Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2JYGR

Calculation Name: 4Y5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VEZ3

Base Structure: X-ray

Registration Date: 2023-09-20

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646363.261213
FMO2-HF: Nuclear repulsion 2559052.073954
FMO2-HF: Total energy -87311.187259
FMO2-MP2: Total energy -87567.14185


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:592:ILE)


Summations of interaction energy for fragment #1(A:592:ILE)
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.
-9.452-3.314.334-2.919-7.557-0.015
Interaction energy analysis for fragmet #1(A:592:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / 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].
3A594PRO00.0610.0463.686-0.2681.376-0.010-0.678-0.9550.003
4A595ALA00.049-0.0095.9590.4110.4110.0000.0000.0000.000
5A596GLU-1-0.867-0.9328.197-0.220-0.2200.0000.0000.0000.000
6A597ILE00.0180.0177.3960.0890.0890.0000.0000.0000.000
7A598LEU0-0.051-0.0224.856-0.023-0.0230.0000.0000.0000.000
8A599ASN00.0060.0038.9740.0950.0950.0000.0000.0000.000
9A600GLY00.0440.02212.463-0.008-0.0080.0000.0000.0000.000
10A601LEU0-0.016-0.0218.5900.0010.0010.0000.0000.0000.000
11A602VAL0-0.076-0.04012.8700.0180.0180.0000.0000.0000.000
12A603ASP-1-0.841-0.89215.2640.0710.0710.0000.0000.0000.000
13A604SER00.0220.01317.914-0.003-0.0030.0000.0000.0000.000
14A605ASN00.015-0.01521.439-0.009-0.0090.0000.0000.0000.000
15A606TRP00.048-0.00120.2580.0020.0020.0000.0000.0000.000
16A607LYS10.9450.97120.288-0.012-0.0120.0000.0000.0000.000
17A608ASN0-0.0080.00117.536-0.038-0.0380.0000.0000.0000.000
18A609ARG10.7860.92015.622-0.162-0.1620.0000.0000.0000.000
19A610LEU0-0.030-0.00815.5530.0010.0010.0000.0000.0000.000
20A611ALA00.0380.03416.632-0.019-0.0190.0000.0000.0000.000
21A612ALA0-0.005-0.00811.912-0.043-0.0430.0000.0000.0000.000
22A613VAL0-0.023-0.01611.584-0.035-0.0350.0000.0000.0000.000
23A614GLU-1-0.886-0.95712.561-0.126-0.1260.0000.0000.0000.000
24A615GLN0-0.019-0.00210.589-0.066-0.0660.0000.0000.0000.000
25A616LEU0-0.021-0.0135.968-0.040-0.0400.0000.0000.0000.000
26A617LEU0-0.056-0.0429.147-0.079-0.0790.0000.0000.0000.000
27A618GLY0-0.024-0.00811.719-0.013-0.0130.0000.0000.0000.000
28A619GLU-1-0.897-0.9607.579-1.228-1.2280.0000.0000.0000.000
29A620ILE0-0.061-0.0206.517-0.153-0.1530.0000.0000.0000.000
30A621SER00.003-0.0038.1880.0200.0200.0000.0000.0000.000
31A622GLY0-0.0120.0138.7660.0930.0930.0000.0000.0000.000
32A623PHE0-0.0010.0072.835-2.557-0.6991.298-0.963-2.194-0.015
33A624ASP-1-0.828-0.9305.602-0.195-0.1950.0000.0000.0000.000
34A625ALA00.016-0.0057.0530.1240.1240.0000.0000.0000.000
35A626LYS10.8690.9309.4950.2770.2770.0000.0000.0000.000
36A627GLN00.0290.0352.518-2.213-0.8060.392-0.670-1.129-0.003
37A628ALA00.001-0.0117.3610.0600.0600.0000.0000.0000.000
38A629GLY00.0090.0037.4160.1010.1010.0000.0000.0000.000
39A630ILE00.0240.0202.610-0.0420.0441.248-0.224-1.1100.000
40A631SER00.0810.0344.9250.1360.197-0.0010.000-0.0600.000
41A632GLN0-0.035-0.0177.5840.0770.0770.0000.0000.0000.000
42A633ILE0-0.006-0.0022.399-0.637-0.1681.070-0.238-1.3010.000
43A634LEU00.0220.0192.830-0.3740.2250.338-0.142-0.7950.000
44A635ILE00.0310.0184.734-0.019-0.001-0.001-0.004-0.0130.000
45A636ARG10.9290.9547.298-0.812-0.8120.0000.0000.0000.000
46A637THR0-0.054-0.0195.0470.2360.2360.0000.0000.0000.000
47A638ILE00.0120.0127.650-0.108-0.1080.0000.0000.0000.000
48A639SER0-0.076-0.04110.661-0.047-0.0470.0000.0000.0000.000
49A640GLY0-0.013-0.00311.386-0.045-0.0450.0000.0000.0000.000
50A641ARG10.8420.9288.493-1.032-1.0320.0000.0000.0000.000
51A642LYS10.9580.98213.726-0.376-0.3760.0000.0000.0000.000
52A643PRO00.0330.00216.4000.0210.0210.0000.0000.0000.000
53A644GLY00.0190.02414.859-0.011-0.0110.0000.0000.0000.000
54A645LEU00.0540.01814.953-0.033-0.0330.0000.0000.0000.000
55A646LYS10.9150.95417.821-0.235-0.2350.0000.0000.0000.000
56A647GLU-1-0.799-0.90818.1580.1430.1430.0000.0000.0000.000
57A648MET00.0210.02520.619-0.015-0.0150.0000.0000.0000.000
58A649ASN0-0.0050.00021.920-0.020-0.0200.0000.0000.0000.000
59A650PHE00.0850.02622.0520.0040.0040.0000.0000.0000.000
60A651GLN00.0160.01921.4350.0030.0030.0000.0000.0000.000
61A652VAL00.0050.00117.182-0.007-0.0070.0000.0000.0000.000
62A653LEU0-0.011-0.00917.5650.0080.0080.0000.0000.0000.000
63A654LYS10.8790.94718.1250.0280.0280.0000.0000.0000.000
64A655PHE00.0470.01216.147-0.003-0.0030.0000.0000.0000.000
65A656LYS10.8410.92913.746-0.243-0.2430.0000.0000.0000.000
66A657LEU0-0.025-0.01313.8100.0130.0130.0000.0000.0000.000
67A658ASP-1-0.774-0.88015.571-0.028-0.0280.0000.0000.0000.000
68A659ILE0-0.0050.0329.313-0.012-0.0120.0000.0000.0000.000
69A660ILE0-0.031-0.01911.335-0.008-0.0080.0000.0000.0000.000
70A661ARG10.8500.92012.4570.0570.0570.0000.0000.0000.000
71A662SER00.009-0.02611.739-0.011-0.0110.0000.0000.0000.000
72A663VAL0-0.049-0.0087.758-0.032-0.0320.0000.0000.0000.000
73A664ALA0-0.058-0.03510.407-0.004-0.0040.0000.0000.0000.000
74A665GLU-1-0.855-0.92313.483-0.089-0.0890.0000.0000.0000.000
75A666ASN0-0.044-0.02711.018-0.025-0.0250.0000.0000.0000.000
76A667TYR0-0.067-0.0377.484-0.056-0.0560.0000.0000.0000.000
77A668PRO0-0.009-0.00110.6130.0380.0380.0000.0000.0000.000
78A669LEU00.0090.01811.6950.0450.0450.0000.0000.0000.000
79A670THR00.004-0.00513.420-0.002-0.0020.0000.0000.0000.000
80A671THR00.0790.01715.4260.0130.0130.0000.0000.0000.000
81A672THR00.0210.01915.3850.0010.0010.0000.0000.0000.000
82A673THR00.000-0.00710.8790.0550.0550.0000.0000.0000.000
83A674VAL00.0020.01513.7800.0070.0070.0000.0000.0000.000
84A675ASP-1-0.837-0.87116.6090.1560.1560.0000.0000.0000.000
85A676LEU0-0.084-0.03113.0190.0070.0070.0000.0000.0000.000
86A677VAL00.0350.01013.5960.0060.0060.0000.0000.0000.000
87A678ILE00.0100.00916.836-0.020-0.0200.0000.0000.0000.000
88A679ASN00.0440.01519.655-0.019-0.0190.0000.0000.0000.000
89A680GLU-1-0.893-0.94718.5070.2260.2260.0000.0000.0000.000
90A681ILE0-0.033-0.02016.816-0.013-0.0130.0000.0000.0000.000
91A682ILE00.0230.00720.807-0.015-0.0150.0000.0000.0000.000
92A683GLU-1-0.934-0.97224.1870.1180.1180.0000.0000.0000.000
93A684LYS10.8320.92521.216-0.137-0.1370.0000.0000.0000.000
94A685LEU00.0190.01824.659-0.009-0.0090.0000.0000.0000.000
95A686ALA0-0.031-0.01226.853-0.007-0.0070.0000.0000.0000.000
96A687ASP-1-0.907-0.94125.9570.0570.0570.0000.0000.0000.000
97A688ALA00.013-0.00528.231-0.005-0.0050.0000.0000.0000.000
98A689LYS10.8760.93826.974-0.027-0.0270.0000.0000.0000.000
99A690ASN0-0.021-0.03322.864-0.014-0.0140.0000.0000.0000.000
100A691GLY00.0440.04823.7770.0030.0030.0000.0000.0000.000
101A692ALA0-0.004-0.01325.2320.0020.0020.0000.0000.0000.000
102A693ALA00.0460.02520.586-0.003-0.0030.0000.0000.0000.000
103A694ALA00.0030.00320.5570.0040.0040.0000.0000.0000.000
104A695ALA0-0.006-0.01121.5920.0050.0050.0000.0000.0000.000
105A696ASP-1-0.891-0.95121.092-0.004-0.0040.0000.0000.0000.000
106A697VAL0-0.056-0.01716.675-0.004-0.0040.0000.0000.0000.000
107A698LEU0-0.0170.00418.8290.0030.0030.0000.0000.0000.000
108A699SER00.0130.00221.2750.0010.0010.0000.0000.0000.000
109A700ALA00.0490.03417.181-0.005-0.0050.0000.0000.0000.000
110A701PHE00.011-0.01514.3970.0050.0050.0000.0000.0000.000
111A702ALA0-0.034-0.00818.5250.0020.0020.0000.0000.0000.000
112A703GLU-1-0.850-0.93120.384-0.028-0.0280.0000.0000.0000.000
113A704ALA0-0.0110.01416.115-0.005-0.0050.0000.0000.0000.000
114A705THR0-0.079-0.03717.7730.0110.0110.0000.0000.0000.000
115A706LYS10.9280.93020.065-0.034-0.0340.0000.0000.0000.000
116A707LEU00.0430.03423.7430.0080.0080.0000.0000.0000.000
117A708GLU-1-0.849-0.94025.9570.0480.0480.0000.0000.0000.000
118A709TYR0-0.088-0.09620.8590.0020.0020.0000.0000.0000.000
119A710VAL0-0.0030.00421.4050.0080.0080.0000.0000.0000.000
120A711VAL00.0380.01424.0680.0040.0040.0000.0000.0000.000
121A712GLY00.0280.02627.6990.0010.0010.0000.0000.0000.000
122A713LYS10.8920.94522.329-0.126-0.1260.0000.0000.0000.000
123A714VAL0-0.004-0.00424.7670.0040.0040.0000.0000.0000.000
124A715LEU00.001-0.00726.9050.0000.0000.0000.0000.0000.000
125A716SER0-0.0170.00128.6000.0000.0000.0000.0000.0000.000
126A717PHE0-0.004-0.00426.6330.0000.0000.0000.0000.0000.000
127A718ALA0-0.020-0.02028.7180.0000.0000.0000.0000.0000.000
128A719PHE0-0.041-0.02230.870-0.003-0.0030.0000.0000.0000.000
129A720GLU-1-0.956-0.95929.4830.0960.0960.0000.0000.0000.000
130A721GLN0-0.0110.00329.499-0.002-0.0020.0000.0000.0000.000
131A722LYS10.9560.96131.879-0.072-0.0720.0000.0000.0000.000
132A723SER0-0.0100.00032.506-0.007-0.0070.0000.0000.0000.000
133A724PRO00.009-0.01834.0010.0000.0000.0000.0000.0000.000
134A725LYS10.9690.99133.225-0.035-0.0350.0000.0000.0000.000
135A726VAL00.0670.03928.964-0.003-0.0030.0000.0000.0000.000
136A727GLN00.0010.00531.1600.0000.0000.0000.0000.0000.000
137A728SER0-0.043-0.01533.524-0.003-0.0030.0000.0000.0000.000
138A729GLU-1-0.899-0.95530.1080.0280.0280.0000.0000.0000.000
139A730ALA00.0050.01029.371-0.002-0.0020.0000.0000.0000.000
140A731PHE0-0.010-0.01230.375-0.002-0.0020.0000.0000.0000.000
141A732ASN0-0.015-0.01432.382-0.004-0.0040.0000.0000.0000.000
142A733TRP00.002-0.00524.245-0.001-0.0010.0000.0000.0000.000
143A734VAL00.0390.02329.527-0.003-0.0030.0000.0000.0000.000
144A735ASN00.0330.03030.779-0.003-0.0030.0000.0000.0000.000
145A736ARG10.9160.95126.651-0.011-0.0110.0000.0000.0000.000
146A737SER00.011-0.00627.765-0.004-0.0040.0000.0000.0000.000
147A738ILE0-0.004-0.00129.551-0.003-0.0030.0000.0000.0000.000
148A739ILE0-0.036-0.01032.618-0.003-0.0030.0000.0000.0000.000
149A740GLU-1-0.899-0.95227.667-0.005-0.0050.0000.0000.0000.000
150A741PHE00.0280.01223.880-0.004-0.0040.0000.0000.0000.000
151A742GLY00.0110.02329.860-0.002-0.0020.0000.0000.0000.000
152A743PHE0-0.001-0.01532.3340.0030.0030.0000.0000.0000.000
153A744GLN0-0.090-0.03829.9100.0020.0020.0000.0000.0000.000
154A745LEU0-0.005-0.01330.0050.0040.0040.0000.0000.0000.000
155A746GLN00.0190.00633.037-0.004-0.0040.0000.0000.0000.000
156A747PRO00.0050.00235.4800.0020.0020.0000.0000.0000.000
157A748LYS10.9520.97238.518-0.026-0.0260.0000.0000.0000.000
158A749THR00.0800.04334.331-0.001-0.0010.0000.0000.0000.000
159A750LEU00.0640.04533.6920.0010.0010.0000.0000.0000.000
160A751ILE0-0.029-0.02336.5130.0000.0000.0000.0000.0000.000
161A752GLU-1-0.958-0.98438.9170.0390.0390.0000.0000.0000.000
162A753ASP-1-0.896-0.95334.2600.0500.0500.0000.0000.0000.000
163A754VAL00.003-0.02336.9470.0000.0000.0000.0000.0000.000
164A755ARG10.8420.92538.904-0.029-0.0290.0000.0000.0000.000
165A756LYS10.9190.97036.579-0.052-0.0520.0000.0000.0000.000
166A757GLY00.0080.00739.0960.0000.0000.0000.0000.0000.000
167A758VAL0-0.006-0.01639.838-0.001-0.0010.0000.0000.0000.000
168A759GLN0-0.077-0.04543.1760.0000.0000.0000.0000.0000.000
169A760SER00.0210.03840.9410.0020.0020.0000.0000.0000.000
170A761THR00.015-0.01143.203-0.002-0.0020.0000.0000.0000.000
171A762ASN00.0160.00540.747-0.003-0.0030.0000.0000.0000.000
172A763PRO00.0450.00842.5600.0000.0000.0000.0000.0000.000
173A764THR00.0060.00238.290-0.002-0.0020.0000.0000.0000.000
174A765VAL0-0.028-0.01237.228-0.001-0.0010.0000.0000.0000.000
175A766ARG10.9120.98539.264-0.027-0.0270.0000.0000.0000.000
176A767ALA0-0.016-0.00741.754-0.001-0.0010.0000.0000.0000.000
177A768SER00.0190.01236.5650.0000.0000.0000.0000.0000.000
178A769ALA00.0250.01538.143-0.001-0.0010.0000.0000.0000.000
179A770ILE0-0.021-0.02839.364-0.001-0.0010.0000.0000.0000.000
180A771GLN0-0.006-0.00939.5660.0000.0000.0000.0000.0000.000
181A772MET00.0000.01634.872-0.001-0.0010.0000.0000.0000.000
182A773VAL0-0.035-0.02038.499-0.001-0.0010.0000.0000.0000.000
183A774GLY00.0410.02141.610-0.001-0.0010.0000.0000.0000.000
184A775THR00.005-0.00236.328-0.003-0.0030.0000.0000.0000.000
185A776MET0-0.002-0.00737.781-0.001-0.0010.0000.0000.0000.000
186A777SER0-0.052-0.02739.841-0.001-0.0010.0000.0000.0000.000
187A778MET00.0080.01539.134-0.001-0.0010.0000.0000.0000.000
188A779TYR0-0.051-0.03236.022-0.001-0.0010.0000.0000.0000.000
189A780MET0-0.059-0.02239.5660.0010.0010.0000.0000.0000.000
190A781GLY00.0260.03243.0610.0000.0000.0000.0000.0000.000
191A782LYS11.0020.96246.528-0.004-0.0040.0000.0000.0000.000
192A783ALA00.0250.02048.1380.0010.0010.0000.0000.0000.000
193A784LEU00.0090.01442.5710.0010.0010.0000.0000.0000.000
194A785MET00.0220.01346.4310.0020.0020.0000.0000.0000.000
195A786MET00.0200.01148.9930.0000.0000.0000.0000.0000.000
196A787PHE0-0.093-0.02545.9060.0010.0010.0000.0000.0000.000
197A788PHE00.0570.00742.7480.0020.0020.0000.0000.0000.000
198A789ASP-1-0.819-0.90548.7910.0150.0150.0000.0000.0000.000
199A790SER0-0.039-0.01151.736-0.001-0.0010.0000.0000.0000.000
200A791GLU-1-0.875-0.91847.9150.0270.0270.0000.0000.0000.000
201A792LYS10.9690.96651.655-0.025-0.0250.0000.0000.0000.000
202A793PRO00.0570.02553.1690.0000.0000.0000.0000.0000.000
203A794ALA00.0050.01053.459-0.001-0.0010.0000.0000.0000.000
204A795LEU00.0050.00746.648-0.001-0.0010.0000.0000.0000.000
205A796LYS10.8890.93549.915-0.016-0.0160.0000.0000.0000.000
206A797SER0-0.021-0.00651.701-0.001-0.0010.0000.0000.0000.000
207A798GLN00.0030.00046.5630.0000.0000.0000.0000.0000.000
208A799ILE0-0.001-0.01846.165-0.001-0.0010.0000.0000.0000.000
209A800GLN0-0.033-0.03148.1210.0000.0000.0000.0000.0000.000
210A801VAL00.0160.02049.717-0.001-0.0010.0000.0000.0000.000
211A802GLU-1-0.950-0.97943.5780.0100.0100.0000.0000.0000.000
212A803PHE00.000-0.00946.045-0.001-0.0010.0000.0000.0000.000
213A804ASP-1-0.885-0.93547.6840.0070.0070.0000.0000.0000.000
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