FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: J2VJ9

Calculation Name: 3B5K-A-Xray540

Preferred Name: Interleukin-5

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 3B5K

Chain ID: A

ChEMBL ID: CHEMBL1163111

UniProt ID: P04401

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 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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -738040.618232
FMO2-HF: Nuclear repulsion 695681.518115
FMO2-HF: Total energy -42359.100116
FMO2-MP2: Total energy -42483.725642


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:7:THR)


Summations of interaction energy for fragment #1(A:7:THR)
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.
-4.53-1.3180.12-1.578-1.7530.004
Interaction energy analysis for fragmet #1(A:7:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.036
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].
4A8SER00.0000.1034.147-0.2640.0640.002-0.151-0.1790.000
5A9THR0-0.027-0.1073.812-3.009-1.226-0.020-1.035-0.7280.003
6A9THR0-0.0060.0786.912-0.163-0.1630.0000.0000.0000.000
7A10VAL00.189-0.1053.847-0.404-0.2420.004-0.035-0.1300.000
8A10VAL0-0.0370.1542.919-0.1400.1810.121-0.176-0.2650.001
9A11VAL00.034-0.0754.979-0.711-0.706-0.002-0.0030.0000.000
10A11VAL0-0.0280.1295.983-0.009-0.0090.0000.0000.0000.000
11A12LYS00.075-0.1216.877-0.095-0.0950.0000.0000.0000.000
12A12LYS10.9501.1039.549-0.367-0.3670.0000.0000.0000.000
13A13GLU00.106-0.1028.372-0.068-0.0680.0000.0000.0000.000
14A13GLU-1-0.846-0.7398.2730.4810.4810.0000.0000.0000.000
15A14THR0-0.013-0.1358.5160.0840.0840.0000.0000.0000.000
16A14THR0-0.0410.0597.355-0.109-0.1090.0000.0000.0000.000
17A15LEU00.022-0.09610.005-0.047-0.0470.0000.0000.0000.000
18A15LEU0-0.0610.11511.0150.0100.0100.0000.0000.0000.000
19A16THR00.038-0.09112.520-0.009-0.0090.0000.0000.0000.000
20A16THR0-0.0550.07413.1060.0200.0200.0000.0000.0000.000
21A17GLN00.101-0.09113.1790.0370.0370.0000.0000.0000.000
22A17GLN0-0.0910.08110.4490.0770.0770.0000.0000.0000.000
23A18LEU00.140-0.05814.1800.0320.0320.0000.0000.0000.000
24A18LEU0-0.1080.09714.235-0.014-0.0140.0000.0000.0000.000
25A19SER00.029-0.07415.9610.0040.0040.0000.0000.0000.000
26A19SER0-0.0630.05217.9290.0050.0050.0000.0000.0000.000
27A20ALA00.103-0.09417.962-0.004-0.0040.0000.0000.0000.000
28A20ALA0-0.0730.10518.0830.0090.0090.0000.0000.0000.000
29A21HIS0-0.044-0.10219.0010.0310.0310.0000.0000.0000.000
30A21HIS0-0.0790.08517.0480.0170.0170.0000.0000.0000.000
31A22ARG00.200-0.06720.300-0.025-0.0250.0000.0000.0000.000
32A22ARG10.8661.08520.4080.2550.2550.0000.0000.0000.000
33A23ALA00.127-0.08921.950-0.016-0.0160.0000.0000.0000.000
34A23ALA0-0.0670.10425.6490.0050.0050.0000.0000.0000.000
35A24LEU00.110-0.06323.7390.0040.0040.0000.0000.0000.000
36A24LEU0-0.0930.08622.0870.0010.0010.0000.0000.0000.000
37A25LEU00.074-0.06921.2690.0120.0120.0000.0000.0000.000
38A25LEU0-0.1160.06317.991-0.010-0.0100.0000.0000.0000.000
39A26THR00.006-0.06922.683-0.013-0.0130.0000.0000.0000.000
40A26THR0-0.0830.04224.529-0.004-0.0040.0000.0000.0000.000
41A27SER00.066-0.09225.2700.0080.0080.0000.0000.0000.000
42A27SER0-0.0640.05026.4690.0040.0040.0000.0000.0000.000
43A28ASN00.112-0.03126.9430.0160.0160.0000.0000.0000.000
44A28ASN0-0.0840.08027.1750.0120.0120.0000.0000.0000.000
45A29GLU00.072-0.13427.908-0.021-0.0210.0000.0000.0000.000
46A29GLU-1-0.968-0.79930.493-0.133-0.1330.0000.0000.0000.000
47A30THR0-0.027-0.14030.5920.0010.0010.0000.0000.0000.000
48A30THR0-0.0450.06131.293-0.002-0.0020.0000.0000.0000.000
49A31LEU00.097-0.09527.1370.0040.0040.0000.0000.0000.000
50A31LEU0-0.0860.12524.044-0.002-0.0020.0000.0000.0000.000
51A32ARG00.031-0.11727.647-0.001-0.0010.0000.0000.0000.000
52A32ARG10.7801.01828.9960.1980.1980.0000.0000.0000.000
53A33LEU00.010-0.11023.2790.0070.0070.0000.0000.0000.000
54A33LEU0-0.0260.10321.187-0.009-0.0090.0000.0000.0000.000
55A34PRO0-0.007-0.09421.4540.0180.0180.0000.0000.0000.000
56A35VAL00.073-0.03022.010-0.041-0.0410.0000.0000.0000.000
57A35VAL0-0.0800.12522.1970.0010.0010.0000.0000.0000.000
58A36PRO0-0.011-0.11019.7270.0280.0280.0000.0000.0000.000
59A37THR00.0790.01623.0330.0040.0040.0000.0000.0000.000
60A37THR0-0.0300.09227.0860.0000.0000.0000.0000.0000.000
61A38HIS00.045-0.05823.6220.0300.0300.0000.0000.0000.000
62A38HIS0-0.0470.08421.3730.0010.0010.0000.0000.0000.000
63A39LYS00.097-0.04620.255-0.030-0.0300.0000.0000.0000.000
64A39LYS10.8551.04420.2640.3090.3090.0000.0000.0000.000
65A40ASN00.191-0.06819.141-0.022-0.0220.0000.0000.0000.000
66A40ASN0-0.0830.09919.039-0.051-0.0510.0000.0000.0000.000
67A41HIS00.094-0.11515.6000.0230.0230.0000.0000.0000.000
68A41HIS0-0.0970.08014.8910.0260.0260.0000.0000.0000.000
69A42GLN00.076-0.09614.532-0.057-0.0570.0000.0000.0000.000
70A42GLN0-0.0710.11112.103-0.132-0.1320.0000.0000.0000.000
71A43LEU00.090-0.11115.489-0.060-0.0600.0000.0000.0000.000
72A43LEU0-0.0660.11620.0720.0080.0080.0000.0000.0000.000
73A44CYS00.026-0.09517.8200.0280.0280.0000.0000.0000.000
74A44CYS0-0.1040.10118.7340.0240.0240.0000.0000.0000.000
75A45ILE00.150-0.09514.3390.0320.0320.0000.0000.0000.000
76A45ILE0-0.1170.09212.021-0.030-0.0300.0000.0000.0000.000
77A46GLY00.041-0.09615.365-0.038-0.0380.0000.0000.0000.000
78A47GLU00.086-0.03317.732-0.019-0.0190.0000.0000.0000.000
79A47GLU-1-0.883-0.80420.197-0.499-0.4990.0000.0000.0000.000
80A48ILE00.079-0.07015.8450.0630.0630.0000.0000.0000.000
81A48ILE0-0.1240.08114.198-0.014-0.0140.0000.0000.0000.000
82A49PHE00.019-0.09014.3120.0510.0510.0000.0000.0000.000
83A49PHE0-0.1240.0649.607-0.055-0.0550.0000.0000.0000.000
84A50GLN00.155-0.09715.358-0.005-0.0050.0000.0000.0000.000
85A50GLN0-0.0870.10118.593-0.016-0.0160.0000.0000.0000.000
86A51GLY00.035-0.08618.9620.0530.0530.0000.0000.0000.000
87A52LEU00.1300.01315.7720.0720.0720.0000.0000.0000.000
88A52LEU0-0.1320.07913.051-0.029-0.0290.0000.0000.0000.000
89A53ASP0-0.047-0.11517.2940.0330.0330.0000.0000.0000.000
90A53ASP-1-0.861-0.79317.689-0.555-0.5550.0000.0000.0000.000
91A54ILE00.127-0.08418.7060.0280.0280.0000.0000.0000.000
92A54ILE0-0.0540.09522.5270.0040.0040.0000.0000.0000.000
93A55LEU00.168-0.06620.3850.0420.0420.0000.0000.0000.000
94A55LEU0-0.1390.08318.501-0.007-0.0070.0000.0000.0000.000
95A56LYS00.043-0.10118.9480.0480.0480.0000.0000.0000.000
96A56LYS10.7330.96615.2970.6130.6130.0000.0000.0000.000
97A57ASN00.033-0.05520.0760.0300.0300.0000.0000.0000.000
98A57ASN0-0.1390.04621.4070.0010.0010.0000.0000.0000.000
99A58GLN00.118-0.08923.2370.0240.0240.0000.0000.0000.000
100A58GLN0-0.0390.11325.061-0.007-0.0070.0000.0000.0000.000
101A59THR00.032-0.10122.2720.0280.0280.0000.0000.0000.000
102A59THR0-0.0770.04921.069-0.002-0.0020.0000.0000.0000.000
103A60VAL00.082-0.09923.584-0.014-0.0140.0000.0000.0000.000
104A60VAL0-0.0640.12326.0530.0020.0020.0000.0000.0000.000
105A61ARG00.009-0.12921.9560.0000.0000.0000.0000.0000.000
106A61ARG10.7931.03118.5550.3180.3180.0000.0000.0000.000
107A62GLY0-0.020-0.11921.1880.0210.0210.0000.0000.0000.000
108A63GLY00.0160.00221.7200.0220.0220.0000.0000.0000.000
109A64THR00.0660.00718.638-0.005-0.0050.0000.0000.0000.000
110A64THR0-0.0330.06418.2870.0110.0110.0000.0000.0000.000
111A65VAL0-0.003-0.13616.8330.0080.0080.0000.0000.0000.000
112A65VAL0-0.0050.13517.4830.0010.0010.0000.0000.0000.000
113A66GLU00.097-0.08016.064-0.081-0.0810.0000.0000.0000.000
114A66GLU-1-0.843-0.74616.806-0.278-0.2780.0000.0000.0000.000
115A67ARG00.108-0.05513.128-0.090-0.0900.0000.0000.0000.000
116A67ARG10.7810.99512.327-0.166-0.1660.0000.0000.0000.000
117A68LEU00.125-0.12111.667-0.055-0.0550.0000.0000.0000.000
118A68LEU0-0.1340.09512.2490.0010.0010.0000.0000.0000.000
119A69PHE0-0.005-0.13311.466-0.204-0.2040.0000.0000.0000.000
120A69PHE0-0.0360.11714.782-0.003-0.0030.0000.0000.0000.000
121A70GLN00.091-0.09911.246-0.193-0.1930.0000.0000.0000.000
122A70GLN0-0.0590.1109.6540.0420.0420.0000.0000.0000.000
123A71ASN00.127-0.0907.632-0.288-0.2880.0000.0000.0000.000
124A71ASN0-0.1200.0807.9850.0920.0920.0000.0000.0000.000
125A72LEU00.063-0.1306.723-0.842-0.8420.0000.0000.0000.000
126A72LEU0-0.0670.1309.3820.0110.0110.0000.0000.0000.000
127A73SER00.052-0.0548.433-0.407-0.4070.0000.0000.0000.000
128A73SER0-0.0290.06910.2820.0080.0080.0000.0000.0000.000
129A74LEU00.048-0.1055.4860.1400.161-0.002-0.001-0.0170.000
130A74LEU0-0.0460.1043.939-0.135-0.030-0.001-0.009-0.0950.000
131A75ILE00.094-0.0844.295-1.662-1.5860.001-0.046-0.0310.000
132A75ILE0-0.0870.0924.336-0.162-0.0640.000-0.040-0.0580.000
133A76LYS00.092-0.0895.258-0.194-0.196-0.002-0.0020.0060.000
134A76LYS10.7060.9779.7321.2811.2810.0000.0000.0000.000
135A77LYS00.044-0.1107.9990.1430.1430.0000.0000.0000.000
136A77LYS10.8151.0447.4301.4461.4460.0000.0000.0000.000
137A78TYR00.189-0.0344.5761.0071.0470.000-0.009-0.0320.000
138A78TYR0-0.1180.0643.791-1.349-1.0760.021-0.072-0.2220.000
139A79ILE00.021-0.1245.9250.4580.460-0.0020.001-0.0020.000
140A79ILE0-0.0670.0917.2250.0040.0040.0000.0000.0000.000
141A80ASP00.136-0.0568.8450.3120.3120.0000.0000.0000.000
142A80ASP-1-0.928-0.81110.872-1.275-1.2750.0000.0000.0000.000
143A81ARG00.125-0.0719.6410.3040.3040.0000.0000.0000.000
144A81ARG10.6630.9318.7340.6500.6500.0000.0000.0000.000
145A82GLN00.052-0.1369.6110.3050.3050.0000.0000.0000.000
146A82GLN0-0.0670.1088.3520.1130.1130.0000.0000.0000.000
147A83LYS00.117-0.08710.9990.1880.1880.0000.0000.0000.000
148A83LYS10.8521.07713.7240.6520.6520.0000.0000.0000.000
149A84GLU00.026-0.16614.0020.1200.1200.0000.0000.0000.000
150A84GLU-1-0.858-0.78514.070-0.721-0.7210.0000.0000.0000.000
151A85LYS00.070-0.04313.5820.1200.1200.0000.0000.0000.000
152A85LYS10.7941.0239.5050.8560.8560.0000.0000.0000.000
153A86CYS00.046-0.12814.8850.0650.0650.0000.0000.0000.000
154A86CYS0-0.1490.07716.622-0.026-0.0260.0000.0000.0000.000
155A87GLY0-0.013-0.10017.6400.0560.0560.0000.0000.0000.000
156A88GLU00.1100.00018.2780.0450.0450.0000.0000.0000.000
157A88GLU-1-0.916-0.76815.996-0.445-0.4450.0000.0000.0000.000
158A89GLU00.042-0.13819.6250.0370.0370.0000.0000.0000.000
159A89GLU-1-0.867-0.76518.115-0.183-0.1830.0000.0000.0000.000
160A90ARG0-0.016-0.12021.103-0.017-0.0170.0000.0000.0000.000
161A90ARG10.9091.08824.3180.2360.2360.0000.0000.0000.000
162A91ARG00.061-0.06724.7220.0150.0150.0000.0000.0000.000
163A91ARG10.7640.96420.7120.1400.1400.0000.0000.0000.000
164A92ARG00.141-0.05626.227-0.007-0.0070.0000.0000.0000.000
165A92ARG10.8391.03829.6410.0720.0720.0000.0000.0000.000
166A93THR00.065-0.09228.626-0.008-0.0080.0000.0000.0000.000
167A93THR00.0120.08432.1680.0010.0010.0000.0000.0000.000
168A94ARG00.195-0.00930.492-0.008-0.0080.0000.0000.0000.000
169A94ARG10.7631.01727.6350.0760.0760.0000.0000.0000.000
170A95GLN00.041-0.09026.190-0.002-0.0020.0000.0000.0000.000
171A95GLN0-0.0740.08825.1370.0050.0050.0000.0000.0000.000
172A96PHE00.104-0.07925.319-0.012-0.0120.0000.0000.0000.000
173A96PHE0-0.1100.06825.6060.0020.0020.0000.0000.0000.000
174A97LEU00.083-0.08026.614-0.020-0.0200.0000.0000.0000.000
175A97LEU0-0.0940.08030.6170.0020.0020.0000.0000.0000.000
176A98ASP00.097-0.06626.780-0.009-0.0090.0000.0000.0000.000
177A98ASP-1-0.892-0.84426.101-0.099-0.0990.0000.0000.0000.000
178A99TYR00.189-0.04823.3940.0050.0050.0000.0000.0000.000
179A99TYR0-0.1160.08618.288-0.013-0.0130.0000.0000.0000.000
180A100LEU00.105-0.08824.061-0.024-0.0240.0000.0000.0000.000
181A100LEU0-0.1120.08026.8510.0010.0010.0000.0000.0000.000
182A101GLN00.074-0.10226.539-0.010-0.0100.0000.0000.0000.000
183A101GLN0-0.1230.07728.1200.0050.0050.0000.0000.0000.000
184A102GLU00.058-0.13724.2780.0060.0060.0000.0000.0000.000
185A102GLU-1-0.967-0.83721.205-0.203-0.2030.0000.0000.0000.000
186A103PHE00.099-0.05423.017-0.008-0.0080.0000.0000.0000.000
187A103PHE0-0.1290.05722.427-0.004-0.0040.0000.0000.0000.000
188A104LEU00.026-0.13023.963-0.012-0.0120.0000.0000.0000.000
189A104LEU0-0.1030.09328.2420.0020.0020.0000.0000.0000.000
190A105GLY0-0.011-0.10926.7040.0080.0080.0000.0000.0000.000
191A106VAL00.0560.01523.1850.0230.0230.0000.0000.0000.000
192A106VAL0-0.0470.11021.390-0.002-0.0020.0000.0000.0000.000
193A107LEU00.137-0.12224.607-0.016-0.0160.0000.0000.0000.000
194A107LEU0-0.1220.10724.874-0.001-0.0010.0000.0000.0000.000
195A108SER0-0.047-0.11126.168-0.004-0.0040.0000.0000.0000.000
196A108SER0-0.0380.07328.665-0.001-0.0010.0000.0000.0000.000
197A109THR0-0.025-0.10726.4780.0150.0150.0000.0000.0000.000
198A109THR0-0.0020.09924.7810.0070.0070.0000.0000.0000.000
199A110GLU00.048-0.08023.9620.0060.0060.0000.0000.0000.000
200A110GLU-1-1.039-0.87020.630-0.360-0.3600.0000.0000.0000.000
201A111TRP0-0.089-0.13624.690-0.018-0.0180.0000.0000.0000.000
202A111TRP00.019-0.00825.6880.0020.0020.0000.0000.0000.000