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: VQ6Y1

Calculation Name: 1WDZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WDZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UQB8

Base Structure: X-ray

Registration Date: 2023-09-23

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 231
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2291492.397827
FMO2-HF: Nuclear repulsion 2198067.963499
FMO2-HF: Total energy -93424.434328
FMO2-MP2: Total energy -93695.168561


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
0.7182.969-0.007-0.815-1.4290.002
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.012
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].
3A4SER0-0.007-0.0203.8101.0722.439-0.012-0.608-0.7480.002
4A5ARG11.0390.9934.7341.1461.223-0.001-0.006-0.0700.000
5A6SER00.0170.0067.0620.3380.3380.0000.0000.0000.000
6A7GLU-1-0.901-0.9364.1332.6742.9900.006-0.099-0.2220.000
7A8GLU-1-0.951-0.9814.065-1.304-0.8130.000-0.102-0.3890.000
8A9MET0-0.030-0.0236.081-0.253-0.2530.0000.0000.0000.000
9A10HIS00.0580.0728.950-0.244-0.2440.0000.0000.0000.000
10A11ARG10.9620.9826.313-2.002-2.0020.0000.0000.0000.000
11A12LEU00.0010.0069.299-0.180-0.1800.0000.0000.0000.000
12A13THR00.0150.01311.661-0.118-0.1180.0000.0000.0000.000
13A14GLU-1-0.904-0.96411.5160.8010.8010.0000.0000.0000.000
14A15ASN0-0.019-0.01612.048-0.112-0.1120.0000.0000.0000.000
15A16VAL00.0260.04214.480-0.053-0.0530.0000.0000.0000.000
16A17TYR0-0.010-0.01717.174-0.033-0.0330.0000.0000.0000.000
17A18LYS10.9040.95716.753-0.352-0.3520.0000.0000.0000.000
18A19THR00.0420.02317.542-0.026-0.0260.0000.0000.0000.000
19A20ILE0-0.053-0.02120.070-0.026-0.0260.0000.0000.0000.000
20A21MET0-0.077-0.04221.422-0.019-0.0190.0000.0000.0000.000
21A22GLU-1-0.886-0.95420.2720.2530.2530.0000.0000.0000.000
22A23GLN0-0.002-0.00120.5280.0090.0090.0000.0000.0000.000
23A24PHE0-0.030-0.00124.312-0.013-0.0130.0000.0000.0000.000
24A25ASN00.038-0.01426.211-0.017-0.0170.0000.0000.0000.000
25A26PRO0-0.039-0.00326.782-0.011-0.0110.0000.0000.0000.000
26A27SER00.0210.00227.997-0.010-0.0100.0000.0000.0000.000
27A28LEU0-0.0040.01430.221-0.008-0.0080.0000.0000.0000.000
28A29ARG10.9140.95731.963-0.099-0.0990.0000.0000.0000.000
29A30ASN00.0110.00733.475-0.006-0.0060.0000.0000.0000.000
30A31PHE00.0030.00934.228-0.005-0.0050.0000.0000.0000.000
31A32ILE00.0310.01335.876-0.005-0.0050.0000.0000.0000.000
32A33ALA0-0.017-0.00737.986-0.004-0.0040.0000.0000.0000.000
33A34MET0-0.031-0.02038.344-0.004-0.0040.0000.0000.0000.000
34A35GLY00.0350.01740.050-0.004-0.0040.0000.0000.0000.000
35A36LYS10.9640.97141.757-0.049-0.0490.0000.0000.0000.000
36A37ASN0-0.019-0.00843.731-0.003-0.0030.0000.0000.0000.000
37A38TYR0-0.0110.00344.276-0.002-0.0020.0000.0000.0000.000
38A39GLU-1-0.880-0.96145.8790.0320.0320.0000.0000.0000.000
39A40LYS10.8980.94547.035-0.040-0.0400.0000.0000.0000.000
40A41ALA00.0050.01249.444-0.002-0.0020.0000.0000.0000.000
41A42LEU00.0150.00748.598-0.001-0.0010.0000.0000.0000.000
42A43ALA00.0370.02051.986-0.001-0.0010.0000.0000.0000.000
43A44GLY0-0.029-0.01853.811-0.001-0.0010.0000.0000.0000.000
44A45VAL0-0.035-0.02354.945-0.001-0.0010.0000.0000.0000.000
45A46THR0-0.0060.00856.392-0.001-0.0010.0000.0000.0000.000
46A47TYR0-0.072-0.03258.220-0.001-0.0010.0000.0000.0000.000
47A48ALA00.007-0.00260.157-0.001-0.0010.0000.0000.0000.000
48A49ALA0-0.0090.00160.507-0.001-0.0010.0000.0000.0000.000
49A50LYS10.9700.98262.479-0.019-0.0190.0000.0000.0000.000
50A51GLY00.0770.04465.266-0.001-0.0010.0000.0000.0000.000
51A52TYR0-0.031-0.01164.756-0.001-0.0010.0000.0000.0000.000
52A53PHE0-0.006-0.01466.525-0.001-0.0010.0000.0000.0000.000
53A54ASP-1-0.899-0.95168.1750.0130.0130.0000.0000.0000.000
54A55ALA0-0.047-0.01570.504-0.001-0.0010.0000.0000.0000.000
55A56LEU00.015-0.00168.490-0.001-0.0010.0000.0000.0000.000
56A57VAL00.0360.01971.798-0.001-0.0010.0000.0000.0000.000
57A58LYS10.9691.00674.246-0.011-0.0110.0000.0000.0000.000
58A59MET0-0.060-0.03574.9130.0000.0000.0000.0000.0000.000
59A60GLY00.0400.00976.2530.0000.0000.0000.0000.0000.000
60A61GLU-1-0.964-0.99977.6570.0090.0090.0000.0000.0000.000
61A62LEU0-0.024-0.01679.9890.0000.0000.0000.0000.0000.000
62A63ALA0-0.0040.01480.2580.0000.0000.0000.0000.0000.000
63A64SER00.0060.02281.284-0.001-0.0010.0000.0000.0000.000
64A65GLU-1-0.976-0.97783.6310.0080.0080.0000.0000.0000.000
65A66SER0-0.075-0.04285.0720.0000.0000.0000.0000.0000.000
66A67GLN0-0.019-0.03086.9970.0000.0000.0000.0000.0000.000
67A68GLY00.007-0.01288.5540.0000.0000.0000.0000.0000.000
68A69SER0-0.012-0.00883.1620.0000.0000.0000.0000.0000.000
69A70LYS10.9320.96682.854-0.006-0.0060.0000.0000.0000.000
70A71GLU-1-0.847-0.90782.0430.0050.0050.0000.0000.0000.000
71A72LEU0-0.022-0.01878.2030.0000.0000.0000.0000.0000.000
72A73GLY00.005-0.00177.8640.0000.0000.0000.0000.0000.000
73A74ASP-1-0.875-0.94177.6040.0060.0060.0000.0000.0000.000
74A75VAL0-0.036-0.01773.4800.0000.0000.0000.0000.0000.000
75A76LEU00.020-0.00673.2130.0000.0000.0000.0000.0000.000
76A77PHE00.0520.02772.4850.0010.0010.0000.0000.0000.000
77A78GLN0-0.030-0.01671.6090.0000.0000.0000.0000.0000.000
78A79MET0-0.0450.00568.8670.0000.0000.0000.0000.0000.000
79A80ALA00.0300.01267.7920.0010.0010.0000.0000.0000.000
80A81GLU-1-0.793-0.90167.7290.0100.0100.0000.0000.0000.000
81A82VAL0-0.061-0.02964.1360.0000.0000.0000.0000.0000.000
82A83HIS0-0.001-0.00162.0770.0000.0000.0000.0000.0000.000
83A84ARG10.8760.93562.852-0.010-0.0100.0000.0000.0000.000
84A85GLN0-0.074-0.04562.8480.0000.0000.0000.0000.0000.000
85A86ILE00.0000.00058.4250.0010.0010.0000.0000.0000.000
86A87GLN00.0290.00758.3950.0020.0020.0000.0000.0000.000
87A88ASN00.0330.00858.2820.0020.0020.0000.0000.0000.000
88A89GLN0-0.054-0.02956.0010.0010.0010.0000.0000.0000.000
89A90LEU0-0.0100.01252.8020.0000.0000.0000.0000.0000.000
90A91GLU-1-0.841-0.92753.3070.0210.0210.0000.0000.0000.000
91A92GLU-1-0.975-0.98053.4160.0180.0180.0000.0000.0000.000
92A93MET0-0.028-0.00148.4280.0020.0020.0000.0000.0000.000
93A94LEU00.0210.01448.7670.0020.0020.0000.0000.0000.000
94A95LYS10.9730.98648.926-0.017-0.0170.0000.0000.0000.000
95A96SER00.0130.01246.8100.0020.0020.0000.0000.0000.000
96A97PHE0-0.033-0.02342.2070.0020.0020.0000.0000.0000.000
97A98HIS00.0110.01244.2360.0040.0040.0000.0000.0000.000
98A99ASN0-0.048-0.05944.7910.0000.0000.0000.0000.0000.000
99A100GLU-1-0.946-0.97843.1430.0220.0220.0000.0000.0000.000
100A101LEU0-0.018-0.01437.9300.0020.0020.0000.0000.0000.000
101A102LEU0-0.0150.00939.7870.0040.0040.0000.0000.0000.000
102A103THR00.0610.03240.3570.0040.0040.0000.0000.0000.000
103A104GLN0-0.057-0.02639.0360.0030.0030.0000.0000.0000.000
104A105LEU0-0.032-0.03234.5080.0040.0040.0000.0000.0000.000
105A106GLU-1-0.911-0.95135.9630.0570.0570.0000.0000.0000.000
106A107GLN00.0000.00437.2470.0030.0030.0000.0000.0000.000
107A108LYS10.8680.95033.620-0.049-0.0490.0000.0000.0000.000
108A109VAL00.007-0.00331.5280.0070.0070.0000.0000.0000.000
109A110GLU-1-0.990-0.97632.6820.0760.0760.0000.0000.0000.000
110A111LEU00.023-0.01933.4880.0070.0070.0000.0000.0000.000
111A112ASP-1-0.741-0.83928.6800.1150.1150.0000.0000.0000.000
112A113SER00.0440.01126.8410.0060.0060.0000.0000.0000.000
113A114ARG10.9591.00526.768-0.085-0.0850.0000.0000.0000.000
114A115TYR00.008-0.00528.1500.0060.0060.0000.0000.0000.000
115A116LEU00.0030.00723.6100.0080.0080.0000.0000.0000.000
116A117SER0-0.0020.00123.3890.0270.0270.0000.0000.0000.000
117A118ALA0-0.044-0.01823.7120.0170.0170.0000.0000.0000.000
118A119ALA0-0.003-0.00423.6760.0100.0100.0000.0000.0000.000
119A120LEU00.0190.01616.9860.0120.0120.0000.0000.0000.000
120A121LYS10.9871.00019.725-0.211-0.2110.0000.0000.0000.000
121A122LYS10.8910.95721.090-0.115-0.1150.0000.0000.0000.000
122A123TYR00.034-0.01413.236-0.029-0.0290.0000.0000.0000.000
123A124GLN0-0.042-0.05015.481-0.041-0.0410.0000.0000.0000.000
124A125THR0-0.071-0.04417.3470.0230.0230.0000.0000.0000.000
125A126GLU-1-0.833-0.89919.7320.1440.1440.0000.0000.0000.000
126A127GLN0-0.003-0.01912.311-0.007-0.0070.0000.0000.0000.000
127A128ARG10.9671.01015.479-0.379-0.3790.0000.0000.0000.000
128A129SER0-0.040-0.00716.596-0.028-0.0280.0000.0000.0000.000
129A130LYS10.9210.95917.460-0.116-0.1160.0000.0000.0000.000
130A131GLY00.0360.02814.627-0.042-0.0420.0000.0000.0000.000
131A132ASP-1-0.823-0.91115.3460.2760.2760.0000.0000.0000.000
132A133ALA0-0.105-0.05817.503-0.042-0.0420.0000.0000.0000.000
133A134LEU00.0160.00814.030-0.032-0.0320.0000.0000.0000.000
134A135ASP-1-0.838-0.91013.6150.1360.1360.0000.0000.0000.000
135A136LYS10.9110.94516.456-0.103-0.1030.0000.0000.0000.000
136A137CYM-1-0.735-0.75920.000-0.049-0.0490.0000.0000.0000.000
137A138GLN00.0380.00013.9370.0130.0130.0000.0000.0000.000
138A139ALA0-0.061-0.02118.479-0.020-0.0200.0000.0000.0000.000
139A140GLU-1-1.019-1.03219.5620.0080.0080.0000.0000.0000.000
140A141LEU00.0870.06120.250-0.007-0.0070.0000.0000.0000.000
141A142LYS10.9820.99817.2940.0790.0790.0000.0000.0000.000
142A143LYS10.8670.91721.193-0.019-0.0190.0000.0000.0000.000
143A144LEU00.0230.01524.1190.0060.0060.0000.0000.0000.000
144A145ARG10.9920.99021.4160.1580.1580.0000.0000.0000.000
145A146LYS10.8840.96223.5150.0170.0170.0000.0000.0000.000
146A147LYS10.8930.94826.3070.0210.0210.0000.0000.0000.000
147A148SER0-0.052-0.01028.4560.0050.0050.0000.0000.0000.000
148A149GLN00.010-0.00130.2250.0030.0030.0000.0000.0000.000
149A150GLY00.0370.01131.7280.0020.0020.0000.0000.0000.000
150A151SER0-0.033-0.02032.8900.0030.0030.0000.0000.0000.000
151A152LYS10.9590.97636.1260.0470.0470.0000.0000.0000.000
152A153ASN00.0170.02731.0720.0100.0100.0000.0000.0000.000
153A154PRO00.0240.00835.164-0.001-0.0010.0000.0000.0000.000
154A155GLN00.1190.04535.451-0.003-0.0030.0000.0000.0000.000
155A156LYS10.9610.99535.0920.0170.0170.0000.0000.0000.000
156A157TYR0-0.019-0.00827.8380.0030.0030.0000.0000.0000.000
157A158SER00.0660.01330.893-0.004-0.0040.0000.0000.0000.000
158A159ASP-1-0.870-0.92730.613-0.060-0.0600.0000.0000.0000.000
159A160LYS10.8480.92829.1630.0240.0240.0000.0000.0000.000
160A161GLU-1-0.916-0.96825.144-0.121-0.1210.0000.0000.0000.000
161A162LEU00.0330.00325.986-0.011-0.0110.0000.0000.0000.000
162A163GLN00.0250.02527.2970.0030.0030.0000.0000.0000.000
163A164TYR0-0.014-0.01823.3650.0000.0000.0000.0000.0000.000
164A165ILE0-0.043-0.00822.261-0.008-0.0080.0000.0000.0000.000
165A166ASP-1-0.897-0.93722.587-0.101-0.1010.0000.0000.0000.000
166A167ALA00.009-0.00423.879-0.001-0.0010.0000.0000.0000.000
167A168ILE0-0.048-0.03717.8110.0050.0050.0000.0000.0000.000
168A169SER0-0.009-0.01019.339-0.018-0.0180.0000.0000.0000.000
169A170ASN0-0.0110.00120.004-0.014-0.0140.0000.0000.0000.000
170A171LYS10.7450.78219.4270.0080.0080.0000.0000.0000.000
171A172GLN0-0.010-0.00814.8540.0350.0350.0000.0000.0000.000
172A173GLY00.0350.02015.864-0.001-0.0010.0000.0000.0000.000
173A174GLU-1-0.965-0.99117.9420.0150.0150.0000.0000.0000.000
174A175LEU0-0.034-0.01413.2010.0360.0360.0000.0000.0000.000
175A176GLU-1-0.893-0.94412.225-0.319-0.3190.0000.0000.0000.000
176A177ASN0-0.004-0.01214.4340.0220.0220.0000.0000.0000.000
177A178TYR0-0.046-0.04616.9170.0260.0260.0000.0000.0000.000
178A179VAL0-0.0090.00111.2730.0230.0230.0000.0000.0000.000
179A180SER0-0.048-0.03714.533-0.002-0.0020.0000.0000.0000.000
180A181ASP-1-1.004-0.99815.2720.0350.0350.0000.0000.0000.000
181A182GLY00.0310.01317.418-0.001-0.0010.0000.0000.0000.000
182A183TYR00.0080.00913.980-0.027-0.0270.0000.0000.0000.000
183A184LYS10.9870.99416.194-0.017-0.0170.0000.0000.0000.000
184A185THR00.0260.01819.215-0.016-0.0160.0000.0000.0000.000
185A186ALA00.0090.00517.560-0.006-0.0060.0000.0000.0000.000
186A187LEU00.0260.00316.736-0.012-0.0120.0000.0000.0000.000
187A188THR0-0.036-0.01320.273-0.020-0.0200.0000.0000.0000.000
188A189GLU-1-0.883-0.94022.4560.1060.1060.0000.0000.0000.000
189A190GLU-1-0.959-0.97619.7590.0930.0930.0000.0000.0000.000
190A191ARG10.9660.98123.185-0.026-0.0260.0000.0000.0000.000
191A192ARG10.8620.91325.123-0.086-0.0860.0000.0000.0000.000
192A193ARG10.7750.86526.067-0.110-0.1100.0000.0000.0000.000
193A194PHE00.0490.02123.670-0.005-0.0050.0000.0000.0000.000
194A195CYS0-0.049-0.02628.805-0.007-0.0070.0000.0000.0000.000
195A196PHE00.0060.00730.945-0.003-0.0030.0000.0000.0000.000
196A197LEU00.0050.00231.815-0.002-0.0020.0000.0000.0000.000
197A198VAL00.0140.00531.854-0.003-0.0030.0000.0000.0000.000
198A199GLU-1-0.880-0.93734.7440.0230.0230.0000.0000.0000.000
199A200LYS10.9450.98437.196-0.033-0.0330.0000.0000.0000.000
200A201GLN00.0110.01437.263-0.003-0.0030.0000.0000.0000.000
201A202CYS0-0.042-0.02737.975-0.003-0.0030.0000.0000.0000.000
202A203ALA0-0.0110.00640.720-0.002-0.0020.0000.0000.0000.000
203A204VAL00.0470.01942.600-0.001-0.0010.0000.0000.0000.000
204A205ALA00.0060.00242.547-0.001-0.0010.0000.0000.0000.000
205A206LYS10.9350.96144.499-0.010-0.0100.0000.0000.0000.000
206A207ASN0-0.014-0.01746.620-0.002-0.0020.0000.0000.0000.000
207A208SER00.0070.00447.032-0.001-0.0010.0000.0000.0000.000
208A209ALA0-0.0150.00148.504-0.001-0.0010.0000.0000.0000.000
209A210ALA00.0000.00250.164-0.001-0.0010.0000.0000.0000.000
210A211TYR00.0270.01751.838-0.001-0.0010.0000.0000.0000.000
211A212HIS0-0.014-0.01949.6390.0000.0000.0000.0000.0000.000
212A213SER0-0.068-0.03153.941-0.001-0.0010.0000.0000.0000.000
213A214LYS10.9770.99755.714-0.008-0.0080.0000.0000.0000.000
214A215GLY00.0250.00657.3820.0000.0000.0000.0000.0000.000
215A216LYS10.9560.97356.599-0.003-0.0030.0000.0000.0000.000
216A217GLU-1-0.950-0.97259.4980.0030.0030.0000.0000.0000.000
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