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: 3ZJRL

Calculation Name: 3KB8-B-Xray547

Preferred Name:

Target Type:

Ligand Name: guanosine-5'-monophosphate | beta-d-fructofuranose | alpha-d-glucopyranose | phosphate ion | glycerol | magnesium ion

Ligand 3-letter code: 5GP | FRU | GLC | PO4 | GOL | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KB8

Chain ID: B

ChEMBL ID:

UniProt ID: B9ZW32

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2014071.558118
FMO2-HF: Nuclear repulsion 1939671.149071
FMO2-HF: Total energy -74400.409047
FMO2-MP2: Total energy -74617.745676


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:-8:GLU)


Summations of interaction energy for fragment #1(A:-8:GLU)
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.
-4.356-2.798-0.009-0.709-0.8410.001
Interaction energy analysis for fragmet #1(A:-8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.111 / q_NPA : -0.060
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].
3A-6LEU0-0.0040.0033.835-7.452-5.894-0.009-0.709-0.8410.001
4A-5TYR00.0270.0096.2502.2302.2300.0000.0000.0000.000
5A-4PHE0-0.008-0.0079.185-0.173-0.1730.0000.0000.0000.000
6A-3GLN00.0270.03012.9110.3380.3380.0000.0000.0000.000
7A-2SER00.002-0.00916.0140.3410.3410.0000.0000.0000.000
8A-1ASN0-0.014-0.01318.042-0.112-0.1120.0000.0000.0000.000
9A0ALA00.0030.01519.6820.1950.1950.0000.0000.0000.000
10A1MET0-0.007-0.01121.296-0.124-0.1240.0000.0000.0000.000
11A2MET00.0510.02821.8260.1040.1040.0000.0000.0000.000
12A3ASN00.0070.00023.9470.0390.0390.0000.0000.0000.000
13A4GLN0-0.009-0.00224.475-0.003-0.0030.0000.0000.0000.000
14A5ASP-1-0.769-0.85921.463-0.554-0.5540.0000.0000.0000.000
15A6ILE0-0.066-0.02424.6220.1070.1070.0000.0000.0000.000
16A7GLU-1-0.910-0.95427.886-0.173-0.1730.0000.0000.0000.000
17A8LYS10.9150.95030.707-0.016-0.0160.0000.0000.0000.000
18A9VAL00.0090.01132.1700.0220.0220.0000.0000.0000.000
19A10LEU0-0.096-0.05433.8590.0030.0030.0000.0000.0000.000
20A11ILE00.0220.01535.0640.0090.0090.0000.0000.0000.000
21A12SER00.018-0.00235.349-0.010-0.0100.0000.0000.0000.000
22A13GLU-1-0.881-0.95035.143-0.261-0.2610.0000.0000.0000.000
23A14GLU-1-0.971-0.98436.814-0.136-0.1360.0000.0000.0000.000
24A15GLN00.0310.01339.8260.0240.0240.0000.0000.0000.000
25A16ILE00.0010.00634.5920.0250.0250.0000.0000.0000.000
26A17GLN0-0.045-0.04636.6880.0270.0270.0000.0000.0000.000
27A18GLU-1-0.976-0.97040.667-0.002-0.0020.0000.0000.0000.000
28A19LYS10.8970.94341.775-0.062-0.0620.0000.0000.0000.000
29A20VAL0-0.013-0.00938.4200.0210.0210.0000.0000.0000.000
30A21LEU0-0.030-0.01641.7900.0070.0070.0000.0000.0000.000
31A22GLU-1-0.858-0.90044.9310.0670.0670.0000.0000.0000.000
32A23LEU0-0.005-0.01741.5600.0120.0120.0000.0000.0000.000
33A24GLY00.0330.02344.5270.0130.0130.0000.0000.0000.000
34A25ALA0-0.002-0.00645.1360.0040.0040.0000.0000.0000.000
35A26ILE0-0.030-0.01547.9290.0060.0060.0000.0000.0000.000
36A27ILE0-0.007-0.00943.1870.0110.0110.0000.0000.0000.000
37A28ALA0-0.001-0.00247.3840.0080.0080.0000.0000.0000.000
38A29GLU-1-0.862-0.91849.3840.0650.0650.0000.0000.0000.000
39A30ASP-1-0.848-0.90949.5150.1440.1440.0000.0000.0000.000
40A31TYR0-0.059-0.03245.7650.0160.0160.0000.0000.0000.000
41A32LYS10.8500.93250.293-0.077-0.0770.0000.0000.0000.000
42A33ASN0-0.078-0.03853.309-0.004-0.0040.0000.0000.0000.000
43A34THR0-0.067-0.05649.1150.0080.0080.0000.0000.0000.000
44A35VAL00.0440.04046.182-0.011-0.0110.0000.0000.0000.000
45A36PRO0-0.0150.00744.4330.0160.0160.0000.0000.0000.000
46A37LEU0-0.021-0.00339.345-0.011-0.0110.0000.0000.0000.000
47A38ALA00.0140.00239.2590.0190.0190.0000.0000.0000.000
48A39ILE0-0.012-0.01134.5610.0010.0010.0000.0000.0000.000
49A40GLY00.0560.01932.9650.0030.0030.0000.0000.0000.000
50A41VAL0-0.026-0.00928.8040.0360.0360.0000.0000.0000.000
51A42LEU0-0.031-0.01325.537-0.025-0.0250.0000.0000.0000.000
52A43LYS10.8040.86918.630-0.916-0.9160.0000.0000.0000.000
53A44GLY00.0390.02125.111-0.085-0.0850.0000.0000.0000.000
54A45ALA00.0430.03226.996-0.079-0.0790.0000.0000.0000.000
55A46MET0-0.045-0.00727.792-0.053-0.0530.0000.0000.0000.000
56A47PRO0-0.011-0.00728.803-0.040-0.0400.0000.0000.0000.000
57A48PHE00.0630.03031.586-0.032-0.0320.0000.0000.0000.000
58A49MET00.0030.01933.663-0.005-0.0050.0000.0000.0000.000
59A50ALA00.0040.00333.257-0.018-0.0180.0000.0000.0000.000
60A51ASP-1-0.791-0.85635.286-0.125-0.1250.0000.0000.0000.000
61A52LEU00.0300.00937.585-0.009-0.0090.0000.0000.0000.000
62A53LEU0-0.0200.00537.902-0.003-0.0030.0000.0000.0000.000
63A54LYS10.8330.90936.2990.1220.1220.0000.0000.0000.000
64A55ARG10.8410.92541.0450.0560.0560.0000.0000.0000.000
65A56THR0-0.005-0.01143.0460.0110.0110.0000.0000.0000.000
66A57ASP-1-0.966-0.96745.182-0.011-0.0110.0000.0000.0000.000
67A58THR0-0.011-0.01747.2850.0020.0020.0000.0000.0000.000
68A59TYR0-0.046-0.01347.001-0.005-0.0050.0000.0000.0000.000
69A60LEU00.0270.00041.7700.0170.0170.0000.0000.0000.000
70A61GLU-1-0.850-0.90441.3480.1690.1690.0000.0000.0000.000
71A62MET0-0.040-0.02236.5550.0060.0060.0000.0000.0000.000
72A63ASP-1-0.759-0.87634.6280.3680.3680.0000.0000.0000.000
73A64PHE0-0.006-0.02230.291-0.008-0.0080.0000.0000.0000.000
74A65MET00.0020.02330.6230.0170.0170.0000.0000.0000.000
75A66ALA00.0060.01025.0240.0100.0100.0000.0000.0000.000
76A67VAL00.0250.01226.0250.0110.0110.0000.0000.0000.000
77A68SER0-0.014-0.01122.7700.1310.1310.0000.0000.0000.000
78A69SER00.0400.01723.544-0.100-0.1000.0000.0000.0000.000
79A70TYR00.0370.01024.2170.1340.1340.0000.0000.0000.000
80A71GLY0-0.047-0.01325.2490.0530.0530.0000.0000.0000.000
81A72HIS0-0.006-0.01225.805-0.129-0.1290.0000.0000.0000.000
82A73SER00.024-0.02429.443-0.074-0.0740.0000.0000.0000.000
83A74THR0-0.001-0.02427.537-0.013-0.0130.0000.0000.0000.000
84A75VAL0-0.028-0.01127.729-0.056-0.0560.0000.0000.0000.000
85A76SER0-0.058-0.02930.590-0.063-0.0630.0000.0000.0000.000
86A77THR0-0.007-0.00933.950-0.070-0.0700.0000.0000.0000.000
87A78GLY00.0080.02432.446-0.041-0.0410.0000.0000.0000.000
88A79GLU-1-0.852-0.89032.1650.9490.9490.0000.0000.0000.000
89A80VAL0-0.024-0.00228.1160.0870.0870.0000.0000.0000.000
90A81LYS10.9440.99623.359-1.650-1.6500.0000.0000.0000.000
91A82ILE00.018-0.00127.2780.0430.0430.0000.0000.0000.000
92A83LEU0-0.096-0.05822.4930.0820.0820.0000.0000.0000.000
93A84LYS10.7720.88626.541-0.462-0.4620.0000.0000.0000.000
94A85ASP-1-0.763-0.85428.9050.5660.5660.0000.0000.0000.000
95A86LEU0-0.009-0.00932.597-0.019-0.0190.0000.0000.0000.000
96A87ASP-1-0.892-0.93733.6910.4090.4090.0000.0000.0000.000
97A88THR0-0.035-0.01636.460-0.026-0.0260.0000.0000.0000.000
98A89SER0-0.038-0.01639.8130.0260.0260.0000.0000.0000.000
99A90VAL00.022-0.00740.201-0.013-0.0130.0000.0000.0000.000
100A91GLU-1-0.941-0.96643.1520.2750.2750.0000.0000.0000.000
101A92GLY0-0.027-0.01146.759-0.016-0.0160.0000.0000.0000.000
102A93ARG10.7780.87743.689-0.232-0.2320.0000.0000.0000.000
103A94ASP-1-0.772-0.82846.5630.2150.2150.0000.0000.0000.000
104A95ILE00.000-0.00940.630-0.006-0.0060.0000.0000.0000.000
105A96LEU0-0.0010.00640.993-0.003-0.0030.0000.0000.0000.000
106A97ILE0-0.007-0.00535.8410.0040.0040.0000.0000.0000.000
107A98VAL0-0.011-0.00635.243-0.022-0.0220.0000.0000.0000.000
108A99GLU-1-0.830-0.94031.9280.5420.5420.0000.0000.0000.000
109A100ASP-1-0.844-0.93328.6890.4350.4350.0000.0000.0000.000
110A101ILE0-0.057-0.04430.242-0.045-0.0450.0000.0000.0000.000
111A102ILE0-0.0070.01732.5200.0550.0550.0000.0000.0000.000
112A103ASP-1-0.816-0.91131.7110.5630.5630.0000.0000.0000.000
113A104SER00.0420.01132.254-0.038-0.0380.0000.0000.0000.000
114A105GLY00.0580.02134.570-0.021-0.0210.0000.0000.0000.000
115A106LEU0-0.012-0.00232.910-0.010-0.0100.0000.0000.0000.000
116A107THR00.028-0.01730.011-0.001-0.0010.0000.0000.0000.000
117A108LEU00.0010.01633.044-0.010-0.0100.0000.0000.0000.000
118A109SER00.0060.00735.260-0.037-0.0370.0000.0000.0000.000
119A110TYR00.0230.01133.026-0.019-0.0190.0000.0000.0000.000
120A111LEU0-0.006-0.00932.118-0.009-0.0090.0000.0000.0000.000
121A112VAL00.0150.00736.580-0.029-0.0290.0000.0000.0000.000
122A113ASP-1-0.798-0.90140.0930.4090.4090.0000.0000.0000.000
123A114LEU0-0.028-0.00435.850-0.014-0.0140.0000.0000.0000.000
124A115PHE00.019-0.01135.949-0.014-0.0140.0000.0000.0000.000
125A116LYS10.8840.94241.316-0.396-0.3960.0000.0000.0000.000
126A117TYR0-0.042-0.01141.632-0.020-0.0200.0000.0000.0000.000
127A118ARG10.7540.84036.251-0.521-0.5210.0000.0000.0000.000
128A119LYS10.9450.96443.496-0.359-0.3590.0000.0000.0000.000
129A120ALA00.0490.03943.930-0.019-0.0190.0000.0000.0000.000
130A121LYS10.7830.89646.014-0.195-0.1950.0000.0000.0000.000
131A122SER0-0.068-0.06847.551-0.008-0.0080.0000.0000.0000.000
132A123VAL0-0.010-0.01141.7280.0090.0090.0000.0000.0000.000
133A124LYS10.8920.98543.778-0.184-0.1840.0000.0000.0000.000
134A125ILE0-0.028-0.01738.3850.0180.0180.0000.0000.0000.000
135A126VAL00.0020.00739.102-0.021-0.0210.0000.0000.0000.000
136A127THR0-0.018-0.02136.1810.0210.0210.0000.0000.0000.000
137A128LEU00.0160.02733.713-0.031-0.0310.0000.0000.0000.000
138A129LEU0-0.004-0.01032.733-0.023-0.0230.0000.0000.0000.000
139A130ASP-1-0.796-0.88036.3500.3800.3800.0000.0000.0000.000
140A131LYS10.8950.96230.994-0.530-0.5300.0000.0000.0000.000
141A132PRO00.0420.01237.2090.0350.0350.0000.0000.0000.000
142A133THR0-0.024-0.02338.5020.0170.0170.0000.0000.0000.000
143A134GLY00.0060.00835.6380.0170.0170.0000.0000.0000.000
144A135ARG10.6980.84436.044-0.360-0.3600.0000.0000.0000.000
145A136LYS10.8640.91734.929-0.600-0.6000.0000.0000.0000.000
146A137VAL00.0130.01837.9520.0130.0130.0000.0000.0000.000
147A138ASP-1-0.913-0.95040.3790.3900.3900.0000.0000.0000.000
148A139LEU0-0.030-0.00338.053-0.006-0.0060.0000.0000.0000.000
149A140LYS10.9540.97441.471-0.237-0.2370.0000.0000.0000.000
150A141ALA00.0410.02040.5870.0090.0090.0000.0000.0000.000
151A142ASP-1-0.900-0.95042.6520.2490.2490.0000.0000.0000.000
152A143TYR0-0.060-0.07642.885-0.016-0.0160.0000.0000.0000.000
153A144VAL00.006-0.00540.2650.0230.0230.0000.0000.0000.000
154A145GLY0-0.0040.00740.047-0.021-0.0210.0000.0000.0000.000
155A146PHE0-0.018-0.02438.679-0.020-0.0200.0000.0000.0000.000
156A147THR0-0.019-0.00739.2540.0220.0220.0000.0000.0000.000
157A148VAL0-0.021-0.00734.792-0.027-0.0270.0000.0000.0000.000
158A149PRO00.0230.00236.7630.0270.0270.0000.0000.0000.000
159A150HIS0-0.071-0.03033.5230.0480.0480.0000.0000.0000.000
160A151GLU-1-0.926-0.96732.5170.2210.2210.0000.0000.0000.000
161A152PHE0-0.049-0.02923.8370.0290.0290.0000.0000.0000.000
162A153VAL0-0.032-0.01328.901-0.057-0.0570.0000.0000.0000.000
163A154VAL0-0.012-0.01023.8780.0600.0600.0000.0000.0000.000
164A155GLY00.0130.00526.354-0.061-0.0610.0000.0000.0000.000
165A156TYR0-0.057-0.06327.8080.0850.0850.0000.0000.0000.000
166A157GLY00.0350.02426.9730.0330.0330.0000.0000.0000.000
167A158LEU0-0.0100.00325.7190.0940.0940.0000.0000.0000.000
168A159ASP-1-0.861-0.93120.4220.7740.7740.0000.0000.0000.000
169A160TYR00.011-0.02118.4410.0530.0530.0000.0000.0000.000
170A161LYS10.8330.91515.462-2.029-2.0290.0000.0000.0000.000
171A162GLU-1-0.800-0.89516.0031.0431.0430.0000.0000.0000.000
172A163GLN0-0.0280.00716.067-0.456-0.4560.0000.0000.0000.000
173A164TYR0-0.028-0.07119.1350.1670.1670.0000.0000.0000.000
174A165ARG10.8010.89620.500-0.660-0.6600.0000.0000.0000.000
175A166ASN00.006-0.00222.3440.0750.0750.0000.0000.0000.000
176A167LEU0-0.0090.00825.468-0.080-0.0800.0000.0000.0000.000
177A168PRO00.0290.01627.8390.0650.0650.0000.0000.0000.000
178A169TYR0-0.006-0.00829.051-0.003-0.0030.0000.0000.0000.000
179A170VAL00.0440.02830.6500.0080.0080.0000.0000.0000.000
180A171GLY00.013-0.01030.167-0.036-0.0360.0000.0000.0000.000
181A172VAL00.0190.02729.4280.0500.0500.0000.0000.0000.000
182A173LEU00.0220.00822.722-0.064-0.0640.0000.0000.0000.000
183A174LYS10.8660.92525.6990.3980.3980.0000.0000.0000.000
184A175PRO00.016-0.00725.1140.0260.0260.0000.0000.0000.000
185A176SER0-0.041-0.01723.7410.0680.0680.0000.0000.0000.000
186A177VAL0-0.0230.00720.323-0.050-0.0500.0000.0000.0000.000
187A178TYR0-0.026-0.00419.5790.0600.0600.0000.0000.0000.000
188A179SER0-0.051-0.01916.7760.1150.1150.0000.0000.0000.000
189A180ASN-1-0.820-0.88216.5222.1812.1810.0000.0000.0000.000