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: 9G9V2

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005059.669272
FMO2-HF: Nuclear repulsion 1933608.500474
FMO2-HF: Total energy -71451.168798
FMO2-MP2: Total energy -71666.044193


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.
-1.7240.7360.24-0.762-1.9360.003
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 : -0.011 / q_NPA : -0.016
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].
3A21PRO00.002-0.0013.855-1.3730.262-0.008-0.607-1.0190.003
4A22THR00.0130.0065.1910.4150.485-0.001-0.004-0.0640.000
5A23VAL00.0420.0118.029-0.109-0.1090.0000.0000.0000.000
6A24GLY00.0300.03410.545-0.027-0.0270.0000.0000.0000.000
7A25LEU00.0880.0462.633-0.710-0.1090.250-0.132-0.7180.000
8A26GLY0-0.004-0.0037.277-0.072-0.0720.0000.0000.0000.000
9A27ARG10.7820.8699.1660.1350.1350.0000.0000.0000.000
10A28GLU-1-0.844-0.9418.763-0.110-0.1100.0000.0000.0000.000
11A29TYR0-0.003-0.0083.950-0.0940.060-0.001-0.019-0.1350.000
12A30LEU0-0.0360.0069.7580.0270.0270.0000.0000.0000.000
13A31VAL0-0.024-0.01813.3040.0240.0240.0000.0000.0000.000
14A32LEU00.0220.01110.2980.0200.0200.0000.0000.0000.000
15A33GLY00.0390.01713.2510.0130.0130.0000.0000.0000.000
16A34LYS10.8170.89214.7430.1610.1610.0000.0000.0000.000
17A35LEU00.0120.03116.5380.0210.0210.0000.0000.0000.000
18A36LEU00.0320.01414.4130.0170.0170.0000.0000.0000.000
19A37ILE00.0170.02218.2040.0170.0170.0000.0000.0000.000
20A38SER0-0.097-0.06220.4850.0180.0180.0000.0000.0000.000
21A39LEU00.005-0.00119.6800.0100.0100.0000.0000.0000.000
22A40SER00.0170.00021.1560.0080.0080.0000.0000.0000.000
23A41LYS10.9190.95523.8470.1290.1290.0000.0000.0000.000
24A42TRP0-0.008-0.01324.8210.0090.0090.0000.0000.0000.000
25A43ARG10.8240.91426.6880.0940.0940.0000.0000.0000.000
26A44ALA00.0050.00227.9570.0050.0050.0000.0000.0000.000
27A45LYS10.8980.94629.7560.0860.0860.0000.0000.0000.000
28A46GLY00.0510.03931.9380.0050.0050.0000.0000.0000.000
29A47LEU0-0.070-0.03130.3320.0040.0040.0000.0000.0000.000
30A48ILE0-0.046-0.03227.7470.0030.0030.0000.0000.0000.000
31A49ASP-1-0.838-0.91030.994-0.064-0.0640.0000.0000.0000.000
32A50PHE0-0.037-0.01128.1490.0000.0000.0000.0000.0000.000
33A51ASP-1-0.773-0.85526.479-0.101-0.1010.0000.0000.0000.000
34A52VAL0-0.035-0.02822.6390.0060.0060.0000.0000.0000.000
35A53TYR0-0.070-0.06421.479-0.007-0.0070.0000.0000.0000.000
36A54LEU00.0530.03515.1290.0080.0080.0000.0000.0000.000
37A68TYR00.0460.02430.8910.0010.0010.0000.0000.0000.000
38A69GLU-1-0.864-0.92724.887-0.050-0.0500.0000.0000.0000.000
39A70TYR00.0240.00227.8910.0040.0040.0000.0000.0000.000
40A71TYR0-0.029-0.01825.899-0.006-0.0060.0000.0000.0000.000
41A72LYS10.8380.90822.2730.0480.0480.0000.0000.0000.000
42A73GLY0-0.044-0.01723.0700.0020.0020.0000.0000.0000.000
43A74LEU0-0.046-0.03722.0410.0090.0090.0000.0000.0000.000
44A75GLU-1-0.831-0.89418.657-0.061-0.0610.0000.0000.0000.000
45A76ASP-1-0.871-0.92415.016-0.044-0.0440.0000.0000.0000.000
46A77LYS10.7630.88516.4740.0120.0120.0000.0000.0000.000
47A78TYR0-0.064-0.06016.9200.0120.0120.0000.0000.0000.000
48A79ASP-1-0.777-0.87412.016-0.054-0.0540.0000.0000.0000.000
49A80LEU0-0.014-0.00412.676-0.035-0.0350.0000.0000.0000.000
50A81THR0-0.012-0.01115.2930.0270.0270.0000.0000.0000.000
51A82LEU0-0.047-0.00918.696-0.014-0.0140.0000.0000.0000.000
52A83TYR00.0590.01219.0330.0120.0120.0000.0000.0000.000
53A84ILE0-0.032-0.01323.374-0.005-0.0050.0000.0000.0000.000
54A85ARG10.9170.95126.2940.1020.1020.0000.0000.0000.000
55A86ALA0-0.0100.00429.0190.0020.0020.0000.0000.0000.000
56A87LYS10.8620.90131.6060.0550.0550.0000.0000.0000.000
57A88ASP-1-0.827-0.88730.939-0.061-0.0610.0000.0000.0000.000
58A89SER0-0.0090.00428.802-0.004-0.0040.0000.0000.0000.000
59A90TYR00.0280.01024.955-0.004-0.0040.0000.0000.0000.000
60A91TYR00.0420.02426.8650.0050.0050.0000.0000.0000.000
61A92PRO00.0270.02723.047-0.007-0.0070.0000.0000.0000.000
62A93LEU0-0.0170.00624.6400.0080.0080.0000.0000.0000.000
63A94LEU0-0.043-0.02023.3560.0070.0070.0000.0000.0000.000
64A95TRP00.0390.01919.888-0.006-0.0060.0000.0000.0000.000
65A96ILE0-0.034-0.03416.5820.0050.0050.0000.0000.0000.000
66A97ASP-1-0.731-0.85315.699-0.032-0.0320.0000.0000.0000.000
67A98ILE0-0.073-0.04411.862-0.003-0.0030.0000.0000.0000.000
68A99THR0-0.026-0.01113.4060.0170.0170.0000.0000.0000.000
69A100GLY00.0170.00412.742-0.009-0.0090.0000.0000.0000.000
70A101SER0-0.019-0.01913.763-0.021-0.0210.0000.0000.0000.000
71A102SER0-0.059-0.05115.9700.0170.0170.0000.0000.0000.000
72A103TRP00.015-0.01419.0800.0000.0000.0000.0000.0000.000
73A104THR00.0390.02420.9300.0070.0070.0000.0000.0000.000
74A105GLU-1-0.804-0.85118.780-0.055-0.0550.0000.0000.0000.000
75A106GLU-1-0.900-0.92617.6090.0910.0910.0000.0000.0000.000
76A107GLN0-0.052-0.03019.6010.0150.0150.0000.0000.0000.000
77A108SER0-0.022-0.01020.7540.0020.0020.0000.0000.0000.000
78A109LYS10.8510.91022.901-0.047-0.0470.0000.0000.0000.000
79A110GLU-1-0.885-0.92225.9990.0300.0300.0000.0000.0000.000
80A111ARG10.8570.90927.090-0.020-0.0200.0000.0000.0000.000
81A112TYR0-0.003-0.00628.558-0.001-0.0010.0000.0000.0000.000
82A113GLY00.0390.02129.6420.0050.0050.0000.0000.0000.000
83A114GLU-1-0.823-0.88428.500-0.018-0.0180.0000.0000.0000.000
84A115SER00.0170.01622.7380.0080.0080.0000.0000.0000.000
85A116ILE00.009-0.01024.754-0.003-0.0030.0000.0000.0000.000
86A117TYR00.0290.01019.0150.0080.0080.0000.0000.0000.000
87A118ALA00.0120.00620.1780.0040.0040.0000.0000.0000.000
88A119ILE0-0.023-0.00319.7170.0000.0000.0000.0000.0000.000
89A120LEU00.0080.00817.4010.0050.0050.0000.0000.0000.000
90A121SER00.017-0.02721.213-0.013-0.0130.0000.0000.0000.000
91A122VAL00.0490.02821.567-0.008-0.0080.0000.0000.0000.000
92A123LYS10.7940.90215.1500.0000.0000.0000.0000.0000.000
93A124VAL00.0050.01021.804-0.011-0.0110.0000.0000.0000.000
94A125GLU-1-0.858-0.91125.2370.0430.0430.0000.0000.0000.000
95A126THR0-0.036-0.03022.575-0.001-0.0010.0000.0000.0000.000
96A127ALA00.0390.01524.848-0.004-0.0040.0000.0000.0000.000
97A128LYS10.9230.95826.401-0.020-0.0200.0000.0000.0000.000
98A129LYS10.8780.94727.334-0.024-0.0240.0000.0000.0000.000
99A130TYR0-0.002-0.00825.9850.0030.0030.0000.0000.0000.000
100A131ASP-1-0.920-0.94829.669-0.015-0.0150.0000.0000.0000.000
101A132VAL00.0520.02425.565-0.004-0.0040.0000.0000.0000.000
102A133LEU0-0.015-0.00427.376-0.003-0.0030.0000.0000.0000.000
103A134GLY0-0.013-0.00828.417-0.001-0.0010.0000.0000.0000.000
104A135ARG10.8270.89926.5420.0360.0360.0000.0000.0000.000
105A136VAL00.0450.04321.749-0.006-0.0060.0000.0000.0000.000
106A137PHE0-0.022-0.02922.0210.0060.0060.0000.0000.0000.000
107A138PHE00.0520.02819.137-0.008-0.0080.0000.0000.0000.000
108A139ILE0-0.030-0.03117.4980.0020.0020.0000.0000.0000.000
109A140HIS00.0660.04417.426-0.003-0.0030.0000.0000.0000.000
110A141TYR0-0.052-0.05417.603-0.006-0.0060.0000.0000.0000.000
111A142ASN00.0100.01819.4030.0070.0070.0000.0000.0000.000
112A143ASP-1-0.753-0.88319.683-0.111-0.1110.0000.0000.0000.000
113A144THR0-0.064-0.05022.4920.0020.0020.0000.0000.0000.000
114A145GLU-1-0.871-0.93125.436-0.048-0.0480.0000.0000.0000.000
115A146ASP-1-0.786-0.85522.635-0.127-0.1270.0000.0000.0000.000
116A147LYS10.9020.95923.6930.0550.0550.0000.0000.0000.000
117A148LEU0-0.0020.00818.1170.0010.0010.0000.0000.0000.000
118A149LYS10.7720.88021.7380.0520.0520.0000.0000.0000.000
119A150CYS0-0.061-0.02321.696-0.005-0.0050.0000.0000.0000.000
120A151ILE00.0200.01123.3930.0050.0050.0000.0000.0000.000
121A152SER00.0350.03324.2470.0010.0010.0000.0000.0000.000
122A153ALA00.0510.01225.1620.0050.0050.0000.0000.0000.000
123A154LEU0-0.010-0.00826.7370.0060.0060.0000.0000.0000.000
124A155GLN00.0390.01629.0900.0040.0040.0000.0000.0000.000
125A156ILE00.0200.02524.4430.0020.0020.0000.0000.0000.000
126A157LEU00.0220.00929.0710.0030.0030.0000.0000.0000.000
127A158ASN0-0.066-0.03331.8830.0040.0040.0000.0000.0000.000
128A159LEU00.0070.00130.0350.0010.0010.0000.0000.0000.000
129A160GLU-1-0.789-0.87432.0900.0280.0280.0000.0000.0000.000
130A161ARG10.9190.95833.9680.0000.0000.0000.0000.0000.000
131A162GLN0-0.020-0.00536.7190.0000.0000.0000.0000.0000.000
132A163ASN0-0.024-0.00836.7270.0020.0020.0000.0000.0000.000
133A164LYS10.9150.97134.4410.0050.0050.0000.0000.0000.000
134A165ILE0-0.0120.00028.699-0.001-0.0010.0000.0000.0000.000
135A166LYS10.8520.90731.021-0.022-0.0220.0000.0000.0000.000
136A167LYS10.8080.90328.408-0.044-0.0440.0000.0000.0000.000
137A168ASP-1-0.832-0.91227.6940.0580.0580.0000.0000.0000.000
138A169LYS10.7990.87326.610-0.077-0.0770.0000.0000.0000.000
139A170PHE00.0200.01624.6490.0100.0100.0000.0000.0000.000
140A171GLU-1-0.778-0.88522.3120.1300.1300.0000.0000.0000.000
141A172ARG10.8890.94316.250-0.176-0.1760.0000.0000.0000.000
142A173GLY00.0320.01019.601-0.015-0.0150.0000.0000.0000.000
143A174ALA0-0.002-0.00418.730-0.018-0.0180.0000.0000.0000.000
144A175LYS10.8360.91620.700-0.157-0.1570.0000.0000.0000.000
145A176SER0-0.065-0.04920.7910.0080.0080.0000.0000.0000.000
146A177GLU-1-0.767-0.84123.1630.0600.0600.0000.0000.0000.000
147A178TYR00.0160.00517.3820.0090.0090.0000.0000.0000.000
148A179TYR0-0.015-0.02024.090-0.002-0.0020.0000.0000.0000.000
149A180LEU00.0240.01624.186-0.002-0.0020.0000.0000.0000.000
150A181ILE0-0.018-0.02425.274-0.003-0.0030.0000.0000.0000.000
151A182PRO00.0350.03425.619-0.003-0.0030.0000.0000.0000.000
152A183THR00.0370.00124.600-0.004-0.0040.0000.0000.0000.000
153A184SER0-0.065-0.05326.698-0.005-0.0050.0000.0000.0000.000
154A185TYR0-0.052-0.02929.188-0.001-0.0010.0000.0000.0000.000
155A186TRP0-0.039-0.00920.404-0.003-0.0030.0000.0000.0000.000
156A187LYS10.8490.91326.9240.0280.0280.0000.0000.0000.000
157A188ASN00.0460.02926.328-0.009-0.0090.0000.0000.0000.000
158A189LEU00.0530.00921.6440.0050.0050.0000.0000.0000.000
159A190THR0-0.018-0.02125.933-0.003-0.0030.0000.0000.0000.000
160A191GLU-1-0.786-0.87228.704-0.032-0.0320.0000.0000.0000.000
161A192LEU00.0380.02522.3020.0010.0010.0000.0000.0000.000
162A193ARG10.8790.93726.8980.0720.0720.0000.0000.0000.000
163A194ILE0-0.026-0.00928.7170.0010.0010.0000.0000.0000.000
164A195ALA00.0310.01628.4940.0010.0010.0000.0000.0000.000
165A196LEU0-0.0030.00225.0860.0010.0010.0000.0000.0000.000
166A197ARG10.9210.95228.5710.0570.0570.0000.0000.0000.000
167A198GLY00.0310.02832.0210.0020.0020.0000.0000.0000.000
168A199PHE00.0240.00129.7610.0030.0030.0000.0000.0000.000
169A200TYR00.0110.01230.3470.0020.0020.0000.0000.0000.000
170A201GLN0-0.006-0.01231.975-0.002-0.0020.0000.0000.0000.000
171A202SER00.010-0.01734.4470.0030.0030.0000.0000.0000.000
172A203PHE0-0.020-0.01831.5820.0020.0020.0000.0000.0000.000
173A204LYS10.8820.93134.3440.0450.0450.0000.0000.0000.000
174A205GLU-1-0.932-0.94336.127-0.030-0.0300.0000.0000.0000.000
175A206TYR0-0.050-0.02235.5200.0030.0030.0000.0000.0000.000
176A207LEU0-0.058-0.01534.0170.0010.0010.0000.0000.0000.000