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

tag_button

FMODB ID: 5J78Z

Calculation Name: 2WUI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WUI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RG61

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2139609.951423
FMO2-HF: Nuclear repulsion 2059477.532881
FMO2-HF: Total energy -80132.418542
FMO2-MP2: Total energy -80362.643439


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:9:SER)


Summations of interaction energy for fragment #1(A:9: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.
-6.368-2.650.022-1.691-2.0480.005
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.020
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].
3A11LYS10.9010.9493.415-5.703-3.1260.013-1.258-1.3320.004
4A12THR00.004-0.0293.605-1.136-0.1800.010-0.417-0.5490.001
5A13ARG10.8760.9515.727-0.574-0.5740.0000.0000.0000.000
6A14ASP-1-0.822-0.9008.1280.8630.8630.0000.0000.0000.000
7A15GLY00.0340.0308.998-0.091-0.0910.0000.0000.0000.000
8A16ILE00.011-0.0098.949-0.111-0.1110.0000.0000.0000.000
9A17LEU0-0.034-0.00512.092-0.041-0.0410.0000.0000.0000.000
10A18ASP-1-0.924-0.95813.8870.4010.4010.0000.0000.0000.000
11A19ALA00.0450.03014.632-0.040-0.0400.0000.0000.0000.000
12A20ALA00.0030.00015.937-0.034-0.0340.0000.0000.0000.000
13A21GLU-1-0.770-0.88117.8780.3030.3030.0000.0000.0000.000
14A22ARG10.9010.96519.056-0.252-0.2520.0000.0000.0000.000
15A23VAL00.0160.00819.340-0.014-0.0140.0000.0000.0000.000
16A24PHE00.025-0.01419.252-0.015-0.0150.0000.0000.0000.000
17A25LEU0-0.027-0.00323.586-0.006-0.0060.0000.0000.0000.000
18A26GLU-1-0.861-0.91024.9220.0590.0590.0000.0000.0000.000
19A27LYS10.7620.84625.929-0.066-0.0660.0000.0000.0000.000
20A28GLY00.0520.04826.1110.0070.0070.0000.0000.0000.000
21A29VAL00.005-0.00523.476-0.007-0.0070.0000.0000.0000.000
22A30GLY0-0.023-0.01025.218-0.009-0.0090.0000.0000.0000.000
23A31THR0-0.071-0.03627.511-0.011-0.0110.0000.0000.0000.000
24A32THR0-0.061-0.03622.376-0.007-0.0070.0000.0000.0000.000
25A33ALA0-0.002-0.02022.051-0.007-0.0070.0000.0000.0000.000
26A34MET0-0.058-0.02714.6610.0200.0200.0000.0000.0000.000
27A35ALA0-0.066-0.03116.817-0.023-0.0230.0000.0000.0000.000
28A36ASP-1-0.699-0.83417.9110.0090.0090.0000.0000.0000.000
29A37LEU00.0290.01615.9570.0170.0170.0000.0000.0000.000
30A38ALA0-0.052-0.02913.8710.0190.0190.0000.0000.0000.000
31A39ASP-1-0.926-0.96114.453-0.062-0.0620.0000.0000.0000.000
32A40ALA0-0.014-0.00216.8300.0160.0160.0000.0000.0000.000
33A41ALA0-0.034-0.02011.7760.0400.0400.0000.0000.0000.000
34A42GLY0-0.0310.00712.0160.0310.0310.0000.0000.0000.000
35A43VAL0-0.066-0.0338.171-0.067-0.0670.0000.0000.0000.000
36A44SER00.0290.00610.7000.0130.0130.0000.0000.0000.000
37A45ARG11.0440.99511.6160.1450.1450.0000.0000.0000.000
38A46GLY0-0.0070.00512.2900.0200.0200.0000.0000.0000.000
39A47ALA00.0100.0087.283-0.061-0.0610.0000.0000.0000.000
40A48VAL00.0260.0158.6270.0320.0320.0000.0000.0000.000
41A49TYR00.008-0.00611.0970.0540.0540.0000.0000.0000.000
42A50GLY0-0.031-0.0019.0690.0170.0170.0000.0000.0000.000
43A51HIS0-0.049-0.0274.2380.0880.273-0.001-0.016-0.1670.000
44A52TYR0-0.018-0.0209.2160.1710.1710.0000.0000.0000.000
45A53LYS10.8780.93513.041-0.022-0.0220.0000.0000.0000.000
46A54ASN0-0.013-0.00916.234-0.029-0.0290.0000.0000.0000.000
47A55LYS10.8980.92617.5500.0060.0060.0000.0000.0000.000
48A56ILE00.0390.01819.3380.0240.0240.0000.0000.0000.000
49A57GLU-1-0.843-0.91015.9800.0420.0420.0000.0000.0000.000
50A58VAL00.0170.00713.8760.0360.0360.0000.0000.0000.000
51A59CYS00.0420.03316.0480.0390.0390.0000.0000.0000.000
52A60LEU0-0.0240.00019.4130.0180.0180.0000.0000.0000.000
53A61ALA00.0140.00814.5370.0210.0210.0000.0000.0000.000
54A62MET0-0.0400.00316.6640.0470.0470.0000.0000.0000.000
55A63CYS0-0.032-0.02017.6270.0100.0100.0000.0000.0000.000
56A64ASP-1-0.803-0.86617.9470.2170.2170.0000.0000.0000.000
57A65ARG10.7830.86313.359-0.512-0.5120.0000.0000.0000.000
58A66ALA00.0330.01417.3200.0080.0080.0000.0000.0000.000
59A67PHE0-0.011-0.02520.653-0.019-0.0190.0000.0000.0000.000
60A68GLY0-0.024-0.00419.511-0.014-0.0140.0000.0000.0000.000
61A69GLN0-0.034-0.00418.8460.0320.0320.0000.0000.0000.000
62A70ILE0-0.0050.02121.793-0.014-0.0140.0000.0000.0000.000
63A71GLU-1-0.851-0.88225.2150.1810.1810.0000.0000.0000.000
64A72VAL00.002-0.01326.455-0.013-0.0130.0000.0000.0000.000
65A73PRO0-0.011-0.00928.718-0.001-0.0010.0000.0000.0000.000
66A74ASP-1-0.837-0.91832.4050.1250.1250.0000.0000.0000.000
67A75GLU-1-0.784-0.87733.6740.0960.0960.0000.0000.0000.000
68A76ASN0-0.075-0.03035.705-0.013-0.0130.0000.0000.0000.000
69A77ALA00.0670.05336.719-0.003-0.0030.0000.0000.0000.000
70A78ARG10.8810.93738.381-0.086-0.0860.0000.0000.0000.000
71A79VAL0-0.013-0.00640.104-0.001-0.0010.0000.0000.0000.000
72A80PRO00.0130.01342.999-0.001-0.0010.0000.0000.0000.000
73A81ALA00.0410.01142.0880.0050.0050.0000.0000.0000.000
74A82LEU00.007-0.01041.9600.0040.0040.0000.0000.0000.000
75A83ASP-1-0.842-0.91441.6800.0890.0890.0000.0000.0000.000
76A84ILE0-0.061-0.02036.8210.0060.0060.0000.0000.0000.000
77A85LEU0-0.018-0.01537.6510.0060.0060.0000.0000.0000.000
78A86LEU00.0010.00938.7740.0030.0030.0000.0000.0000.000
79A87ARG10.8080.86831.439-0.152-0.1520.0000.0000.0000.000
80A88ALA00.0200.01334.0290.0070.0070.0000.0000.0000.000
81A89GLY00.0080.01434.2840.0060.0060.0000.0000.0000.000
82A90MET0-0.016-0.01036.2080.0020.0020.0000.0000.0000.000
83A91GLY00.0250.02132.5780.0040.0040.0000.0000.0000.000
84A92PHE00.0210.00129.3030.0090.0090.0000.0000.0000.000
85A93LEU00.0280.01531.8720.0020.0020.0000.0000.0000.000
86A94ARG0-0.005-0.00131.2930.0030.0030.0000.0000.0000.000
87A95GLN00.013-0.00525.318-0.005-0.0050.0000.0000.0000.000
88A96CYS0-0.081-0.03428.5360.0060.0060.0000.0000.0000.000
89A97CYS0-0.068-0.03331.015-0.010-0.0100.0000.0000.0000.000
90A98GLU-1-0.907-0.93726.9240.2110.2110.0000.0000.0000.000
91A99PRO0-0.012-0.02226.6180.0020.0020.0000.0000.0000.000
92A100GLY00.0140.01023.8060.0170.0170.0000.0000.0000.000
93A101SER0-0.043-0.05019.814-0.025-0.0250.0000.0000.0000.000
94A102VAL00.0120.01521.874-0.015-0.0150.0000.0000.0000.000
95A103GLN00.0440.03024.485-0.017-0.0170.0000.0000.0000.000
96A104ARG10.7930.88719.933-0.285-0.2850.0000.0000.0000.000
97A105VAL00.009-0.00121.151-0.017-0.0170.0000.0000.0000.000
98A106LEU00.0080.00024.169-0.016-0.0160.0000.0000.0000.000
99A107GLU-1-0.801-0.89527.8570.1010.1010.0000.0000.0000.000
100A108ILE0-0.051-0.03123.620-0.013-0.0130.0000.0000.0000.000
101A109LEU0-0.037-0.03425.455-0.014-0.0140.0000.0000.0000.000
102A110TYR0-0.082-0.06928.323-0.007-0.0070.0000.0000.0000.000
103A111LEU0-0.051-0.02330.909-0.008-0.0080.0000.0000.0000.000
104A112LYS10.7870.91627.800-0.102-0.1020.0000.0000.0000.000
105A113CYS0-0.0040.00228.489-0.002-0.0020.0000.0000.0000.000
106A114GLU-1-0.798-0.88929.4740.0410.0410.0000.0000.0000.000
107A115ARG10.9260.95131.216-0.039-0.0390.0000.0000.0000.000
108A116SER0-0.016-0.01830.615-0.006-0.0060.0000.0000.0000.000
109A117ASP-1-0.851-0.93931.7780.0150.0150.0000.0000.0000.000
110A118GLU-1-0.856-0.92726.1060.0100.0100.0000.0000.0000.000
111A119ASN0-0.012-0.00826.7870.0020.0020.0000.0000.0000.000
112A120GLU-1-0.744-0.84528.4660.0510.0510.0000.0000.0000.000
113A121PRO0-0.041-0.02324.8750.0080.0080.0000.0000.0000.000
114A122LEU00.0190.00222.9730.0120.0120.0000.0000.0000.000
115A123LEU0-0.0010.02026.7130.0080.0080.0000.0000.0000.000
116A124ARG10.8410.88928.607-0.040-0.0400.0000.0000.0000.000
117A125ARG10.7960.87220.876-0.154-0.1540.0000.0000.0000.000
118A126ARG10.8340.88827.226-0.070-0.0700.0000.0000.0000.000
119A127GLU-1-0.797-0.88829.6750.0630.0630.0000.0000.0000.000
120A128LEU0-0.080-0.03326.867-0.004-0.0040.0000.0000.0000.000
121A129LEU00.0510.03527.438-0.001-0.0010.0000.0000.0000.000
122A130GLU-1-0.722-0.80530.3230.0810.0810.0000.0000.0000.000
123A131LYS10.8730.91433.979-0.070-0.0700.0000.0000.0000.000
124A132GLN0-0.066-0.01827.625-0.004-0.0040.0000.0000.0000.000
125A133GLY00.0510.03833.1630.0000.0000.0000.0000.0000.000
126A134GLN00.0550.01934.6980.0010.0010.0000.0000.0000.000
127A135ARG10.8360.88932.878-0.092-0.0920.0000.0000.0000.000
128A136PHE00.0080.01334.811-0.003-0.0030.0000.0000.0000.000
129A137GLY00.0440.01636.927-0.002-0.0020.0000.0000.0000.000
130A138LEU0-0.085-0.04740.043-0.003-0.0030.0000.0000.0000.000
131A139ARG10.8610.92334.308-0.104-0.1040.0000.0000.0000.000
132A140GLN0-0.0060.00238.065-0.006-0.0060.0000.0000.0000.000
133A141ILE00.0410.00941.680-0.002-0.0020.0000.0000.0000.000
134A142ARG10.7620.89044.418-0.062-0.0620.0000.0000.0000.000
135A143ARG10.8400.89339.249-0.091-0.0910.0000.0000.0000.000
136A144ALA00.0410.02845.229-0.002-0.0020.0000.0000.0000.000
137A145VAL0-0.031-0.01347.314-0.002-0.0020.0000.0000.0000.000
138A146GLU-1-0.902-0.95346.0240.0630.0630.0000.0000.0000.000
139A147ARG10.7970.89543.472-0.073-0.0730.0000.0000.0000.000
140A148GLY0-0.0080.01149.833-0.001-0.0010.0000.0000.0000.000
141A149GLU-1-0.856-0.92646.5010.0730.0730.0000.0000.0000.000
142A150LEU0-0.022-0.00848.3720.0000.0000.0000.0000.0000.000
143A151PRO00.0170.02152.191-0.001-0.0010.0000.0000.0000.000
144A152ALA00.0550.01554.6290.0000.0000.0000.0000.0000.000
145A153ARG10.8590.91355.503-0.038-0.0380.0000.0000.0000.000
146A154LEU00.0370.02750.399-0.001-0.0010.0000.0000.0000.000
147A155ASP-1-0.868-0.93852.2050.0450.0450.0000.0000.0000.000
148A156VAL0-0.003-0.01547.1770.0020.0020.0000.0000.0000.000
149A157GLU-1-0.755-0.86646.4500.0590.0590.0000.0000.0000.000
150A158LEU00.0120.01347.8120.0020.0020.0000.0000.0000.000
151A159ALA00.0140.00548.8810.0020.0020.0000.0000.0000.000
152A160SER0-0.039-0.02943.6730.0030.0030.0000.0000.0000.000
153A161ILE00.0300.01644.7160.0030.0030.0000.0000.0000.000
154A162TYR0-0.0270.00246.3720.0000.0000.0000.0000.0000.000
155A163LEU00.007-0.00443.1480.0010.0010.0000.0000.0000.000
156A164GLN0-0.050-0.02938.8660.0070.0070.0000.0000.0000.000
157A165SER0-0.008-0.01142.4730.0010.0010.0000.0000.0000.000
158A166LEU0-0.074-0.01844.3890.0000.0000.0000.0000.0000.000
159A167TRP0-0.031-0.03134.4640.0000.0000.0000.0000.0000.000
160A168ASP-1-0.826-0.92739.1650.0840.0840.0000.0000.0000.000
161A169GLY0-0.0100.00340.8620.0000.0000.0000.0000.0000.000
162A170ILE0-0.049-0.03440.8290.0000.0000.0000.0000.0000.000
163A171CYS0-0.0110.01436.2410.0040.0040.0000.0000.0000.000
164A172GLY00.0770.04238.9410.0020.0020.0000.0000.0000.000
165A173THR0-0.137-0.08340.886-0.003-0.0030.0000.0000.0000.000
166A174LEU0-0.0070.02137.736-0.001-0.0010.0000.0000.0000.000
167A175ALA00.0090.00735.6390.0000.0000.0000.0000.0000.000
168A176TRP00.0330.00636.046-0.001-0.0010.0000.0000.0000.000
169A177THR0-0.129-0.07939.834-0.007-0.0070.0000.0000.0000.000
170A178GLU-1-0.756-0.87042.1260.0770.0770.0000.0000.0000.000
171A179ARG10.8800.93944.122-0.058-0.0580.0000.0000.0000.000
172A180LEU0-0.0140.00242.500-0.002-0.0020.0000.0000.0000.000
173A181ARG10.8770.93441.231-0.070-0.0700.0000.0000.0000.000
174A182ASP-1-0.829-0.91241.8660.0750.0750.0000.0000.0000.000
175A183ASP-1-0.835-0.93543.2770.0860.0860.0000.0000.0000.000
176A184PRO00.0680.04339.136-0.002-0.0020.0000.0000.0000.000
177A185TRP00.0300.01135.259-0.003-0.0030.0000.0000.0000.000
178A186ASN00.019-0.01240.5160.0000.0000.0000.0000.0000.000
179A187ARG10.7590.88843.734-0.077-0.0770.0000.0000.0000.000
180A188ALA00.0770.04141.138-0.003-0.0030.0000.0000.0000.000
181A189GLU-1-0.860-0.91941.3070.0900.0900.0000.0000.0000.000
182A190ARG10.8880.93843.223-0.077-0.0770.0000.0000.0000.000
183A191MET0-0.038-0.00945.429-0.003-0.0030.0000.0000.0000.000
184A192PHE00.0530.02039.333-0.003-0.0030.0000.0000.0000.000
185A193ARG10.8260.89643.440-0.090-0.0900.0000.0000.0000.000
186A194ALA00.0040.00647.125-0.003-0.0030.0000.0000.0000.000
187A195GLY00.009-0.00247.583-0.003-0.0030.0000.0000.0000.000
188A196LEU00.003-0.01443.872-0.003-0.0030.0000.0000.0000.000
189A197ASP-1-0.800-0.87348.3370.0580.0580.0000.0000.0000.000
190A198SER0-0.056-0.00951.636-0.004-0.0040.0000.0000.0000.000
191A199LEU0-0.014-0.01247.116-0.002-0.0020.0000.0000.0000.000
192A200ARG10.7950.86851.687-0.059-0.0590.0000.0000.0000.000
193A201SER0-0.044-0.03853.610-0.002-0.0020.0000.0000.0000.000
194A202SER00.0110.01855.689-0.003-0.0030.0000.0000.0000.000
195A203PRO00.012-0.01757.4730.0000.0000.0000.0000.0000.000
196A204TYR0-0.033-0.02257.929-0.001-0.0010.0000.0000.0000.000
197A205LEU00.0270.03052.1320.0000.0000.0000.0000.0000.000
198A206LEU0-0.0340.00555.1530.0010.0010.0000.0000.0000.000
199A207LEU00.0000.01654.694-0.002-0.0020.0000.0000.0000.000
200A208ALA0-0.016-0.00558.240-0.002-0.0020.0000.0000.0000.000