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: V56Q1

Calculation Name: 4O9H-H-Xray372

Preferred Name: Interleukin-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4O9H

Chain ID: H

ChEMBL ID: CHEMBL1795129

UniProt ID: P05231

Base Structure: X-ray

Registration Date: 2023-06-26

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2036902.20072
FMO2-HF: Nuclear repulsion 1958215.189007
FMO2-HF: Total energy -78687.011713
FMO2-MP2: Total energy -78915.417735


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(H:1:GLU)


Summations of interaction energy for fragment #1(H: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.
-65.411-60.3041.313-2.459-3.9590.015
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.922 / q_NPA : -0.961
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].
3H3GLN00.009-0.0032.88411.26514.3191.195-1.521-2.7280.007
4H4LEU0-0.033-0.0235.476-6.542-6.526-0.001-0.003-0.0110.000
5H5VAL00.0200.0148.4750.4070.4070.0000.0000.0000.000
6H6GLU-1-0.773-0.88511.17723.38623.3860.0000.0000.0000.000
7H7SER0-0.065-0.02714.294-0.511-0.5110.0000.0000.0000.000
8H8GLY00.0620.02317.6690.2040.2040.0000.0000.0000.000
9H9GLY0-0.0060.01020.423-0.576-0.5760.0000.0000.0000.000
10H10GLY00.003-0.01522.268-0.017-0.0170.0000.0000.0000.000
11H11LEU0-0.047-0.01325.2700.0170.0170.0000.0000.0000.000
12H12VAL0-0.0040.00228.802-0.123-0.1230.0000.0000.0000.000
13H13GLN00.0270.01730.836-0.158-0.1580.0000.0000.0000.000
14H14PRO0-0.001-0.01633.9350.1320.1320.0000.0000.0000.000
15H15GLY0-0.023-0.01034.742-0.236-0.2360.0000.0000.0000.000
16H16GLY0-0.0100.00533.202-0.093-0.0930.0000.0000.0000.000
17H17SER0-0.061-0.04530.5400.1790.1790.0000.0000.0000.000
18H18LEU00.0200.01123.876-0.003-0.0030.0000.0000.0000.000
19H19ARG10.9370.98523.845-12.330-12.3300.0000.0000.0000.000
20H20LEU0-0.0280.00519.0150.2410.2410.0000.0000.0000.000
21H21SER0-0.016-0.02318.149-0.605-0.6050.0000.0000.0000.000
22H22CYS0-0.077-0.04712.613-0.040-0.0400.0000.0000.0000.000
23H23ALA00.0080.02512.901-0.456-0.4560.0000.0000.0000.000
24H24ALA00.0180.01010.0852.2172.2170.0000.0000.0000.000
25H25SER0-0.055-0.0316.999-2.372-2.3720.0000.0000.0000.000
26H26GLY00.0900.0344.7243.5373.520-0.001-0.0180.0370.000
27H27PHE00.0350.0145.5240.9270.9270.0000.0000.0000.000
28H28THR00.0240.0168.288-1.055-1.0550.0000.0000.0000.000
29H29PHE00.0760.03512.085-0.913-0.9130.0000.0000.0000.000
30H30SER0-0.0140.00913.548-0.195-0.1950.0000.0000.0000.000
31H31SER0-0.023-0.00614.989-1.190-1.1900.0000.0000.0000.000
32H32TYR00.0080.01311.2840.2110.2110.0000.0000.0000.000
33H33ARG10.8960.96215.519-15.363-15.3630.0000.0000.0000.000
34H34MET0-0.0270.00311.9131.2341.2340.0000.0000.0000.000
35H35TYR0-0.142-0.11914.282-1.876-1.8760.0000.0000.0000.000
36H36TRP00.0480.02515.7791.2061.2060.0000.0000.0000.000
37H37VAL0-0.018-0.00316.624-1.047-1.0470.0000.0000.0000.000
38H38ARG10.8370.92018.092-11.903-11.9030.0000.0000.0000.000
39H39GLN0-0.012-0.02219.0130.6160.6160.0000.0000.0000.000
40H40PRO00.0200.01221.221-0.025-0.0250.0000.0000.0000.000
41H41PRO00.0270.01024.3580.2940.2940.0000.0000.0000.000
42H42GLY00.0000.00124.912-0.443-0.4430.0000.0000.0000.000
43H43LYS10.9080.96625.167-10.999-10.9990.0000.0000.0000.000
44H44GLY00.0440.01923.2180.5680.5680.0000.0000.0000.000
45H45LEU00.0170.00217.042-0.124-0.1240.0000.0000.0000.000
46H46GLU-1-0.881-0.93121.24811.50011.5000.0000.0000.0000.000
47H47TRP0-0.017-0.00519.6140.3090.3090.0000.0000.0000.000
48H48VAL00.0070.00921.162-0.742-0.7420.0000.0000.0000.000
49H49SER00.006-0.02221.362-0.763-0.7630.0000.0000.0000.000
50H50ALA0-0.024-0.02220.2770.8910.8910.0000.0000.0000.000
51H51ILE0-0.0100.02219.468-0.862-0.8620.0000.0000.0000.000
52H52SER0-0.040-0.01819.8980.7480.7480.0000.0000.0000.000
53H53ALA00.0330.00718.819-0.039-0.0390.0000.0000.0000.000
54H54GLY00.0470.01919.8010.2630.2630.0000.0000.0000.000
55H55GLY0-0.034-0.02622.664-0.408-0.4080.0000.0000.0000.000
56H56GLY00.0000.02024.265-0.319-0.3190.0000.0000.0000.000
57H57SER0-0.017-0.01425.451-0.276-0.2760.0000.0000.0000.000
58H58THR00.0030.00324.7790.5420.5420.0000.0000.0000.000
59H59TYR0-0.014-0.01524.107-0.271-0.2710.0000.0000.0000.000
60H60TYR00.0370.03924.8780.5270.5270.0000.0000.0000.000
61H61GLY00.0950.04926.212-0.274-0.2740.0000.0000.0000.000
62H62ASP-1-0.912-0.97627.56110.00210.0020.0000.0000.0000.000
63H63SER00.0110.02429.149-0.287-0.2870.0000.0000.0000.000
64H64VAL0-0.029-0.03126.379-0.148-0.1480.0000.0000.0000.000
65H65LYS10.8880.95529.421-10.580-10.5800.0000.0000.0000.000
66H66GLY00.0230.02731.1000.0210.0210.0000.0000.0000.000
67H67ARG10.7930.89730.551-10.231-10.2310.0000.0000.0000.000
68H68PHE00.009-0.00624.8510.1280.1280.0000.0000.0000.000
69H69THR0-0.012-0.01326.960-0.339-0.3390.0000.0000.0000.000
70H70ILE0-0.0020.01320.0740.3830.3830.0000.0000.0000.000
71H71SER0-0.013-0.01322.678-0.514-0.5140.0000.0000.0000.000
72H72ARG10.8200.88515.995-16.346-16.3460.0000.0000.0000.000
73H73ASP-1-0.882-0.94619.82212.82112.8210.0000.0000.0000.000
74H74ASN00.008-0.01617.9531.6771.6770.0000.0000.0000.000
75H75ALA00.0180.02817.502-0.680-0.6800.0000.0000.0000.000
76H76LYS10.9950.98516.618-13.630-13.6300.0000.0000.0000.000
77H77ASN0-0.0050.01111.691-0.590-0.5900.0000.0000.0000.000
78H78THR00.0040.00214.5161.3471.3470.0000.0000.0000.000
79H79VAL0-0.030-0.00815.431-0.951-0.9510.0000.0000.0000.000
80H80TYR0-0.031-0.03118.0410.3440.3440.0000.0000.0000.000
81H81LEU00.000-0.00420.658-0.234-0.2340.0000.0000.0000.000
82H82GLN0-0.033-0.02122.3560.0850.0850.0000.0000.0000.000
83H83MET0-0.020-0.01124.2750.0010.0010.0000.0000.0000.000
84H84ASN00.0850.04727.4800.0200.0200.0000.0000.0000.000
85H85SER0-0.002-0.02731.294-0.002-0.0020.0000.0000.0000.000
86H86LEU0-0.0320.01627.590-0.032-0.0320.0000.0000.0000.000
87H87LYS10.9370.97831.355-9.539-9.5390.0000.0000.0000.000
88H88PRO00.0500.02231.0540.3670.3670.0000.0000.0000.000
89H89GLU-1-0.855-0.94130.5749.5969.5960.0000.0000.0000.000
90H90ASP-1-0.800-0.88427.28911.12011.1200.0000.0000.0000.000
91H91THR0-0.0040.01225.9910.4990.4990.0000.0000.0000.000
92H92ALA0-0.009-0.01022.424-0.071-0.0710.0000.0000.0000.000
93H93VAL0-0.0210.01516.983-0.117-0.1170.0000.0000.0000.000
94H94TYR0-0.047-0.05018.388-0.106-0.1060.0000.0000.0000.000
95H95TYR00.0450.01112.7040.4200.4200.0000.0000.0000.000
96H97ALA00.0820.03311.0852.2532.2530.0000.0000.0000.000
97H98ASN00.008-0.0029.442-0.087-0.0870.0000.0000.0000.000
98H99ARG10.9100.95612.539-15.772-15.7720.0000.0000.0000.000
99H100ALA00.0150.02212.3910.4350.4350.0000.0000.0000.000
100H101GLY00.002-0.00912.840-2.022-2.0220.0000.0000.0000.000
101H102TRP0-0.043-0.03412.6441.1171.1170.0000.0000.0000.000
102H103GLY00.0220.02112.7020.4830.4830.0000.0000.0000.000
103H104MET0-0.0250.0207.2162.0662.0660.0000.0000.0000.000
104H105GLY00.0510.0088.782-2.914-2.9140.0000.0000.0000.000
105H106ASP-1-0.844-0.9049.50324.00324.0030.0000.0000.0000.000
106H107TYR00.0250.0213.246-8.715-6.6610.120-0.917-1.2570.008
107H108TRP0-0.021-0.0427.702-5.240-5.2400.0000.0000.0000.000
108H109GLY00.0720.0397.3465.0765.0760.0000.0000.0000.000
109H110GLN0-0.040-0.0268.8891.0731.0730.0000.0000.0000.000
110H111GLY00.0150.02410.947-1.603-1.6030.0000.0000.0000.000
111H112THR0-0.061-0.04214.337-0.789-0.7890.0000.0000.0000.000
112H113GLN0-0.007-0.00317.590-0.770-0.7700.0000.0000.0000.000
113H114VAL00.0070.00821.010-0.246-0.2460.0000.0000.0000.000
114H115THR0-0.031-0.02224.023-0.058-0.0580.0000.0000.0000.000
115H116VAL00.0230.01627.426-0.189-0.1890.0000.0000.0000.000
116H117SER00.007-0.01030.588-0.243-0.2430.0000.0000.0000.000
117H118SER00.0140.00633.8130.0660.0660.0000.0000.0000.000
118H119ALA0-0.0140.01435.710-0.199-0.1990.0000.0000.0000.000
119H120SER00.010-0.00735.4410.1410.1410.0000.0000.0000.000
120H121THR0-0.017-0.02031.472-0.002-0.0020.0000.0000.0000.000
121H122LYS10.8370.94134.380-8.545-8.5450.0000.0000.0000.000
122H123GLY00.0520.02733.9460.3010.3010.0000.0000.0000.000
123H124PRO0-0.023-0.02332.227-0.185-0.1850.0000.0000.0000.000
124H125SER0-0.027-0.00535.396-0.103-0.1030.0000.0000.0000.000
125H126VAL00.0020.00034.7540.0730.0730.0000.0000.0000.000
126H127PHE0-0.013-0.01337.601-0.264-0.2640.0000.0000.0000.000
127H128PRO00.0050.00738.5180.2130.2130.0000.0000.0000.000
128H129LEU0-0.045-0.00236.335-0.208-0.2080.0000.0000.0000.000
129H130ALA00.011-0.00939.5270.1330.1330.0000.0000.0000.000
130H131PRO00.0510.03340.599-0.018-0.0180.0000.0000.0000.000
131H132SER0-0.031-0.01342.316-0.224-0.2240.0000.0000.0000.000
132H133SER00.002-0.02545.4280.1130.1130.0000.0000.0000.000
133H134LYS10.8450.94543.729-7.563-7.5630.0000.0000.0000.000
134H135SER00.1180.07947.463-0.059-0.0590.0000.0000.0000.000
135H136THR0-0.003-0.01948.8030.1850.1850.0000.0000.0000.000
136H137SER00.0470.03546.3990.0340.0340.0000.0000.0000.000
137H138GLY00.0190.02444.4010.1920.1920.0000.0000.0000.000
138H139GLY0-0.009-0.02343.2830.0270.0270.0000.0000.0000.000
139H140THR0-0.031-0.02437.142-0.034-0.0340.0000.0000.0000.000
140H141ALA0-0.004-0.00139.649-0.097-0.0970.0000.0000.0000.000
141H142ALA00.0250.02236.4080.2090.2090.0000.0000.0000.000
142H143LEU0-0.0220.00735.774-0.286-0.2860.0000.0000.0000.000
143H144GLY00.076-0.00434.8410.3370.3370.0000.0000.0000.000
144H145CYS0-0.074-0.02431.787-0.017-0.0170.0000.0000.0000.000
145H146LEU00.0050.01534.3920.2260.2260.0000.0000.0000.000
146H147VAL0-0.018-0.00931.617-0.188-0.1880.0000.0000.0000.000
147H148LYS10.9710.97534.548-7.757-7.7570.0000.0000.0000.000
148H149ASP-1-0.854-0.93136.9438.0798.0790.0000.0000.0000.000
149H150TYR00.0310.02629.3650.0120.0120.0000.0000.0000.000
150H151PHE00.0340.03032.0040.1340.1340.0000.0000.0000.000
151H152PRO00.0470.02228.173-0.207-0.2070.0000.0000.0000.000
152H153GLU-1-0.831-0.92525.78111.85311.8530.0000.0000.0000.000
153H154PRO0-0.057-0.03422.1050.1620.1620.0000.0000.0000.000
154H155VAL00.006-0.00825.201-0.222-0.2220.0000.0000.0000.000
155H156THR0-0.054-0.02622.6910.5670.5670.0000.0000.0000.000
156H157VAL0-0.009-0.01125.100-0.401-0.4010.0000.0000.0000.000
157H158SER0-0.008-0.00124.9910.4810.4810.0000.0000.0000.000
158H159TRP00.0600.03926.807-0.592-0.5920.0000.0000.0000.000
159H160ASN00.0900.03627.9610.3640.3640.0000.0000.0000.000
160H161SER0-0.047-0.01427.7410.1310.1310.0000.0000.0000.000
161H162GLY0-0.0120.00625.9500.5250.5250.0000.0000.0000.000
162H163ALA0-0.043-0.03222.9470.0410.0410.0000.0000.0000.000
163H164LEU00.0290.01924.9350.1360.1360.0000.0000.0000.000
164H165THR00.013-0.00723.040-0.494-0.4940.0000.0000.0000.000
165H166SER0-0.034-0.01326.450-0.046-0.0460.0000.0000.0000.000
166H167GLY00.029-0.00128.710-0.421-0.4210.0000.0000.0000.000
167H168VAL0-0.057-0.02726.372-0.237-0.2370.0000.0000.0000.000
168H169HIS00.0220.01626.7520.7050.7050.0000.0000.0000.000
169H170THR0-0.007-0.01125.579-0.708-0.7080.0000.0000.0000.000
170H171PHE0-0.004-0.00126.5550.3480.3480.0000.0000.0000.000
171H172PRO00.0050.00327.0450.1340.1340.0000.0000.0000.000
172H173ALA0-0.014-0.00228.219-0.452-0.4520.0000.0000.0000.000
173H174VAL0-0.0130.00130.4480.0260.0260.0000.0000.0000.000
174H175LEU0-0.002-0.00132.525-0.039-0.0390.0000.0000.0000.000
175H176GLN0-0.032-0.00434.541-0.043-0.0430.0000.0000.0000.000
176H177SER00.050-0.00138.1650.1360.1360.0000.0000.0000.000
177H178SER0-0.038-0.01539.7630.0060.0060.0000.0000.0000.000
178H179GLY00.0480.03536.834-0.049-0.0490.0000.0000.0000.000
179H180LEU0-0.089-0.03735.2690.2520.2520.0000.0000.0000.000
180H181TYR00.0460.00729.946-0.084-0.0840.0000.0000.0000.000
181H182SER0-0.002-0.00933.634-0.195-0.1950.0000.0000.0000.000
182H183LEU00.0100.01728.1490.0530.0530.0000.0000.0000.000
183H184SER00.000-0.01231.868-0.425-0.4250.0000.0000.0000.000
184H185SER0-0.0020.02228.7090.2530.2530.0000.0000.0000.000
185H186VAL00.005-0.00931.054-0.379-0.3790.0000.0000.0000.000
186H187VAL00.0140.01130.5390.4210.4210.0000.0000.0000.000
187H188THR0-0.0150.00932.462-0.453-0.4530.0000.0000.0000.000
188H198THR00.0470.02837.233-0.184-0.1840.0000.0000.0000.000
189H199TYR0-0.009-0.00733.8370.1710.1710.0000.0000.0000.000
190H200ILE0-0.026-0.02134.306-0.273-0.2730.0000.0000.0000.000
191H202ASN00.014-0.03228.775-0.048-0.0480.0000.0000.0000.000
192H203VAL00.0080.00128.7230.4260.4260.0000.0000.0000.000
193H204ASN00.001-0.00626.227-0.222-0.2220.0000.0000.0000.000
194H205HIS00.0400.03827.2030.1990.1990.0000.0000.0000.000
195H206LYS11.0030.99121.420-14.503-14.5030.0000.0000.0000.000
196H207PRO0-0.022-0.01026.376-0.143-0.1430.0000.0000.0000.000
197H208SER00.001-0.01328.466-0.305-0.3050.0000.0000.0000.000
198H209ASN0-0.055-0.03529.2050.0370.0370.0000.0000.0000.000
199H210THR00.0290.02530.953-0.329-0.3290.0000.0000.0000.000
200H211LYS10.8890.94928.714-10.425-10.4250.0000.0000.0000.000
201H212VAL0-0.015-0.00431.909-0.338-0.3380.0000.0000.0000.000
202H213ASP-1-0.791-0.86232.46810.15910.1590.0000.0000.0000.000
203H214LYS10.9080.94234.797-8.306-8.3060.0000.0000.0000.000
204H215LYS10.8990.95336.699-7.490-7.4900.0000.0000.0000.000
205H216VAL0-0.046-0.02436.998-0.225-0.2250.0000.0000.0000.000
206H217GLU-1-0.903-0.95539.8207.3567.3560.0000.0000.0000.000
207H218PRO0-0.004-0.01243.041-0.016-0.0160.0000.0000.0000.000
208H219LYS10.9660.97444.691-7.277-7.2770.0000.0000.0000.000
209H220SER00.0020.02648.187-0.112-0.1120.0000.0000.0000.000