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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QV16Y

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:


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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2352569.346512
FMO2-HF: Nuclear repulsion 2273132.70398
FMO2-HF: Total energy -79436.642531
FMO2-MP2: Total energy -79668.974355


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.
0.7432.5820.003-0.697-1.1460.001
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 : 0.001 / q_NPA : -0.007
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-1-0.881-0.9313.807-1.1330.4340.000-0.652-0.9150.001
4A13ALA0-0.0050.0073.5840.4790.7290.004-0.044-0.2110.000
5A14LEU00.0410.0185.2770.2020.224-0.001-0.001-0.0200.000
6A15VAL0-0.028-0.0029.0160.2030.2030.0000.0000.0000.000
7A16ARG10.9580.97310.6660.0230.0230.0000.0000.0000.000
8A17LEU00.0140.01114.1140.0170.0170.0000.0000.0000.000
9A18ALA0-0.005-0.01317.0950.0270.0270.0000.0000.0000.000
10A19ARG10.7260.82319.2080.1090.1090.0000.0000.0000.000
11A20GLU-1-0.889-0.93818.847-0.166-0.1660.0000.0000.0000.000
12A21ARG10.8060.89921.8450.0480.0480.0000.0000.0000.000
13A22PHE00.046-0.00318.2580.0000.0000.0000.0000.0000.000
14A23ASP-1-0.878-0.91123.908-0.018-0.0180.0000.0000.0000.000
15A24LEU0-0.021-0.00925.4570.0000.0000.0000.0000.0000.000
16A25PRO00.0550.01728.8990.0030.0030.0000.0000.0000.000
17A26ASP-1-0.799-0.89131.031-0.049-0.0490.0000.0000.0000.000
18A27GLN0-0.0120.00131.938-0.009-0.0090.0000.0000.0000.000
19A28VAL00.0620.02229.021-0.005-0.0050.0000.0000.0000.000
20A29ARG10.8770.94325.4430.0390.0390.0000.0000.0000.000
21A30ARG10.8160.89027.3000.0580.0580.0000.0000.0000.000
22A31LEU0-0.0420.00729.105-0.005-0.0050.0000.0000.0000.000
23A32ALA00.0450.02527.132-0.009-0.0090.0000.0000.0000.000
24A33ARG10.9430.96621.2580.2740.2740.0000.0000.0000.000
25A34PRO0-0.042-0.00225.8830.0050.0050.0000.0000.0000.000
26A35PRO00.0320.01328.272-0.013-0.0130.0000.0000.0000.000
27A36VAL0-0.003-0.00328.080-0.003-0.0030.0000.0000.0000.000
28A37PRO0-0.0140.00730.6080.0070.0070.0000.0000.0000.000
29A38SER00.002-0.00633.169-0.008-0.0080.0000.0000.0000.000
30A39LEU0-0.045-0.03335.1160.0080.0080.0000.0000.0000.000
31A40GLU-1-0.899-0.93437.643-0.100-0.1000.0000.0000.0000.000
32A41PRO00.0640.02539.782-0.001-0.0010.0000.0000.0000.000
33A42PRO0-0.082-0.04740.3540.0050.0050.0000.0000.0000.000
34A43TYR0-0.059-0.04437.085-0.003-0.0030.0000.0000.0000.000
35A44GLY00.0670.04634.4820.0020.0020.0000.0000.0000.000
36A45LEU0-0.040-0.01631.094-0.002-0.0020.0000.0000.0000.000
37A46ARG10.7660.85424.0320.2600.2600.0000.0000.0000.000
38A47VAL00.0190.00422.9080.0000.0000.0000.0000.0000.000
39A48ALA0-0.0080.00121.433-0.005-0.0050.0000.0000.0000.000
40A49GLN00.002-0.01220.010-0.036-0.0360.0000.0000.0000.000
41A50LEU00.0460.02813.1190.0060.0060.0000.0000.0000.000
42A51THR00.020-0.00316.107-0.036-0.0360.0000.0000.0000.000
43A52ASP-1-0.775-0.84718.223-0.288-0.2880.0000.0000.0000.000
44A53ALA0-0.007-0.00214.8950.0370.0370.0000.0000.0000.000
45A54GLU-1-0.894-0.96214.972-0.540-0.5400.0000.0000.0000.000
46A55MET0-0.0280.00418.1450.0430.0430.0000.0000.0000.000
47A56LEU00.0140.00419.3240.0320.0320.0000.0000.0000.000
48A57ALA00.0040.01516.7970.0280.0280.0000.0000.0000.000
49A58GLU-1-0.841-0.88618.887-0.144-0.1440.0000.0000.0000.000
50A59TRP0-0.017-0.03521.9380.0240.0240.0000.0000.0000.000
51A60MET0-0.029-0.02320.9410.0280.0280.0000.0000.0000.000
52A61ASN0-0.035-0.02318.7460.0320.0320.0000.0000.0000.000
53A62ARG10.7520.87322.8940.1670.1670.0000.0000.0000.000
54A63PRO00.001-0.01526.6210.0030.0030.0000.0000.0000.000
55A64HIS0-0.043-0.03629.0590.0080.0080.0000.0000.0000.000
56A65LEU0-0.024-0.01225.8890.0040.0040.0000.0000.0000.000
57A66ALA00.0680.04624.194-0.002-0.0020.0000.0000.0000.000
58A67ALA0-0.021-0.00825.1480.0070.0070.0000.0000.0000.000
59A68ALA0-0.085-0.04327.9230.0060.0060.0000.0000.0000.000
60A69TRP0-0.038-0.02923.104-0.001-0.0010.0000.0000.0000.000
61A70GLU-1-0.927-0.94522.955-0.057-0.0570.0000.0000.0000.000
62A71TYR0-0.035-0.03319.2990.0030.0030.0000.0000.0000.000
63A72ASP-1-0.876-0.92019.353-0.137-0.1370.0000.0000.0000.000
64A73TRP0-0.037-0.01714.307-0.007-0.0070.0000.0000.0000.000
65A74PRO00.0370.00712.409-0.007-0.0070.0000.0000.0000.000
66A75ALA00.0590.02513.554-0.037-0.0370.0000.0000.0000.000
67A76SER00.0240.0028.5040.0140.0140.0000.0000.0000.000
68A77ARG10.9881.01010.0590.1520.1520.0000.0000.0000.000
69A78TRP00.024-0.00911.363-0.019-0.0190.0000.0000.0000.000
70A79ARG10.9020.94810.5491.2031.2030.0000.0000.0000.000
71A80GLN0-0.0020.0046.3360.2460.2460.0000.0000.0000.000
72A81HIS0-0.077-0.03511.3050.0510.0510.0000.0000.0000.000
73A82LEU0-0.011-0.01314.7770.0420.0420.0000.0000.0000.000
74A83ASN0-0.003-0.01811.706-0.009-0.0090.0000.0000.0000.000
75A84ALA00.0200.00613.2350.0420.0420.0000.0000.0000.000
76A85GLN0-0.0560.00014.5870.0780.0780.0000.0000.0000.000
77A86LEU0-0.063-0.03617.1430.0360.0360.0000.0000.0000.000
78A87GLU-1-0.899-0.94713.895-0.501-0.5010.0000.0000.0000.000
79A88GLY00.0040.03017.1510.0340.0340.0000.0000.0000.000
80A89THR0-0.054-0.05519.6150.0030.0030.0000.0000.0000.000
81A90TYR0-0.006-0.02220.6130.0180.0180.0000.0000.0000.000
82A91SER00.007-0.02521.5470.0230.0230.0000.0000.0000.000
83A92LEU0-0.0080.00122.108-0.028-0.0280.0000.0000.0000.000
84A93PRO00.0040.02120.1700.0200.0200.0000.0000.0000.000
85A94LEU0-0.028-0.01923.398-0.008-0.0080.0000.0000.0000.000
86A95ILE0-0.013-0.00923.1040.0020.0020.0000.0000.0000.000
87A96GLY0-0.009-0.01227.1070.0090.0090.0000.0000.0000.000
88A97SER0-0.023-0.01430.702-0.001-0.0010.0000.0000.0000.000
89A98TRP00.019-0.00532.7500.0090.0090.0000.0000.0000.000
90A99HIS0-0.037-0.02236.054-0.004-0.0040.0000.0000.0000.000
91A100GLY00.0140.01334.6070.0010.0010.0000.0000.0000.000
92A101THR0-0.042-0.00932.029-0.005-0.0050.0000.0000.0000.000
93A102ASP-1-0.749-0.87927.308-0.205-0.2050.0000.0000.0000.000
94A103GLY00.027-0.00429.8300.0010.0010.0000.0000.0000.000
95A104GLY0-0.039-0.02229.3080.0120.0120.0000.0000.0000.000
96A105TYR00.0090.00021.493-0.022-0.0220.0000.0000.0000.000
97A106LEU0-0.030-0.02426.4150.0190.0190.0000.0000.0000.000
98A107GLU-1-0.739-0.83921.952-0.211-0.2110.0000.0000.0000.000
99A108LEU00.0010.01726.0510.0170.0170.0000.0000.0000.000
100A109TYR00.0090.00825.422-0.011-0.0110.0000.0000.0000.000
101A110TRP00.0050.00226.9160.0150.0150.0000.0000.0000.000
102A111ALA00.020-0.00227.9730.0000.0000.0000.0000.0000.000
103A112ALA00.0140.00629.8030.0050.0050.0000.0000.0000.000
104A113LYS10.8170.91025.1560.1260.1260.0000.0000.0000.000
105A114ASP-1-0.712-0.81224.963-0.099-0.0990.0000.0000.0000.000
106A115LEU00.0260.02625.1400.0110.0110.0000.0000.0000.000
107A116ILE0-0.015-0.02827.2310.0090.0090.0000.0000.0000.000
108A117SER0-0.058-0.01729.5000.0070.0070.0000.0000.0000.000
109A118HIS0-0.014-0.00627.6950.0060.0060.0000.0000.0000.000
110A119TYR0-0.079-0.04630.0040.0050.0050.0000.0000.0000.000
111A120TYR0-0.060-0.07333.672-0.001-0.0010.0000.0000.0000.000
112A121ASP-1-0.915-0.94435.922-0.024-0.0240.0000.0000.0000.000
113A122ALA0-0.031-0.01034.110-0.002-0.0020.0000.0000.0000.000
114A123ASP-1-0.827-0.90736.097-0.049-0.0490.0000.0000.0000.000
115A124PRO0-0.045-0.04434.315-0.004-0.0040.0000.0000.0000.000
116A125TYR0-0.029-0.02233.466-0.007-0.0070.0000.0000.0000.000
117A126ASP-1-0.698-0.80634.286-0.060-0.0600.0000.0000.0000.000
118A127LEU00.009-0.00330.928-0.006-0.0060.0000.0000.0000.000
119A128GLY0-0.0030.02130.4730.0090.0090.0000.0000.0000.000
120A129LEU0-0.015-0.01729.996-0.010-0.0100.0000.0000.0000.000
121A130HIS10.7940.90825.1700.1300.1300.0000.0000.0000.000
122A131ALA00.029-0.00328.555-0.009-0.0090.0000.0000.0000.000
123A132ALA0-0.0100.01027.2620.0100.0100.0000.0000.0000.000
124A133ILE0-0.019-0.01229.367-0.006-0.0060.0000.0000.0000.000
125A134ALA00.0790.04628.0880.0050.0050.0000.0000.0000.000
126A135ASP-1-0.857-0.91629.393-0.115-0.1150.0000.0000.0000.000
127A136LEU00.0160.00432.1200.0060.0060.0000.0000.0000.000
128A137SER00.0460.00733.8320.0050.0050.0000.0000.0000.000
129A138LYS10.8890.92735.7010.1120.1120.0000.0000.0000.000
130A139VAL00.0360.03433.4960.0030.0030.0000.0000.0000.000
131A140ASN0-0.035-0.03736.7400.0030.0030.0000.0000.0000.000
132A141ARG10.8620.93639.7580.0730.0730.0000.0000.0000.000
133A142GLY00.0260.03640.5140.0020.0020.0000.0000.0000.000
134A143PHE00.0000.00135.7970.0020.0020.0000.0000.0000.000
135A144GLY00.0480.01636.838-0.002-0.0020.0000.0000.0000.000
136A145PRO0-0.005-0.01637.480-0.001-0.0010.0000.0000.0000.000
137A146LEU00.0040.02740.6400.0020.0020.0000.0000.0000.000
138A147LEU0-0.002-0.01137.1170.0010.0010.0000.0000.0000.000
139A148LEU00.0130.01134.413-0.002-0.0020.0000.0000.0000.000
140A149PRO00.0200.01137.942-0.002-0.0020.0000.0000.0000.000
141A150ARG10.9570.98339.6460.0830.0830.0000.0000.0000.000
142A151ILE00.0230.01433.626-0.002-0.0020.0000.0000.0000.000
143A152VAL00.0080.01036.785-0.003-0.0030.0000.0000.0000.000
144A153ALA00.0130.01438.0840.0010.0010.0000.0000.0000.000
145A154SER00.0310.01936.7920.0000.0000.0000.0000.0000.000
146A155VAL0-0.012-0.00833.448-0.001-0.0010.0000.0000.0000.000
147A156PHE0-0.006-0.01436.1010.0000.0000.0000.0000.0000.000
148A157ALA0-0.041-0.00939.1610.0030.0030.0000.0000.0000.000
149A158ASN0-0.072-0.05335.220-0.003-0.0030.0000.0000.0000.000
150A159GLU-1-0.804-0.86734.917-0.088-0.0880.0000.0000.0000.000
151A160PRO00.0420.02037.3980.0040.0040.0000.0000.0000.000
152A161ARG10.7800.87135.3120.0840.0840.0000.0000.0000.000
153A162CYS0-0.106-0.04235.7530.0040.0040.0000.0000.0000.000
154A163ARG10.8730.92338.1290.0470.0470.0000.0000.0000.000
155A164ARG10.7490.83737.4280.0530.0530.0000.0000.0000.000
156A165ILE00.0100.00734.190-0.004-0.0040.0000.0000.0000.000
157A166MET0-0.063-0.03332.9590.0060.0060.0000.0000.0000.000
158A167PHE00.0260.00233.133-0.008-0.0080.0000.0000.0000.000
159A168ASP-1-0.749-0.87029.267-0.074-0.0740.0000.0000.0000.000
160A169PRO00.0420.03531.104-0.003-0.0030.0000.0000.0000.000
161A170ASP-1-0.745-0.85130.885-0.034-0.0340.0000.0000.0000.000
162A171HIS0-0.014-0.01232.5500.0020.0020.0000.0000.0000.000
163A172ARG10.9140.92830.2850.0340.0340.0000.0000.0000.000
164A173ASN0-0.0130.01632.7250.0010.0010.0000.0000.0000.000
165A174THR00.0660.00836.010-0.001-0.0010.0000.0000.0000.000
166A175ALA0-0.068-0.02537.8980.0000.0000.0000.0000.0000.000
167A176THR00.033-0.00334.466-0.003-0.0030.0000.0000.0000.000
168A177ARG10.8200.89637.5480.0330.0330.0000.0000.0000.000
169A178ARG10.9900.99339.4060.0420.0420.0000.0000.0000.000
170A179LEU0-0.0370.00038.4460.0000.0000.0000.0000.0000.000
171A180CYS0-0.025-0.02338.160-0.001-0.0010.0000.0000.0000.000
172A181GLU-1-0.833-0.90440.873-0.037-0.0370.0000.0000.0000.000
173A182TRP0-0.046-0.03744.1130.0000.0000.0000.0000.0000.000
174A183ALA0-0.029-0.00742.6040.0000.0000.0000.0000.0000.000
175A184GLY00.0060.01444.6790.0000.0000.0000.0000.0000.000
176A185CYS0-0.106-0.03240.959-0.001-0.0010.0000.0000.0000.000
177A186LYS10.9600.98742.6670.0350.0350.0000.0000.0000.000
178A187PHE0-0.013-0.01439.496-0.001-0.0010.0000.0000.0000.000
179A188LEU00.001-0.02138.2780.0030.0030.0000.0000.0000.000
180A189GLY00.0200.03039.6670.0020.0020.0000.0000.0000.000
181A190GLU-1-0.825-0.90937.361-0.026-0.0260.0000.0000.0000.000
182A191HIS10.8320.90034.0990.0280.0280.0000.0000.0000.000
183A192ASP-1-0.786-0.85032.703-0.011-0.0110.0000.0000.0000.000
184A193THR0-0.058-0.05528.289-0.002-0.0020.0000.0000.0000.000
185A194THR00.005-0.02423.6910.0040.0040.0000.0000.0000.000
186A195ASN0-0.0340.00023.7010.0180.0180.0000.0000.0000.000
187A196ARG10.9200.98425.8360.0620.0620.0000.0000.0000.000
188A197ARG10.8310.90828.9980.0140.0140.0000.0000.0000.000
189A198MET0-0.064-0.01330.981-0.004-0.0040.0000.0000.0000.000
190A199ALA00.0170.00733.2460.0050.0050.0000.0000.0000.000
191A200LEU0-0.002-0.00233.675-0.005-0.0050.0000.0000.0000.000
192A201TYR0-0.058-0.05636.3540.0050.0050.0000.0000.0000.000
193A202ALA00.0560.02937.105-0.005-0.0050.0000.0000.0000.000
194A203LEU00.0150.01538.9360.0030.0030.0000.0000.0000.000
195A204GLU-1-0.790-0.87840.440-0.050-0.0500.0000.0000.0000.000
196A205ALA00.0260.01841.643-0.001-0.0010.0000.0000.0000.000
197A206PRO0-0.035-0.02043.1400.0030.0030.0000.0000.0000.000
198A207THR0-0.0140.00446.5210.0000.0000.0000.0000.0000.000