Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LJ439

Calculation Name: 2W8M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W8M

Chain ID: A

ChEMBL ID:

UniProt ID: Q6TRV5

Base Structure: X-ray

Registration Date: 2023-06-20

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2002250.803674
FMO2-HF: Nuclear repulsion 1930800.077904
FMO2-HF: Total energy -71450.72577
FMO2-MP2: Total energy -71665.577698


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:19:ILE)


Summations of interaction energy for fragment #1(A:19:ILE)
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.
-1.9160.6680.127-0.865-1.8440.003
Interaction energy analysis for fragmet #1(A:19:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.017
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].
3A21PRO00.006-0.0013.818-1.5570.273-0.015-0.736-1.0790.003
4A22THR00.0240.0135.3720.3560.416-0.001-0.003-0.0550.000
5A23VAL00.0440.0088.177-0.124-0.1240.0000.0000.0000.000
6A24GLY00.0250.02210.557-0.031-0.0310.0000.0000.0000.000
7A25LEU00.0730.0402.762-0.615-0.0830.143-0.106-0.5700.000
8A26GLY0-0.009-0.0077.493-0.073-0.0730.0000.0000.0000.000
9A27ARG10.8080.8709.0990.1070.1070.0000.0000.0000.000
10A28GLU-1-0.865-0.9429.019-0.072-0.0720.0000.0000.0000.000
11A29TYR0-0.004-0.0073.833-0.1080.0540.000-0.020-0.1400.000
12A30LEU0-0.0420.0029.8020.0210.0210.0000.0000.0000.000
13A31VAL0-0.009-0.01213.1890.0220.0220.0000.0000.0000.000
14A32LEU00.0170.01110.4140.0170.0170.0000.0000.0000.000
15A33GLY00.0380.01413.2960.0120.0120.0000.0000.0000.000
16A34LYS10.8790.93714.8450.1580.1580.0000.0000.0000.000
17A35LEU00.0130.01816.8850.0180.0180.0000.0000.0000.000
18A36LEU00.0370.01514.7600.0160.0160.0000.0000.0000.000
19A37ILE00.0130.02118.4960.0160.0160.0000.0000.0000.000
20A38SER0-0.087-0.05020.8910.0160.0160.0000.0000.0000.000
21A39LEU00.0170.00919.9110.0100.0100.0000.0000.0000.000
22A40SER00.0140.00021.4970.0060.0060.0000.0000.0000.000
23A41LYS10.9170.95224.1820.1220.1220.0000.0000.0000.000
24A42TRP0-0.008-0.01925.2040.0080.0080.0000.0000.0000.000
25A43ARG10.8630.94827.1590.0910.0910.0000.0000.0000.000
26A44ALA0-0.0080.00028.4740.0040.0040.0000.0000.0000.000
27A45LYS10.9020.94430.2690.0840.0840.0000.0000.0000.000
28A46GLY00.0570.04832.2070.0040.0040.0000.0000.0000.000
29A47LEU0-0.090-0.03330.3500.0040.0040.0000.0000.0000.000
30A48ILE0-0.037-0.02028.0550.0040.0040.0000.0000.0000.000
31A49ASP-1-0.859-0.92831.252-0.062-0.0620.0000.0000.0000.000
32A50PHE0-0.038-0.02428.3370.0010.0010.0000.0000.0000.000
33A51ASP-1-0.797-0.88326.755-0.097-0.0970.0000.0000.0000.000
34A52VAL0-0.019-0.01522.9460.0060.0060.0000.0000.0000.000
35A53TYR0-0.066-0.05821.744-0.008-0.0080.0000.0000.0000.000
36A54LEU00.0630.04415.8190.0090.0090.0000.0000.0000.000
37A68TYR00.0220.01331.5220.0010.0010.0000.0000.0000.000
38A69GLU-1-0.882-0.93125.170-0.049-0.0490.0000.0000.0000.000
39A70TYR00.024-0.00828.6780.0040.0040.0000.0000.0000.000
40A71TYR0-0.029-0.02325.882-0.006-0.0060.0000.0000.0000.000
41A72LYS10.8750.91422.8280.0430.0430.0000.0000.0000.000
42A73GLY0-0.034-0.00823.2550.0010.0010.0000.0000.0000.000
43A74LEU0-0.057-0.04322.4810.0090.0090.0000.0000.0000.000
44A75GLU-1-0.865-0.90618.717-0.057-0.0570.0000.0000.0000.000
45A76ASP-1-0.892-0.94215.430-0.043-0.0430.0000.0000.0000.000
46A77LYS10.8340.93916.498-0.010-0.0100.0000.0000.0000.000
47A78TYR0-0.069-0.06117.0320.0150.0150.0000.0000.0000.000
48A79ASP-1-0.799-0.87612.410-0.052-0.0520.0000.0000.0000.000
49A80LEU0-0.009-0.00413.319-0.030-0.0300.0000.0000.0000.000
50A81THR00.0000.00415.6770.0240.0240.0000.0000.0000.000
51A82LEU0-0.043-0.01319.028-0.013-0.0130.0000.0000.0000.000
52A83TYR00.0560.00819.2820.0120.0120.0000.0000.0000.000
53A84ILE0-0.020-0.00123.727-0.005-0.0050.0000.0000.0000.000
54A85ARG10.9400.96026.4410.1000.1000.0000.0000.0000.000
55A86ALA0-0.0250.00929.2820.0030.0030.0000.0000.0000.000
56A87LYS10.8680.89531.8440.0540.0540.0000.0000.0000.000
57A88ASP-1-0.805-0.87831.008-0.061-0.0610.0000.0000.0000.000
58A89SER0-0.044-0.00728.717-0.001-0.0010.0000.0000.0000.000
59A90TYR00.0210.00424.821-0.003-0.0030.0000.0000.0000.000
60A91TYR00.0470.02626.7420.0040.0040.0000.0000.0000.000
61A92PRO00.0010.01723.273-0.006-0.0060.0000.0000.0000.000
62A93LEU0-0.029-0.01424.9490.0070.0070.0000.0000.0000.000
63A94LEU0-0.026-0.01223.5260.0070.0070.0000.0000.0000.000
64A95TRP00.0300.02020.284-0.006-0.0060.0000.0000.0000.000
65A96ILE0-0.033-0.03416.9270.0070.0070.0000.0000.0000.000
66A97ASP-1-0.747-0.86416.185-0.017-0.0170.0000.0000.0000.000
67A98ILE0-0.091-0.05512.302-0.001-0.0010.0000.0000.0000.000
68A99THR0-0.010-0.01014.1490.0220.0220.0000.0000.0000.000
69A100GLY00.0270.01212.984-0.015-0.0150.0000.0000.0000.000
70A101SER0-0.025-0.02113.987-0.020-0.0200.0000.0000.0000.000
71A102SER0-0.058-0.04715.8840.0170.0170.0000.0000.0000.000
72A103TRP0-0.001-0.01619.0660.0040.0040.0000.0000.0000.000
73A104THR00.0430.03621.2260.0070.0070.0000.0000.0000.000
74A105GLU-1-0.803-0.85919.014-0.036-0.0360.0000.0000.0000.000
75A106GLU-1-0.928-0.94317.5930.1090.1090.0000.0000.0000.000
76A107GLN0-0.037-0.03719.8300.0160.0160.0000.0000.0000.000
77A108SER0-0.0120.01920.9750.0020.0020.0000.0000.0000.000
78A109LYS10.8500.90523.153-0.056-0.0560.0000.0000.0000.000
79A110GLU-1-0.885-0.92326.1200.0370.0370.0000.0000.0000.000
80A111ARG10.8680.91827.165-0.027-0.0270.0000.0000.0000.000
81A112TYR0-0.017-0.01629.071-0.001-0.0010.0000.0000.0000.000
82A113GLY00.0400.01429.7080.0040.0040.0000.0000.0000.000
83A114GLU-1-0.822-0.87728.963-0.008-0.0080.0000.0000.0000.000
84A115SER00.0110.00922.9190.0080.0080.0000.0000.0000.000
85A116ILE00.026-0.00724.853-0.002-0.0020.0000.0000.0000.000
86A117TYR00.0430.01619.2080.0060.0060.0000.0000.0000.000
87A118ALA00.0190.02020.4490.0010.0010.0000.0000.0000.000
88A119ILE0-0.0050.00220.1210.0000.0000.0000.0000.0000.000
89A120LEU00.0090.01217.6370.0040.0040.0000.0000.0000.000
90A121SER00.024-0.01721.635-0.013-0.0130.0000.0000.0000.000
91A122VAL00.0290.01321.999-0.007-0.0070.0000.0000.0000.000
92A123LYS10.8180.90415.655-0.019-0.0190.0000.0000.0000.000
93A124VAL00.0070.01022.377-0.011-0.0110.0000.0000.0000.000
94A125GLU-1-0.859-0.92625.7950.0470.0470.0000.0000.0000.000
95A126THR0-0.039-0.02222.976-0.002-0.0020.0000.0000.0000.000
96A127ALA00.0470.01925.399-0.005-0.0050.0000.0000.0000.000
97A128LYS10.9370.97226.925-0.023-0.0230.0000.0000.0000.000
98A129LYS10.8910.96027.830-0.025-0.0250.0000.0000.0000.000
99A130TYR0-0.025-0.02626.2030.0020.0020.0000.0000.0000.000
100A131ASP-1-0.920-0.94329.715-0.011-0.0110.0000.0000.0000.000
101A132VAL00.023-0.00326.291-0.005-0.0050.0000.0000.0000.000
102A133LEU0-0.0020.00527.829-0.003-0.0030.0000.0000.0000.000
103A134GLY0-0.003-0.01128.416-0.001-0.0010.0000.0000.0000.000
104A135ARG10.8380.91726.8600.0330.0330.0000.0000.0000.000
105A136VAL00.0290.03122.373-0.006-0.0060.0000.0000.0000.000
106A137PHE0-0.025-0.03122.4990.0050.0050.0000.0000.0000.000
107A138PHE00.0300.02219.593-0.003-0.0030.0000.0000.0000.000
108A139ILE0-0.020-0.03317.988-0.001-0.0010.0000.0000.0000.000
109A140HIS00.0730.04217.760-0.002-0.0020.0000.0000.0000.000
110A141TYR0-0.060-0.06117.719-0.005-0.0050.0000.0000.0000.000
111A142ASN00.0040.01319.5380.0040.0040.0000.0000.0000.000
112A143ASP-1-0.793-0.90319.910-0.099-0.0990.0000.0000.0000.000
113A144THR0-0.053-0.03422.6150.0000.0000.0000.0000.0000.000
114A145GLU-1-0.866-0.93726.145-0.041-0.0410.0000.0000.0000.000
115A146ASP-1-0.836-0.87423.169-0.112-0.1120.0000.0000.0000.000
116A147LYS10.9040.94723.8110.0560.0560.0000.0000.0000.000
117A148LEU0-0.019-0.00218.3030.0030.0030.0000.0000.0000.000
118A149LYS10.7920.89321.9350.0420.0420.0000.0000.0000.000
119A150CYS0-0.092-0.04522.166-0.003-0.0030.0000.0000.0000.000
120A151ILE00.0400.02223.9440.0050.0050.0000.0000.0000.000
121A152SER00.0510.03724.5860.0000.0000.0000.0000.0000.000
122A153ALA00.0760.02525.6260.0050.0050.0000.0000.0000.000
123A154LEU0-0.035-0.01527.1810.0050.0050.0000.0000.0000.000
124A155GLN00.0550.01929.5950.0040.0040.0000.0000.0000.000
125A156ILE00.0260.02924.9180.0020.0020.0000.0000.0000.000
126A157LEU00.0270.01029.5260.0030.0030.0000.0000.0000.000
127A158ASN0-0.074-0.04032.1870.0040.0040.0000.0000.0000.000
128A159LEU00.0110.00030.4390.0000.0000.0000.0000.0000.000
129A160GLU-1-0.820-0.88732.4550.0330.0330.0000.0000.0000.000
130A161ARG10.9210.95434.305-0.004-0.0040.0000.0000.0000.000
131A162GLN0-0.022-0.00237.1680.0000.0000.0000.0000.0000.000
132A163ASN0-0.035-0.01037.0410.0020.0020.0000.0000.0000.000
133A164LYS10.9150.96834.7150.0000.0000.0000.0000.0000.000
134A165ILE0-0.0110.00129.0260.0000.0000.0000.0000.0000.000
135A166LYS10.8650.91331.231-0.027-0.0270.0000.0000.0000.000
136A167LYS10.8300.93228.846-0.046-0.0460.0000.0000.0000.000
137A168ASP-1-0.827-0.91328.0630.0570.0570.0000.0000.0000.000
138A169LYS10.8010.88726.526-0.081-0.0810.0000.0000.0000.000
139A170PHE00.007-0.00425.3460.0120.0120.0000.0000.0000.000
140A171GLU-1-0.760-0.87022.6070.1350.1350.0000.0000.0000.000
141A172ARG10.8900.94516.311-0.186-0.1860.0000.0000.0000.000
142A173GLY00.0400.01219.527-0.015-0.0150.0000.0000.0000.000
143A174ALA0-0.003-0.00619.273-0.021-0.0210.0000.0000.0000.000
144A175LYS10.8360.91221.175-0.162-0.1620.0000.0000.0000.000
145A176SER0-0.072-0.05021.2810.0040.0040.0000.0000.0000.000
146A177GLU-1-0.793-0.85323.5130.0670.0670.0000.0000.0000.000
147A178TYR00.0220.00117.7930.0110.0110.0000.0000.0000.000
148A179TYR0-0.017-0.03224.516-0.003-0.0030.0000.0000.0000.000
149A180LEU00.0200.01224.685-0.002-0.0020.0000.0000.0000.000
150A181ILE0-0.019-0.02125.644-0.004-0.0040.0000.0000.0000.000
151A182PRO00.0380.02626.082-0.002-0.0020.0000.0000.0000.000
152A183THR00.0530.01424.992-0.005-0.0050.0000.0000.0000.000
153A184SER0-0.072-0.05527.151-0.005-0.0050.0000.0000.0000.000
154A185TYR0-0.051-0.02629.602-0.002-0.0020.0000.0000.0000.000
155A186TRP0-0.057-0.01120.698-0.005-0.0050.0000.0000.0000.000
156A187LYS10.8550.91627.2470.0230.0230.0000.0000.0000.000
157A188ASN00.0420.02826.618-0.008-0.0080.0000.0000.0000.000
158A189LEU00.0630.01122.0600.0040.0040.0000.0000.0000.000
159A190THR0-0.029-0.02226.365-0.003-0.0030.0000.0000.0000.000
160A191GLU-1-0.792-0.87328.753-0.027-0.0270.0000.0000.0000.000
161A192LEU00.0370.02022.5910.0010.0010.0000.0000.0000.000
162A193ARG10.8870.95027.0950.0660.0660.0000.0000.0000.000
163A194ILE0-0.016-0.01428.8520.0000.0000.0000.0000.0000.000
164A195ALA00.0290.02428.6740.0020.0020.0000.0000.0000.000
165A196LEU0-0.014-0.00525.4600.0010.0010.0000.0000.0000.000
166A197ARG10.9260.94528.9140.0530.0530.0000.0000.0000.000
167A198GLY00.0230.02332.3400.0020.0020.0000.0000.0000.000
168A199PHE00.025-0.00430.0960.0030.0030.0000.0000.0000.000
169A200TYR00.0020.00830.5540.0020.0020.0000.0000.0000.000
170A201GLN0-0.002-0.00632.355-0.002-0.0020.0000.0000.0000.000
171A202SER0-0.011-0.01534.8550.0030.0030.0000.0000.0000.000
172A203PHE0-0.006-0.01531.9390.0020.0020.0000.0000.0000.000
173A204LYS10.9270.96334.8440.0440.0440.0000.0000.0000.000
174A205GLU-1-0.965-0.97836.385-0.027-0.0270.0000.0000.0000.000
175A206TYR0-0.067-0.01936.0120.0020.0020.0000.0000.0000.000
176A207LEU0-0.0340.00334.0680.0010.0010.0000.0000.0000.000