003-0.00237.3940.0000.0000.0000.0000.0000.000
174A179GLU-1-0.846-0.93430.782-0.143-0.1430.0000.0000.0000.000
175A180ASN00.0180.00531.312-0.004-0.0040.0000.0000.0000.000
176A181ALA00.0300.01527.339-0.001-0.0010.0000.0000.0000.000
177A182LEU0-0.0160.01928.641-0.006-0.0060.0000.0000.0000.000
178A183GLY0-0.035-0.02731.2150.0050.0050.0000.0000.0000.000
179A184LYS10.8130.90531.5230.1320.1320.0000.0000.0000.000
180A185VAL0-0.039-0.01534.4350.0030.0030.0000.0000.0000.000
181A186THR00.0080.00338.126-0.001-0.0010.0000.0000.0000.000
182A187SER0-0.0070.00040.8470.0010.0010.0000.0000.0000.000
183A188ASP-1-0.847-0.92044.414-0.065-0.0650.0000.0000.0000.000
184A189HIS10.8340.90242.7320.0700.0700.0000.0000.0000.000
185A190ILE0-0.0130.00447.5070.0020.0020.0000.0000.0000.000
186A191ASN00.008-0.01549.6750.0010.0010.0000.0000.0000.000
187A192PHE0-0.025-0.02050.5350.0020.0020.0000.0000.0000.000
188A193ASP-1-0.690-0.83753.726-0.038-0.0380.0000.0000.0000.000
189A194PRO00.015-0.01352.5740.0010.0010.0000.0000.0000.000
190A195VAL0-0.045-0.00555.2230.0010.0010.0000.0000.0000.000
191A196TYR0-0.034-0.01958.4140.0020.0020.0000.0000.0000.000
192A197LYS10.8950.95354.7890.0410.0410.0000.0000.0000.000
193A198VAL00.0400.02256.722-0.001-0.0010.0000.0000.0000.000
194A199LYS10.7750.90558.1150.0310.0310.0000.0000.0000.000
195A200PRO0-0.031-0.01659.4930.0000.0000.0000.0000.0000.000
196A201ASN0-0.022-0.01359.3350.0000.0000.0000.0000.0000.000
197A202PRO00.0030.00862.5720.0000.0000.0000.0000.0000.000
198A203PRO0-0.043-0.03465.9960.0000.0000.0000.0000.0000.000
199A204HIS00.0350.01766.9970.0010.0010.0000.0000.0000.000
200A205ASN0-0.008-0.01669.6600.0000.0000.0000.0000.0000.000
201A206LEU0-0.021-0.00572.5920.0000.0000.0000.0000.0000.000
202A207SER0-0.029-0.01574.8330.0010.0010.0000.0000.0000.000
203A208VAL0-0.0120.00278.4380.0000.0000.0000.0000.0000.000
204A209ILE0-0.011-0.01281.6480.0000.0000.0000.0000.0000.000
205A210ASN0-0.0030.00184.7290.0000.0000.0000.0000.0000.000
206A211SER0-0.027-0.02386.9230.0000.0000.0000.0000.0000.000
207A212GLU-1-0.909-0.95788.881-0.012-0.0120.0000.0000.0000.000
208A213GLU-1-0.878-0.93692.031-0.010-0.0100.0000.0000.0000.000
209A214LEU0-0.024-0.00993.8230.0000.0000.0000.0000.0000.000
210A215SER0-0.019-0.03293.7070.0000.0000.0000.0000.0000.000
211A216SER00.004-0.00591.8830.0000.0000.0000.0000.0000.000
212A217ILE0-0.023-0.01788.3450.0000.0000.0000.0000.0000.000
213A218LEU0-0.0150.00684.7720.0000.0000.0000.0000.0000.000
214A219LYS10.9120.97282.6190.0140.0140.0000.0000.0000.000
215A220LEU00.0190.01378.1580.0000.0000.0000.0000.0000.000
216A221THR0-0.011-0.02578.3920.0000.0000.0000.0000.0000.000
217A222TRP0-0.017-0.00172.2590.0000.0000.0000.0000.0000.000
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