Manual

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: 3959L

Calculation Name: 2WST-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WST

Chain ID: A

ChEMBL ID:

UniProt ID: Q83467

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1729211.959931
FMO2-HF: Nuclear repulsion 1662781.414541
FMO2-HF: Total energy -66430.54539
FMO2-MP2: Total energy -66624.021829


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:116:LEU)


Summations of interaction energy for fragment #1(A:116:LEU)
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.
-3.310.6680.612-1.451-3.139-0.006
Interaction energy analysis for fragmet #1(A:116:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.023
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].
3A118TYR0-0.009-0.0102.626-3.0080.4030.607-1.335-2.683-0.005
4A119PRO00.0300.0305.0120.2700.346-0.001-0.005-0.0700.000
5A120THR0-0.001-0.0138.367-0.096-0.0960.0000.0000.0000.000
6A121LEU0-0.0240.00911.6450.0750.0750.0000.0000.0000.000
7A122TRP00.011-0.01014.395-0.020-0.0200.0000.0000.0000.000
8A123THR00.0130.00417.9800.0080.0080.0000.0000.0000.000
9A124GLY00.0410.02620.4270.0190.0190.0000.0000.0000.000
10A125PRO0-0.032-0.00321.805-0.011-0.0110.0000.0000.0000.000
11A126ALA0-0.056-0.05223.403-0.003-0.0030.0000.0000.0000.000
12A127PRO0-0.0530.00725.0750.0090.0090.0000.0000.0000.000
13A128GLU-1-0.893-0.95527.354-0.034-0.0340.0000.0000.0000.000
14A129ALA0-0.040-0.02729.844-0.007-0.0070.0000.0000.0000.000
15A130ASN0-0.006-0.01025.8660.0040.0040.0000.0000.0000.000
16A131VAL00.0090.00427.834-0.008-0.0080.0000.0000.0000.000
17A132THR0-0.017-0.00130.3720.0060.0060.0000.0000.0000.000
18A133PHE00.0280.03532.307-0.007-0.0070.0000.0000.0000.000
19A134SER00.002-0.02234.5730.0050.0050.0000.0000.0000.000
20A135GLY0-0.0030.00035.9570.0020.0020.0000.0000.0000.000
21A136GLU-1-0.819-0.86737.361-0.050-0.0500.0000.0000.0000.000
22A137ASN0-0.057-0.03337.970-0.002-0.0020.0000.0000.0000.000
23A138SER0-0.001-0.01237.3800.0020.0020.0000.0000.0000.000
24A139PRO0-0.002-0.00132.861-0.002-0.0020.0000.0000.0000.000
25A140SER00.0240.01434.7960.0020.0020.0000.0000.0000.000
26A141GLY00.0310.00132.9650.0010.0010.0000.0000.0000.000
27A142ILE0-0.030-0.00628.697-0.001-0.0010.0000.0000.0000.000
28A143LEU0-0.0060.00324.213-0.004-0.0040.0000.0000.0000.000
29A144ARG10.9690.97924.2750.0870.0870.0000.0000.0000.000
30A145LEU00.0270.01119.301-0.008-0.0080.0000.0000.0000.000
31A146CYS0-0.012-0.01915.9520.0140.0140.0000.0000.0000.000
32A147LEU0-0.0190.01213.865-0.005-0.0050.0000.0000.0000.000
33A148SER00.0410.01311.3180.0050.0050.0000.0000.0000.000
34A149ARG10.8340.8915.5041.3351.3350.0000.0000.0000.000
35A150THR0-0.0180.0047.619-0.086-0.0860.0000.0000.0000.000
36A151GLY00.0260.0176.6350.2030.2030.0000.0000.0000.000
37A152GLY00.0240.0086.508-0.149-0.1490.0000.0000.0000.000
38A153THR0-0.0100.0038.7090.1120.1120.0000.0000.0000.000
39A154VAL00.0020.00710.507-0.131-0.1310.0000.0000.0000.000
40A155ILE0-0.041-0.03012.2180.0780.0780.0000.0000.0000.000
41A156GLY00.0310.00915.228-0.010-0.0100.0000.0000.0000.000
42A157THR0-0.048-0.02917.9560.0150.0150.0000.0000.0000.000
43A158LEU0-0.002-0.01320.8330.0000.0000.0000.0000.0000.000
44A159SER0-0.0030.01123.8130.0070.0070.0000.0000.0000.000
45A160VAL00.0220.00327.139-0.002-0.0020.0000.0000.0000.000
46A161GLN00.0560.03729.7170.0030.0030.0000.0000.0000.000
47A162GLY0-0.021-0.00532.767-0.002-0.0020.0000.0000.0000.000
48A163SER0-0.061-0.02635.3010.0040.0040.0000.0000.0000.000
49A164LEU0-0.021-0.00537.717-0.001-0.0010.0000.0000.0000.000
50A165THR0-0.072-0.05440.7230.0040.0040.0000.0000.0000.000
51A166ASN0-0.015-0.00643.2910.0020.0020.0000.0000.0000.000
52A167PRO00.004-0.01043.938-0.002-0.0020.0000.0000.0000.000
53A168SER00.0060.01141.5800.0010.0010.0000.0000.0000.000
54A169THR0-0.007-0.00343.5840.0000.0000.0000.0000.0000.000
55A170GLY0-0.015-0.02242.0790.0000.0000.0000.0000.0000.000
56A171GLN00.0260.01040.658-0.003-0.0030.0000.0000.0000.000
57A172THR0-0.023-0.00735.529-0.004-0.0040.0000.0000.0000.000
58A173LEU00.0520.02434.4380.0040.0040.0000.0000.0000.000
59A174GLY00.0040.01131.623-0.006-0.0060.0000.0000.0000.000
60A175MET0-0.050-0.02327.2860.0100.0100.0000.0000.0000.000
61A176ASN00.012-0.00326.251-0.013-0.0130.0000.0000.0000.000
62A177LEU0-0.0040.00121.4130.0090.0090.0000.0000.0000.000
63A178TYR00.0410.00822.001-0.009-0.0090.0000.0000.0000.000
64A179PHE00.0270.01417.2320.0050.0050.0000.0000.0000.000
65A180ASP-1-0.784-0.88617.289-0.183-0.1830.0000.0000.0000.000
66A181ALA0-0.005-0.02814.897-0.026-0.0260.0000.0000.0000.000
67A182ASP-1-0.899-0.94512.851-0.251-0.2510.0000.0000.0000.000
68A183GLY0-0.011-0.00813.237-0.033-0.0330.0000.0000.0000.000
69A184ASN0-0.027-0.01814.7050.0140.0140.0000.0000.0000.000
70A185VAL0-0.0170.00918.030-0.002-0.0020.0000.0000.0000.000
71A186LEU00.0220.00021.0400.0180.0180.0000.0000.0000.000
72A187SER0-0.022-0.02723.7000.0010.0010.0000.0000.0000.000
73A188GLU-1-0.961-0.97827.067-0.098-0.0980.0000.0000.0000.000
74A189SER0-0.043-0.02124.438-0.007-0.0070.0000.0000.0000.000
75A190ASN0-0.009-0.02026.7830.0020.0020.0000.0000.0000.000
76A191LEU0-0.0140.01722.7750.0040.0040.0000.0000.0000.000
77A192VAL00.0200.00326.6280.0010.0010.0000.0000.0000.000
78A193ARG11.0050.97423.8790.0690.0690.0000.0000.0000.000
79A194GLY0-0.055-0.02223.655-0.002-0.0020.0000.0000.0000.000
80A195SER0-0.021-0.03124.0760.0070.0070.0000.0000.0000.000
81A196TRP0-0.0030.01916.357-0.004-0.0040.0000.0000.0000.000
82A197GLY00.0480.02117.6340.0120.0120.0000.0000.0000.000
83A198MET0-0.0070.00410.165-0.013-0.0130.0000.0000.0000.000
84A199LYS10.8810.95313.9640.1350.1350.0000.0000.0000.000
85A200ASP-1-0.904-0.94214.3330.1170.1170.0000.0000.0000.000
86A201GLN0-0.025-0.01316.816-0.006-0.0060.0000.0000.0000.000
87A202ASP-1-0.890-0.95018.894-0.053-0.0530.0000.0000.0000.000
88A203THR0-0.079-0.05220.133-0.007-0.0070.0000.0000.0000.000
89A204LEU00.0210.00919.030-0.015-0.0150.0000.0000.0000.000
90A205VAL0-0.005-0.00316.2280.0200.0200.0000.0000.0000.000
91A206THR00.007-0.01317.365-0.020-0.0200.0000.0000.0000.000
92A207PRO0-0.0350.00316.903-0.014-0.0140.0000.0000.0000.000
93A208ILE00.0190.01312.8300.0100.0100.0000.0000.0000.000
94A209ALA00.0190.00610.5850.0060.0060.0000.0000.0000.000
95A210ASN0-0.050-0.0386.439-0.098-0.0980.0000.0000.0000.000
96A211GLY00.0900.0358.269-0.158-0.1580.0000.0000.0000.000
97A212GLN00.0860.0387.833-0.010-0.0100.0000.0000.0000.000
98A213TYR0-0.054-0.0114.163-0.740-0.2490.006-0.111-0.386-0.001
99A214LEU0-0.0140.0047.455-0.062-0.0620.0000.0000.0000.000
100A215MET0-0.0290.02910.6720.1070.1070.0000.0000.0000.000
101A216PRO00.016-0.00312.210-0.061-0.0610.0000.0000.0000.000
102A217ASN0-0.011-0.00511.5290.0800.0800.0000.0000.0000.000
103A218LEU00.019-0.00313.8460.0400.0400.0000.0000.0000.000
104A219THR0-0.055-0.02115.5280.0390.0390.0000.0000.0000.000
105A220ALA0-0.061-0.02216.2120.0210.0210.0000.0000.0000.000
106A221TYR0-0.006-0.00215.5710.0050.0050.0000.0000.0000.000
107A222PRO00.0300.02919.406-0.005-0.0050.0000.0000.0000.000
108A223ARG10.9280.96119.9660.1810.1810.0000.0000.0000.000
109A224LEU0-0.062-0.01622.3370.0110.0110.0000.0000.0000.000
110A225ILE0-0.0070.00825.1140.0130.0130.0000.0000.0000.000
111A226GLN00.004-0.00326.291-0.010-0.0100.0000.0000.0000.000
112A227THR0-0.014-0.02128.730-0.002-0.0020.0000.0000.0000.000
113A228LEU00.0290.03124.5060.0040.0040.0000.0000.0000.000
114A229THR00.0540.00326.608-0.005-0.0050.0000.0000.0000.000
115A230SER0-0.026-0.01322.9550.0000.0000.0000.0000.0000.000
116A231SER00.0060.01021.997-0.021-0.0210.0000.0000.0000.000
117A232TYR0-0.055-0.02022.999-0.002-0.0020.0000.0000.0000.000
118A233ILE0-0.0120.00220.029-0.006-0.0060.0000.0000.0000.000
119A234TYR0-0.023-0.01524.5090.0100.0100.0000.0000.0000.000
120A235THR00.001-0.00626.043-0.001-0.0010.0000.0000.0000.000
121A236GLN0-0.038-0.02228.3360.0100.0100.0000.0000.0000.000
122A237ALA0-0.0090.02030.275-0.005-0.0050.0000.0000.0000.000
123A238HIS0-0.039-0.02631.7710.0090.0090.0000.0000.0000.000
124A239LEU0-0.034-0.02234.209-0.002-0.0020.0000.0000.0000.000
125A240ASP-1-0.828-0.92736.793-0.059-0.0590.0000.0000.0000.000
126A241HIS0-0.078-0.02838.2460.0060.0060.0000.0000.0000.000
127A242ASN0-0.066-0.04941.624-0.003-0.0030.0000.0000.0000.000
128A243ASN00.0440.01338.494-0.004-0.0040.0000.0000.0000.000
129A244SER0-0.0200.01540.2530.0000.0000.0000.0000.0000.000
130A245VAL00.0320.01535.716-0.002-0.0020.0000.0000.0000.000
131A246VAL0-0.023-0.01733.1680.0040.0040.0000.0000.0000.000
132A247ASP-1-0.883-0.94132.868-0.108-0.1080.0000.0000.0000.000
133A248ILE0-0.031-0.02027.3520.0010.0010.0000.0000.0000.000
134A249LYS10.9340.96228.0280.1230.1230.0000.0000.0000.000
135A250ILE0-0.014-0.00721.7620.0040.0040.0000.0000.0000.000
136A251GLY00.0240.01124.359-0.003-0.0030.0000.0000.0000.000
137A252LEU0-0.034-0.01618.384-0.006-0.0060.0000.0000.0000.000
138A253ASN00.003-0.02016.8910.0080.0080.0000.0000.0000.000
139A254THR0-0.014-0.00121.1410.0070.0070.0000.0000.0000.000
140A255ASP-1-0.828-0.90624.838-0.127-0.1270.0000.0000.0000.000
141A256LEU0-0.048-0.04721.736-0.009-0.0090.0000.0000.0000.000
142A257ARG10.9540.98625.5180.1050.1050.0000.0000.0000.000
143A258PRO0-0.004-0.01725.605-0.007-0.0070.0000.0000.0000.000
144A259THR0-0.016-0.02024.904-0.006-0.0060.0000.0000.0000.000
145A260ALA0-0.0140.02422.050-0.004-0.0040.0000.0000.0000.000
146A261ALA0-0.054-0.01717.2650.0040.0040.0000.0000.0000.000
147A262TYR0-0.010-0.02012.888-0.025-0.0250.0000.0000.0000.000
148A263GLY00.003-0.00218.2880.0210.0210.0000.0000.0000.000
149A264LEU0-0.0170.01017.913-0.018-0.0180.0000.0000.0000.000
150A265SER0-0.035-0.00621.4400.0100.0100.0000.0000.0000.000
151A266PHE00.0410.02421.840-0.008-0.0080.0000.0000.0000.000
152A267THR0-0.020-0.01527.1230.0120.0120.0000.0000.0000.000
153A268MET0-0.031-0.01830.735-0.006-0.0060.0000.0000.0000.000
154A269THR00.0080.01033.1110.0070.0070.0000.0000.0000.000
155A270PHE00.0320.01035.997-0.002-0.0020.0000.0000.0000.000
156A271THR0-0.002-0.00138.8480.0020.0020.0000.0000.0000.000
157A272ASN0-0.005-0.00941.3580.0010.0010.0000.0000.0000.000
158A273SER0-0.023-0.00942.730-0.002-0.0020.0000.0000.0000.000
159A274PRO0-0.0100.01139.4340.0010.0010.0000.0000.0000.000
160A275PRO0-0.0080.00539.7030.0040.0040.0000.0000.0000.000
161A276THR00.0040.00241.210-0.002-0.0020.0000.0000.0000.000
162A277SER0-0.008-0.01539.834-0.001-0.0010.0000.0000.0000.000
163A278PHE00.0310.01533.6220.0000.0000.0000.0000.0000.000
164A279GLY00.0290.01434.236-0.001-0.0010.0000.0000.0000.000
165A280THR0-0.018-0.00229.9770.0010.0010.0000.0000.0000.000
166A281ASP-1-0.858-0.91930.968-0.107-0.1070.0000.0000.0000.000
167A282LEU0-0.058-0.03223.737-0.005-0.0050.0000.0000.0000.000
168A283VAL00.0510.02625.041-0.003-0.0030.0000.0000.0000.000
169A284GLN0-0.004-0.00720.6230.0090.0090.0000.0000.0000.000
170A285PHE0-0.027-0.01818.9640.0090.0090.0000.0000.0000.000
171A286GLY00.0260.02416.690-0.026-0.0260.0000.0000.0000.000
172A287TYR0-0.067-0.05913.8480.0560.0560.0000.0000.0000.000
173A288LEU00.0110.01012.438-0.068-0.0680.0000.0000.0000.000
174A289GLY00.0650.0239.7000.0500.0500.0000.0000.0000.000
175A290GLN00.0430.0179.8650.0200.0200.0000.0000.0000.000
176A291ASP-1-0.939-0.9665.533-0.804-0.8040.0000.0000.0000.000