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: 94642

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 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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1733183.110414
FMO2-HF: Nuclear repulsion 1666751.69844
FMO2-HF: Total energy -66431.411974
FMO2-MP2: Total energy -66624.961028


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.
-4.9610.31.3-2.17-4.39-0.01
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 : -0.032 / q_NPA : -0.024
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].
3A118TYR0-0.013-0.0062.675-4.2200.0801.250-1.876-3.674-0.008
4A119PRO00.0130.0204.9580.2540.343-0.001-0.005-0.0820.000
5A120THR00.005-0.0178.262-0.058-0.0580.0000.0000.0000.000
6A121LEU0-0.041-0.00511.1620.0700.0700.0000.0000.0000.000
7A122TRP0-0.011-0.02413.839-0.010-0.0100.0000.0000.0000.000
8A123THR00.0340.02117.6170.0100.0100.0000.0000.0000.000
9A124GLY00.0130.02020.1940.0190.0190.0000.0000.0000.000
10A125PRO0-0.022-0.01221.842-0.011-0.0110.0000.0000.0000.000
11A126ALA0-0.034-0.04723.512-0.002-0.0020.0000.0000.0000.000
12A127PRO0-0.0240.01724.9220.0090.0090.0000.0000.0000.000
13A128GLU-1-0.888-0.95127.309-0.039-0.0390.0000.0000.0000.000
14A129ALA0-0.047-0.02629.736-0.007-0.0070.0000.0000.0000.000
15A130ASN0-0.019-0.01725.7020.0030.0030.0000.0000.0000.000
16A131VAL0-0.0050.00127.473-0.006-0.0060.0000.0000.0000.000
17A132THR00.0240.02129.9300.0060.0060.0000.0000.0000.000
18A133PHE00.0230.01431.964-0.006-0.0060.0000.0000.0000.000
19A134SER00.004-0.01433.9910.0040.0040.0000.0000.0000.000
20A135GLY0-0.0020.00135.4450.0020.0020.0000.0000.0000.000
21A136GLU-1-0.806-0.83936.440-0.051-0.0510.0000.0000.0000.000
22A137ASN0-0.036-0.01537.5960.0000.0000.0000.0000.0000.000
23A138SER00.005-0.01536.3650.0020.0020.0000.0000.0000.000
24A139PRO0-0.025-0.01731.981-0.002-0.0020.0000.0000.0000.000
25A140SER0-0.007-0.02133.9420.0020.0020.0000.0000.0000.000
26A141GLY00.0460.00632.7640.0010.0010.0000.0000.0000.000
27A142ILE0-0.059-0.01528.5310.0000.0000.0000.0000.0000.000
28A143LEU00.0060.00723.662-0.003-0.0030.0000.0000.0000.000
29A144ARG10.9140.96224.2420.0870.0870.0000.0000.0000.000
30A145LEU00.0480.01119.220-0.007-0.0070.0000.0000.0000.000
31A146CYS0-0.017-0.00715.8030.0080.0080.0000.0000.0000.000
32A147LEU00.0260.02713.478-0.003-0.0030.0000.0000.0000.000
33A148SER00.017-0.00710.6650.0190.0190.0000.0000.0000.000
34A149ARG10.8320.8975.4951.3271.3270.0000.0000.0000.000
35A150THR00.0110.0167.195-0.170-0.1700.0000.0000.0000.000
36A151GLY00.0250.0126.0790.2370.2370.0000.0000.0000.000
37A152GLY00.0270.0156.019-0.142-0.1420.0000.0000.0000.000
38A153THR0-0.021-0.0088.3580.0750.0750.0000.0000.0000.000
39A154VAL0-0.0090.00910.043-0.116-0.1160.0000.0000.0000.000
40A155ILE0-0.014-0.01211.8180.0810.0810.0000.0000.0000.000
41A156GLY00.0290.00714.285-0.026-0.0260.0000.0000.0000.000
42A157THR0-0.052-0.02417.0140.0170.0170.0000.0000.0000.000
43A158LEU0-0.005-0.01120.256-0.002-0.0020.0000.0000.0000.000
44A159SER0-0.036-0.01523.3510.0090.0090.0000.0000.0000.000
45A160VAL00.003-0.00626.745-0.003-0.0030.0000.0000.0000.000
46A161GLN00.0270.01229.4390.0030.0030.0000.0000.0000.000
47A162GLY00.008-0.00332.623-0.003-0.0030.0000.0000.0000.000
48A163SER0-0.049-0.02435.3340.0020.0020.0000.0000.0000.000
49A164LEU00.0030.02637.0250.0000.0000.0000.0000.0000.000
50A165THR0-0.061-0.05940.1050.0040.0040.0000.0000.0000.000
51A166ASN0-0.066-0.02342.8390.0030.0030.0000.0000.0000.000
52A167PRO00.0170.00243.377-0.002-0.0020.0000.0000.0000.000
53A168SER00.0270.01640.2500.0010.0010.0000.0000.0000.000
54A169THR0-0.010-0.01142.9820.0010.0010.0000.0000.0000.000
55A170GLY0-0.008-0.01541.7750.0000.0000.0000.0000.0000.000
56A171GLN00.0420.01940.328-0.002-0.0020.0000.0000.0000.000
57A172THR0-0.071-0.02934.857-0.003-0.0030.0000.0000.0000.000
58A173LEU00.0080.00133.8680.0040.0040.0000.0000.0000.000
59A174GLY0-0.0070.00831.194-0.006-0.0060.0000.0000.0000.000
60A175MET0-0.042-0.01727.2120.0080.0080.0000.0000.0000.000
61A176ASN00.006-0.01825.610-0.012-0.0120.0000.0000.0000.000
62A177LEU00.0000.00820.9660.0090.0090.0000.0000.0000.000
63A178TYR00.0230.00721.653-0.011-0.0110.0000.0000.0000.000
64A179PHE00.0350.01616.9230.0030.0030.0000.0000.0000.000
65A180ASP-1-0.741-0.85916.372-0.184-0.1840.0000.0000.0000.000
66A181ALA0-0.004-0.02215.098-0.026-0.0260.0000.0000.0000.000
67A182ASP-1-0.897-0.95112.090-0.246-0.2460.0000.0000.0000.000
68A183GLY00.0150.00211.873-0.053-0.0530.0000.0000.0000.000
69A184ASN0-0.068-0.04614.0590.0140.0140.0000.0000.0000.000
70A185VAL0-0.0170.00017.330-0.001-0.0010.0000.0000.0000.000
71A186LEU00.005-0.00620.3220.0190.0190.0000.0000.0000.000
72A187SER00.001-0.01123.1320.0010.0010.0000.0000.0000.000
73A188GLU-1-0.844-0.89326.706-0.096-0.0960.0000.0000.0000.000
74A189SER0-0.017-0.00924.125-0.006-0.0060.0000.0000.0000.000
75A190ASN0-0.008-0.00726.4680.0010.0010.0000.0000.0000.000
76A191LEU0-0.0200.01022.1930.0060.0060.0000.0000.0000.000
77A192VAL00.0390.00625.809-0.001-0.0010.0000.0000.0000.000
78A193ARG10.9530.95622.9800.0750.0750.0000.0000.0000.000
79A194GLY0-0.0190.00722.672-0.003-0.0030.0000.0000.0000.000
80A195SER0-0.029-0.01723.6130.0070.0070.0000.0000.0000.000
81A196TRP0-0.014-0.02315.628-0.008-0.0080.0000.0000.0000.000
82A197GLY00.0380.02216.8110.0170.0170.0000.0000.0000.000
83A198MET00.0050.0219.539-0.018-0.0180.0000.0000.0000.000
84A199LYS10.7950.90913.7070.1460.1460.0000.0000.0000.000
85A200ASP-1-0.836-0.90113.6660.0820.0820.0000.0000.0000.000
86A201GLN0-0.047-0.03316.010-0.007-0.0070.0000.0000.0000.000
87A202ASP-1-0.881-0.93618.430-0.080-0.0800.0000.0000.0000.000
88A203THR0-0.052-0.03219.181-0.002-0.0020.0000.0000.0000.000
89A204LEU00.0160.00518.412-0.019-0.0190.0000.0000.0000.000
90A205VAL00.0030.00115.2300.0190.0190.0000.0000.0000.000
91A206THR00.0340.00216.512-0.024-0.0240.0000.0000.0000.000
92A207PRO0-0.053-0.01216.617-0.014-0.0140.0000.0000.0000.000
93A208ILE00.001-0.00112.1960.0050.0050.0000.0000.0000.000
94A209ALA00.0310.00110.6250.0190.0190.0000.0000.0000.000
95A210ASN0-0.052-0.0325.576-0.051-0.0510.0000.0000.0000.000
96A211GLY00.0770.0387.004-0.206-0.2060.0000.0000.0000.000
97A212GLN00.0520.0136.935-0.042-0.0420.0000.0000.0000.000
98A213TYR0-0.051-0.0133.308-1.108-0.2360.051-0.289-0.634-0.002
99A214LEU00.0020.0127.171-0.072-0.0720.0000.0000.0000.000
100A215MET0-0.0060.03210.2240.1120.1120.0000.0000.0000.000
101A216PRO00.008-0.00711.887-0.059-0.0590.0000.0000.0000.000
102A217ASN0-0.015-0.01010.6990.0820.0820.0000.0000.0000.000
103A218LEU00.0260.00213.2540.0380.0380.0000.0000.0000.000
104A219THR0-0.072-0.02615.0920.0360.0360.0000.0000.0000.000
105A220ALA0-0.045-0.01815.6120.0190.0190.0000.0000.0000.000
106A221TYR0-0.0090.00015.0840.0010.0010.0000.0000.0000.000
107A222PRO00.0220.03018.778-0.004-0.0040.0000.0000.0000.000
108A223ARG10.8630.89919.6430.1820.1820.0000.0000.0000.000
109A224LEU0-0.048-0.02122.1150.0110.0110.0000.0000.0000.000
110A225ILE0-0.0110.01224.6580.0120.0120.0000.0000.0000.000
111A226GLN0-0.043-0.04526.3590.0000.0000.0000.0000.0000.000
112A227THR0-0.023-0.01228.131-0.001-0.0010.0000.0000.0000.000
113A228LEU00.0020.01123.7790.0030.0030.0000.0000.0000.000
114A229THR00.0310.00425.666-0.007-0.0070.0000.0000.0000.000
115A230SER0-0.012-0.00422.4470.0010.0010.0000.0000.0000.000
116A231SER0-0.005-0.00421.367-0.024-0.0240.0000.0000.0000.000
117A232TYR0-0.049-0.02422.4150.0040.0040.0000.0000.0000.000
118A233ILE0-0.018-0.00419.478-0.005-0.0050.0000.0000.0000.000
119A234TYR0-0.012-0.01024.1790.0080.0080.0000.0000.0000.000
120A235THR0-0.010-0.00525.561-0.002-0.0020.0000.0000.0000.000
121A236GLN0-0.046-0.03428.3680.0090.0090.0000.0000.0000.000
122A237ALA0-0.0120.01329.648-0.007-0.0070.0000.0000.0000.000
123A238HIS0-0.036-0.03431.2670.0090.0090.0000.0000.0000.000
124A239LEU0-0.043-0.03333.748-0.002-0.0020.0000.0000.0000.000
125A240ASP-1-0.818-0.89636.279-0.060-0.0600.0000.0000.0000.000
126A241HIS0-0.044-0.02737.7200.0070.0070.0000.0000.0000.000
127A242ASN0-0.071-0.05140.991-0.003-0.0030.0000.0000.0000.000
128A243ASN0-0.003-0.01438.194-0.003-0.0030.0000.0000.0000.000
129A244SER00.0000.02540.033-0.002-0.0020.0000.0000.0000.000
130A245VAL00.0340.01935.457-0.002-0.0020.0000.0000.0000.000
131A246VAL0-0.031-0.01432.6520.0040.0040.0000.0000.0000.000
132A247ASP-1-0.835-0.90232.633-0.105-0.1050.0000.0000.0000.000
133A248ILE0-0.029-0.03327.1530.0010.0010.0000.0000.0000.000
134A249LYS10.9070.97327.2850.1250.1250.0000.0000.0000.000
135A250ILE00.0170.00921.3500.0040.0040.0000.0000.0000.000
136A251GLY00.014-0.00423.4920.0010.0010.0000.0000.0000.000
137A252LEU0-0.026-0.00717.943-0.010-0.0100.0000.0000.0000.000
138A253ASN0-0.004-0.03616.3910.0080.0080.0000.0000.0000.000
139A254THR00.018-0.00420.6570.0090.0090.0000.0000.0000.000
140A255ASP-1-0.804-0.85524.074-0.127-0.1270.0000.0000.0000.000
141A256LEU0-0.033-0.01521.105-0.008-0.0080.0000.0000.0000.000
142A257ARG10.8810.92424.8230.1020.1020.0000.0000.0000.000
143A258PRO00.016-0.00125.006-0.008-0.0080.0000.0000.0000.000
144A259THR0-0.022-0.02124.1910.0000.0000.0000.0000.0000.000
145A260ALA0-0.0130.01821.557-0.003-0.0030.0000.0000.0000.000
146A261ALA0-0.0100.01616.9780.0050.0050.0000.0000.0000.000
147A262TYR0-0.007-0.01112.770-0.021-0.0210.0000.0000.0000.000
148A263GLY0-0.012-0.01918.0890.0230.0230.0000.0000.0000.000
149A264LEU0-0.0150.00617.175-0.018-0.0180.0000.0000.0000.000
150A265SER0-0.038-0.02021.1550.0100.0100.0000.0000.0000.000
151A266PHE00.0290.00321.056-0.012-0.0120.0000.0000.0000.000
152A267THR0-0.017-0.01326.6410.0120.0120.0000.0000.0000.000
153A268MET00.0090.01930.123-0.004-0.0040.0000.0000.0000.000
154A269THR0-0.012-0.01232.2590.0060.0060.0000.0000.0000.000
155A270PHE00.0550.02535.623-0.002-0.0020.0000.0000.0000.000
156A271THR00.007-0.00238.4610.0020.0020.0000.0000.0000.000
157A272ASN0-0.038-0.01741.1610.0020.0020.0000.0000.0000.000
158A273SER00.002-0.00642.5980.0000.0000.0000.0000.0000.000
159A274PRO0-0.0100.00738.7340.0000.0000.0000.0000.0000.000
160A275PRO0-0.0160.00339.3240.0040.0040.0000.0000.0000.000
161A276THR0-0.004-0.00241.012-0.002-0.0020.0000.0000.0000.000
162A277SER0-0.006-0.01939.6150.0010.0010.0000.0000.0000.000
163A278PHE0-0.032-0.00433.1970.0010.0010.0000.0000.0000.000
164A279GLY00.003-0.01233.838-0.001-0.0010.0000.0000.0000.000
165A280THR0-0.032-0.00829.4670.0010.0010.0000.0000.0000.000
166A281ASP-1-0.783-0.87030.264-0.105-0.1050.0000.0000.0000.000
167A282LEU0-0.042-0.01623.106-0.004-0.0040.0000.0000.0000.000
168A283VAL00.0560.04124.275-0.004-0.0040.0000.0000.0000.000
169A284GLN0-0.016-0.01420.4570.0040.0040.0000.0000.0000.000
170A285PHE0-0.019-0.01818.9600.0080.0080.0000.0000.0000.000
171A286GLY00.0420.01116.437-0.026-0.0260.0000.0000.0000.000
172A287TYR0-0.061-0.03413.1980.0600.0600.0000.0000.0000.000
173A288LEU00.0180.01112.180-0.072-0.0720.0000.0000.0000.000
174A289GLY00.0780.0349.2640.0580.0580.0000.0000.0000.000
175A290GLN00.0100.0089.5320.0270.0270.0000.0000.0000.000
176A291ASP-1-0.898-0.9335.631-0.761-0.7610.0000.0000.0000.000