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: 2LN4R

Calculation Name: 1YW5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YW5

Chain ID: A

ChEMBL ID:

UniProt ID: Q59KZ2

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 177
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1822461.687863
FMO2-HF: Nuclear repulsion 1753198.93849
FMO2-HF: Total energy -69262.749373
FMO2-MP2: Total energy -69467.154767


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.023-0.5670.071-1.17-1.357-0.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.013
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].
3A3SER00.015-0.0123.076-3.062-0.9750.067-1.085-1.069-0.003
4A4THR0-0.008-0.0105.7110.2490.2490.0000.0000.0000.000
5A5SER00.0090.0098.7870.0580.0580.0000.0000.0000.000
6A6THR00.0610.01910.0380.0880.0880.0000.0000.0000.000
7A7GLY00.0140.00312.0490.0440.0440.0000.0000.0000.000
8A8LEU0-0.0120.00912.753-0.028-0.0280.0000.0000.0000.000
9A9PRO00.0200.02016.577-0.019-0.0190.0000.0000.0000.000
10A10PRO00.022-0.00819.1300.0090.0090.0000.0000.0000.000
11A11ASN00.000-0.00620.871-0.001-0.0010.0000.0000.0000.000
12A12TRP00.0140.02220.3020.0090.0090.0000.0000.0000.000
13A13THR0-0.065-0.04919.1560.0070.0070.0000.0000.0000.000
14A14ILE00.0150.01415.2750.0020.0020.0000.0000.0000.000
15A15ARG10.7870.88419.804-0.094-0.0940.0000.0000.0000.000
16A16VAL00.0410.00720.9390.0130.0130.0000.0000.0000.000
17A17SER0-0.002-0.00423.606-0.007-0.0070.0000.0000.0000.000
18A18ARG10.9470.96126.890-0.072-0.0720.0000.0000.0000.000
19A19SER00.0360.00529.286-0.003-0.0030.0000.0000.0000.000
20A20HIS00.0340.04027.8820.0050.0050.0000.0000.0000.000
21A21ASN0-0.0120.01022.773-0.002-0.0020.0000.0000.0000.000
22A22LYS10.8920.94022.493-0.110-0.1100.0000.0000.0000.000
23A23GLU-1-0.792-0.89017.7720.1940.1940.0000.0000.0000.000
24A24TYR0-0.032-0.01421.058-0.005-0.0050.0000.0000.0000.000
25A25PHE00.010-0.00117.5910.0130.0130.0000.0000.0000.000
26A26LEU0-0.008-0.00522.076-0.009-0.0090.0000.0000.0000.000
27A27ASN00.0270.00923.6650.0000.0000.0000.0000.0000.000
28A28GLN00.006-0.03224.082-0.002-0.0020.0000.0000.0000.000
29A29SER0-0.063-0.02526.891-0.003-0.0030.0000.0000.0000.000
30A30THR00.0060.00129.058-0.001-0.0010.0000.0000.0000.000
31A31ASN0-0.063-0.03029.6720.0020.0020.0000.0000.0000.000
32A32GLU-1-0.864-0.91828.0370.0340.0340.0000.0000.0000.000
33A33SER0-0.034-0.03126.7120.0060.0060.0000.0000.0000.000
34A34SER0-0.026-0.02123.993-0.007-0.0070.0000.0000.0000.000
35A35TRP0-0.004-0.01023.4930.0110.0110.0000.0000.0000.000
36A36ASP-1-0.881-0.92321.8470.0800.0800.0000.0000.0000.000
37A37PRO0-0.024-0.02417.643-0.003-0.0030.0000.0000.0000.000
38A38PRO00.0240.04619.522-0.013-0.0130.0000.0000.0000.000
39A39TYR00.0200.00920.3200.0010.0010.0000.0000.0000.000
40A40GLY00.012-0.00119.485-0.002-0.0020.0000.0000.0000.000
41A41THR0-0.033-0.03115.211-0.002-0.0020.0000.0000.0000.000
42A42ASP-1-0.776-0.88110.4200.0780.0780.0000.0000.0000.000
43A43LYS10.8260.87710.0140.0820.0820.0000.0000.0000.000
44A44GLU-1-0.975-0.9566.841-0.090-0.0900.0000.0000.0000.000
45A45VAL0-0.012-0.0137.6580.3240.3240.0000.0000.0000.000
46A46LEU00.0440.0348.7450.0910.0910.0000.0000.0000.000
47A47ASN0-0.007-0.00410.417-0.014-0.0140.0000.0000.0000.000
48A48ALA0-0.008-0.0065.746-0.0050.047-0.001-0.003-0.0480.000
49A49TYR0-0.033-0.0367.808-0.114-0.1140.0000.0000.0000.000
50A50ILE00.015-0.00410.174-0.071-0.0710.0000.0000.0000.000
51A51ALA0-0.037-0.0169.703-0.067-0.0670.0000.0000.0000.000
52A52LYS10.9450.9743.236-0.929-0.6120.005-0.082-0.2400.001
53A53PHE00.0160.01010.251-0.069-0.0690.0000.0000.0000.000
54A54LYS10.8300.90113.576-0.279-0.2790.0000.0000.0000.000
55A55ASN0-0.0170.00112.382-0.041-0.0410.0000.0000.0000.000
56A56ASN0-0.067-0.02813.088-0.015-0.0150.0000.0000.0000.000
57A57GLY0-0.013-0.01414.955-0.020-0.0200.0000.0000.0000.000
58A58TYR0-0.053-0.03817.523-0.017-0.0170.0000.0000.0000.000
59A59LYS10.9801.00917.230-0.158-0.1580.0000.0000.0000.000
60A60PRO00.0130.01115.6510.0280.0280.0000.0000.0000.000
61A61LEU0-0.0250.0098.9680.0060.0060.0000.0000.0000.000
62A62VAL0-0.0090.00511.929-0.036-0.0360.0000.0000.0000.000
63A63ASN0-0.059-0.0668.951-0.034-0.0340.0000.0000.0000.000
64A64GLU-1-0.874-0.9296.0380.6860.6860.0000.0000.0000.000
65A65ASP-1-0.875-0.9138.9510.3610.3610.0000.0000.0000.000
66A66GLY0-0.045-0.02212.073-0.050-0.0500.0000.0000.0000.000
67A67GLN0-0.081-0.05113.368-0.044-0.0440.0000.0000.0000.000
68A68VAL0-0.032-0.02113.6360.0000.0000.0000.0000.0000.000
69A69ARG10.8680.91715.242-0.013-0.0130.0000.0000.0000.000
70A70VAL0-0.001-0.00416.985-0.004-0.0040.0000.0000.0000.000
71A71SER0-0.017-0.00519.970-0.005-0.0050.0000.0000.0000.000
72A72HIS00.020-0.07122.7750.0050.0050.0000.0000.0000.000
73A73LEU00.0300.01226.306-0.003-0.0030.0000.0000.0000.000
74A74LEU0-0.075-0.02129.9170.0020.0020.0000.0000.0000.000
75A75ILE00.0080.01232.357-0.003-0.0030.0000.0000.0000.000
76A76LYS10.8430.90735.652-0.025-0.0250.0000.0000.0000.000
77A77ASN00.014-0.01038.149-0.001-0.0010.0000.0000.0000.000
78A78ASN0-0.011-0.00141.6160.0020.0020.0000.0000.0000.000
79A79GLN00.0060.01842.211-0.001-0.0010.0000.0000.0000.000
80A80SER0-0.048-0.01838.1470.0020.0020.0000.0000.0000.000
81A81ARG10.9310.92935.976-0.043-0.0430.0000.0000.0000.000
82A82LYS10.9370.97036.181-0.030-0.0300.0000.0000.0000.000
83A83PRO00.0620.05439.3740.0000.0000.0000.0000.0000.000
84A84LYS10.9690.97440.288-0.021-0.0210.0000.0000.0000.000
85A85SER0-0.060-0.05237.1920.0020.0020.0000.0000.0000.000
86A86TRP0-0.012-0.01234.372-0.002-0.0020.0000.0000.0000.000
87A87LYS10.8490.94636.860-0.015-0.0150.0000.0000.0000.000
88A88SER0-0.058-0.04739.9980.0000.0000.0000.0000.0000.000
89A89PRO00.0220.02642.3470.0020.0020.0000.0000.0000.000
90A90ASP-1-0.894-0.96243.2590.0130.0130.0000.0000.0000.000
91A91GLY0-0.045-0.01844.9990.0010.0010.0000.0000.0000.000
92A92ILE0-0.064-0.01940.189-0.001-0.0010.0000.0000.0000.000
93A93SER00.0230.00544.4150.0010.0010.0000.0000.0000.000
94A94ARG10.8050.89338.900-0.019-0.0190.0000.0000.0000.000
95A95THR00.020-0.04244.5190.0020.0020.0000.0000.0000.000
96A96ARG10.8080.86839.845-0.030-0.0300.0000.0000.0000.000
97A97ASP-1-0.813-0.89441.4820.0260.0260.0000.0000.0000.000
98A98GLU-1-0.808-0.86642.9200.0170.0170.0000.0000.0000.000
99A99SER0-0.052-0.04038.7540.0000.0000.0000.0000.0000.000
100A100ILE00.0150.00738.1500.0000.0000.0000.0000.0000.000
101A101GLN00.010-0.00838.7160.0000.0000.0000.0000.0000.000
102A102ILE0-0.053-0.02037.994-0.001-0.0010.0000.0000.0000.000
103A103LEU0-0.010-0.00232.456-0.001-0.0010.0000.0000.0000.000
104A104LYS10.8110.88034.912-0.022-0.0220.0000.0000.0000.000
105A105LYS10.9771.00135.876-0.015-0.0150.0000.0000.0000.000
106A106HIS00.0380.01933.119-0.002-0.0020.0000.0000.0000.000
107A107LEU00.0150.00729.602-0.001-0.0010.0000.0000.0000.000
108A108GLU-1-0.815-0.90231.8330.0210.0210.0000.0000.0000.000
109A109ARG10.8660.92333.897-0.007-0.0070.0000.0000.0000.000
110A110ILE0-0.060-0.01727.496-0.002-0.0020.0000.0000.0000.000
111A111LEU0-0.064-0.02827.996-0.001-0.0010.0000.0000.0000.000
112A112SER0-0.010-0.02830.1730.0000.0000.0000.0000.0000.000
113A113GLY0-0.0050.00729.642-0.002-0.0020.0000.0000.0000.000
114A114GLU-1-0.844-0.88230.5390.0040.0040.0000.0000.0000.000
115A115VAL0-0.0210.00231.418-0.001-0.0010.0000.0000.0000.000
116A116LYS10.9300.96524.932-0.001-0.0010.0000.0000.0000.000
117A117LEU00.0290.02224.7460.0000.0000.0000.0000.0000.000
118A118SER00.0250.00524.5480.0020.0020.0000.0000.0000.000
119A119GLU-1-0.898-0.95426.650-0.005-0.0050.0000.0000.0000.000
120A120LEU00.0270.00829.8010.0010.0010.0000.0000.0000.000
121A121ALA0-0.048-0.02328.3360.0010.0010.0000.0000.0000.000
122A122ASN00.0190.00430.4020.0020.0020.0000.0000.0000.000
123A123THR0-0.033-0.03231.6460.0000.0000.0000.0000.0000.000
124A124GLU-1-0.813-0.89634.1640.0120.0120.0000.0000.0000.000
125A125SER00.0390.03830.0520.0030.0030.0000.0000.0000.000
126A126ASP-1-0.742-0.83333.0360.0190.0190.0000.0000.0000.000
127A127CYM-1-0.861-0.73629.6950.0320.0320.0000.0000.0000.000
128A128SER00.026-0.00730.170-0.002-0.0020.0000.0000.0000.000
129A129SER0-0.042-0.14526.405-0.002-0.0020.0000.0000.0000.000
130A130HIS10.7720.90027.708-0.013-0.0130.0000.0000.0000.000
131A131ASP-1-0.832-0.91529.3330.0090.0090.0000.0000.0000.000
132A132ARG10.8200.90521.928-0.025-0.0250.0000.0000.0000.000
133A133GLY00.0170.01224.458-0.001-0.0010.0000.0000.0000.000
134A134GLY00.0500.01525.2890.0010.0010.0000.0000.0000.000
135A135ASP-1-0.830-0.87120.1040.0310.0310.0000.0000.0000.000
136A136LEU0-0.013-0.01621.7970.0010.0010.0000.0000.0000.000
137A137GLY0-0.0130.00718.7110.0050.0050.0000.0000.0000.000
138A138PHE00.005-0.02111.898-0.004-0.0040.0000.0000.0000.000
139A139PHE00.0000.00117.141-0.001-0.0010.0000.0000.0000.000
140A140SER00.0830.04218.1720.0080.0080.0000.0000.0000.000
141A141LYS10.8210.89519.415-0.132-0.1320.0000.0000.0000.000
142A142GLY0-0.011-0.01021.8220.0040.0040.0000.0000.0000.000
143A143GLN00.0030.01521.4100.0040.0040.0000.0000.0000.000
144A144MET0-0.018-0.00223.426-0.009-0.0090.0000.0000.0000.000
145A145GLN00.0310.01326.2760.0000.0000.0000.0000.0000.000
146A146PRO00.0660.02428.0050.0000.0000.0000.0000.0000.000
147A147PRO00.0230.01027.7490.0030.0030.0000.0000.0000.000
148A148PHE00.0240.01423.9640.0010.0010.0000.0000.0000.000
149A149GLU-1-0.800-0.87522.8140.1040.1040.0000.0000.0000.000
150A150GLU-1-0.871-0.93522.9450.1000.1000.0000.0000.0000.000
151A151ALA0-0.013-0.00323.8970.0040.0040.0000.0000.0000.000
152A152ALA00.012-0.00720.5760.0030.0030.0000.0000.0000.000
153A153PHE0-0.028-0.03017.0350.0010.0010.0000.0000.0000.000
154A154ASN0-0.091-0.05318.9880.0170.0170.0000.0000.0000.000
155A155LEU0-0.0530.00319.9440.0000.0000.0000.0000.0000.000
156A156HIS00.0460.03716.2790.0230.0230.0000.0000.0000.000
157A157VAL0-0.031-0.02412.226-0.011-0.0110.0000.0000.0000.000
158A158GLY00.0140.00715.3730.0040.0040.0000.0000.0000.000
159A159GLU-1-0.779-0.84018.1660.0800.0800.0000.0000.0000.000
160A160VAL0-0.001-0.01420.975-0.003-0.0030.0000.0000.0000.000
161A161SER0-0.020-0.00724.2510.0030.0030.0000.0000.0000.000
162A162ASN00.0440.00826.298-0.006-0.0060.0000.0000.0000.000
163A163ILE00.0230.01429.5470.0010.0010.0000.0000.0000.000
164A164ILE0-0.027-0.00227.8700.0030.0030.0000.0000.0000.000
165A165GLU-1-0.798-0.86931.3650.0320.0320.0000.0000.0000.000
166A166THR0-0.029-0.03130.5640.0030.0030.0000.0000.0000.000
167A167ASN00.020-0.00333.942-0.004-0.0040.0000.0000.0000.000
168A168SER0-0.032-0.02032.777-0.002-0.0020.0000.0000.0000.000
169A169GLY00.0170.01935.157-0.002-0.0020.0000.0000.0000.000
170A170VAL0-0.0070.00534.2870.0030.0030.0000.0000.0000.000
171A171HIS00.006-0.00329.306-0.002-0.0020.0000.0000.0000.000
172A172ILE00.0100.03027.3040.0010.0010.0000.0000.0000.000
173A173LEU00.003-0.00623.354-0.002-0.0020.0000.0000.0000.000
174A174GLN00.0140.00520.639-0.003-0.0030.0000.0000.0000.000
175A175ARG10.8040.90412.944-0.107-0.1070.0000.0000.0000.000
176A176THR00.003-0.01016.430-0.001-0.0010.0000.0000.0000.000
177A177GLY00.0270.04912.320-0.018-0.0180.0000.0000.0000.000