FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

tag_button

FMODB ID: KG353

Calculation Name: 1YK3-A-Xray372

Preferred Name:

Target Type:

Ligand Name: octyl beta-d-glucopyranoside

ligand 3-letter code: BOG

PDB ID: 1YK3

Chain ID: A

ChEMBL ID:

UniProt ID: P9WK15

Base Structure: X-ray

Registration Date: 2023-09-21

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

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357534.774322
FMO2-HF: Nuclear repulsion 2278097.716453
FMO2-HF: Total energy -79437.057869
FMO2-MP2: Total energy -79669.341476


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:10:ALA)


Summations of interaction energy for fragment #1(A:10:ALA)
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.
1.1332.9490.003-0.713-1.1040.001
Interaction energy analysis for fragmet #1(A:10:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.001
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].
3A12ASP-1-0.867-0.9303.886-1.0030.479-0.005-0.649-0.8270.001
4A13ALA0-0.0190.0033.5140.7371.0320.009-0.063-0.2410.000
5A14LEU00.0420.0265.2590.2770.316-0.001-0.001-0.0360.000
6A15VAL0-0.0110.0078.8020.2260.2260.0000.0000.0000.000
7A16ARG10.9490.97610.396-0.072-0.0720.0000.0000.0000.000
8A17LEU00.0260.01213.9550.0140.0140.0000.0000.0000.000
9A18ALA0-0.008-0.01416.8690.0230.0230.0000.0000.0000.000
10A19ARG10.7370.82818.8570.0760.0760.0000.0000.0000.000
11A20GLU-1-0.884-0.94118.382-0.112-0.1120.0000.0000.0000.000
12A21ARG10.7780.88321.6620.0220.0220.0000.0000.0000.000
13A22PHE00.0270.00118.197-0.001-0.0010.0000.0000.0000.000
14A23ASP-1-0.848-0.90823.9860.0120.0120.0000.0000.0000.000
15A24LEU0-0.0100.00425.408-0.002-0.0020.0000.0000.0000.000
16A25PRO00.0760.02728.9450.0040.0040.0000.0000.0000.000
17A26ASP-1-0.764-0.86731.008-0.026-0.0260.0000.0000.0000.000
18A27GLN00.0070.01931.692-0.008-0.0080.0000.0000.0000.000
19A28VAL00.0350.01428.918-0.006-0.0060.0000.0000.0000.000
20A29ARG10.7950.88125.9260.0040.0040.0000.0000.0000.000
21A30ARG10.8160.89127.3050.0360.0360.0000.0000.0000.000
22A31LEU0-0.0370.01529.054-0.007-0.0070.0000.0000.0000.000
23A32ALA00.0620.02526.831-0.005-0.0050.0000.0000.0000.000
24A33ARG10.9110.95921.1800.2460.2460.0000.0000.0000.000
25A34PRO0-0.050-0.00825.6250.0030.0030.0000.0000.0000.000
26A35PRO00.0340.01427.924-0.013-0.0130.0000.0000.0000.000
27A36VAL00.0100.00127.848-0.003-0.0030.0000.0000.0000.000
28A37PRO0-0.0160.00430.3610.0060.0060.0000.0000.0000.000
29A38SER00.0210.01932.885-0.008-0.0080.0000.0000.0000.000
30A39LEU0-0.037-0.02934.8240.0060.0060.0000.0000.0000.000
31A40GLU-1-0.877-0.93137.306-0.096-0.0960.0000.0000.0000.000
32A41PRO00.0400.01640.0160.0000.0000.0000.0000.0000.000
33A42PRO0-0.068-0.03140.7740.0050.0050.0000.0000.0000.000
34A43TYR0-0.043-0.03837.110-0.003-0.0030.0000.0000.0000.000
35A44GLY00.0660.03634.5830.0010.0010.0000.0000.0000.000
36A45LEU0-0.061-0.02130.770-0.001-0.0010.0000.0000.0000.000
37A46ARG10.7710.83423.8820.2450.2450.0000.0000.0000.000
38A47VAL00.0180.00922.6550.0020.0020.0000.0000.0000.000
39A48ALA0-0.0130.00721.014-0.009-0.0090.0000.0000.0000.000
40A49GLN00.003-0.01419.525-0.037-0.0370.0000.0000.0000.000
41A50LEU00.005-0.00112.9000.0050.0050.0000.0000.0000.000
42A51THR00.011-0.00915.440-0.077-0.0770.0000.0000.0000.000
43A52ASP-1-0.755-0.83618.212-0.269-0.2690.0000.0000.0000.000
44A53ALA0-0.0050.00914.7770.0340.0340.0000.0000.0000.000
45A54GLU-1-0.863-0.95614.550-0.562-0.5620.0000.0000.0000.000
46A55MET0-0.0290.00417.7240.0430.0430.0000.0000.0000.000
47A56LEU0-0.001-0.00619.2100.0330.0330.0000.0000.0000.000
48A57ALA00.0210.02916.6520.0270.0270.0000.0000.0000.000
49A58GLU-1-0.839-0.88018.765-0.135-0.1350.0000.0000.0000.000
50A59TRP0-0.006-0.03121.7650.0230.0230.0000.0000.0000.000
51A60MET0-0.031-0.00920.8900.0280.0280.0000.0000.0000.000
52A61ASN0-0.031-0.03218.7290.0340.0340.0000.0000.0000.000
53A62ARG10.7550.86222.8510.1600.1600.0000.0000.0000.000
54A63PRO00.014-0.00526.6320.0040.0040.0000.0000.0000.000
55A64HIS0-0.067-0.04628.8950.0100.0100.0000.0000.0000.000
56A65LEU0-0.042-0.01625.9530.0030.0030.0000.0000.0000.000
57A66ALA00.0940.05124.1660.0030.0030.0000.0000.0000.000
58A67ALA0-0.017-0.01325.1560.0070.0070.0000.0000.0000.000
59A68ALA0-0.095-0.04627.6190.0080.0080.0000.0000.0000.000
60A69TRP0-0.053-0.03623.459-0.001-0.0010.0000.0000.0000.000
61A70GLU-1-0.877-0.91822.988-0.024-0.0240.0000.0000.0000.000
62A71TYR0-0.015-0.02919.5350.0070.0070.0000.0000.0000.000
63A72ASP-1-0.888-0.93219.343-0.113-0.1130.0000.0000.0000.000
64A73TRP0-0.032-0.00714.5840.0040.0040.0000.0000.0000.000
65A74PRO00.027-0.00712.151-0.018-0.0180.0000.0000.0000.000
66A75ALA00.0500.02413.653-0.023-0.0230.0000.0000.0000.000
67A76SER00.0330.0188.2770.0420.0420.0000.0000.0000.000
68A77ARG10.9651.00210.3870.1260.1260.0000.0000.0000.000
69A78TRP00.012-0.01411.2900.0210.0210.0000.0000.0000.000
70A79ARG10.8460.91710.6341.1451.1450.0000.0000.0000.000
71A80GLN0-0.009-0.0076.4490.2000.2000.0000.0000.0000.000
72A81HIS0-0.056-0.02511.0460.0720.0720.0000.0000.0000.000
73A82LEU0-0.011-0.00314.6080.0540.0540.0000.0000.0000.000
74A83ASN0-0.021-0.02811.7160.0140.0140.0000.0000.0000.000
75A84ALA00.0220.00212.9550.0480.0480.0000.0000.0000.000
76A85GLN0-0.055-0.00214.4450.0780.0780.0000.0000.0000.000
77A86LEU0-0.059-0.02317.0020.0330.0330.0000.0000.0000.000
78A87GLU-1-0.869-0.92213.912-0.478-0.4780.0000.0000.0000.000
79A88GLY00.0080.02317.2350.0370.0370.0000.0000.0000.000
80A89THR0-0.014-0.03719.4880.0040.0040.0000.0000.0000.000
81A90TYR0-0.020-0.03020.4250.0110.0110.0000.0000.0000.000
82A91SER0-0.002-0.03621.5970.0190.0190.0000.0000.0000.000
83A92LEU0-0.0010.00722.318-0.023-0.0230.0000.0000.0000.000
84A93PRO00.0090.02319.6900.0170.0170.0000.0000.0000.000
85A94LEU0-0.017-0.01922.872-0.010-0.0100.0000.0000.0000.000
86A95ILE0-0.002-0.00322.9620.0020.0020.0000.0000.0000.000
87A96GLY0-0.002-0.00426.8750.0080.0080.0000.0000.0000.000
88A97SER0-0.026-0.01830.563-0.004-0.0040.0000.0000.0000.000
89A98TRP00.020-0.00932.7390.0100.0100.0000.0000.0000.000
90A99HIS0-0.031-0.01435.800-0.006-0.0060.0000.0000.0000.000
91A100GLY00.0240.02635.0430.0020.0020.0000.0000.0000.000
92A101THR0-0.065-0.02832.170-0.005-0.0050.0000.0000.0000.000
93A102ASP-1-0.746-0.86227.689-0.196-0.1960.0000.0000.0000.000
94A103GLY00.014-0.01129.7550.0010.0010.0000.0000.0000.000
95A104GLY0-0.031-0.01829.0810.0120.0120.0000.0000.0000.000
96A105TYR00.001-0.00821.358-0.021-0.0210.0000.0000.0000.000
97A106LEU0-0.028-0.02426.1780.0190.0190.0000.0000.0000.000
98A107GLU-1-0.740-0.83721.803-0.174-0.1740.0000.0000.0000.000
99A108LEU00.0100.01625.6610.0170.0170.0000.0000.0000.000
100A109TYR0-0.0010.00225.327-0.010-0.0100.0000.0000.0000.000
101A110TRP00.0300.00526.8550.0130.0130.0000.0000.0000.000
102A111ALA00.006-0.00528.0430.0020.0020.0000.0000.0000.000
103A112ALA00.007-0.00229.7650.0060.0060.0000.0000.0000.000
104A113LYS10.7950.90125.0820.0950.0950.0000.0000.0000.000
105A114ASP-1-0.714-0.80024.863-0.062-0.0620.0000.0000.0000.000
106A115LEU00.0290.02625.0660.0080.0080.0000.0000.0000.000
107A116ILE0-0.018-0.01827.0940.0070.0070.0000.0000.0000.000
108A117SER0-0.029-0.00829.3730.0050.0050.0000.0000.0000.000
109A118HIS0-0.031-0.01327.4960.0040.0040.0000.0000.0000.000
110A119TYR0-0.091-0.06729.5770.0050.0050.0000.0000.0000.000
111A120TYR0-0.065-0.06733.553-0.001-0.0010.0000.0000.0000.000
112A121ASP-1-0.887-0.93835.392-0.008-0.0080.0000.0000.0000.000
113A122ALA0-0.051-0.02533.737-0.003-0.0030.0000.0000.0000.000
114A123ASP-1-0.797-0.88235.669-0.034-0.0340.0000.0000.0000.000
115A124PRO0-0.064-0.04934.107-0.003-0.0030.0000.0000.0000.000
116A125TYR0-0.008-0.02433.299-0.006-0.0060.0000.0000.0000.000
117A126ASP-1-0.719-0.82834.476-0.043-0.0430.0000.0000.0000.000
118A127LEU00.0100.00330.616-0.003-0.0030.0000.0000.0000.000
119A128GLY0-0.0050.00430.5220.0090.0090.0000.0000.0000.000
120A129LEU0-0.012-0.00429.786-0.010-0.0100.0000.0000.0000.000
121A130HIS10.7700.87925.1060.1020.1020.0000.0000.0000.000
122A131ALA00.0290.00028.741-0.008-0.0080.0000.0000.0000.000
123A132ALA00.0180.02427.1710.0080.0080.0000.0000.0000.000
124A133ILE0-0.022-0.01429.206-0.005-0.0050.0000.0000.0000.000
125A134ALA00.0650.04827.7360.0070.0070.0000.0000.0000.000
126A135ASP-1-0.846-0.90829.194-0.109-0.1090.0000.0000.0000.000
127A136LEU00.0050.00231.9510.0070.0070.0000.0000.0000.000
128A137SER00.0270.00233.6970.0050.0050.0000.0000.0000.000
129A138LYS10.9120.94435.3420.1080.1080.0000.0000.0000.000
130A139VAL00.0210.02333.6480.0040.0040.0000.0000.0000.000
131A140ASN0-0.028-0.02736.9150.0030.0030.0000.0000.0000.000
132A141ARG10.8570.92939.9470.0660.0660.0000.0000.0000.000
133A142GLY00.0270.02840.8270.0010.0010.0000.0000.0000.000
134A143PHE00.0070.00036.0460.0010.0010.0000.0000.0000.000
135A144GLY00.0500.02136.717-0.002-0.0020.0000.0000.0000.000
136A145PRO00.014-0.00537.403-0.001-0.0010.0000.0000.0000.000
137A146LEU0-0.0010.03140.6450.0020.0020.0000.0000.0000.000
138A147LEU00.002-0.00836.9880.0000.0000.0000.0000.0000.000
139A148LEU00.0240.01134.131-0.002-0.0020.0000.0000.0000.000
140A149PRO00.0330.01537.648-0.001-0.0010.0000.0000.0000.000
141A150ARG10.9040.95639.2650.0750.0750.0000.0000.0000.000
142A151ILE00.0300.01833.222-0.001-0.0010.0000.0000.0000.000
143A152VAL00.0010.00136.411-0.002-0.0020.0000.0000.0000.000
144A153ALA00.0070.00437.8840.0010.0010.0000.0000.0000.000
145A154SER0-0.011-0.01236.6650.0000.0000.0000.0000.0000.000
146A155VAL00.0000.00133.212-0.002-0.0020.0000.0000.0000.000
147A156PHE0-0.008-0.01535.8900.0000.0000.0000.0000.0000.000
148A157ALA0-0.029-0.00839.0000.0020.0020.0000.0000.0000.000
149A158ASN0-0.062-0.03734.768-0.004-0.0040.0000.0000.0000.000
150A159GLU-1-0.812-0.87434.624-0.072-0.0720.0000.0000.0000.000
151A160PRO00.0390.01437.0000.0040.0040.0000.0000.0000.000
152A161ARG10.7720.86835.0350.0690.0690.0000.0000.0000.000
153A162CYS0-0.091-0.02735.3490.0040.0040.0000.0000.0000.000
154A163ARG10.8790.92037.8210.0340.0340.0000.0000.0000.000
155A164ARG10.7470.83337.0610.0370.0370.0000.0000.0000.000
156A165ILE00.0000.00933.822-0.004-0.0040.0000.0000.0000.000
157A166MET0-0.048-0.01832.8140.0040.0040.0000.0000.0000.000
158A167PHE00.0330.00532.869-0.008-0.0080.0000.0000.0000.000
159A168ASP-1-0.735-0.85128.915-0.050-0.0500.0000.0000.0000.000
160A169PRO00.0520.03931.001-0.001-0.0010.0000.0000.0000.000
161A170ASP-1-0.737-0.84730.920-0.015-0.0150.0000.0000.0000.000
162A171HIS0-0.030-0.02332.6940.0010.0010.0000.0000.0000.000
163A172ARG10.9240.92930.0580.0150.0150.0000.0000.0000.000
164A173ASN00.0170.03832.6520.0000.0000.0000.0000.0000.000
165A174THR00.061-0.00136.001-0.001-0.0010.0000.0000.0000.000
166A175ALA0-0.056-0.01437.6600.0000.0000.0000.0000.0000.000
167A176THR00.025-0.00634.490-0.003-0.0030.0000.0000.0000.000
168A177ARG10.7860.88637.5340.0200.0200.0000.0000.0000.000
169A178ARG10.9720.98539.5650.0320.0320.0000.0000.0000.000
170A179LEU0-0.032-0.00538.1410.0000.0000.0000.0000.0000.000
171A180CYS0-0.017-0.01738.028-0.002-0.0020.0000.0000.0000.000
172A181GLU-1-0.827-0.89840.745-0.027-0.0270.0000.0000.0000.000
173A182TRP0-0.041-0.03644.1620.0000.0000.0000.0000.0000.000
174A183ALA0-0.038-0.00942.2220.0000.0000.0000.0000.0000.000
175A184GLY00.0040.01144.315-0.001-0.0010.0000.0000.0000.000
176A185CYS0-0.090-0.02640.6590.0000.0000.0000.0000.0000.000
177A186LYS10.9460.97442.7430.0220.0220.0000.0000.0000.000
178A187PHE00.0220.00939.624-0.001-0.0010.0000.0000.0000.000
179A188LEU0-0.003-0.01037.6020.0020.0020.0000.0000.0000.000
180A189GLY00.0400.04239.2440.0030.0030.0000.0000.0000.000
181A190GLU-1-0.809-0.90337.392-0.012-0.0120.0000.0000.0000.000
182A191HIS10.8300.90133.9650.0100.0100.0000.0000.0000.000
183A192ASP-1-0.762-0.83832.8760.0080.0080.0000.0000.0000.000
184A193THR0-0.049-0.03928.156-0.001-0.0010.0000.0000.0000.000
185A194THR00.005-0.02223.3690.0050.0050.0000.0000.0000.000
186A195ASN0-0.081-0.02023.8050.0200.0200.0000.0000.0000.000
187A196ARG10.8860.96525.8880.0370.0370.0000.0000.0000.000
188A197ARG10.8120.88929.128-0.002-0.0020.0000.0000.0000.000
189A198MET0-0.062-0.01130.938-0.006-0.0060.0000.0000.0000.000
190A199ALA00.017-0.00133.2810.0050.0050.0000.0000.0000.000
191A200LEU0-0.017-0.00433.416-0.005-0.0050.0000.0000.0000.000
192A201TYR0-0.075-0.07436.2280.0040.0040.0000.0000.0000.000
193A202ALA00.0610.02136.789-0.004-0.0040.0000.0000.0000.000
194A203LEU00.0010.00338.4580.0020.0020.0000.0000.0000.000
195A204GLU-1-0.788-0.87939.903-0.036-0.0360.0000.0000.0000.000
196A205ALA00.0270.01441.446-0.002-0.0020.0000.0000.0000.000
197A206PRO0-0.057-0.02942.7900.0030.0030.0000.0000.0000.000
198A207THR0-0.0140.01046.0400.0000.0000.0000.0000.0000.000