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: 173NZ

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2038905.960454
FMO2-HF: Nuclear repulsion 1960217.838106
FMO2-HF: Total energy -78688.122347
FMO2-MP2: Total energy -78916.530639


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.
-97.104-98.416.99-8.957-6.7350.087
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 : -0.841 / q_NPA : -0.908
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].
3H3GLN0-0.012-0.0123.4133.2405.9040.023-1.271-1.4170.004
4H4LEU0-0.016-0.0115.683-4.690-4.6900.0000.0000.0000.000
5H5VAL00.0090.0039.3100.4400.4400.0000.0000.0000.000
6H6GLU-1-0.773-0.87611.86722.20622.2060.0000.0000.0000.000
7H7SER0-0.061-0.02815.318-0.421-0.4210.0000.0000.0000.000
8H8GLY00.0540.02318.4600.1990.1990.0000.0000.0000.000
9H9GLY0-0.0030.01221.441-0.524-0.5240.0000.0000.0000.000
10H10GLY00.006-0.01223.407-0.025-0.0250.0000.0000.0000.000
11H11LEU0-0.050-0.00926.3570.0240.0240.0000.0000.0000.000
12H12VAL00.0070.00229.427-0.110-0.1100.0000.0000.0000.000
13H13GLN00.0270.01731.984-0.124-0.1240.0000.0000.0000.000
14H14PRO0-0.006-0.02135.1330.1240.1240.0000.0000.0000.000
15H15GLY0-0.021-0.00935.958-0.227-0.2270.0000.0000.0000.000
16H16GLY0-0.0080.00534.420-0.091-0.0910.0000.0000.0000.000
17H17SER0-0.065-0.05831.7130.1870.1870.0000.0000.0000.000
18H18LEU00.0010.00525.2700.0200.0200.0000.0000.0000.000
19H19ARG10.9040.97823.934-12.202-12.2020.0000.0000.0000.000
20H20LEU0-0.0240.00520.3950.2260.2260.0000.0000.0000.000
21H21SER0-0.009-0.02318.678-0.556-0.5560.0000.0000.0000.000
22H22CYS0-0.082-0.03913.901-0.030-0.0300.0000.0000.0000.000
23H23ALA00.0130.02413.048-0.331-0.3310.0000.0000.0000.000
24H24ALA00.0200.00910.2301.8851.8850.0000.0000.0000.000
25H25SER0-0.042-0.0297.451-1.572-1.5720.0000.0000.0000.000
26H26GLY00.0830.0334.7252.8912.874-0.001-0.0180.0380.000
27H27PHE00.0360.0165.5251.4821.4820.0000.0000.0000.000
28H28THR00.0230.0158.248-1.276-1.2760.0000.0000.0000.000
29H29PHE00.0550.03112.043-0.830-0.8300.0000.0000.0000.000
30H30SER0-0.016-0.00613.520-0.176-0.1760.0000.0000.0000.000
31H31SER0-0.0040.00114.977-1.203-1.2030.0000.0000.0000.000
32H32TYR0-0.006-0.00511.0010.3260.3260.0000.0000.0000.000
33H33ARG10.8780.95415.489-15.290-15.2900.0000.0000.0000.000
34H34MET0-0.0220.00712.3631.3211.3210.0000.0000.0000.000
35H35TYR0-0.149-0.11614.252-1.978-1.9780.0000.0000.0000.000
36H36TRP00.0530.02816.7491.1041.1040.0000.0000.0000.000
37H37VAL0-0.015-0.00117.306-0.960-0.9600.0000.0000.0000.000
38H38ARG10.7880.87519.200-11.698-11.6980.0000.0000.0000.000
39H39GLN00.002-0.01019.4600.6840.6840.0000.0000.0000.000
40H40PRO00.0250.01222.086-0.058-0.0580.0000.0000.0000.000
41H41PRO00.0240.01225.0980.2860.2860.0000.0000.0000.000
42H42GLY00.0070.00025.515-0.425-0.4250.0000.0000.0000.000
43H43LYS10.8930.96025.822-10.873-10.8730.0000.0000.0000.000
44H44GLY00.0390.01723.5900.5410.5410.0000.0000.0000.000
45H45LEU00.0160.00317.245-0.140-0.1400.0000.0000.0000.000
46H46GLU-1-0.838-0.90421.68011.47011.4700.0000.0000.0000.000
47H47TRP0-0.027-0.00420.0730.2640.2640.0000.0000.0000.000
48H48VAL00.0000.00621.910-0.716-0.7160.0000.0000.0000.000
49H49SER00.013-0.01622.206-0.704-0.7040.0000.0000.0000.000
50H50ALA0-0.032-0.02320.9190.8810.8810.0000.0000.0000.000
51H51ILE00.0120.02119.775-0.835-0.8350.0000.0000.0000.000
52H52SER0-0.022-0.00919.9690.7840.7840.0000.0000.0000.000
53H53ALA00.021-0.00118.817-0.063-0.0630.0000.0000.0000.000
54H54GLY00.0530.02219.7970.2270.2270.0000.0000.0000.000
55H55GLY0-0.037-0.02522.712-0.417-0.4170.0000.0000.0000.000
56H56GLY0-0.0040.01824.320-0.320-0.3200.0000.0000.0000.000
57H57SER0-0.003-0.00725.505-0.322-0.3220.0000.0000.0000.000
58H58THR0-0.0130.00124.8480.5500.5500.0000.0000.0000.000
59H59TYR00.003-0.01124.386-0.222-0.2220.0000.0000.0000.000
60H60TYR00.0760.04725.5880.5810.5810.0000.0000.0000.000
61H61GLY00.0990.06226.958-0.288-0.2880.0000.0000.0000.000
62H62ASP-1-0.846-0.94428.18110.07610.0760.0000.0000.0000.000
63H63SER00.0010.02529.651-0.294-0.2940.0000.0000.0000.000
64H64VAL0-0.026-0.03227.431-0.153-0.1530.0000.0000.0000.000
65H65LYS10.7880.89230.444-10.343-10.3430.0000.0000.0000.000
66H66GLY00.0270.02932.0470.0180.0180.0000.0000.0000.000
67H67ARG10.7540.85131.459-10.143-10.1430.0000.0000.0000.000
68H68PHE0-0.008-0.01726.4860.1080.1080.0000.0000.0000.000
69H69THR0-0.002-0.00528.160-0.302-0.3020.0000.0000.0000.000
70H70ILE0-0.0180.00820.6660.3300.3300.0000.0000.0000.000
71H71SER0-0.012-0.01323.540-0.468-0.4680.0000.0000.0000.000
72H72ARG10.8440.91016.189-16.089-16.0890.0000.0000.0000.000
73H73ASP-1-0.812-0.88019.87312.79912.7990.0000.0000.0000.000
74H74ASN00.0420.01417.8271.5151.5150.0000.0000.0000.000
75H75ALA00.0050.01517.586-0.657-0.6570.0000.0000.0000.000
76H76LYS10.9110.93816.615-13.243-13.2430.0000.0000.0000.000
77H77ASN00.0170.01211.980-0.351-0.3510.0000.0000.0000.000
78H78THR0-0.002-0.00114.5161.0651.0650.0000.0000.0000.000
79H79VAL0-0.023-0.00516.187-0.815-0.8150.0000.0000.0000.000
80H80TYR0-0.043-0.06418.6700.2210.2210.0000.0000.0000.000
81H81LEU00.001-0.00221.505-0.188-0.1880.0000.0000.0000.000
82H82GLN0-0.021-0.00723.4660.1040.1040.0000.0000.0000.000
83H83MET0-0.022-0.01425.2550.0470.0470.0000.0000.0000.000
84H84ASN00.0890.05228.741-0.070-0.0700.0000.0000.0000.000
85H85SER00.008-0.01932.5440.0030.0030.0000.0000.0000.000
86H86LEU0-0.0270.01728.886-0.016-0.0160.0000.0000.0000.000
87H87LYS10.9090.94632.552-9.338-9.3380.0000.0000.0000.000
88H88PRO00.0480.01932.1770.3370.3370.0000.0000.0000.000
89H89GLU-1-0.820-0.90931.5889.4739.4730.0000.0000.0000.000
90H90ASP-1-0.768-0.83228.52210.87310.8730.0000.0000.0000.000
91H91THR00.0010.02427.0980.4810.4810.0000.0000.0000.000
92H92ALA0-0.021-0.01723.419-0.060-0.0600.0000.0000.0000.000
93H93VAL0-0.0050.02317.935-0.126-0.1260.0000.0000.0000.000
94H94TYR0-0.038-0.04819.521-0.063-0.0630.0000.0000.0000.000
95H95TYR00.0400.00713.9930.4100.4100.0000.0000.0000.000
96H97ALA00.0740.03011.9942.0362.0360.0000.0000.0000.000
97H98ASN00.007-0.0079.550-0.259-0.2590.0000.0000.0000.000
98H99ARG10.9100.95612.449-15.868-15.8680.0000.0000.0000.000
99H100ALA0-0.0070.01012.2480.4320.4320.0000.0000.0000.000
100H101GLY0-0.001-0.01112.723-2.218-2.2180.0000.0000.0000.000
101H102TRP0-0.047-0.03112.4841.2551.2550.0000.0000.0000.000
102H103GLY00.0240.02212.4520.5180.5180.0000.0000.0000.000
103H104MET0-0.0230.0206.9972.7952.7950.0000.0000.0000.000
104H105GLY00.0510.0118.327-3.390-3.3900.0000.0000.0000.000
105H106ASP-1-0.804-0.8889.19024.01724.0170.0000.0000.0000.000
106H107TYR0-0.027-0.0231.658-34.971-38.91416.968-7.668-5.3560.083
107H108TRP0-0.036-0.0517.851-5.346-5.3460.0000.0000.0000.000
108H109GLY00.0600.0378.4594.1414.1410.0000.0000.0000.000
109H110GLN0-0.056-0.0318.9552.1022.1020.0000.0000.0000.000
110H111GLY00.0120.00911.866-1.351-1.3510.0000.0000.0000.000
111H112THR0-0.050-0.04015.377-0.741-0.7410.0000.0000.0000.000
112H113GLN0-0.015-0.00518.676-0.428-0.4280.0000.0000.0000.000
113H114VAL00.0020.00622.011-0.257-0.2570.0000.0000.0000.000
114H115THR0-0.028-0.02225.114-0.024-0.0240.0000.0000.0000.000
115H116VAL00.0210.01628.448-0.185-0.1850.0000.0000.0000.000
116H117SER00.008-0.00731.665-0.225-0.2250.0000.0000.0000.000
117H118SER00.0200.00734.8350.0710.0710.0000.0000.0000.000
118H119ALA0-0.0220.01036.635-0.196-0.1960.0000.0000.0000.000
119H120SER00.016-0.00336.4180.1370.1370.0000.0000.0000.000
120H121THR0-0.021-0.01932.4340.0140.0140.0000.0000.0000.000
121H122LYS10.8180.92235.187-8.427-8.4270.0000.0000.0000.000
122H123GLY00.0610.03334.6210.2860.2860.0000.0000.0000.000
123H124PRO0-0.022-0.01232.883-0.200-0.2000.0000.0000.0000.000
124H125SER0-0.016-0.00535.937-0.092-0.0920.0000.0000.0000.000
125H126VAL00.0220.00935.1660.0630.0630.0000.0000.0000.000
126H127PHE0-0.004-0.01337.934-0.265-0.2650.0000.0000.0000.000
127H128PRO00.0130.01038.6870.2010.2010.0000.0000.0000.000
128H129LEU0-0.0340.00036.586-0.202-0.2020.0000.0000.0000.000
129H130ALA00.010-0.01139.4550.1280.1280.0000.0000.0000.000
130H131PRO00.0390.03540.632-0.012-0.0120.0000.0000.0000.000
131H132SER00.000-0.00442.100-0.218-0.2180.0000.0000.0000.000
132H133SER0-0.035-0.03845.1900.1150.1150.0000.0000.0000.000
133H134LYS10.8370.92443.286-7.508-7.5080.0000.0000.0000.000
134H135SER00.1140.07847.232-0.053-0.0530.0000.0000.0000.000
135H136THR0-0.012-0.02749.0690.1490.1490.0000.0000.0000.000
136H137SER00.0510.03546.5580.0190.0190.0000.0000.0000.000
137H138GLY00.0200.02844.3430.1810.1810.0000.0000.0000.000
138H139GLY0-0.001-0.01343.0950.0450.0450.0000.0000.0000.000
139H140THR0-0.017-0.00937.083-0.022-0.0220.0000.0000.0000.000
140H141ALA0-0.005-0.00339.362-0.102-0.1020.0000.0000.0000.000
141H142ALA00.0250.02036.2080.2020.2020.0000.0000.0000.000
142H143LEU0-0.024-0.00235.890-0.276-0.2760.0000.0000.0000.000
143H144GLY00.0670.00834.7770.3260.3260.0000.0000.0000.000
144H145CYS0-0.079-0.02131.808-0.025-0.0250.0000.0000.0000.000
145H146LEU00.0100.02034.5270.2250.2250.0000.0000.0000.000
146H147VAL0-0.017-0.00731.852-0.193-0.1930.0000.0000.0000.000
147H148LYS10.9020.92134.916-7.676-7.6760.0000.0000.0000.000
148H149ASP-1-0.770-0.86437.4207.9297.9290.0000.0000.0000.000
149H150TYR00.0150.01929.763-0.158-0.1580.0000.0000.0000.000
150H151PHE00.0510.03532.7330.1340.1340.0000.0000.0000.000
151H152PRO00.0400.02429.045-0.199-0.1990.0000.0000.0000.000
152H153GLU-1-0.836-0.92526.42211.56711.5670.0000.0000.0000.000
153H154PRO0-0.042-0.02922.7660.1290.1290.0000.0000.0000.000
154H155VAL00.001-0.00925.821-0.213-0.2130.0000.0000.0000.000
155H156THR0-0.056-0.02822.9560.5310.5310.0000.0000.0000.000
156H157VAL0-0.016-0.01525.454-0.387-0.3870.0000.0000.0000.000
157H158SER0-0.033-0.01924.9110.4590.4590.0000.0000.0000.000
158H159TRP00.0620.04326.847-0.545-0.5450.0000.0000.0000.000
159H160ASN00.0290.00427.7910.3410.3410.0000.0000.0000.000
160H161SER0-0.019-0.00328.7690.1650.1650.0000.0000.0000.000
161H162GLY00.001-0.02225.5020.3250.3250.0000.0000.0000.000
162H163ALA00.0160.00023.021-0.278-0.2780.0000.0000.0000.000
163H164LEU00.0310.04324.4420.0910.0910.0000.0000.0000.000
164H165THR0-0.008-0.01822.655-0.447-0.4470.0000.0000.0000.000
165H166SER0-0.011-0.00826.020-0.037-0.0370.0000.0000.0000.000
166H167GLY00.0220.00328.491-0.370-0.3700.0000.0000.0000.000
167H168VAL0-0.051-0.02526.114-0.231-0.2310.0000.0000.0000.000
168H169HIS00.0100.01126.4690.6830.6830.0000.0000.0000.000
169H170THR00.0100.00525.606-0.674-0.6740.0000.0000.0000.000
170H171PHE0-0.008-0.00126.5800.3470.3470.0000.0000.0000.000
171H172PRO00.002-0.00326.9580.1060.1060.0000.0000.0000.000
172H173ALA0-0.0150.00128.439-0.418-0.4180.0000.0000.0000.000
173H174VAL0-0.017-0.00230.8080.0390.0390.0000.0000.0000.000
174H175LEU0-0.010-0.00533.208-0.036-0.0360.0000.0000.0000.000
175H176GLN0-0.045-0.01735.070-0.062-0.0620.0000.0000.0000.000
176H177SER00.0490.00238.7830.1350.1350.0000.0000.0000.000
177H178SER0-0.025-0.00940.512-0.006-0.0060.0000.0000.0000.000
178H179GLY00.0410.03137.543-0.047-0.0470.0000.0000.0000.000
179H180LEU0-0.105-0.04235.9490.2380.2380.0000.0000.0000.000
180H181TYR00.0330.00530.600-0.067-0.0670.0000.0000.0000.000
181H182SER0-0.004-0.01634.183-0.178-0.1780.0000.0000.0000.000
182H183LEU00.0280.02828.4890.0540.0540.0000.0000.0000.000
183H184SER00.008-0.01232.061-0.417-0.4170.0000.0000.0000.000
184H185SER0-0.0050.00028.5420.2610.2610.0000.0000.0000.000
185H186VAL0-0.008-0.01430.985-0.367-0.3670.0000.0000.0000.000
186H187VAL00.0140.02030.3690.4040.4040.0000.0000.0000.000
187H188THR0-0.0050.00732.174-0.443-0.4430.0000.0000.0000.000
188H198THR00.0510.02937.150-0.176-0.1760.0000.0000.0000.000
189H199TYR0-0.007-0.00933.4230.1690.1690.0000.0000.0000.000
190H200ILE0-0.020-0.01434.388-0.279-0.2790.0000.0000.0000.000
191H202ASN00.025-0.00329.224-0.280-0.2800.0000.0000.0000.000
192H203VAL00.0160.00628.9480.3970.3970.0000.0000.0000.000
193H204ASN00.0400.01626.721-0.335-0.3350.0000.0000.0000.000
194H205HIS00.0370.03927.7080.1710.1710.0000.0000.0000.000
195H206LYS11.0010.98521.927-14.018-14.0180.0000.0000.0000.000
196H207PRO0-0.016-0.00627.077-0.126-0.1260.0000.0000.0000.000
197H208SER0-0.006-0.01329.323-0.270-0.2700.0000.0000.0000.000
198H209ASN0-0.026-0.02929.135-0.018-0.0180.0000.0000.0000.000
199H210THR00.0200.02331.529-0.314-0.3140.0000.0000.0000.000
200H211LYS10.8330.92028.725-10.291-10.2910.0000.0000.0000.000
201H212VAL0-0.021-0.01132.388-0.327-0.3270.0000.0000.0000.000
202H213ASP-1-0.804-0.87632.9169.8889.8880.0000.0000.0000.000
203H214LYS10.8610.91835.028-8.264-8.2640.0000.0000.0000.000
204H215LYS10.8450.92436.775-7.295-7.2950.0000.0000.0000.000
205H216VAL0-0.046-0.02636.933-0.222-0.2220.0000.0000.0000.000
206H217GLU-1-0.839-0.91839.7887.3237.3230.0000.0000.0000.000
207H218PRO00.010-0.00842.936-0.019-0.0190.0000.0000.0000.000
208H219LYS10.9570.97144.727-7.191-7.1910.0000.0000.0000.000
209H220SER00.0010.02648.079-0.100-0.1000.0000.0000.0000.000