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: Z6R9N

Calculation Name: 3WY8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WY8

Chain ID: A

ChEMBL ID:

UniProt ID: K7ZK39

Base Structure: X-ray

Registration Date: 2023-06-21

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456196.124205
FMO2-HF: Nuclear repulsion 2375274.748499
FMO2-HF: Total energy -80921.375707
FMO2-MP2: Total energy -81155.259721


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:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-8.521-3.38410.597-7.254-8.476-0.041
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.021
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].
3A3GLN00.0140.0153.096-3.2140.8410.174-1.926-2.3030.001
4A4SER00.0200.0044.8420.0400.083-0.001-0.008-0.0330.000
5A5GLU-1-0.790-0.8556.467-1.607-1.6070.0000.0000.0000.000
6A6THR00.0290.0179.9990.0940.0940.0000.0000.0000.000
7A7PRO00.005-0.00513.181-0.056-0.0560.0000.0000.0000.000
8A8VAL00.0200.01212.7360.0160.0160.0000.0000.0000.000
9A9LYS10.9200.97415.8850.2360.2360.0000.0000.0000.000
10A10HIS10.8890.93915.7560.4470.4470.0000.0000.0000.000
11A11ILE0-0.0120.00813.3730.0040.0040.0000.0000.0000.000
12A12GLY00.0430.00917.4150.0160.0160.0000.0000.0000.000
13A13LYS10.8630.95218.8630.2410.2410.0000.0000.0000.000
14A14ILE0-0.030-0.02020.4010.0220.0220.0000.0000.0000.000
15A15PHE0-0.007-0.00423.387-0.006-0.0060.0000.0000.0000.000
16A16PHE0-0.016-0.02023.5820.0060.0060.0000.0000.0000.000
17A17THR00.0150.00728.3990.0010.0010.0000.0000.0000.000
18A18LEU0-0.012-0.01127.9190.0000.0000.0000.0000.0000.000
19A19GLY00.1120.06331.2160.0010.0010.0000.0000.0000.000
20A20GLY0-0.062-0.02433.9260.0050.0050.0000.0000.0000.000
21A21SER0-0.0120.00830.9660.0040.0040.0000.0000.0000.000
22A22ASN0-0.029-0.01629.899-0.008-0.0080.0000.0000.0000.000
23A23TYR00.0230.02124.851-0.001-0.0010.0000.0000.0000.000
24A24VAL0-0.019-0.01921.078-0.004-0.0040.0000.0000.0000.000
25A25CYS0-0.146-0.05419.718-0.002-0.0020.0000.0000.0000.000
26A26SER00.0100.01816.497-0.028-0.0280.0000.0000.0000.000
27A27GLY00.0730.03018.4890.0210.0210.0000.0000.0000.000
28A28ASN0-0.005-0.00617.521-0.050-0.0500.0000.0000.0000.000
29A29SER00.0060.01119.4980.0350.0350.0000.0000.0000.000
30A30VAL0-0.024-0.01320.523-0.021-0.0210.0000.0000.0000.000
31A31THR0-0.008-0.02522.9200.0170.0170.0000.0000.0000.000
32A32ALA00.0310.02625.5090.0030.0030.0000.0000.0000.000
33A33ALA00.0260.02428.8010.0010.0010.0000.0000.0000.000
34A34ASN00.0490.04330.718-0.006-0.0060.0000.0000.0000.000
35A35LYS10.8340.91129.4350.1340.1340.0000.0000.0000.000
36A36SER0-0.038-0.03629.394-0.004-0.0040.0000.0000.0000.000
37A37THR00.0220.00725.8740.0030.0030.0000.0000.0000.000
38A38VAL0-0.020-0.00422.628-0.015-0.0150.0000.0000.0000.000
39A39SER0-0.035-0.02419.4900.0100.0100.0000.0000.0000.000
40A40THR00.0410.00019.841-0.020-0.0200.0000.0000.0000.000
41A41ALA00.0270.01919.0870.0060.0060.0000.0000.0000.000
42A42GLY00.0430.02020.9520.0100.0100.0000.0000.0000.000
43A43HIS10.8510.88818.9550.2330.2330.0000.0000.0000.000
44A45LEU0-0.044-0.02723.8860.0030.0030.0000.0000.0000.000
45A46ASN00.000-0.01327.2830.0120.0120.0000.0000.0000.000
46A47GLU-1-0.841-0.91727.988-0.095-0.0950.0000.0000.0000.000
47A48GLY0-0.0380.02328.242-0.001-0.0010.0000.0000.0000.000
48A49PRO0-0.014-0.01429.2110.0010.0010.0000.0000.0000.000
49A50GLY00.017-0.00632.1390.0020.0020.0000.0000.0000.000
50A51ALA0-0.024-0.00734.267-0.002-0.0020.0000.0000.0000.000
51A52TYR00.021-0.01330.406-0.009-0.0090.0000.0000.0000.000
52A53ALA0-0.029-0.02129.6220.0040.0040.0000.0000.0000.000
53A54THR00.0130.00531.7790.0010.0010.0000.0000.0000.000
54A55ASN0-0.015-0.01232.7100.0020.0020.0000.0000.0000.000
55A56PHE00.0400.01224.664-0.006-0.0060.0000.0000.0000.000
56A57ILE0-0.025-0.00727.6090.0040.0040.0000.0000.0000.000
57A58PHE0-0.0070.01120.697-0.013-0.0130.0000.0000.0000.000
58A59VAL00.004-0.01723.3010.0180.0180.0000.0000.0000.000
59A60PRO0-0.0010.00221.096-0.028-0.0280.0000.0000.0000.000
60A61ALA0-0.022-0.02318.4950.0200.0200.0000.0000.0000.000
61A62TYR0-0.057-0.04119.5830.0180.0180.0000.0000.0000.000
62A63LEU00.0070.00117.027-0.048-0.0480.0000.0000.0000.000
63A64ASN0-0.034-0.02219.1500.0120.0120.0000.0000.0000.000
64A65GLY00.0670.04121.8040.0190.0190.0000.0000.0000.000
65A66ALA0-0.056-0.01123.4520.0130.0130.0000.0000.0000.000
66A67ALA00.032-0.00923.660-0.020-0.0200.0000.0000.0000.000
67A68PRO0-0.0190.00222.4670.0150.0150.0000.0000.0000.000
68A69TYR00.0350.00822.0780.0100.0100.0000.0000.0000.000
69A70GLY00.0350.02826.7640.0060.0060.0000.0000.0000.000
70A71LYS10.9270.95227.0790.1240.1240.0000.0000.0000.000
71A72TRP0-0.0030.00127.1540.0130.0130.0000.0000.0000.000
72A73THR00.0670.03129.158-0.010-0.0100.0000.0000.0000.000
73A74ALA00.0060.01130.0680.0020.0020.0000.0000.0000.000
74A75LYS10.9120.96531.8510.1210.1210.0000.0000.0000.000
75A76ALA0-0.011-0.00133.2030.0070.0070.0000.0000.0000.000
76A77LEU0-0.009-0.01028.932-0.013-0.0130.0000.0000.0000.000
77A78TYR00.0190.01129.5040.0090.0090.0000.0000.0000.000
78A79ALA00.0520.01427.989-0.015-0.0150.0000.0000.0000.000
79A80PRO00.0060.02326.6290.0100.0100.0000.0000.0000.000
80A81THR00.0600.01529.795-0.002-0.0020.0000.0000.0000.000
81A82GLN00.0160.00629.014-0.002-0.0020.0000.0000.0000.000
82A83TRP0-0.0120.00624.609-0.001-0.0010.0000.0000.0000.000
83A84ALA00.0370.00428.6980.0040.0040.0000.0000.0000.000
84A85SER0-0.013-0.00431.6300.0050.0050.0000.0000.0000.000
85A86ASN0-0.053-0.04031.4500.0070.0070.0000.0000.0000.000
86A87GLY00.0430.05228.3690.0030.0030.0000.0000.0000.000
87A88ASN0-0.019-0.01526.521-0.004-0.0040.0000.0000.0000.000
88A89MET00.0510.01620.584-0.009-0.0090.0000.0000.0000.000
89A90GLN0-0.0100.01421.864-0.012-0.0120.0000.0000.0000.000
90A91TYR0-0.084-0.06422.656-0.011-0.0110.0000.0000.0000.000
91A92ASP-1-0.685-0.77820.472-0.213-0.2130.0000.0000.0000.000
92A93THR0-0.094-0.06220.451-0.037-0.0370.0000.0000.0000.000
93A94ALA0-0.0210.00522.3540.0230.0230.0000.0000.0000.000
94A95PHE0-0.008-0.01322.762-0.024-0.0240.0000.0000.0000.000
95A96ALA00.0220.02426.1320.0170.0170.0000.0000.0000.000
96A97VAL0-0.030-0.01327.877-0.008-0.0080.0000.0000.0000.000
97A98MET0-0.043-0.01327.7200.0060.0060.0000.0000.0000.000
98A99ASN0-0.025-0.03231.0620.0120.0120.0000.0000.0000.000
99A100THR0-0.002-0.00432.687-0.006-0.0060.0000.0000.0000.000
100A101LEU0-0.0060.00830.7540.0050.0050.0000.0000.0000.000
101A102ASN0-0.012-0.02134.0990.0010.0010.0000.0000.0000.000
102A103GLY00.0340.02336.6800.0010.0010.0000.0000.0000.000
103A104GLN0-0.023-0.00132.7310.0000.0000.0000.0000.0000.000
104A105LYS10.9720.97931.8770.1120.1120.0000.0000.0000.000
105A106LEU00.0660.03524.904-0.003-0.0030.0000.0000.0000.000
106A107ALA0-0.018-0.01426.145-0.009-0.0090.0000.0000.0000.000
107A108ASP-1-0.867-0.92727.093-0.139-0.1390.0000.0000.0000.000
108A109VAL0-0.0280.01027.0310.0020.0020.0000.0000.0000.000
109A110VAL0-0.052-0.04622.644-0.007-0.0070.0000.0000.0000.000
110A111GLY00.0090.02022.381-0.024-0.0240.0000.0000.0000.000
111A112SER0-0.046-0.02522.0400.0020.0020.0000.0000.0000.000
112A113SER00.0090.01617.574-0.009-0.0090.0000.0000.0000.000
113A114GLY00.0630.04620.2390.0220.0220.0000.0000.0000.000
114A115VAL0-0.017-0.01519.689-0.038-0.0380.0000.0000.0000.000
115A116GLN00.0060.00119.1020.0310.0310.0000.0000.0000.000
116A117PHE00.0200.00120.634-0.017-0.0170.0000.0000.0000.000
117A118ASN0-0.058-0.04122.8740.0080.0080.0000.0000.0000.000
118A119ALA00.0430.04419.1210.0110.0110.0000.0000.0000.000
119A120ALA00.0290.01818.6150.0090.0090.0000.0000.0000.000
120A121ARG10.8150.88717.4280.0370.0370.0000.0000.0000.000
121A122GLY0-0.0050.00114.2140.0220.0220.0000.0000.0000.000
122A123LEU0-0.030-0.00213.4030.0380.0380.0000.0000.0000.000
123A124SER00.014-0.0048.3310.0200.0200.0000.0000.0000.000
124A125TYR0-0.020-0.0267.8220.0230.0230.0000.0000.0000.000
125A126LYS10.8420.9164.7061.5271.646-0.001-0.007-0.1110.000
126A127SER0-0.052-0.0286.8210.4420.4420.0000.0000.0000.000
127A128PHE00.039-0.0028.193-0.359-0.3590.0000.0000.0000.000
128A129GLY00.023-0.00310.7980.1300.1300.0000.0000.0000.000
129A130TYR0-0.049-0.04112.916-0.071-0.0710.0000.0000.0000.000
130A131PRO0-0.060-0.00812.1040.0540.0540.0000.0000.0000.000
131A132ALA00.017-0.03015.1180.0180.0180.0000.0000.0000.000
132A133ALA0-0.0030.03117.2750.0370.0370.0000.0000.0000.000
133A134SER00.0710.06116.545-0.032-0.0320.0000.0000.0000.000
134A135PRO00.0300.00713.0190.0020.0020.0000.0000.0000.000
135A136PHE0-0.055-0.0319.599-0.019-0.0190.0000.0000.0000.000
136A137ASN00.0670.01215.5270.0000.0000.0000.0000.0000.000
137A138GLY00.0190.02417.2420.0190.0190.0000.0000.0000.000
138A139GLU-1-0.837-0.88318.235-0.240-0.2400.0000.0000.0000.000
139A140SER00.019-0.00714.690-0.009-0.0090.0000.0000.0000.000
140A141LEU0-0.0290.01311.498-0.020-0.0200.0000.0000.0000.000
141A142LYS10.8370.9219.1270.5720.5720.0000.0000.0000.000
142A143SER0-0.025-0.0595.420-0.168-0.1680.0000.0000.0000.000
143A144CYS0-0.080-0.0144.009-1.397-1.122-0.001-0.119-0.1540.000
144A145SER00.0300.0111.991-3.650-4.3208.737-3.914-4.152-0.026
145A146GLY00.0240.0232.464-1.688-0.4711.691-1.267-1.641-0.016
146A147THR00.0130.0005.108-0.319-0.306-0.001-0.003-0.0080.000
147A148ALA0-0.0230.0118.7950.0380.0380.0000.0000.0000.000
148A149THR0-0.0010.00211.0280.0770.0770.0000.0000.0000.000
149A150ASN00.0610.02013.389-0.080-0.0800.0000.0000.0000.000
150A151ASP-1-0.713-0.80415.608-0.009-0.0090.0000.0000.0000.000
151A152PRO0-0.041-0.02315.783-0.001-0.0010.0000.0000.0000.000
152A153TYR0-0.023-0.00616.3470.0130.0130.0000.0000.0000.000
153A154ASN0-0.010-0.01120.398-0.002-0.0020.0000.0000.0000.000
154A155PRO00.0210.01720.885-0.018-0.0180.0000.0000.0000.000
155A156GLN00.008-0.00721.906-0.002-0.0020.0000.0000.0000.000
156A157PHE0-0.003-0.00321.192-0.006-0.0060.0000.0000.0000.000
157A158ALA0-0.013-0.00621.278-0.017-0.0170.0000.0000.0000.000
158A159THR00.0000.00716.827-0.005-0.0050.0000.0000.0000.000
159A160GLN00.008-0.00213.5860.0780.0780.0000.0000.0000.000
160A161GLY00.0400.01911.418-0.064-0.0640.0000.0000.0000.000
161A162ILE0-0.024-0.0075.9010.0950.0950.0000.0000.0000.000
162A163PRO00.0280.0054.166-0.176-0.091-0.001-0.010-0.0740.000
163A165ASN00.0600.0186.1550.1410.1410.0000.0000.0000.000
164A166MET0-0.028-0.0168.2700.1710.1710.0000.0000.0000.000
165A167THR00.0420.01410.5570.0510.0510.0000.0000.0000.000
166A168GLY00.0690.03414.204-0.042-0.0420.0000.0000.0000.000
167A169GLY00.0520.03317.4990.0020.0020.0000.0000.0000.000
168A170SER0-0.038-0.02312.804-0.021-0.0210.0000.0000.0000.000
169A171SER00.010-0.00214.894-0.028-0.0280.0000.0000.0000.000
170A172GLY00.0440.00016.8190.0140.0140.0000.0000.0000.000
171A173GLY0-0.018-0.00914.3830.0120.0120.0000.0000.0000.000
172A174PRO0-0.048-0.00613.6310.0060.0060.0000.0000.0000.000
173A175TRP0-0.005-0.01010.987-0.173-0.1730.0000.0000.0000.000
174A176PHE0-0.022-0.03010.8950.1480.1480.0000.0000.0000.000
175A177ILE00.0270.01110.627-0.113-0.1130.0000.0000.0000.000
176A178GLY0-0.029-0.00910.7420.0310.0310.0000.0000.0000.000
177A179ASN00.011-0.0096.725-0.154-0.1540.0000.0000.0000.000
178A180SER00.0520.0307.809-0.102-0.1020.0000.0000.0000.000
179A181SER00.0090.00910.3030.0370.0370.0000.0000.0000.000
180A182SER0-0.085-0.05812.2610.0810.0810.0000.0000.0000.000
181A183GLY00.0350.03213.9460.0570.0570.0000.0000.0000.000
182A184TYR00.0150.00715.2490.0120.0120.0000.0000.0000.000
183A185GLN0-0.0120.00615.343-0.032-0.0320.0000.0000.0000.000
184A186ASN0-0.060-0.04415.3570.0500.0500.0000.0000.0000.000
185A187SER00.0640.02014.1430.0220.0220.0000.0000.0000.000
186A188VAL0-0.019-0.00315.100-0.042-0.0420.0000.0000.0000.000
187A189ASN0-0.0210.02311.345-0.036-0.0360.0000.0000.0000.000
188A190SER0-0.024-0.04614.0750.0520.0520.0000.0000.0000.000
189A191TYR0-0.019-0.03115.5600.0110.0110.0000.0000.0000.000
190A192GLY00.0980.05114.484-0.042-0.0420.0000.0000.0000.000
191A193TYR0-0.060-0.04615.1280.0200.0200.0000.0000.0000.000
192A194GLY00.0420.01816.9510.0260.0260.0000.0000.0000.000
193A195SER0-0.021-0.02416.734-0.024-0.0240.0000.0000.0000.000
194A196ASN0-0.067-0.04714.362-0.030-0.0300.0000.0000.0000.000
195A197SER0-0.0030.02712.5310.0450.0450.0000.0000.0000.000
196A198SER00.0230.0089.423-0.093-0.0930.0000.0000.0000.000
197A199THR0-0.036-0.0238.3010.0500.0500.0000.0000.0000.000
198A200MET0-0.0160.0198.9980.0470.0470.0000.0000.0000.000
199A201TYR00.0600.01110.616-0.011-0.0110.0000.0000.0000.000
200A202GLY00.0600.03213.377-0.034-0.0340.0000.0000.0000.000
201A203PRO0-0.034-0.00714.9350.0390.0390.0000.0000.0000.000
202A204TYR0-0.004-0.01017.718-0.028-0.0280.0000.0000.0000.000
203A205TRP00.000-0.00219.2570.0000.0000.0000.0000.0000.000
204A206GLY00.0460.02821.0250.0080.0080.0000.0000.0000.000
205A207THR00.0680.02224.406-0.009-0.0090.0000.0000.0000.000
206A208VAL00.0010.02327.322-0.002-0.0020.0000.0000.0000.000
207A209ILE00.0260.00322.0430.0010.0010.0000.0000.0000.000
208A210GLN00.0280.02825.7830.0000.0000.0000.0000.0000.000
209A211SER0-0.017-0.01726.9660.0020.0020.0000.0000.0000.000
210A212THR0-0.037-0.01527.4690.0040.0040.0000.0000.0000.000
211A213TYR0-0.045-0.03925.4590.0020.0020.0000.0000.0000.000
212A214ASN0-0.004-0.01127.709-0.005-0.0050.0000.0000.0000.000
213A215THR00.0190.01730.8560.0050.0050.0000.0000.0000.000
214A216ALA0-0.0140.01029.0440.0030.0030.0000.0000.0000.000
215A217ALA0-0.010-0.01428.8780.0010.0010.0000.0000.0000.000
216A218ALA00.0040.00030.6330.0010.0010.0000.0000.0000.000
217A219SER0-0.067-0.02833.7310.0020.0020.0000.0000.0000.000