FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: K2ZN3

Calculation Name: 3F62-A-Xray540

Preferred Name: Interleukin-18

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3F62

Chain ID: A

ChEMBL ID: CHEMBL1741305

UniProt ID: Q14116

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -822211.042004
FMO2-HF: Nuclear repulsion 777906.536635
FMO2-HF: Total energy -44304.50537
FMO2-MP2: Total energy -44428.320043


3D Structure Molmil
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:18:GLY)


Summations of interaction energy for fragment #1(A:18:GLY)
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.
2.4663.488-0.002-0.379-0.640.001
Interaction energy analysis for fragmet #1(A:18:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : -0.008
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].
3A19ALA0-0.0990.1084.4960.4480.6060.000-0.062-0.0950.000
4A20MET00.023-0.0813.8440.3521.216-0.002-0.317-0.5450.001
5A20MET0-0.1110.0754.9340.2790.2790.0000.0000.0000.000
6A21VAL00.056-0.0975.9780.2030.2030.0000.0000.0000.000
7A21VAL0-0.0640.0667.2360.0290.0290.0000.0000.0000.000
8A22GLU00.129-0.1088.1460.1280.1280.0000.0000.0000.000
9A22GLU-1-0.988-0.83812.4020.0190.0190.0000.0000.0000.000
10A23THR0-0.024-0.11710.5690.0570.0570.0000.0000.0000.000
11A23THR00.0100.1048.9130.1040.1040.0000.0000.0000.000
12A24LYS00.060-0.08910.993-0.060-0.0600.0000.0000.0000.000
13A24LYS10.7981.02613.932-0.224-0.2240.0000.0000.0000.000
14A25CYS00.127-0.10714.4710.0580.0580.0000.0000.0000.000
15A25CYS0-0.0830.13215.0080.0050.0050.0000.0000.0000.000
16A26PRO0-0.016-0.10016.515-0.040-0.0400.0000.0000.0000.000
17A27ASN00.0860.03316.2670.0240.0240.0000.0000.0000.000
18A27ASN0-0.1080.06515.562-0.027-0.0270.0000.0000.0000.000
19A28LEU00.144-0.09417.5390.0420.0420.0000.0000.0000.000
20A28LEU0-0.0890.09521.271-0.005-0.0050.0000.0000.0000.000
21A29ASP0-0.008-0.12919.403-0.026-0.0260.0000.0000.0000.000
22A29ASP-1-0.840-0.76518.7840.2250.2250.0000.0000.0000.000
23A30ILE00.084-0.09520.5650.0180.0180.0000.0000.0000.000
24A30ILE0-0.0990.08224.040-0.002-0.0020.0000.0000.0000.000
25A31VAL00.143-0.05421.611-0.017-0.0170.0000.0000.0000.000
26A31VAL0-0.0750.10019.4500.0020.0020.0000.0000.0000.000
27A32THR0-0.015-0.11922.708-0.002-0.0020.0000.0000.0000.000
28A32THR0-0.0010.08926.068-0.003-0.0030.0000.0000.0000.000
29A33SER00.008-0.05525.4190.0020.0020.0000.0000.0000.000
30A33SER0-0.0540.03525.6710.0040.0040.0000.0000.0000.000
31A34SER00.043-0.09827.423-0.004-0.0040.0000.0000.0000.000
32A34SER0-0.0580.06830.914-0.002-0.0020.0000.0000.0000.000
33A35GLY00.022-0.07730.9940.0010.0010.0000.0000.0000.000
34A36GLU00.035-0.03829.011-0.004-0.0040.0000.0000.0000.000
35A36GLU-1-0.830-0.74427.8580.1290.1290.0000.0000.0000.000
36A37PHE00.030-0.08427.1750.0000.0000.0000.0000.0000.000
37A37PHE0-0.0320.09027.5530.0000.0000.0000.0000.0000.000
38A38HIS00.101-0.08423.438-0.008-0.0080.0000.0000.0000.000
39A38HIS0-0.1390.06122.4820.0180.0180.0000.0000.0000.000
40A39CYS00.147-0.09322.5360.0160.0160.0000.0000.0000.000
41A39CYS0-0.2290.19723.9590.0050.0050.0000.0000.0000.000
42A40SER0-0.017-0.09918.770-0.005-0.0050.0000.0000.0000.000
43A40SER0-0.0350.06617.8830.0250.0250.0000.0000.0000.000
44A41GLY00.026-0.09017.870-0.020-0.0200.0000.0000.0000.000
45A42CYS00.0250.00115.538-0.012-0.0120.0000.0000.0000.000
46A42CYS0-0.1170.11215.1320.0220.0220.0000.0000.0000.000
47A43VAL00.127-0.11516.876-0.034-0.0340.0000.0000.0000.000
48A43VAL0-0.0610.10619.084-0.004-0.0040.0000.0000.0000.000
49A44GLU00.069-0.09115.6400.0460.0460.0000.0000.0000.000
50A44GLU-1-0.999-0.86414.1210.2440.2440.0000.0000.0000.000
51A45HIS00.180-0.08316.751-0.004-0.0040.0000.0000.0000.000
52A45HIS0-0.0870.10519.9320.0030.0030.0000.0000.0000.000
53A46MET0-0.012-0.09319.9760.0090.0090.0000.0000.0000.000
54A46MET0-0.1290.07323.743-0.004-0.0040.0000.0000.0000.000
55A47PRO00.092-0.07218.932-0.002-0.0020.0000.0000.0000.000
56A48GLU00.0970.02621.1750.0120.0120.0000.0000.0000.000
57A48GLU-1-0.860-0.81323.4400.1620.1620.0000.0000.0000.000
58A49PHE0-0.017-0.09724.316-0.003-0.0030.0000.0000.0000.000
59A49PHE0-0.1040.07326.294-0.004-0.0040.0000.0000.0000.000
60A50SER00.077-0.11023.687-0.008-0.0080.0000.0000.0000.000
61A50SER0-0.0390.06422.7650.0100.0100.0000.0000.0000.000
62A51TYR00.002-0.10225.1750.0060.0060.0000.0000.0000.000
63A51TYR0-0.0550.09727.831-0.003-0.0030.0000.0000.0000.000
64A52MET00.113-0.09724.887-0.004-0.0040.0000.0000.0000.000
65A52MET0-0.1180.09921.3720.0020.0020.0000.0000.0000.000
66A53TYR00.050-0.09526.2150.0000.0000.0000.0000.0000.000
67A53TYR0-0.0790.08229.361-0.004-0.0040.0000.0000.0000.000
68A54TRP00.058-0.10028.9510.0070.0070.0000.0000.0000.000
69A54TRP0-0.1000.09126.824-0.003-0.0030.0000.0000.0000.000
70A55LEU00.124-0.09431.113-0.004-0.0040.0000.0000.0000.000
71A55LEU0-0.1120.08333.3670.0000.0000.0000.0000.0000.000
72A56ALA00.093-0.09933.7920.0050.0050.0000.0000.0000.000
73A56ALA0-0.0700.10235.9860.0000.0000.0000.0000.0000.000
74A57LYS00.079-0.10436.513-0.002-0.0020.0000.0000.0000.000
75A57LYS10.6970.96838.908-0.051-0.0510.0000.0000.0000.000
76A58ASP00.111-0.09539.3790.0030.0030.0000.0000.0000.000
77A58ASP-1-0.861-0.76443.1430.0480.0480.0000.0000.0000.000
78A59MET00.059-0.08841.151-0.001-0.0010.0000.0000.0000.000
79A59MET0-0.1300.09139.0980.0010.0010.0000.0000.0000.000
80A60LYS00.099-0.09042.304-0.002-0.0020.0000.0000.0000.000
81A60LYS10.7771.03445.068-0.043-0.0430.0000.0000.0000.000
82A61SER0-0.012-0.09945.413-0.003-0.0030.0000.0000.0000.000
83A61SER0-0.0630.03346.1700.0000.0000.0000.0000.0000.000
84A62ASP00.029-0.13145.8020.0020.0020.0000.0000.0000.000
85A62ASP-1-0.903-0.80648.8740.0380.0380.0000.0000.0000.000
86A63GLU00.094-0.10246.4570.0010.0010.0000.0000.0000.000
87A63GLU-1-0.936-0.80745.0510.0480.0480.0000.0000.0000.000
88A64ASP00.122-0.11343.9120.0020.0020.0000.0000.0000.000
89A64ASP-1-0.962-0.80943.0840.0540.0540.0000.0000.0000.000
90A65THR00.011-0.09539.2440.0000.0000.0000.0000.0000.000
91A65THR0-0.0720.04737.1290.0010.0010.0000.0000.0000.000
92A66LYS00.013-0.07639.242-0.001-0.0010.0000.0000.0000.000
93A66LYS10.7490.97940.514-0.055-0.0550.0000.0000.0000.000
94A67PHE00.076-0.09536.3020.0040.0040.0000.0000.0000.000
95A67PHE0-0.0540.10534.9320.0000.0000.0000.0000.0000.000
96A68ILE00.112-0.09035.428-0.006-0.0060.0000.0000.0000.000
97A68ILE0-0.0930.11133.4620.0010.0010.0000.0000.0000.000
98A69GLU00.088-0.10236.772-0.003-0.0030.0000.0000.0000.000
99A69GLU-1-0.904-0.81737.6470.0800.0800.0000.0000.0000.000
100A70HIS00.015-0.13139.182-0.004-0.0040.0000.0000.0000.000
101A70HIS0-0.0980.06940.616-0.001-0.0010.0000.0000.0000.000
102A71LEU0-0.013-0.11840.528-0.004-0.0040.0000.0000.0000.000
103A71LEU0-0.0530.12537.7010.0000.0000.0000.0000.0000.000
104A72GLY00.019-0.08441.826-0.003-0.0030.0000.0000.0000.000
105A73ASP00.033-0.05041.6810.0040.0040.0000.0000.0000.000
106A73ASP-1-0.923-0.80944.3340.0530.0530.0000.0000.0000.000
107A74GLY00.015-0.09540.846-0.001-0.0010.0000.0000.0000.000
108A75ILE00.052-0.01936.8320.0010.0010.0000.0000.0000.000
109A75ILE0-0.0810.10935.2780.0000.0000.0000.0000.0000.000
110A76ASN00.042-0.06435.092-0.004-0.0040.0000.0000.0000.000
111A76ASN0-0.1240.03232.743-0.003-0.0030.0000.0000.0000.000
112A77GLU00.150-0.06331.2110.0020.0020.0000.0000.0000.000
113A77GLU-1-0.863-0.82130.3360.1170.1170.0000.0000.0000.000
114A78ASP00.078-0.09929.029-0.010-0.0100.0000.0000.0000.000
115A78ASP-1-0.914-0.79428.1570.1250.1250.0000.0000.0000.000
116A79GLU00.060-0.10928.6940.0030.0030.0000.0000.0000.000
117A79GLU-1-0.921-0.81828.4120.1270.1270.0000.0000.0000.000
118A80THR00.024-0.09325.3190.0090.0090.0000.0000.0000.000
119A80THR0-0.0860.05923.742-0.004-0.0040.0000.0000.0000.000
120A81VAL00.108-0.08722.091-0.006-0.0060.0000.0000.0000.000
121A81VAL0-0.1030.10420.1200.0030.0030.0000.0000.0000.000
122A82ARG00.126-0.08820.2630.0230.0230.0000.0000.0000.000
123A82ARG10.7521.01520.559-0.216-0.2160.0000.0000.0000.000
124A83THR0-0.052-0.09216.312-0.029-0.0290.0000.0000.0000.000
125A83THR0-0.0650.02915.3650.0260.0260.0000.0000.0000.000
126A84THR00.061-0.07914.5680.0190.0190.0000.0000.0000.000
127A84THR0-0.0480.06114.645-0.022-0.0220.0000.0000.0000.000
128A85ASP00.038-0.11610.395-0.100-0.1000.0000.0000.0000.000
129A85ASP-1-0.913-0.8128.2441.0661.0660.0000.0000.0000.000
130A86GLY0-0.046-0.1118.4920.0700.0700.0000.0000.0000.000
131A87GLY0-0.032-0.0149.361-0.058-0.0580.0000.0000.0000.000
132A88ILE00.090-0.00411.526-0.117-0.1170.0000.0000.0000.000
133A88ILE0-0.0870.11710.3520.0050.0050.0000.0000.0000.000
134A89THR00.086-0.08413.0310.0470.0470.0000.0000.0000.000
135A89THR0-0.0240.10116.842-0.017-0.0170.0000.0000.0000.000
136A90THR00.004-0.09815.286-0.015-0.0150.0000.0000.0000.000
137A90THR0-0.0820.05013.8380.0330.0330.0000.0000.0000.000
138A91LEU00.092-0.07416.386-0.003-0.0030.0000.0000.0000.000
139A91LEU0-0.0420.11920.146-0.006-0.0060.0000.0000.0000.000
140A92ARG00.095-0.10119.5860.0210.0210.0000.0000.0000.000
141A92ARG10.8411.04514.086-0.454-0.4540.0000.0000.0000.000
142A93LYS00.095-0.09521.382-0.005-0.0050.0000.0000.0000.000
143A93LYS10.6901.01225.352-0.141-0.1410.0000.0000.0000.000
144A94VAL00.098-0.12125.0850.0020.0020.0000.0000.0000.000
145A94VAL0-0.0520.13124.9770.0010.0010.0000.0000.0000.000
146A95LEU00.132-0.07826.854-0.005-0.0050.0000.0000.0000.000
147A95LEU0-0.1380.09529.6210.0000.0000.0000.0000.0000.000
148A96HIS00.068-0.09630.2200.0020.0020.0000.0000.0000.000
149A96HIS10.7140.95929.582-0.115-0.1150.0000.0000.0000.000
150A97VAL00.073-0.09732.437-0.003-0.0030.0000.0000.0000.000
151A97VAL0-0.0820.10632.984-0.001-0.0010.0000.0000.0000.000
152A98THR00.065-0.05335.3080.0000.0000.0000.0000.0000.000
153A98THR0-0.0600.04236.3810.0000.0000.0000.0000.0000.000
154A99ASP00.122-0.09537.838-0.003-0.0030.0000.0000.0000.000
155A99ASP-1-0.939-0.80441.4790.0530.0530.0000.0000.0000.000
156A100THR00.030-0.11738.4680.0010.0010.0000.0000.0000.000
157A100THR0-0.0520.06236.509-0.002-0.0020.0000.0000.0000.000
158A101ASN00.126-0.03839.1670.0000.0000.0000.0000.0000.000
159A101ASN0-0.1470.04943.653-0.001-0.0010.0000.0000.0000.000
160A102LYS00.115-0.11342.741-0.001-0.0010.0000.0000.0000.000
161A102LYS10.7291.01642.717-0.057-0.0570.0000.0000.0000.000
162A103PHE00.038-0.09938.994-0.002-0.0020.0000.0000.0000.000
163A103PHE0-0.0920.09138.1110.0010.0010.0000.0000.0000.000
164A104ALA00.117-0.11438.8330.0040.0040.0000.0000.0000.000
165A104ALA0-0.0630.10041.009-0.001-0.0010.0000.0000.0000.000
166A105HIS0-0.021-0.08439.9640.0000.0000.0000.0000.0000.000
167A105HIS0-0.0740.06842.864-0.001-0.0010.0000.0000.0000.000
168A106TYR00.089-0.10838.735-0.003-0.0030.0000.0000.0000.000
169A106TYR0-0.0580.11937.9690.0010.0010.0000.0000.0000.000
170A107ARG00.143-0.07735.5400.0030.0030.0000.0000.0000.000
171A107ARG10.7631.02034.024-0.076-0.0760.0000.0000.0000.000
172A108PHE00.046-0.09532.785-0.003-0.0030.0000.0000.0000.000
173A108PHE0-0.0850.10532.0850.0010.0010.0000.0000.0000.000
174A109THR00.004-0.09730.5020.0020.0020.0000.0000.0000.000
175A109THR0-0.0890.03130.525-0.004-0.0040.0000.0000.0000.000
176A110CYS00.195-0.05226.784-0.006-0.0060.0000.0000.0000.000
177A111VAL00.038-0.13527.7290.0010.0010.0000.0000.0000.000
178A111VAL0-0.0790.10529.043-0.002-0.0020.0000.0000.0000.000
179A112LEU00.141-0.08124.0300.0000.0000.0000.0000.0000.000
180A112LEU0-0.1310.10320.9090.0030.0030.0000.0000.0000.000
181A113THR0-0.015-0.09525.503-0.003-0.0030.0000.0000.0000.000
182A113THR0-0.0100.05828.410-0.001-0.0010.0000.0000.0000.000
183A114THR00.002-0.07024.0440.0110.0110.0000.0000.0000.000
184A114THR00.0080.06422.1380.0030.0030.0000.0000.0000.000
185A115LEU00.077-0.08125.382-0.008-0.0080.0000.0000.0000.000
186A115LEU0-0.0720.10525.9610.0000.0000.0000.0000.0000.000
187A116ASP00.106-0.10424.522-0.013-0.0130.0000.0000.0000.000
188A116ASP-1-0.970-0.82422.6210.1360.1360.0000.0000.0000.000
189A117GLY0-0.037-0.11225.925-0.010-0.0100.0000.0000.0000.000
190A118VAL00.0780.00826.7130.0130.0130.0000.0000.0000.000
191A118VAL0-0.0830.09228.670-0.002-0.0020.0000.0000.0000.000
192A119SER0-0.023-0.11124.589-0.011-0.0110.0000.0000.0000.000
193A119SER0-0.0040.08524.1000.0070.0070.0000.0000.0000.000
194A120LYS00.092-0.08226.0900.0060.0060.0000.0000.0000.000
195A120LYS10.8751.05428.853-0.094-0.0940.0000.0000.0000.000
196A121LYS00.053-0.09325.382-0.003-0.0030.0000.0000.0000.000
197A121LYS10.7190.98121.374-0.184-0.1840.0000.0000.0000.000
198A122ASN00.058-0.07526.8090.0020.0020.0000.0000.0000.000
199A122ASN0-0.0640.06830.477-0.002-0.0020.0000.0000.0000.000
200A123ILE00.040-0.08028.6460.0030.0030.0000.0000.0000.000
201A123ILE0-0.0380.11027.0680.0010.0010.0000.0000.0000.000
202A124TRP00.035-0.13230.470-0.002-0.0020.0000.0000.0000.000
203A124TRP0-0.0010.11632.786-0.002-0.0020.0000.0000.0000.000
204A125LEU0-0.064-0.11832.4380.0040.0040.0000.0000.0000.000
205A125LEU00.0740.06433.5770.0000.0000.0000.0000.0000.000