FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 9Y6R2

Calculation Name: 1J6R-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J6R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYA6

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 199
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2194350.987424
FMO2-HF: Nuclear repulsion 2116925.612614
FMO2-HF: Total energy -77425.37481
FMO2-MP2: Total energy -77654.219075


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:0:ACE )


Summations of interaction energy for fragment #1(A:0: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.
0.5381.362-0.005-0.381-0.439-0.001
Interaction energy analysis for fragmet #1(A:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / 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].
3A2HIS 00.0010.0143.8590.9601.784-0.005-0.381-0.439-0.001
4A3MET 0-0.027-0.0036.3370.0300.0300.0000.0000.0000.000
5A4PRO 0-0.0290.0029.6550.1250.1250.0000.0000.0000.000
6A5LYS 10.9430.96612.4230.2130.2130.0000.0000.0000.000
7A6VAL 0-0.044-0.01415.8010.0290.0290.0000.0000.0000.000
8A7GLU -1-0.921-0.95619.246-0.108-0.1080.0000.0000.0000.000
9A8ILE 0-0.064-0.03522.1870.0100.0100.0000.0000.0000.000
10A9ALA 00.0470.01825.4890.0000.0000.0000.0000.0000.000
11A10PRO 00.0570.01328.856-0.001-0.0010.0000.0000.0000.000
12A11SER 00.0300.01331.0130.0000.0000.0000.0000.0000.000
13A12GLU -1-0.973-0.97129.759-0.041-0.0410.0000.0000.0000.000
14A13ILE 0-0.086-0.04327.947-0.003-0.0030.0000.0000.0000.000
15A14LYS 10.9460.98131.5530.0500.0500.0000.0000.0000.000
16A15ILE 00.0350.01134.199-0.003-0.0030.0000.0000.0000.000
17A16PRO 0-0.080-0.05035.5630.0050.0050.0000.0000.0000.000
18A17ASP -1-0.771-0.88238.809-0.040-0.0400.0000.0000.0000.000
19A18ASN 0-0.032-0.03342.1850.0010.0010.0000.0000.0000.000
20A19VAL 0-0.0380.00236.5900.0000.0000.0000.0000.0000.000
21A20LEU 00.0530.01938.766-0.001-0.0010.0000.0000.0000.000
22A21LYS 10.8870.94740.4560.0360.0360.0000.0000.0000.000
23A22ALA 0-0.019-0.01142.1940.0010.0010.0000.0000.0000.000
24A23LYS 10.8780.96036.6510.0670.0670.0000.0000.0000.000
25A24LEU 0-0.063-0.03040.4860.0000.0000.0000.0000.0000.000
26A25GLY 00.0220.01543.5590.0020.0020.0000.0000.0000.000
27A26PHE 0-0.006-0.00446.3340.0020.0020.0000.0000.0000.000
28A27GLY 00.010-0.00446.5020.0000.0000.0000.0000.0000.000
29A28GLY 0-0.039-0.01347.3860.0010.0010.0000.0000.0000.000
30A29ALA 00.0140.01649.4680.0010.0010.0000.0000.0000.000
31A30GLU -1-0.933-0.97049.725-0.027-0.0270.0000.0000.0000.000
32A31GLU -1-0.899-0.96549.295-0.031-0.0310.0000.0000.0000.000
33A32ILE 0-0.088-0.02647.036-0.001-0.0010.0000.0000.0000.000
34A33PRO 00.0130.01249.8700.0010.0010.0000.0000.0000.000
35A34GLU -1-0.916-0.97252.275-0.023-0.0230.0000.0000.0000.000
36A35GLU -1-0.967-0.98753.923-0.027-0.0270.0000.0000.0000.000
37A36PHE 00.001-0.00449.309-0.001-0.0010.0000.0000.0000.000
38A37ARG 10.9900.99848.7750.0240.0240.0000.0000.0000.000
39A38LYS 10.9720.97147.9590.0230.0230.0000.0000.0000.000
40A39THR 00.0110.01546.5950.0000.0000.0000.0000.0000.000
41A40VAL 00.0450.03743.425-0.002-0.0020.0000.0000.0000.000
42A41ASN 0-0.039-0.02543.2480.0000.0000.0000.0000.0000.000
43A42ARG 10.9670.99942.8660.0310.0310.0000.0000.0000.000
44A43ALA 00.0390.00841.099-0.001-0.0010.0000.0000.0000.000
45A44TYR 0-0.012-0.01736.186-0.002-0.0020.0000.0000.0000.000
46A45GLU -1-0.912-0.97238.085-0.036-0.0360.0000.0000.0000.000
47A46GLU -1-0.923-0.97138.400-0.038-0.0380.0000.0000.0000.000
48A47LEU 0-0.044-0.02632.994-0.002-0.0020.0000.0000.0000.000
49A48LEU 0-0.053-0.02933.755-0.004-0.0040.0000.0000.0000.000
50A49ASP -1-0.941-0.95933.517-0.042-0.0420.0000.0000.0000.000
51A50ALA 0-0.019-0.01032.805-0.001-0.0010.0000.0000.0000.000
52A51ALA 0-0.070-0.03129.875-0.006-0.0060.0000.0000.0000.000
53A52LYS 10.9120.94125.3350.0680.0680.0000.0000.0000.000
54A53PRO 0-0.030-0.01224.889-0.011-0.0110.0000.0000.0000.000
55A54VAL 00.0390.03218.9800.0010.0010.0000.0000.0000.000
56A55VAL 0-0.050-0.02619.430-0.007-0.0070.0000.0000.0000.000
57A56LEU 00.0390.01914.2380.0010.0010.0000.0000.0000.000
58A57TRP 0-0.042-0.02614.2240.0220.0220.0000.0000.0000.000
59A58ARG 11.0231.0047.5621.2561.2560.0000.0000.0000.000
60A59ASP -1-0.840-0.88411.138-0.250-0.2500.0000.0000.0000.000
61A60PHE 00.0080.00010.611-0.161-0.1610.0000.0000.0000.000
62A61GLU -1-0.927-0.97511.978-0.130-0.1300.0000.0000.0000.000
63A62VAL 0-0.058-0.03813.856-0.019-0.0190.0000.0000.0000.000
64A63ASP -1-0.974-0.98716.746-0.082-0.0820.0000.0000.0000.000
65A64GLY 0-0.0180.00919.8670.0090.0090.0000.0000.0000.000
66A65SER 0-0.040-0.01718.7050.0050.0050.0000.0000.0000.000
67A66LEU 00.0250.00420.663-0.010-0.0100.0000.0000.0000.000
68A67SER 0-0.074-0.04418.9310.0110.0110.0000.0000.0000.000
69A68PHE 00.015-0.00213.6170.0050.0050.0000.0000.0000.000
70A69ASP -1-0.951-0.97510.380-0.738-0.7380.0000.0000.0000.000
71A70ASP -1-0.851-0.90312.967-0.272-0.2720.0000.0000.0000.000
72A71MET 0-0.055-0.01915.7490.0660.0660.0000.0000.0000.000
73A72ARG 10.9790.96718.4300.1510.1510.0000.0000.0000.000
74A73LEU 0-0.037-0.01120.4210.0150.0150.0000.0000.0000.000
75A74THR 0-0.052-0.03523.4480.0100.0100.0000.0000.0000.000
76A75GLY 00.0180.00727.0280.0080.0080.0000.0000.0000.000
77A76GLU -1-0.886-0.94929.680-0.076-0.0760.0000.0000.0000.000
78A77LEU 0-0.063-0.03729.1720.0000.0000.0000.0000.0000.000
79A78ALA 00.0170.00025.683-0.002-0.0020.0000.0000.0000.000
80A79THR 00.0400.02426.937-0.005-0.0050.0000.0000.0000.000
81A80LYS 10.9341.00428.8360.0720.0720.0000.0000.0000.000
82A81HIS 0-0.039-0.03327.5870.0030.0030.0000.0000.0000.000
83A82LEU 00.0180.00122.304-0.001-0.0010.0000.0000.0000.000
84A83SER 0-0.060-0.02423.739-0.007-0.0070.0000.0000.0000.000
85A84GLY 0-0.0070.00125.0080.0060.0060.0000.0000.0000.000
86A85SER 0-0.032-0.03221.7070.0020.0020.0000.0000.0000.000
87A86LYS 11.0331.02017.0280.0920.0920.0000.0000.0000.000
88A87ILE 00.008-0.00514.707-0.018-0.0180.0000.0000.0000.000
89A88ILE 0-0.0120.00316.3020.0300.0300.0000.0000.0000.000
90A89THR 0-0.036-0.02315.395-0.040-0.0400.0000.0000.0000.000
91A90VAL 00.0080.00914.3130.0380.0380.0000.0000.0000.000
92A91PHE 0-0.007-0.02915.936-0.031-0.0310.0000.0000.0000.000
93A92LEU 00.0240.01317.4550.0070.0070.0000.0000.0000.000
94A93ALA 0-0.0070.00419.2880.0020.0020.0000.0000.0000.000
95A94THR 00.022-0.01521.5520.0090.0090.0000.0000.0000.000
96A95LEU 00.0190.00923.9640.0050.0050.0000.0000.0000.000
97A96GLY 00.0630.04325.1070.0080.0080.0000.0000.0000.000
98A97LYS 10.9690.96226.0290.0770.0770.0000.0000.0000.000
99A98LYN 00.0390.02528.2650.0030.0030.0000.0000.0000.000
100A99VAL 00.0190.02230.3370.0050.0050.0000.0000.0000.000
101A100ASP -1-0.836-0.92330.350-0.086-0.0860.0000.0000.0000.000
102A101GLU -1-0.937-0.97531.549-0.058-0.0580.0000.0000.0000.000
103A102LYS 10.9010.96934.6380.0480.0480.0000.0000.0000.000
104A103ILE 0-0.039-0.01834.6150.0020.0020.0000.0000.0000.000
105A104GLU -1-0.894-0.95137.030-0.048-0.0480.0000.0000.0000.000
106A105GLU -1-0.940-0.97238.633-0.036-0.0360.0000.0000.0000.000
107A106TYR 0-0.050-0.04040.6060.0040.0040.0000.0000.0000.000
108A107PHE 00.0190.01739.4750.0010.0010.0000.0000.0000.000
109A108ARG 10.8910.95338.5930.0470.0470.0000.0000.0000.000
110A109LYS 10.8430.93444.0520.0350.0350.0000.0000.0000.000
111A110GLY 00.0250.02546.6530.0020.0020.0000.0000.0000.000
112A111GLU -1-0.993-0.99445.872-0.030-0.0300.0000.0000.0000.000
113A112ASP -1-0.832-0.94245.159-0.040-0.0400.0000.0000.0000.000
114A113LEU 0-0.036-0.01244.933-0.002-0.0020.0000.0000.0000.000
115A114LEU 00.0290.01242.887-0.002-0.0020.0000.0000.0000.000
116A115ALA 00.0410.01941.024-0.002-0.0020.0000.0000.0000.000
117A116PHE 0-0.0300.00240.261-0.004-0.0040.0000.0000.0000.000
118A117PHE 00.009-0.02040.999-0.002-0.0020.0000.0000.0000.000
119A118ILE 0-0.0070.00836.757-0.003-0.0030.0000.0000.0000.000
120A119ASP -1-0.813-0.90336.316-0.072-0.0720.0000.0000.0000.000
121A120GLY 00.0170.00635.947-0.005-0.0050.0000.0000.0000.000
122A121ILE 0-0.003-0.01935.870-0.002-0.0020.0000.0000.0000.000
123A122ALA 00.0050.01432.686-0.003-0.0030.0000.0000.0000.000
124A123SER 0-0.029-0.02931.837-0.009-0.0090.0000.0000.0000.000
125A124GLU -1-0.879-0.95031.832-0.077-0.0770.0000.0000.0000.000
126A125MET 0-0.0230.00030.606-0.004-0.0040.0000.0000.0000.000
127A126VAL 00.0260.00925.969-0.004-0.0040.0000.0000.0000.000
128A127GLU -1-0.804-0.87827.015-0.115-0.1150.0000.0000.0000.000
129A128TYR 0-0.030-0.04628.173-0.003-0.0030.0000.0000.0000.000
130A129ALA 00.0250.02625.4400.0010.0010.0000.0000.0000.000
131A130LEU 00.0210.01522.160-0.006-0.0060.0000.0000.0000.000
132A131ARG 10.7710.87024.2250.0830.0830.0000.0000.0000.000
133A132LYS 10.9500.98425.6180.0710.0710.0000.0000.0000.000
134A133VAL 00.0340.02319.6370.0040.0040.0000.0000.0000.000
135A134ASP -1-0.843-0.90621.980-0.133-0.1330.0000.0000.0000.000
136A135ALA 00.019-0.00423.2780.0030.0030.0000.0000.0000.000
137A136GLU -1-0.914-0.94922.254-0.069-0.0690.0000.0000.0000.000
138A137LEU 0-0.069-0.03417.6310.0040.0040.0000.0000.0000.000
139A138ARG 10.7620.86121.0670.1190.1190.0000.0000.0000.000
140A139MET 0-0.030-0.00724.1130.0090.0090.0000.0000.0000.000
141A140LYS 10.9290.97017.0070.1110.1110.0000.0000.0000.000
142A141ARG 10.7820.89415.0450.2190.2190.0000.0000.0000.000
143A142SER 00.0870.03721.9520.0000.0000.0000.0000.0000.000
144A143ASN 0-0.089-0.03320.2250.0010.0010.0000.0000.0000.000
145A144LEU 0-0.050-0.02519.202-0.005-0.0050.0000.0000.0000.000
146A145GLU -1-0.891-0.93423.882-0.065-0.0650.0000.0000.0000.000
147A146GLY 0-0.025-0.01223.829-0.010-0.0100.0000.0000.0000.000
148A147SER 0-0.060-0.06524.3570.0050.0050.0000.0000.0000.000
149A148PHE 00.0310.00426.2750.0010.0010.0000.0000.0000.000
150A149ARG 10.9361.02024.2350.1100.1100.0000.0000.0000.000
151A150ILE 0-0.023-0.01024.8290.0110.0110.0000.0000.0000.000
152A151SER 00.0590.01324.574-0.013-0.0130.0000.0000.0000.000
153A152PRO 0-0.027-0.02523.2940.0100.0100.0000.0000.0000.000
154A153GLY 00.014-0.01026.1640.0050.0050.0000.0000.0000.000
155A154TYR 0-0.047-0.00629.3740.0100.0100.0000.0000.0000.000
156A155GLY 00.0140.00030.692-0.004-0.0040.0000.0000.0000.000
157A156ASP -1-0.823-0.90531.422-0.091-0.0910.0000.0000.0000.000
158A157LEU 0-0.063-0.01624.694-0.005-0.0050.0000.0000.0000.000
159A158PRO 00.0370.01126.1700.0030.0030.0000.0000.0000.000
160A159LEU 00.0900.05226.167-0.011-0.0110.0000.0000.0000.000
161A160SER 0-0.028-0.01325.466-0.010-0.0100.0000.0000.0000.000
162A161LEU 0-0.017-0.01821.004-0.014-0.0140.0000.0000.0000.000
163A162ASN 00.0240.01620.817-0.034-0.0340.0000.0000.0000.000
164A163LYS 10.9820.98620.8410.1590.1590.0000.0000.0000.000
165A164LYS 10.8600.93917.6830.2270.2270.0000.0000.0000.000
166A165ILE 00.023-0.00116.377-0.044-0.0440.0000.0000.0000.000
167A166ALA 00.0130.00516.164-0.032-0.0320.0000.0000.0000.000
168A167GLU -1-0.867-0.93014.651-0.287-0.2870.0000.0000.0000.000
169A168ILE 0-0.053-0.02211.075-0.061-0.0610.0000.0000.0000.000
170A169PHE 0-0.030-0.02711.453-0.108-0.1080.0000.0000.0000.000
171A170LYS 10.8880.95313.7360.2780.2780.0000.0000.0000.000
172A171GLU -1-0.914-0.95011.053-0.222-0.2220.0000.0000.0000.000
173A172GLU -1-0.981-0.9899.573-0.460-0.4600.0000.0000.0000.000
174A173VAL 0-0.039-0.03913.6180.0510.0510.0000.0000.0000.000
175A174ASP -1-0.924-0.94717.302-0.133-0.1330.0000.0000.0000.000
176A175VAL 0-0.035-0.02219.1420.0100.0100.0000.0000.0000.000
177A176ASN 0-0.044-0.02319.908-0.019-0.0190.0000.0000.0000.000
178A177VAL 0-0.010-0.00321.9960.0000.0000.0000.0000.0000.000
179A178ILE 0-0.027-0.00624.5650.0040.0040.0000.0000.0000.000
180A179GLU -1-0.861-0.91726.737-0.095-0.0950.0000.0000.0000.000
181A180ASP -1-0.888-0.95428.154-0.109-0.1090.0000.0000.0000.000
182A181SER 0-0.078-0.03929.8330.0030.0030.0000.0000.0000.000
183A182TYR 0-0.053-0.04825.652-0.005-0.0050.0000.0000.0000.000
184A183VAL 0-0.0020.00726.971-0.007-0.0070.0000.0000.0000.000
185A184LEU 0-0.020-0.00922.352-0.005-0.0050.0000.0000.0000.000
186A185VAL 00.0080.03025.0350.0120.0120.0000.0000.0000.000
187A186PRO 00.059-0.01124.072-0.011-0.0110.0000.0000.0000.000
188A187ARG 10.9360.97326.6040.0690.0690.0000.0000.0000.000
189A188LYS 10.7510.89728.8910.0790.0790.0000.0000.0000.000
190A189THR 00.0120.00322.679-0.006-0.0060.0000.0000.0000.000
191A190ILE 0-0.0140.00624.0840.0050.0050.0000.0000.0000.000
192A191THR 00.0640.02820.771-0.020-0.0200.0000.0000.0000.000
193A192ALA 0-0.056-0.03121.0690.0220.0220.0000.0000.0000.000
194A193PHE 00.0200.02018.416-0.028-0.0280.0000.0000.0000.000
195A194VAL 0-0.016-0.01120.1410.0250.0250.0000.0000.0000.000
196A195GLY 00.0290.02820.010-0.024-0.0240.0000.0000.0000.000
197A196TRP 00.008-0.00418.5020.0320.0320.0000.0000.0000.000
198A197ARG 10.9370.95921.4340.0930.0930.0000.0000.0000.000
199A198NME 00.0460.03123.0810.0050.0050.0000.0000.0000.000