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: QMZQY

Calculation Name: 5LS0-B-Xray547

Preferred Name:

Target Type:

Ligand Name: di(hydroxyethyl)ether

Ligand 3-letter code: PEG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5LS0

Chain ID: B

ChEMBL ID:

UniProt ID: Q93V56

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 -2017308.72159
FMO2-HF: Nuclear repulsion 1945295.841736
FMO2-HF: Total energy -72012.879854
FMO2-MP2: Total energy -72222.499208


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:30:SER)


Summations of interaction energy for fragment #1(A:30:SER)
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.
-94.204-92.834-0.019-0.565-0.785-0.001
Interaction energy analysis for fragmet #1(A:30:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.903
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].
3A32ALA00.0050.0093.8511.3392.709-0.019-0.565-0.785-0.001
4A33ALA00.0110.0016.7021.2411.2410.0000.0000.0000.000
5A34HIS00.0530.0248.9911.5961.5960.0000.0000.0000.000
6A35PRO00.001-0.00812.5960.1890.1890.0000.0000.0000.000
7A36TRP00.0250.00614.6460.3240.3240.0000.0000.0000.000
8A37HIS10.8630.93914.09218.84918.8490.0000.0000.0000.000
9A38ASP-1-0.838-0.9059.552-28.044-28.0440.0000.0000.0000.000
10A39LEU0-0.041-0.01011.254-1.555-1.5550.0000.0000.0000.000
11A40GLU-1-0.907-0.96612.870-18.145-18.1450.0000.0000.0000.000
12A41ILE00.0610.03115.2280.1560.1560.0000.0000.0000.000
13A42GLY00.0670.04517.9610.6170.6170.0000.0000.0000.000
14A43PRO0-0.037-0.04218.4860.6140.6140.0000.0000.0000.000
15A44GLY0-0.022-0.00121.2690.5450.5450.0000.0000.0000.000
16A45ALA0-0.0120.02223.0050.5850.5850.0000.0000.0000.000
17A46PRO00.0410.01524.880-0.019-0.0190.0000.0000.0000.000
18A47GLN00.009-0.00627.372-0.125-0.1250.0000.0000.0000.000
19A48ILE0-0.067-0.05424.0630.2150.2150.0000.0000.0000.000
20A49PHE0-0.0120.00022.144-0.340-0.3400.0000.0000.0000.000
21A50ASN0-0.056-0.04316.6280.7050.7050.0000.0000.0000.000
22A51VAL00.009-0.00919.9690.3070.3070.0000.0000.0000.000
23A52VAL0-0.0090.00016.992-0.485-0.4850.0000.0000.0000.000
24A53VAL0-0.024-0.00719.6890.7690.7690.0000.0000.0000.000
25A54GLU-1-0.830-0.92921.369-13.308-13.3080.0000.0000.0000.000
26A55ILE0-0.075-0.04323.5900.0760.0760.0000.0000.0000.000
27A56THR0-0.032-0.02325.7680.0360.0360.0000.0000.0000.000
28A57LYS10.9410.97227.7439.6139.6130.0000.0000.0000.000
29A58GLY00.015-0.00131.030-0.001-0.0010.0000.0000.0000.000
30A59SER0-0.042-0.00830.0010.2230.2230.0000.0000.0000.000
31A60LYS10.9660.97932.1518.2988.2980.0000.0000.0000.000
32A61VAL0-0.038-0.01428.8560.2010.2010.0000.0000.0000.000
33A62LYS10.8720.93028.32410.76110.7610.0000.0000.0000.000
34A63TYR00.007-0.02424.8420.0380.0380.0000.0000.0000.000
35A64GLU-1-0.805-0.89325.104-10.905-10.9050.0000.0000.0000.000
36A65LEU00.0230.01418.507-0.560-0.5600.0000.0000.0000.000
37A66ASP-1-0.838-0.89220.777-14.246-14.2460.0000.0000.0000.000
38A67LYS10.8560.90919.88511.52011.5200.0000.0000.0000.000
39A68LYS10.9100.96619.65613.29413.2940.0000.0000.0000.000
40A69THR0-0.080-0.08717.150-0.985-0.9850.0000.0000.0000.000
41A70GLY0-0.0150.00315.499-1.530-1.5300.0000.0000.0000.000
42A71LEU0-0.031-0.01715.257-0.471-0.4710.0000.0000.0000.000
43A72ILE00.0110.01117.7670.5670.5670.0000.0000.0000.000
44A73LYS10.8740.94120.82911.56611.5660.0000.0000.0000.000
45A74VAL00.004-0.01223.9950.1350.1350.0000.0000.0000.000
46A75ASP-1-0.872-0.91027.380-10.336-10.3360.0000.0000.0000.000
47A76ARG10.8170.88229.7029.7319.7310.0000.0000.0000.000
48A77ILE0-0.034-0.01232.295-0.184-0.1840.0000.0000.0000.000
49A78LEU00.0160.00634.5870.1640.1640.0000.0000.0000.000
50A79TYR00.0380.01036.9370.0730.0730.0000.0000.0000.000
51A80SER00.0290.03040.3880.2840.2840.0000.0000.0000.000
52A81SER0-0.084-0.04140.441-0.224-0.2240.0000.0000.0000.000
53A82VAL00.0120.00438.3170.1310.1310.0000.0000.0000.000
54A83VAL0-0.027-0.01835.427-0.127-0.1270.0000.0000.0000.000
55A84TYR00.0760.03931.7980.1810.1810.0000.0000.0000.000
56A85PRO00.0110.01833.968-0.126-0.1260.0000.0000.0000.000
57A86HIS0-0.009-0.01731.4640.3540.3540.0000.0000.0000.000
58A87ASN00.0260.00226.3020.0150.0150.0000.0000.0000.000
59A88TYR00.018-0.00727.4030.3230.3230.0000.0000.0000.000
60A89GLY00.0270.01724.044-0.400-0.4000.0000.0000.0000.000
61A90PHE00.0520.04618.5970.2000.2000.0000.0000.0000.000
62A91VAL00.0160.02021.716-0.642-0.6420.0000.0000.0000.000
63A92PRO0-0.045-0.00516.8230.0860.0860.0000.0000.0000.000
64A93ARG10.8040.88112.10622.11122.1110.0000.0000.0000.000
65A94THR00.0230.01019.4300.6430.6430.0000.0000.0000.000
66A95LEU0-0.075-0.03622.994-0.601-0.6010.0000.0000.0000.000
67A96CYS00.0180.02525.6370.3330.3330.0000.0000.0000.000
68A97GLU-1-0.796-0.90829.375-9.731-9.7310.0000.0000.0000.000
69A98ASP-1-0.825-0.89729.867-10.557-10.5570.0000.0000.0000.000
70A99ASN0-0.141-0.07527.582-0.142-0.1420.0000.0000.0000.000
71A100ASP-1-0.802-0.88625.570-12.636-12.6360.0000.0000.0000.000
72A101PRO0-0.059-0.03721.8740.0900.0900.0000.0000.0000.000
73A102ILE00.0420.00924.4590.3090.3090.0000.0000.0000.000
74A103ASP-1-0.754-0.86225.939-11.410-11.4100.0000.0000.0000.000
75A104VAL0-0.054-0.04025.7540.3290.3290.0000.0000.0000.000
76A105LEU0-0.026-0.00427.956-0.138-0.1380.0000.0000.0000.000
77A106VAL0-0.006-0.01525.5170.1530.1530.0000.0000.0000.000
78A107ILE0-0.050-0.02928.9750.1080.1080.0000.0000.0000.000
79A108MET0-0.045-0.01825.481-0.358-0.3580.0000.0000.0000.000
80A109GLN0-0.064-0.04630.8930.3100.3100.0000.0000.0000.000
81A110GLU-1-0.913-0.94928.161-10.077-10.0770.0000.0000.0000.000
82A111PRO0-0.030-0.00728.303-0.149-0.1490.0000.0000.0000.000
83A112VAL00.014-0.00422.161-0.311-0.3110.0000.0000.0000.000
84A113LEU00.0070.01221.2490.3090.3090.0000.0000.0000.000
85A114PRO00.0370.01421.465-0.435-0.4350.0000.0000.0000.000
86A115GLY0-0.030-0.00917.840-0.472-0.4720.0000.0000.0000.000
87A116CYS0-0.079-0.01916.356-1.284-1.2840.0000.0000.0000.000
88A117PHE0-0.008-0.00713.0600.2650.2650.0000.0000.0000.000
89A118LEU0-0.0140.00418.075-0.021-0.0210.0000.0000.0000.000
90A119ARG10.8710.89519.77013.65113.6510.0000.0000.0000.000
91A120ALA0-0.008-0.00722.0130.5010.5010.0000.0000.0000.000
92A121ARG10.8580.92625.5049.8769.8760.0000.0000.0000.000
93A122ALA00.0190.01928.5240.1600.1600.0000.0000.0000.000
94A123ILE0-0.031-0.01630.6550.1600.1600.0000.0000.0000.000
95A124GLY00.0290.00734.1060.3580.3580.0000.0000.0000.000
96A125LEU0-0.026-0.00234.082-0.324-0.3240.0000.0000.0000.000
97A126MET0-0.015-0.00235.8320.3790.3790.0000.0000.0000.000
98A127PRO00.0300.02636.997-0.191-0.1910.0000.0000.0000.000
99A128MET0-0.057-0.02737.2040.1920.1920.0000.0000.0000.000
100A129ILE00.0250.03338.800-0.126-0.1260.0000.0000.0000.000
101A130ASP-1-0.802-0.87837.448-8.433-8.4330.0000.0000.0000.000
102A131GLN00.012-0.01239.6910.0450.0450.0000.0000.0000.000
103A132GLY0-0.025-0.01141.9300.0710.0710.0000.0000.0000.000
104A133GLU-1-0.921-0.95237.430-8.305-8.3050.0000.0000.0000.000
105A134LYS10.8090.89733.9239.3919.3910.0000.0000.0000.000
106A135ASP-1-0.812-0.92134.086-9.578-9.5780.0000.0000.0000.000
107A136ASP-1-0.876-0.94534.433-8.798-8.7980.0000.0000.0000.000
108A137LYS10.7590.87531.8459.4319.4310.0000.0000.0000.000
109A138ILE0-0.0090.00229.2070.3180.3180.0000.0000.0000.000
110A139ILE0-0.030-0.01631.362-0.100-0.1000.0000.0000.0000.000
111A140ALA00.0420.00828.6210.0180.0180.0000.0000.0000.000
112A141VAL0-0.0010.01630.1450.1710.1710.0000.0000.0000.000
113A142CYS0-0.0180.00924.515-0.370-0.3700.0000.0000.0000.000
114A143VAL0-0.039-0.03324.6320.3810.3810.0000.0000.0000.000
115A144ASP-1-0.803-0.88922.592-13.431-13.4310.0000.0000.0000.000
116A145ASP-1-0.753-0.85925.676-10.088-10.0880.0000.0000.0000.000
117A146PRO0-0.072-0.05228.5690.2010.2010.0000.0000.0000.000
118A147GLU-1-0.951-0.96631.336-8.378-8.3780.0000.0000.0000.000
119A148TYR0-0.007-0.02031.3570.1850.1850.0000.0000.0000.000
120A149LYS10.9460.99129.29010.49910.4990.0000.0000.0000.000
121A150HIS0-0.015-0.01530.903-0.151-0.1510.0000.0000.0000.000
122A151TYR0-0.0350.01634.2580.1980.1980.0000.0000.0000.000
123A152THR0-0.083-0.05633.757-0.325-0.3250.0000.0000.0000.000
124A153ASP-1-0.744-0.88935.775-8.021-8.0210.0000.0000.0000.000
125A154ILE00.0370.01936.8530.0870.0870.0000.0000.0000.000
126A155LYS10.8170.89838.9547.7577.7570.0000.0000.0000.000
127A156GLU-1-0.829-0.90038.351-8.082-8.0820.0000.0000.0000.000
128A157LEU0-0.0210.00236.634-0.014-0.0140.0000.0000.0000.000
129A158PRO00.003-0.00840.7120.2000.2000.0000.0000.0000.000
130A159PRO00.0450.01542.806-0.100-0.1000.0000.0000.0000.000
131A160HIS0-0.029-0.00943.1730.0770.0770.0000.0000.0000.000
132A161ARG10.8170.88337.3628.1338.1330.0000.0000.0000.000
133A162LEU00.0540.03239.076-0.134-0.1340.0000.0000.0000.000
134A163SER0-0.020-0.00441.334-0.014-0.0140.0000.0000.0000.000
135A164GLU-1-0.841-0.90939.370-7.967-7.9670.0000.0000.0000.000
136A165ILE0-0.002-0.00136.318-0.092-0.0920.0000.0000.0000.000
137A166ARG10.8390.89039.1057.0087.0080.0000.0000.0000.000
138A167ARG10.8550.93941.7276.9066.9060.0000.0000.0000.000
139A168PHE0-0.008-0.01035.1240.0340.0340.0000.0000.0000.000
140A169PHE00.020-0.00633.281-0.068-0.0680.0000.0000.0000.000
141A170GLU-1-0.805-0.88239.210-7.002-7.0020.0000.0000.0000.000
142A171ASP-1-0.862-0.93842.262-6.958-6.9580.0000.0000.0000.000
143A172TYR0-0.081-0.04634.471-0.045-0.0450.0000.0000.0000.000
144A173LYS10.8270.89635.9588.6788.6780.0000.0000.0000.000
145A174LYS10.8890.95340.3636.9996.9990.0000.0000.0000.000
146A175ASN0-0.061-0.04443.3920.2280.2280.0000.0000.0000.000
147A176GLU-1-0.807-0.88537.593-8.646-8.6460.0000.0000.0000.000
148A177ASN0-0.086-0.05242.2960.0970.0970.0000.0000.0000.000
149A178LYS10.8200.91438.4958.1938.1930.0000.0000.0000.000
150A179GLU-1-0.937-0.96043.266-6.767-6.7670.0000.0000.0000.000
151A180VAL0-0.014-0.01239.364-0.169-0.1690.0000.0000.0000.000
152A181ALA0-0.0200.00042.3480.1630.1630.0000.0000.0000.000
153A182VAL00.0110.00740.338-0.145-0.1450.0000.0000.0000.000
154A183ASN0-0.054-0.02442.1750.1690.1690.0000.0000.0000.000
155A184ASP-1-0.876-0.93242.701-6.954-6.9540.0000.0000.0000.000
156A185PHE0-0.023-0.02538.315-0.072-0.0720.0000.0000.0000.000
157A186LEU0-0.013-0.00139.4410.2000.2000.0000.0000.0000.000
158A187PRO00.028-0.00138.912-0.177-0.1770.0000.0000.0000.000
159A188SER0-0.030-0.00235.224-0.201-0.2010.0000.0000.0000.000
160A189GLU-1-0.878-0.93934.844-8.464-8.4640.0000.0000.0000.000
161A190SER00.0540.01735.619-0.126-0.1260.0000.0000.0000.000
162A191ALA0-0.0240.00332.924-0.151-0.1510.0000.0000.0000.000
163A192VAL0-0.004-0.01230.748-0.346-0.3460.0000.0000.0000.000
164A193GLU-1-0.930-0.96931.288-8.758-8.7580.0000.0000.0000.000
165A194ALA0-0.0010.00332.410-0.167-0.1670.0000.0000.0000.000
166A195ILE0-0.040-0.00726.268-0.326-0.3260.0000.0000.0000.000
167A196GLN0-0.021-0.02827.149-0.442-0.4420.0000.0000.0000.000
168A197TYR00.0070.01128.283-0.272-0.2720.0000.0000.0000.000
169A198SER00.011-0.00327.069-0.280-0.2800.0000.0000.0000.000
170A199MET0-0.030-0.00923.593-0.517-0.5170.0000.0000.0000.000
171A200ASP-1-0.870-0.92424.545-11.422-11.4220.0000.0000.0000.000
172A201LEU00.0340.02026.655-0.177-0.1770.0000.0000.0000.000
173A202TYR00.0190.02116.989-0.648-0.6480.0000.0000.0000.000
174A203ALA0-0.017-0.01422.308-0.530-0.5300.0000.0000.0000.000
175A204GLU-1-0.886-0.93923.362-10.651-10.6510.0000.0000.0000.000
176A205TYR0-0.051-0.02825.501-0.040-0.0400.0000.0000.0000.000
177A206ILE0-0.107-0.05319.054-0.270-0.2700.0000.0000.0000.000
178A207LEU0-0.109-0.04217.230-0.937-0.9370.0000.0000.0000.000
179A208HIS0-0.052-0.00920.320-0.370-0.3700.0000.0000.0000.000