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: N824Q

Calculation Name: 3PPB-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: PG4 | PEG | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3PPB

Chain ID: A

ChEMBL ID:

UniProt ID: A3QHM2

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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1990471.140826
FMO2-HF: Nuclear repulsion 1916466.378058
FMO2-HF: Total energy -74004.762768
FMO2-MP2: Total energy -74221.321702


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:7:ARG)


Summations of interaction energy for fragment #1(A:7:ARG)
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.
-115.338-111.8420.065-1.397-2.166-0.005
Interaction energy analysis for fragmet #1(A:7:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.888 / q_NPA : 1.938
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].
3A9LYS11.0351.0103.78348.48649.888-0.007-0.692-0.7030.001
5A11GLN0-0.027-0.0233.0057.5688.4820.065-0.297-0.683-0.003
6A12ALA00.0030.0123.1060.0310.6040.008-0.199-0.383-0.002
7A13ILE00.0020.0074.2398.8829.010-0.001-0.033-0.0940.000
9A15GLU-1-0.873-0.9293.963-96.648-96.1690.000-0.176-0.303-0.001
4A10LYS10.9931.0096.24345.54345.5430.0000.0000.0000.000
8A14LEU00.0160.0167.4064.3524.3520.0000.0000.0000.000
10A16THR0-0.017-0.0177.2775.5435.5430.0000.0000.0000.000
11A17ALA0-0.005-0.0099.4523.9483.9480.0000.0000.0000.000
12A18LEU00.0020.00711.1132.9652.9650.0000.0000.0000.000
13A19GLN00.0150.00711.6452.5822.5820.0000.0000.0000.000
14A20LEU00.0050.01813.4002.5482.5480.0000.0000.0000.000
15A21PHE00.018-0.00615.4361.9791.9790.0000.0000.0000.000
16A22VAL00.0130.03016.6661.8201.8200.0000.0000.0000.000
17A23SER0-0.067-0.04616.8131.6291.6290.0000.0000.0000.000
18A24GLN0-0.013-0.01018.3601.2641.2640.0000.0000.0000.000
19A25GLY00.0540.04320.2351.1441.1440.0000.0000.0000.000
20A26PHE0-0.009-0.00319.311-0.526-0.5260.0000.0000.0000.000
21A27HIS00.006-0.01720.918-0.841-0.8410.0000.0000.0000.000
22A28GLY00.0230.03423.1700.3580.3580.0000.0000.0000.000
23A29THR00.0100.01216.347-0.868-0.8680.0000.0000.0000.000
24A30SER00.0190.00519.441-0.094-0.0940.0000.0000.0000.000
25A31THR00.0580.00916.397-1.091-1.0910.0000.0000.0000.000
26A32ALA00.001-0.00615.611-1.903-1.9030.0000.0000.0000.000
27A33THR0-0.050-0.01515.694-0.757-0.7570.0000.0000.0000.000
28A34ILE00.0390.01411.235-1.570-1.5700.0000.0000.0000.000
29A35ALA0-0.038-0.02211.208-3.270-3.2700.0000.0000.0000.000
30A36ARG10.8930.95211.37529.54829.5480.0000.0000.0000.000
31A37GLU-1-0.866-0.93511.626-37.479-37.4790.0000.0000.0000.000
32A38ALA0-0.0170.0067.293-3.272-3.2720.0000.0000.0000.000
33A39GLY0-0.0180.0027.100-6.812-6.8120.0000.0000.0000.000
34A40VAL0-0.111-0.0638.233-1.076-1.0760.0000.0000.0000.000
35A41ALA00.0580.02711.0162.9062.9060.0000.0000.0000.000
36A42THR00.0630.00914.009-1.578-1.5780.0000.0000.0000.000
37A43GLY00.0260.02116.127-0.135-0.1350.0000.0000.0000.000
38A44THR0-0.058-0.03810.719-1.045-1.0450.0000.0000.0000.000
39A45LEU0-0.0010.00212.398-1.858-1.8580.0000.0000.0000.000
40A46PHE00.021-0.00913.408-0.129-0.1290.0000.0000.0000.000
41A47HIS0-0.032-0.00114.2971.9731.9730.0000.0000.0000.000
42A48HIS0-0.065-0.03310.9870.5670.5670.0000.0000.0000.000
43A49PHE00.008-0.00610.507-0.885-0.8850.0000.0000.0000.000
44A50PRO00.0160.01615.9900.4720.4720.0000.0000.0000.000
45A51SER0-0.020-0.02019.1771.0581.0580.0000.0000.0000.000
46A52LYS10.8760.94117.91124.54324.5430.0000.0000.0000.000
47A53GLU-1-0.796-0.89518.438-26.290-26.2900.0000.0000.0000.000
48A54GLN00.0610.03418.524-1.223-1.2230.0000.0000.0000.000
49A55LEU0-0.062-0.03011.914-1.453-1.4530.0000.0000.0000.000
50A56LEU0-0.0080.00115.155-1.753-1.7530.0000.0000.0000.000
51A57GLU-1-0.873-0.94617.522-26.378-26.3780.0000.0000.0000.000
52A58GLN0-0.041-0.03014.173-1.618-1.6180.0000.0000.0000.000
53A59LEU0-0.035-0.00611.446-1.449-1.4490.0000.0000.0000.000
54A60PHE0-0.017-0.00714.104-0.311-0.3110.0000.0000.0000.000
55A61LEU00.0230.00717.4680.2110.2110.0000.0000.0000.000
56A62GLY00.0080.01213.4700.0710.0710.0000.0000.0000.000
57A63VAL0-0.009-0.01513.246-0.187-0.1870.0000.0000.0000.000
58A64LYS10.8940.95615.27626.17626.1760.0000.0000.0000.000
59A65GLN0-0.016-0.01516.2471.5481.5480.0000.0000.0000.000
60A66GLU-1-0.836-0.90211.635-44.124-44.1240.0000.0000.0000.000
61A67PHE0-0.033-0.00715.9820.7980.7980.0000.0000.0000.000
62A68ALA00.0560.02519.2780.9660.9660.0000.0000.0000.000
63A69ASP-1-0.859-0.91417.533-30.714-30.7140.0000.0000.0000.000
64A70ALA0-0.045-0.02218.1500.8030.8030.0000.0000.0000.000
65A71ILE0-0.041-0.01420.0380.9660.9660.0000.0000.0000.000
66A72GLN0-0.012-0.01223.3601.7111.7110.0000.0000.0000.000
67A73ALA0-0.019-0.00921.5150.6600.6600.0000.0000.0000.000
68A74SER0-0.082-0.04423.2090.0850.0850.0000.0000.0000.000
69A75VAL0-0.037-0.01025.3890.9320.9320.0000.0000.0000.000
70A76SER0-0.035-0.00928.660-0.148-0.1480.0000.0000.0000.000
71A77SER0-0.028-0.04131.0880.6330.6330.0000.0000.0000.000
72A78ARG10.7950.86633.26718.13918.1390.0000.0000.0000.000
73A79GLY0-0.0260.00137.2360.4810.4810.0000.0000.0000.000
74A80ASP-1-0.898-0.93039.070-15.052-15.0520.0000.0000.0000.000
75A81LEU00.0820.05336.170-0.499-0.4990.0000.0000.0000.000
76A82LYS10.9640.99736.76714.35214.3520.0000.0000.0000.000
77A83GLN00.0700.02636.125-0.497-0.4970.0000.0000.0000.000
78A84ASP-1-0.807-0.87633.481-18.509-18.5090.0000.0000.0000.000
79A85ALA0-0.004-0.00532.233-0.712-0.7120.0000.0000.0000.000
80A86GLU-1-0.963-0.98032.596-17.063-17.0630.0000.0000.0000.000
81A87GLN0-0.031-0.02930.222-0.846-0.8460.0000.0000.0000.000
82A88LEU00.0220.01327.363-0.770-0.7700.0000.0000.0000.000
83A89TRP0-0.020-0.00627.780-0.887-0.8870.0000.0000.0000.000
84A90PHE0-0.001-0.01828.629-0.526-0.5260.0000.0000.0000.000
85A91ALA00.0160.03624.916-0.631-0.6310.0000.0000.0000.000
86A92ALA00.0120.00624.118-1.146-1.1460.0000.0000.0000.000
87A93LEU00.006-0.01024.127-0.784-0.7840.0000.0000.0000.000
88A94THR0-0.042-0.03523.004-0.308-0.3080.0000.0000.0000.000
89A95TRP0-0.020-0.00616.540-0.590-0.5900.0000.0000.0000.000
90A96ALA0-0.003-0.00720.061-1.267-1.2670.0000.0000.0000.000
91A97MET0-0.033-0.02021.437-0.479-0.4790.0000.0000.0000.000
92A98ALA0-0.0230.00019.000-0.420-0.4200.0000.0000.0000.000
93A99ASN0-0.082-0.03315.403-3.978-3.9780.0000.0000.0000.000
94A100PRO00.0690.03317.157-0.129-0.1290.0000.0000.0000.000
95A101LEU0-0.012-0.00812.5360.7460.7460.0000.0000.0000.000
96A102LYS10.8310.89010.32645.66545.6650.0000.0000.0000.000
97A103GLN00.0810.05816.3270.3740.3740.0000.0000.0000.000
98A104ALA0-0.021-0.01119.2391.2311.2310.0000.0000.0000.000
99A105PHE00.007-0.00317.0440.8300.8300.0000.0000.0000.000
100A106PHE00.001-0.01018.7440.8650.8650.0000.0000.0000.000
101A107GLN0-0.031-0.02421.3671.2981.2980.0000.0000.0000.000
102A108LEU0-0.0410.00420.7290.8370.8370.0000.0000.0000.000
103A109TYR0-0.038-0.05119.5850.9900.9900.0000.0000.0000.000
104A110SER0-0.097-0.04323.1610.2540.2540.0000.0000.0000.000
105A111MET00.0340.01824.3730.2560.2560.0000.0000.0000.000
106A112SER0-0.049-0.00925.5170.6600.6600.0000.0000.0000.000
107A113PRO00.021-0.01827.957-0.222-0.2220.0000.0000.0000.000
108A114THR0-0.043-0.01724.2080.1820.1820.0000.0000.0000.000
109A115VAL0-0.030-0.00722.185-0.699-0.6990.0000.0000.0000.000
110A116GLU-1-0.838-0.92624.742-19.559-19.5590.0000.0000.0000.000
111A117GLN0-0.028-0.00126.404-0.326-0.3260.0000.0000.0000.000
112A118SER00.0480.02627.485-0.390-0.3900.0000.0000.0000.000
113A119VAL0-0.016-0.00721.529-0.488-0.4880.0000.0000.0000.000
114A120ARG10.8940.94323.93419.68819.6880.0000.0000.0000.000
115A121ASP-1-0.831-0.91625.925-19.502-19.5020.0000.0000.0000.000
116A122GLN0-0.011-0.00622.7430.6510.6510.0000.0000.0000.000
117A123ALA0-0.037-0.03322.496-0.548-0.5480.0000.0000.0000.000
118A124MET0-0.0260.00323.905-0.074-0.0740.0000.0000.0000.000
119A125HIS0-0.007-0.03127.426-0.380-0.3800.0000.0000.0000.000
120A126GLY0-0.0140.00325.9390.2870.2870.0000.0000.0000.000
121A127ILE0-0.075-0.03219.6250.0890.0890.0000.0000.0000.000
122A128LEU0-0.022-0.01223.340-0.280-0.2800.0000.0000.0000.000
123A129GLY00.0530.04226.0770.7720.7720.0000.0000.0000.000
124A130PHE0-0.022-0.02424.8090.7770.7770.0000.0000.0000.000
125A131ILE0-0.0010.00727.3700.5860.5860.0000.0000.0000.000
126A132ALA00.0490.01831.1220.6340.6340.0000.0000.0000.000
127A133GLU-1-0.847-0.90332.991-16.330-16.3300.0000.0000.0000.000
128A134LEU00.008-0.00231.3510.4690.4690.0000.0000.0000.000
129A135ILE0-0.002-0.00734.4760.4690.4690.0000.0000.0000.000
130A136ARG10.8810.93134.51117.37117.3710.0000.0000.0000.000
131A137GLN0-0.068-0.04135.9420.4290.4290.0000.0000.0000.000
132A138GLY00.0630.00939.2320.3250.3250.0000.0000.0000.000
133A139GLN0-0.078-0.03140.9710.2610.2610.0000.0000.0000.000
134A140ALA0-0.045-0.02242.8650.3680.3680.0000.0000.0000.000
135A141SER0-0.080-0.07042.9430.3140.3140.0000.0000.0000.000
136A142GLY00.0020.01045.2600.2700.2700.0000.0000.0000.000
137A143GLU-1-0.883-0.91842.112-14.746-14.7460.0000.0000.0000.000
138A144LEU0-0.073-0.04138.596-0.046-0.0460.0000.0000.0000.000
139A145ALA00.0330.01943.0880.2360.2360.0000.0000.0000.000
140A146GLU-1-0.920-0.95843.351-13.220-13.2200.0000.0000.0000.000
141A147TYR0-0.050-0.02941.9220.3170.3170.0000.0000.0000.000
142A148PRO00.003-0.01941.096-0.216-0.2160.0000.0000.0000.000
143A149ILE00.0260.01036.467-0.260-0.2600.0000.0000.0000.000
144A150GLU-1-0.854-0.92033.994-17.614-17.6140.0000.0000.0000.000
145A151LEU00.0140.01135.193-0.314-0.3140.0000.0000.0000.000
146A152MET0-0.0090.01637.089-0.081-0.0810.0000.0000.0000.000
147A153GLN00.0200.01828.8240.1460.1460.0000.0000.0000.000
148A154ASP-1-0.856-0.94231.980-18.778-18.7780.0000.0000.0000.000
149A155ASN0-0.087-0.04033.196-0.045-0.0450.0000.0000.0000.000
150A156CYS0-0.046-0.02631.590-0.159-0.1590.0000.0000.0000.000
151A157HIS0-0.007-0.01125.716-1.120-1.1200.0000.0000.0000.000
152A158GLY00.0460.00929.710-0.479-0.4790.0000.0000.0000.000
153A159GLN0-0.007-0.01432.263-0.151-0.1510.0000.0000.0000.000
154A160TYR00.0330.00723.022-0.108-0.1080.0000.0000.0000.000
155A161LEU0-0.0410.00725.571-0.483-0.4830.0000.0000.0000.000
156A162ALA00.0340.02228.823-0.125-0.1250.0000.0000.0000.000
157A163ALA00.0040.00130.9120.1090.1090.0000.0000.0000.000
158A164THR0-0.027-0.04425.833-0.309-0.3090.0000.0000.0000.000
159A165ARG10.7910.87926.58820.04520.0450.0000.0000.0000.000
160A166TYR0-0.034-0.02929.309-0.023-0.0230.0000.0000.0000.000
161A167PHE00.007-0.01728.8150.2180.2180.0000.0000.0000.000
162A168VAL0-0.027-0.01524.529-0.424-0.4240.0000.0000.0000.000
163A169ASP-1-0.859-0.88727.214-19.722-19.7220.0000.0000.0000.000
164A170HIS0-0.076-0.02530.3470.7080.7080.0000.0000.0000.000
165A171PRO00.0490.02327.5620.0350.0350.0000.0000.0000.000
166A172GLU-1-0.842-0.93529.543-17.760-17.7600.0000.0000.0000.000
167A173ARG10.8380.90632.80516.75016.7500.0000.0000.0000.000
168A174TRP00.0380.03526.5410.4480.4480.0000.0000.0000.000
169A175GLN00.0230.01428.0320.1370.1370.0000.0000.0000.000
170A176GLN0-0.044-0.01632.3710.6460.6460.0000.0000.0000.000
171A177ALA00.0440.01335.647-0.151-0.1510.0000.0000.0000.000
172A178HIS0-0.0090.00437.196-0.038-0.0380.0000.0000.0000.000
173A179GLU-1-0.767-0.85635.723-15.948-15.9480.0000.0000.0000.000
174A180ARG10.8660.93631.28218.48018.4800.0000.0000.0000.000
175A181SER00.005-0.00134.843-0.088-0.0880.0000.0000.0000.000
176A182ALA0-0.007-0.00437.9640.1430.1430.0000.0000.0000.000
177A183SER0-0.046-0.03333.847-0.117-0.1170.0000.0000.0000.000
178A184PHE00.0400.03034.527-0.026-0.0260.0000.0000.0000.000
179A185ALA00.005-0.00236.1390.2300.2300.0000.0000.0000.000
180A186LEU0-0.032-0.02537.7430.2850.2850.0000.0000.0000.000
181A187PHE00.0050.01432.7080.1320.1320.0000.0000.0000.000
182A188TRP00.0540.02136.7240.0060.0060.0000.0000.0000.000
183A189ASN0-0.024-0.03739.0300.2500.2500.0000.0000.0000.000
184A190ALA0-0.0450.00139.0590.3590.3590.0000.0000.0000.000
185A191MET0-0.018-0.00735.8400.0040.0040.0000.0000.0000.000
186A192ALA0-0.0100.00340.7700.1520.1520.0000.0000.0000.000
187A193VAL0-0.023-0.00243.6180.1610.1610.0000.0000.0000.000
188A194ARG0-0.017-0.00147.1160.4030.4030.0000.0000.0000.000