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: LZ2Z9

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1729699.48179
FMO2-HF: Nuclear repulsion 1663268.296289
FMO2-HF: Total energy -66431.185501
FMO2-MP2: Total energy -66624.632291


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.
-3.7460.5340.834-1.582-3.533-0.005
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 : -0.030 / q_NPA : -0.025
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].
3A118TYR0-0.026-0.0142.629-3.3810.2180.824-1.415-3.008-0.004
4A119PRO00.0220.0274.8770.2500.338-0.001-0.006-0.0810.000
5A120THR00.017-0.0098.368-0.110-0.1100.0000.0000.0000.000
6A121LEU0-0.0290.00311.5410.0740.0740.0000.0000.0000.000
7A122TRP00.019-0.00114.335-0.013-0.0130.0000.0000.0000.000
8A123THR00.0240.01817.8880.0070.0070.0000.0000.0000.000
9A124GLY00.0200.01420.3170.0180.0180.0000.0000.0000.000
10A125PRO0-0.031-0.00921.741-0.010-0.0100.0000.0000.0000.000
11A126ALA0-0.050-0.04823.274-0.003-0.0030.0000.0000.0000.000
12A127PRO0-0.0500.00324.9080.0080.0080.0000.0000.0000.000
13A128GLU-1-0.899-0.95327.283-0.030-0.0300.0000.0000.0000.000
14A129ALA0-0.037-0.02529.777-0.007-0.0070.0000.0000.0000.000
15A130ASN0-0.025-0.01425.8650.0020.0020.0000.0000.0000.000
16A131VAL00.0180.00327.702-0.007-0.0070.0000.0000.0000.000
17A132THR0-0.0080.00730.2220.0050.0050.0000.0000.0000.000
18A133PHE00.0330.03232.166-0.006-0.0060.0000.0000.0000.000
19A134SER00.014-0.01934.4320.0040.0040.0000.0000.0000.000
20A135GLY0-0.0060.00035.8230.0020.0020.0000.0000.0000.000
21A136GLU-1-0.798-0.85837.151-0.044-0.0440.0000.0000.0000.000
22A137ASN0-0.043-0.02337.786-0.001-0.0010.0000.0000.0000.000
23A138SER00.000-0.01236.9660.0010.0010.0000.0000.0000.000
24A139PRO0-0.018-0.01032.581-0.002-0.0020.0000.0000.0000.000
25A140SER0-0.006-0.00534.5660.0020.0020.0000.0000.0000.000
26A141GLY00.0390.00432.8280.0010.0010.0000.0000.0000.000
27A142ILE0-0.043-0.01428.531-0.001-0.0010.0000.0000.0000.000
28A143LEU0-0.011-0.00723.925-0.004-0.0040.0000.0000.0000.000
29A144ARG10.9720.98224.0990.0750.0750.0000.0000.0000.000
30A145LEU00.0330.00719.164-0.008-0.0080.0000.0000.0000.000
31A146CYS0-0.028-0.02716.0450.0080.0080.0000.0000.0000.000
32A147LEU0-0.0050.01913.589-0.003-0.0030.0000.0000.0000.000
33A148SER00.0410.01511.031-0.004-0.0040.0000.0000.0000.000
34A149ARG10.8280.8875.6241.1681.1680.0000.0000.0000.000
35A150THR0-0.0030.0147.455-0.076-0.0760.0000.0000.0000.000
36A151GLY00.0210.0116.4280.2060.2060.0000.0000.0000.000
37A152GLY00.0360.0146.430-0.116-0.1160.0000.0000.0000.000
38A153THR0-0.022-0.0048.6070.0930.0930.0000.0000.0000.000
39A154VAL0-0.0010.00710.309-0.121-0.1210.0000.0000.0000.000
40A155ILE0-0.038-0.02612.2910.0740.0740.0000.0000.0000.000
41A156GLY00.0350.01114.965-0.010-0.0100.0000.0000.0000.000
42A157THR0-0.046-0.03117.6180.0140.0140.0000.0000.0000.000
43A158LEU0-0.010-0.01220.5100.0000.0000.0000.0000.0000.000
44A159SER0-0.0130.00923.5280.0070.0070.0000.0000.0000.000
45A160VAL00.010-0.00126.872-0.002-0.0020.0000.0000.0000.000
46A161GLN00.0410.02929.4900.0030.0030.0000.0000.0000.000
47A162GLY0-0.0080.00032.596-0.002-0.0020.0000.0000.0000.000
48A163SER0-0.052-0.02335.1280.0030.0030.0000.0000.0000.000
49A164LEU0-0.0160.00237.370-0.001-0.0010.0000.0000.0000.000
50A165THR0-0.084-0.05840.5800.0030.0030.0000.0000.0000.000
51A166ASN0-0.027-0.00543.1180.0020.0020.0000.0000.0000.000
52A167PRO00.012-0.00743.762-0.002-0.0020.0000.0000.0000.000
53A168SER00.0030.00341.1210.0010.0010.0000.0000.0000.000
54A169THR0-0.003-0.00343.3890.0000.0000.0000.0000.0000.000
55A170GLY0-0.018-0.01941.8610.0000.0000.0000.0000.0000.000
56A171GLN00.0350.01740.455-0.002-0.0020.0000.0000.0000.000
57A172THR0-0.027-0.01335.406-0.003-0.0030.0000.0000.0000.000
58A173LEU00.0390.02034.2770.0040.0040.0000.0000.0000.000
59A174GLY00.0060.01131.406-0.005-0.0050.0000.0000.0000.000
60A175MET0-0.062-0.02527.1310.0080.0080.0000.0000.0000.000
61A176ASN00.001-0.01926.076-0.011-0.0110.0000.0000.0000.000
62A177LEU0-0.0010.00521.2290.0070.0070.0000.0000.0000.000
63A178TYR00.0300.00021.908-0.008-0.0080.0000.0000.0000.000
64A179PHE00.0350.01417.2130.0050.0050.0000.0000.0000.000
65A180ASP-1-0.759-0.86216.857-0.163-0.1630.0000.0000.0000.000
66A181ALA00.008-0.02215.095-0.023-0.0230.0000.0000.0000.000
67A182ASP-1-0.906-0.95512.534-0.225-0.2250.0000.0000.0000.000
68A183GLY0-0.007-0.00312.756-0.032-0.0320.0000.0000.0000.000
69A184ASN0-0.045-0.03614.5090.0100.0100.0000.0000.0000.000
70A185VAL0-0.0170.00217.563-0.001-0.0010.0000.0000.0000.000
71A186LEU00.0140.00420.7380.0160.0160.0000.0000.0000.000
72A187SER0-0.013-0.03023.4640.0010.0010.0000.0000.0000.000
73A188GLU-1-0.845-0.89726.980-0.087-0.0870.0000.0000.0000.000
74A189SER0-0.033-0.01024.375-0.006-0.0060.0000.0000.0000.000
75A190ASN00.000-0.00226.7180.0010.0010.0000.0000.0000.000
76A191LEU0-0.0180.01922.4500.0040.0040.0000.0000.0000.000
77A192VAL00.0330.00726.2730.0000.0000.0000.0000.0000.000
78A193ARG10.9970.97423.3030.0610.0610.0000.0000.0000.000
79A194GLY0-0.056-0.02223.089-0.002-0.0020.0000.0000.0000.000
80A195SER0-0.021-0.00824.0070.0070.0070.0000.0000.0000.000
81A196TRP00.006-0.00616.050-0.005-0.0050.0000.0000.0000.000
82A197GLY00.0460.02117.1270.0110.0110.0000.0000.0000.000
83A198MET00.0040.0239.941-0.016-0.0160.0000.0000.0000.000
84A199LYS10.8300.91713.9720.1130.1130.0000.0000.0000.000
85A200ASP-1-0.881-0.93214.1000.1060.1060.0000.0000.0000.000
86A201GLN0-0.007-0.00216.440-0.005-0.0050.0000.0000.0000.000
87A202ASP-1-0.880-0.93618.743-0.053-0.0530.0000.0000.0000.000
88A203THR0-0.076-0.04919.730-0.007-0.0070.0000.0000.0000.000
89A204LEU00.0110.00718.858-0.014-0.0140.0000.0000.0000.000
90A205VAL00.0040.00215.8070.0180.0180.0000.0000.0000.000
91A206THR00.009-0.01516.893-0.019-0.0190.0000.0000.0000.000
92A207PRO0-0.044-0.00116.722-0.012-0.0120.0000.0000.0000.000
93A208ILE00.0160.00312.2770.0080.0080.0000.0000.0000.000
94A209ALA00.008-0.00710.4900.0070.0070.0000.0000.0000.000
95A210ASN0-0.055-0.0385.980-0.064-0.0640.0000.0000.0000.000
96A211GLY00.0910.0417.678-0.152-0.1520.0000.0000.0000.000
97A212GLN00.0620.0307.322-0.030-0.0300.0000.0000.0000.000
98A213TYR0-0.059-0.0173.714-0.820-0.2270.011-0.161-0.444-0.001
99A214LEU00.0020.0107.316-0.052-0.0520.0000.0000.0000.000
100A215MET0-0.0290.02310.4650.0970.0970.0000.0000.0000.000
101A216PRO00.010-0.00811.991-0.051-0.0510.0000.0000.0000.000
102A217ASN0-0.025-0.01211.3040.0690.0690.0000.0000.0000.000
103A218LEU00.0420.00513.6110.0360.0360.0000.0000.0000.000
104A219THR0-0.072-0.02815.3340.0310.0310.0000.0000.0000.000
105A220ALA0-0.056-0.01916.1480.0180.0180.0000.0000.0000.000
106A221TYR0-0.0020.00115.6230.0040.0040.0000.0000.0000.000
107A222PRO00.0290.02819.202-0.004-0.0040.0000.0000.0000.000
108A223ARG10.8710.91419.5880.1630.1630.0000.0000.0000.000
109A224LEU0-0.064-0.02022.2020.0100.0100.0000.0000.0000.000
110A225ILE0-0.0150.00424.9940.0110.0110.0000.0000.0000.000
111A226GLN0-0.030-0.03926.067-0.002-0.0020.0000.0000.0000.000
112A227THR0-0.035-0.02228.503-0.001-0.0010.0000.0000.0000.000
113A228LEU00.0140.02524.4130.0030.0030.0000.0000.0000.000
114A229THR00.0510.00426.440-0.005-0.0050.0000.0000.0000.000
115A230SER0-0.020-0.01022.8470.0000.0000.0000.0000.0000.000
116A231SER00.0060.00721.855-0.020-0.0200.0000.0000.0000.000
117A232TYR0-0.029-0.00822.7790.0000.0000.0000.0000.0000.000
118A233ILE0-0.023-0.00419.876-0.005-0.0050.0000.0000.0000.000
119A234TYR0-0.017-0.01324.5360.0080.0080.0000.0000.0000.000
120A235THR0-0.008-0.00925.7670.0000.0000.0000.0000.0000.000
121A236GLN0-0.050-0.03828.3890.0080.0080.0000.0000.0000.000
122A237ALA0-0.0120.02030.055-0.005-0.0050.0000.0000.0000.000
123A238HIS0-0.045-0.03731.4640.0080.0080.0000.0000.0000.000
124A239LEU0-0.043-0.02533.877-0.002-0.0020.0000.0000.0000.000
125A240ASP-1-0.813-0.91036.462-0.051-0.0510.0000.0000.0000.000
126A241HIS0-0.059-0.02637.9400.0050.0050.0000.0000.0000.000
127A242ASN0-0.073-0.05541.294-0.002-0.0020.0000.0000.0000.000
128A243ASN00.0260.01438.152-0.004-0.0040.0000.0000.0000.000
129A244SER0-0.0170.01139.9310.0000.0000.0000.0000.0000.000
130A245VAL00.0330.01435.603-0.001-0.0010.0000.0000.0000.000
131A246VAL0-0.020-0.01432.8850.0030.0030.0000.0000.0000.000
132A247ASP-1-0.858-0.92132.860-0.095-0.0950.0000.0000.0000.000
133A248ILE0-0.019-0.01527.1110.0000.0000.0000.0000.0000.000
134A249LYS10.9170.96427.7730.1150.1150.0000.0000.0000.000
135A250ILE0-0.017-0.00921.5010.0030.0030.0000.0000.0000.000
136A251GLY00.0370.00624.095-0.002-0.0020.0000.0000.0000.000
137A252LEU0-0.041-0.01418.097-0.006-0.0060.0000.0000.0000.000
138A253ASN0-0.006-0.02916.6510.0070.0070.0000.0000.0000.000
139A254THR00.0140.00020.9570.0080.0080.0000.0000.0000.000
140A255ASP-1-0.825-0.86724.640-0.115-0.1150.0000.0000.0000.000
141A256LEU0-0.028-0.02321.495-0.008-0.0080.0000.0000.0000.000
142A257ARG10.8520.91725.4140.0910.0910.0000.0000.0000.000
143A258PRO00.019-0.00725.569-0.007-0.0070.0000.0000.0000.000
144A259THR0-0.004-0.01324.418-0.002-0.0020.0000.0000.0000.000
145A260ALA0-0.0260.01322.084-0.003-0.0030.0000.0000.0000.000
146A261ALA0-0.0280.01017.3210.0040.0040.0000.0000.0000.000
147A262TYR00.006-0.00812.830-0.019-0.0190.0000.0000.0000.000
148A263GLY00.000-0.00318.1970.0190.0190.0000.0000.0000.000
149A264LEU0-0.0320.00617.461-0.015-0.0150.0000.0000.0000.000
150A265SER0-0.033-0.02821.2410.0090.0090.0000.0000.0000.000
151A266PHE00.0390.02121.441-0.007-0.0070.0000.0000.0000.000
152A267THR0-0.034-0.02026.8810.0100.0100.0000.0000.0000.000
153A268MET0-0.004-0.00630.482-0.005-0.0050.0000.0000.0000.000
154A269THR0-0.0070.00032.8390.0060.0060.0000.0000.0000.000
155A270PHE00.0510.02035.927-0.001-0.0010.0000.0000.0000.000
156A271THR00.0080.00138.6740.0020.0020.0000.0000.0000.000
157A272ASN0-0.013-0.01441.2780.0010.0010.0000.0000.0000.000
158A273SER0-0.024-0.00642.486-0.002-0.0020.0000.0000.0000.000
159A274PRO0-0.0160.00739.1950.0010.0010.0000.0000.0000.000
160A275PRO0-0.0150.00439.4820.0030.0030.0000.0000.0000.000
161A276THR00.0060.00340.996-0.002-0.0020.0000.0000.0000.000
162A277SER00.013-0.00239.6410.0000.0000.0000.0000.0000.000
163A278PHE0-0.010-0.00433.5080.0000.0000.0000.0000.0000.000
164A279GLY00.007-0.00433.992-0.001-0.0010.0000.0000.0000.000
165A280THR0-0.029-0.01029.6450.0010.0010.0000.0000.0000.000
166A281ASP-1-0.811-0.88930.640-0.093-0.0930.0000.0000.0000.000
167A282LEU0-0.048-0.02723.377-0.004-0.0040.0000.0000.0000.000
168A283VAL00.0400.02324.875-0.002-0.0020.0000.0000.0000.000
169A284GLN0-0.008-0.00920.5310.0030.0030.0000.0000.0000.000
170A285PHE0-0.013-0.01519.0570.0080.0080.0000.0000.0000.000
171A286GLY00.0280.02616.732-0.023-0.0230.0000.0000.0000.000
172A287TYR0-0.055-0.04513.7070.0510.0510.0000.0000.0000.000
173A288LEU00.0160.01112.617-0.062-0.0620.0000.0000.0000.000
174A289GLY00.0750.0269.5480.0430.0430.0000.0000.0000.000
175A290GLN00.0130.0059.8020.0460.0460.0000.0000.0000.000
176A291ASP-1-0.893-0.9345.088-0.661-0.6610.0000.0000.0000.000