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: 5YQKZ

Calculation Name: 4YGU-D-Xray547

Preferred Name:

Target Type:

Ligand Name: triethylene glycol | di(hydroxyethyl)ether | 1,2-ethanediol

Ligand 3-letter code: PGE | PEG | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YGU

Chain ID: D

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-04

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1763460.207658
FMO2-HF: Nuclear repulsion 1696010.379323
FMO2-HF: Total energy -67449.828336
FMO2-MP2: Total energy -67647.47528


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:28:LYS)


Summations of interaction energy for fragment #1(A:28:LYS)
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.
-169.132-168.91343.896-22.963-21.147-0.275
Interaction energy analysis for fragmet #1(A:28:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.556 / q_NPA : 1.760
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].
3A30SER00.024-0.0033.504-0.7781.175-0.003-0.796-1.153-0.003
35A62GLU-1-0.832-0.9191.819-191.423-194.40923.886-10.948-9.951-0.133
36A63GLY00.0520.0232.9773.2784.4810.249-0.496-0.955-0.002
37A64ARG10.9170.9642.40970.14073.4492.837-2.594-3.552-0.030
38A65GLU-1-0.737-0.8561.698-151.126-154.59816.929-8.114-5.343-0.107
73A100THR0-0.0200.0034.6553.1443.232-0.001-0.002-0.0840.000
75A102TRP0-0.009-0.0073.930-0.368-0.244-0.001-0.013-0.1090.000
4A31GLU-1-0.853-0.9055.517-46.512-46.5120.0000.0000.0000.000
5A32VAL00.006-0.0068.899-0.719-0.7190.0000.0000.0000.000
6A33ARG10.7390.84211.40046.50746.5070.0000.0000.0000.000
7A34LYS10.8640.93415.16727.59827.5980.0000.0000.0000.000
8A35VAL00.0130.01118.3520.2540.2540.0000.0000.0000.000
9A36ASP-1-0.872-0.93120.311-24.196-24.1960.0000.0000.0000.000
10A37ALA00.008-0.00322.958-0.813-0.8130.0000.0000.0000.000
11A38PHE0-0.007-0.00618.9800.4400.4400.0000.0000.0000.000
12A39SER00.0160.01224.6490.2900.2900.0000.0000.0000.000
13A40SER00.0040.00524.4220.8400.8400.0000.0000.0000.000
14A41ILE0-0.020-0.01018.048-0.767-0.7670.0000.0000.0000.000
15A42GLU-1-0.837-0.89321.317-23.785-23.7850.0000.0000.0000.000
16A43ILE0-0.025-0.02015.889-1.379-1.3790.0000.0000.0000.000
17A44THR00.0140.00218.7271.0771.0770.0000.0000.0000.000
18A45SER0-0.015-0.02813.700-1.835-1.8350.0000.0000.0000.000
19A46VAL0-0.035-0.00711.6441.9581.9580.0000.0000.0000.000
20A47GLY0-0.006-0.0119.969-3.823-3.8230.0000.0000.0000.000
21A48THR00.0030.0178.3713.4933.4930.0000.0000.0000.000
22A49ILE0-0.030-0.0209.309-4.844-4.8440.0000.0000.0000.000
23A50HIS00.0100.0157.9154.9484.9480.0000.0000.0000.000
24A51PHE00.0410.01112.415-0.873-0.8730.0000.0000.0000.000
25A52THR0-0.066-0.05015.395-0.340-0.3400.0000.0000.0000.000
26A53GLN00.0200.00617.269-0.429-0.4290.0000.0000.0000.000
27A54SER0-0.011-0.02419.9920.2030.2030.0000.0000.0000.000
28A55ASP-1-0.879-0.93321.835-22.444-22.4440.0000.0000.0000.000
29A56THR0-0.093-0.03519.6770.1950.1950.0000.0000.0000.000
30A57TYR00.0020.01220.080-0.813-0.8130.0000.0000.0000.000
31A58SER0-0.084-0.05215.667-1.378-1.3780.0000.0000.0000.000
32A59PHE00.0700.02711.947-0.267-0.2670.0000.0000.0000.000
33A60ARG10.9350.9785.31371.01371.0130.0000.0000.0000.000
34A61ILE00.0170.0187.5540.0730.0730.0000.0000.0000.000
39A66LYS10.8710.9455.40255.45455.4540.0000.0000.0000.000
40A67TYR00.012-0.0037.0516.5976.5970.0000.0000.0000.000
41A68VAL00.0490.0455.4434.2294.2290.0000.0000.0000.000
42A69LYS10.8560.9027.47567.33667.3360.0000.0000.0000.000
43A70ASN0-0.009-0.00810.7444.6914.6910.0000.0000.0000.000
44A71THR00.0280.01711.2082.5612.5610.0000.0000.0000.000
45A72GLU-1-0.976-0.98613.490-29.789-29.7890.0000.0000.0000.000
46A73THR0-0.0110.00014.594-1.439-1.4390.0000.0000.0000.000
47A74THR0-0.023-0.00717.6720.7000.7000.0000.0000.0000.000
48A75VAL00.0240.01421.290-0.414-0.4140.0000.0000.0000.000
49A76LYS10.9350.96923.85123.64923.6490.0000.0000.0000.000
50A77ASP-1-0.879-0.93527.357-19.907-19.9070.0000.0000.0000.000
51A78GLY00.0270.02627.2940.2600.2600.0000.0000.0000.000
52A79ARG10.8120.89724.28022.00422.0040.0000.0000.0000.000
53A80LEU0-0.030-0.01217.237-0.339-0.3390.0000.0000.0000.000
54A81LEU00.0010.00621.1370.0120.0120.0000.0000.0000.000
55A82ILE00.008-0.01414.524-1.548-1.5480.0000.0000.0000.000
56A83GLY00.0350.02017.3101.1461.1460.0000.0000.0000.000
57A84PHE0-0.054-0.02613.666-2.634-2.6340.0000.0000.0000.000
58A85LYS10.9000.96014.22939.95039.9500.0000.0000.0000.000
59A86ASP-1-0.869-0.93117.216-30.898-30.8980.0000.0000.0000.000
60A87LYS10.9720.99218.68022.76822.7680.0000.0000.0000.000
61A88LYS10.8970.94815.14536.11936.1190.0000.0000.0000.000
62A89ASN00.0340.00318.471-1.446-1.4460.0000.0000.0000.000
63A90LYS11.0091.00119.90824.98524.9850.0000.0000.0000.000
64A91SER00.0770.03315.641-1.549-1.5490.0000.0000.0000.000
65A92ARG10.8520.92714.76425.69025.6900.0000.0000.0000.000
66A93ARG0-0.0160.00314.2580.2080.2080.0000.0000.0000.000
67A94ASN0-0.026-0.01411.6270.3680.3680.0000.0000.0000.000
68A95GLN00.027-0.00214.6140.7710.7710.0000.0000.0000.000
69A96LYS10.9330.96613.82132.84632.8460.0000.0000.0000.000
70A97ASP-1-0.822-0.9068.290-59.919-59.9190.0000.0000.0000.000
71A98GLY0-0.020-0.0238.2843.7203.7200.0000.0000.0000.000
72A99VAL0-0.072-0.0256.004-9.128-9.1280.0000.0000.0000.000
74A101ILE00.004-0.0106.541-3.409-3.4090.0000.0000.0000.000
76A103ILE0-0.002-0.00110.9970.2250.2250.0000.0000.0000.000
77A104SER0-0.0020.00514.792-0.142-0.1420.0000.0000.0000.000
78A105ALA00.0310.00717.7180.1590.1590.0000.0000.0000.000
79A106PRO00.0470.03421.498-0.196-0.1960.0000.0000.0000.000
80A107ASP-1-0.815-0.90324.668-20.433-20.4330.0000.0000.0000.000
81A108LEU0-0.072-0.04221.063-1.047-1.0470.0000.0000.0000.000
82A109LYS10.9250.95524.90520.65820.6580.0000.0000.0000.000
83A110GLU-1-0.917-0.95726.132-20.237-20.2370.0000.0000.0000.000
84A111VAL0-0.028-0.00220.341-1.071-1.0710.0000.0000.0000.000
85A112GLU-1-0.796-0.88122.644-22.031-22.0310.0000.0000.0000.000
86A113PHE0-0.037-0.01515.701-1.094-1.0940.0000.0000.0000.000
87A114THR00.004-0.00220.7541.3081.3080.0000.0000.0000.000
88A115GLY00.009-0.01217.890-0.879-0.8790.0000.0000.0000.000
89A116VAL0-0.099-0.04615.2781.4851.4850.0000.0000.0000.000
90A117GLY00.0400.02713.563-2.638-2.6380.0000.0000.0000.000
91A118GLU-1-0.834-0.90413.031-37.579-37.5790.0000.0000.0000.000
92A119PHE0-0.015-0.01913.868-2.341-2.3410.0000.0000.0000.000
93A120ASN00.020-0.00312.3753.5273.5270.0000.0000.0000.000
94A121CYS0-0.047-0.02515.413-1.042-1.0420.0000.0000.0000.000
95A122GLU-1-0.855-0.94314.824-30.316-30.3160.0000.0000.0000.000
96A123LYS10.8360.92314.23235.28935.2890.0000.0000.0000.000
97A124PRO00.0210.01619.481-0.063-0.0630.0000.0000.0000.000
98A125LEU0-0.0480.00021.554-0.601-0.6010.0000.0000.0000.000
99A126LYS10.9680.97824.01419.36419.3640.0000.0000.0000.000
100A127LEU0-0.031-0.01024.478-0.246-0.2460.0000.0000.0000.000
101A128ASP-1-0.843-0.90428.724-16.868-16.8680.0000.0000.0000.000
102A129GLU-1-0.868-0.93931.859-16.906-16.9060.0000.0000.0000.000
103A130VAL0-0.025-0.01125.273-0.540-0.5400.0000.0000.0000.000
104A131SER0-0.035-0.02727.4640.5310.5310.0000.0000.0000.000
105A132PHE00.0460.01521.594-0.944-0.9440.0000.0000.0000.000
106A133GLU-1-0.808-0.88925.352-20.228-20.2280.0000.0000.0000.000
107A134VAL0-0.0130.00421.765-1.071-1.0710.0000.0000.0000.000
108A135LYS10.8190.89823.40023.18923.1890.0000.0000.0000.000
109A136GLY0-0.023-0.01922.464-1.153-1.1530.0000.0000.0000.000
110A137VAL0-0.061-0.04719.7261.0051.0050.0000.0000.0000.000
111A138GLY00.0260.03418.554-1.468-1.4680.0000.0000.0000.000
112A139GLU-1-0.870-0.92617.546-29.170-29.1700.0000.0000.0000.000
113A140VAL0-0.033-0.02918.081-1.458-1.4580.0000.0000.0000.000
114A141ASN00.003-0.00116.4982.6692.6690.0000.0000.0000.000
115A142VAL0-0.024-0.02718.850-1.091-1.0910.0000.0000.0000.000
116A143ALA00.0450.02819.9971.0961.0960.0000.0000.0000.000
117A144ASP-1-0.909-0.96121.896-21.154-21.1540.0000.0000.0000.000
118A145LEU0-0.0030.00724.046-0.604-0.6040.0000.0000.0000.000
119A146THR0-0.018-0.01026.2490.9700.9700.0000.0000.0000.000
120A147CYS0-0.089-0.04129.229-0.435-0.4350.0000.0000.0000.000
121A148ASN00.0200.00831.2310.5190.5190.0000.0000.0000.000
122A149VAL0-0.024-0.02133.1580.3900.3900.0000.0000.0000.000
123A150LEU00.0450.03027.538-0.680-0.6800.0000.0000.0000.000
124A151LYS10.8660.93430.07318.09718.0970.0000.0000.0000.000
125A152VAL00.0320.01427.051-0.788-0.7880.0000.0000.0000.000
126A153ALA0-0.023-0.01928.3200.8190.8190.0000.0000.0000.000
127A154LEU0-0.0040.02025.658-0.735-0.7350.0000.0000.0000.000
128A155ARG10.8480.88227.37420.19620.1960.0000.0000.0000.000
129A156GLY0-0.019-0.00726.694-0.867-0.8670.0000.0000.0000.000
130A157VAL0-0.052-0.04124.0580.7310.7310.0000.0000.0000.000
131A158GLY0-0.0120.02123.231-0.689-0.6890.0000.0000.0000.000
132A159SER00.000-0.01822.5981.3641.3640.0000.0000.0000.000
133A160ALA0-0.016-0.02222.496-0.910-0.9100.0000.0000.0000.000
134A161ASP-1-0.889-0.93522.107-22.583-22.5830.0000.0000.0000.000
135A162ILE00.003-0.00222.740-0.841-0.8410.0000.0000.0000.000
136A163HIS0-0.036-0.01424.8981.3321.3320.0000.0000.0000.000
137A164VAL00.000-0.01826.442-0.476-0.4760.0000.0000.0000.000
138A165VAL00.0010.01129.1710.6730.6730.0000.0000.0000.000
139A166CYS0-0.044-0.01332.034-0.251-0.2510.0000.0000.0000.000
140A167ASP-1-0.865-0.92234.238-15.219-15.2190.0000.0000.0000.000
141A168TYR0-0.193-0.12736.1320.2700.2700.0000.0000.0000.000
142A169LEU00.0700.03831.658-0.538-0.5380.0000.0000.0000.000
143A170SER0-0.028-0.00233.6410.4040.4040.0000.0000.0000.000
144A171ALA00.0470.00932.182-0.696-0.6960.0000.0000.0000.000
145A172GLN00.0060.02032.3740.2440.2440.0000.0000.0000.000
146A173MET00.0210.02629.424-0.751-0.7510.0000.0000.0000.000
147A174GLY00.0230.00131.8050.6930.6930.0000.0000.0000.000
148A175GLY0-0.020-0.01330.4270.0650.0650.0000.0000.0000.000
149A176VAL0-0.038-0.02728.7270.5970.5970.0000.0000.0000.000
150A177GLY00.0560.03826.344-0.552-0.5520.0000.0000.0000.000
151A178SER0-0.038-0.03726.0920.9120.9120.0000.0000.0000.000
152A179VAL00.0300.01926.270-0.808-0.8080.0000.0000.0000.000
153A180THR0-0.0090.00526.3701.0471.0470.0000.0000.0000.000
154A181LEU00.0020.00127.319-0.488-0.4880.0000.0000.0000.000
155A182SER0-0.011-0.00428.0730.4560.4560.0000.0000.0000.000
156A183GLY00.0760.05130.211-0.375-0.3750.0000.0000.0000.000
157A184SER0-0.113-0.08432.1340.7770.7770.0000.0000.0000.000
158A185ALA00.0260.00934.273-0.395-0.3950.0000.0000.0000.000
159A186GLY00.004-0.00236.3030.3480.3480.0000.0000.0000.000
160A187ARG10.9610.98138.95914.97414.9740.0000.0000.0000.000
161A188ALA00.0210.00136.661-0.465-0.4650.0000.0000.0000.000
162A189ASP-1-0.846-0.87837.853-14.693-14.6930.0000.0000.0000.000
163A190ILE0-0.020-0.01334.774-0.498-0.4980.0000.0000.0000.000
164A191SER0-0.037-0.02336.1260.4300.4300.0000.0000.0000.000
165A192LYS10.8840.93634.53316.52416.5240.0000.0000.0000.000
166A193GLY0-0.0130.00236.3130.4830.4830.0000.0000.0000.000
167A194GLY0-0.041-0.00334.0730.1770.1770.0000.0000.0000.000
168A195ILE0-0.008-0.01732.9120.3410.3410.0000.0000.0000.000
169A196GLY0-0.009-0.00131.204-0.302-0.3020.0000.0000.0000.000
170A197GLY0-0.015-0.01830.6730.6610.6610.0000.0000.0000.000
171A198VAL00.003-0.01730.975-0.394-0.3940.0000.0000.0000.000
172A199ASN0-0.0290.00430.4020.6770.6770.0000.0000.0000.000
173A200THR00.0730.02031.612-0.453-0.4530.0000.0000.0000.000
174A201ASP-1-0.895-0.92834.130-16.653-16.6530.0000.0000.0000.000
175A202ASN0-0.070-0.04331.7430.6090.6090.0000.0000.0000.000
176A203LEU0-0.0080.00932.588-0.339-0.3390.0000.0000.0000.000
177A204LYS10.8680.93834.55015.85715.8570.0000.0000.0000.000
178A205ILE0-0.002-0.01737.213-0.399-0.3990.0000.0000.0000.000
179A206GLY-1-0.922-0.93739.719-13.574-13.5740.0000.0000.0000.000