FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 4JN7N

Calculation Name: 4LOG-A-Xray372

Preferred Name: Maltose/maltodextrin-binding periplasmic protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4LOG

Chain ID: A

ChEMBL ID: CHEMBL4295571

UniProt ID: P0AEX9

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 553
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -10941604.816667
FMO2-HF: Nuclear repulsion 10728025.974262
FMO2-HF: Total energy -213578.842405
FMO2-MP2: Total energy -214208.452163


3D Structure
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:5:GLU)


Summations of interaction energy for fragment #1(A:5: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.
63.68362.41320.339-10.778-8.2910.08
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.928 / q_NPA : -0.952
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].
3A7GLY00.0090.0103.380-10.148-6.6380.001-1.928-1.5830.004
4A8LYS10.7460.8481.836-86.339-92.97720.191-8.190-5.3630.071
5A9LEU00.0150.0184.2413.8633.8790.000-0.0350.0190.000
6A10VAL00.0190.0183.142-8.362-7.1230.152-0.558-0.8340.005
7A11ILE0-0.013-0.0136.103-2.267-2.2670.0000.0000.0000.000
8A12TRP0-0.041-0.0338.718-1.409-1.4090.0000.0000.0000.000
9A13ILE00.000-0.00511.550-1.411-1.4110.0000.0000.0000.000
10A14ASN00.011-0.01215.2780.5360.5360.0000.0000.0000.000
11A15GLY00.0390.00818.323-0.031-0.0310.0000.0000.0000.000
12A16ASP-1-0.852-0.90020.34513.35813.3580.0000.0000.0000.000
13A17LYS10.8900.93819.941-13.917-13.9170.0000.0000.0000.000
14A18GLY00.0410.04321.5190.1790.1790.0000.0000.0000.000
15A19TYR0-0.003-0.02916.8480.2600.2600.0000.0000.0000.000
16A20ASN0-0.020-0.02217.3201.6571.6570.0000.0000.0000.000
17A21GLY00.0240.01119.7230.0380.0380.0000.0000.0000.000
18A22LEU00.0020.01214.699-0.034-0.0340.0000.0000.0000.000
19A23ALA00.0630.02515.3500.7110.7110.0000.0000.0000.000
20A24GLU-1-0.871-0.91316.36716.82416.8240.0000.0000.0000.000
21A25VAL00.0040.01017.582-0.349-0.3490.0000.0000.0000.000
22A26GLY0-0.002-0.00713.9730.2670.2670.0000.0000.0000.000
23A27LYS10.8180.87713.910-17.434-17.4340.0000.0000.0000.000
24A28LYS10.8450.91115.910-14.656-14.6560.0000.0000.0000.000
25A29PHE00.0750.04011.385-0.493-0.4930.0000.0000.0000.000
26A30GLU-1-0.873-0.91811.61425.83625.8360.0000.0000.0000.000
27A31LYS10.8280.91113.512-16.047-16.0470.0000.0000.0000.000
28A32ASP-1-0.819-0.87216.85314.49314.4930.0000.0000.0000.000
29A33THR0-0.023-0.03413.2910.2220.2220.0000.0000.0000.000
30A34GLY0-0.041-0.00612.5520.4250.4250.0000.0000.0000.000
31A35ILE0-0.049-0.0108.2082.2452.2450.0000.0000.0000.000
32A36LYS10.9340.9636.727-31.171-31.1710.0000.0000.0000.000
33A37VAL00.0210.0157.8123.1733.1730.0000.0000.0000.000
34A38THR0-0.051-0.0147.750-2.976-2.9760.0000.0000.0000.000
35A39VAL0-0.017-0.0099.0572.0752.0750.0000.0000.0000.000
36A40GLU-1-0.883-0.9268.85535.97535.9750.0000.0000.0000.000
37A41HIS0-0.049-0.02712.038-0.284-0.2840.0000.0000.0000.000
38A42PRO0-0.001-0.00112.003-1.536-1.5360.0000.0000.0000.000
39A43ASP-1-0.765-0.87514.98217.64417.6440.0000.0000.0000.000
40A44LYS10.8310.94218.181-16.239-16.2390.0000.0000.0000.000
41A45LEU00.0310.00513.5240.6210.6210.0000.0000.0000.000
42A46GLU-1-0.797-0.90915.27617.38217.3820.0000.0000.0000.000
43A47GLU-1-0.878-0.95517.79514.52214.5220.0000.0000.0000.000
44A48LYS10.7910.89813.239-20.446-20.4460.0000.0000.0000.000
45A49PHE00.0740.04010.0350.7380.7380.0000.0000.0000.000
46A50PRO0-0.051-0.03812.7240.7880.7880.0000.0000.0000.000
47A51GLN0-0.135-0.06114.124-0.710-0.7100.0000.0000.0000.000
48A52VAL00.0100.0028.727-0.774-0.7740.0000.0000.0000.000
49A53ALA00.0390.0319.9071.3441.3440.0000.0000.0000.000
50A54ALA0-0.062-0.03710.921-0.771-0.7710.0000.0000.0000.000
51A55THR0-0.100-0.03811.692-0.732-0.7320.0000.0000.0000.000
52A56GLY00.006-0.0138.765-1.304-1.3040.0000.0000.0000.000
53A57ASP-1-0.899-0.9345.12152.50152.581-0.001-0.004-0.0750.000
54A58GLY0-0.004-0.0115.493-6.335-6.3350.0000.0000.0000.000
55A59PRO0-0.0270.0074.4818.5598.760-0.001-0.005-0.1940.000
56A60ASP-1-0.704-0.8124.76449.91750.012-0.001-0.002-0.0920.000
57A61ILE0-0.049-0.0087.017-4.848-4.8480.0000.0000.0000.000
58A62ILE00.0160.00910.2511.3431.3430.0000.0000.0000.000
59A63PHE00.001-0.01512.636-1.616-1.6160.0000.0000.0000.000
60A64TRP0-0.011-0.02016.0820.2500.2500.0000.0000.0000.000
61A65ALA0-0.0010.01519.049-0.183-0.1830.0000.0000.0000.000
62A66HIS00.013-0.00221.5430.6970.6970.0000.0000.0000.000
63A67ASP-1-0.864-0.92823.14912.89612.8960.0000.0000.0000.000
64A68ARG10.9360.95219.856-14.977-14.9770.0000.0000.0000.000
65A69PHE0-0.022-0.02016.8000.4560.4560.0000.0000.0000.000
66A70GLY00.0220.01520.3780.1040.1040.0000.0000.0000.000
67A71GLY0-0.027-0.01921.993-0.125-0.1250.0000.0000.0000.000
68A72TYR0-0.011-0.03316.1860.1080.1080.0000.0000.0000.000
69A73ALA00.0340.03118.5450.3310.3310.0000.0000.0000.000
70A74GLN0-0.078-0.02720.113-0.553-0.5530.0000.0000.0000.000
71A75SER0-0.040-0.02118.710-0.518-0.5180.0000.0000.0000.000
72A76GLY0-0.019-0.00617.4720.6800.6800.0000.0000.0000.000
73A77LEU00.0020.01614.2150.7720.7720.0000.0000.0000.000
74A78LEU0-0.040-0.01913.4201.5411.5410.0000.0000.0000.000
75A79ALA0-0.023-0.01813.074-0.846-0.8460.0000.0000.0000.000
76A80GLU-1-0.860-0.90415.14213.14613.1460.0000.0000.0000.000
77A81ILE0-0.049-0.00516.6970.2800.2800.0000.0000.0000.000
78A82THR0-0.021-0.02118.861-0.826-0.8260.0000.0000.0000.000
79A83PRO00.0350.03721.431-0.018-0.0180.0000.0000.0000.000
80A84ASP-1-0.849-0.92623.32812.12712.1270.0000.0000.0000.000
81A85LYS10.8670.89926.433-9.754-9.7540.0000.0000.0000.000
82A86ALA0-0.044-0.02528.791-0.212-0.2120.0000.0000.0000.000
83A87PHE00.0110.00322.805-0.186-0.1860.0000.0000.0000.000
84A88GLN00.000-0.00926.576-0.296-0.2960.0000.0000.0000.000
85A89ASP-1-0.808-0.86728.1829.5059.5050.0000.0000.0000.000
86A90LYS10.9660.99226.166-12.021-12.0210.0000.0000.0000.000
87A91LEU00.0380.04024.335-0.022-0.0220.0000.0000.0000.000
88A92TYR00.0210.01029.102-0.429-0.4290.0000.0000.0000.000
89A93PRO00.005-0.01030.4980.2660.2660.0000.0000.0000.000
90A94PHE00.0190.00631.4900.1490.1490.0000.0000.0000.000
91A95THR00.000-0.01327.4460.2660.2660.0000.0000.0000.000
92A96TRP00.030-0.00622.9500.5650.5650.0000.0000.0000.000
93A97ASP-1-0.852-0.89027.03510.28110.2810.0000.0000.0000.000
94A98ALA00.0110.01826.795-0.116-0.1160.0000.0000.0000.000
95A99VAL0-0.031-0.00422.3110.2840.2840.0000.0000.0000.000
96A100ARG10.8160.90323.359-10.314-10.3140.0000.0000.0000.000
97A101TYR00.0920.02423.720-0.262-0.2620.0000.0000.0000.000
98A102ASN00.0120.01925.401-0.153-0.1530.0000.0000.0000.000
99A103GLY00.0250.00927.796-0.112-0.1120.0000.0000.0000.000
100A104LYS10.7720.87022.683-12.963-12.9630.0000.0000.0000.000
101A105LEU0-0.001-0.00522.562-0.013-0.0130.0000.0000.0000.000
102A106ILE00.0100.00419.2780.4260.4260.0000.0000.0000.000
103A107ALA00.001-0.00718.1690.9250.9250.0000.0000.0000.000
104A108TYR0-0.030-0.05816.965-0.683-0.6830.0000.0000.0000.000
105A109PRO0-0.024-0.00720.4080.3680.3680.0000.0000.0000.000
106A110ILE00.004-0.00519.7930.0860.0860.0000.0000.0000.000
107A111ALA0-0.0390.00523.264-0.413-0.4130.0000.0000.0000.000
108A112VAL0-0.057-0.02625.7990.1410.1410.0000.0000.0000.000
109A113GLU-1-0.905-0.95027.48311.22511.2250.0000.0000.0000.000
110A114ALA00.022-0.00230.656-0.022-0.0220.0000.0000.0000.000
111A115LEU0-0.0370.00433.939-0.098-0.0980.0000.0000.0000.000
112A116SER00.0110.00236.943-0.128-0.1280.0000.0000.0000.000
113A117LEU0-0.009-0.00739.631-0.056-0.0560.0000.0000.0000.000
114A118ILE0-0.0130.00338.844-0.023-0.0230.0000.0000.0000.000
115A119TYR00.005-0.00443.379-0.152-0.1520.0000.0000.0000.000
116A120ASN00.0760.02946.5300.0540.0540.0000.0000.0000.000
117A121LYS10.9000.94546.546-6.984-6.9840.0000.0000.0000.000
118A122ASP-1-0.867-0.92550.8436.2146.2140.0000.0000.0000.000
119A123LEU0-0.103-0.05252.062-0.140-0.1400.0000.0000.0000.000
120A124LEU0-0.007-0.01851.316-0.112-0.1120.0000.0000.0000.000
121A125PRO00.0020.01252.0220.1320.1320.0000.0000.0000.000
122A126ASN0-0.074-0.05152.907-0.030-0.0300.0000.0000.0000.000
123A127PRO00.0040.00848.681-0.076-0.0760.0000.0000.0000.000
124A128PRO00.0160.02750.989-0.035-0.0350.0000.0000.0000.000
125A129LYS10.9440.96848.038-6.520-6.5200.0000.0000.0000.000
126A130THR0-0.078-0.04050.4380.0840.0840.0000.0000.0000.000
127A131TRP00.058-0.00745.314-0.053-0.0530.0000.0000.0000.000
128A132GLU-1-0.814-0.92951.7865.9775.9770.0000.0000.0000.000
129A133GLU-1-0.914-0.92754.6285.7895.7890.0000.0000.0000.000
130A134ILE0-0.008-0.00750.264-0.011-0.0110.0000.0000.0000.000
131A135PRO00.0060.00154.545-0.041-0.0410.0000.0000.0000.000
132A136ALA0-0.046-0.02757.126-0.045-0.0450.0000.0000.0000.000
133A137LEU00.0600.03853.906-0.058-0.0580.0000.0000.0000.000
134A138ASP-1-0.771-0.87655.4945.8475.8470.0000.0000.0000.000
135A139LYS10.9330.96457.106-5.042-5.0420.0000.0000.0000.000
136A140GLU-1-0.953-0.97459.9715.3305.3300.0000.0000.0000.000
137A141LEU00.0280.00854.558-0.034-0.0340.0000.0000.0000.000
138A142LYS10.8330.89855.394-5.815-5.8150.0000.0000.0000.000
139A143ALA0-0.0230.01159.622-0.050-0.0500.0000.0000.0000.000
140A144LYS10.8780.94659.974-5.278-5.2780.0000.0000.0000.000
141A145GLY00.001-0.00359.5050.0640.0640.0000.0000.0000.000
142A146LYS10.8500.92754.278-5.855-5.8550.0000.0000.0000.000
143A147SER00.011-0.01552.092-0.021-0.0210.0000.0000.0000.000
144A148ALA00.0680.04352.8590.0660.0660.0000.0000.0000.000
145A149LEU0-0.0120.00146.2090.0990.0990.0000.0000.0000.000
146A150MET0-0.0020.00146.924-0.104-0.1040.0000.0000.0000.000
147A151PHE00.0220.01042.2420.1180.1180.0000.0000.0000.000
148A152ASN00.0410.02137.992-0.259-0.2590.0000.0000.0000.000
149A153LEU0-0.016-0.00741.5140.0770.0770.0000.0000.0000.000
150A154GLN0-0.040-0.01840.403-0.006-0.0060.0000.0000.0000.000
151A155GLU-1-0.822-0.89135.7119.0059.0050.0000.0000.0000.000
152A156PRO00.0180.02137.149-0.114-0.1140.0000.0000.0000.000
153A157TYR0-0.010-0.01132.359-0.142-0.1420.0000.0000.0000.000
154A158PHE00.000-0.01935.1930.0230.0230.0000.0000.0000.000
155A159THR00.0000.00839.069-0.152-0.1520.0000.0000.0000.000
156A160TRP0-0.0270.00138.363-0.268-0.2680.0000.0000.0000.000
157A161PRO00.0210.01239.187-0.132-0.1320.0000.0000.0000.000
158A162LEU0-0.0380.00441.493-0.116-0.1160.0000.0000.0000.000
159A163ILE0-0.025-0.02143.288-0.155-0.1550.0000.0000.0000.000
160A164ALA00.0530.03241.509-0.130-0.1300.0000.0000.0000.000
161A165ALA00.0000.00943.570-0.094-0.0940.0000.0000.0000.000
162A166ASP-1-0.873-0.92745.6826.2176.2170.0000.0000.0000.000
163A167GLY00.000-0.00946.077-0.145-0.1450.0000.0000.0000.000
164A168GLY0-0.062-0.01244.2940.0570.0570.0000.0000.0000.000
165A169TYR0-0.068-0.09139.7900.0080.0080.0000.0000.0000.000
166A170ALA00.0110.00836.194-0.093-0.0930.0000.0000.0000.000
167A171PHE0-0.007-0.01234.544-0.081-0.0810.0000.0000.0000.000
168A172LYS10.9000.95436.937-7.586-7.5860.0000.0000.0000.000
169A173TYR0-0.080-0.06231.7580.2290.2290.0000.0000.0000.000
170A174GLU-1-0.869-0.91436.5027.5777.5770.0000.0000.0000.000
171A175ASN0-0.025-0.02236.5050.0860.0860.0000.0000.0000.000
172A176GLY0-0.018-0.00232.5210.1550.1550.0000.0000.0000.000
173A177LYS10.8550.92127.626-10.697-10.6970.0000.0000.0000.000
174A178TYR00.0210.00430.230-0.093-0.0930.0000.0000.0000.000
175A179ASP-1-0.864-0.92634.0648.2248.2240.0000.0000.0000.000
176A180ILE0-0.045-0.03433.533-0.142-0.1420.0000.0000.0000.000
177A181LYS10.8100.90536.462-8.357-8.3570.0000.0000.0000.000
178A182ASP-1-0.866-0.89139.8987.3087.3080.0000.0000.0000.000
179A183VAL00.0600.01339.3470.2000.2000.0000.0000.0000.000
180A184GLY00.0160.03041.490-0.239-0.2390.0000.0000.0000.000
181A185VAL00.0070.00141.1990.0020.0020.0000.0000.0000.000
182A186ASP-1-0.853-0.92844.0886.3516.3510.0000.0000.0000.000
183A187ASN00.0120.01845.591-0.173-0.1730.0000.0000.0000.000
184A188ALA00.013-0.01348.889-0.068-0.0680.0000.0000.0000.000
185A189GLY00.013-0.01249.418-0.061-0.0610.0000.0000.0000.000
186A190ALA0-0.0170.01246.6700.0700.0700.0000.0000.0000.000
187A191LYS10.8760.92048.023-6.084-6.0840.0000.0000.0000.000
188A192ALA0-0.072-0.00551.076-0.090-0.0900.0000.0000.0000.000
189A193GLY00.0770.02948.431-0.075-0.0750.0000.0000.0000.000
190A194LEU00.0250.01946.826-0.007-0.0070.0000.0000.0000.000
191A195THR0-0.006-0.02549.184-0.071-0.0710.0000.0000.0000.000
192A196PHE0-0.0170.00351.186-0.063-0.0630.0000.0000.0000.000
193A197LEU00.011-0.00546.113-0.037-0.0370.0000.0000.0000.000
194A198VAL00.002-0.00450.375-0.021-0.0210.0000.0000.0000.000
195A199ASP-1-0.814-0.90552.4805.5955.5950.0000.0000.0000.000
196A200LEU0-0.027-0.00650.370-0.091-0.0910.0000.0000.0000.000
197A201ILE0-0.0200.00049.440-0.062-0.0620.0000.0000.0000.000
198A202LYS10.8350.92053.870-5.602-5.6020.0000.0000.0000.000
199A203ASN0-0.048-0.02156.844-0.132-0.1320.0000.0000.0000.000
200A204LYS10.7710.87754.434-5.952-5.9520.0000.0000.0000.000
201A205HIS0-0.036-0.02654.880-0.073-0.0730.0000.0000.0000.000
202A206MET0-0.0170.00648.8430.1410.1410.0000.0000.0000.000
203A207ASN0-0.039-0.03650.091-0.232-0.2320.0000.0000.0000.000
204A208ALA00.0750.05548.6690.1480.1480.0000.0000.0000.000
205A209ASP-1-0.831-0.90447.4366.4986.4980.0000.0000.0000.000
206A210THR0-0.085-0.04444.9530.0320.0320.0000.0000.0000.000
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