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: KGRN3

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 OptH
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 -10938365.298314
FMO2-HF: Nuclear repulsion 10724790.895069
FMO2-HF: Total energy -213574.403244
FMO2-MP2: Total energy -214204.224432


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.
86.92894.6285.376-6.011-7.0640.051
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 : -0.992 / q_NPA : -1.003
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].
3A7GLY0-0.0070.0043.185-9.643-6.2540.001-1.804-1.5860.003
4A8LYS10.8200.8982.289-76.757-74.4065.341-3.698-3.9940.047
5A9LEU00.0150.0144.2475.2625.3360.000-0.033-0.0420.000
6A10VAL00.0190.0153.614-8.487-7.8680.014-0.236-0.3970.001
7A11ILE0-0.022-0.0176.500-1.182-1.1820.0000.0000.0000.000
8A12TRP0-0.033-0.0288.693-1.333-1.3330.0000.0000.0000.000
9A13ILE00.000-0.00711.961-1.193-1.1930.0000.0000.0000.000
10A14ASN0-0.003-0.03615.6860.3520.3520.0000.0000.0000.000
11A15GLY00.0400.00818.824-0.050-0.0500.0000.0000.0000.000
12A16ASP-1-0.899-0.92221.00013.45413.4540.0000.0000.0000.000
13A17LYS10.9420.97920.341-14.353-14.3530.0000.0000.0000.000
14A18GLY00.0470.04422.0730.1340.1340.0000.0000.0000.000
15A19TYR0-0.013-0.03317.4620.3720.3720.0000.0000.0000.000
16A20ASN00.021-0.00617.9301.9181.9180.0000.0000.0000.000
17A21GLY00.0350.02020.1730.0120.0120.0000.0000.0000.000
18A22LEU00.0060.01214.866-0.013-0.0130.0000.0000.0000.000
19A23ALA00.0190.00115.3740.7640.7640.0000.0000.0000.000
20A24GLU-1-0.975-0.97916.39515.56515.5650.0000.0000.0000.000
21A25VAL0-0.012-0.00117.700-0.329-0.3290.0000.0000.0000.000
22A26GLY00.000-0.00913.9950.3310.3310.0000.0000.0000.000
23A27LYS10.9730.97513.929-18.150-18.1500.0000.0000.0000.000
24A28LYS10.9480.97915.934-13.947-13.9470.0000.0000.0000.000
25A29PHE00.0680.03311.313-0.476-0.4760.0000.0000.0000.000
26A30GLU-1-0.911-0.93911.25823.80723.8070.0000.0000.0000.000
27A31LYS10.8250.90913.512-15.551-15.5510.0000.0000.0000.000
28A32ASP-1-0.913-0.95616.90014.37914.3790.0000.0000.0000.000
29A33THR0-0.030-0.03513.1550.3680.3680.0000.0000.0000.000
30A34GLY0-0.040-0.01012.5520.4550.4550.0000.0000.0000.000
31A35ILE0-0.038-0.0018.1132.2462.2460.0000.0000.0000.000
32A36LYS10.9230.9556.720-31.347-31.3470.0000.0000.0000.000
33A37VAL00.0500.0297.8323.2663.2660.0000.0000.0000.000
34A38THR0-0.081-0.0288.012-2.719-2.7190.0000.0000.0000.000
35A39VAL00.0010.0019.6492.2132.2130.0000.0000.0000.000
36A40GLU-1-0.899-0.9309.18334.54334.5430.0000.0000.0000.000
37A41HIS0-0.036-0.02112.8450.0350.0350.0000.0000.0000.000
38A42PRO0-0.020-0.00712.335-1.455-1.4550.0000.0000.0000.000
39A43ASP-1-0.841-0.92415.17016.52116.5210.0000.0000.0000.000
40A44LYS10.9350.99717.286-17.396-17.3960.0000.0000.0000.000
41A45LEU00.0430.01713.6670.7520.7520.0000.0000.0000.000
42A46GLU-1-0.839-0.93215.14217.33917.3390.0000.0000.0000.000
43A47GLU-1-0.952-1.00017.60414.69314.6930.0000.0000.0000.000
44A48LYS10.8170.90212.703-20.631-20.6310.0000.0000.0000.000
45A49PHE00.0640.04110.0170.8910.8910.0000.0000.0000.000
46A50PRO0-0.047-0.04012.0481.0711.0710.0000.0000.0000.000
47A51GLN0-0.105-0.03813.085-0.177-0.1770.0000.0000.0000.000
48A52VAL00.006-0.0057.662-0.746-0.7460.0000.0000.0000.000
49A53ALA00.0480.0388.6801.8931.8930.0000.0000.0000.000
50A54ALA0-0.067-0.04210.038-0.780-0.7800.0000.0000.0000.000
51A55THR0-0.109-0.03710.771-0.763-0.7630.0000.0000.0000.000
52A56GLY00.003-0.0198.354-1.566-1.5660.0000.0000.0000.000
53A57ASP-1-0.918-0.9473.65963.89264.4180.023-0.118-0.4300.000
54A58GLY00.0140.0024.385-8.574-8.596-0.001-0.0150.0390.000
55A59PRO0-0.0080.0094.43610.78311.005-0.001-0.011-0.2100.000
56A60ASP-1-0.710-0.8114.44360.76960.922-0.001-0.015-0.1370.000
57A61ILE0-0.042-0.0016.551-5.341-5.3410.0000.0000.0000.000
58A62ILE00.0100.01010.1181.0531.0530.0000.0000.0000.000
59A63PHE00.016-0.01512.589-1.626-1.6260.0000.0000.0000.000
60A64TRP0-0.026-0.03416.1300.1730.1730.0000.0000.0000.000
61A65ALA00.0060.02519.099-0.165-0.1650.0000.0000.0000.000
62A66HIS00.0100.00321.4300.7790.7790.0000.0000.0000.000
63A67ASP-1-0.874-0.94022.87713.16113.1610.0000.0000.0000.000
64A68ARG10.9750.98120.057-15.016-15.0160.0000.0000.0000.000
65A69PHE0-0.003-0.01616.6460.5590.5590.0000.0000.0000.000
66A70GLY0-0.003-0.00620.0620.1540.1540.0000.0000.0000.000
67A71GLY00.009-0.00621.621-0.099-0.0990.0000.0000.0000.000
68A72TYR0-0.002-0.02516.2820.1720.1720.0000.0000.0000.000
69A73ALA00.0310.02717.9980.3980.3980.0000.0000.0000.000
70A74GLN0-0.045-0.00819.510-0.453-0.4530.0000.0000.0000.000
71A75SER0-0.056-0.02718.016-0.556-0.5560.0000.0000.0000.000
72A76GLY0-0.017-0.00517.1410.7800.7800.0000.0000.0000.000
73A77LEU00.0040.01813.5120.8870.8870.0000.0000.0000.000
74A78LEU0-0.043-0.01812.8171.7601.7600.0000.0000.0000.000
75A79ALA0-0.022-0.02212.510-0.938-0.9380.0000.0000.0000.000
76A80GLU-1-0.985-0.98514.57314.00314.0030.0000.0000.0000.000
77A81ILE0-0.056-0.00416.0250.3250.3250.0000.0000.0000.000
78A82THR00.027-0.00818.062-0.936-0.9360.0000.0000.0000.000
79A83PRO00.0120.01620.7350.0080.0080.0000.0000.0000.000
80A84ASP-1-0.842-0.91822.61812.42412.4240.0000.0000.0000.000
81A85LYS10.9700.97525.892-9.920-9.9200.0000.0000.0000.000
82A86ALA0-0.050-0.03128.538-0.229-0.2290.0000.0000.0000.000
83A87PHE00.0150.00922.112-0.204-0.2040.0000.0000.0000.000
84A88GLN0-0.018-0.02125.8650.0060.0060.0000.0000.0000.000
85A89ASP-1-0.877-0.92927.5659.7769.7760.0000.0000.0000.000
86A90LYS10.9500.97826.869-11.804-11.8040.0000.0000.0000.000
87A91LEU00.0300.04023.999-0.053-0.0530.0000.0000.0000.000
88A92TYR00.013-0.00128.696-0.411-0.4110.0000.0000.0000.000
89A93PRO0-0.014-0.01830.0680.2840.2840.0000.0000.0000.000
90A94PHE00.0390.01430.9750.1820.1820.0000.0000.0000.000
91A95THR0-0.004-0.00427.0910.2980.2980.0000.0000.0000.000
92A96TRP00.014-0.01122.3560.5920.5920.0000.0000.0000.000
93A97ASP-1-0.992-0.98826.49210.57610.5760.0000.0000.0000.000
94A98ALA00.0100.00926.314-0.115-0.1150.0000.0000.0000.000
95A99VAL0-0.025-0.00321.7550.3070.3070.0000.0000.0000.000
96A100ARG10.9330.98222.778-10.794-10.7940.0000.0000.0000.000
97A101TYR00.0500.00223.074-0.229-0.2290.0000.0000.0000.000
98A102ASN0-0.042-0.00724.846-0.284-0.2840.0000.0000.0000.000
99A103GLY00.0120.00227.213-0.108-0.1080.0000.0000.0000.000
100A104LYS10.9020.95722.486-13.061-13.0610.0000.0000.0000.000
101A105LEU0-0.004-0.00121.834-0.024-0.0240.0000.0000.0000.000
102A106ILE00.0120.00618.6460.4760.4760.0000.0000.0000.000
103A107ALA0-0.004-0.01017.6351.0011.0010.0000.0000.0000.000
104A108TYR0-0.012-0.05916.346-0.742-0.7420.0000.0000.0000.000
105A109PRO0-0.032-0.01219.9670.3670.3670.0000.0000.0000.000
106A110ILE00.0120.00419.7250.0560.0560.0000.0000.0000.000
107A111ALA0-0.0320.00323.110-0.448-0.4480.0000.0000.0000.000
108A112VAL0-0.055-0.02325.7610.1760.1760.0000.0000.0000.000
109A113GLU-1-0.923-0.95628.57111.15711.1570.0000.0000.0000.000
110A114ALA00.016-0.00830.693-0.009-0.0090.0000.0000.0000.000
111A115LEU0-0.0360.01233.970-0.109-0.1090.0000.0000.0000.000
112A116SER00.0300.01537.044-0.165-0.1650.0000.0000.0000.000
113A117LEU0-0.019-0.01439.737-0.061-0.0610.0000.0000.0000.000
114A118ILE0-0.0090.00839.229-0.018-0.0180.0000.0000.0000.000
115A119TYR00.002-0.01443.621-0.166-0.1660.0000.0000.0000.000
116A120ASN00.0760.02346.8360.0930.0930.0000.0000.0000.000
117A121LYS10.8860.94047.072-6.961-6.9610.0000.0000.0000.000
118A122ASP-1-0.908-0.94851.1516.1276.1270.0000.0000.0000.000
119A123LEU0-0.110-0.05652.339-0.131-0.1310.0000.0000.0000.000
120A124LEU00.008-0.01451.847-0.107-0.1070.0000.0000.0000.000
121A125PRO0-0.0010.01552.2650.1390.1390.0000.0000.0000.000
122A126ASN0-0.065-0.05253.044-0.026-0.0260.0000.0000.0000.000
123A127PRO0-0.0030.01148.885-0.076-0.0760.0000.0000.0000.000
124A128PRO00.0240.03451.126-0.032-0.0320.0000.0000.0000.000
125A129LYS10.9670.97248.571-6.513-6.5130.0000.0000.0000.000
126A130THR0-0.055-0.03650.4060.1060.1060.0000.0000.0000.000
127A131TRP00.0400.00545.423-0.065-0.0650.0000.0000.0000.000
128A132GLU-1-0.801-0.92351.8076.0426.0420.0000.0000.0000.000
129A133GLU-1-0.963-0.94954.6905.7925.7920.0000.0000.0000.000
130A134ILE0-0.012-0.00850.180-0.018-0.0180.0000.0000.0000.000
131A135PRO00.003-0.00454.665-0.043-0.0430.0000.0000.0000.000
132A136ALA0-0.043-0.02857.268-0.050-0.0500.0000.0000.0000.000
133A137LEU00.0440.03454.123-0.061-0.0610.0000.0000.0000.000
134A138ASP-1-0.734-0.86755.8835.9055.9050.0000.0000.0000.000
135A139LYS10.9130.95857.348-5.074-5.0740.0000.0000.0000.000
136A140GLU-1-0.949-0.97460.2165.3755.3750.0000.0000.0000.000
137A141LEU00.0280.00654.824-0.041-0.0410.0000.0000.0000.000
138A142LYS10.7910.89355.261-5.874-5.8740.0000.0000.0000.000
139A143ALA0-0.0150.01559.965-0.053-0.0530.0000.0000.0000.000
140A144LYS10.8630.93960.289-5.269-5.2690.0000.0000.0000.000
141A145GLY00.002-0.00359.9410.0620.0620.0000.0000.0000.000
142A146LYS10.8450.91754.515-5.883-5.8830.0000.0000.0000.000
143A147SER00.023-0.01051.865-0.069-0.0690.0000.0000.0000.000
144A148ALA00.0970.05653.1890.0650.0650.0000.0000.0000.000
145A149LEU0-0.0060.00446.4250.1010.1010.0000.0000.0000.000
146A150MET0-0.0020.00247.120-0.079-0.0790.0000.0000.0000.000
147A151PHE00.0180.01642.5300.1220.1220.0000.0000.0000.000
148A152ASN00.0700.03038.382-0.281-0.2810.0000.0000.0000.000
149A153LEU0-0.015-0.00741.7500.0800.0800.0000.0000.0000.000
150A154GLN0-0.031-0.02640.385-0.029-0.0290.0000.0000.0000.000
151A155GLU-1-0.933-0.95736.0838.9748.9740.0000.0000.0000.000
152A156PRO00.0110.01237.001-0.107-0.1070.0000.0000.0000.000
153A157TYR00.008-0.00632.432-0.146-0.1460.0000.0000.0000.000
154A158PHE0-0.010-0.02235.5370.0310.0310.0000.0000.0000.000
155A159THR0-0.0070.00439.204-0.126-0.1260.0000.0000.0000.000
156A160TRP0-0.0480.01938.307-0.266-0.2660.0000.0000.0000.000
157A161PRO00.0130.01139.158-0.132-0.1320.0000.0000.0000.000
158A162LEU0-0.0190.01041.447-0.111-0.1110.0000.0000.0000.000
159A163ILE0-0.034-0.02142.845-0.151-0.1510.0000.0000.0000.000
160A164ALA00.0410.02441.356-0.125-0.1250.0000.0000.0000.000
161A165ALA0-0.023-0.00143.405-0.088-0.0880.0000.0000.0000.000
162A166ASP-1-0.958-0.98245.5206.3466.3460.0000.0000.0000.000
163A167GLY0-0.021-0.01745.812-0.140-0.1400.0000.0000.0000.000
164A168GLY0-0.058-0.01444.0610.0640.0640.0000.0000.0000.000
165A169TYR0-0.082-0.10539.512-0.003-0.0030.0000.0000.0000.000
166A170ALA00.0400.01935.928-0.095-0.0950.0000.0000.0000.000
167A171PHE00.000-0.01334.254-0.088-0.0880.0000.0000.0000.000
168A172LYS10.9731.00536.536-7.663-7.6630.0000.0000.0000.000
169A173TYR0-0.075-0.04130.7730.2380.2380.0000.0000.0000.000
170A174GLU-1-0.904-0.94835.9877.7947.7940.0000.0000.0000.000
171A175ASN0-0.026-0.02335.8030.0850.0850.0000.0000.0000.000
172A176GLY0-0.024-0.00331.8040.1770.1770.0000.0000.0000.000
173A177LYS10.8880.94627.479-10.938-10.9380.0000.0000.0000.000
174A178TYR00.0320.01429.649-0.111-0.1110.0000.0000.0000.000
175A179ASP-1-0.865-0.93133.5388.4208.4200.0000.0000.0000.000
176A180ILE0-0.047-0.03733.238-0.170-0.1700.0000.0000.0000.000
177A181LYS10.9020.95636.030-8.585-8.5850.0000.0000.0000.000
178A182ASP-1-0.868-0.89039.4627.4737.4730.0000.0000.0000.000
179A183VAL00.0590.01338.7910.2030.2030.0000.0000.0000.000
180A184GLY00.0050.01941.151-0.248-0.2480.0000.0000.0000.000
181A185VAL00.0020.00041.0550.0010.0010.0000.0000.0000.000
182A186ASP-1-0.879-0.95443.8786.4816.4810.0000.0000.0000.000
183A187ASN00.0240.01245.897-0.210-0.2100.0000.0000.0000.000
184A188ALA0-0.022-0.02848.618-0.076-0.0760.0000.0000.0000.000
185A189GLY00.015-0.01249.173-0.064-0.0640.0000.0000.0000.000
186A190ALA0-0.0130.01446.5610.0720.0720.0000.0000.0000.000
187A191LYS10.9750.97147.848-6.158-6.1580.0000.0000.0000.000
188A192ALA0-0.077-0.01750.946-0.093-0.0930.0000.0000.0000.000
189A193GLY00.0640.02348.352-0.081-0.0810.0000.0000.0000.000
190A194LEU00.0410.02446.651-0.011-0.0110.0000.0000.0000.000
191A195THR0-0.003-0.00649.162-0.082-0.0820.0000.0000.0000.000
192A196PHE0-0.0210.00451.016-0.062-0.0620.0000.0000.0000.000
193A197LEU00.006-0.00646.369-0.040-0.0400.0000.0000.0000.000
194A198VAL0-0.006-0.00950.447-0.023-0.0230.0000.0000.0000.000
195A199ASP-1-0.847-0.95552.5795.6845.6840.0000.0000.0000.000
196A200LEU0-0.0110.00250.467-0.095-0.0950.0000.0000.0000.000
197A201ILE0-0.0110.00749.636-0.068-0.0680.0000.0000.0000.000
198A202LYS10.8700.96254.080-5.626-5.6260.0000.0000.0000.000
199A203ASN0-0.044-0.02157.052-0.119-0.1190.0000.0000.0000.000
200A204LYS10.8030.90354.893-5.957-5.9570.0000.0000.0000.000
201A205HIS0-0.015-0.01354.946-0.076-0.0760.0000.0000.0000.000
202A206MET0-0.0240.01148.7790.1250.1250.0000.0000.0000.000
203A207ASN0-0.035-0.04250.392-0.191-0.1910.0000.0000.0000.000
204A208ALA00.0540.02348.8140.1370.1370.0000.0000.0000.000
205A209ASP-1-0.900-0.93647.5126.6046.6040.0000.0000.0000.000
206A210THR0-0.059-0.02845.1310.0250.0250.0000.0000.0000.000
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