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: 6NL5Z

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2455478.686034
FMO2-HF: Nuclear repulsion 2374557.542427
FMO2-HF: Total energy -80921.143606
FMO2-MP2: Total energy -81155.039327


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.
-6.141-3.20815.655-8.958-9.629-0.034
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 : 0.034 / 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].
3A3GLN0-0.012-0.0032.915-4.2390.2180.552-2.206-2.803-0.007
4A4SER0-0.005-0.0104.7590.1970.242-0.001-0.010-0.0340.000
5A5GLU-1-0.802-0.8796.336-1.742-1.7420.0000.0000.0000.000
6A6THR00.0240.0169.8830.1130.1130.0000.0000.0000.000
7A7PRO00.011-0.00313.069-0.053-0.0530.0000.0000.0000.000
8A8VAL00.0110.00912.6070.0130.0130.0000.0000.0000.000
9A9LYS10.9430.97515.7630.2710.2710.0000.0000.0000.000
10A10HIS10.8790.93815.5250.4480.4480.0000.0000.0000.000
11A11ILE0-0.0060.01213.1880.0100.0100.0000.0000.0000.000
12A12GLY00.0370.00717.2460.0100.0100.0000.0000.0000.000
13A13LYS10.8350.94018.6600.2490.2490.0000.0000.0000.000
14A14ILE0-0.031-0.01920.1950.0200.0200.0000.0000.0000.000
15A15PHE00.0050.00123.172-0.003-0.0030.0000.0000.0000.000
16A16PHE0-0.017-0.02123.4980.0040.0040.0000.0000.0000.000
17A17THR00.0230.01528.2300.0010.0010.0000.0000.0000.000
18A18LEU0-0.015-0.01627.771-0.001-0.0010.0000.0000.0000.000
19A19GLY00.1050.05831.0820.0020.0020.0000.0000.0000.000
20A20GLY0-0.052-0.01933.8120.0040.0040.0000.0000.0000.000
21A21SER00.0010.01230.9060.0030.0030.0000.0000.0000.000
22A22ASN0-0.027-0.01629.744-0.008-0.0080.0000.0000.0000.000
23A23TYR00.0150.01824.6780.0010.0010.0000.0000.0000.000
24A24VAL0-0.023-0.01821.021-0.007-0.0070.0000.0000.0000.000
25A25CYS0-0.147-0.05919.5650.0050.0050.0000.0000.0000.000
26A26SER00.0060.01416.268-0.034-0.0340.0000.0000.0000.000
27A27GLY00.0720.03118.2890.0250.0250.0000.0000.0000.000
28A28ASN00.002-0.00217.452-0.061-0.0610.0000.0000.0000.000
29A29SER00.0100.01619.3200.0360.0360.0000.0000.0000.000
30A30VAL0-0.027-0.01220.681-0.022-0.0220.0000.0000.0000.000
31A31THR0-0.004-0.01922.9080.0150.0150.0000.0000.0000.000
32A32ALA00.0340.03425.4860.0050.0050.0000.0000.0000.000
33A33ALA00.0290.02728.910-0.001-0.0010.0000.0000.0000.000
34A34ASN00.0400.02130.812-0.008-0.0080.0000.0000.0000.000
35A35LYS10.8320.91829.3040.1310.1310.0000.0000.0000.000
36A36SER0-0.028-0.02129.252-0.006-0.0060.0000.0000.0000.000
37A37THR00.0230.00825.8670.0040.0040.0000.0000.0000.000
38A38VAL0-0.012-0.00122.400-0.016-0.0160.0000.0000.0000.000
39A39SER0-0.034-0.02719.5200.0130.0130.0000.0000.0000.000
40A40THR00.032-0.00219.647-0.020-0.0200.0000.0000.0000.000
41A41ALA00.0290.01818.9980.0070.0070.0000.0000.0000.000
42A42GLY00.0440.02020.7950.0050.0050.0000.0000.0000.000
43A43HIS10.8290.87418.9380.1690.1690.0000.0000.0000.000
44A45LEU0-0.043-0.02323.7350.0000.0000.0000.0000.0000.000
45A46ASN00.013-0.00627.1410.0110.0110.0000.0000.0000.000
46A47GLU-1-0.849-0.92527.868-0.070-0.0700.0000.0000.0000.000
47A48GLY0-0.0420.02528.1440.0010.0010.0000.0000.0000.000
48A49PRO0-0.010-0.01329.1380.0030.0030.0000.0000.0000.000
49A50GLY00.016-0.00532.0490.0020.0020.0000.0000.0000.000
50A51ALA0-0.031-0.01034.143-0.003-0.0030.0000.0000.0000.000
51A52TYR00.016-0.01530.246-0.007-0.0070.0000.0000.0000.000
52A53ALA0-0.031-0.02129.4800.0040.0040.0000.0000.0000.000
53A54THR0-0.005-0.00431.6180.0000.0000.0000.0000.0000.000
54A55ASN00.0070.00632.5210.0040.0040.0000.0000.0000.000
55A56PHE00.0310.00524.462-0.005-0.0050.0000.0000.0000.000
56A57ILE0-0.021-0.00727.3870.0030.0030.0000.0000.0000.000
57A58PHE00.0030.00920.567-0.011-0.0110.0000.0000.0000.000
58A59VAL00.003-0.01623.0250.0150.0150.0000.0000.0000.000
59A60PRO0-0.0030.00320.932-0.028-0.0280.0000.0000.0000.000
60A61ALA0-0.023-0.02218.3410.0170.0170.0000.0000.0000.000
61A62TYR0-0.068-0.03719.4220.0150.0150.0000.0000.0000.000
62A63LEU00.004-0.00316.866-0.051-0.0510.0000.0000.0000.000
63A64ASN0-0.043-0.01819.0750.0170.0170.0000.0000.0000.000
64A65GLY00.0770.04421.7210.0190.0190.0000.0000.0000.000
65A66ALA0-0.056-0.01423.3590.0140.0140.0000.0000.0000.000
66A67ALA00.029-0.01023.498-0.019-0.0190.0000.0000.0000.000
67A68PRO0-0.0230.00522.3170.0170.0170.0000.0000.0000.000
68A69TYR00.0260.00221.8630.0100.0100.0000.0000.0000.000
69A70GLY00.0310.02526.6220.0070.0070.0000.0000.0000.000
70A71LYS10.9350.95626.9090.1200.1200.0000.0000.0000.000
71A72TRP0-0.0040.00026.9270.0130.0130.0000.0000.0000.000
72A73THR00.0400.02028.963-0.005-0.0050.0000.0000.0000.000
73A74ALA0-0.005-0.00429.8290.0010.0010.0000.0000.0000.000
74A75LYS10.9290.97331.6510.1100.1100.0000.0000.0000.000
75A76ALA0-0.0050.00232.9920.0070.0070.0000.0000.0000.000
76A77LEU0-0.008-0.01128.732-0.012-0.0120.0000.0000.0000.000
77A78TYR00.0150.01229.3230.0080.0080.0000.0000.0000.000
78A79ALA00.0540.01427.826-0.013-0.0130.0000.0000.0000.000
79A80PRO00.0050.02126.5130.0080.0080.0000.0000.0000.000
80A81THR00.0550.01929.653-0.001-0.0010.0000.0000.0000.000
81A82GLN00.0130.00228.933-0.002-0.0020.0000.0000.0000.000
82A83TRP0-0.0140.00624.5120.0020.0020.0000.0000.0000.000
83A84ALA00.0430.00628.5910.0040.0040.0000.0000.0000.000
84A85SER0-0.024-0.01331.5100.0040.0040.0000.0000.0000.000
85A86ASN0-0.051-0.03631.4990.0060.0060.0000.0000.0000.000
86A87GLY00.0410.05128.2860.0040.0040.0000.0000.0000.000
87A88ASN0-0.016-0.01526.4910.0020.0020.0000.0000.0000.000
88A89MET00.0520.01420.523-0.011-0.0110.0000.0000.0000.000
89A90GLN0-0.0160.01321.795-0.007-0.0070.0000.0000.0000.000
90A91TYR0-0.079-0.05922.569-0.007-0.0070.0000.0000.0000.000
91A92ASP-1-0.672-0.78520.594-0.153-0.1530.0000.0000.0000.000
92A93THR0-0.094-0.06620.269-0.031-0.0310.0000.0000.0000.000
93A94ALA0-0.0190.00522.2000.0200.0200.0000.0000.0000.000
94A95PHE0-0.012-0.01422.774-0.023-0.0230.0000.0000.0000.000
95A96ALA00.0290.03025.9360.0150.0150.0000.0000.0000.000
96A97VAL0-0.014-0.00527.779-0.009-0.0090.0000.0000.0000.000
97A98MET0-0.067-0.03027.6420.0050.0050.0000.0000.0000.000
98A99ASN00.003-0.00730.8780.0090.0090.0000.0000.0000.000
99A100THR0-0.014-0.01332.513-0.007-0.0070.0000.0000.0000.000
100A101LEU00.0110.01930.5650.0040.0040.0000.0000.0000.000
101A102ASN0-0.017-0.02033.9360.0020.0020.0000.0000.0000.000
102A103GLY00.0230.01536.5280.0010.0010.0000.0000.0000.000
103A104GLN0-0.0080.00332.4570.0000.0000.0000.0000.0000.000
104A105LYS10.9840.98531.6720.1110.1110.0000.0000.0000.000
105A106LEU00.0680.03724.756-0.004-0.0040.0000.0000.0000.000
106A107ALA0-0.025-0.01626.011-0.010-0.0100.0000.0000.0000.000
107A108ASP-1-0.873-0.93926.979-0.142-0.1420.0000.0000.0000.000
108A109VAL0-0.0460.00026.9040.0000.0000.0000.0000.0000.000
109A110VAL0-0.051-0.04022.472-0.009-0.0090.0000.0000.0000.000
110A111GLY00.0070.01522.265-0.026-0.0260.0000.0000.0000.000
111A112SER0-0.044-0.03121.9080.0040.0040.0000.0000.0000.000
112A113SER00.0000.01317.714-0.012-0.0120.0000.0000.0000.000
113A114GLY00.0760.05220.1260.0230.0230.0000.0000.0000.000
114A115VAL0-0.021-0.01419.830-0.033-0.0330.0000.0000.0000.000
115A116GLN00.0070.00319.2850.0300.0300.0000.0000.0000.000
116A117PHE00.0200.00120.740-0.012-0.0120.0000.0000.0000.000
117A118ASN0-0.057-0.03822.9420.0080.0080.0000.0000.0000.000
118A119ALA00.0470.04819.1940.0080.0080.0000.0000.0000.000
119A120ALA00.0290.02018.6030.0110.0110.0000.0000.0000.000
120A121ARG10.8040.88617.368-0.025-0.0250.0000.0000.0000.000
121A122GLY00.0050.00414.2050.0140.0140.0000.0000.0000.000
122A123LEU0-0.033-0.00413.4050.0290.0290.0000.0000.0000.000
123A124SER00.0280.0058.3250.0950.0950.0000.0000.0000.000
124A125TYR0-0.028-0.0367.8960.0020.0020.0000.0000.0000.000
125A126LYS10.8960.9574.7831.5541.657-0.001-0.005-0.0970.000
126A127SER0-0.064-0.0376.8150.3350.3350.0000.0000.0000.000
127A128PHE00.0490.0038.092-0.344-0.3440.0000.0000.0000.000
128A129GLY00.017-0.00710.5930.1390.1390.0000.0000.0000.000
129A130TYR0-0.042-0.03712.702-0.079-0.0790.0000.0000.0000.000
130A131PRO0-0.066-0.01012.0080.0610.0610.0000.0000.0000.000
131A132ALA00.011-0.03314.9960.0060.0060.0000.0000.0000.000
132A133ALA00.0030.03317.2040.0330.0330.0000.0000.0000.000
133A134SER00.0650.05616.554-0.030-0.0300.0000.0000.0000.000
134A135PRO00.0420.00912.9990.0130.0130.0000.0000.0000.000
135A136PHE0-0.067-0.0389.602-0.037-0.0370.0000.0000.0000.000
136A137ASN00.0700.01315.4460.0020.0020.0000.0000.0000.000
137A138GLY0-0.0060.01817.1590.0180.0180.0000.0000.0000.000
138A139GLU-1-0.788-0.87218.218-0.235-0.2350.0000.0000.0000.000
139A140SER0-0.003-0.01914.469-0.019-0.0190.0000.0000.0000.000
140A141LEU0-0.0280.01011.237-0.011-0.0110.0000.0000.0000.000
141A142LYS10.8670.9378.9850.5820.5820.0000.0000.0000.000
142A143SER0-0.030-0.0535.252-0.116-0.1160.0000.0000.0000.000
143A144CYS0-0.075-0.0063.814-1.355-1.050-0.001-0.123-0.1810.000
144A145SER0-0.0040.0011.697-0.124-3.64313.236-5.016-4.701-0.008
145A146GLY00.0490.0302.418-1.815-0.3681.872-1.585-1.734-0.019
146A147THR0-0.016-0.0065.084-0.331-0.313-0.001-0.004-0.0130.000
147A148ALA0-0.022-0.0018.8030.0840.0840.0000.0000.0000.000
148A149THR0-0.0030.00411.0210.0490.0490.0000.0000.0000.000
149A150ASN00.0550.01913.444-0.072-0.0720.0000.0000.0000.000
150A151ASP-1-0.695-0.79615.6920.1010.1010.0000.0000.0000.000
151A152PRO0-0.041-0.02115.885-0.011-0.0110.0000.0000.0000.000
152A153TYR0-0.032-0.01316.7470.0010.0010.0000.0000.0000.000
153A154ASN0-0.011-0.02420.477-0.011-0.0110.0000.0000.0000.000
154A155PRO00.0200.01720.926-0.015-0.0150.0000.0000.0000.000
155A156GLN00.003-0.00321.954-0.002-0.0020.0000.0000.0000.000
156A157PHE00.0050.00321.207-0.010-0.0100.0000.0000.0000.000
157A158ALA0-0.0040.00121.295-0.016-0.0160.0000.0000.0000.000
158A159THR0-0.021-0.01616.743-0.006-0.0060.0000.0000.0000.000
159A160GLN00.0310.00813.5480.0670.0670.0000.0000.0000.000
160A161GLY00.0400.02011.408-0.068-0.0680.0000.0000.0000.000
161A162ILE0-0.021-0.0055.5590.0820.0820.0000.0000.0000.000
162A163PRO00.0360.0114.295-0.259-0.182-0.001-0.009-0.0660.000
163A165ASN00.0690.0226.1780.0660.0660.0000.0000.0000.000
164A166MET0-0.031-0.0258.2570.0820.0820.0000.0000.0000.000
165A167THR00.0470.01910.4930.0580.0580.0000.0000.0000.000
166A168GLY00.0630.02314.159-0.043-0.0430.0000.0000.0000.000
167A169GLY00.0480.03117.428-0.004-0.0040.0000.0000.0000.000
168A170SER0-0.036-0.01612.651-0.023-0.0230.0000.0000.0000.000
169A171SER00.0200.00514.730-0.025-0.0250.0000.0000.0000.000
170A172GLY00.037-0.00316.6730.0050.0050.0000.0000.0000.000
171A173GLY0-0.016-0.00714.1760.0060.0060.0000.0000.0000.000
172A174PRO0-0.044-0.00713.6200.0160.0160.0000.0000.0000.000
173A175TRP00.000-0.00310.948-0.155-0.1550.0000.0000.0000.000
174A176PHE0-0.020-0.03011.1500.1220.1220.0000.0000.0000.000
175A177ILE00.0280.01210.817-0.093-0.0930.0000.0000.0000.000
176A178GLY0-0.034-0.01310.6850.0170.0170.0000.0000.0000.000
177A179ASN00.016-0.0056.660-0.105-0.1050.0000.0000.0000.000
178A180SER00.0540.0327.740-0.130-0.1300.0000.0000.0000.000
179A181SER00.0020.00710.2090.0530.0530.0000.0000.0000.000
180A182SER0-0.091-0.06412.1690.0880.0880.0000.0000.0000.000
181A183GLY00.0390.03513.8320.0550.0550.0000.0000.0000.000
182A184TYR00.0190.00615.1440.0150.0150.0000.0000.0000.000
183A185GLN0-0.0060.01015.547-0.034-0.0340.0000.0000.0000.000
184A186ASN0-0.055-0.03315.4640.0520.0520.0000.0000.0000.000
185A187SER00.0640.02213.9990.0250.0250.0000.0000.0000.000
186A188VAL0-0.014-0.00414.935-0.047-0.0470.0000.0000.0000.000
187A189ASN0-0.0120.02211.205-0.003-0.0030.0000.0000.0000.000
188A190SER0-0.020-0.02413.9370.0360.0360.0000.0000.0000.000
189A191TYR0-0.011-0.02315.5030.0010.0010.0000.0000.0000.000
190A192GLY00.0970.04914.465-0.021-0.0210.0000.0000.0000.000
191A193TYR0-0.073-0.04515.148-0.002-0.0020.0000.0000.0000.000
192A194GLY00.0550.02617.0470.0300.0300.0000.0000.0000.000
193A195SER0-0.027-0.03116.782-0.016-0.0160.0000.0000.0000.000
194A196ASN0-0.062-0.03513.929-0.037-0.0370.0000.0000.0000.000
195A197SER0-0.0210.01313.3700.0400.0400.0000.0000.0000.000
196A198SER00.0250.0139.554-0.083-0.0830.0000.0000.0000.000
197A199THR0-0.034-0.0228.4380.1620.1620.0000.0000.0000.000
198A200MET0-0.0090.0239.025-0.007-0.0070.0000.0000.0000.000
199A201TYR00.0520.00610.5930.0140.0140.0000.0000.0000.000
200A202GLY00.0540.02713.345-0.045-0.0450.0000.0000.0000.000
201A203PRO0-0.030-0.00414.8430.0400.0400.0000.0000.0000.000
202A204TYR0-0.004-0.01117.602-0.026-0.0260.0000.0000.0000.000
203A205TRP0-0.002-0.00419.125-0.005-0.0050.0000.0000.0000.000
204A206GLY00.0510.02420.8850.0050.0050.0000.0000.0000.000
205A207THR00.0580.01824.280-0.009-0.0090.0000.0000.0000.000
206A208VAL0-0.0070.01127.237-0.004-0.0040.0000.0000.0000.000
207A209ILE00.0220.00521.762-0.001-0.0010.0000.0000.0000.000
208A210GLN00.0240.02125.629-0.001-0.0010.0000.0000.0000.000
209A211SER0-0.014-0.00926.847-0.001-0.0010.0000.0000.0000.000
210A212THR0-0.031-0.00827.3450.0030.0030.0000.0000.0000.000
211A213TYR0-0.046-0.04925.5310.0000.0000.0000.0000.0000.000
212A214ASN00.002-0.00927.621-0.007-0.0070.0000.0000.0000.000
213A215THR0-0.0120.00730.8580.0010.0010.0000.0000.0000.000
214A216ALA00.0340.03928.9450.0010.0010.0000.0000.0000.000
215A217ALA0-0.015-0.01628.983-0.001-0.0010.0000.0000.0000.000
216A218ALA0-0.002-0.00330.723-0.001-0.0010.0000.0000.0000.000
217A219SER0-0.075-0.03233.7770.0030.0030.0000.0000.0000.000