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: ML97Z

Calculation Name: 2DD4-F-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-d-fructofuranose | l(+)-tartaric acid

Ligand 3-letter code: FRU | TLA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DD4

Chain ID: F

ChEMBL ID:

UniProt ID: O66187

Base Structure: X-ray

Registration Date: 2025-10-05

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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2487275.543948
FMO2-HF: Nuclear repulsion 2402061.148988
FMO2-HF: Total energy -85214.39496
FMO2-MP2: Total energy -85462.801811


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:24:VAL)


Summations of interaction energy for fragment #1(A:24: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.
-17.575-12.0358.813-6.02-8.334-0.057
Interaction energy analysis for fragmet #1(A:24:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.904
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].
3A26ASP-1-0.809-0.9123.544-42.244-40.2190.005-0.939-1.091-0.002
5A28GLU-1-0.806-0.8682.169-76.873-74.7857.050-4.369-4.769-0.048
6A29ILE00.0040.0042.4320.9881.3941.577-0.364-1.619-0.004
7A30LEU00.0070.0045.0144.2814.335-0.001-0.004-0.0490.000
213A236ASN0-0.017-0.0154.6971.9021.929-0.001-0.001-0.0250.000
214A237ARG10.8350.8852.88650.13551.0750.183-0.343-0.781-0.003
4A27PHE0-0.020-0.0175.9693.0493.0490.0000.0000.0000.000
8A31GLU-1-0.877-0.9317.640-23.245-23.2450.0000.0000.0000.000
9A32MET00.0240.0225.6342.5842.5840.0000.0000.0000.000
10A33ALA00.0420.0288.5122.4352.4350.0000.0000.0000.000
11A34VAL0-0.027-0.02310.3082.0372.0370.0000.0000.0000.000
12A35ARG10.8140.8939.21625.36025.3600.0000.0000.0000.000
13A36GLU-1-0.920-0.95810.963-22.082-22.0820.0000.0000.0000.000
14A37LEU00.0270.01013.7571.3881.3880.0000.0000.0000.000
15A38ALA0-0.032-0.01816.1851.1161.1160.0000.0000.0000.000
16A39ILE0-0.029-0.00615.6170.8890.8890.0000.0000.0000.000
17A40GLU-1-0.959-0.98215.877-15.710-15.7100.0000.0000.0000.000
18A41LYS10.8480.92119.61014.15014.1500.0000.0000.0000.000
19A42GLY00.0070.01421.8640.5270.5270.0000.0000.0000.000
20A43LEU0-0.068-0.02920.8140.4120.4120.0000.0000.0000.000
21A44PHE0-0.034-0.02016.5460.1090.1090.0000.0000.0000.000
22A45SER00.006-0.02220.836-0.475-0.4750.0000.0000.0000.000
23A46ALA00.015-0.02017.738-0.401-0.4010.0000.0000.0000.000
24A47GLU-1-0.814-0.87418.781-13.041-13.0410.0000.0000.0000.000
25A48ASP-1-0.791-0.86321.668-12.159-12.1590.0000.0000.0000.000
26A49HIS0-0.015-0.01413.4950.0600.0600.0000.0000.0000.000
27A50ARG10.8100.88817.95113.57913.5790.0000.0000.0000.000
28A51VAL00.0840.04119.4220.0410.0410.0000.0000.0000.000
29A52TRP00.007-0.00620.6450.4790.4790.0000.0000.0000.000
30A53LYS10.9290.96113.12719.33919.3390.0000.0000.0000.000
31A54ASP-1-0.889-0.94319.407-13.737-13.7370.0000.0000.0000.000
32A55TYR00.0260.00722.0370.5020.5020.0000.0000.0000.000
33A56VAL0-0.046-0.02920.2930.2590.2590.0000.0000.0000.000
34A57HIS0-0.025-0.00720.491-0.243-0.2430.0000.0000.0000.000
35A58THR0-0.065-0.03822.2910.4300.4300.0000.0000.0000.000
36A59LEU0-0.071-0.00825.2180.4470.4470.0000.0000.0000.000
37A60GLY00.019-0.01325.914-0.429-0.4290.0000.0000.0000.000
38A61PRO0-0.051-0.04128.3820.2820.2820.0000.0000.0000.000
39A62LEU00.0520.05031.5800.2560.2560.0000.0000.0000.000
40A63PRO00.0470.02232.8380.2890.2890.0000.0000.0000.000
41A64ALA00.0450.01934.6400.2710.2710.0000.0000.0000.000
42A65ALA0-0.007-0.00335.8090.2450.2450.0000.0000.0000.000
43A66ARG10.9350.94737.5837.9787.9780.0000.0000.0000.000
44A67LEU00.0030.02039.2830.2090.2090.0000.0000.0000.000
45A68VAL0-0.010-0.01939.9080.2120.2120.0000.0000.0000.000
46A69ALA0-0.0100.00441.8860.1960.1960.0000.0000.0000.000
47A70LYS10.8630.91743.0927.1997.1990.0000.0000.0000.000
48A71ALA0-0.0030.00245.0940.1870.1870.0000.0000.0000.000
49A72TRP0-0.072-0.06543.2160.1350.1350.0000.0000.0000.000
50A73LEU0-0.031-0.01347.4850.1340.1340.0000.0000.0000.000
51A74ASP-1-0.820-0.89649.421-6.040-6.0400.0000.0000.0000.000
52A75PRO00.006-0.02050.421-0.099-0.0990.0000.0000.0000.000
53A76GLU-1-0.967-0.96452.470-5.818-5.8180.0000.0000.0000.000
54A77TYR0-0.001-0.02942.624-0.118-0.1180.0000.0000.0000.000
55A78LYS10.9390.97547.6576.3476.3470.0000.0000.0000.000
56A79LYS10.9130.95148.3935.6535.6530.0000.0000.0000.000
57A80LEU00.0240.02346.665-0.046-0.0460.0000.0000.0000.000
58A81CYS0-0.056-0.03944.321-0.161-0.1610.0000.0000.0000.000
59A82ILE0-0.083-0.04044.323-0.139-0.1390.0000.0000.0000.000
60A83GLU-1-0.988-0.97746.270-6.413-6.4130.0000.0000.0000.000
61A84ASP-1-0.830-0.92043.852-7.204-7.2040.0000.0000.0000.000
62A85GLY00.0280.00041.282-0.019-0.0190.0000.0000.0000.000
63A86VAL0-0.072-0.03738.795-0.230-0.2300.0000.0000.0000.000
64A87GLU-1-0.823-0.90140.744-7.024-7.0240.0000.0000.0000.000
65A88ALA00.0280.01542.969-0.028-0.0280.0000.0000.0000.000
66A89SER0-0.012-0.01637.402-0.101-0.1010.0000.0000.0000.000
67A90LYS10.8190.89939.0646.9856.9850.0000.0000.0000.000
68A91ALA0-0.0080.00840.902-0.027-0.0270.0000.0000.0000.000
69A92VAL0-0.083-0.04037.8040.0500.0500.0000.0000.0000.000
70A93GLY00.0010.00337.281-0.216-0.2160.0000.0000.0000.000
71A94VAL0-0.0220.00433.527-0.171-0.1710.0000.0000.0000.000
72A95ASN00.0730.04635.9010.0850.0850.0000.0000.0000.000
73A96TRP0-0.011-0.02232.683-0.306-0.3060.0000.0000.0000.000
74A97VAL00.0270.00834.209-0.230-0.2300.0000.0000.0000.000
75A98THR0-0.034-0.03934.739-0.169-0.1690.0000.0000.0000.000
76A99SER00.0330.02632.6950.0170.0170.0000.0000.0000.000
77A100PRO0-0.067-0.02029.254-0.291-0.2910.0000.0000.0000.000
78A101PRO00.0160.00226.0200.2400.2400.0000.0000.0000.000
79A102THR0-0.025-0.02328.2010.0240.0240.0000.0000.0000.000
80A103GLN0-0.053-0.01530.4810.4240.4240.0000.0000.0000.000
81A104PHE00.0320.00629.9940.2300.2300.0000.0000.0000.000
82A105GLY00.0470.02032.5090.0560.0560.0000.0000.0000.000
83A106THR0-0.028-0.02926.908-0.111-0.1110.0000.0000.0000.000
84A107PRO00.0280.00525.8040.2390.2390.0000.0000.0000.000
85A108SER0-0.026-0.00425.275-0.068-0.0680.0000.0000.0000.000
86A109ASP-1-0.840-0.87827.319-11.203-11.2030.0000.0000.0000.000
87A110TYR00.0120.00329.8880.4150.4150.0000.0000.0000.000
88A111CYS00.0460.04132.750-0.065-0.0650.0000.0000.0000.000
89A112ASN00.0010.00735.8560.2270.2270.0000.0000.0000.000
90A113LEU00.0280.03035.409-0.146-0.1460.0000.0000.0000.000
91A114ARG10.9750.98437.8797.4687.4680.0000.0000.0000.000
92A115VAL00.0310.01439.456-0.220-0.2200.0000.0000.0000.000
93A116LEU0-0.052-0.02639.4110.1910.1910.0000.0000.0000.000
94A117ALA00.0230.01442.626-0.073-0.0730.0000.0000.0000.000
95A118ASP-1-0.746-0.84843.323-7.297-7.2970.0000.0000.0000.000
96A119SER0-0.027-0.02946.3370.1590.1590.0000.0000.0000.000
97A120PRO00.0420.00349.429-0.092-0.0920.0000.0000.0000.000
98A121THR00.0010.01451.5350.0430.0430.0000.0000.0000.000
99A122LEU0-0.078-0.02446.532-0.008-0.0080.0000.0000.0000.000
100A123LYS10.8210.91540.4127.6937.6930.0000.0000.0000.000
101A124HIS0-0.012-0.02440.977-0.019-0.0190.0000.0000.0000.000
102A125VAL00.0020.00836.070-0.092-0.0920.0000.0000.0000.000
103A126VAL00.0180.01933.6440.0830.0830.0000.0000.0000.000
104A127VAL0-0.0140.00331.273-0.307-0.3070.0000.0000.0000.000
105A128CYS0-0.0230.02329.4080.0610.0610.0000.0000.0000.000
106A129THR0-0.027-0.05530.089-0.393-0.3930.0000.0000.0000.000
107A130LEU00.0140.01430.193-0.351-0.3510.0000.0000.0000.000
108A131CYS0-0.011-0.01625.564-0.338-0.3380.0000.0000.0000.000
109A132SER0-0.029-0.02823.974-0.225-0.2250.0000.0000.0000.000
110A133CYS00.002-0.00126.431-0.181-0.1810.0000.0000.0000.000
111A134TYR00.0730.02627.2010.2190.2190.0000.0000.0000.000
112A135PRO00.0240.01629.266-0.116-0.1160.0000.0000.0000.000
113A136ARG10.8350.89122.82412.50412.5040.0000.0000.0000.000
114A137PRO00.0130.00728.375-0.088-0.0880.0000.0000.0000.000
115A138ILE0-0.0040.01230.4770.1140.1140.0000.0000.0000.000
116A139LEU0-0.023-0.00730.2230.1460.1460.0000.0000.0000.000
117A140GLY00.0510.03826.231-0.161-0.1610.0000.0000.0000.000
118A141GLN00.0440.00820.5040.3950.3950.0000.0000.0000.000
119A142SER00.0020.01223.7580.0720.0720.0000.0000.0000.000
120A143PRO0-0.043-0.02322.970-0.589-0.5890.0000.0000.0000.000
121A144GLU-1-0.804-0.89418.617-15.905-15.9050.0000.0000.0000.000
122A145TRP00.007-0.01222.1510.0270.0270.0000.0000.0000.000
123A146TYR0-0.040-0.01825.4570.2690.2690.0000.0000.0000.000
124A147ARG10.9010.93818.76015.27815.2780.0000.0000.0000.000
125A148SER0-0.031-0.01023.8820.0670.0670.0000.0000.0000.000
126A149PRO00.037-0.00723.8320.4620.4620.0000.0000.0000.000
127A150ASN0-0.0170.00027.0400.6170.6170.0000.0000.0000.000
128A151TYR00.0490.00428.5510.3840.3840.0000.0000.0000.000
129A152ARG10.8480.92624.89812.11312.1130.0000.0000.0000.000
130A153ARG10.9150.96028.56710.99110.9910.0000.0000.0000.000
131A154ARG10.7650.85432.3869.6179.6170.0000.0000.0000.000
132A155LEU00.0400.02434.2720.2950.2950.0000.0000.0000.000
133A156VAL00.014-0.00936.0780.2290.2290.0000.0000.0000.000
134A157ARG10.9210.97538.4057.9247.9240.0000.0000.0000.000
135A158TRP0-0.021-0.00336.8170.1030.1030.0000.0000.0000.000
136A159PRO00.0610.03838.883-0.129-0.1290.0000.0000.0000.000
137A160ARG10.8480.91139.9266.7126.7120.0000.0000.0000.000
138A161GLN00.0620.02539.585-0.058-0.0580.0000.0000.0000.000
139A162VAL00.0130.00734.165-0.126-0.1260.0000.0000.0000.000
140A163LEU0-0.014-0.00636.201-0.191-0.1910.0000.0000.0000.000
141A164ALA00.0380.03138.327-0.053-0.0530.0000.0000.0000.000
142A165GLU-1-0.840-0.87934.257-9.146-9.1460.0000.0000.0000.000
143A166PHE0-0.074-0.04330.248-0.338-0.3380.0000.0000.0000.000
144A167GLY0-0.0160.00835.275-0.034-0.0340.0000.0000.0000.000
145A168LEU0-0.067-0.02838.5180.1900.1900.0000.0000.0000.000
146A169GLN0-0.001-0.01040.650-0.057-0.0570.0000.0000.0000.000
147A170LEU0-0.001-0.01043.5570.0480.0480.0000.0000.0000.000
148A171PRO00.0630.03146.753-0.038-0.0380.0000.0000.0000.000
149A172SER0-0.062-0.03049.620-0.085-0.0850.0000.0000.0000.000
150A173GLU-1-0.811-0.90751.130-6.037-6.0370.0000.0000.0000.000
151A174VAL0-0.0400.00048.0070.0180.0180.0000.0000.0000.000
152A175GLN00.0550.02647.596-0.206-0.2060.0000.0000.0000.000
153A176ILE00.0030.00042.311-0.088-0.0880.0000.0000.0000.000
154A177ARG10.8740.93243.0956.8306.8300.0000.0000.0000.000
155A178VAL00.003-0.00337.716-0.140-0.1400.0000.0000.0000.000
156A179ALA0-0.0060.00038.2920.1580.1580.0000.0000.0000.000
157A180ASP-1-0.769-0.86234.458-9.350-9.3500.0000.0000.0000.000
158A181SER0-0.018-0.01332.4210.2010.2010.0000.0000.0000.000
159A182ASN00.008-0.00832.673-0.296-0.2960.0000.0000.0000.000
160A183GLN00.0440.02934.353-0.072-0.0720.0000.0000.0000.000
161A184LYS10.9430.97933.5478.5258.5250.0000.0000.0000.000
162A185THR0-0.0150.00434.840-0.061-0.0610.0000.0000.0000.000
163A186ARG10.7590.86330.1029.4849.4840.0000.0000.0000.000
164A187TYR00.0230.00334.6990.3100.3100.0000.0000.0000.000
165A188ILE00.0230.01034.564-0.325-0.3250.0000.0000.0000.000
166A189VAL0-0.049-0.02136.9350.2320.2320.0000.0000.0000.000
167A190MET00.0040.00739.481-0.027-0.0270.0000.0000.0000.000
168A191PRO0-0.0010.00340.4450.1760.1760.0000.0000.0000.000
169A192VAL00.0110.00243.2420.0880.0880.0000.0000.0000.000
170A193ARG10.8720.93745.6686.2466.2460.0000.0000.0000.000
171A194PRO0-0.041-0.00444.6540.1220.1220.0000.0000.0000.000
172A195GLU-1-0.874-0.94247.738-5.965-5.9650.0000.0000.0000.000
173A196GLY00.0190.00549.300-0.119-0.1190.0000.0000.0000.000
174A197THR0-0.031-0.02446.599-0.068-0.0680.0000.0000.0000.000
175A198ASP-1-0.885-0.93349.540-5.935-5.9350.0000.0000.0000.000
176A199GLY0-0.012-0.01852.528-0.011-0.0110.0000.0000.0000.000
177A200TRP0-0.077-0.02243.775-0.121-0.1210.0000.0000.0000.000
178A201THR00.024-0.01346.350-0.018-0.0180.0000.0000.0000.000
179A202GLU-1-0.739-0.86143.154-7.189-7.1890.0000.0000.0000.000
180A203ASP-1-0.876-0.94640.856-7.615-7.6150.0000.0000.0000.000
181A204GLN00.0520.04941.005-0.086-0.0860.0000.0000.0000.000
182A205LEU0-0.052-0.02042.605-0.080-0.0800.0000.0000.0000.000
183A206ALA0-0.022-0.01638.785-0.107-0.1070.0000.0000.0000.000
184A207GLU-1-0.950-0.97137.600-8.186-8.1860.0000.0000.0000.000
185A208ILE0-0.010-0.00237.465-0.187-0.1870.0000.0000.0000.000
186A209VAL0-0.058-0.01837.733-0.038-0.0380.0000.0000.0000.000
187A210THR00.0440.02833.526-0.229-0.2290.0000.0000.0000.000
188A211ARG10.8970.92625.70111.24211.2420.0000.0000.0000.000
189A212ASP-1-0.719-0.86430.512-10.269-10.2690.0000.0000.0000.000
190A213CYS0-0.054-0.00733.1260.1880.1880.0000.0000.0000.000
191A214LEU00.0170.02034.2550.1330.1330.0000.0000.0000.000
192A215ILE0-0.036-0.01530.859-0.004-0.0040.0000.0000.0000.000
193A216GLY00.0220.01534.3490.1020.1020.0000.0000.0000.000
194A217VAL0-0.018-0.01732.4660.1510.1510.0000.0000.0000.000
195A218ALA0-0.025-0.01135.7460.0560.0560.0000.0000.0000.000
196A219VAL00.017-0.00937.4540.0810.0810.0000.0000.0000.000
197A220PRO00.0350.02440.116-0.092-0.0920.0000.0000.0000.000
198A221LYS10.9440.96039.2278.0428.0420.0000.0000.0000.000
199A222PRO00.0830.03641.960-0.188-0.1880.0000.0000.0000.000
200A223GLY00.0220.02041.9890.0090.0090.0000.0000.0000.000
201A224ILE0-0.096-0.04337.181-0.203-0.2030.0000.0000.0000.000
202A225THR00.0690.03936.561-0.068-0.0680.0000.0000.0000.000
203A226VAL0-0.021-0.00331.650-0.295-0.2950.0000.0000.0000.000
204A227ASN0-0.030-0.02028.7370.4100.4100.0000.0000.0000.000
205A228ALA00.0470.02931.523-0.064-0.0640.0000.0000.0000.000
206A229LYS10.9590.97528.34210.42510.4250.0000.0000.0000.000
207A230ARG10.8410.92226.25110.75810.7580.0000.0000.0000.000
208A231PRO0-0.002-0.01724.273-0.222-0.2220.0000.0000.0000.000
209A232VAL0-0.0030.00019.5240.0130.0130.0000.0000.0000.000
210A233LEU00.0060.01315.850-0.065-0.0650.0000.0000.0000.000
211A234LYS10.9590.97414.64918.35818.3580.0000.0000.0000.000
212A235ALA00.0430.02111.163-0.499-0.4990.0000.0000.0000.000
215A238PRO0-0.076-0.0248.4790.6190.6190.0000.0000.0000.000
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