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

tag_button

FMODB ID: MMK7Z

Calculation Name: 2W8M-A-Xray316

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2012790.259037
FMO2-HF: Nuclear repulsion 1940998.717527
FMO2-HF: Total energy -71791.54151
FMO2-MP2: Total energy -72007.364042


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:18:ACE )


Summations of interaction energy for fragment #1(A:18:ACE )
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.
1.3022.103-0.005-0.341-0.455-0.001
Interaction energy analysis for fragmet #1(A:18:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.006
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].
3A20LEU 00.0120.0163.8471.1531.954-0.005-0.341-0.455-0.001
4A21PRO 00.0100.0046.352-0.057-0.0570.0000.0000.0000.000
5A22THR 00.0300.01310.0120.1160.1160.0000.0000.0000.000
6A23VAL 00.0340.00412.490-0.005-0.0050.0000.0000.0000.000
7A24GLY 00.0220.01815.4000.0160.0160.0000.0000.0000.000
8A25LEU 00.0760.0429.6420.0060.0060.0000.0000.0000.000
9A26GLY 0-0.013-0.00813.7730.0240.0240.0000.0000.0000.000
10A27ARG 10.9250.96415.8390.2150.2150.0000.0000.0000.000
11A28GLU -1-0.860-0.93614.958-0.408-0.4080.0000.0000.0000.000
12A29TYR 00.007-0.00111.2510.0720.0720.0000.0000.0000.000
13A30LEU 0-0.048-0.00117.6210.0360.0360.0000.0000.0000.000
14A31VAL 0-0.001-0.00920.8470.0290.0290.0000.0000.0000.000
15A32LEU 00.0190.01218.1020.0230.0230.0000.0000.0000.000
16A33GLY 00.0400.01321.2120.0200.0200.0000.0000.0000.000
17A34LYS 10.9410.96522.7640.1480.1480.0000.0000.0000.000
18A35LEU 00.0080.00824.4810.0170.0170.0000.0000.0000.000
19A36LEU 00.0440.01922.0150.0160.0160.0000.0000.0000.000
20A37ILE 00.0050.02126.2720.0160.0160.0000.0000.0000.000
21A38SER 0-0.070-0.03728.7570.0140.0140.0000.0000.0000.000
22A39LEU 00.0180.00927.4550.0100.0100.0000.0000.0000.000
23A40SER 00.015-0.00129.1460.0080.0080.0000.0000.0000.000
24A41LYS 10.9120.94731.8340.0930.0930.0000.0000.0000.000
25A42TRP 00.000-0.01432.5910.0060.0060.0000.0000.0000.000
26A43ARG 10.9320.99034.6430.0700.0700.0000.0000.0000.000
27A44ALA 0-0.006-0.00436.0770.0040.0040.0000.0000.0000.000
28A45LYS 10.8860.93737.1660.0720.0720.0000.0000.0000.000
29A46GLY 00.0610.05139.8560.0030.0030.0000.0000.0000.000
30A47LEU 0-0.092-0.03338.0580.0000.0000.0000.0000.0000.000
31A48ILE 0-0.051-0.03635.5570.0000.0000.0000.0000.0000.000
32A49ASP -1-0.857-0.92438.695-0.053-0.0530.0000.0000.0000.000
33A50PHE 0-0.055-0.02734.9490.0020.0020.0000.0000.0000.000
34A51ASP -1-0.874-0.94333.299-0.073-0.0730.0000.0000.0000.000
35A52VAL 0-0.017-0.01929.6440.0010.0010.0000.0000.0000.000
36A53TYR 0-0.024-0.02627.841-0.001-0.0010.0000.0000.0000.000
37A54LEU 00.0130.00322.802-0.002-0.0020.0000.0000.0000.000
38A55NME 00.0400.03621.4520.0070.0070.0000.0000.0000.000
39A67ACE 00.015-0.00437.0020.0000.0000.0000.0000.0000.000
40A68TYR 0-0.024-0.02234.7530.0000.0000.0000.0000.0000.000
41A69GLU -1-0.891-0.93328.648-0.073-0.0730.0000.0000.0000.000
42A70TYR 00.019-0.00632.140-0.001-0.0010.0000.0000.0000.000
43A71TYR 0-0.037-0.02629.977-0.005-0.0050.0000.0000.0000.000
44A72LYS 11.0131.02326.4570.0670.0670.0000.0000.0000.000
45A73GLY 0-0.052-0.02026.316-0.005-0.0050.0000.0000.0000.000
46A74LEU 0-0.063-0.04425.987-0.004-0.0040.0000.0000.0000.000
47A75GLU -1-0.934-0.95821.749-0.130-0.1300.0000.0000.0000.000
48A76ASP -1-0.886-0.93918.471-0.187-0.1870.0000.0000.0000.000
49A77LYS 10.8540.95119.7090.1150.1150.0000.0000.0000.000
50A78TYR 0-0.082-0.05521.7300.0020.0020.0000.0000.0000.000
51A79ASP -1-0.782-0.85718.235-0.295-0.2950.0000.0000.0000.000
52A80LEU 0-0.025-0.01519.158-0.010-0.0100.0000.0000.0000.000
53A81THR 00.0050.00921.8650.0200.0200.0000.0000.0000.000
54A82LEU 0-0.058-0.02324.801-0.001-0.0010.0000.0000.0000.000
55A83TYR 00.0630.01224.4910.0070.0070.0000.0000.0000.000
56A84ILE 0-0.0220.00029.4970.0010.0010.0000.0000.0000.000
57A85ARG 10.9570.97431.8450.0670.0670.0000.0000.0000.000
58A86ALA 0-0.0260.01034.7300.0020.0020.0000.0000.0000.000
59A87LYS 10.9620.95536.7670.0410.0410.0000.0000.0000.000
60A88ASP -1-0.888-0.92235.659-0.045-0.0450.0000.0000.0000.000
61A89SER 0-0.063-0.02833.100-0.001-0.0010.0000.0000.0000.000
62A90TYR 00.015-0.00329.661-0.001-0.0010.0000.0000.0000.000
63A91TYR 00.0530.02031.388-0.001-0.0010.0000.0000.0000.000
64A92PRO 00.0010.01628.282-0.002-0.0020.0000.0000.0000.000
65A93LEU 0-0.035-0.01630.1740.0050.0050.0000.0000.0000.000
66A94LEU 0-0.040-0.02830.0560.0040.0040.0000.0000.0000.000
67A95TRP 00.0400.02425.337-0.002-0.0020.0000.0000.0000.000
68A96ILE 0-0.033-0.03524.1550.0100.0100.0000.0000.0000.000
69A97ASP -1-0.794-0.90321.979-0.222-0.2220.0000.0000.0000.000
70A98ILE 0-0.092-0.05319.4200.0250.0250.0000.0000.0000.000
71A99THR 0-0.002-0.00620.334-0.006-0.0060.0000.0000.0000.000
72A100GLY 00.015-0.00319.2540.0120.0120.0000.0000.0000.000
73A101SER 0-0.031-0.02219.1420.0140.0140.0000.0000.0000.000
74A102SER 0-0.040-0.02621.2600.0050.0050.0000.0000.0000.000
75A103TRP 0-0.003-0.00823.7490.0000.0000.0000.0000.0000.000
76A104THR 00.0090.01925.6630.0060.0060.0000.0000.0000.000
77A105GLU -1-0.871-0.93023.918-0.151-0.1510.0000.0000.0000.000
78A106GLU -1-0.977-0.97221.553-0.163-0.1630.0000.0000.0000.000
79A107GLN 0-0.040-0.03323.8460.0130.0130.0000.0000.0000.000
80A108SER 00.006-0.00225.0620.0040.0040.0000.0000.0000.000
81A109LYS 10.8920.96027.7470.0720.0720.0000.0000.0000.000
82A110GLU -1-0.802-0.89431.167-0.049-0.0490.0000.0000.0000.000
83A111ARG 10.8290.88731.8820.0530.0530.0000.0000.0000.000
84A112TYR 00.0180.01034.548-0.002-0.0020.0000.0000.0000.000
85A113GLY 00.009-0.01234.351-0.002-0.0020.0000.0000.0000.000
86A114GLU -1-0.846-0.87634.368-0.075-0.0750.0000.0000.0000.000
87A115SER 00.0130.00928.637-0.001-0.0010.0000.0000.0000.000
88A116ILE 00.024-0.00629.2950.0030.0030.0000.0000.0000.000
89A117TYR 00.0440.01924.995-0.011-0.0110.0000.0000.0000.000
90A118ALA 00.0170.02224.7560.0100.0100.0000.0000.0000.000
91A119ILE 0-0.0030.00224.839-0.014-0.0140.0000.0000.0000.000
92A120LEU 00.0100.01020.8250.0120.0120.0000.0000.0000.000
93A121SER 00.0420.00925.4410.0020.0020.0000.0000.0000.000
94A122VAL 00.0530.02424.6400.0030.0030.0000.0000.0000.000
95A123LYS 10.8380.91220.0520.2140.2140.0000.0000.0000.000
96A124VAL 00.0090.00526.2460.0040.0040.0000.0000.0000.000
97A125GLU -1-0.937-0.97329.798-0.074-0.0740.0000.0000.0000.000
98A126THR 0-0.053-0.02726.5630.0060.0060.0000.0000.0000.000
99A127ALA 00.0430.02129.3230.0040.0040.0000.0000.0000.000
100A128LYS 10.9330.96731.1570.0650.0650.0000.0000.0000.000
101A129LYS 10.9150.97229.9920.0770.0770.0000.0000.0000.000
102A130TYR 0-0.041-0.03229.2690.0030.0030.0000.0000.0000.000
103A131ASP -1-0.921-0.94433.460-0.059-0.0590.0000.0000.0000.000
104A132VAL 00.019-0.00531.2420.0010.0010.0000.0000.0000.000
105A133LEU 00.0000.00333.032-0.005-0.0050.0000.0000.0000.000
106A134GLY 0-0.006-0.01133.979-0.004-0.0040.0000.0000.0000.000
107A135ARG 10.8420.92832.6190.0780.0780.0000.0000.0000.000
108A136VAL 00.0210.03227.700-0.006-0.0060.0000.0000.0000.000
109A137PHE 0-0.023-0.03128.6450.0070.0070.0000.0000.0000.000
110A138PHE 00.0290.02225.272-0.009-0.0090.0000.0000.0000.000
111A139ILE 0-0.026-0.03225.1690.0150.0150.0000.0000.0000.000
112A140HIS 00.0730.04324.575-0.010-0.0100.0000.0000.0000.000
113A141TYR 0-0.083-0.06424.9420.0100.0100.0000.0000.0000.000
114A142ASN 00.0080.00926.736-0.004-0.0040.0000.0000.0000.000
115A143ASP -1-0.831-0.93126.385-0.132-0.1320.0000.0000.0000.000
116A144THR 0-0.061-0.03329.3800.0070.0070.0000.0000.0000.000
117A145GLU -1-0.953-0.98432.999-0.075-0.0750.0000.0000.0000.000
118A146ASP -1-0.890-0.89330.977-0.096-0.0960.0000.0000.0000.000
119A147LYS 10.8920.94031.1540.0820.0820.0000.0000.0000.000
120A148LEU 0-0.029-0.00926.133-0.004-0.0040.0000.0000.0000.000
121A149LYS 10.8330.91729.2060.0990.0990.0000.0000.0000.000
122A150CYS 0-0.068-0.03229.238-0.008-0.0080.0000.0000.0000.000
123A151ILE 00.0310.01730.2410.0100.0100.0000.0000.0000.000
124A152SER 00.0480.04030.898-0.006-0.0060.0000.0000.0000.000
125A153ALA 00.0830.02930.8750.0020.0020.0000.0000.0000.000
126A154LEU 0-0.030-0.01532.5490.0040.0040.0000.0000.0000.000
127A155GLN 00.0410.01035.6670.0060.0060.0000.0000.0000.000
128A156ILE 00.0190.02430.4110.0040.0040.0000.0000.0000.000
129A157LEU 00.0320.01134.8560.0050.0050.0000.0000.0000.000
130A158ASN 0-0.075-0.03937.0050.0070.0070.0000.0000.0000.000
131A159LEU 0-0.010-0.01136.0180.0040.0040.0000.0000.0000.000
132A160GLU -1-0.851-0.92136.771-0.063-0.0630.0000.0000.0000.000
133A161ARG 10.9090.95438.9180.0580.0580.0000.0000.0000.000
134A162GLN 0-0.048-0.01942.1540.0020.0020.0000.0000.0000.000
135A163ASN 0-0.033-0.01541.5160.0000.0000.0000.0000.0000.000
136A164LYS 10.9470.98640.0340.0550.0550.0000.0000.0000.000
137A165ILE 0-0.0150.00133.926-0.002-0.0020.0000.0000.0000.000
138A166LYS 10.8930.93435.5320.0550.0550.0000.0000.0000.000
139A167LYS 10.9160.98532.4240.0630.0630.0000.0000.0000.000
140A168ASP -1-0.831-0.91231.558-0.061-0.0610.0000.0000.0000.000
141A169LYS 10.8690.93629.0910.0550.0550.0000.0000.0000.000
142A170PHE 00.0260.02128.264-0.002-0.0020.0000.0000.0000.000
143A171GLU -1-0.749-0.84424.785-0.130-0.1300.0000.0000.0000.000
144A172ARG 10.8420.88520.5020.1450.1450.0000.0000.0000.000
145A173GLY 00.0100.02224.0700.0060.0060.0000.0000.0000.000
146A174ALA 00.017-0.00526.7950.0040.0040.0000.0000.0000.000
147A175LYS 10.8880.92921.3360.0950.0950.0000.0000.0000.000
148A176SER 0-0.025-0.03023.501-0.010-0.0100.0000.0000.0000.000
149A177GLU -1-0.897-0.93825.752-0.073-0.0730.0000.0000.0000.000
150A178TYR 00.009-0.01421.415-0.011-0.0110.0000.0000.0000.000
151A179TYR 0-0.010-0.01628.2410.0080.0080.0000.0000.0000.000
152A180LEU 00.0320.01928.851-0.009-0.0090.0000.0000.0000.000
153A181ILE 0-0.034-0.02630.6870.0080.0080.0000.0000.0000.000
154A182PRO 00.0360.02231.558-0.006-0.0060.0000.0000.0000.000
155A183THR 00.0670.01731.4390.0010.0010.0000.0000.0000.000
156A184SER 0-0.070-0.04833.2860.0000.0000.0000.0000.0000.000
157A185TYR 0-0.041-0.02035.5310.0040.0040.0000.0000.0000.000
158A186TRP 0-0.043-0.00827.139-0.001-0.0010.0000.0000.0000.000
159A187LYS 10.9740.98134.0920.0750.0750.0000.0000.0000.000
160A188ASN 00.0320.01433.764-0.006-0.0060.0000.0000.0000.000
161A189LEU 00.0600.01229.7540.0030.0030.0000.0000.0000.000
162A190THR 0-0.047-0.03133.8920.0000.0000.0000.0000.0000.000
163A191GLU -1-0.889-0.93935.718-0.070-0.0700.0000.0000.0000.000
164A192LEU 00.0370.02229.7130.0020.0020.0000.0000.0000.000
165A193ARG 10.8870.96334.3010.0760.0760.0000.0000.0000.000
166A194ILE 0-0.014-0.01436.2740.0030.0030.0000.0000.0000.000
167A195ALA 00.0350.02635.5300.0030.0030.0000.0000.0000.000
168A196LEU 0-0.022-0.00532.4800.0020.0020.0000.0000.0000.000
169A197ARG 10.9460.96135.8370.0630.0630.0000.0000.0000.000
170A198GLY 00.0190.02139.3370.0030.0030.0000.0000.0000.000
171A199PHE 00.040-0.00636.7270.0020.0020.0000.0000.0000.000
172A200TYR 0-0.0040.00436.8030.0020.0020.0000.0000.0000.000
173A201GLN 00.002-0.00538.6680.0010.0010.0000.0000.0000.000
174A202SER 00.0020.00140.7480.0030.0030.0000.0000.0000.000
175A203PHE 00.007-0.00637.2560.0020.0020.0000.0000.0000.000
176A204LYS 10.9210.95940.3420.0470.0470.0000.0000.0000.000
177A205GLU -1-0.978-0.98142.091-0.039-0.0390.0000.0000.0000.000
178A206TYR 0-0.060-0.02140.5460.0010.0010.0000.0000.0000.000
179A207LEU 0-0.083-0.03139.0570.0010.0010.0000.0000.0000.000
180A208NME 00.0300.02943.2920.0010.0010.0000.0000.0000.000