FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: R8528

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 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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2351547.252134
FMO2-HF: Nuclear repulsion 2272111.491109
FMO2-HF: Total energy -79435.761025
FMO2-MP2: Total energy -79668.161144


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.
0.8532.608-0.003-0.611-1.1420
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 : -0.026 / q_NPA : -0.034
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-1-0.951-0.9673.796-0.6310.860-0.005-0.568-0.9190.000
4A13ALA00.0030.0083.6260.7080.9570.003-0.042-0.2100.000
5A14LEU00.0300.0125.269-0.176-0.161-0.001-0.001-0.0130.000
6A15VAL0-0.0220.0008.8690.0880.0880.0000.0000.0000.000
7A16ARG10.9620.97210.649-0.058-0.0580.0000.0000.0000.000
8A17LEU00.0210.01314.098-0.025-0.0250.0000.0000.0000.000
9A18ALA0-0.011-0.01517.0760.0210.0210.0000.0000.0000.000
10A19ARG10.7480.85819.1670.0550.0550.0000.0000.0000.000
11A20GLU-1-0.886-0.92919.2720.0160.0160.0000.0000.0000.000
12A21ARG10.7950.89121.830-0.014-0.0140.0000.0000.0000.000
13A22PHE00.053-0.00318.2550.0050.0050.0000.0000.0000.000
14A23ASP-1-0.882-0.91223.9000.0470.0470.0000.0000.0000.000
15A24LEU0-0.045-0.02125.344-0.006-0.0060.0000.0000.0000.000
16A25PRO00.0430.01028.8940.0060.0060.0000.0000.0000.000
17A26ASP-1-0.878-0.93931.0280.0510.0510.0000.0000.0000.000
18A27GLN0-0.020-0.02631.937-0.002-0.0020.0000.0000.0000.000
19A28VAL00.0620.02828.850-0.002-0.0020.0000.0000.0000.000
20A29ARG10.9080.96025.595-0.066-0.0660.0000.0000.0000.000
21A30ARG10.8700.93227.298-0.049-0.0490.0000.0000.0000.000
22A31LEU0-0.0120.02229.028-0.001-0.0010.0000.0000.0000.000
23A32ALA00.0400.02327.1310.0030.0030.0000.0000.0000.000
24A33ARG10.9670.97621.4150.0450.0450.0000.0000.0000.000
25A34PRO0-0.049-0.00425.9050.0010.0010.0000.0000.0000.000
26A35PRO00.0250.01128.262-0.005-0.0050.0000.0000.0000.000
27A36VAL00.0080.00128.049-0.004-0.0040.0000.0000.0000.000
28A37PRO0-0.0050.00930.5970.0020.0020.0000.0000.0000.000
29A38SER0-0.020-0.02133.156-0.004-0.0040.0000.0000.0000.000
30A39LEU0-0.058-0.04034.9700.0020.0020.0000.0000.0000.000
31A40GLU-1-0.866-0.91837.585-0.036-0.0360.0000.0000.0000.000
32A41PRO00.0330.01139.676-0.003-0.0030.0000.0000.0000.000
33A42PRO0-0.084-0.05040.3010.0030.0030.0000.0000.0000.000
34A43TYR0-0.059-0.04436.940-0.004-0.0040.0000.0000.0000.000
35A44GLY00.0730.04734.3780.0030.0030.0000.0000.0000.000
36A45LEU0-0.032-0.01630.636-0.005-0.0050.0000.0000.0000.000
37A46ARG10.7920.88523.8220.1400.1400.0000.0000.0000.000
38A47VAL00.0130.00822.859-0.003-0.0030.0000.0000.0000.000
39A48ALA0-0.019-0.00621.283-0.005-0.0050.0000.0000.0000.000
40A49GLN00.010-0.01420.0000.0000.0000.0000.0000.0000.000
41A50LEU00.0340.02113.178-0.017-0.0170.0000.0000.0000.000
42A51THR00.007-0.01016.000-0.041-0.0410.0000.0000.0000.000
43A52ASP-1-0.748-0.83518.115-0.169-0.1690.0000.0000.0000.000
44A53ALA0-0.014-0.00514.8010.0140.0140.0000.0000.0000.000
45A54GLU-1-0.901-0.96415.320-0.409-0.4090.0000.0000.0000.000
46A55MET00.0000.01918.0440.0220.0220.0000.0000.0000.000
47A56LEU00.007-0.00119.1820.0190.0190.0000.0000.0000.000
48A57ALA00.0190.01816.7180.0150.0150.0000.0000.0000.000
49A58GLU-1-0.911-0.93018.796-0.159-0.1590.0000.0000.0000.000
50A59TRP0-0.051-0.05721.8480.0210.0210.0000.0000.0000.000
51A60MET0-0.011-0.01720.8970.0220.0220.0000.0000.0000.000
52A61ASN0-0.037-0.02218.6230.0170.0170.0000.0000.0000.000
53A62ARG10.8070.92422.8170.1420.1420.0000.0000.0000.000
54A63PRO00.004-0.01126.5420.0030.0030.0000.0000.0000.000
55A64HIS0-0.023-0.00828.9880.0010.0010.0000.0000.0000.000
56A65LEU0-0.025-0.01725.7630.0060.0060.0000.0000.0000.000
57A66ALA00.0670.04624.1220.0010.0010.0000.0000.0000.000
58A67ALA0-0.019-0.00725.0850.0030.0030.0000.0000.0000.000
59A68ALA0-0.086-0.04327.8590.0060.0060.0000.0000.0000.000
60A69TRP0-0.030-0.03122.8370.0050.0050.0000.0000.0000.000
61A70GLU-1-0.954-0.95622.862-0.075-0.0750.0000.0000.0000.000
62A71TYR0-0.037-0.02619.251-0.002-0.0020.0000.0000.0000.000
63A72ASP-1-0.853-0.91519.275-0.168-0.1680.0000.0000.0000.000
64A73TRP0-0.025-0.01214.148-0.025-0.0250.0000.0000.0000.000
65A74PRO00.021-0.00612.2950.0070.0070.0000.0000.0000.000
66A75ALA00.0720.03013.468-0.024-0.0240.0000.0000.0000.000
67A76SER00.013-0.0038.4290.0580.0580.0000.0000.0000.000
68A77ARG10.9911.0189.9600.2310.2310.0000.0000.0000.000
69A78TRP00.025-0.00711.2770.0330.0330.0000.0000.0000.000
70A79ARG10.9600.98110.8010.6870.6870.0000.0000.0000.000
71A80GLN00.0160.0126.4820.1790.1790.0000.0000.0000.000
72A81HIS0-0.072-0.03211.2130.0810.0810.0000.0000.0000.000
73A82LEU0-0.030-0.01814.6910.0500.0500.0000.0000.0000.000
74A83ASN00.034-0.00612.1210.0770.0770.0000.0000.0000.000
75A84ALA00.0260.01413.3420.0540.0540.0000.0000.0000.000
76A85GLN0-0.0450.02114.5740.0620.0620.0000.0000.0000.000
77A86LEU0-0.076-0.04317.0870.0260.0260.0000.0000.0000.000
78A87GLU-1-0.908-0.95113.984-0.011-0.0110.0000.0000.0000.000
79A88GLY0-0.0050.02717.1470.0330.0330.0000.0000.0000.000
80A89THR0-0.056-0.05319.609-0.010-0.0100.0000.0000.0000.000
81A90TYR0-0.018-0.03620.6140.0010.0010.0000.0000.0000.000
82A91SER0-0.012-0.04921.4610.0020.0020.0000.0000.0000.000
83A92LEU0-0.009-0.00122.095-0.005-0.0050.0000.0000.0000.000
84A93PRO00.0030.02320.2630.0030.0030.0000.0000.0000.000
85A94LEU0-0.015-0.02023.3810.0010.0010.0000.0000.0000.000
86A95ILE00.0030.00323.240-0.007-0.0070.0000.0000.0000.000
87A96GLY0-0.021-0.01927.0030.0090.0090.0000.0000.0000.000
88A97SER0-0.024-0.01330.598-0.004-0.0040.0000.0000.0000.000
89A98TRP0-0.019-0.01732.6450.0080.0080.0000.0000.0000.000
90A99HIS0-0.041-0.02235.949-0.005-0.0050.0000.0000.0000.000
91A100GLY00.0150.01734.499-0.001-0.0010.0000.0000.0000.000
92A101THR0-0.025-0.00131.914-0.004-0.0040.0000.0000.0000.000
93A102ASP-1-0.791-0.90827.160-0.115-0.1150.0000.0000.0000.000
94A103GLY00.040-0.00729.727-0.004-0.0040.0000.0000.0000.000
95A104GLY0-0.043-0.02529.2100.0050.0050.0000.0000.0000.000
96A105TYR0-0.011-0.00821.231-0.010-0.0100.0000.0000.0000.000
97A106LEU0-0.029-0.02626.3050.0090.0090.0000.0000.0000.000
98A107GLU-1-0.752-0.86221.757-0.118-0.1180.0000.0000.0000.000
99A108LEU0-0.0010.01925.9630.0060.0060.0000.0000.0000.000
100A109TYR00.0020.00525.392-0.001-0.0010.0000.0000.0000.000
101A110TRP0-0.004-0.00126.7440.0010.0010.0000.0000.0000.000
102A111ALA00.025-0.00127.9590.0010.0010.0000.0000.0000.000
103A112ALA00.0120.00629.7880.0020.0020.0000.0000.0000.000
104A113LYS10.8150.91125.005-0.013-0.0130.0000.0000.0000.000
105A114ASP-1-0.709-0.82224.950-0.030-0.0300.0000.0000.0000.000
106A115LEU00.0250.03525.3880.0050.0050.0000.0000.0000.000
107A116ILE0-0.027-0.04027.2130.0030.0030.0000.0000.0000.000
108A117SER0-0.061-0.02729.4680.0030.0030.0000.0000.0000.000
109A118HIS0-0.0010.00327.8010.0020.0020.0000.0000.0000.000
110A119TYR0-0.079-0.04629.9520.0000.0000.0000.0000.0000.000
111A120TYR0-0.070-0.07933.515-0.003-0.0030.0000.0000.0000.000
112A121ASP-1-0.907-0.94135.9060.0090.0090.0000.0000.0000.000
113A122ALA0-0.044-0.01734.088-0.002-0.0020.0000.0000.0000.000
114A123ASP-1-0.899-0.95536.0830.0070.0070.0000.0000.0000.000
115A124PRO0-0.052-0.04534.306-0.001-0.0010.0000.0000.0000.000
116A125TYR0-0.015-0.00733.4560.0000.0000.0000.0000.0000.000
117A126ASP-1-0.731-0.83034.246-0.009-0.0090.0000.0000.0000.000
118A127LEU00.008-0.00530.8850.0000.0000.0000.0000.0000.000
119A128GLY0-0.0030.02230.4600.0010.0010.0000.0000.0000.000
120A129LEU0-0.009-0.01429.878-0.003-0.0030.0000.0000.0000.000
121A130HIS10.8170.93625.3020.0630.0630.0000.0000.0000.000
122A131ALA00.034-0.00128.467-0.003-0.0030.0000.0000.0000.000
123A132ALA00.0010.00827.1110.0030.0030.0000.0000.0000.000
124A133ILE0-0.037-0.00929.277-0.001-0.0010.0000.0000.0000.000
125A134ALA00.0590.03127.984-0.001-0.0010.0000.0000.0000.000
126A135ASP-1-0.898-0.96529.299-0.092-0.0920.0000.0000.0000.000
127A136LEU0-0.005-0.01132.2800.0060.0060.0000.0000.0000.000
128A137SER00.0630.01133.7450.0050.0050.0000.0000.0000.000
129A138LYS10.9690.97435.9360.0720.0720.0000.0000.0000.000
130A139VAL00.0510.04933.5310.0040.0040.0000.0000.0000.000
131A140ASN0-0.041-0.03936.6510.0020.0020.0000.0000.0000.000
132A141ARG10.8370.92739.4750.0610.0610.0000.0000.0000.000
133A142GLY00.0400.04340.4320.0020.0020.0000.0000.0000.000
134A143PHE0-0.0060.00135.7580.0020.0020.0000.0000.0000.000
135A144GLY00.0510.01636.7420.0010.0010.0000.0000.0000.000
136A145PRO0-0.009-0.01837.3870.0010.0010.0000.0000.0000.000
137A146LEU00.0090.02740.5500.0030.0030.0000.0000.0000.000
138A147LEU00.001-0.00837.0180.0020.0020.0000.0000.0000.000
139A148LEU00.0110.01234.6110.0010.0010.0000.0000.0000.000
140A149PRO00.0090.00537.8490.0020.0020.0000.0000.0000.000
141A150ARG10.9660.98639.6130.0420.0420.0000.0000.0000.000
142A151ILE00.0330.02133.6490.0010.0010.0000.0000.0000.000
143A152VAL00.0100.01136.7680.0010.0010.0000.0000.0000.000
144A153ALA00.0190.01638.0600.0030.0030.0000.0000.0000.000
145A154SER00.0320.03336.8400.0020.0020.0000.0000.0000.000
146A155VAL00.0040.00133.5080.0020.0020.0000.0000.0000.000
147A156PHE00.000-0.01536.0860.0020.0020.0000.0000.0000.000
148A157ALA0-0.043-0.01139.1480.0030.0030.0000.0000.0000.000
149A158ASN0-0.092-0.06435.1420.0010.0010.0000.0000.0000.000
150A159GLU-1-0.850-0.92234.925-0.002-0.0020.0000.0000.0000.000
151A160PRO00.0410.01937.3880.0010.0010.0000.0000.0000.000
152A161ARG10.8300.92335.909-0.002-0.0020.0000.0000.0000.000
153A162CYS0-0.087-0.02235.9120.0010.0010.0000.0000.0000.000
154A163ARG10.9590.97938.117-0.002-0.0020.0000.0000.0000.000
155A164ARG10.7880.88637.4970.0060.0060.0000.0000.0000.000
156A165ILE00.0090.00834.2630.0000.0000.0000.0000.0000.000
157A166MET0-0.058-0.03332.9360.0000.0000.0000.0000.0000.000
158A167PHE00.0230.00333.059-0.004-0.0040.0000.0000.0000.000
159A168ASP-1-0.763-0.90129.138-0.041-0.0410.0000.0000.0000.000
160A169PRO00.0080.02131.041-0.005-0.0050.0000.0000.0000.000
161A170ASP-1-0.739-0.86030.887-0.043-0.0430.0000.0000.0000.000
162A171HIS0-0.035-0.02332.4920.0010.0010.0000.0000.0000.000
163A172ARG10.9330.93530.3970.0500.0500.0000.0000.0000.000
164A173ASN0-0.0090.02032.6460.0010.0010.0000.0000.0000.000
165A174THR00.0790.01135.9460.0020.0020.0000.0000.0000.000
166A175ALA0-0.087-0.02837.8030.0020.0020.0000.0000.0000.000
167A176THR00.0390.00534.4500.0000.0000.0000.0000.0000.000
168A177ARG10.8320.89837.4730.0290.0290.0000.0000.0000.000
169A178ARG10.9820.97939.3370.0360.0360.0000.0000.0000.000
170A179LEU0-0.0150.00538.4800.0010.0010.0000.0000.0000.000
171A180CYS0-0.037-0.01838.1020.0010.0010.0000.0000.0000.000
172A181GLU-1-0.893-0.95640.798-0.023-0.0230.0000.0000.0000.000
173A182TRP0-0.039-0.03244.1960.0000.0000.0000.0000.0000.000
174A183ALA0-0.033-0.01042.5330.0010.0010.0000.0000.0000.000
175A184GLY00.0050.01344.5980.0010.0010.0000.0000.0000.000
176A185CYS0-0.088-0.02240.5850.0010.0010.0000.0000.0000.000
177A186LYS10.9650.99042.5990.0100.0100.0000.0000.0000.000
178A187PHE0-0.020-0.01339.515-0.001-0.0010.0000.0000.0000.000
179A188LEU00.007-0.01738.3950.0020.0020.0000.0000.0000.000
180A189GLY00.0280.03339.6180.0020.0020.0000.0000.0000.000
181A190GLU-1-0.842-0.90637.322-0.025-0.0250.0000.0000.0000.000
182A191HIS10.8150.88834.0250.0140.0140.0000.0000.0000.000
183A192ASP-1-0.820-0.89032.580-0.018-0.0180.0000.0000.0000.000
184A193THR0-0.075-0.05828.1350.0010.0010.0000.0000.0000.000
185A194THR0-0.025-0.03623.137-0.002-0.0020.0000.0000.0000.000
186A195ASN00.0230.01923.6650.0040.0040.0000.0000.0000.000
187A196ARG10.9531.00825.8060.0450.0450.0000.0000.0000.000
188A197ARG10.8900.94828.9600.0220.0220.0000.0000.0000.000
189A198MET0-0.052-0.00630.835-0.003-0.0030.0000.0000.0000.000
190A199ALA00.0110.00533.1950.0040.0040.0000.0000.0000.000
191A200LEU00.001-0.00333.712-0.003-0.0030.0000.0000.0000.000
192A201TYR0-0.035-0.01236.2930.0020.0020.0000.0000.0000.000
193A202ALA00.0520.02537.037-0.001-0.0010.0000.0000.0000.000
194A203LEU00.0250.01838.8940.0010.0010.0000.0000.0000.000
195A204GLU-1-0.823-0.90940.422-0.009-0.0090.0000.0000.0000.000
196A205ALA00.0170.01041.636-0.001-0.0010.0000.0000.0000.000
197A206PRO0-0.045-0.02443.1240.0010.0010.0000.0000.0000.000
198A207THR0-0.0080.00746.5050.0010.0010.0000.0000.0000.000