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: YY932

Calculation Name: 1I39-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1I39

Chain ID: A

ChEMBL ID:

UniProt ID: O29634

Base Structure: X-ray

Registration Date: 2023-03-13

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2259544.89386
FMO2-HF: Nuclear repulsion 2179960.62212
FMO2-HF: Total energy -79584.27174
FMO2-MP2: Total energy -79814.965211


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.
-14.515-5.8034.137-3.893-8.958-0.01
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 : 0.026 / q_NPA : 0.019
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].
3A3ALA00.019-0.0153.033-1.7701.8280.150-1.935-1.8130.002
4A4GLY0-0.0100.0165.577-0.227-0.2270.0000.0000.0000.000
5A5ILE0-0.033-0.0309.1080.2140.2140.0000.0000.0000.000
6A6ASP-1-0.789-0.90312.107-0.095-0.0950.0000.0000.0000.000
7A7GLU-1-0.904-0.98415.617-0.009-0.0090.0000.0000.0000.000
8A8ALA00.0390.02918.8600.0140.0140.0000.0000.0000.000
9A9GLY00.013-0.00221.8900.0020.0020.0000.0000.0000.000
10A10LYS10.9570.99623.3230.0940.0940.0000.0000.0000.000
11A11GLY0-0.024-0.01925.856-0.006-0.0060.0000.0000.0000.000
12A12CYS0-0.1000.01528.7270.0060.0060.0000.0000.0000.000
13A13VAL0-0.001-0.00930.567-0.007-0.0070.0000.0000.0000.000
14A14ILE00.0080.00532.754-0.002-0.0020.0000.0000.0000.000
15A15GLY00.0570.03929.8570.0040.0040.0000.0000.0000.000
16A16PRO0-0.017-0.01725.424-0.012-0.0120.0000.0000.0000.000
17A17LEU0-0.0450.00622.3360.0030.0030.0000.0000.0000.000
18A18VAL0-0.020-0.01618.8560.0030.0030.0000.0000.0000.000
19A19VAL00.0180.00815.677-0.013-0.0130.0000.0000.0000.000
20A20ALA0-0.005-0.00713.9300.0330.0330.0000.0000.0000.000
21A21GLY00.0400.01710.326-0.121-0.1210.0000.0000.0000.000
22A22VAL0-0.029-0.0117.3290.2330.2330.0000.0000.0000.000
23A23ALA00.0430.0282.794-1.467-0.9150.380-0.249-0.6830.002
24A24CYS0-0.036-0.0323.4070.2821.5210.215-0.312-1.142-0.001
25A25SER00.0190.0102.375-3.656-1.7423.240-1.687-3.468-0.012
26A26ASP-1-0.841-0.9233.3180.306-0.5250.1020.971-0.2430.001
27A27GLU-1-0.899-0.9686.565-0.388-0.3880.0000.0000.0000.000
28A28ASP-1-0.889-0.9538.2960.3090.3090.0000.0000.0000.000
29A29ARG10.9560.98210.211-1.323-1.3230.0000.0000.0000.000
30A30LEU00.001-0.0118.643-0.095-0.0950.0000.0000.0000.000
31A31ARG10.8500.92610.568-0.394-0.3940.0000.0000.0000.000
32A32LYS10.9470.99214.143-0.578-0.5780.0000.0000.0000.000
33A33LEU0-0.028-0.01013.229-0.055-0.0550.0000.0000.0000.000
34A34GLY0-0.0040.00616.771-0.046-0.0460.0000.0000.0000.000
35A35VAL00.0110.00313.127-0.046-0.0460.0000.0000.0000.000
36A36LYS10.9560.99416.414-0.112-0.1120.0000.0000.0000.000
37A37ASP-1-0.942-0.96417.8470.1590.1590.0000.0000.0000.000
38A38SER00.059-0.00318.290-0.002-0.0020.0000.0000.0000.000
39A39LYS10.8410.90920.961-0.024-0.0240.0000.0000.0000.000
40A40LYS10.9310.97723.327-0.170-0.1700.0000.0000.0000.000
41A41LEU0-0.0320.00021.361-0.004-0.0040.0000.0000.0000.000
42A42SER00.0290.01825.394-0.007-0.0070.0000.0000.0000.000
43A43GLN00.0560.01325.6390.0060.0060.0000.0000.0000.000
44A44GLY00.0370.01825.3680.0160.0160.0000.0000.0000.000
45A45ARG10.8780.91124.437-0.209-0.2090.0000.0000.0000.000
46A46ARG10.8290.90221.585-0.130-0.1300.0000.0000.0000.000
47A47GLU-1-0.923-0.96120.3530.2790.2790.0000.0000.0000.000
48A48GLU-1-0.842-0.90720.3510.3070.3070.0000.0000.0000.000
49A49LEU00.0010.00316.5930.0450.0450.0000.0000.0000.000
50A50ALA00.004-0.00716.0760.0890.0890.0000.0000.0000.000
51A51GLU-1-0.911-0.95815.2140.5680.5680.0000.0000.0000.000
52A52GLU-1-0.976-0.98715.3640.6770.6770.0000.0000.0000.000
53A53ILE0-0.041-0.02610.8690.1540.1540.0000.0000.0000.000
54A54ARG10.9260.95210.585-0.269-0.2690.0000.0000.0000.000
55A55LYS10.9350.98410.656-0.500-0.5000.0000.0000.0000.000
56A56ILE0-0.047-0.0279.2370.0240.0240.0000.0000.0000.000
57A57CYS0-0.0410.0215.8960.4410.545-0.001-0.004-0.0990.000
58A58ARG10.8880.9594.601-1.572-1.394-0.001-0.016-0.1610.000
59A59THR0-0.028-0.0306.420-0.094-0.0940.0000.0000.0000.000
60A60GLU-1-0.821-0.9049.7180.2600.2600.0000.0000.0000.000
61A61VAL00.005-0.00312.151-0.052-0.0520.0000.0000.0000.000
62A62LEU00.0000.01915.896-0.014-0.0140.0000.0000.0000.000
63A63LYS10.9470.96318.686-0.125-0.1250.0000.0000.0000.000
64A64VAL00.0050.00822.214-0.008-0.0080.0000.0000.0000.000
65A65SER00.0300.00825.1120.0010.0010.0000.0000.0000.000
66A66PRO00.022-0.00328.543-0.010-0.0100.0000.0000.0000.000
67A67GLU-1-0.886-0.92731.379-0.003-0.0030.0000.0000.0000.000
68A68ASN00.0680.02128.115-0.011-0.0110.0000.0000.0000.000
69A69LEU0-0.082-0.03626.359-0.013-0.0130.0000.0000.0000.000
70A70ASP-1-0.761-0.88529.950-0.031-0.0310.0000.0000.0000.000
71A71GLU-1-0.973-0.97132.074-0.044-0.0440.0000.0000.0000.000
72A72ARG10.9260.95723.2720.0860.0860.0000.0000.0000.000
73A73MET0-0.048-0.03130.581-0.006-0.0060.0000.0000.0000.000
74A74ALA0-0.082-0.02132.3480.0000.0000.0000.0000.0000.000
75A75ALA0-0.007-0.00732.680-0.001-0.0010.0000.0000.0000.000
76A76LYS10.8590.92726.6270.1400.1400.0000.0000.0000.000
77A77THR00.0040.00529.2420.0110.0110.0000.0000.0000.000
78A78ILE00.0400.00126.380-0.006-0.0060.0000.0000.0000.000
79A79ASN00.0340.00024.9560.0060.0060.0000.0000.0000.000
80A80GLU-1-0.879-0.92723.951-0.172-0.1720.0000.0000.0000.000
81A81ILE00.0060.00524.007-0.015-0.0150.0000.0000.0000.000
82A82LEU00.007-0.00619.876-0.002-0.0020.0000.0000.0000.000
83A83LYS10.9591.00519.8320.2360.2360.0000.0000.0000.000
84A84GLU-1-0.819-0.89819.134-0.200-0.2000.0000.0000.0000.000
85A85CYS0-0.064-0.02518.912-0.001-0.0010.0000.0000.0000.000
86A86TYR0-0.005-0.01915.5670.0130.0130.0000.0000.0000.000
87A87ALA00.0410.02514.322-0.060-0.0600.0000.0000.0000.000
88A88GLU-1-0.859-0.91814.472-0.152-0.1520.0000.0000.0000.000
89A89ILE0-0.015-0.01511.145-0.002-0.0020.0000.0000.0000.000
90A90ILE00.0110.0009.876-0.001-0.0010.0000.0000.0000.000
91A91LEU00.0020.0059.698-0.215-0.2150.0000.0000.0000.000
92A92ARG10.7600.89111.266-0.027-0.0270.0000.0000.0000.000
93A93LEU0-0.063-0.0456.1160.1230.1230.0000.0000.0000.000
94A94LYS10.8900.9605.9270.5170.5170.0000.0000.0000.000
95A95PRO0-0.026-0.0053.739-0.615-0.3680.000-0.056-0.1910.000
96A96GLU-1-0.943-0.9673.150-5.630-4.0930.053-0.586-1.004-0.002
97A97ILE0-0.018-0.0264.6311.4991.673-0.001-0.019-0.1540.000
98A98ALA0-0.022-0.0086.640-0.466-0.4660.0000.0000.0000.000
99A99TYR00.0030.0007.5730.0790.0790.0000.0000.0000.000
100A100VAL00.009-0.00611.2630.1200.1200.0000.0000.0000.000
101A101ASP-1-0.829-0.91414.137-0.162-0.1620.0000.0000.0000.000
102A102SER00.005-0.00417.3060.0010.0010.0000.0000.0000.000
103A103PRO0-0.106-0.06820.4950.0360.0360.0000.0000.0000.000
104A104ASP-1-0.911-0.94723.653-0.202-0.2020.0000.0000.0000.000
105A105VAL00.001-0.02524.613-0.011-0.0110.0000.0000.0000.000
106A106ILE0-0.057-0.01125.765-0.005-0.0050.0000.0000.0000.000
107A107PRO00.0610.04620.455-0.008-0.0080.0000.0000.0000.000
108A108GLU-1-0.853-0.94521.492-0.341-0.3410.0000.0000.0000.000
109A109ARG10.8570.92621.8410.1940.1940.0000.0000.0000.000
110A110LEU00.0490.03018.996-0.007-0.0070.0000.0000.0000.000
111A111SER00.014-0.00317.552-0.046-0.0460.0000.0000.0000.000
112A112ARG10.9730.98317.8010.2910.2910.0000.0000.0000.000
113A113GLU-1-0.873-0.94019.721-0.296-0.2960.0000.0000.0000.000
114A114LEU00.0080.00015.8370.0090.0090.0000.0000.0000.000
115A115GLU-1-0.894-0.95114.548-0.890-0.8900.0000.0000.0000.000
116A116GLU-1-1.024-0.99216.114-0.381-0.3810.0000.0000.0000.000
117A117ILE0-0.007-0.00218.1080.0120.0120.0000.0000.0000.000
118A118THR0-0.104-0.06213.047-0.047-0.0470.0000.0000.0000.000
119A119GLY00.0340.02514.231-0.022-0.0220.0000.0000.0000.000
120A120LEU0-0.072-0.0378.249-0.091-0.0910.0000.0000.0000.000
121A121ARG10.9470.9899.6161.1881.1880.0000.0000.0000.000
122A122VAL0-0.027-0.02410.286-0.249-0.2490.0000.0000.0000.000
123A123VAL0-0.025-0.01312.7370.0930.0930.0000.0000.0000.000
124A124ALA0-0.0010.01214.2420.0140.0140.0000.0000.0000.000
125A125GLU-1-0.843-0.92516.677-0.426-0.4260.0000.0000.0000.000
126A126HIS00.003-0.01618.6410.0240.0240.0000.0000.0000.000
127A127LYS10.9470.99120.4390.1140.1140.0000.0000.0000.000
128A128ALA00.0540.02315.1970.0110.0110.0000.0000.0000.000
129A129ASP-1-0.783-0.90315.610-0.034-0.0340.0000.0000.0000.000
130A130GLU-1-1.043-1.01516.8120.0110.0110.0000.0000.0000.000
131A131LYS10.8510.93915.8530.3610.3610.0000.0000.0000.000
132A132TYR0-0.069-0.05811.217-0.058-0.0580.0000.0000.0000.000
133A133PRO00.0280.00810.9590.0470.0470.0000.0000.0000.000
134A134LEU00.0350.0105.1690.1290.1290.0000.0000.0000.000
135A135VAL00.0050.0199.4170.0770.0770.0000.0000.0000.000
136A136ALA00.0330.02512.2270.0540.0540.0000.0000.0000.000
137A137ALA0-0.017-0.01510.7190.0310.0310.0000.0000.0000.000
138A138ALA0-0.0030.00311.2910.0550.0550.0000.0000.0000.000
139A139SER00.0200.00912.8510.0020.0020.0000.0000.0000.000
140A140ILE0-0.062-0.03015.751-0.010-0.0100.0000.0000.0000.000
141A141ILE0-0.008-0.00112.994-0.015-0.0150.0000.0000.0000.000
142A142ALA00.0170.00516.252-0.025-0.0250.0000.0000.0000.000
143A143LYS10.9420.95418.166-0.121-0.1210.0000.0000.0000.000
144A144VAL00.0130.02919.652-0.016-0.0160.0000.0000.0000.000
145A145GLU-1-0.909-0.95918.9240.2250.2250.0000.0000.0000.000
146A146ARG10.8370.88921.570-0.087-0.0870.0000.0000.0000.000
147A147GLU-1-0.847-0.93024.0810.1140.1140.0000.0000.0000.000
148A148ARG10.9600.99420.294-0.294-0.2940.0000.0000.0000.000
149A149GLU-1-0.835-0.87826.1940.0780.0780.0000.0000.0000.000
150A150ILE0-0.064-0.03827.980-0.013-0.0130.0000.0000.0000.000
151A151GLU-1-0.868-0.94429.7640.0960.0960.0000.0000.0000.000
152A152ARG10.8690.91329.366-0.093-0.0930.0000.0000.0000.000
153A153LEU0-0.074-0.05131.496-0.010-0.0100.0000.0000.0000.000
154A154LYS10.8530.94533.904-0.073-0.0730.0000.0000.0000.000
155A155GLU-1-0.945-0.95034.2550.0950.0950.0000.0000.0000.000
156A156LYS10.8750.95236.539-0.055-0.0550.0000.0000.0000.000
157A157PHE0-0.076-0.07336.348-0.006-0.0060.0000.0000.0000.000
158A158GLY00.0530.04339.566-0.005-0.0050.0000.0000.0000.000
159A159ASP-1-0.849-0.93038.1840.0560.0560.0000.0000.0000.000
160A160PHE00.002-0.00233.565-0.005-0.0050.0000.0000.0000.000
161A161GLY00.016-0.00337.191-0.006-0.0060.0000.0000.0000.000
162A162SER0-0.052-0.05232.3520.0030.0030.0000.0000.0000.000
163A163GLY00.0570.02532.1450.0040.0040.0000.0000.0000.000
164A164TYR00.045-0.00127.142-0.012-0.0120.0000.0000.0000.000
165A165ALA00.009-0.01033.8730.0010.0010.0000.0000.0000.000
166A166SER0-0.022-0.01835.670-0.001-0.0010.0000.0000.0000.000
167A167ASP-1-0.793-0.87336.1890.0330.0330.0000.0000.0000.000
168A168PRO0-0.053-0.06238.038-0.003-0.0030.0000.0000.0000.000
169A169ARG11.0691.04939.834-0.031-0.0310.0000.0000.0000.000
170A170THR00.0040.00236.5350.0000.0000.0000.0000.0000.000
171A171ARG10.8990.97239.447-0.007-0.0070.0000.0000.0000.000
172A172GLU-1-0.969-0.98041.9870.0170.0170.0000.0000.0000.000
173A173VAL00.0480.03041.274-0.001-0.0010.0000.0000.0000.000
174A174LEU0-0.002-0.00938.361-0.002-0.0020.0000.0000.0000.000
175A175LYS10.9090.96142.356-0.005-0.0050.0000.0000.0000.000
176A176GLU-1-0.917-0.96045.9140.0200.0200.0000.0000.0000.000
177A177TRP00.0440.01138.577-0.001-0.0010.0000.0000.0000.000
178A178ILE0-0.039-0.01843.070-0.002-0.0020.0000.0000.0000.000
179A179ALA0-0.042-0.01846.211-0.001-0.0010.0000.0000.0000.000
180A180SER0-0.032-0.01247.2050.0000.0000.0000.0000.0000.000
181A181GLY0-0.0060.00148.5700.0000.0000.0000.0000.0000.000
182A182ARG10.8740.93446.251-0.019-0.0190.0000.0000.0000.000
183A183ILE00.0090.00240.5250.0020.0020.0000.0000.0000.000
184A184PRO00.0080.02038.592-0.001-0.0010.0000.0000.0000.000
185A185SER00.0740.01836.309-0.002-0.0020.0000.0000.0000.000
186A186CYS0-0.069-0.01033.563-0.004-0.0040.0000.0000.0000.000
187A187VAL00.0310.00633.8760.0000.0000.0000.0000.0000.000
188A188ARG10.7950.91327.3130.0020.0020.0000.0000.0000.000
189A189MET00.031-0.00234.781-0.001-0.0010.0000.0000.0000.000
190A190ARG10.8480.91835.2880.0440.0440.0000.0000.0000.000
191A191TRP0-0.0090.00929.683-0.005-0.0050.0000.0000.0000.000
192A192LYS10.9870.98836.2230.0460.0460.0000.0000.0000.000
193A193THR0-0.012-0.01837.7580.0000.0000.0000.0000.0000.000
194A194VAL00.0540.03438.0490.0030.0030.0000.0000.0000.000
195A195SER00.0380.02140.5090.0010.0010.0000.0000.0000.000
196A196ASN0-0.036-0.03542.4640.0000.0000.0000.0000.0000.000
197A197LEU0-0.023-0.01342.3690.0010.0010.0000.0000.0000.000
198A198ARG10.9540.98343.1870.0150.0150.0000.0000.0000.000
199A199GLN0-0.045-0.01245.820-0.001-0.0010.0000.0000.0000.000
200A200LYS10.9230.98947.5390.0100.0100.0000.0000.0000.000