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

tag_button

FMODB ID: 971K2

Calculation Name: 6I4Y-B-Xray547

Preferred Name: Maltose/maltodextrin-binding periplasmic protein

Target Type: SINGLE PROTEIN

Ligand Name: alpha-d-glucopyranose

Ligand 3-letter code: GLC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6I4Y

Chain ID: B

ChEMBL ID: CHEMBL4295571

UniProt ID: P0AEX9

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1485883.562465
FMO2-HF: Nuclear repulsion 1417543.358026
FMO2-HF: Total energy -68340.204439
FMO2-MP2: Total energy -68537.829179


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:ASP)


Summations of interaction energy for fragment #1(A:-1:ASP)
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.
0.2232.777-0.027-1.068-1.4590.002
Interaction energy analysis for fragmet #1(A:-1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.009
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].
3A1MET00.0340.0143.840-0.9441.430-0.026-1.066-1.2820.002
137A135VAL0-0.006-0.0064.9831.2741.454-0.001-0.002-0.1770.000
4A2LYS10.8290.9126.5054.5024.5020.0000.0000.0000.000
5A3ILE0-0.0010.0069.3850.1140.1140.0000.0000.0000.000
6A4TRP00.0570.03112.0320.2350.2350.0000.0000.0000.000
7A5THR0-0.055-0.05413.959-0.438-0.4380.0000.0000.0000.000
8A6SER0-0.0460.00016.2720.0830.0830.0000.0000.0000.000
9A7GLU-1-0.892-0.95420.025-1.089-1.0890.0000.0000.0000.000
10A8HIS0-0.012-0.00522.9590.0750.0750.0000.0000.0000.000
11A9VAL0-0.012-0.00726.436-0.010-0.0100.0000.0000.0000.000
12A10PHE0-0.0090.00427.1760.0280.0280.0000.0000.0000.000
13A11ASP-1-0.879-0.92832.026-0.383-0.3830.0000.0000.0000.000
14A12HIS00.0180.00434.3280.0160.0160.0000.0000.0000.000
15A13PRO00.1230.08933.981-0.030-0.0300.0000.0000.0000.000
16A14TRP00.0260.02727.5100.0320.0320.0000.0000.0000.000
17A15GLU-1-0.793-0.89131.871-0.313-0.3130.0000.0000.0000.000
18A16THR0-0.054-0.02534.1850.0210.0210.0000.0000.0000.000
19A17VAL00.0180.01429.1980.0150.0150.0000.0000.0000.000
20A18THR00.028-0.00228.916-0.003-0.0030.0000.0000.0000.000
21A19THR0-0.066-0.04630.3710.0280.0280.0000.0000.0000.000
22A20ALA0-0.003-0.01132.7390.0210.0210.0000.0000.0000.000
23A21ALA0-0.014-0.00627.3110.0140.0140.0000.0000.0000.000
24A22MET0-0.043-0.01027.2730.0380.0380.0000.0000.0000.000
25A23GLN0-0.038-0.01330.3040.0300.0300.0000.0000.0000.000
26A24LYS10.9420.99225.6880.3030.3030.0000.0000.0000.000
27A25TYR00.0030.02225.053-0.017-0.0170.0000.0000.0000.000
28A26PRO00.0550.02731.9490.0110.0110.0000.0000.0000.000
29A27ASN0-0.010-0.03130.578-0.014-0.0140.0000.0000.0000.000
30A28PRO00.029-0.00934.1110.0060.0060.0000.0000.0000.000
31A29MET00.0150.02231.8850.0080.0080.0000.0000.0000.000
32A30ASN0-0.056-0.02727.838-0.028-0.0280.0000.0000.0000.000
33A31PRO00.0480.02830.7540.0210.0210.0000.0000.0000.000
34A32SER00.0190.01528.5290.0130.0130.0000.0000.0000.000
35A33VAL0-0.033-0.00827.0850.0330.0330.0000.0000.0000.000
36A34VAL00.006-0.00329.755-0.004-0.0040.0000.0000.0000.000
37A35GLY0-0.0030.00230.7970.0080.0080.0000.0000.0000.000
38A36VAL0-0.058-0.02028.2910.0080.0080.0000.0000.0000.000
39A37ASP-1-0.857-0.90928.5720.1120.1120.0000.0000.0000.000
40A38VAL0-0.078-0.05027.883-0.011-0.0110.0000.0000.0000.000
41A39LEU0-0.048-0.02123.9510.0160.0160.0000.0000.0000.000
42A40ASP-1-0.883-0.94926.3270.1660.1660.0000.0000.0000.000
43A41ARG10.8850.92927.4860.0240.0240.0000.0000.0000.000
44A42HIS00.0510.04727.8790.0060.0060.0000.0000.0000.000
45A43ILE0-0.006-0.00728.676-0.033-0.0330.0000.0000.0000.000
46A44ASP-1-0.768-0.83725.318-0.114-0.1140.0000.0000.0000.000
47A45PRO00.013-0.02627.659-0.018-0.0180.0000.0000.0000.000
48A46SER0-0.108-0.06726.978-0.026-0.0260.0000.0000.0000.000
49A47GLY00.0130.01129.258-0.028-0.0280.0000.0000.0000.000
50A48LYS10.8560.93424.2000.3110.3110.0000.0000.0000.000
51A49LEU0-0.026-0.01127.9380.0450.0450.0000.0000.0000.000
52A50HIS0-0.015-0.01922.007-0.016-0.0160.0000.0000.0000.000
53A51SER0-0.010-0.01424.5520.0280.0280.0000.0000.0000.000
54A52HIS00.0100.01620.761-0.010-0.0100.0000.0000.0000.000
55A53ARG10.8780.92123.2410.0990.0990.0000.0000.0000.000
56A54LEU00.0030.01423.1350.0350.0350.0000.0000.0000.000
57A55LEU00.0020.00523.673-0.026-0.0260.0000.0000.0000.000
58A56SER0-0.065-0.04524.8230.0480.0480.0000.0000.0000.000
59A57THR00.0210.00125.245-0.048-0.0480.0000.0000.0000.000
60A58GLU-1-0.946-0.97327.4160.1450.1450.0000.0000.0000.000
61A59TRP00.003-0.01323.309-0.051-0.0510.0000.0000.0000.000
62A60GLY00.0270.01629.6150.0120.0120.0000.0000.0000.000
63A61LEU00.0110.00830.805-0.012-0.0120.0000.0000.0000.000
64A62PRO00.0310.01434.0250.0190.0190.0000.0000.0000.000
65A63SER0-0.067-0.04737.659-0.012-0.0120.0000.0000.0000.000
66A64ILE00.0530.01836.3280.0040.0040.0000.0000.0000.000
67A65VAL00.0230.03034.7060.0160.0160.0000.0000.0000.000
68A66LYS10.9730.97336.988-0.061-0.0610.0000.0000.0000.000
69A67SER0-0.0170.00839.5060.0110.0110.0000.0000.0000.000
70A68LEU00.010-0.00131.7890.0130.0130.0000.0000.0000.000
71A69ILE00.001-0.00834.6520.0230.0230.0000.0000.0000.000
72A70GLY0-0.0170.00435.8530.0100.0100.0000.0000.0000.000
73A71ALA0-0.032-0.00535.4030.0130.0130.0000.0000.0000.000
74A72ALA0-0.010-0.01830.4420.0350.0350.0000.0000.0000.000
75A73ARG10.9380.97324.667-0.515-0.5150.0000.0000.0000.000
76A74THR00.0730.02629.3250.0140.0140.0000.0000.0000.000
77A75LYS10.8650.94928.970-0.168-0.1680.0000.0000.0000.000
78A76THR0-0.062-0.02123.2470.0360.0360.0000.0000.0000.000
79A77TYR00.016-0.00923.158-0.047-0.0470.0000.0000.0000.000
80A78VAL00.0130.00619.5430.0610.0610.0000.0000.0000.000
81A79GLN0-0.0060.01318.7770.0500.0500.0000.0000.0000.000
82A80GLU-1-0.869-0.96318.673-0.208-0.2080.0000.0000.0000.000
83A81HIS0-0.047-0.01518.3980.0590.0590.0000.0000.0000.000
84A82SER00.000-0.00519.733-0.074-0.0740.0000.0000.0000.000
85A83VAL0-0.005-0.00520.9080.0640.0640.0000.0000.0000.000
86A84VAL0-0.013-0.00723.431-0.069-0.0690.0000.0000.0000.000
87A85ASP-1-0.766-0.87326.107-0.309-0.3090.0000.0000.0000.000
88A86PRO0-0.011-0.01927.848-0.024-0.0240.0000.0000.0000.000
89A87VAL0-0.046-0.02630.8310.0090.0090.0000.0000.0000.000
90A88GLU-1-0.950-0.98526.315-0.511-0.5110.0000.0000.0000.000
91A89LYS10.7910.90229.0100.2810.2810.0000.0000.0000.000
92A90THR00.0230.00724.089-0.047-0.0470.0000.0000.0000.000
93A91MET0-0.036-0.00724.7020.0590.0590.0000.0000.0000.000
94A92GLU-1-0.799-0.87216.942-0.936-0.9360.0000.0000.0000.000
95A93LEU0-0.003-0.01019.4400.1100.1100.0000.0000.0000.000
96A94LYS10.8910.94213.0760.5420.5420.0000.0000.0000.000
97A95SER00.0050.00516.1800.1250.1250.0000.0000.0000.000
98A96THR00.020-0.00213.041-0.134-0.1340.0000.0000.0000.000
99A97ASN0-0.023-0.00515.2810.0150.0150.0000.0000.0000.000
100A98ILE00.0610.01516.4500.1290.1290.0000.0000.0000.000
101A99SER0-0.066-0.03018.8400.0450.0450.0000.0000.0000.000
102A100PHE00.001-0.01518.5790.0060.0060.0000.0000.0000.000
103A101THR00.0560.03513.0190.0660.0660.0000.0000.0000.000
104A102ASN0-0.013-0.00613.5570.2810.2810.0000.0000.0000.000
105A103MET0-0.080-0.04014.8730.2440.2440.0000.0000.0000.000
106A104VAL00.011-0.00513.0750.0210.0210.0000.0000.0000.000
107A105SER0-0.052-0.02510.2570.0100.0100.0000.0000.0000.000
108A106VAL0-0.041-0.02511.111-0.191-0.1910.0000.0000.0000.000
109A107ASP-1-0.804-0.87110.4400.2920.2920.0000.0000.0000.000
110A108GLU-1-0.911-0.96112.515-1.074-1.0740.0000.0000.0000.000
111A109ARG10.7700.86713.5491.6291.6290.0000.0000.0000.000
112A110LEU00.0160.00915.735-0.126-0.1260.0000.0000.0000.000
113A111ILE0-0.010-0.01317.6430.0450.0450.0000.0000.0000.000
114A112TYR00.0270.02121.284-0.026-0.0260.0000.0000.0000.000
115A113LYS10.9220.94524.9930.7000.7000.0000.0000.0000.000
116A114PRO00.0600.03727.428-0.012-0.0120.0000.0000.0000.000
117A115HIS00.0320.02629.760-0.045-0.0450.0000.0000.0000.000
118A116PRO0-0.063-0.04428.6370.0280.0280.0000.0000.0000.000
119A117GLN0-0.035-0.02131.6130.0290.0290.0000.0000.0000.000
120A118ASP-1-0.828-0.91734.371-0.363-0.3630.0000.0000.0000.000
121A119PRO0-0.023-0.01734.871-0.014-0.0140.0000.0000.0000.000
122A120GLU-1-0.910-0.95135.522-0.296-0.2960.0000.0000.0000.000
123A121LYS10.8090.90833.3840.4120.4120.0000.0000.0000.000
124A122THR0-0.045-0.03628.497-0.014-0.0140.0000.0000.0000.000
125A123VAL0-0.023-0.00724.951-0.002-0.0020.0000.0000.0000.000
126A124LEU0-0.017-0.00722.2220.0310.0310.0000.0000.0000.000
127A125THR00.0040.00719.735-0.034-0.0340.0000.0000.0000.000
128A126GLN00.000-0.00818.4310.0800.0800.0000.0000.0000.000
129A127GLU-1-0.840-0.89812.644-2.823-2.8230.0000.0000.0000.000
130A128ALA00.0460.02513.7400.2570.2570.0000.0000.0000.000
131A129ILE0-0.063-0.0407.066-0.754-0.7540.0000.0000.0000.000
132A130ILE00.0400.0249.7880.4780.4780.0000.0000.0000.000
133A131THR0-0.055-0.0066.369-0.114-0.1140.0000.0000.0000.000
134A132VAL0-0.0060.0018.6320.0190.0190.0000.0000.0000.000
135A133LYS10.9140.9469.536-1.885-1.8850.0000.0000.0000.000
136A134GLY00.0500.0476.3030.8090.8090.0000.0000.0000.000
138A136SER00.0470.0186.042-0.847-0.8470.0000.0000.0000.000
139A137LEU00.0610.0167.4160.4020.4020.0000.0000.0000.000
140A138SER00.0170.00510.7570.2170.2170.0000.0000.0000.000
141A139SER00.0530.0248.3320.6140.6140.0000.0000.0000.000
142A140TYR00.0160.00310.7880.3020.3020.0000.0000.0000.000
143A141LEU00.0160.00612.4070.0180.0180.0000.0000.0000.000
144A142GLU-1-0.901-0.95813.334-0.537-0.5370.0000.0000.0000.000
145A143GLY00.0150.00914.2010.0320.0320.0000.0000.0000.000
146A144LEU0-0.029-0.01715.1890.0080.0080.0000.0000.0000.000
147A145MET0-0.0110.00918.130-0.060-0.0600.0000.0000.0000.000
148A146ALA00.0330.01817.599-0.017-0.0170.0000.0000.0000.000
149A147SER0-0.0120.01318.795-0.043-0.0430.0000.0000.0000.000
150A148THR0-0.011-0.02720.550-0.070-0.0700.0000.0000.0000.000
151A149ILE00.0130.00923.129-0.036-0.0360.0000.0000.0000.000
152A150SER0-0.037-0.03222.159-0.012-0.0120.0000.0000.0000.000
153A151SER00.0200.01124.571-0.036-0.0360.0000.0000.0000.000
154A152ASN00.023-0.00226.4100.0040.0040.0000.0000.0000.000
155A153ALA00.0210.01727.763-0.027-0.0270.0000.0000.0000.000
156A154SER0-0.031-0.02028.699-0.025-0.0250.0000.0000.0000.000
157A155LYS10.9270.97428.267-0.427-0.4270.0000.0000.0000.000
158A156GLY00.0000.00432.529-0.019-0.0190.0000.0000.0000.000
159A157ARG10.9130.94727.940-0.338-0.3380.0000.0000.0000.000
160A158GLU-1-0.911-0.95033.3030.3480.3480.0000.0000.0000.000
161A159ALA0-0.016-0.00936.537-0.013-0.0130.0000.0000.0000.000
162A160MET0-0.021-0.00937.931-0.019-0.0190.0000.0000.0000.000
163A161GLU-1-0.894-0.94938.1910.1960.1960.0000.0000.0000.000
164A162TRP0-0.043-0.01340.640-0.014-0.0140.0000.0000.0000.000
165A163VAL0-0.032-0.02442.522-0.010-0.0100.0000.0000.0000.000
166A164ILE00.0100.00741.415-0.011-0.0110.0000.0000.0000.000
167A165HIS00.0020.00244.606-0.006-0.0060.0000.0000.0000.000
168A166LYS10.9420.96446.447-0.127-0.1270.0000.0000.0000.000
169A167LEU0-0.020-0.01048.075-0.006-0.0060.0000.0000.0000.000
170A168ASN0-0.044-0.03248.641-0.006-0.0060.0000.0000.0000.000
171A169ALA0-0.032-0.00850.5680.0010.0010.0000.0000.0000.000
172A170GLU-1-1.057-1.01552.6590.0860.0860.0000.0000.0000.000
173A171ILE-1-0.973-0.97554.3140.0910.0910.0000.0000.0000.000