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: 5Y2VZ

Calculation Name: 3EU9-C-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3EU9

Chain ID: C

ChEMBL ID:

UniProt ID: Q8IUH5

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2625610.405856
FMO2-HF: Nuclear repulsion 2536540.907826
FMO2-HF: Total energy -89069.49803
FMO2-MP2: Total energy -89327.271942


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:59:TRP)


Summations of interaction energy for fragment #1(A:59:TRP)
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.
57.49268.5348.146-5.22-13.969-0.008
Interaction energy analysis for fragmet #1(A:59:TRP)
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 : 0.922
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].
3A61ILE00.1000.0422.956-8.128-5.5300.421-1.475-1.544-0.010
5A63LYS10.8650.9192.07433.36435.1482.880-1.343-3.320-0.004
6A64ALA0-0.016-0.0012.6710.7832.2270.321-0.484-1.281-0.004
7A65THR00.0220.0033.8835.1735.3610.011-0.032-0.1670.000
9A67TYR0-0.014-0.0132.819-1.7541.9272.493-1.122-5.0530.012
11A69ILE0-0.018-0.0092.387-0.665-0.1702.002-0.527-1.970-0.001
14A72ARG10.8920.9613.32452.93953.7910.018-0.237-0.634-0.001
4A62VAL00.0150.0435.7342.7122.7120.0000.0000.0000.000
8A66GLN00.0090.0126.626-0.042-0.0420.0000.0000.0000.000
10A68GLY00.0040.0067.0211.0091.0090.0000.0000.0000.000
12A70TYR00.0370.0066.250-2.319-2.3190.0000.0000.0000.000
13A71GLU-1-0.771-0.8819.213-23.112-23.1120.0000.0000.0000.000
15A73CYS0-0.051-0.0326.574-2.098-2.0980.0000.0000.0000.000
16A74ARG10.8150.8937.74021.44521.4450.0000.0000.0000.000
17A75GLU-1-0.891-0.9398.019-27.924-27.9240.0000.0000.0000.000
18A76LEU0-0.058-0.0355.073-0.179-0.1790.0000.0000.0000.000
19A77VAL0-0.023-0.0129.4821.8441.8440.0000.0000.0000.000
20A78GLU-1-0.924-0.95112.532-18.157-18.1570.0000.0000.0000.000
21A79ALA0-0.030-0.01211.4131.2131.2130.0000.0000.0000.000
22A80GLY00.0010.00513.4990.4640.4640.0000.0000.0000.000
23A81TYR0-0.071-0.03410.916-0.188-0.1880.0000.0000.0000.000
24A82ASP-1-0.821-0.91113.436-15.967-15.9670.0000.0000.0000.000
25A83VAL0-0.026-0.03113.598-0.837-0.8370.0000.0000.0000.000
26A84ARG10.8120.89215.10313.60113.6010.0000.0000.0000.000
27A85GLN0-0.0190.00414.1891.2371.2370.0000.0000.0000.000
28A86PRO0-0.031-0.01614.078-1.299-1.2990.0000.0000.0000.000
29A87ASP-1-0.810-0.90211.541-21.460-21.4600.0000.0000.0000.000
30A88LYS10.8220.87013.10619.08819.0880.0000.0000.0000.000
31A89GLU-1-0.788-0.86315.070-16.824-16.8240.0000.0000.0000.000
32A90ASN0-0.006-0.00517.2400.3730.3730.0000.0000.0000.000
33A91VAL0-0.0110.00413.9940.6220.6220.0000.0000.0000.000
34A92THR00.0450.03413.933-1.101-1.1010.0000.0000.0000.000
35A93LEU00.0420.0129.4140.0450.0450.0000.0000.0000.000
36A94LEU00.0250.02012.388-0.499-0.4990.0000.0000.0000.000
37A95HIS10.8430.91915.18915.89715.8970.0000.0000.0000.000
38A96TRP00.0210.00210.206-0.112-0.1120.0000.0000.0000.000
39A97ALA00.0240.00212.273-0.452-0.4520.0000.0000.0000.000
40A98ALA00.0140.00913.2040.3750.3750.0000.0000.0000.000
41A99ILE00.0160.00814.0320.4150.4150.0000.0000.0000.000
42A100ASN0-0.045-0.03211.6390.1140.1140.0000.0000.0000.000
43A101ASN00.0210.00014.081-0.247-0.2470.0000.0000.0000.000
44A102ARG10.8680.95110.13323.37023.3700.0000.0000.0000.000
45A103ILE00.007-0.01214.437-0.053-0.0530.0000.0000.0000.000
46A104ASP-1-0.813-0.91014.983-16.209-16.2090.0000.0000.0000.000
47A105LEU0-0.005-0.0039.406-0.009-0.0090.0000.0000.0000.000
48A106VAL0-0.010-0.00413.8720.1440.1440.0000.0000.0000.000
49A107LYS10.8730.94416.96014.86114.8610.0000.0000.0000.000
50A108TYR00.0080.01513.0730.1170.1170.0000.0000.0000.000
51A109TYR00.044-0.0149.2770.2790.2790.0000.0000.0000.000
52A110ILE00.0180.01816.1190.4740.4740.0000.0000.0000.000
53A111SER0-0.081-0.04418.6330.4940.4940.0000.0000.0000.000
54A112LYS10.9120.95715.85917.11217.1120.0000.0000.0000.000
55A113GLY00.0500.03518.894-0.075-0.0750.0000.0000.0000.000
56A114ALA0-0.032-0.01717.5070.3710.3710.0000.0000.0000.000
57A115ILE0-0.0070.00019.6150.4940.4940.0000.0000.0000.000
58A116VAL00.012-0.00221.067-0.494-0.4940.0000.0000.0000.000
59A117ASP-1-0.794-0.90921.852-11.933-11.9330.0000.0000.0000.000
60A118GLN0-0.060-0.03420.2870.4550.4550.0000.0000.0000.000
61A119LEU00.011-0.00721.527-0.473-0.4730.0000.0000.0000.000
62A120GLY00.018-0.00419.648-0.244-0.2440.0000.0000.0000.000
63A121GLY00.0060.01118.8940.1720.1720.0000.0000.0000.000
64A122ASP-1-0.909-0.95219.687-13.397-13.3970.0000.0000.0000.000
65A123LEU0-0.012-0.00222.5150.5430.5430.0000.0000.0000.000
66A124ASN0-0.035-0.00723.6710.0320.0320.0000.0000.0000.000
67A125SER00.0390.01022.4650.2650.2650.0000.0000.0000.000
68A126THR00.0220.02021.863-0.658-0.6580.0000.0000.0000.000
69A127PRO0-0.031-0.02618.449-0.200-0.2000.0000.0000.0000.000
70A128LEU00.0570.03320.023-0.273-0.2730.0000.0000.0000.000
71A129HIS00.0360.02523.194-0.315-0.3150.0000.0000.0000.000
72A130TRP00.0010.00014.921-0.333-0.3330.0000.0000.0000.000
73A131ALA0-0.025-0.01720.165-0.133-0.1330.0000.0000.0000.000
74A132THR0-0.053-0.04220.9840.2520.2520.0000.0000.0000.000
75A133ARG10.7570.84222.36611.71711.7170.0000.0000.0000.000
76A134GLN0-0.0250.00018.1490.3860.3860.0000.0000.0000.000
77A135GLY00.0380.03421.527-0.077-0.0770.0000.0000.0000.000
78A136HIS0-0.051-0.03017.3280.6130.6130.0000.0000.0000.000
79A137LEU00.0260.00722.3240.0170.0170.0000.0000.0000.000
80A138SER00.002-0.01321.8490.2810.2810.0000.0000.0000.000
81A139MET0-0.0230.03017.2480.0700.0700.0000.0000.0000.000
82A140VAL00.0320.02321.7690.0610.0610.0000.0000.0000.000
83A141VAL0-0.030-0.02124.9570.2600.2600.0000.0000.0000.000
84A142GLN0-0.045-0.03020.357-0.105-0.1050.0000.0000.0000.000
85A143LEU00.0350.00119.9990.0250.0250.0000.0000.0000.000
86A144MET00.0180.01823.7420.2390.2390.0000.0000.0000.000
87A145LYS10.8520.93725.97310.71310.7130.0000.0000.0000.000
88A146TYR0-0.043-0.02222.150-0.021-0.0210.0000.0000.0000.000
89A147GLY00.0070.00626.099-0.040-0.0400.0000.0000.0000.000
90A148ALA0-0.035-0.00524.9810.1360.1360.0000.0000.0000.000
91A149ASP-1-0.791-0.88127.048-9.137-9.1370.0000.0000.0000.000
92A150PRO0-0.035-0.05029.026-0.158-0.1580.0000.0000.0000.000
93A151SER0-0.050-0.04830.0130.1310.1310.0000.0000.0000.000
94A152LEU00.0550.04128.0940.1370.1370.0000.0000.0000.000
95A153ILE0-0.0050.00930.292-0.096-0.0960.0000.0000.0000.000
96A154ASP-1-0.784-0.88626.131-10.986-10.9860.0000.0000.0000.000
97A155GLY00.000-0.00926.8600.3780.3780.0000.0000.0000.000
98A156GLU-1-0.879-0.91427.470-10.473-10.4730.0000.0000.0000.000
99A157GLY00.0000.00730.0600.3370.3370.0000.0000.0000.000
100A158CYS0-0.070-0.03829.9360.2970.2970.0000.0000.0000.000
101A159SER00.0450.01830.083-0.225-0.2250.0000.0000.0000.000
102A160CYS0-0.033-0.00527.588-0.173-0.1730.0000.0000.0000.000
103A161ILE00.0160.00429.507-0.120-0.1200.0000.0000.0000.000
104A162HIS00.019-0.01032.358-0.154-0.1540.0000.0000.0000.000
105A163LEU0-0.058-0.01126.009-0.044-0.0440.0000.0000.0000.000
106A164ALA0-0.009-0.01429.093-0.124-0.1240.0000.0000.0000.000
107A165ALA0-0.014-0.00729.9950.0310.0310.0000.0000.0000.000
108A166GLN00.0090.00829.978-0.050-0.0500.0000.0000.0000.000
109A167PHE0-0.019-0.01226.744-0.055-0.0550.0000.0000.0000.000
110A168GLY00.0450.02828.861-0.136-0.1360.0000.0000.0000.000
111A169HIS0-0.0020.02225.3050.2970.2970.0000.0000.0000.000
112A170THR00.016-0.01329.7960.1280.1280.0000.0000.0000.000
113A171SER00.0060.00028.6900.1650.1650.0000.0000.0000.000
114A172ILE0-0.0050.00425.6060.0630.0630.0000.0000.0000.000
115A173VAL00.0060.00630.1210.1240.1240.0000.0000.0000.000
116A174ALA00.0150.01033.4490.1740.1740.0000.0000.0000.000
117A175TYR0-0.019-0.01430.1970.0880.0880.0000.0000.0000.000
118A176LEU00.022-0.00629.5940.0990.0990.0000.0000.0000.000
119A177ILE00.0200.02633.2350.1020.1020.0000.0000.0000.000
120A178ALA0-0.022-0.00235.8880.1760.1760.0000.0000.0000.000
121A179LYS10.8130.90232.3748.9698.9690.0000.0000.0000.000
122A180GLY00.0250.02235.700-0.009-0.0090.0000.0000.0000.000
123A181GLN0-0.039-0.02233.7840.0070.0070.0000.0000.0000.000
124A182ASP-1-0.826-0.92237.094-7.282-7.2820.0000.0000.0000.000
125A183VAL0-0.014-0.01538.412-0.230-0.2300.0000.0000.0000.000
126A184ASP-1-0.791-0.87440.187-6.900-6.9000.0000.0000.0000.000
127A185MET0-0.0460.00335.191-0.031-0.0310.0000.0000.0000.000
128A186MET0-0.033-0.01538.953-0.105-0.1050.0000.0000.0000.000
129A187ASP-1-0.713-0.83034.808-8.525-8.5250.0000.0000.0000.000
130A188GLN00.006-0.00435.1750.3320.3320.0000.0000.0000.000
131A189ASN0-0.102-0.06933.8410.2280.2280.0000.0000.0000.000
132A190GLY0-0.051-0.03738.0940.2090.2090.0000.0000.0000.000
133A191MET0-0.009-0.01437.3810.2940.2940.0000.0000.0000.000
134A192THR00.0620.01538.274-0.159-0.1590.0000.0000.0000.000
135A193PRO00.0260.00336.369-0.102-0.1020.0000.0000.0000.000
136A194LEU00.0300.02337.537-0.098-0.0980.0000.0000.0000.000
137A195MET0-0.0530.01240.193-0.003-0.0030.0000.0000.0000.000
138A196TRP0-0.020-0.03034.103-0.060-0.0600.0000.0000.0000.000
139A197ALA00.0170.01536.030-0.121-0.1210.0000.0000.0000.000
140A198ALA0-0.010-0.00537.165-0.008-0.0080.0000.0000.0000.000
141A199TYR0-0.065-0.03836.1150.0310.0310.0000.0000.0000.000
142A200ARG10.8770.93930.3759.2939.2930.0000.0000.0000.000
143A201THR00.0220.02032.780-0.203-0.2030.0000.0000.0000.000
144A202HIS0-0.0220.00035.0090.1000.1000.0000.0000.0000.000
145A203SER0-0.043-0.04535.3670.0030.0030.0000.0000.0000.000
146A204VAL00.015-0.00137.4160.1050.1050.0000.0000.0000.000
147A205ASP-1-0.810-0.87436.405-7.770-7.7700.0000.0000.0000.000
148A206PRO00.0290.01734.292-0.101-0.1010.0000.0000.0000.000
149A207THR00.0310.01036.8640.0800.0800.0000.0000.0000.000
150A208ARG10.9250.94539.1587.6297.6290.0000.0000.0000.000
151A209LEU0-0.0210.00936.4380.1240.1240.0000.0000.0000.000
152A210LEU0-0.010-0.01537.3140.0680.0680.0000.0000.0000.000
153A211LEU00.001-0.00440.9350.1100.1100.0000.0000.0000.000
154A212THR0-0.063-0.03642.9750.1700.1700.0000.0000.0000.000
155A213PHE0-0.062-0.04238.2130.0300.0300.0000.0000.0000.000
156A214ASN0-0.038-0.01243.6270.0750.0750.0000.0000.0000.000
157A215VAL00.0000.01242.2060.0480.0480.0000.0000.0000.000
158A216SER0-0.003-0.02945.3610.2210.2210.0000.0000.0000.000
159A217VAL0-0.037-0.03546.846-0.085-0.0850.0000.0000.0000.000
160A218ASN0-0.058-0.02647.858-0.063-0.0630.0000.0000.0000.000
161A219LEU00.0180.02745.1310.1000.1000.0000.0000.0000.000
162A220GLY00.000-0.01847.042-0.038-0.0380.0000.0000.0000.000
163A221ASP-1-0.789-0.90942.597-6.974-6.9740.0000.0000.0000.000
164A222LYS10.9190.97042.5997.2927.2920.0000.0000.0000.000
165A223TYR0-0.0110.00540.4460.2040.2040.0000.0000.0000.000
166A224HIS10.8530.91241.2607.1657.1650.0000.0000.0000.000
167A225LYS10.9410.99846.3556.1126.1120.0000.0000.0000.000
168A226ASN00.0090.01243.7570.2700.2700.0000.0000.0000.000
169A227THR00.0600.00545.610-0.119-0.1190.0000.0000.0000.000
170A228ALA00.0340.01443.611-0.086-0.0860.0000.0000.0000.000
171A229LEU00.0510.02844.341-0.090-0.0900.0000.0000.0000.000
172A230HIS0-0.0080.02246.447-0.115-0.1150.0000.0000.0000.000
173A231TRP00.000-0.00640.823-0.060-0.0600.0000.0000.0000.000
174A232ALA00.0520.03641.886-0.117-0.1170.0000.0000.0000.000
175A233VAL0-0.022-0.00843.179-0.046-0.0460.0000.0000.0000.000
176A234LEU0-0.045-0.02542.290-0.004-0.0040.0000.0000.0000.000
177A235ALA00.0170.01938.686-0.045-0.0450.0000.0000.0000.000
178A236GLY0-0.051-0.01739.829-0.090-0.0900.0000.0000.0000.000
179A237ASN0-0.012-0.01838.7460.1030.1030.0000.0000.0000.000
180A238THR00.0310.00041.5540.0260.0260.0000.0000.0000.000
181A239THR00.0100.01440.2630.1910.1910.0000.0000.0000.000
182A240VAL00.0280.02239.9510.0930.0930.0000.0000.0000.000
183A241ILE0-0.014-0.01443.1100.1180.1180.0000.0000.0000.000
184A242SER0-0.019-0.02346.3710.1610.1610.0000.0000.0000.000
185A243LEU0-0.0170.00142.5970.0820.0820.0000.0000.0000.000
186A244LEU0-0.003-0.00344.3640.0510.0510.0000.0000.0000.000
187A245LEU0-0.056-0.03547.8470.0950.0950.0000.0000.0000.000
188A246GLU-1-0.926-0.94749.824-5.836-5.8360.0000.0000.0000.000
189A247ALA0-0.044-0.01548.8560.0600.0600.0000.0000.0000.000
190A248GLY00.0490.03250.8460.0070.0070.0000.0000.0000.000
191A249ALA0-0.025-0.01949.6160.0270.0270.0000.0000.0000.000
192A250ASN00.008-0.00251.6700.1630.1630.0000.0000.0000.000
193A251VAL00.003-0.00753.290-0.066-0.0660.0000.0000.0000.000
194A252ASP-1-0.816-0.89654.359-5.329-5.3290.0000.0000.0000.000
195A253ALA0-0.038-0.00852.5390.0550.0550.0000.0000.0000.000
196A254GLN0-0.012-0.01453.203-0.076-0.0760.0000.0000.0000.000
197A255ASN0-0.008-0.01648.1920.0780.0780.0000.0000.0000.000
198A256ILE0-0.036-0.03448.2470.1140.1140.0000.0000.0000.000
199A257LYS10.8020.89447.7556.2956.2950.0000.0000.0000.000
200A258GLY00.0350.02852.3750.0880.0880.0000.0000.0000.000
201A259GLU-1-0.794-0.86849.646-6.090-6.0900.0000.0000.0000.000
202A260SER0-0.002-0.02552.307-0.091-0.0910.0000.0000.0000.000
203A261ALA00.0270.01150.111-0.054-0.0540.0000.0000.0000.000
204A262LEU00.0260.00451.235-0.043-0.0430.0000.0000.0000.000
205A263ASP-1-0.857-0.90053.865-5.454-5.4540.0000.0000.0000.000
206A264LEU0-0.0070.00447.292-0.024-0.0240.0000.0000.0000.000
207A265ALA00.0170.00549.804-0.064-0.0640.0000.0000.0000.000
208A266LYS10.9260.96151.0425.3105.3100.0000.0000.0000.000
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