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: 63Q8Z

Calculation Name: 1WYZ-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WYZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A031

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 230
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2632019.696755
FMO2-HF: Nuclear repulsion 2543020.851949
FMO2-HF: Total energy -88998.844806
FMO2-MP2: Total energy -89260.086577


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:1:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
-3.215-1.9910.023-0.554-0.6920
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.054
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].
3A3THR 0-0.0120.0203.8441.2182.129-0.005-0.411-0.495-0.001
4A4ALA 0-0.049-0.0495.0750.6890.6890.0000.0000.0000.000
5A5LEU 00.0340.0176.841-0.174-0.1740.0000.0000.0000.000
6A6TYR 00.0430.0114.6260.0410.0380.000-0.0310.0350.000
7A7LEU 0-0.045-0.0319.3490.0210.0210.0000.0000.0000.000
8A8LEU 0-0.006-0.02111.607-0.011-0.0110.0000.0000.0000.000
9A9PRO 0-0.0240.01014.1770.0180.0180.0000.0000.0000.000
10A10VAL 00.0310.01817.285-0.025-0.0250.0000.0000.0000.000
11A11THR 0-0.036-0.03220.5850.0080.0080.0000.0000.0000.000
12A12LEU 0-0.023-0.01923.7070.0070.0070.0000.0000.0000.000
13A13GLY 00.020-0.00826.0660.0060.0060.0000.0000.0000.000
14A14ASP -1-1.002-0.97828.050-0.068-0.0680.0000.0000.0000.000
15A15THR 00.0020.01026.6350.0010.0010.0000.0000.0000.000
16A16PRO 0-0.010-0.00527.103-0.007-0.0070.0000.0000.0000.000
17A17LEU 00.0630.01621.0230.0010.0010.0000.0000.0000.000
18A18GLU -1-0.907-0.95521.862-0.130-0.1300.0000.0000.0000.000
19A19GLN 0-0.087-0.04622.9530.0030.0030.0000.0000.0000.000
20A20VAL 0-0.054-0.04022.1050.0110.0110.0000.0000.0000.000
21A21LEU 0-0.009-0.00117.6520.0050.0050.0000.0000.0000.000
22A22PRO 0-0.0100.00314.494-0.005-0.0050.0000.0000.0000.000
23A23SER 00.0420.01115.864-0.026-0.0260.0000.0000.0000.000
24A24TYR 00.0240.0206.0190.0350.0350.0000.0000.0000.000
25A25ASN 00.031-0.00711.841-0.136-0.1360.0000.0000.0000.000
26A26THR 00.0150.00413.070-0.027-0.0270.0000.0000.0000.000
27A27GLU -1-0.983-0.98811.538-0.618-0.6180.0000.0000.0000.000
28A28ILE 00.0240.0217.784-0.021-0.0210.0000.0000.0000.000
29A29ILE 0-0.034-0.01810.5710.0410.0410.0000.0000.0000.000
30A30ARG 10.8560.90513.6220.3960.3960.0000.0000.0000.000
31A31GLY 0-0.0190.01511.6510.0260.0260.0000.0000.0000.000
32A32ILE 0-0.093-0.0359.6370.0500.0500.0000.0000.0000.000
33A33ARG 10.9660.98213.2780.3750.3750.0000.0000.0000.000
34A34HIS 00.0210.02015.3550.0210.0210.0000.0000.0000.000
35A35PHE 00.0490.00915.255-0.017-0.0170.0000.0000.0000.000
36A36ILE 0-0.0260.00416.9650.0250.0250.0000.0000.0000.000
37A37VAL 0-0.008-0.02018.471-0.003-0.0030.0000.0000.0000.000
38A38GLU -1-0.786-0.90021.168-0.021-0.0210.0000.0000.0000.000
39A39ASP -1-0.801-0.92524.124-0.055-0.0550.0000.0000.0000.000
40A40VAL 00.0120.01124.705-0.009-0.0090.0000.0000.0000.000
41A41ARG 10.8990.96125.7780.0560.0560.0000.0000.0000.000
42A42SER 0-0.0060.00325.937-0.011-0.0110.0000.0000.0000.000
43A43ALA 00.0830.04921.706-0.009-0.0090.0000.0000.0000.000
44A44ARG 10.9080.96222.6500.0970.0970.0000.0000.0000.000
45A45ARG 10.8720.92424.4880.0730.0730.0000.0000.0000.000
46A46PHE 00.0680.03318.056-0.004-0.0040.0000.0000.0000.000
47A47LEU 00.0370.01317.841-0.009-0.0090.0000.0000.0000.000
48A48LYS 10.8120.92721.4030.1530.1530.0000.0000.0000.000
49A49LYN 0-0.0070.01124.156-0.001-0.0010.0000.0000.0000.000
50A50VAL 0-0.0250.00817.713-0.004-0.0040.0000.0000.0000.000
51A51ASP -1-0.809-0.89819.814-0.281-0.2810.0000.0000.0000.000
52A52ARG 10.8970.92621.9110.1570.1570.0000.0000.0000.000
53A53GLU -1-0.912-0.95822.141-0.165-0.1650.0000.0000.0000.000
54A54ILE 0-0.044-0.00818.171-0.006-0.0060.0000.0000.0000.000
55A55ASP -1-0.825-0.92021.752-0.136-0.1360.0000.0000.0000.000
56A56ILE 0-0.076-0.04023.289-0.002-0.0020.0000.0000.0000.000
57A57ASP -1-0.933-0.95824.618-0.106-0.1060.0000.0000.0000.000
58A58SER 0-0.0170.00620.6640.0010.0010.0000.0000.0000.000
59A59LEU 0-0.080-0.05921.851-0.006-0.0060.0000.0000.0000.000
60A60THR 0-0.014-0.00520.1640.0080.0080.0000.0000.0000.000
61A61PHE 0-0.031-0.01520.9600.0020.0020.0000.0000.0000.000
62A62TYR 00.0210.00919.0260.0110.0110.0000.0000.0000.000
63A63PRO 0-0.027-0.02422.0930.0010.0010.0000.0000.0000.000
64A64LEU 00.0060.01721.0320.0070.0070.0000.0000.0000.000
65A65ASN 00.0270.00324.134-0.001-0.0010.0000.0000.0000.000
66A66LYS 10.9800.98225.584-0.013-0.0130.0000.0000.0000.000
67A67HIS 0-0.022-0.02927.4730.0080.0080.0000.0000.0000.000
68A68THR 0-0.0370.00524.057-0.004-0.0040.0000.0000.0000.000
69A69SER 00.0620.03426.5940.0090.0090.0000.0000.0000.000
70A70PRO 00.013-0.04724.007-0.002-0.0020.0000.0000.0000.000
71A71GLU -1-0.916-0.97423.4630.0260.0260.0000.0000.0000.000
72A72ASP -1-0.833-0.93124.388-0.005-0.0050.0000.0000.0000.000
73A73ILE 0-0.031-0.00519.574-0.008-0.0080.0000.0000.0000.000
74A74SER 00.0170.01219.860-0.003-0.0030.0000.0000.0000.000
75A75GLY 0-0.028-0.02919.883-0.005-0.0050.0000.0000.0000.000
76A76TYR 0-0.027-0.01319.616-0.014-0.0140.0000.0000.0000.000
77A77LEU 00.0160.00115.102-0.023-0.0230.0000.0000.0000.000
78A78LYS 10.9420.99115.7250.0130.0130.0000.0000.0000.000
79A79PRO 00.0200.00315.7390.0000.0000.0000.0000.0000.000
80A80LEU 00.0330.0319.312-0.017-0.0170.0000.0000.0000.000
81A81ALA 0-0.080-0.03912.2470.0210.0210.0000.0000.0000.000
82A82GLY 0-0.033-0.01214.5750.0200.0200.0000.0000.0000.000
83A83GLY 0-0.0180.00010.894-0.005-0.0050.0000.0000.0000.000
84A84ALA 0-0.058-0.02510.665-0.125-0.1250.0000.0000.0000.000
85A85SER 00.008-0.0167.1330.1540.1540.0000.0000.0000.000
86A86MET 0-0.037-0.0039.9190.0740.0740.0000.0000.0000.000
87A87GLY 00.0230.01910.933-0.035-0.0350.0000.0000.0000.000
88A88VAL 0-0.046-0.01913.1320.0420.0420.0000.0000.0000.000
89A89ILE 00.0040.00015.666-0.014-0.0140.0000.0000.0000.000
90A90SER 00.024-0.00918.4090.0130.0130.0000.0000.0000.000
91A91GLU -1-0.945-0.97721.345-0.045-0.0450.0000.0000.0000.000
92A92NME 0-0.044-0.00523.8680.0010.0010.0000.0000.0000.000
93A98ACE 00.0460.01422.000-0.003-0.0030.0000.0000.0000.000
94A99ASP -1-0.956-0.98522.8740.0280.0280.0000.0000.0000.000
95A100PRO 0-0.0290.00522.5790.0100.0100.0000.0000.0000.000
96A101GLY 00.0460.01918.9960.0020.0020.0000.0000.0000.000
97A102ALA 0-0.021-0.02018.0200.0150.0150.0000.0000.0000.000
98A103ASP -1-0.909-0.95919.3180.0580.0580.0000.0000.0000.000
99A104VAL 0-0.006-0.00615.9130.0080.0080.0000.0000.0000.000
100A105VAL 00.0050.01013.8370.0180.0180.0000.0000.0000.000
101A106ALA 0-0.0070.00715.7810.0360.0360.0000.0000.0000.000
102A107ILE 0-0.0440.02418.4640.0170.0170.0000.0000.0000.000
103A108ALA 00.0380.00513.1620.0120.0120.0000.0000.0000.000
104A109GLN 00.002-0.00412.1300.0500.0500.0000.0000.0000.000
105A110ARG 10.9080.97614.999-0.077-0.0770.0000.0000.0000.000
106A111GLN 0-0.068-0.03115.978-0.005-0.0050.0000.0000.0000.000
107A112LYS 10.9170.96311.726-0.501-0.5010.0000.0000.0000.000
108A113LEU 00.0220.01211.0870.0770.0770.0000.0000.0000.000
109A114LYS 10.9250.9683.161-4.324-4.0910.028-0.101-0.1600.001
110A115VAL 00.0360.0227.856-0.189-0.1890.0000.0000.0000.000
111A116ILE 0-0.052-0.0294.4220.2710.3540.000-0.011-0.0720.000
112A117PRO 00.0030.0147.427-0.187-0.1870.0000.0000.0000.000
113A118LEU 00.0250.0178.1770.0150.0150.0000.0000.0000.000
114A119VAL 0-0.011-0.01411.4860.0340.0340.0000.0000.0000.000
115A120GLY 00.0710.02214.679-0.038-0.0380.0000.0000.0000.000
116A121PRO 0-0.0280.01817.8940.0230.0230.0000.0000.0000.000
117A122SER 00.0850.03220.9350.0030.0030.0000.0000.0000.000
118A123SER 00.0490.01222.6870.0050.0050.0000.0000.0000.000
119A124ILE 00.0200.01324.3790.0030.0030.0000.0000.0000.000
120A125ILE 00.043-0.00220.8450.0040.0040.0000.0000.0000.000
121A126LEU 00.0210.01524.2700.0010.0010.0000.0000.0000.000
122A127SER 0-0.003-0.00426.488-0.001-0.0010.0000.0000.0000.000
123A128VAL 0-0.030-0.00827.4990.0000.0000.0000.0000.0000.000
124A129MET 0-0.042-0.02024.7760.0020.0020.0000.0000.0000.000
125A130ALA 00.0370.02829.096-0.001-0.0010.0000.0000.0000.000
126A131SER 0-0.057-0.02332.0990.0000.0000.0000.0000.0000.000
127A132GLY 00.0270.01933.002-0.001-0.0010.0000.0000.0000.000
128A133PHE 0-0.068-0.05233.3670.0020.0020.0000.0000.0000.000
129A134ASN 0-0.017-0.00631.4260.0040.0040.0000.0000.0000.000
130A135GLY 00.1110.04028.4480.0000.0000.0000.0000.0000.000
131A136GLN 0-0.065-0.02226.8950.0120.0120.0000.0000.0000.000
132A137SER 00.0240.00728.3990.0070.0070.0000.0000.0000.000
133A138PHE 0-0.015-0.01824.066-0.008-0.0080.0000.0000.0000.000
134A139ALA 00.0260.02228.4590.0060.0060.0000.0000.0000.000
135A140PHE 00.0340.02626.849-0.007-0.0070.0000.0000.0000.000
136A141HIS 0-0.050-0.04929.1520.0030.0030.0000.0000.0000.000
137A142GLY 00.0420.02730.400-0.001-0.0010.0000.0000.0000.000
138A143TYR 00.0240.02631.014-0.003-0.0030.0000.0000.0000.000
139A144LEU 0-0.029-0.02234.4490.0030.0030.0000.0000.0000.000
140A145PRO 0-0.014-0.01837.562-0.002-0.0020.0000.0000.0000.000
141A146ILE 00.0510.01739.704-0.001-0.0010.0000.0000.0000.000
142A147GLU -1-0.953-0.96042.3550.0110.0110.0000.0000.0000.000
143A148PRO 00.061-0.00145.5490.0010.0010.0000.0000.0000.000
144A149GLY 00.0370.03947.7060.0000.0000.0000.0000.0000.000
145A150GLU -1-0.848-0.93543.1710.0200.0200.0000.0000.0000.000
146A151ARG 10.7680.87341.491-0.006-0.0060.0000.0000.0000.000
147A152ALA 00.0000.00743.3370.0010.0010.0000.0000.0000.000
148A153LYS 10.9510.98344.609-0.021-0.0210.0000.0000.0000.000
149A154LYS 10.8870.97135.448-0.027-0.0270.0000.0000.0000.000
150A155LEU 00.0050.00640.3350.0020.0020.0000.0000.0000.000
151A156LYS 10.9520.98441.885-0.016-0.0160.0000.0000.0000.000
152A157THR 0-0.012-0.00739.8590.0010.0010.0000.0000.0000.000
153A158LEU 00.005-0.00636.0810.0020.0020.0000.0000.0000.000
154A159GLU -1-0.708-0.80638.9080.0210.0210.0000.0000.0000.000
155A160GLN 0-0.052-0.03941.3470.0010.0010.0000.0000.0000.000
156A161ARG 11.0141.00334.373-0.046-0.0460.0000.0000.0000.000
157A162VAL 0-0.0420.01637.5980.0020.0020.0000.0000.0000.000
158A163TYR 0-0.115-0.08438.6610.0010.0010.0000.0000.0000.000
159A164ALA 0-0.040-0.00839.9960.0010.0010.0000.0000.0000.000
160A165GLU -1-0.903-0.95634.4310.0560.0560.0000.0000.0000.000
161A166SER 0-0.079-0.03135.3860.0010.0010.0000.0000.0000.000
162A167GLN 00.0190.02431.023-0.001-0.0010.0000.0000.0000.000
163A168THR 0-0.029-0.01231.623-0.005-0.0050.0000.0000.0000.000
164A169GLN 0-0.050-0.03532.4010.0030.0030.0000.0000.0000.000
165A170LEU 00.007-0.00528.659-0.004-0.0040.0000.0000.0000.000
166A171PHE 0-0.005-0.00632.1320.0030.0030.0000.0000.0000.000
167A172ILE 00.0270.00630.054-0.002-0.0020.0000.0000.0000.000
168A173GLU -1-0.776-0.91933.5420.0050.0050.0000.0000.0000.000
169A174THR 0-0.0420.00535.815-0.004-0.0040.0000.0000.0000.000
170A175PRO 00.0540.00835.8630.0010.0010.0000.0000.0000.000
171A176TYR 00.0460.01138.4500.0010.0010.0000.0000.0000.000
172A177ARG 10.9110.96340.523-0.002-0.0020.0000.0000.0000.000
173A178ASN 00.0170.00637.8230.0030.0030.0000.0000.0000.000
174A179HIS 00.0400.01541.3920.0020.0020.0000.0000.0000.000
175A180LYS 10.9310.97444.821-0.003-0.0030.0000.0000.0000.000
176A181MET 0-0.017-0.00439.6690.0020.0020.0000.0000.0000.000
177A182ILE 00.0100.01542.3460.0020.0020.0000.0000.0000.000
178A183GLU -1-0.857-0.93644.1920.0050.0050.0000.0000.0000.000
179A184ASP -1-0.820-0.91244.7200.0080.0080.0000.0000.0000.000
180A185ILE 0-0.041-0.00740.7200.0020.0020.0000.0000.0000.000
181A186LEU 0-0.038-0.03044.6250.0010.0010.0000.0000.0000.000
182A187GLN 0-0.0300.00747.7250.0010.0010.0000.0000.0000.000
183A188ASN 0-0.078-0.06446.4320.0010.0010.0000.0000.0000.000
184A189CYS 0-0.076-0.02643.0070.0020.0020.0000.0000.0000.000
185A190ARG 10.8690.93544.586-0.023-0.0230.0000.0000.0000.000
186A191PRO 0-0.008-0.01947.3730.0000.0000.0000.0000.0000.000
187A192GLN 00.042-0.00647.651-0.001-0.0010.0000.0000.0000.000
188A193THR 0-0.060-0.04342.0680.0010.0010.0000.0000.0000.000
189A194LYS 10.9150.96540.520-0.017-0.0170.0000.0000.0000.000
190A195LEU 00.0220.01138.9170.0020.0020.0000.0000.0000.000
191A196CYS 0-0.0560.00735.666-0.002-0.0020.0000.0000.0000.000
192A197ILE 0-0.0030.00036.8460.0010.0010.0000.0000.0000.000
193A198ALA 00.0660.02332.774-0.001-0.0010.0000.0000.0000.000
194A199ALA 0-0.013-0.03733.8750.0000.0000.0000.0000.0000.000
195A200ASN 00.0370.02632.993-0.002-0.0020.0000.0000.0000.000
196A201ILE 00.0280.02128.201-0.002-0.0020.0000.0000.0000.000
197A202THR 0-0.047-0.02625.885-0.007-0.0070.0000.0000.0000.000
198A203CYS 0-0.006-0.00329.155-0.006-0.0060.0000.0000.0000.000
199A204GLU -1-0.877-0.94031.779-0.033-0.0330.0000.0000.0000.000
200A205GLY 0-0.0270.02334.2760.0020.0020.0000.0000.0000.000
201A206GLU -1-0.957-1.01231.639-0.018-0.0180.0000.0000.0000.000
202A207PHE 0-0.0080.00635.2950.0020.0020.0000.0000.0000.000
203A208ILE 00.0150.00031.8800.0020.0020.0000.0000.0000.000
204A209GLN 00.0100.02236.1570.0010.0010.0000.0000.0000.000
205A210THR 0-0.015-0.03437.1990.0010.0010.0000.0000.0000.000
206A211ARG 10.8850.94339.713-0.002-0.0020.0000.0000.0000.000
207A212THR 00.0090.03243.0980.0010.0010.0000.0000.0000.000
208A213VAL 00.0770.04344.609-0.002-0.0020.0000.0000.0000.000
209A214LYS 10.9140.94246.556-0.009-0.0090.0000.0000.0000.000
210A215ASP -1-0.907-0.97847.6570.0060.0060.0000.0000.0000.000
211A216TRP 0-0.051-0.03241.143-0.002-0.0020.0000.0000.0000.000
212A217LYS 10.8580.95647.368-0.008-0.0080.0000.0000.0000.000
213A218GLY 00.0020.01550.595-0.001-0.0010.0000.0000.0000.000
214A219HIS 0-0.011-0.01848.3190.0000.0000.0000.0000.0000.000
215A220ILE 00.0290.01944.5440.0010.0010.0000.0000.0000.000
216A221PRO 00.0190.01942.461-0.001-0.0010.0000.0000.0000.000
217A222GLU -1-0.888-0.97342.806-0.013-0.0130.0000.0000.0000.000
218A223LEU 00.0510.01540.5730.0000.0000.0000.0000.0000.000
219A224SER 0-0.053-0.02044.365-0.001-0.0010.0000.0000.0000.000
220A225LYS 10.8810.94639.4980.0090.0090.0000.0000.0000.000
221A226ILE 00.0470.02035.805-0.002-0.0020.0000.0000.0000.000
222A227PRO 0-0.063-0.02133.2990.0030.0030.0000.0000.0000.000
223A228CYS 00.0030.01133.737-0.002-0.0020.0000.0000.0000.000
224A229ILE 0-0.042-0.00129.8910.0020.0020.0000.0000.0000.000
225A230PHE 0-0.016-0.00933.362-0.001-0.0010.0000.0000.0000.000
226A231LEU 0-0.003-0.00131.2200.0040.0040.0000.0000.0000.000
227A232LEU 00.0060.01035.268-0.002-0.0020.0000.0000.0000.000
228A233TYR 00.017-0.00935.9900.0040.0040.0000.0000.0000.000
229A234LYS 10.9680.97838.339-0.037-0.0370.0000.0000.0000.000
230A235NME 00.0240.04040.866-0.001-0.0010.0000.0000.0000.000