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: ZL5JN

Calculation Name: 5WB5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: di(hydroxyethyl)ether

Ligand 3-letter code: PEG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5WB5

Chain ID: A

ChEMBL ID:

UniProt ID: E9ADE1

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1962347.244716
FMO2-HF: Nuclear repulsion 1890413.331549
FMO2-HF: Total energy -71933.913167
FMO2-MP2: Total energy -72141.310795


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:13:ALA)


Summations of interaction energy for fragment #1(A:13:ALA)
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.
9.36611.150.041-0.607-1.218-0.001
Interaction energy analysis for fragmet #1(A:13:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.915
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].
3A15LEU0-0.0010.0133.0685.7847.5680.041-0.607-1.218-0.001
4A16HIS0-0.002-0.0215.5862.5002.5000.0000.0000.0000.000
5A17LYS10.8820.9306.70636.64836.6480.0000.0000.0000.000
6A18LEU00.0070.02710.6450.8340.8340.0000.0000.0000.000
7A19GLN0-0.0170.01314.318-0.377-0.3770.0000.0000.0000.000
8A20ARG10.7250.83017.23714.02614.0260.0000.0000.0000.000
9A21ALA00.0000.00415.363-0.742-0.7420.0000.0000.0000.000
10A22TRP00.0150.00516.6581.4111.4110.0000.0000.0000.000
11A23THR0-0.008-0.01017.987-0.732-0.7320.0000.0000.0000.000
12A24LEU0-0.019-0.01220.1530.6260.6260.0000.0000.0000.000
13A25TRP00.006-0.01621.9110.0320.0320.0000.0000.0000.000
14A26TYR0-0.040-0.02725.2920.0820.0820.0000.0000.0000.000
15A27ASP-1-0.817-0.88327.948-9.188-9.1880.0000.0000.0000.000
16A28SER00.0400.00331.7360.1090.1090.0000.0000.0000.000
17A29PRO0-0.029-0.02934.8190.0380.0380.0000.0000.0000.000
18A30SER0-0.031-0.01035.1490.1640.1640.0000.0000.0000.000
19A31THR0-0.033-0.02731.258-0.018-0.0180.0000.0000.0000.000
20A32TYR0-0.036-0.01334.5940.0230.0230.0000.0000.0000.000
21A33ASN00.0570.03736.4320.3450.3450.0000.0000.0000.000
22A34THR0-0.030-0.03138.5430.0500.0500.0000.0000.0000.000
23A35GLU-1-0.954-0.95541.244-7.162-7.1620.0000.0000.0000.000
24A36ASN0-0.006-0.02637.0140.1040.1040.0000.0000.0000.000
25A37TRP00.0370.02536.263-0.254-0.2540.0000.0000.0000.000
26A38GLU-1-0.802-0.87232.706-9.470-9.4700.0000.0000.0000.000
27A39MET0-0.065-0.03933.247-0.239-0.2390.0000.0000.0000.000
28A40SER0-0.005-0.00733.8190.0510.0510.0000.0000.0000.000
29A41LEU0-0.064-0.00629.636-0.158-0.1580.0000.0000.0000.000
30A42VAL00.0140.00426.257-0.100-0.1000.0000.0000.0000.000
31A43PRO0-0.0130.00223.174-0.183-0.1830.0000.0000.0000.000
32A44ILE0-0.045-0.02720.2380.0030.0030.0000.0000.0000.000
33A45MET0-0.002-0.00613.314-0.293-0.2930.0000.0000.0000.000
34A46THR0-0.0100.01215.8660.8130.8130.0000.0000.0000.000
35A47VAL0-0.056-0.00713.342-1.195-1.1950.0000.0000.0000.000
36A48HIS10.8710.90410.77122.30722.3070.0000.0000.0000.000
37A49SER0-0.043-0.0517.927-1.554-1.5540.0000.0000.0000.000
38A50VAL00.0790.04810.5541.2461.2460.0000.0000.0000.000
39A51GLU-1-0.764-0.8606.788-33.086-33.0860.0000.0000.0000.000
40A52GLU-1-0.835-0.9068.852-24.475-24.4750.0000.0000.0000.000
41A53PHE00.0430.02211.0291.5231.5230.0000.0000.0000.000
42A54PHE00.0480.00813.1871.2221.2220.0000.0000.0000.000
43A55VAL0-0.082-0.03610.7070.8850.8850.0000.0000.0000.000
44A56MET00.0110.00413.8201.0711.0710.0000.0000.0000.000
45A57LEU00.004-0.00716.5910.8940.8940.0000.0000.0000.000
46A58ARG10.8590.95312.52519.51719.5170.0000.0000.0000.000
47A59TYR0-0.011-0.01415.3930.1560.1560.0000.0000.0000.000
48A60MET0-0.0180.01820.2140.4180.4180.0000.0000.0000.000
49A61LYS10.9250.96722.61011.22211.2220.0000.0000.0000.000
50A62PRO00.0530.03926.147-0.009-0.0090.0000.0000.0000.000
51A63LEU00.025-0.00127.7670.2660.2660.0000.0000.0000.000
52A64HIS0-0.060-0.01830.6320.5020.5020.0000.0000.0000.000
53A65ALA00.0180.00130.8540.2530.2530.0000.0000.0000.000
54A66LEU0-0.0450.00629.4270.1120.1120.0000.0000.0000.000
55A67ARG10.9810.98732.2028.4208.4200.0000.0000.0000.000
56A68THR00.0340.00035.114-0.136-0.1360.0000.0000.0000.000
57A69SER0-0.067-0.02837.0930.2190.2190.0000.0000.0000.000
58A70SER00.001-0.01631.967-0.077-0.0770.0000.0000.0000.000
59A71GLN0-0.0270.00931.5620.0160.0160.0000.0000.0000.000
60A72TYR0-0.017-0.00825.967-0.263-0.2630.0000.0000.0000.000
61A73HIS0-0.009-0.02326.8500.0550.0550.0000.0000.0000.000
62A74PHE00.004-0.01618.414-0.429-0.4290.0000.0000.0000.000
63A75PHE00.0810.03123.4670.2920.2920.0000.0000.0000.000
64A76GLN00.0640.04821.282-0.360-0.3600.0000.0000.0000.000
65A77GLU-1-0.870-0.95716.888-17.068-17.0680.0000.0000.0000.000
66A78GLY0-0.038-0.02520.7890.0550.0550.0000.0000.0000.000
67A79VAL0-0.064-0.01623.8000.4970.4970.0000.0000.0000.000
68A80LYS10.8670.91125.9869.6489.6480.0000.0000.0000.000
69A81PRO0-0.0020.01127.9880.1380.1380.0000.0000.0000.000
70A82MET0-0.046-0.02130.2520.3600.3600.0000.0000.0000.000
71A83TRP00.0030.00733.580-0.174-0.1740.0000.0000.0000.000
72A84GLU-1-0.826-0.94435.744-8.308-8.3080.0000.0000.0000.000
73A85ASP-1-0.808-0.88129.751-10.520-10.5200.0000.0000.0000.000
74A86PRO0-0.043-0.04231.4620.1830.1830.0000.0000.0000.000
75A87ALA00.0280.01229.3150.1630.1630.0000.0000.0000.000
76A88ASN0-0.005-0.00830.471-0.087-0.0870.0000.0000.0000.000
77A89LYS10.9240.97733.5948.8658.8650.0000.0000.0000.000
78A90LYS10.9190.95536.4368.6118.6110.0000.0000.0000.000
79A91GLY00.0300.03435.4940.1650.1650.0000.0000.0000.000
80A92GLY00.030-0.00935.4900.3050.3050.0000.0000.0000.000
81A93LYS10.8590.95534.6837.9087.9080.0000.0000.0000.000
82A94LEU00.0240.02434.5600.3330.3330.0000.0000.0000.000
83A95TRP0-0.082-0.05734.610-0.235-0.2350.0000.0000.0000.000
84A96VAL00.0430.02034.9540.2130.2130.0000.0000.0000.000
85A97ASN0-0.050-0.01537.171-0.222-0.2220.0000.0000.0000.000
86A98LEU00.0380.01933.3260.0850.0850.0000.0000.0000.000
87A99ASP-1-0.856-0.93837.839-7.293-7.2930.0000.0000.0000.000
88A100ILE-1-0.931-0.96137.000-8.357-8.3570.0000.0000.0000.000
89A122ALA10.8340.90834.1078.6978.6970.0000.0000.0000.000
90A123ALA00.1030.05329.820-0.003-0.0030.0000.0000.0000.000
91A124GLU-1-0.876-0.93731.075-8.682-8.6820.0000.0000.0000.000
92A125ALA0-0.016-0.00930.464-0.362-0.3620.0000.0000.0000.000
93A126LYS10.9010.96123.41312.37712.3770.0000.0000.0000.000
94A127THR00.0440.00229.8180.1740.1740.0000.0000.0000.000
95A128ASP-1-0.817-0.91630.973-9.356-9.3560.0000.0000.0000.000
96A129LEU00.0180.01531.773-0.208-0.2080.0000.0000.0000.000
97A130ASP-1-0.817-0.90027.658-10.402-10.4020.0000.0000.0000.000
98A131LYS10.8610.92327.0949.3379.3370.0000.0000.0000.000
99A132ALA00.0310.02927.187-0.339-0.3390.0000.0000.0000.000
100A133TRP00.015-0.00425.384-0.151-0.1510.0000.0000.0000.000
101A134GLU-1-0.870-0.95422.964-12.923-12.9230.0000.0000.0000.000
102A135ASN0-0.036-0.01523.026-0.895-0.8950.0000.0000.0000.000
103A136VAL00.0060.00424.436-0.312-0.3120.0000.0000.0000.000
104A137LEU00.0010.01421.212-0.301-0.3010.0000.0000.0000.000
105A138MET0-0.030-0.01619.276-0.845-0.8450.0000.0000.0000.000
106A139ALA00.0060.00820.597-0.512-0.5120.0000.0000.0000.000
107A140THR0-0.068-0.04121.9250.2940.2940.0000.0000.0000.000
108A141VAL0-0.036-0.01816.678-0.230-0.2300.0000.0000.0000.000
109A142GLY0-0.013-0.00717.903-0.828-0.8280.0000.0000.0000.000
110A143GLU-1-0.727-0.86119.151-14.037-14.0370.0000.0000.0000.000
111A144TYR00.010-0.00221.0520.4340.4340.0000.0000.0000.000
112A145LEU0-0.068-0.03224.6320.5330.5330.0000.0000.0000.000
113A146ASP-1-0.717-0.89326.703-10.934-10.9340.0000.0000.0000.000
114A147CYS00.0150.02925.0790.2890.2890.0000.0000.0000.000
115A148VAL00.0110.01426.8850.0610.0610.0000.0000.0000.000
116A149ASP-1-0.865-0.95529.925-9.442-9.4420.0000.0000.0000.000
117A150LYS10.8690.93627.46910.08910.0890.0000.0000.0000.000
118A151LYS10.8310.95324.08711.98511.9850.0000.0000.0000.000
119A152ASP-1-0.922-0.97019.922-15.699-15.6990.0000.0000.0000.000
120A153THR0-0.059-0.03022.1270.0480.0480.0000.0000.0000.000
121A154PRO0-0.0020.00422.047-0.039-0.0390.0000.0000.0000.000
122A155THR0-0.068-0.05423.5920.7150.7150.0000.0000.0000.000
123A156GLU-1-0.927-0.96126.503-10.616-10.6160.0000.0000.0000.000
124A157PRO0-0.0180.01824.9780.2200.2200.0000.0000.0000.000
125A158PHE0-0.014-0.02227.6550.2860.2860.0000.0000.0000.000
126A159VAL0-0.030-0.01026.5310.2590.2590.0000.0000.0000.000
127A160THR0-0.003-0.01926.572-0.499-0.4990.0000.0000.0000.000
128A161GLY00.0300.00725.552-0.499-0.4990.0000.0000.0000.000
129A162ILE0-0.067-0.00824.5910.4350.4350.0000.0000.0000.000
130A163VAL0-0.0010.00127.464-0.169-0.1690.0000.0000.0000.000
131A164MET00.0060.02128.9830.3120.3120.0000.0000.0000.000
132A165SER0-0.033-0.01830.7340.0460.0460.0000.0000.0000.000
133A166LYS10.8860.94033.4588.9028.9020.0000.0000.0000.000
134A167ARG10.8610.91835.1997.7607.7600.0000.0000.0000.000
135A168LYS10.9430.96339.0327.0007.0000.0000.0000.0000.000
136A169TYR0-0.0100.00742.1560.0910.0910.0000.0000.0000.000
137A170HIS00.0800.04440.471-0.114-0.1140.0000.0000.0000.000
138A171ASN0-0.049-0.02734.846-0.064-0.0640.0000.0000.0000.000
139A172ARG10.8760.93436.0937.6977.6970.0000.0000.0000.000
140A173LEU00.0440.04129.454-0.204-0.2040.0000.0000.0000.000
141A174ALA0-0.032-0.03231.8800.3160.3160.0000.0000.0000.000
142A175VAL00.0320.02128.909-0.363-0.3630.0000.0000.0000.000
143A176TRP0-0.033-0.02130.0370.4540.4540.0000.0000.0000.000
144A177VAL00.0240.01130.116-0.355-0.3550.0000.0000.0000.000
145A178SER00.0750.03530.7790.2870.2870.0000.0000.0000.000
146A179ASP-1-0.858-0.92332.749-8.134-8.1340.0000.0000.0000.000
147A180ALA0-0.039-0.02136.065-0.053-0.0530.0000.0000.0000.000
148A181SER0-0.104-0.05639.0580.2360.2360.0000.0000.0000.000
149A182ALA00.0160.00237.0910.1490.1490.0000.0000.0000.000
150A183THR00.020-0.01138.543-0.149-0.1490.0000.0000.0000.000
151A184ASP-1-0.843-0.91038.745-7.937-7.9370.0000.0000.0000.000
152A185LYS10.8450.93733.0339.3369.3360.0000.0000.0000.000
153A186ILE00.0310.01834.945-0.215-0.2150.0000.0000.0000.000
154A187GLU-1-1.006-0.99537.060-7.804-7.8040.0000.0000.0000.000
155A188ALA0-0.003-0.00333.548-0.078-0.0780.0000.0000.0000.000
156A189LEU00.0290.01930.618-0.146-0.1460.0000.0000.0000.000
157A190LYS10.9710.98133.3797.6777.6770.0000.0000.0000.000
158A191LYS10.9180.98134.9148.4168.4160.0000.0000.0000.000
159A192ALA00.0190.01329.876-0.046-0.0460.0000.0000.0000.000
160A193LEU00.021-0.00231.250-0.159-0.1590.0000.0000.0000.000
161A194THR0-0.047-0.05732.4650.0860.0860.0000.0000.0000.000
162A195LYS10.8650.95329.01810.55110.5510.0000.0000.0000.000
163A196GLU-1-0.863-0.94427.268-11.438-11.4380.0000.0000.0000.000
164A197ALA0-0.0160.00430.130-0.144-0.1440.0000.0000.0000.000
165A198SER0-0.035-0.03131.3840.1940.1940.0000.0000.0000.000
166A199LEU00.0030.00533.358-0.070-0.0700.0000.0000.0000.000
167A200ALA00.0220.01536.3330.1130.1130.0000.0000.0000.000
168A201PRO0-0.037-0.03839.669-0.109-0.1090.0000.0000.0000.000
169A202ILE00.0340.03237.3530.0950.0950.0000.0000.0000.000
170A203ALA00.0440.02440.7600.1340.1340.0000.0000.0000.000
171A204SER0-0.072-0.05241.5300.1730.1730.0000.0000.0000.000
172A205MET00.0090.00636.854-0.195-0.1950.0000.0000.0000.000
173A206VAL0-0.0220.00640.0520.1720.1720.0000.0000.0000.000
174A207PHE00.0390.02136.536-0.210-0.2100.0000.0000.0000.000
175A208THR0-0.067-0.04039.3550.2470.2470.0000.0000.0000.000
176A209LYS10.9520.98639.2077.2417.2410.0000.0000.0000.000
177A210HIS-1-0.900-0.92934.691-7.286-7.2860.0000.0000.0000.000