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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: 2K1YR

Calculation Name: 2I1S-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I1S

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PRU3

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 181
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1982316.827677
FMO2-HF: Nuclear repulsion 1909130.150948
FMO2-HF: Total energy -73186.67673
FMO2-MP2: Total energy -73401.769772


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:3:ACE )


Summations of interaction energy for fragment #1(A:3:ACE )
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.
0.1812.1190.523-1.123-1.339-0.002
Interaction energy analysis for fragmet #1(A:3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.002
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].
3A5PHE 00.0110.0193.6400.1791.5770.003-0.694-0.707-0.001
4A6GLU -1-0.882-0.9394.3120.1590.3530.000-0.024-0.1710.000
5A7LYS 10.8670.9266.5670.2230.2230.0000.0000.0000.000
6A8VAL 00.0020.0059.928-0.036-0.0360.0000.0000.0000.000
7A9TYR 00.022-0.00112.108-0.008-0.0080.0000.0000.0000.000
8A10HIS 0-0.003-0.01215.2210.0030.0030.0000.0000.0000.000
9A11LEU 00.0380.02218.416-0.012-0.0120.0000.0000.0000.000
10A12LYS 10.8650.92921.051-0.012-0.0120.0000.0000.0000.000
11A13LEU 00.0510.02422.318-0.009-0.0090.0000.0000.0000.000
12A14SER 0-0.088-0.05426.0510.0060.0060.0000.0000.0000.000
13A15ILE 00.1330.08429.831-0.005-0.0050.0000.0000.0000.000
14A16LYS 10.8370.90332.3700.0130.0130.0000.0000.0000.000
15A17GLY 00.008-0.00235.108-0.001-0.0010.0000.0000.0000.000
16A18ILE 00.0940.08137.0150.0000.0000.0000.0000.0000.000
17A19THR 0-0.154-0.07637.6350.0010.0010.0000.0000.0000.000
18A20PRO 00.1140.03038.2480.0000.0000.0000.0000.0000.000
19A21GLN 0-0.0100.01832.5300.0030.0030.0000.0000.0000.000
20A22ILE 00.1050.08631.2160.0030.0030.0000.0000.0000.000
21A23TRP 0-0.079-0.04926.250-0.001-0.0010.0000.0000.0000.000
22A24ARG 10.8920.94324.440-0.024-0.0240.0000.0000.0000.000
23A25ARG 10.7540.87422.431-0.050-0.0500.0000.0000.0000.000
24A26ILE 00.0940.05418.3940.0100.0100.0000.0000.0000.000
25A27GLN 0-0.075-0.04414.7670.0190.0190.0000.0000.0000.000
26A28VAL 00.0660.02713.5470.0180.0180.0000.0000.0000.000
27A29PRO 00.0410.0168.7850.0200.0200.0000.0000.0000.000
28A30GLU -1-0.817-0.9179.104-0.309-0.3090.0000.0000.0000.000
29A31ASN 0-0.053-0.0327.9520.1380.1380.0000.0000.0000.000
30A32TYR 00.0580.02811.469-0.008-0.0080.0000.0000.0000.000
31A33THR 0-0.048-0.01113.7100.0100.0100.0000.0000.0000.000
32A34PHE 00.031-0.00316.9270.0210.0210.0000.0000.0000.000
33A35LEU 0-0.0250.00819.3490.0140.0140.0000.0000.0000.000
34A36ASP -1-0.839-0.93214.504-0.177-0.1770.0000.0000.0000.000
35A37LEU 0-0.028-0.01617.3690.0220.0220.0000.0000.0000.000
36A38HIS 0-0.0520.00219.2140.0150.0150.0000.0000.0000.000
37A39LYS 10.9890.98318.9380.0930.0930.0000.0000.0000.000
38A40ALA 00.0140.02517.8900.0110.0110.0000.0000.0000.000
39A41ILE 0-0.051-0.04219.9310.0120.0120.0000.0000.0000.000
40A42GLN 00.020-0.00123.4240.0080.0080.0000.0000.0000.000
41A43ALA 00.0550.05221.2700.0040.0040.0000.0000.0000.000
42A44VAL 0-0.079-0.05621.7100.0070.0070.0000.0000.0000.000
43A45MET 0-0.107-0.06024.2910.0060.0060.0000.0000.0000.000
44A46ASP -1-0.912-0.93726.6810.0170.0170.0000.0000.0000.000
45A47TRP 0-0.092-0.04327.726-0.005-0.0050.0000.0000.0000.000
46A48GLU -1-0.890-0.97428.0860.0000.0000.0000.0000.0000.000
47A49ASP -1-0.945-0.95926.290-0.042-0.0420.0000.0000.0000.000
48A50TYR 00.0170.02529.042-0.003-0.0030.0000.0000.0000.000
49A51HIS 10.7730.90331.9820.0130.0130.0000.0000.0000.000
50A52LEU 0-0.022-0.00631.316-0.004-0.0040.0000.0000.0000.000
51A53HIS 10.8610.91425.2260.0580.0580.0000.0000.0000.000
52A54GLU -1-0.941-0.97228.539-0.050-0.0500.0000.0000.0000.000
53A55PHE 0-0.025-0.01723.0270.0050.0050.0000.0000.0000.000
54A56GLU -1-0.913-0.94627.899-0.037-0.0370.0000.0000.0000.000
55A57MET 0-0.036-0.01823.4310.0010.0010.0000.0000.0000.000
56A58VAL 00.0260.02728.391-0.003-0.0030.0000.0000.0000.000
57A59ASN 00.0250.01226.285-0.008-0.0080.0000.0000.0000.000
58A60PRO 0-0.0100.01423.6170.0050.0050.0000.0000.0000.000
59A61LYS 10.8920.94121.3690.1350.1350.0000.0000.0000.000
60A62THR 0-0.016-0.01727.4300.0030.0030.0000.0000.0000.000
61A63GLY 0-0.0100.00130.0930.0050.0050.0000.0000.0000.000
62A64MET 0-0.034-0.01331.8800.0060.0060.0000.0000.0000.000
63A65LEU 0-0.029-0.01031.097-0.003-0.0030.0000.0000.0000.000
64A66ASP -1-0.784-0.87228.122-0.077-0.0770.0000.0000.0000.000
65A67LYS 10.9300.96929.8560.0440.0440.0000.0000.0000.000
66A68ILE 0-0.039-0.01723.896-0.007-0.0070.0000.0000.0000.000
67A69GLY 00.0860.02926.9010.0070.0070.0000.0000.0000.000
68A70ALA 00.0120.00726.635-0.009-0.0090.0000.0000.0000.000
69A71GLU -1-0.905-0.96124.645-0.121-0.1210.0000.0000.0000.000
70A72GLY 00.0420.04628.3040.0050.0050.0000.0000.0000.000
71A73ASP -1-0.953-0.98231.323-0.064-0.0640.0000.0000.0000.000
72A74NME 0-0.080-0.03233.586-0.003-0.0030.0000.0000.0000.000
73A80ACE 00.021-0.00233.2780.0000.0000.0000.0000.0000.000
74A81PRO 0-0.044-0.02033.061-0.002-0.0020.0000.0000.0000.000
75A82LEU 00.0020.01329.7260.0020.0020.0000.0000.0000.000
76A83VAL 0-0.0020.00625.178-0.006-0.0060.0000.0000.0000.000
77A84SER 0-0.042-0.04224.5000.0010.0010.0000.0000.0000.000
78A85GLU -1-0.753-0.88722.699-0.091-0.0910.0000.0000.0000.000
79A86LYS 10.9320.97220.1180.1020.1020.0000.0000.0000.000
80A87LYS 10.9000.94719.0570.1100.1100.0000.0000.0000.000
81A88ALA 00.0040.00919.562-0.021-0.0210.0000.0000.0000.000
82A89LYS 10.9570.98313.3740.3530.3530.0000.0000.0000.000
83A90LEU 00.0400.00915.9110.0220.0220.0000.0000.0000.000
84A91SER 00.0010.00214.4410.0070.0070.0000.0000.0000.000
85A92ASP -1-0.980-0.97316.591-0.198-0.1980.0000.0000.0000.000
86A93TYR 0-0.099-0.09919.7000.0120.0120.0000.0000.0000.000
87A94PHE 0-0.009-0.00219.2700.0140.0140.0000.0000.0000.000
88A95THR 00.001-0.00319.600-0.006-0.0060.0000.0000.0000.000
89A96LEU 0-0.011-0.03120.3850.0100.0100.0000.0000.0000.000
90A97GLU -1-0.945-0.96323.318-0.028-0.0280.0000.0000.0000.000
91A98ASN 0-0.061-0.03524.7390.0050.0050.0000.0000.0000.000
92A99LYS 10.9330.97023.844-0.002-0.0020.0000.0000.0000.000
93A100GLU -1-0.892-0.94324.515-0.006-0.0060.0000.0000.0000.000
94A101ALA 00.0220.02025.177-0.006-0.0060.0000.0000.0000.000
95A102LEU 0-0.046-0.02627.1770.0080.0080.0000.0000.0000.000
96A103TYR 0-0.006-0.03225.851-0.004-0.0040.0000.0000.0000.000
97A104THR 00.0380.01728.7070.0060.0060.0000.0000.0000.000
98A105TYR 0-0.047-0.08029.604-0.008-0.0080.0000.0000.0000.000
99A106ASP -1-0.764-0.89331.611-0.012-0.0120.0000.0000.0000.000
100A107PHE 0-0.103-0.06332.8190.0010.0010.0000.0000.0000.000
101A108GLY 0-0.045-0.01037.3280.0000.0000.0000.0000.0000.000
102A109ASP -1-0.802-0.89937.724-0.007-0.0070.0000.0000.0000.000
103A110ASN 0-0.124-0.06736.682-0.001-0.0010.0000.0000.0000.000
104A111TRP 00.0610.05933.1100.0020.0020.0000.0000.0000.000
105A112GLN 0-0.021-0.02832.354-0.001-0.0010.0000.0000.0000.000
106A113VAL 00.0220.00826.8590.0040.0040.0000.0000.0000.000
107A114LYS 10.8720.93929.0450.0010.0010.0000.0000.0000.000
108A115VAL 00.0480.02922.6690.0060.0060.0000.0000.0000.000
109A116ARG 10.8630.92625.117-0.004-0.0040.0000.0000.0000.000
110A117LEU 0-0.0140.00118.2500.0090.0090.0000.0000.0000.000
111A118GLU -1-0.934-0.97621.6610.0360.0360.0000.0000.0000.000
112A119LYS 10.8820.94119.038-0.083-0.0830.0000.0000.0000.000
113A120ILE 00.0500.04914.4920.0030.0030.0000.0000.0000.000
114A121LEU 0-0.062-0.04114.4260.0020.0020.0000.0000.0000.000
115A122PRO 0-0.025-0.00710.474-0.014-0.0140.0000.0000.0000.000
116A123ARG 10.9260.9862.772-1.342-0.9960.520-0.405-0.461-0.001
117A124LYS 10.9330.9579.424-0.254-0.2540.0000.0000.0000.000
118A125GLU -1-0.923-0.9778.7321.1001.1000.0000.0000.0000.000
119A126GLY 00.0080.0078.612-0.159-0.1590.0000.0000.0000.000
120A127VAL 0-0.080-0.03010.228-0.114-0.1140.0000.0000.0000.000
121A128GLU -1-0.921-0.9539.2250.4150.4150.0000.0000.0000.000
122A129TYR 0-0.084-0.0288.830-0.039-0.0390.0000.0000.0000.000
123A130PRO 00.0450.01210.998-0.015-0.0150.0000.0000.0000.000
124A131ILE 0-0.0200.00813.8670.0180.0180.0000.0000.0000.000
125A132CYS 00.0390.02716.351-0.021-0.0210.0000.0000.0000.000
126A133THR 0-0.076-0.04218.9020.0050.0050.0000.0000.0000.000
127A134ALA 0-0.002-0.01021.3660.0000.0000.0000.0000.0000.000
128A135GLY 00.0400.00025.026-0.004-0.0040.0000.0000.0000.000
129A136LYS 10.8610.93627.712-0.034-0.0340.0000.0000.0000.000
130A137ARG 10.8660.90731.466-0.020-0.0200.0000.0000.0000.000
131A138ALA 00.1010.06632.0270.0020.0020.0000.0000.0000.000
132A139ALA 0-0.053-0.03630.237-0.002-0.0020.0000.0000.0000.000
133A140VAL 0-0.047-0.00532.3530.0000.0000.0000.0000.0000.000
134A141PRO 00.0950.04433.888-0.001-0.0010.0000.0000.0000.000
135A142GLU -1-0.715-0.82431.806-0.012-0.0120.0000.0000.0000.000
136A143ASP -1-0.863-0.92735.637-0.007-0.0070.0000.0000.0000.000
137A144SER 0-0.056-0.02938.1080.0000.0000.0000.0000.0000.000
138A145GLY 00.0760.03040.5140.0010.0010.0000.0000.0000.000
139A146GLY 00.0050.00539.093-0.001-0.0010.0000.0000.0000.000
140A147VAL 0-0.089-0.06737.8960.0020.0020.0000.0000.0000.000
141A148TRP 0-0.058-0.03140.3800.0010.0010.0000.0000.0000.000
142A149GLY 00.0830.05843.5110.0010.0010.0000.0000.0000.000
143A150TYR 00.0500.01937.8000.0010.0010.0000.0000.0000.000
144A151GLU -1-0.889-0.98441.7170.0090.0090.0000.0000.0000.000
145A152GLU -1-0.980-0.97743.7230.0000.0000.0000.0000.0000.000
146A153MET 00.0230.02341.6870.0010.0010.0000.0000.0000.000
147A154LEU 0-0.022-0.01740.3590.0020.0020.0000.0000.0000.000
148A155GLU -1-0.924-0.95744.8720.0090.0090.0000.0000.0000.000
149A156VAL 00.0220.03148.3130.0010.0010.0000.0000.0000.000
150A157LEU 00.000-0.00743.8590.0010.0010.0000.0000.0000.000
151A158LYS 10.7030.85246.114-0.009-0.0090.0000.0000.0000.000
152A159ASP -1-0.879-0.94749.8110.0080.0080.0000.0000.0000.000
153A160SER 0-0.011-0.02252.5860.0000.0000.0000.0000.0000.000
154A161GLU -1-1.041-1.01353.7360.0080.0080.0000.0000.0000.000
155A162HIS 0-0.0180.00753.657-0.001-0.0010.0000.0000.0000.000
156A163GLU -1-0.974-1.00055.7340.0040.0040.0000.0000.0000.000
157A164GLU -1-0.913-0.95651.8460.0020.0020.0000.0000.0000.000
158A165TYR 0-0.0360.01749.3150.0000.0000.0000.0000.0000.000
159A166GLU -1-0.910-0.96550.3030.0070.0070.0000.0000.0000.000
160A167ASP -1-0.939-0.96950.3940.0040.0040.0000.0000.0000.000
161A168THR 0-0.076-0.06346.2380.0000.0000.0000.0000.0000.000
162A169VAL 0-0.006-0.00645.8450.0000.0000.0000.0000.0000.000
163A170LEU 0-0.056-0.01545.4160.0010.0010.0000.0000.0000.000
164A171TRP 0-0.072-0.02140.1590.0000.0000.0000.0000.0000.000
165A172LEU 0-0.056-0.04340.2330.0000.0000.0000.0000.0000.000
166A173GLY 00.0150.02240.6500.0010.0010.0000.0000.0000.000
167A174ASP -1-0.937-0.98442.6920.0150.0150.0000.0000.0000.000
168A175ASP -1-1.013-1.00238.5860.0200.0200.0000.0000.0000.000
169A176PHE 0-0.023-0.00236.7020.0020.0020.0000.0000.0000.000
170A177ASP -1-0.831-0.92637.8990.0260.0260.0000.0000.0000.000
171A178PRO 00.0160.00537.3030.0010.0010.0000.0000.0000.000
172A179GLU -1-0.866-0.91936.6950.0210.0210.0000.0000.0000.000
173A180TYR 0-0.104-0.05530.7460.0040.0040.0000.0000.0000.000
174A181PHE 0-0.012-0.01825.2430.0000.0000.0000.0000.0000.000
175A182ASP -1-0.828-0.90927.3600.0730.0730.0000.0000.0000.000
176A183PRO 0-0.067-0.04723.3360.0000.0000.0000.0000.0000.000
177A184LYS 10.8090.89422.943-0.080-0.0800.0000.0000.0000.000
178A185ASP -1-0.778-0.86424.0340.0550.0550.0000.0000.0000.000
179A186VAL 0-0.077-0.03121.019-0.005-0.0050.0000.0000.0000.000
180A187SER 0-0.016-0.01120.5230.0170.0170.0000.0000.0000.000
181A188PHE -1-0.959-0.97616.5910.0130.0130.0000.0000.0000.000