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: R9N48

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2457015.271415
FMO2-HF: Nuclear repulsion 2376093.855605
FMO2-HF: Total energy -80921.41581
FMO2-MP2: Total energy -81155.270534


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.
-8.706-3.8679.648-6.698-7.785-0.046
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 : 0.032 / q_NPA : 0.027
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].
3A3GLN0-0.013-0.0032.793-2.9160.8590.469-1.933-2.310-0.004
4A4SER00.0090.0024.8720.0710.112-0.001-0.008-0.0310.000
5A5GLU-1-0.772-0.8456.504-1.567-1.5670.0000.0000.0000.000
6A6THR00.0300.0179.9950.0900.0900.0000.0000.0000.000
7A7PRO0-0.004-0.01613.406-0.051-0.0510.0000.0000.0000.000
8A8VAL00.0080.01612.6660.0370.0370.0000.0000.0000.000
9A9LYS10.9300.97915.7360.2200.2200.0000.0000.0000.000
10A10HIS10.8570.93316.0580.4490.4490.0000.0000.0000.000
11A11ILE0-0.010-0.00113.549-0.004-0.0040.0000.0000.0000.000
12A12GLY00.0310.00517.5870.0230.0230.0000.0000.0000.000
13A13LYS10.8190.93218.8750.2370.2370.0000.0000.0000.000
14A14ILE0-0.032-0.01620.4040.0200.0200.0000.0000.0000.000
15A15PHE00.0200.00423.364-0.007-0.0070.0000.0000.0000.000
16A16PHE0-0.020-0.01724.1460.0060.0060.0000.0000.0000.000
17A17THR00.005-0.00228.8190.0000.0000.0000.0000.0000.000
18A18LEU0-0.007-0.00428.4310.0000.0000.0000.0000.0000.000
19A19GLY00.1020.06331.8990.0010.0010.0000.0000.0000.000
20A20GLY0-0.058-0.02734.2930.0040.0040.0000.0000.0000.000
21A21SER0-0.0340.00031.8800.0050.0050.0000.0000.0000.000
22A22ASN0-0.023-0.01330.613-0.008-0.0080.0000.0000.0000.000
23A23TYR00.0180.01625.563-0.002-0.0020.0000.0000.0000.000
24A24VAL0-0.014-0.01721.839-0.001-0.0010.0000.0000.0000.000
25A25CYS0-0.142-0.05020.258-0.008-0.0080.0000.0000.0000.000
26A26SER00.0130.01016.470-0.022-0.0220.0000.0000.0000.000
27A27GLY00.0680.02918.5150.0170.0170.0000.0000.0000.000
28A28ASN0-0.013-0.01517.613-0.037-0.0370.0000.0000.0000.000
29A29SER00.0180.01219.5110.0330.0330.0000.0000.0000.000
30A30VAL0-0.039-0.02520.875-0.022-0.0220.0000.0000.0000.000
31A31THR0-0.006-0.02023.2430.0180.0180.0000.0000.0000.000
32A32ALA00.0210.02925.7750.0030.0030.0000.0000.0000.000
33A33ALA00.0280.02429.1470.0020.0020.0000.0000.0000.000
34A34ASN00.0410.03330.854-0.005-0.0050.0000.0000.0000.000
35A35LYS10.8530.92829.4320.1390.1390.0000.0000.0000.000
36A36SER0-0.019-0.02429.253-0.005-0.0050.0000.0000.0000.000
37A37THR00.0150.00926.2590.0030.0030.0000.0000.0000.000
38A38VAL0-0.021-0.01422.605-0.013-0.0130.0000.0000.0000.000
39A39SER0-0.036-0.01719.7720.0070.0070.0000.0000.0000.000
40A40THR00.0370.00020.168-0.020-0.0200.0000.0000.0000.000
41A41ALA00.0240.02019.2890.0060.0060.0000.0000.0000.000
42A42GLY00.0410.02221.1790.0140.0140.0000.0000.0000.000
43A43HIS10.8640.89719.3920.2730.2730.0000.0000.0000.000
44A45LEU0-0.043-0.02424.2800.0040.0040.0000.0000.0000.000
45A46ASN0-0.009-0.02127.6420.0130.0130.0000.0000.0000.000
46A47GLU-1-0.805-0.90728.242-0.115-0.1150.0000.0000.0000.000
47A48GLY0-0.0240.01828.377-0.002-0.0020.0000.0000.0000.000
48A49PRO0-0.020-0.00929.4140.0000.0000.0000.0000.0000.000
49A50GLY00.015-0.00732.3000.0030.0030.0000.0000.0000.000
50A51ALA0-0.019-0.00234.505-0.002-0.0020.0000.0000.0000.000
51A52TYR00.015-0.01130.721-0.011-0.0110.0000.0000.0000.000
52A53ALA0-0.032-0.02230.0550.0050.0050.0000.0000.0000.000
53A54THR00.0220.00932.2160.0010.0010.0000.0000.0000.000
54A55ASN0-0.002-0.00832.9540.0030.0030.0000.0000.0000.000
55A56PHE00.0220.00624.907-0.008-0.0080.0000.0000.0000.000
56A57ILE0-0.0200.00127.8400.0060.0060.0000.0000.0000.000
57A58PHE00.0100.01520.629-0.011-0.0110.0000.0000.0000.000
58A59VAL0-0.008-0.02123.2670.0210.0210.0000.0000.0000.000
59A60PRO00.0070.00421.082-0.027-0.0270.0000.0000.0000.000
60A61ALA0-0.023-0.02418.4090.0210.0210.0000.0000.0000.000
61A62TYR0-0.083-0.05419.4900.0160.0160.0000.0000.0000.000
62A63LEU00.0110.00317.221-0.047-0.0470.0000.0000.0000.000
63A64ASN0-0.031-0.02019.4510.0120.0120.0000.0000.0000.000
64A65GLY00.0550.03922.0320.0180.0180.0000.0000.0000.000
65A66ALA0-0.041-0.00823.4350.0100.0100.0000.0000.0000.000
66A67ALA00.032-0.01023.637-0.020-0.0200.0000.0000.0000.000
67A68PRO0-0.023-0.00122.2810.0150.0150.0000.0000.0000.000
68A69TYR00.0370.01222.0690.0100.0100.0000.0000.0000.000
69A70GLY00.0330.02726.4940.0040.0040.0000.0000.0000.000
70A71LYS10.9280.94826.9330.1320.1320.0000.0000.0000.000
71A72TRP0-0.009-0.00927.2010.0130.0130.0000.0000.0000.000
72A73THR00.0580.02829.081-0.012-0.0120.0000.0000.0000.000
73A74ALA0-0.0090.00230.2690.0030.0030.0000.0000.0000.000
74A75LYS10.8770.94131.8740.1320.1320.0000.0000.0000.000
75A76ALA0-0.0030.00533.3590.0080.0080.0000.0000.0000.000
76A77LEU0-0.002-0.01229.458-0.014-0.0140.0000.0000.0000.000
77A78TYR00.001-0.00229.7380.0100.0100.0000.0000.0000.000
78A79ALA00.0590.01228.052-0.018-0.0180.0000.0000.0000.000
79A80PRO00.0060.02326.9070.0120.0120.0000.0000.0000.000
80A81THR00.0590.01630.025-0.002-0.0020.0000.0000.0000.000
81A82GLN00.0250.01129.1680.0000.0000.0000.0000.0000.000
82A83TRP0-0.031-0.00124.754-0.004-0.0040.0000.0000.0000.000
83A84ALA00.020-0.00828.9720.0050.0050.0000.0000.0000.000
84A85SER0-0.011-0.00131.9940.0060.0060.0000.0000.0000.000
85A86ASN0-0.039-0.03131.8420.0070.0070.0000.0000.0000.000
86A87GLY00.0460.04428.7900.0030.0030.0000.0000.0000.000
87A88ASN0-0.001-0.00526.311-0.010-0.0100.0000.0000.0000.000
88A89MET00.0490.01620.666-0.007-0.0070.0000.0000.0000.000
89A90GLN0-0.0100.00921.917-0.015-0.0150.0000.0000.0000.000
90A91TYR0-0.063-0.06223.054-0.009-0.0090.0000.0000.0000.000
91A92ASP-1-0.709-0.78120.608-0.253-0.2530.0000.0000.0000.000
92A93THR0-0.123-0.08020.592-0.044-0.0440.0000.0000.0000.000
93A94ALA0-0.0110.00522.5550.0250.0250.0000.0000.0000.000
94A95PHE0-0.006-0.01823.010-0.027-0.0270.0000.0000.0000.000
95A96ALA00.0430.03826.3010.0180.0180.0000.0000.0000.000
96A97VAL0-0.035-0.02328.048-0.008-0.0080.0000.0000.0000.000
97A98MET0-0.033-0.00527.6390.0060.0060.0000.0000.0000.000
98A99ASN0-0.010-0.01931.0620.0130.0130.0000.0000.0000.000
99A100THR0-0.006-0.00832.800-0.006-0.0060.0000.0000.0000.000
100A101LEU0-0.0030.01430.6250.0050.0050.0000.0000.0000.000
101A102ASN0-0.014-0.02233.9750.0000.0000.0000.0000.0000.000
102A103GLY00.0490.03436.7110.0030.0030.0000.0000.0000.000
103A104GLN0-0.048-0.01532.6590.0000.0000.0000.0000.0000.000
104A105LYS10.9170.94131.8570.1220.1220.0000.0000.0000.000
105A106LEU00.0590.03324.692-0.002-0.0020.0000.0000.0000.000
106A107ALA0-0.010-0.01226.011-0.007-0.0070.0000.0000.0000.000
107A108ASP-1-0.846-0.91227.046-0.138-0.1380.0000.0000.0000.000
108A109VAL0-0.0200.01127.2600.0040.0040.0000.0000.0000.000
109A110VAL0-0.059-0.05322.725-0.006-0.0060.0000.0000.0000.000
110A111GLY00.0240.03122.387-0.023-0.0230.0000.0000.0000.000
111A112SER0-0.057-0.02821.8640.0020.0020.0000.0000.0000.000
112A113SER00.0100.02317.221-0.007-0.0070.0000.0000.0000.000
113A114GLY00.0630.04020.0820.0220.0220.0000.0000.0000.000
114A115VAL0-0.024-0.01719.771-0.042-0.0420.0000.0000.0000.000
115A116GLN00.0100.00019.1800.0330.0330.0000.0000.0000.000
116A117PHE00.0270.00920.611-0.022-0.0220.0000.0000.0000.000
117A118ASN0-0.037-0.03922.8410.0140.0140.0000.0000.0000.000
118A119ALA00.0170.03718.9430.0140.0140.0000.0000.0000.000
119A120ALA00.0450.02818.3900.0090.0090.0000.0000.0000.000
120A121ARG10.8210.88117.1050.0910.0910.0000.0000.0000.000
121A122GLY0-0.0040.00413.8030.0270.0270.0000.0000.0000.000
122A123LEU0-0.0120.00313.3360.0420.0420.0000.0000.0000.000
123A124SER0-0.006-0.0108.2110.0040.0040.0000.0000.0000.000
124A125TYR0-0.015-0.0217.9150.0850.0850.0000.0000.0000.000
125A126LYS10.8300.9134.4581.4301.556-0.001-0.008-0.1160.000
126A127SER0-0.040-0.0207.2630.4620.4620.0000.0000.0000.000
127A128PHE00.036-0.0048.310-0.359-0.3590.0000.0000.0000.000
128A129GLY00.002-0.01310.6510.1260.1260.0000.0000.0000.000
129A130TYR0-0.037-0.04012.810-0.060-0.0600.0000.0000.0000.000
130A131PRO0-0.055-0.00812.0230.0480.0480.0000.0000.0000.000
131A132ALA00.020-0.02315.3440.0210.0210.0000.0000.0000.000
132A133ALA00.0180.03217.5240.0380.0380.0000.0000.0000.000
133A134SER00.0610.05116.733-0.034-0.0340.0000.0000.0000.000
134A135PRO00.0320.01212.9170.0020.0020.0000.0000.0000.000
135A136PHE0-0.055-0.0319.634-0.018-0.0180.0000.0000.0000.000
136A137ASN00.0650.01415.508-0.003-0.0030.0000.0000.0000.000
137A138GLY00.0280.03017.0440.0190.0190.0000.0000.0000.000
138A139GLU-1-0.802-0.86918.077-0.240-0.2400.0000.0000.0000.000
139A140SER00.0430.01914.837-0.003-0.0030.0000.0000.0000.000
140A141LEU0-0.0300.01411.529-0.027-0.0270.0000.0000.0000.000
141A142LYS10.8150.8949.2340.5990.5990.0000.0000.0000.000
142A143SER0-0.014-0.0555.508-0.123-0.1230.0000.0000.0000.000
143A144CYS0-0.0720.0074.653-1.024-0.892-0.002-0.052-0.0780.000
144A145SER00.005-0.0032.033-2.934-3.5187.258-3.183-3.491-0.023
145A146GLY00.0380.0252.348-3.669-2.4601.927-1.493-1.643-0.019
146A147THR00.005-0.0044.829-0.145-0.127-0.001-0.006-0.0100.000
147A148ALA0-0.0240.0088.5680.0300.0300.0000.0000.0000.000
148A149THR0-0.019-0.00410.7910.1220.1220.0000.0000.0000.000
149A150ASN00.0710.02213.133-0.084-0.0840.0000.0000.0000.000
150A151ASP-1-0.702-0.79815.422-0.096-0.0960.0000.0000.0000.000
151A152PRO0-0.043-0.02715.7700.0100.0100.0000.0000.0000.000
152A153TYR0-0.020-0.00816.3720.0220.0220.0000.0000.0000.000
153A154ASN0-0.029-0.01220.5590.0060.0060.0000.0000.0000.000
154A155PRO00.0300.01721.002-0.019-0.0190.0000.0000.0000.000
155A156GLN00.0240.00922.001-0.003-0.0030.0000.0000.0000.000
156A157PHE00.000-0.00121.408-0.004-0.0040.0000.0000.0000.000
157A158ALA0-0.028-0.01121.486-0.016-0.0160.0000.0000.0000.000
158A159THR0-0.0080.00017.143-0.005-0.0050.0000.0000.0000.000
159A160GLN0-0.005-0.00113.5490.0770.0770.0000.0000.0000.000
160A161GLY00.0480.01611.663-0.049-0.0490.0000.0000.0000.000
161A162ILE0-0.010-0.0026.1690.1010.1010.0000.0000.0000.000
162A163PRO00.0410.0133.830-0.0880.034-0.001-0.015-0.1060.000
163A165ASN00.0520.0016.5590.1950.1950.0000.0000.0000.000
164A166MET0-0.034-0.0188.8340.1740.1740.0000.0000.0000.000
165A167THR00.0430.01811.1920.0210.0210.0000.0000.0000.000
166A168GLY00.0670.03414.741-0.051-0.0510.0000.0000.0000.000
167A169GLY00.0410.02817.7650.0040.0040.0000.0000.0000.000
168A170SER0-0.049-0.02813.235-0.020-0.0200.0000.0000.0000.000
169A171SER00.0400.01215.224-0.035-0.0350.0000.0000.0000.000
170A172GLY00.027-0.00217.2440.0200.0200.0000.0000.0000.000
171A173GLY00.000-0.00614.6120.0120.0120.0000.0000.0000.000
172A174PRO0-0.058-0.00913.796-0.008-0.0080.0000.0000.0000.000
173A175TRP0-0.005-0.01711.323-0.181-0.1810.0000.0000.0000.000
174A176PHE0-0.026-0.02511.3330.1600.1600.0000.0000.0000.000
175A177ILE00.0260.00910.829-0.134-0.1340.0000.0000.0000.000
176A178GLY0-0.026-0.01010.6270.0460.0460.0000.0000.0000.000
177A179ASN00.021-0.0056.557-0.183-0.1830.0000.0000.0000.000
178A180SER00.0480.0247.420-0.131-0.1310.0000.0000.0000.000
179A181SER00.0090.01310.1140.0440.0440.0000.0000.0000.000
180A182SER0-0.049-0.03512.2780.0860.0860.0000.0000.0000.000
181A183GLY00.0300.03213.7530.0580.0580.0000.0000.0000.000
182A184TYR00.002-0.00415.0290.0000.0000.0000.0000.0000.000
183A185GLN0-0.0070.01115.588-0.027-0.0270.0000.0000.0000.000
184A186ASN0-0.040-0.03515.5580.0470.0470.0000.0000.0000.000
185A187SER00.0550.01914.1760.0190.0190.0000.0000.0000.000
186A188VAL0-0.021-0.00815.148-0.036-0.0360.0000.0000.0000.000
187A189ASN0-0.0200.03411.658-0.049-0.0490.0000.0000.0000.000
188A190SER0-0.030-0.04514.3590.0630.0630.0000.0000.0000.000
189A191TYR0-0.024-0.04615.8320.0180.0180.0000.0000.0000.000
190A192GLY00.0960.03714.633-0.064-0.0640.0000.0000.0000.000
191A193TYR0-0.046-0.02615.3070.0320.0320.0000.0000.0000.000
192A194GLY00.0410.01117.3410.0350.0350.0000.0000.0000.000
193A195SER0-0.039-0.02916.763-0.031-0.0310.0000.0000.0000.000
194A196ASN0-0.037-0.03214.420-0.033-0.0330.0000.0000.0000.000
195A197SER00.0040.03012.8850.0430.0430.0000.0000.0000.000
196A198SER00.0210.0119.554-0.121-0.1210.0000.0000.0000.000
197A199THR0-0.064-0.0508.5790.0590.0590.0000.0000.0000.000
198A200MET0-0.0280.0179.3440.0870.0870.0000.0000.0000.000
199A201TYR00.0450.01710.673-0.048-0.0480.0000.0000.0000.000
200A202GLY00.0670.03413.470-0.034-0.0340.0000.0000.0000.000
201A203PRO0-0.0220.00215.4760.0360.0360.0000.0000.0000.000
202A204TYR0-0.003-0.01717.988-0.032-0.0320.0000.0000.0000.000
203A205TRP0-0.020-0.00719.0520.0140.0140.0000.0000.0000.000
204A206GLY00.0820.04120.9860.0070.0070.0000.0000.0000.000
205A207THR00.0350.01224.411-0.009-0.0090.0000.0000.0000.000
206A208VAL00.0220.03927.5170.0000.0000.0000.0000.0000.000
207A209ILE00.0210.01522.0850.0010.0010.0000.0000.0000.000
208A210GLN00.0290.01825.793-0.002-0.0020.0000.0000.0000.000
209A211SER0-0.017-0.02126.9310.0050.0050.0000.0000.0000.000
210A212THR0-0.044-0.02027.3400.0050.0050.0000.0000.0000.000
211A213TYR0-0.048-0.03825.6030.0020.0020.0000.0000.0000.000
212A214ASN0-0.003-0.01227.717-0.003-0.0030.0000.0000.0000.000
213A215THR00.0110.01130.9440.0070.0070.0000.0000.0000.000
214A216ALA0-0.0150.01629.0880.0040.0040.0000.0000.0000.000
215A217ALA0-0.002-0.01229.0320.0030.0030.0000.0000.0000.000
216A218ALA00.0320.01130.7700.0020.0020.0000.0000.0000.000
217A219SER0-0.039-0.00533.8620.0040.0040.0000.0000.0000.000