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: 1VMYZ

Calculation Name: 1AF6-A-Xray549

Preferred Name:

Target Type:

Ligand Name: beta-d-fructofuranose | alpha-d-glucopyranose

Ligand 3-letter code: FRU | GLC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AF6

Chain ID: A

ChEMBL ID:

UniProt ID: P02943

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 420
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -7353451.602982
FMO2-HF: Nuclear repulsion 7186060.321769
FMO2-HF: Total energy -167391.281213
FMO2-MP2: Total energy -167878.283668


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:1:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-167.995-162.9599.878-5.96-8.954-0.069
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.791 / q_NPA : 0.894
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].
3A3PHE0-0.009-0.0093.7204.9786.512-0.006-0.356-1.172-0.001
4A4HIS10.8380.8784.82835.77635.836-0.001-0.009-0.0500.000
45A46LEU0-0.023-0.0062.652-4.403-3.7770.423-0.188-0.8610.000
46A47GLY00.0650.0493.7875.2665.5310.005-0.074-0.1960.000
47A48GLN0-0.018-0.0171.905-54.735-52.2839.454-5.288-6.618-0.068
48A49GLU-1-0.809-0.8943.899-21.127-21.0280.003-0.045-0.0570.000
5A5GLY00.0490.0188.1170.0150.0150.0000.0000.0000.000
6A6TYR0-0.017-0.00711.2750.6290.6290.0000.0000.0000.000
7A7ALA0-0.015-0.01514.966-0.247-0.2470.0000.0000.0000.000
8A8ARG10.7810.89416.95212.56712.5670.0000.0000.0000.000
9A9SER00.014-0.00720.652-0.058-0.0580.0000.0000.0000.000
10A10GLY0-0.004-0.01222.741-0.015-0.0150.0000.0000.0000.000
11A11ILE00.0100.02826.3360.0440.0440.0000.0000.0000.000
12A12GLY00.0330.00229.7080.0290.0290.0000.0000.0000.000
13A13TRP0-0.052-0.02032.955-0.067-0.0670.0000.0000.0000.000
14A14THR00.009-0.03636.540-0.105-0.1050.0000.0000.0000.000
15A15GLY0-0.020-0.00439.1810.0910.0910.0000.0000.0000.000
16A16SER0-0.085-0.06742.4870.1290.1290.0000.0000.0000.000
17A17GLY0-0.023-0.01442.5270.1520.1520.0000.0000.0000.000
18A18GLY0-0.019-0.01239.512-0.057-0.0570.0000.0000.0000.000
19A19GLU-1-0.893-0.94233.582-8.770-8.7700.0000.0000.0000.000
20A20GLN0-0.041-0.00730.5180.0970.0970.0000.0000.0000.000
21A21GLN00.0400.03033.865-0.094-0.0940.0000.0000.0000.000
22A22CYS0-0.038-0.02228.310-0.063-0.0630.0000.0000.0000.000
23A23PHE0-0.016-0.00634.3810.1630.1630.0000.0000.0000.000
24A24GLN0-0.045-0.04032.988-0.380-0.3800.0000.0000.0000.000
25A25THR0-0.028-0.02136.6210.1890.1890.0000.0000.0000.000
26A26THR0-0.035-0.05138.864-0.215-0.2150.0000.0000.0000.000
27A27GLY00.0340.01439.4270.1860.1860.0000.0000.0000.000
28A28ALA0-0.0250.00837.033-0.045-0.0450.0000.0000.0000.000
29A29GLN0-0.008-0.00133.196-0.266-0.2660.0000.0000.0000.000
30A30SER0-0.065-0.02831.165-0.359-0.3590.0000.0000.0000.000
31A31LYS10.9570.96828.68310.38510.3850.0000.0000.0000.000
32A32TYR00.0320.02531.166-0.270-0.2700.0000.0000.0000.000
33A33ARG10.8000.88823.39512.18712.1870.0000.0000.0000.000
34A34LEU0-0.019-0.00528.540-0.158-0.1580.0000.0000.0000.000
35A35GLY00.0280.00529.7890.3450.3450.0000.0000.0000.000
36A36ASN0-0.021-0.00430.4010.4160.4160.0000.0000.0000.000
37A37GLU-1-0.809-0.89425.087-11.931-11.9310.0000.0000.0000.000
38A39GLU-1-0.797-0.87824.121-11.056-11.0560.0000.0000.0000.000
39A40THR0-0.017-0.00120.303-0.382-0.3820.0000.0000.0000.000
40A41TYR0-0.071-0.06018.0710.0030.0030.0000.0000.0000.000
41A42ALA0-0.001-0.01515.012-0.346-0.3460.0000.0000.0000.000
42A43GLU-1-0.777-0.85813.455-16.695-16.6950.0000.0000.0000.000
43A44LEU0-0.004-0.0029.221-1.140-1.1400.0000.0000.0000.000
44A45LYS10.7750.8507.86825.46625.4660.0000.0000.0000.000
49A50VAL0-0.064-0.0356.638-3.496-3.4960.0000.0000.0000.000
50A51TRP0-0.049-0.0258.2921.2931.2930.0000.0000.0000.000
51A52LYS10.8770.92611.41524.70524.7050.0000.0000.0000.000
52A53GLU-1-0.914-0.94113.240-16.867-16.8670.0000.0000.0000.000
53A54GLY0-0.008-0.00716.7590.9300.9300.0000.0000.0000.000
54A55ASP-1-0.884-0.95316.202-16.525-16.5250.0000.0000.0000.000
55A56LYS10.8490.95217.29213.91813.9180.0000.0000.0000.000
56A57SER00.017-0.00212.197-1.203-1.2030.0000.0000.0000.000
57A58PHE0-0.0060.00612.1591.5111.5110.0000.0000.0000.000
58A59TYR0-0.072-0.0655.525-0.492-0.4920.0000.0000.0000.000
59A60PHE0-0.015-0.0075.7983.5093.5090.0000.0000.0000.000
60A61ASP-1-0.792-0.8956.659-33.150-33.1500.0000.0000.0000.000
61A62THR0-0.019-0.0246.5583.2673.2670.0000.0000.0000.000
62A63ASN0-0.067-0.0389.023-0.803-0.8030.0000.0000.0000.000
63A64VAL0-0.0090.00510.2611.4391.4390.0000.0000.0000.000
64A65ALA00.0130.01112.611-0.456-0.4560.0000.0000.0000.000
65A66TYR0-0.003-0.00713.0410.1320.1320.0000.0000.0000.000
66A67SER00.011-0.00217.982-0.012-0.0120.0000.0000.0000.000
67A68VAL00.0030.00921.2490.1650.1650.0000.0000.0000.000
68A69ALA00.0350.01023.790-0.001-0.0010.0000.0000.0000.000
69A70GLN00.0080.02125.053-0.188-0.1880.0000.0000.0000.000
70A71GLN0-0.019-0.00926.6470.3660.3660.0000.0000.0000.000
71A72ASN0-0.122-0.06528.1210.4060.4060.0000.0000.0000.000
72A73ASP-1-0.913-0.94724.439-11.931-11.9310.0000.0000.0000.000
73A74TRP0-0.022-0.01622.567-0.582-0.5820.0000.0000.0000.000
74A75GLU-1-0.788-0.89424.031-10.650-10.6500.0000.0000.0000.000
75A76ALA0-0.050-0.02222.877-0.516-0.5160.0000.0000.0000.000
76A77THR0-0.017-0.01920.3560.3590.3590.0000.0000.0000.000
77A78ASP-1-0.904-0.94221.271-12.065-12.0650.0000.0000.0000.000
78A79PRO0-0.067-0.02116.165-0.212-0.2120.0000.0000.0000.000
79A80ALA00.0410.01518.2180.1340.1340.0000.0000.0000.000
80A81PHE00.0070.00311.513-0.865-0.8650.0000.0000.0000.000
81A82ARG10.8970.95115.01015.71215.7120.0000.0000.0000.000
82A83GLU-1-0.797-0.89112.228-20.036-20.0360.0000.0000.0000.000
83A84ALA00.000-0.01511.073-1.056-1.0560.0000.0000.0000.000
84A85ASN0-0.056-0.00311.2081.4831.4830.0000.0000.0000.000
85A86VAL00.0240.01110.968-2.244-2.2440.0000.0000.0000.000
86A87GLN0-0.017-0.02012.5941.6481.6480.0000.0000.0000.000
87A88GLY00.0360.01713.456-1.564-1.5640.0000.0000.0000.000
88A89LYS10.8880.95012.30623.86123.8610.0000.0000.0000.000
89A90ASN00.0450.00917.3640.3260.3260.0000.0000.0000.000
90A91LEU0-0.027-0.00317.3720.4790.4790.0000.0000.0000.000
91A92ILE00.0150.00921.1660.4710.4710.0000.0000.0000.000
92A93GLU-1-0.931-0.96824.710-11.468-11.4680.0000.0000.0000.000
93A94TRP0-0.017-0.01426.8130.0270.0270.0000.0000.0000.000
94A95LEU0-0.034-0.00425.9320.3370.3370.0000.0000.0000.000
95A96PRO00.0410.03624.439-0.639-0.6390.0000.0000.0000.000
96A97GLY00.007-0.00321.6790.2950.2950.0000.0000.0000.000
97A98SER0-0.067-0.02521.369-0.461-0.4610.0000.0000.0000.000
98A99THR0-0.010-0.02916.597-1.146-1.1460.0000.0000.0000.000
99A100ILE0-0.0020.01218.9730.7610.7610.0000.0000.0000.000
100A101TRP0-0.005-0.01316.548-1.579-1.5790.0000.0000.0000.000
101A102ALA00.0190.01016.6531.0751.0750.0000.0000.0000.000
102A103GLY00.0240.01715.799-1.280-1.2800.0000.0000.0000.000
103A104LYS10.8420.90815.54616.17816.1780.0000.0000.0000.000
104A105ARG10.8340.88114.55815.92615.9260.0000.0000.0000.000
105A106PHE00.005-0.00815.3091.2831.2830.0000.0000.0000.000
106A107TYR0-0.054-0.02817.577-0.713-0.7130.0000.0000.0000.000
107A108GLN0-0.045-0.03319.7201.0951.0950.0000.0000.0000.000
108A109ARG10.9280.98617.99715.93715.9370.0000.0000.0000.000
109A110HIS10.7970.90422.70811.36611.3660.0000.0000.0000.000
110A111ASP-1-0.894-0.95623.152-12.596-12.5960.0000.0000.0000.000
111A112VAL00.0170.01926.0520.0260.0260.0000.0000.0000.000
112A113HIS00.1090.05423.2290.4820.4820.0000.0000.0000.000
113A114MET0-0.039-0.01825.972-0.024-0.0240.0000.0000.0000.000
114A115ILE0-0.003-0.00428.9270.2180.2180.0000.0000.0000.000
115A116ASP-1-0.813-0.91323.916-12.364-12.3640.0000.0000.0000.000
116A117PHE00.0080.00826.603-0.092-0.0920.0000.0000.0000.000
117A118TYR00.0220.00721.070-0.208-0.2080.0000.0000.0000.000
118A119TYR0-0.028-0.03326.7320.2740.2740.0000.0000.0000.000
119A120TRP0-0.043-0.01727.7110.2570.2570.0000.0000.0000.000
120A121ASP-1-0.811-0.89822.994-13.744-13.7440.0000.0000.0000.000
121A122ILE00.0050.01923.9570.3430.3430.0000.0000.0000.000
122A123SER0-0.054-0.06019.760-0.415-0.4150.0000.0000.0000.000
123A124GLY00.0280.01720.2340.4450.4450.0000.0000.0000.000
124A125PRO0-0.063-0.03319.508-0.815-0.8150.0000.0000.0000.000
125A126GLY00.0460.01619.9910.7220.7220.0000.0000.0000.000
126A127ALA0-0.039-0.01920.217-0.672-0.6720.0000.0000.0000.000
127A128GLY00.0250.01421.3420.6030.6030.0000.0000.0000.000
128A129LEU0-0.059-0.01121.877-0.567-0.5670.0000.0000.0000.000
129A130GLU-1-0.770-0.84618.895-15.661-15.6610.0000.0000.0000.000
130A131ASN00.007-0.02020.9720.0180.0180.0000.0000.0000.000
131A132ILE00.0210.01723.757-0.070-0.0700.0000.0000.0000.000
132A133ASP-1-0.846-0.91226.624-10.863-10.8630.0000.0000.0000.000
133A134VAL0-0.004-0.00328.5590.2110.2110.0000.0000.0000.000
134A135GLY0-0.0220.00331.7500.3930.3930.0000.0000.0000.000
135A136PHE0-0.068-0.04433.5780.0420.0420.0000.0000.0000.000
136A137GLY00.0740.04030.9410.1320.1320.0000.0000.0000.000
137A138LYS10.8150.90125.08312.10612.1060.0000.0000.0000.000
138A139LEU00.0180.01528.1920.1260.1260.0000.0000.0000.000
139A140SER0-0.030-0.02124.591-0.737-0.7370.0000.0000.0000.000
140A141LEU0-0.0030.00625.8860.4670.4670.0000.0000.0000.000
141A142ALA00.000-0.00723.791-0.600-0.6000.0000.0000.0000.000
142A143ALA00.0050.01024.8230.5700.5700.0000.0000.0000.000
143A144THR0-0.061-0.04022.613-0.455-0.4550.0000.0000.0000.000
144A145ARG10.7970.88624.28410.97510.9750.0000.0000.0000.000
145A146SER00.0210.00424.934-0.424-0.4240.0000.0000.0000.000
146A147SER0-0.047-0.06027.4350.0610.0610.0000.0000.0000.000
147A148GLU-1-0.745-0.81429.966-8.482-8.4820.0000.0000.0000.000
148A149ALA00.018-0.01332.1210.0820.0820.0000.0000.0000.000
149A150GLY00.0140.00633.2700.0910.0910.0000.0000.0000.000
150A151GLY00.0470.01636.683-0.124-0.1240.0000.0000.0000.000
151A152SER0-0.015-0.02538.6220.1390.1390.0000.0000.0000.000
152A153SER00.0010.02040.470-0.057-0.0570.0000.0000.0000.000
153A154SER00.004-0.01442.520-0.029-0.0290.0000.0000.0000.000
154A155PHE0-0.041-0.01443.9180.1020.1020.0000.0000.0000.000
155A156ALA0-0.034-0.01547.590-0.055-0.0550.0000.0000.0000.000
156A157SER0-0.004-0.02548.9200.1450.1450.0000.0000.0000.000
157A158ASN0-0.0020.00350.110-0.028-0.0280.0000.0000.0000.000
158A159ASN00.0000.00649.6640.0040.0040.0000.0000.0000.000
159A160ILE00.0460.01144.881-0.083-0.0830.0000.0000.0000.000
160A161TYR0-0.059-0.06645.234-0.223-0.2230.0000.0000.0000.000
161A162ASP-1-0.808-0.86944.966-6.385-6.3850.0000.0000.0000.000
162A163TYR0-0.129-0.07542.547-0.141-0.1410.0000.0000.0000.000
163A164THR00.0380.00940.179-0.194-0.1940.0000.0000.0000.000
164A165ASN0-0.084-0.04337.684-0.257-0.2570.0000.0000.0000.000
165A166GLU-1-0.878-0.91230.031-9.785-9.7850.0000.0000.0000.000
166A167THR0-0.093-0.03234.4310.1140.1140.0000.0000.0000.000
167A168ALA00.0300.01130.711-0.246-0.2460.0000.0000.0000.000
168A169ASN0-0.020-0.01430.5380.4320.4320.0000.0000.0000.000
169A170ASP-1-0.798-0.86029.492-10.336-10.3360.0000.0000.0000.000
170A171VAL00.0230.00728.0980.3610.3610.0000.0000.0000.000
171A172PHE0-0.038-0.01928.555-0.371-0.3710.0000.0000.0000.000
172A173ASP-1-0.754-0.82526.981-11.122-11.1220.0000.0000.0000.000
173A174VAL00.003-0.00628.851-0.190-0.1900.0000.0000.0000.000
174A175ARG10.8270.89225.10012.07212.0720.0000.0000.0000.000
175A176LEU0-0.009-0.01129.629-0.117-0.1170.0000.0000.0000.000
176A177ALA00.0640.03027.1920.2100.2100.0000.0000.0000.000
177A178GLN0-0.038-0.02924.7780.0170.0170.0000.0000.0000.000
178A179MET00.0670.05829.6950.1630.1630.0000.0000.0000.000
179A180GLU-1-0.916-0.96931.571-10.010-10.0100.0000.0000.0000.000
180A181ILE0-0.033-0.00935.0310.2660.2660.0000.0000.0000.000
181A182ASN0-0.030-0.01637.6800.2640.2640.0000.0000.0000.000
182A183PRO00.009-0.00537.428-0.247-0.2470.0000.0000.0000.000
183A184GLY00.0160.01034.2760.0610.0610.0000.0000.0000.000
184A185GLY00.0080.01634.135-0.220-0.2200.0000.0000.0000.000
185A186THR0-0.035-0.01730.437-0.016-0.0160.0000.0000.0000.000
186A187LEU0-0.013-0.01133.2370.1140.1140.0000.0000.0000.000
187A188GLU-1-0.873-0.95127.598-11.739-11.7390.0000.0000.0000.000
188A189LEU0-0.012-0.01031.6560.2820.2820.0000.0000.0000.000
189A190GLY00.010-0.00131.459-0.336-0.3360.0000.0000.0000.000
190A191VAL0-0.046-0.01832.1810.3290.3290.0000.0000.0000.000
191A192ASP0-0.030-0.04628.773-0.312-0.3120.0000.0000.0000.000
192A193TYR0-0.037-0.03532.5490.1900.1900.0000.0000.0000.000
193A194GLY00.021-0.01332.903-0.355-0.3550.0000.0000.0000.000
194A195ARG10.9240.95233.6568.4178.4170.0000.0000.0000.000
195A196ALA00.0360.03434.039-0.284-0.2840.0000.0000.0000.000
196A197ASN0-0.147-0.08732.9390.4060.4060.0000.0000.0000.000
197A198LEU0-0.0060.00735.317-0.099-0.0990.0000.0000.0000.000
198A199ARG10.9550.97735.1468.0428.0420.0000.0000.0000.000
199A200ASP-1-0.837-0.94038.171-6.927-6.9270.0000.0000.0000.000
200A201ASN0-0.083-0.04641.4340.1360.1360.0000.0000.0000.000
201A202TYR0-0.0380.00240.0220.0780.0780.0000.0000.0000.000
202A203ARG10.8840.94442.7556.4686.4680.0000.0000.0000.000
203A204LEU00.0200.01739.157-0.087-0.0870.0000.0000.0000.000
204A205VAL00.0350.01843.0990.1490.1490.0000.0000.0000.000
205A206ASP-1-0.896-0.96545.853-6.135-6.1350.0000.0000.0000.000
206A207GLY0-0.047-0.02348.3940.0010.0010.0000.0000.0000.000
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