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: LVYY9

Calculation Name: 3TEO-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol

Ligand 3-letter code: PE3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TEO

Chain ID: A

ChEMBL ID:

UniProt ID: G0WXL9

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
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. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2171647.770036
FMO2-HF: Nuclear repulsion 2090539.970826
FMO2-HF: Total energy -81107.79921
FMO2-MP2: Total energy -81346.565389


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-105.048-104.8514.899-8.519-6.579-0.1
Interaction energy analysis for fragmet #1(A:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.799 / q_NPA : 0.883
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].
3A4GLU-1-0.797-0.8841.691-112.415-113.19014.731-8.329-5.627-0.099
4A5TYR0-0.022-0.0054.0218.3828.7900.000-0.061-0.3470.000
5A6ILE00.0140.0042.7316.0726.6370.168-0.129-0.605-0.001
6A7ASP-1-0.878-0.9496.218-33.879-33.8790.0000.0000.0000.000
7A8SER0-0.066-0.0298.5044.5584.5580.0000.0000.0000.000
8A9GLU-1-0.874-0.9539.395-21.549-21.5490.0000.0000.0000.000
9A10LEU0-0.018-0.0149.1452.5292.5290.0000.0000.0000.000
10A11LYS10.9840.99812.06224.37624.3760.0000.0000.0000.000
11A12ARG10.9400.98613.62222.34122.3410.0000.0000.0000.000
12A13LEU00.0000.00414.5831.4341.4340.0000.0000.0000.000
13A14GLU-1-0.850-0.91916.178-15.804-15.8040.0000.0000.0000.000
14A15ASP-1-0.900-0.95818.153-15.534-15.5340.0000.0000.0000.000
15A16TYR0-0.132-0.09019.3700.8060.8060.0000.0000.0000.000
16A17ALA0-0.005-0.01220.3870.7690.7690.0000.0000.0000.000
17A18LEU00.0070.00521.8310.7260.7260.0000.0000.0000.000
18A19ARG10.8460.93723.48113.09613.0960.0000.0000.0000.000
19A20ARG10.8610.92625.64511.01511.0150.0000.0000.0000.000
20A21VAL0-0.0210.00226.5600.3890.3890.0000.0000.0000.000
21A22LYS10.7770.86919.95115.65315.6530.0000.0000.0000.000
22A23GLY00.0040.02326.672-0.014-0.0140.0000.0000.0000.000
23A24ILE0-0.029-0.00523.1780.0920.0920.0000.0000.0000.000
24A25PRO0-0.0020.01027.5290.2110.2110.0000.0000.0000.000
25A26ASN00.0070.00028.203-0.473-0.4730.0000.0000.0000.000
26A27ASN00.0540.00825.443-0.131-0.1310.0000.0000.0000.000
27A28ARG10.9040.96028.3809.7169.7160.0000.0000.0000.000
28A29ARG10.8790.95330.39210.37510.3750.0000.0000.0000.000
29A30LEU00.0500.03833.7700.3220.3220.0000.0000.0000.000
30A31TRP00.014-0.00435.744-0.093-0.0930.0000.0000.0000.000
31A32VAL00.0170.00138.0210.1360.1360.0000.0000.0000.000
32A33LEU0-0.0110.01840.484-0.053-0.0530.0000.0000.0000.000
33A34THR0-0.018-0.03741.4190.0730.0730.0000.0000.0000.000
34A35CYS-1-0.748-0.76344.450-6.580-6.5800.0000.0000.0000.000
35A36MET0-0.021-0.01643.543-0.202-0.2020.0000.0000.0000.000
36A37ASP-1-0.782-0.84744.099-6.605-6.6050.0000.0000.0000.000
37A38GLU-1-0.826-0.91942.803-6.867-6.8670.0000.0000.0000.000
38A39ARG10.7420.82242.6006.1236.1230.0000.0000.0000.000
39A40VAL0-0.020-0.00442.521-0.046-0.0460.0000.0000.0000.000
40A41HIS10.8480.93738.7647.3787.3780.0000.0000.0000.000
41A42ILE00.0810.02837.436-0.081-0.0810.0000.0000.0000.000
42A43GLU-1-0.866-0.92532.038-9.499-9.4990.0000.0000.0000.000
43A44GLN0-0.031-0.02535.626-0.081-0.0810.0000.0000.0000.000
44A45SER0-0.072-0.04036.4780.1050.1050.0000.0000.0000.000
45A46LEU00.011-0.00637.4690.1790.1790.0000.0000.0000.000
46A47GLY0-0.0220.00935.464-0.067-0.0670.0000.0000.0000.000
47A48ILE0-0.106-0.04632.541-0.216-0.2160.0000.0000.0000.000
48A49GLN0-0.012-0.01127.492-0.188-0.1880.0000.0000.0000.000
49A50PRO00.0660.02627.2170.0730.0730.0000.0000.0000.000
50A51ASP-1-0.850-0.88824.135-12.513-12.5130.0000.0000.0000.000
51A52ASP-1-0.852-0.94827.740-10.816-10.8160.0000.0000.0000.000
52A53ALA0-0.007-0.00530.3050.1560.1560.0000.0000.0000.000
53A54HIS0-0.0420.00331.4870.0740.0740.0000.0000.0000.000
54A55ILE00.0270.00535.1210.2640.2640.0000.0000.0000.000
55A56TYR0-0.068-0.05037.5480.0040.0040.0000.0000.0000.000
56A57ARG10.8670.91239.2127.7337.7330.0000.0000.0000.000
57A58ASN0-0.009-0.00942.7090.0250.0250.0000.0000.0000.000
58A59ALA00.0360.00446.298-0.010-0.0100.0000.0000.0000.000
59A60GLY00.041-0.00949.1200.1120.1120.0000.0000.0000.000
60A61GLY00.0420.01947.4420.0770.0770.0000.0000.0000.000
61A62ILE0-0.0130.00248.4510.0060.0060.0000.0000.0000.000
62A63VAL0-0.0020.00549.276-0.122-0.1220.0000.0000.0000.000
63A64THR00.0100.00448.2210.1200.1200.0000.0000.0000.000
64A65ASP-1-0.843-0.93149.382-6.415-6.4150.0000.0000.0000.000
65A66ASP-1-0.717-0.82544.650-7.309-7.3090.0000.0000.0000.000
66A67ALA00.0020.01944.794-0.210-0.2100.0000.0000.0000.000
67A68ILE00.0270.01044.852-0.160-0.1600.0000.0000.0000.000
68A69ARG10.8440.92641.0527.2987.2980.0000.0000.0000.000
69A70SER0-0.027-0.02440.843-0.227-0.2270.0000.0000.0000.000
70A71ALA00.0130.00840.638-0.218-0.2180.0000.0000.0000.000
71A72SER0-0.024-0.00841.861-0.161-0.1610.0000.0000.0000.000
72A73LEU00.0100.01238.972-0.132-0.1320.0000.0000.0000.000
73A74THR00.002-0.01235.997-0.240-0.2400.0000.0000.0000.000
74A75THR0-0.043-0.04537.154-0.156-0.1560.0000.0000.0000.000
75A76ASN0-0.093-0.04938.861-0.097-0.0970.0000.0000.0000.000
76A77PHE0-0.0130.00036.876-0.078-0.0780.0000.0000.0000.000
77A78PHE0-0.041-0.01933.301-0.330-0.3300.0000.0000.0000.000
78A79GLY00.0150.01933.342-0.296-0.2960.0000.0000.0000.000
79A80THR0-0.034-0.03235.021-0.221-0.2210.0000.0000.0000.000
80A81LYS10.8140.88036.4558.5898.5890.0000.0000.0000.000
81A82GLU-1-0.932-0.95438.214-7.949-7.9490.0000.0000.0000.000
82A83ILE00.0080.00039.450-0.119-0.1190.0000.0000.0000.000
83A84ILE0-0.004-0.00239.7260.1790.1790.0000.0000.0000.000
84A85VAL00.0000.00743.025-0.059-0.0590.0000.0000.0000.000
85A86VAL0-0.015-0.01242.8070.0450.0450.0000.0000.0000.000
86A87THR00.0590.03745.813-0.070-0.0700.0000.0000.0000.000
87A88HIS10.7160.75947.7266.3776.3770.0000.0000.0000.000
88A89THR0-0.023-0.04849.6840.1000.1000.0000.0000.0000.000
89A90ASP-1-0.823-0.89651.594-5.874-5.8740.0000.0000.0000.000
90A91CYS0-0.0230.02752.115-0.072-0.0720.0000.0000.0000.000
91A92GLY00.0810.03252.5470.1120.1120.0000.0000.0000.000
92A93MET0-0.007-0.01153.1090.1000.1000.0000.0000.0000.000
93A94LEU0-0.0060.00255.9080.0830.0830.0000.0000.0000.000
94A95ARG10.7690.87756.4205.5585.5580.0000.0000.0000.000
95A96PHE00.0190.02957.2490.0380.0380.0000.0000.0000.000
96A97THR00.0290.01860.928-0.058-0.0580.0000.0000.0000.000
97A98GLY00.0750.02961.519-0.006-0.0060.0000.0000.0000.000
98A99GLU0-0.074-0.08462.3640.0370.0370.0000.0000.0000.000
99A100GLU-1-0.893-0.94863.693-4.907-4.9070.0000.0000.0000.000
100A101VAL0-0.017-0.00658.6000.0110.0110.0000.0000.0000.000
101A102ALA00.0260.01661.968-0.017-0.0170.0000.0000.0000.000
102A103LYS11.0000.99363.8614.5484.5480.0000.0000.0000.000
103A104TYR00.0050.02359.0060.0530.0530.0000.0000.0000.000
104A105PHE00.006-0.00156.9130.0040.0040.0000.0000.0000.000
105A106ILE00.0280.02362.9340.0160.0160.0000.0000.0000.000
106A107SER0-0.117-0.06465.7740.0490.0490.0000.0000.0000.000
107A108LYS10.8850.93260.8215.1625.1620.0000.0000.0000.000
108A109GLY00.0010.01164.743-0.033-0.0330.0000.0000.0000.000
109A110ILE0-0.046-0.01660.711-0.011-0.0110.0000.0000.0000.000
110A111LYS10.9560.97563.9304.7644.7640.0000.0000.0000.000
111A112PRO00.022-0.00363.232-0.054-0.0540.0000.0000.0000.000
112A113THR00.0090.00063.236-0.041-0.0410.0000.0000.0000.000
113A114GLU-1-0.921-0.96163.384-4.809-4.8090.0000.0000.0000.000
114A115VAL0-0.049-0.01058.142-0.065-0.0650.0000.0000.0000.000
115A116GLN00.006-0.00855.158-0.001-0.0010.0000.0000.0000.000
116A117LEU0-0.014-0.01055.433-0.094-0.0940.0000.0000.0000.000
117A118ASP-1-0.813-0.90650.322-6.468-6.4680.0000.0000.0000.000
118A119PRO0-0.056-0.04050.7870.0500.0500.0000.0000.0000.000
119A120LEU0-0.0270.00145.454-0.026-0.0260.0000.0000.0000.000
120A121LEU0-0.045-0.00849.615-0.003-0.0030.0000.0000.0000.000
121A122PRO00.0780.03651.9620.1090.1090.0000.0000.0000.000
122A123ALA0-0.054-0.03754.9930.1360.1360.0000.0000.0000.000
123A124PHE0-0.029-0.00854.7720.0970.0970.0000.0000.0000.000
124A125ARG10.8870.94156.9585.3725.3720.0000.0000.0000.000
125A126ILE0-0.0070.01159.998-0.022-0.0220.0000.0000.0000.000
126A127SER0-0.013-0.01362.5580.0500.0500.0000.0000.0000.000
127A128SER0-0.006-0.00365.4850.0660.0660.0000.0000.0000.000
128A129GLU-1-0.931-0.96465.447-4.740-4.7400.0000.0000.0000.000
129A130GLU-1-0.848-0.93065.512-4.707-4.7070.0000.0000.0000.000
130A131ASP-1-0.864-0.93762.827-5.061-5.0610.0000.0000.0000.000
131A132PHE0-0.032-0.02159.198-0.111-0.1110.0000.0000.0000.000
132A133ILE0-0.041-0.02260.722-0.100-0.1000.0000.0000.0000.000
133A134LYS10.9140.96260.8544.9254.9250.0000.0000.0000.000
134A135TRP0-0.010-0.00153.627-0.093-0.0930.0000.0000.0000.000
135A136PHE00.0240.00456.199-0.151-0.1510.0000.0000.0000.000
136A137LYS10.8090.91753.6515.7945.7940.0000.0000.0000.000
137A138PHE00.0650.02956.637-0.083-0.0830.0000.0000.0000.000
138A139TYR0-0.011-0.03352.6570.0310.0310.0000.0000.0000.000
139A140GLU-1-0.905-0.94959.232-4.925-4.9250.0000.0000.0000.000
140A141ASP-1-0.789-0.85661.794-4.989-4.9890.0000.0000.0000.000
141A142LEU0-0.092-0.05457.1010.0180.0180.0000.0000.0000.000
142A143GLY0-0.034-0.00761.487-0.008-0.0080.0000.0000.0000.000
143A144VAL0-0.061-0.01757.4300.0040.0040.0000.0000.0000.000
144A145LYS10.9820.97960.8814.9084.9080.0000.0000.0000.000
145A146SER0-0.011-0.01157.768-0.033-0.0330.0000.0000.0000.000
146A147PRO00.0480.02652.495-0.013-0.0130.0000.0000.0000.000
147A148ASP-1-0.739-0.83853.121-6.014-6.0140.0000.0000.0000.000
148A149GLU-1-0.820-0.91754.276-5.402-5.4020.0000.0000.0000.000
149A150MET00.0120.02052.868-0.029-0.0290.0000.0000.0000.000
150A151ALA0-0.0140.00150.006-0.081-0.0810.0000.0000.0000.000
151A152LEU0-0.028-0.02351.199-0.078-0.0780.0000.0000.0000.000
152A153LYS10.9470.98853.5535.5145.5140.0000.0000.0000.000
153A154GLY00.0290.00650.7110.0000.0000.0000.0000.0000.000
154A155VAL0-0.022-0.01848.319-0.071-0.0710.0000.0000.0000.000
155A156GLU-1-0.893-0.94350.464-5.763-5.7630.0000.0000.0000.000
156A157ILE00.0390.02052.149-0.032-0.0320.0000.0000.0000.000
157A158LEU0-0.030-0.02246.478-0.045-0.0450.0000.0000.0000.000
158A159ARG10.8620.92249.0286.3236.3230.0000.0000.0000.000
159A160ASN0-0.029-0.03450.846-0.026-0.0260.0000.0000.0000.000
160A161HIS00.0060.01750.258-0.015-0.0150.0000.0000.0000.000
161A162PRO00.004-0.00950.677-0.115-0.1150.0000.0000.0000.000
162A163LEU0-0.016-0.00547.351-0.076-0.0760.0000.0000.0000.000
163A164ILE00.0050.00944.531-0.204-0.2040.0000.0000.0000.000
164A165PRO00.0100.01842.6080.1730.1730.0000.0000.0000.000
165A166LYS10.8620.91745.0456.5016.5010.0000.0000.0000.000
166A167ASP-1-0.830-0.89540.983-7.792-7.7920.0000.0000.0000.000
167A168VAL0-0.057-0.01741.028-0.121-0.1210.0000.0000.0000.000
168A169ARG10.9270.97342.0787.5117.5110.0000.0000.0000.000
169A170ILE00.0370.02143.160-0.100-0.1000.0000.0000.0000.000
170A171THR0-0.011-0.00244.2450.2460.2460.0000.0000.0000.000
171A172GLY00.0360.01546.153-0.054-0.0540.0000.0000.0000.000
172A173TYR0-0.036-0.02943.3910.1020.1020.0000.0000.0000.000
173A174VAL0-0.0180.01147.9420.0260.0260.0000.0000.0000.000
174A175TYR00.020-0.00541.905-0.100-0.1000.0000.0000.0000.000
175A176GLU-1-0.762-0.85247.001-6.092-6.0920.0000.0000.0000.000
176A177VAL0-0.004-0.01347.094-0.119-0.1190.0000.0000.0000.000
177A178GLU-1-0.830-0.88148.417-6.145-6.1450.0000.0000.0000.000
178A179THR0-0.074-0.05947.3560.0340.0340.0000.0000.0000.000
179A180HIS0-0.0160.01342.790-0.245-0.2450.0000.0000.0000.000
180A181ARG10.9540.99043.0596.4466.4460.0000.0000.0000.000
181A182LEU00.0210.01542.4590.1410.1410.0000.0000.0000.000
182A183ARG10.7960.86146.0066.0236.0230.0000.0000.0000.000
183A184LYS10.8950.93449.1045.9895.9890.0000.0000.0000.000
184A185PRO0-0.008-0.00950.2070.1080.1080.0000.0000.0000.000
185A186ASN0-0.039-0.03253.3170.0210.0210.0000.0000.0000.000
186A187GLN00.0160.02852.4670.0810.0810.0000.0000.0000.000
187A188ILE0-0.010-0.00654.386-0.101-0.1010.0000.0000.0000.000
188A189ILE00.1170.06253.5810.0660.0660.0000.0000.0000.000
189A190TYR0-0.062-0.04551.3730.0580.0580.0000.0000.0000.000
190A191ASN00.000-0.00557.881-0.001-0.0010.0000.0000.0000.000
191A192GLU-1-0.948-0.96758.874-5.356-5.3560.0000.0000.0000.000
192A193THR0-0.003-0.03456.5960.0580.0580.0000.0000.0000.000
193A194SER0-0.039-0.00460.0390.0130.0130.0000.0000.0000.000
194A195LYS10.8890.94862.6554.9454.9450.0000.0000.0000.000
195A196PHE0-0.0090.00364.989-0.036-0.0360.0000.0000.0000.000
196A197GLU-1-0.908-0.96462.005-5.183-5.1830.0000.0000.0000.000
197A198HIS0-0.050-0.01666.0190.0330.0330.0000.0000.0000.000
198A199GLY00.0500.03463.102-0.050-0.0500.0000.0000.0000.000
199A200THR0-0.040-0.03061.2860.0690.0690.0000.0000.0000.000
200A201ILE0-0.019-0.01062.350-0.045-0.0450.0000.0000.0000.000
201A202VAL00.0230.01557.649-0.003-0.0030.0000.0000.0000.000
202A203LYS0-0.017-0.00457.828-0.358-0.3580.0000.0000.0000.000