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: G6451

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2040930.162051
FMO2-HF: Nuclear repulsion 1962241.470415
FMO2-HF: Total energy -78688.691636
FMO2-MP2: Total energy -78917.06046


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.
-101.909-105.99622.166-10.905-7.1740.08
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 : -0.852 / q_NPA : -0.901
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].
3H3GLN00.0010.0002.7980.8103.6270.427-1.449-1.795-0.004
4H4LEU0-0.009-0.0045.582-4.311-4.3110.0000.0000.0000.000
5H5VAL00.0280.0119.0220.6720.6720.0000.0000.0000.000
6H6GLU-1-0.786-0.88812.14521.18921.1890.0000.0000.0000.000
7H7SER0-0.054-0.02915.348-0.462-0.4620.0000.0000.0000.000
8H8GLY00.030-0.01118.483-0.156-0.1560.0000.0000.0000.000
9H9GLY0-0.0270.00921.088-0.511-0.5110.0000.0000.0000.000
10H10GLY0-0.007-0.01623.4730.0270.0270.0000.0000.0000.000
11H11LEU0-0.041-0.00626.7410.0530.0530.0000.0000.0000.000
12H12VAL0-0.014-0.00529.293-0.112-0.1120.0000.0000.0000.000
13H13GLN00.0430.02332.122-0.150-0.1500.0000.0000.0000.000
14H14PRO0-0.001-0.01634.9100.1460.1460.0000.0000.0000.000
15H15GLY0-0.0100.00436.099-0.218-0.2180.0000.0000.0000.000
16H16GLY0-0.0090.00134.454-0.048-0.0480.0000.0000.0000.000
17H17SER0-0.071-0.06031.4630.1550.1550.0000.0000.0000.000
18H18LEU00.0070.00625.365-0.034-0.0340.0000.0000.0000.000
19H19ARG10.8750.94323.208-12.072-12.0720.0000.0000.0000.000
20H20LEU00.0150.02120.0170.2160.2160.0000.0000.0000.000
21H21SER00.005-0.00318.807-0.539-0.5390.0000.0000.0000.000
22H22CYS0-0.103-0.04313.099-0.144-0.1440.0000.0000.0000.000
23H23ALA00.0220.03913.576-0.165-0.1650.0000.0000.0000.000
24H24ALA00.007-0.0059.9761.6291.6290.0000.0000.0000.000
25H25SER0-0.037-0.0237.333-1.281-1.2810.0000.0000.0000.000
26H26GLY00.0870.0334.3882.3992.415-0.001-0.0410.0270.000
27H27PHE00.0370.0145.1081.7531.846-0.001-0.009-0.0830.000
28H28THR00.0270.0187.804-1.238-1.2380.0000.0000.0000.000
29H29PHE00.0360.02011.557-1.102-1.1020.0000.0000.0000.000
30H30SER0-0.013-0.00413.052-0.315-0.3150.0000.0000.0000.000
31H31SER0-0.0080.00214.760-1.193-1.1930.0000.0000.0000.000
32H32TYR00.003-0.00411.0670.2930.2930.0000.0000.0000.000
33H33ARG10.8430.93415.283-15.067-15.0670.0000.0000.0000.000
34H34MET00.0030.02511.3591.3131.3130.0000.0000.0000.000
35H35TYR0-0.143-0.11114.460-1.801-1.8010.0000.0000.0000.000
36H36TRP00.0510.02815.8931.0761.0760.0000.0000.0000.000
37H37VAL0-0.024-0.01017.254-0.842-0.8420.0000.0000.0000.000
38H38ARG10.8200.89819.134-11.521-11.5210.0000.0000.0000.000
39H39GLN00.0270.00719.9380.7820.7820.0000.0000.0000.000
40H40PRO00.0270.01422.626-0.019-0.0190.0000.0000.0000.000
41H41PRO00.0090.00925.5780.3190.3190.0000.0000.0000.000
42H42GLY00.0250.01626.142-0.409-0.4090.0000.0000.0000.000
43H43LYS10.8610.92825.929-11.249-11.2490.0000.0000.0000.000
44H44GLY00.0620.03423.3950.5170.5170.0000.0000.0000.000
45H45LEU00.0130.00317.436-0.154-0.1540.0000.0000.0000.000
46H46GLU-1-0.814-0.87521.98711.22311.2230.0000.0000.0000.000
47H47TRP0-0.039-0.02319.9000.1790.1790.0000.0000.0000.000
48H48VAL00.0000.01121.577-0.670-0.6700.0000.0000.0000.000
49H49SER00.026-0.01521.582-0.661-0.6610.0000.0000.0000.000
50H50ALA0-0.015-0.01219.8860.8770.8770.0000.0000.0000.000
51H51ILE0-0.0100.01218.917-0.839-0.8390.0000.0000.0000.000
52H52SER0-0.006-0.00919.2350.7910.7910.0000.0000.0000.000
53H53ALA00.0170.00818.3430.1010.1010.0000.0000.0000.000
54H54GLY00.0650.02919.3210.1490.1490.0000.0000.0000.000
55H55GLY0-0.040-0.01521.915-0.474-0.4740.0000.0000.0000.000
56H56GLY0-0.0010.00023.442-0.180-0.1800.0000.0000.0000.000
57H57SER0-0.0010.00924.986-0.337-0.3370.0000.0000.0000.000
58H58THR00.004-0.00124.1280.5760.5760.0000.0000.0000.000
59H59TYR00.0220.00323.639-0.176-0.1760.0000.0000.0000.000
60H60TYR00.0700.05024.6980.5490.5490.0000.0000.0000.000
61H61GLY00.0880.05526.154-0.285-0.2850.0000.0000.0000.000
62H62ASP-1-0.848-0.93727.6199.8839.8830.0000.0000.0000.000
63H63SER0-0.0160.00028.570-0.321-0.3210.0000.0000.0000.000
64H64VAL0-0.033-0.03026.532-0.161-0.1610.0000.0000.0000.000
65H65LYS10.8050.88829.749-10.279-10.2790.0000.0000.0000.000
66H66GLY00.0290.03031.1970.0050.0050.0000.0000.0000.000
67H67ARG10.7240.83130.793-10.116-10.1160.0000.0000.0000.000
68H68PHE00.002-0.00425.5510.1010.1010.0000.0000.0000.000
69H69THR0-0.022-0.01926.932-0.325-0.3250.0000.0000.0000.000
70H70ILE0-0.0200.00719.4270.2240.2240.0000.0000.0000.000
71H71SER0-0.013-0.02122.165-0.473-0.4730.0000.0000.0000.000
72H72ARG10.8230.89815.771-15.643-15.6430.0000.0000.0000.000
73H73ASP-1-0.789-0.84519.15812.57312.5730.0000.0000.0000.000
74H74ASN00.0380.00917.4611.3581.3580.0000.0000.0000.000
75H75ALA00.0440.02817.235-0.676-0.6760.0000.0000.0000.000
76H76LYS10.8420.91616.120-12.893-12.8930.0000.0000.0000.000
77H77ASN00.0330.00411.869-0.641-0.6410.0000.0000.0000.000
78H78THR00.0150.00914.2651.0641.0640.0000.0000.0000.000
79H79VAL0-0.025-0.00614.815-0.790-0.7900.0000.0000.0000.000
80H80TYR0-0.031-0.06317.4950.1600.1600.0000.0000.0000.000
81H81LEU0-0.005-0.00820.596-0.084-0.0840.0000.0000.0000.000
82H82GLN0-0.0020.00622.6840.1360.1360.0000.0000.0000.000
83H83MET0-0.027-0.01224.5180.1880.1880.0000.0000.0000.000
84H84ASN00.0850.04727.991-0.064-0.0640.0000.0000.0000.000
85H85SER00.0220.00731.837-0.051-0.0510.0000.0000.0000.000
86H86LEU0-0.0120.01428.4800.0360.0360.0000.0000.0000.000
87H87LYS10.8570.90532.246-9.194-9.1940.0000.0000.0000.000
88H88PRO00.0560.02632.2500.3220.3220.0000.0000.0000.000
89H89GLU-1-0.806-0.89331.8949.3799.3790.0000.0000.0000.000
90H90ASP-1-0.769-0.83228.34810.71410.7140.0000.0000.0000.000
91H91THR0-0.028-0.00527.1540.4760.4760.0000.0000.0000.000
92H92ALA0-0.011-0.01323.788-0.059-0.0590.0000.0000.0000.000
93H93VAL00.0160.03018.496-0.083-0.0830.0000.0000.0000.000
94H94TYR0-0.037-0.04019.551-0.150-0.1500.0000.0000.0000.000
95H95TYR00.0400.00614.3470.4010.4010.0000.0000.0000.000
96H97ALA00.0810.03611.1711.9471.9470.0000.0000.0000.000
97H98ASN0-0.014-0.0278.883-0.367-0.3670.0000.0000.0000.000
98H99ARG10.9120.95712.015-15.954-15.9540.0000.0000.0000.000
99H100ALA0-0.0110.00212.1260.6190.6190.0000.0000.0000.000
100H101GLY0-0.004-0.01212.563-2.133-2.1330.0000.0000.0000.000
101H102TRP0-0.054-0.03212.2751.4221.4220.0000.0000.0000.000
102H103GLY00.0390.03411.9100.0900.0900.0000.0000.0000.000
103H104MET0-0.0290.0166.5593.0203.0200.0000.0000.0000.000
104H105GLY00.0600.0138.284-3.488-3.4880.0000.0000.0000.000
105H106ASP-1-0.789-0.8839.16923.36223.3620.0000.0000.0000.000
106H107TYR0-0.028-0.0281.587-35.399-42.41221.741-9.406-5.3230.084
107H108TRP0-0.036-0.0467.641-5.380-5.3800.0000.0000.0000.000
108H109GLY00.0220.0218.1573.5413.5410.0000.0000.0000.000
109H110GLN0-0.061-0.0449.1812.3592.3590.0000.0000.0000.000
110H111GLY00.0050.00512.261-1.191-1.1910.0000.0000.0000.000
111H112THR0-0.048-0.03715.629-0.630-0.6300.0000.0000.0000.000
112H113GLN00.0080.00618.890-0.195-0.1950.0000.0000.0000.000
113H114VAL0-0.0140.00522.436-0.268-0.2680.0000.0000.0000.000
114H115THR0-0.044-0.03425.341-0.049-0.0490.0000.0000.0000.000
115H116VAL00.0160.02228.967-0.146-0.1460.0000.0000.0000.000
116H117SER00.014-0.00632.063-0.238-0.2380.0000.0000.0000.000
117H118SER00.0280.01035.4050.0730.0730.0000.0000.0000.000
118H119ALA0-0.0270.00136.944-0.178-0.1780.0000.0000.0000.000
119H120SER00.014-0.00336.8630.1530.1530.0000.0000.0000.000
120H121THR0-0.024-0.01233.3190.0060.0060.0000.0000.0000.000
121H122LYS10.8260.91835.750-8.374-8.3740.0000.0000.0000.000
122H123GLY00.0480.02734.8250.2840.2840.0000.0000.0000.000
123H124PRO0-0.049-0.01533.043-0.243-0.2430.0000.0000.0000.000
124H125SER00.0150.01236.096-0.105-0.1050.0000.0000.0000.000
125H126VAL00.0150.00735.4990.0730.0730.0000.0000.0000.000
126H127PHE0-0.002-0.01538.266-0.244-0.2440.0000.0000.0000.000
127H128PRO00.0160.01439.0090.1810.1810.0000.0000.0000.000
128H129LEU0-0.035-0.01936.934-0.269-0.2690.0000.0000.0000.000
129H130ALA00.0150.00139.6190.1430.1430.0000.0000.0000.000
130H131PRO00.0350.03540.8730.0100.0100.0000.0000.0000.000
131H132SER00.0030.00142.265-0.229-0.2290.0000.0000.0000.000
132H133SER00.0180.00645.0990.1570.1570.0000.0000.0000.000
133H134LYS10.8340.91642.924-7.543-7.5430.0000.0000.0000.000
134H135SER00.0640.02946.916-0.014-0.0140.0000.0000.0000.000
135H136THR0-0.003-0.01648.8840.1470.1470.0000.0000.0000.000
136H137SER00.0410.03146.6750.0120.0120.0000.0000.0000.000
137H138GLY00.0230.03544.2870.1870.1870.0000.0000.0000.000
138H139GLY0-0.005-0.01543.2820.0310.0310.0000.0000.0000.000
139H140THR0-0.020-0.01437.357-0.032-0.0320.0000.0000.0000.000
140H141ALA0-0.016-0.01339.213-0.166-0.1660.0000.0000.0000.000
141H142ALA00.0310.01836.1240.2170.2170.0000.0000.0000.000
142H143LEU0-0.025-0.00436.037-0.312-0.3120.0000.0000.0000.000
143H144GLY00.0530.00434.8960.3410.3410.0000.0000.0000.000
144H145CYS0-0.077-0.00932.079-0.061-0.0610.0000.0000.0000.000
145H146LEU00.0330.04434.5980.2640.2640.0000.0000.0000.000
146H147VAL0-0.021-0.02232.298-0.142-0.1420.0000.0000.0000.000
147H148LYS10.9130.92934.908-7.604-7.6040.0000.0000.0000.000
148H149ASP-1-0.798-0.86837.4837.8197.8190.0000.0000.0000.000
149H150TYR00.0060.00930.227-0.165-0.1650.0000.0000.0000.000
150H151PHE00.0540.02833.2830.1120.1120.0000.0000.0000.000
151H152PRO00.0460.02829.695-0.183-0.1830.0000.0000.0000.000
152H153GLU-1-0.848-0.92826.81711.40111.4010.0000.0000.0000.000
153H154PRO0-0.031-0.02423.2210.0590.0590.0000.0000.0000.000
154H155VAL00.003-0.01226.125-0.262-0.2620.0000.0000.0000.000
155H156THR0-0.035-0.00623.5400.5930.5930.0000.0000.0000.000
156H157VAL0-0.002-0.01725.949-0.504-0.5040.0000.0000.0000.000
157H158SER0-0.050-0.02425.3640.3950.3950.0000.0000.0000.000
158H159TRP00.0640.03527.230-0.616-0.6160.0000.0000.0000.000
159H160ASN00.0210.01727.9740.3500.3500.0000.0000.0000.000
160H161SER00.0210.00629.1440.1920.1920.0000.0000.0000.000
161H162GLY0-0.019-0.02225.5110.3780.3780.0000.0000.0000.000
162H163ALA00.0230.00823.400-0.282-0.2820.0000.0000.0000.000
163H164LEU00.0230.03924.6390.0810.0810.0000.0000.0000.000
164H165THR00.006-0.00722.933-0.431-0.4310.0000.0000.0000.000
165H166SER0-0.008-0.00926.267-0.059-0.0590.0000.0000.0000.000
166H167GLY00.0320.01128.702-0.369-0.3690.0000.0000.0000.000
167H168VAL0-0.056-0.02126.069-0.213-0.2130.0000.0000.0000.000
168H169HIS00.0090.01526.4860.7300.7300.0000.0000.0000.000
169H170THR00.001-0.00126.124-0.634-0.6340.0000.0000.0000.000
170H171PHE0-0.0060.00527.0000.3540.3540.0000.0000.0000.000
171H172PRO00.025-0.00326.8770.0460.0460.0000.0000.0000.000
172H173ALA0-0.0130.00428.695-0.399-0.3990.0000.0000.0000.000
173H174VAL0-0.0100.00131.1730.0360.0360.0000.0000.0000.000
174H175LEU0-0.007-0.00633.459-0.086-0.0860.0000.0000.0000.000
175H176GLN0-0.033-0.01635.173-0.229-0.2290.0000.0000.0000.000
176H177SER00.0420.00238.9700.1100.1100.0000.0000.0000.000
177H178SER0-0.0140.00141.001-0.038-0.0380.0000.0000.0000.000
178H179GLY00.0110.01338.088-0.037-0.0370.0000.0000.0000.000
179H180LEU0-0.059-0.02036.5200.2610.2610.0000.0000.0000.000
180H181TYR00.019-0.00330.111-0.165-0.1650.0000.0000.0000.000
181H182SER0-0.024-0.02434.817-0.202-0.2020.0000.0000.0000.000
182H183LEU00.0270.03428.8340.0880.0880.0000.0000.0000.000
183H184SER0-0.003-0.02532.164-0.466-0.4660.0000.0000.0000.000
184H185SER0-0.021-0.00128.8810.2940.2940.0000.0000.0000.000
185H186VAL00.011-0.00530.905-0.421-0.4210.0000.0000.0000.000
186H187VAL00.0150.02630.4000.4160.4160.0000.0000.0000.000
187H188THR0-0.005-0.00932.389-0.443-0.4430.0000.0000.0000.000
188H198THR00.0550.02837.361-0.179-0.1790.0000.0000.0000.000
189H199TYR0-0.035-0.02033.1970.1540.1540.0000.0000.0000.000
190H200ILE0-0.024-0.02934.430-0.288-0.2880.0000.0000.0000.000
191H202ASN00.002-0.01729.764-0.262-0.2620.0000.0000.0000.000
192H203VAL00.0210.01329.4420.4140.4140.0000.0000.0000.000
193H204ASN00.0180.00326.368-0.434-0.4340.0000.0000.0000.000
194H205HIS00.0220.02427.9650.1720.1720.0000.0000.0000.000
195H206LYS11.0110.99422.258-13.737-13.7370.0000.0000.0000.000
196H207PRO0-0.021-0.00427.378-0.123-0.1230.0000.0000.0000.000
197H208SER00.017-0.00729.621-0.277-0.2770.0000.0000.0000.000
198H209ASN00.010-0.00128.948-0.055-0.0550.0000.0000.0000.000
199H210THR00.0390.03531.316-0.155-0.1550.0000.0000.0000.000
200H211LYS10.8000.87729.078-10.060-10.0600.0000.0000.0000.000
201H212VAL0-0.030-0.01732.772-0.333-0.3330.0000.0000.0000.000
202H213ASP-1-0.819-0.88233.2579.6999.6990.0000.0000.0000.000
203H214LYS10.8430.90735.417-8.274-8.2740.0000.0000.0000.000
204H215LYS10.8620.93436.896-7.259-7.2590.0000.0000.0000.000
205H216VAL0-0.044-0.02237.043-0.180-0.1800.0000.0000.0000.000
206H217GLU-1-0.821-0.90340.0537.3447.3440.0000.0000.0000.000
207H218PRO00.025-0.00542.973-0.015-0.0150.0000.0000.0000.000
208H219LYS10.9340.97644.424-7.239-7.2390.0000.0000.0000.000
209H220SER00.0050.02048.334-0.094-0.0940.0000.0000.0000.000