Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 8NN2Y

Calculation Name: 3LB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LB9

Chain ID: A

ChEMBL ID:

UniProt ID: P09850

Base Structure: X-ray

Registration Date: 2023-09-27

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1975562.334987
FMO2-HF: Nuclear repulsion 1906071.439441
FMO2-HF: Total energy -69490.895546
FMO2-MP2: Total energy -69697.318205


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-12.194-10.77212.405-6.409-7.421-0.033
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.005
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].
3A4PHE0-0.058-0.0182.860-0.4661.5070.105-0.836-1.2430.002
4A5THR00.0180.0115.8650.1230.1230.0000.0000.0000.000
5A6GLN0-0.003-0.0019.3750.0020.0020.0000.0000.0000.000
6A7TYR0-0.044-0.05211.3700.1030.1030.0000.0000.0000.000
7A8TRP00.0240.00113.783-0.009-0.0090.0000.0000.0000.000
8A9SER0-0.0210.00017.7260.0290.0290.0000.0000.0000.000
9A10VAL0-0.001-0.00320.531-0.013-0.0130.0000.0000.0000.000
10A11ARG10.8890.96123.0800.1360.1360.0000.0000.0000.000
11A12GLN0-0.051-0.05126.8000.0030.0030.0000.0000.0000.000
12A13SER0-0.029-0.01029.1670.0040.0040.0000.0000.0000.000
13A14LYS10.8640.94028.0040.1120.1120.0000.0000.0000.000
14A15ARG10.8160.88328.2260.1440.1440.0000.0000.0000.000
15A16PRO0-0.004-0.00630.784-0.002-0.0020.0000.0000.0000.000
16A17THR0-0.048-0.02229.747-0.007-0.0070.0000.0000.0000.000
17A18GLY00.0670.03532.8090.0050.0050.0000.0000.0000.000
18A19SER0-0.0280.00535.4970.0040.0040.0000.0000.0000.000
19A20ASN00.0220.00333.793-0.010-0.0100.0000.0000.0000.000
20A21ALA0-0.0080.01430.5090.0040.0040.0000.0000.0000.000
21A22THR00.020-0.00330.095-0.003-0.0030.0000.0000.0000.000
22A23ILE0-0.014-0.00723.859-0.001-0.0010.0000.0000.0000.000
23A24THR00.030-0.01226.691-0.005-0.0050.0000.0000.0000.000
24A25PHE0-0.024-0.01918.2740.0020.0020.0000.0000.0000.000
25A26THR00.0360.01523.684-0.004-0.0040.0000.0000.0000.000
26A27ASN00.0160.00025.4590.0050.0050.0000.0000.0000.000
27A28HIS0-0.0050.00922.298-0.004-0.0040.0000.0000.0000.000
28A29VAL00.0170.01720.069-0.004-0.0040.0000.0000.0000.000
29A30ASN0-0.014-0.02022.0750.0050.0050.0000.0000.0000.000
30A31ALA00.0200.01624.8320.0070.0070.0000.0000.0000.000
31A32TRP0-0.009-0.01117.183-0.007-0.0070.0000.0000.0000.000
32A33LYS10.9390.96321.3010.1630.1630.0000.0000.0000.000
33A34SER0-0.074-0.03922.3550.0120.0120.0000.0000.0000.000
34A35HIS10.8660.92522.0960.1400.1400.0000.0000.0000.000
35A36GLY00.0650.03620.484-0.006-0.0060.0000.0000.0000.000
36A37MET0-0.063-0.00717.1210.0020.0020.0000.0000.0000.000
37A38ASN00.0000.00617.3070.0050.0050.0000.0000.0000.000
38A39LEU00.0120.01914.455-0.026-0.0260.0000.0000.0000.000
39A40GLY00.0020.00812.9960.0350.0350.0000.0000.0000.000
40A41SER0-0.007-0.01213.9850.0010.0010.0000.0000.0000.000
41A42ASN0-0.0030.01313.197-0.019-0.0190.0000.0000.0000.000
42A43TRP00.0370.00913.460-0.061-0.0610.0000.0000.0000.000
43A44ALA0-0.028-0.00811.9350.0150.0150.0000.0000.0000.000
44A45TYR00.0710.03811.7140.0720.0720.0000.0000.0000.000
45A46GLN0-0.0060.01215.693-0.015-0.0150.0000.0000.0000.000
46A47VAL0-0.032-0.00617.4270.0310.0310.0000.0000.0000.000
47A48MET0-0.0080.01520.007-0.015-0.0150.0000.0000.0000.000
48A49ALA0-0.026-0.02018.7100.0120.0120.0000.0000.0000.000
49A50THR00.0150.01620.7420.0210.0210.0000.0000.0000.000
50A51GLU-1-0.814-0.90714.545-0.473-0.4730.0000.0000.0000.000
51A52GLY0-0.005-0.01317.0880.0450.0450.0000.0000.0000.000
52A53TYR0-0.015-0.00813.873-0.044-0.0440.0000.0000.0000.000
53A54GLN00.0150.01417.3190.0130.0130.0000.0000.0000.000
54A55SER0-0.037-0.00719.6420.0140.0140.0000.0000.0000.000
55A56SER00.0380.02322.7250.0020.0020.0000.0000.0000.000
56A57GLY0-0.012-0.00225.479-0.001-0.0010.0000.0000.0000.000
57A58SER0-0.043-0.03327.2710.0040.0040.0000.0000.0000.000
58A59SER00.000-0.01225.2060.0020.0020.0000.0000.0000.000
59A60ASN00.0180.01228.3670.0000.0000.0000.0000.0000.000
60A61VAL00.0100.00526.1250.0040.0040.0000.0000.0000.000
61A62THR00.0050.02328.8580.0000.0000.0000.0000.0000.000
62A63VAL0-0.018-0.00825.0460.0010.0010.0000.0000.0000.000
63A64TRP0-0.026-0.02428.3820.0030.0030.0000.0000.0000.000
64A65GLY00.025-0.00930.352-0.004-0.0040.0000.0000.0000.000
65A66ALA0-0.020-0.00431.3790.0000.0000.0000.0000.0000.000
66A67SER00.0130.00629.3600.0010.0010.0000.0000.0000.000
67A68THR0-0.054-0.01926.260-0.006-0.0060.0000.0000.0000.000
68A69ASP-1-0.776-0.85423.883-0.186-0.1860.0000.0000.0000.000
69A70TYR0-0.035-0.01615.8860.0040.0040.0000.0000.0000.000
70A71TRP00.013-0.02021.7470.0010.0010.0000.0000.0000.000
71A72GLN00.0050.02214.904-0.016-0.0160.0000.0000.0000.000
72A73ASN00.017-0.01118.1750.0190.0190.0000.0000.0000.000
73A74TRP00.0180.00910.480-0.028-0.0280.0000.0000.0000.000
74A75THR00.020-0.00215.1420.0220.0220.0000.0000.0000.000
75A76ASP-1-0.815-0.89512.037-0.254-0.2540.0000.0000.0000.000
76A77GLY0-0.0120.00813.4880.0420.0420.0000.0000.0000.000
77A78GLY0-0.038-0.02316.3850.0340.0340.0000.0000.0000.000
78A79GLY0-0.005-0.00817.7090.0180.0180.0000.0000.0000.000
79A80ILE0-0.033-0.00321.066-0.013-0.0130.0000.0000.0000.000
80A81VAL00.038-0.00419.607-0.004-0.0040.0000.0000.0000.000
81A82ASN0-0.049-0.01022.988-0.001-0.0010.0000.0000.0000.000
82A83ALA00.0290.00122.896-0.006-0.0060.0000.0000.0000.000
83A84VAL0-0.0050.00224.9880.0010.0010.0000.0000.0000.000
84A85ASN00.0490.01426.068-0.006-0.0060.0000.0000.0000.000
85A86GLY00.0290.01527.4890.0090.0090.0000.0000.0000.000
86A87SER00.0070.00030.248-0.003-0.0030.0000.0000.0000.000
87A88GLY00.0190.00431.3410.0000.0000.0000.0000.0000.000
88A89GLY00.0860.04828.818-0.009-0.0090.0000.0000.0000.000
89A90ASN0-0.069-0.05328.670-0.008-0.0080.0000.0000.0000.000
90A91TYR0-0.027-0.01023.482-0.005-0.0050.0000.0000.0000.000
91A92SER00.0220.01127.9720.0070.0070.0000.0000.0000.000
92A93VAL0-0.0020.01322.893-0.006-0.0060.0000.0000.0000.000
93A94ASN0-0.0080.00926.1960.0090.0090.0000.0000.0000.000
94A95TRP0-0.0060.01422.622-0.003-0.0030.0000.0000.0000.000
95A96SER0-0.022-0.02524.2670.0090.0090.0000.0000.0000.000
96A97ASN00.000-0.01122.6350.0020.0020.0000.0000.0000.000
97A98THR0-0.0170.00618.9000.0120.0120.0000.0000.0000.000
98A99GLY00.0650.04115.9380.0160.0160.0000.0000.0000.000
99A100ASN0-0.120-0.09111.453-0.110-0.1100.0000.0000.0000.000
100A101PHE0-0.034-0.02114.442-0.002-0.0020.0000.0000.0000.000
101A102VAL00.0190.02013.4100.0070.0070.0000.0000.0000.000
102A103VAL00.0130.00616.6070.0050.0050.0000.0000.0000.000
103A104GLY00.008-0.00519.9120.0080.0080.0000.0000.0000.000
104A105LYS10.8160.91621.3940.1480.1480.0000.0000.0000.000
105A106GLY0-0.002-0.00622.328-0.003-0.0030.0000.0000.0000.000
106A107TRP0-0.022-0.01421.2960.0120.0120.0000.0000.0000.000
107A108THR00.013-0.03219.293-0.038-0.0380.0000.0000.0000.000
108A109THR0-0.079-0.03618.237-0.016-0.0160.0000.0000.0000.000
109A110GLY0-0.023-0.01917.9170.0200.0200.0000.0000.0000.000
110A111SER00.0140.00019.2330.0160.0160.0000.0000.0000.000
111A112PRO00.0420.01620.658-0.009-0.0090.0000.0000.0000.000
112A113PHE00.0150.00022.0170.0080.0080.0000.0000.0000.000
113A114ARG10.8410.94821.9190.2100.2100.0000.0000.0000.000
114A115THR00.013-0.00125.0700.0030.0030.0000.0000.0000.000
115A116ILE0-0.025-0.00722.982-0.001-0.0010.0000.0000.0000.000
116A117ASN00.0500.03127.2860.0060.0060.0000.0000.0000.000
117A118TYR0-0.024-0.05427.290-0.004-0.0040.0000.0000.0000.000
118A119ASN00.0130.00329.8040.0090.0090.0000.0000.0000.000
119A120ALA0-0.004-0.00728.756-0.002-0.0020.0000.0000.0000.000
120A121GLY00.0090.01230.5780.0060.0060.0000.0000.0000.000
121A122VAL0-0.003-0.00331.3580.0070.0070.0000.0000.0000.000
122A123TRP0-0.021-0.01823.157-0.011-0.0110.0000.0000.0000.000
123A124ALA00.0000.00829.1940.0060.0060.0000.0000.0000.000
124A125PRO0-0.0220.00624.9940.0010.0010.0000.0000.0000.000
125A126ASN0-0.006-0.01026.6870.0070.0070.0000.0000.0000.000
126A127GLY00.0670.01024.5240.0070.0070.0000.0000.0000.000
127A128ASN00.0200.00618.1870.0060.0060.0000.0000.0000.000
128A129GLY00.0770.04419.968-0.006-0.0060.0000.0000.0000.000
129A130TYR0-0.041-0.03716.3250.0390.0390.0000.0000.0000.000
130A131LEU00.0150.04021.094-0.015-0.0150.0000.0000.0000.000
131A132THR0-0.015-0.04818.1000.0100.0100.0000.0000.0000.000
132A133LEU00.0240.02818.577-0.005-0.0050.0000.0000.0000.000
133A134TYR0-0.060-0.05210.849-0.002-0.0020.0000.0000.0000.000
134A135GLY00.0740.03014.2950.0460.0460.0000.0000.0000.000
135A136TRP00.0410.0265.333-0.046-0.0460.0000.0000.0000.000
136A137THR0-0.028-0.00410.6350.1010.1010.0000.0000.0000.000
137A138ARG10.9110.9388.9740.3600.3600.0000.0000.0000.000
138A139SER00.0060.0199.7540.0400.0400.0000.0000.0000.000
139A140PRO00.0710.0369.5120.0350.0350.0000.0000.0000.000
140A141LEU0-0.017-0.0213.102-0.2930.0670.129-0.107-0.3820.000
141A142ILE0-0.031-0.0067.243-0.068-0.0680.0000.0000.0000.000
142A143GLU-1-0.702-0.7558.268-1.073-1.0730.0000.0000.0000.000
143A144TYR0-0.026-0.02910.0270.1030.1030.0000.0000.0000.000
144A145TYR00.018-0.01611.8110.0480.0480.0000.0000.0000.000
145A146VAL0-0.056-0.03316.7760.0270.0270.0000.0000.0000.000
146A147VAL00.0370.02419.3400.0080.0080.0000.0000.0000.000
147A148ASP-1-0.715-0.80521.888-0.144-0.1440.0000.0000.0000.000
148A149SER0-0.005-0.01424.8330.0180.0180.0000.0000.0000.000
149A150TRP00.0420.01723.536-0.021-0.0210.0000.0000.0000.000
150A151GLY00.0430.02923.9630.0150.0150.0000.0000.0000.000
151A152THR0-0.026-0.02524.5210.0030.0030.0000.0000.0000.000
152A153TYR0-0.013-0.00518.5920.0030.0030.0000.0000.0000.000
153A154ARG10.7740.89523.0900.1280.1280.0000.0000.0000.000
154A155PRO00.0260.00718.1190.0090.0090.0000.0000.0000.000
155A156THR0-0.010-0.00719.2270.0180.0180.0000.0000.0000.000
156A157GLY00.0220.00618.048-0.024-0.0240.0000.0000.0000.000
157A158THR0-0.029-0.00817.5280.0360.0360.0000.0000.0000.000
158A159TYR0-0.029-0.01519.797-0.018-0.0180.0000.0000.0000.000
159A160LYS10.9090.93918.2860.1920.1920.0000.0000.0000.000
160A161GLY00.0210.03523.5410.0070.0070.0000.0000.0000.000
161A162THR0-0.015-0.00925.681-0.007-0.0070.0000.0000.0000.000
162A163VAL00.0060.01025.2300.0040.0040.0000.0000.0000.000
163A164LYS10.8730.92428.0080.1060.1060.0000.0000.0000.000
164A165SER00.025-0.01528.4590.0030.0030.0000.0000.0000.000
165A166ASP-1-0.791-0.84428.635-0.138-0.1380.0000.0000.0000.000
166A167GLY00.0640.03631.8310.0000.0000.0000.0000.0000.000
167A168GLY0-0.012-0.01131.5910.0020.0020.0000.0000.0000.000
168A169THR0-0.0040.00629.759-0.003-0.0030.0000.0000.0000.000
169A170TYR0-0.057-0.04124.5550.0030.0030.0000.0000.0000.000
170A171ASP-1-0.733-0.84624.646-0.116-0.1160.0000.0000.0000.000
171A172ILE0-0.029-0.01220.853-0.016-0.0160.0000.0000.0000.000
172A173TYR00.0180.00018.8980.0200.0200.0000.0000.0000.000
173A174THR00.0120.01015.122-0.014-0.0140.0000.0000.0000.000
174A175THR00.011-0.00512.7520.0790.0790.0000.0000.0000.000
175A176THR0-0.004-0.0058.613-0.067-0.0670.0000.0000.0000.000
176A177ARG10.8880.9516.4471.2501.2500.0000.0000.0000.000
177A178TYR00.0560.0045.170-0.789-0.756-0.001-0.020-0.0120.000
178A179ASN0-0.0160.0022.790-0.8410.2871.285-1.162-1.2530.011
179A180ALA00.0110.0162.609-1.751-1.1950.726-0.050-1.2330.000
180A181PRO00.0280.0131.889-9.342-12.11910.161-4.174-3.209-0.046
181A182SER0-0.015-0.0254.068-0.324-0.1750.000-0.060-0.0890.000
182A183ILE0-0.0240.0086.5250.1820.1820.0000.0000.0000.000