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: M9NRZ

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 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 177
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1821512.440852
FMO2-HF: Nuclear repulsion 1752250.713507
FMO2-HF: Total energy -69261.727345
FMO2-MP2: Total energy -69466.158089


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.
-0.1441.3340-0.644-0.8340.002
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 : 0.038 / q_NPA : 0.010
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].
3A3SER00.0680.0353.817-1.3240.0790.001-0.637-0.7670.002
4A4THR0-0.013-0.0135.9920.2910.2910.0000.0000.0000.000
5A5SER0-0.019-0.0128.8190.1110.1110.0000.0000.0000.000
6A6THR00.0720.0219.8920.0230.0230.0000.0000.0000.000
7A7GLY00.0410.01512.4440.0350.0350.0000.0000.0000.000
8A8LEU0-0.0310.00112.9570.0020.0020.0000.0000.0000.000
9A9PRO00.0040.01916.659-0.010-0.0100.0000.0000.0000.000
10A10PRO00.026-0.01019.1550.0010.0010.0000.0000.0000.000
11A11ASN00.0100.00220.9490.0020.0020.0000.0000.0000.000
12A12TRP0-0.0150.01420.3710.0040.0040.0000.0000.0000.000
13A13THR0-0.030-0.02319.163-0.002-0.0020.0000.0000.0000.000
14A14ILE00.0060.00215.0180.0010.0010.0000.0000.0000.000
15A15ARG10.7950.89619.519-0.021-0.0210.0000.0000.0000.000
16A16VAL00.0390.01920.7170.0010.0010.0000.0000.0000.000
17A17SER0-0.0050.00523.2620.0000.0000.0000.0000.0000.000
18A18ARG10.9590.95926.576-0.025-0.0250.0000.0000.0000.000
19A19SER00.0210.00629.0770.0010.0010.0000.0000.0000.000
20A20HIS0-0.008-0.00127.5080.0000.0000.0000.0000.0000.000
21A21ASN0-0.046-0.02222.585-0.002-0.0020.0000.0000.0000.000
22A22LYS10.9831.00222.343-0.012-0.0120.0000.0000.0000.000
23A23GLU-1-0.885-0.94417.6810.0330.0330.0000.0000.0000.000
24A24TYR0-0.028-0.01021.011-0.001-0.0010.0000.0000.0000.000
25A25PHE0-0.002-0.01617.2070.0030.0030.0000.0000.0000.000
26A26LEU0-0.0070.00122.050-0.002-0.0020.0000.0000.0000.000
27A27ASN00.0470.04023.6920.0000.0000.0000.0000.0000.000
28A28GLN0-0.001-0.04124.312-0.001-0.0010.0000.0000.0000.000
29A29SER0-0.042-0.01727.2770.0000.0000.0000.0000.0000.000
30A30THR00.001-0.00829.2750.0000.0000.0000.0000.0000.000
31A31ASN0-0.049-0.02729.6520.0010.0010.0000.0000.0000.000
32A32GLU-1-0.932-0.95528.4640.0020.0020.0000.0000.0000.000
33A33SER0-0.033-0.02926.7380.0020.0020.0000.0000.0000.000
34A34SER0-0.008-0.01924.123-0.002-0.0020.0000.0000.0000.000
35A35TRP0-0.016-0.01723.7110.0030.0030.0000.0000.0000.000
36A36ASP-1-0.875-0.92122.1310.0060.0060.0000.0000.0000.000
37A37PRO0-0.033-0.02018.0140.0000.0000.0000.0000.0000.000
38A38PRO00.0340.04519.666-0.004-0.0040.0000.0000.0000.000
39A39TYR00.0390.01820.5540.0030.0030.0000.0000.0000.000
40A40GLY0-0.005-0.00819.878-0.001-0.0010.0000.0000.0000.000
41A41THR0-0.012-0.02515.4760.0000.0000.0000.0000.0000.000
42A42ASP-1-0.948-0.96711.0750.1730.1730.0000.0000.0000.000
43A43LYS10.9790.95012.493-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.951-0.9527.2800.2180.2180.0000.0000.0000.000
45A45VAL00.0050.0057.7850.1140.1140.0000.0000.0000.000
46A46LEU00.0340.0229.061-0.051-0.0510.0000.0000.0000.000
47A47ASN0-0.034-0.02010.917-0.039-0.0390.0000.0000.0000.000
48A48ALA0-0.0080.0025.830-0.037-0.0370.0000.0000.0000.000
49A49TYR0-0.033-0.0447.972-0.079-0.0790.0000.0000.0000.000
50A50ILE00.013-0.0089.556-0.016-0.0160.0000.0000.0000.000
51A51ALA0-0.039-0.0159.740-0.015-0.0150.0000.0000.0000.000
52A52LYS10.9610.9734.423-0.194-0.119-0.001-0.007-0.0670.000
53A53PHE00.0120.01410.6070.0040.0040.0000.0000.0000.000
54A54LYS10.9070.94613.557-0.044-0.0440.0000.0000.0000.000
55A55ASN0-0.045-0.00712.635-0.017-0.0170.0000.0000.0000.000
56A56ASN0-0.054-0.01813.2950.0310.0310.0000.0000.0000.000
57A57GLY0-0.020-0.01815.297-0.003-0.0030.0000.0000.0000.000
58A58TYR0-0.020-0.01117.525-0.007-0.0070.0000.0000.0000.000
59A59LYS10.9610.99217.115-0.090-0.0900.0000.0000.0000.000
60A60PRO00.0210.01015.3730.0060.0060.0000.0000.0000.000
61A61LEU0-0.0300.0088.8750.0190.0190.0000.0000.0000.000
62A62VAL0-0.0140.00712.337-0.039-0.0390.0000.0000.0000.000
63A63ASN00.0350.0098.9900.0270.0270.0000.0000.0000.000
64A64GLU-1-0.896-0.9526.6040.5390.5390.0000.0000.0000.000
65A65ASP-1-0.906-0.9378.7980.4680.4680.0000.0000.0000.000
66A66GLY0-0.080-0.04912.024-0.067-0.0670.0000.0000.0000.000
67A67GLN0-0.077-0.05513.218-0.053-0.0530.0000.0000.0000.000
68A68VAL0-0.010-0.00613.443-0.011-0.0110.0000.0000.0000.000
69A69ARG10.8460.90814.817-0.007-0.0070.0000.0000.0000.000
70A70VAL00.0090.00216.793-0.012-0.0120.0000.0000.0000.000
71A71SER0-0.0090.00319.9340.0010.0010.0000.0000.0000.000
72A72HIS00.011-0.04822.7500.0010.0010.0000.0000.0000.000
73A73LEU00.0190.02526.232-0.001-0.0010.0000.0000.0000.000
74A74LEU0-0.062-0.02829.8120.0010.0010.0000.0000.0000.000
75A75ILE00.0210.02732.331-0.001-0.0010.0000.0000.0000.000
76A76LYS10.8080.89835.567-0.025-0.0250.0000.0000.0000.000
77A77ASN00.030-0.01238.083-0.001-0.0010.0000.0000.0000.000
78A78ASN0-0.032-0.01841.5700.0020.0020.0000.0000.0000.000
79A79GLN00.0160.02642.295-0.001-0.0010.0000.0000.0000.000
80A80SER0-0.057-0.01238.1360.0010.0010.0000.0000.0000.000
81A81ARG10.9610.94834.402-0.039-0.0390.0000.0000.0000.000
82A82LYS10.9100.96236.538-0.031-0.0310.0000.0000.0000.000
83A83PRO00.0970.05939.2640.0000.0000.0000.0000.0000.000
84A84LYS11.0201.00640.156-0.024-0.0240.0000.0000.0000.000
85A85SER0-0.084-0.06737.0570.0020.0020.0000.0000.0000.000
86A86TRP00.023-0.00434.702-0.001-0.0010.0000.0000.0000.000
87A87LYS10.9811.01437.277-0.014-0.0140.0000.0000.0000.000
88A88SER0-0.072-0.03740.083-0.001-0.0010.0000.0000.0000.000
89A89PRO00.0100.00542.4200.0010.0010.0000.0000.0000.000
90A90ASP-1-0.901-0.94643.3050.0150.0150.0000.0000.0000.000
91A91GLY0-0.049-0.01544.6480.0000.0000.0000.0000.0000.000
92A92ILE0-0.077-0.03439.789-0.001-0.0010.0000.0000.0000.000
93A93SER00.015-0.00944.1670.0010.0010.0000.0000.0000.000
94A94ARG10.8800.96239.698-0.016-0.0160.0000.0000.0000.000
95A95THR00.0500.00944.5520.0010.0010.0000.0000.0000.000
96A96ARG10.8990.92440.165-0.021-0.0210.0000.0000.0000.000
97A97ASP-1-0.864-0.91841.7230.0150.0150.0000.0000.0000.000
98A98GLU-1-0.853-0.92043.1090.0120.0120.0000.0000.0000.000
99A99SER0-0.073-0.05638.8720.0000.0000.0000.0000.0000.000
100A100ILE00.0180.00938.3680.0000.0000.0000.0000.0000.000
101A101GLN0-0.003-0.00938.849-0.001-0.0010.0000.0000.0000.000
102A102ILE0-0.0160.00137.963-0.001-0.0010.0000.0000.0000.000
103A103LEU00.0020.00232.666-0.001-0.0010.0000.0000.0000.000
104A104LYS10.9600.97535.135-0.012-0.0120.0000.0000.0000.000
105A105LYS10.9680.99236.457-0.008-0.0080.0000.0000.0000.000
106A106HIS00.0380.01533.431-0.002-0.0020.0000.0000.0000.000
107A107LEU0-0.003-0.01129.942-0.001-0.0010.0000.0000.0000.000
108A108GLU-1-0.952-0.97232.1910.0060.0060.0000.0000.0000.000
109A109ARG10.9220.96634.071-0.003-0.0030.0000.0000.0000.000
110A110ILE0-0.054-0.01827.804-0.001-0.0010.0000.0000.0000.000
111A111LEU0-0.038-0.02528.057-0.001-0.0010.0000.0000.0000.000
112A112SER00.0110.02230.175-0.001-0.0010.0000.0000.0000.000
113A113GLY0-0.0090.00129.695-0.001-0.0010.0000.0000.0000.000
114A114GLU-1-0.919-0.95230.6850.0000.0000.0000.0000.0000.000
115A115VAL0-0.023-0.00831.2430.0000.0000.0000.0000.0000.000
116A116LYS10.9750.99423.3790.0120.0120.0000.0000.0000.000
117A117LEU00.0560.02525.1670.0010.0010.0000.0000.0000.000
118A118SER00.013-0.00424.5610.0010.0010.0000.0000.0000.000
119A119GLU-1-0.955-0.97726.643-0.001-0.0010.0000.0000.0000.000
120A120LEU00.0240.01029.9250.0010.0010.0000.0000.0000.000
121A121ALA0-0.015-0.01628.5290.0020.0020.0000.0000.0000.000
122A122ASN00.0080.00530.4640.0030.0030.0000.0000.0000.000
123A123THR0-0.049-0.04531.6540.0010.0010.0000.0000.0000.000
124A124GLU-1-0.886-0.93034.2750.0100.0100.0000.0000.0000.000
125A125SER0-0.0040.01330.4040.0020.0020.0000.0000.0000.000
126A126ASP-1-0.797-0.89333.2720.0170.0170.0000.0000.0000.000
127A127CYM-1-0.861-0.81929.5880.0320.0320.0000.0000.0000.000
128A128SER0-0.041-0.03430.107-0.001-0.0010.0000.0000.0000.000
129A129SER00.033-0.05826.171-0.002-0.0020.0000.0000.0000.000
130A130HIS10.8430.92227.578-0.017-0.0170.0000.0000.0000.000
131A131ASP-1-0.928-0.94629.4350.0170.0170.0000.0000.0000.000
132A132ARG10.8860.93321.032-0.029-0.0290.0000.0000.0000.000
133A133GLY00.0030.00724.254-0.001-0.0010.0000.0000.0000.000
134A134GLY00.0490.01724.973-0.002-0.0020.0000.0000.0000.000
135A135ASP-1-0.845-0.88919.8480.0290.0290.0000.0000.0000.000
136A136LEU0-0.012-0.01421.8110.0030.0030.0000.0000.0000.000
137A137GLY0-0.023-0.00218.5400.0070.0070.0000.0000.0000.000
138A138PHE0-0.009-0.02811.716-0.010-0.0100.0000.0000.0000.000
139A139PHE00.0240.02116.9180.0040.0040.0000.0000.0000.000
140A140SER00.0560.03217.9040.0040.0040.0000.0000.0000.000
141A141LYS10.9030.94818.955-0.139-0.1390.0000.0000.0000.000
142A142GLY0-0.011-0.01921.9170.0070.0070.0000.0000.0000.000
143A143GLN0-0.030-0.00622.174-0.003-0.0030.0000.0000.0000.000
144A144MET0-0.0170.00123.045-0.008-0.0080.0000.0000.0000.000
145A145GLN00.000-0.03026.239-0.001-0.0010.0000.0000.0000.000
146A146PRO00.0830.02827.9720.0000.0000.0000.0000.0000.000
147A147PRO00.0390.01628.0850.0020.0020.0000.0000.0000.000
148A148PHE00.0110.01123.587-0.002-0.0020.0000.0000.0000.000
149A149GLU-1-0.856-0.91022.9650.0860.0860.0000.0000.0000.000
150A150GLU-1-0.892-0.95323.3530.0560.0560.0000.0000.0000.000
151A151ALA0-0.003-0.00224.3000.0000.0000.0000.0000.0000.000
152A152ALA00.0310.00720.831-0.002-0.0020.0000.0000.0000.000
153A153PHE0-0.062-0.04817.2340.0000.0000.0000.0000.0000.000
154A154ASN0-0.077-0.03319.4190.0060.0060.0000.0000.0000.000
155A155LEU0-0.0420.01019.997-0.005-0.0050.0000.0000.0000.000
156A156HIS00.0500.05916.2140.0020.0020.0000.0000.0000.000
157A157VAL0-0.026-0.02812.5790.0050.0050.0000.0000.0000.000
158A158GLY0-0.013-0.01015.790-0.002-0.0020.0000.0000.0000.000
159A159GLU-1-0.816-0.87818.5420.0240.0240.0000.0000.0000.000
160A160VAL0-0.018-0.01921.3020.0010.0010.0000.0000.0000.000
161A161SER0-0.0050.00024.4600.0010.0010.0000.0000.0000.000
162A162ASN00.0210.00726.467-0.004-0.0040.0000.0000.0000.000
163A163ILE00.016-0.00529.7590.0010.0010.0000.0000.0000.000
164A164ILE0-0.0070.01328.0080.0010.0010.0000.0000.0000.000
165A165GLU-1-0.822-0.89531.4430.0230.0230.0000.0000.0000.000
166A166THR0-0.035-0.04430.5330.0030.0030.0000.0000.0000.000
167A167ASN00.000-0.00333.839-0.003-0.0030.0000.0000.0000.000
168A168SER0-0.033-0.01833.0040.0000.0000.0000.0000.0000.000
169A169GLY00.0140.02135.221-0.002-0.0020.0000.0000.0000.000
170A170VAL00.0010.01634.2300.0010.0010.0000.0000.0000.000
171A171HIS00.012-0.00229.3270.0000.0000.0000.0000.0000.000
172A172ILE00.0120.03527.4710.0000.0000.0000.0000.0000.000
173A173LEU0-0.003-0.01323.4480.0000.0000.0000.0000.0000.000
174A174GLN00.0570.03320.2960.0010.0010.0000.0000.0000.000
175A175ARG10.7890.88013.003-0.024-0.0240.0000.0000.0000.000
176A176THR0-0.014-0.01816.555-0.006-0.0060.0000.0000.0000.000
177A177GLY00.0310.06412.078-0.030-0.0300.0000.0000.0000.000