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: 52MJZ

Calculation Name: 1LUF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LUF

Chain ID: A

ChEMBL ID:

UniProt ID: Q62838

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 OptHSide
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 279
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4057585.662735
FMO2-HF: Nuclear repulsion 3942075.762898
FMO2-HF: Total energy -115509.899837
FMO2-MP2: Total energy -115834.193139


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:560:LEU)


Summations of interaction energy for fragment #1(A:560:LEU)
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.
-0.9291.2382.43-1.14-3.458-0.003
Interaction energy analysis for fragmet #1(A:560:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.011
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].
3A562PRO00.0450.0043.821-1.0171.001-0.018-0.746-1.2540.001
4A563LYS10.8850.9545.0080.2970.425-0.001-0.005-0.1220.000
5A564LEU00.015-0.0016.3380.1350.1350.0000.0000.0000.000
6A565LEU0-0.008-0.0042.287-0.690-0.6692.449-0.389-2.082-0.004
7A566SER0-0.103-0.0606.2870.0670.0670.0000.0000.0000.000
8A567LEU0-0.008-0.0049.1730.0430.0430.0000.0000.0000.000
9A568GLU-1-0.808-0.8929.0720.2650.2650.0000.0000.0000.000
10A569TYR00.007-0.02711.182-0.032-0.0320.0000.0000.0000.000
11A570PRO00.0040.00014.3910.0340.0340.0000.0000.0000.000
12A571ARG10.9270.94312.392-0.237-0.2370.0000.0000.0000.000
13A572ASN0-0.049-0.03717.1030.0120.0120.0000.0000.0000.000
14A573ASN0-0.034-0.00519.400-0.004-0.0040.0000.0000.0000.000
15A574ILE0-0.035-0.01317.884-0.004-0.0040.0000.0000.0000.000
16A575GLU-1-0.861-0.90322.0280.0420.0420.0000.0000.0000.000
17A576TYR0-0.045-0.06025.814-0.001-0.0010.0000.0000.0000.000
18A577VAL0-0.034-0.00527.018-0.008-0.0080.0000.0000.0000.000
19A578ARG10.9260.95229.328-0.077-0.0770.0000.0000.0000.000
20A579ASP-1-0.780-0.85527.8840.1170.1170.0000.0000.0000.000
21A580ILE0-0.090-0.03726.548-0.008-0.0080.0000.0000.0000.000
22A581GLY00.0400.01628.075-0.005-0.0050.0000.0000.0000.000
23A582GLU-1-0.951-0.96526.3730.1460.1460.0000.0000.0000.000
24A583GLY00.0480.01924.289-0.007-0.0070.0000.0000.0000.000
25A584ALA0-0.024-0.01422.7720.0000.0000.0000.0000.0000.000
26A585PHE00.0300.01216.941-0.004-0.0040.0000.0000.0000.000
27A586GLY00.0420.01620.4230.0110.0110.0000.0000.0000.000
28A587ARG10.8800.96022.382-0.145-0.1450.0000.0000.0000.000
29A588VAL00.0300.01422.3260.0170.0170.0000.0000.0000.000
30A589PHE0-0.016-0.01421.656-0.013-0.0130.0000.0000.0000.000
31A590GLN00.0330.00324.7420.0050.0050.0000.0000.0000.000
32A591ALA0-0.005-0.01223.8260.0000.0000.0000.0000.0000.000
33A592ARG10.8820.92825.897-0.039-0.0390.0000.0000.0000.000
34A593ALA00.0370.02221.2220.0050.0050.0000.0000.0000.000
35A594PRO00.006-0.00723.231-0.009-0.0090.0000.0000.0000.000
36A595GLY00.0060.01122.300-0.001-0.0010.0000.0000.0000.000
37A596LEU0-0.0350.00017.822-0.009-0.0090.0000.0000.0000.000
38A597LEU0-0.0050.00619.852-0.014-0.0140.0000.0000.0000.000
39A598PRO0-0.014-0.03220.8230.0030.0030.0000.0000.0000.000
40A599TYR0-0.044-0.01423.785-0.002-0.0020.0000.0000.0000.000
41A600GLU-1-0.803-0.87026.3390.0070.0070.0000.0000.0000.000
42A601PRO0-0.036-0.01026.739-0.001-0.0010.0000.0000.0000.000
43A602PHE0-0.019-0.02825.9150.0010.0010.0000.0000.0000.000
44A603THR00.001-0.00623.325-0.003-0.0030.0000.0000.0000.000
45A604MET0-0.0570.00924.8620.0080.0080.0000.0000.0000.000
46A605VAL00.010-0.00721.154-0.002-0.0020.0000.0000.0000.000
47A606ALA0-0.011-0.00123.2940.0000.0000.0000.0000.0000.000
48A607VAL0-0.005-0.01419.1620.0110.0110.0000.0000.0000.000
49A608LYS10.8890.96417.968-0.309-0.3090.0000.0000.0000.000
50A609MET0-0.025-0.02817.8500.0210.0210.0000.0000.0000.000
51A610LEU0-0.047-0.01414.213-0.003-0.0030.0000.0000.0000.000
52A611LYS10.8920.92617.738-0.234-0.2340.0000.0000.0000.000
53A612GLU-1-0.873-0.94117.5210.2510.2510.0000.0000.0000.000
54A613GLU-1-0.906-0.96517.8730.2450.2450.0000.0000.0000.000
55A614ALA0-0.043-0.02017.209-0.006-0.0060.0000.0000.0000.000
56A615SER0-0.042-0.04217.8770.0220.0220.0000.0000.0000.000
57A616ALA00.034-0.00314.4610.0390.0390.0000.0000.0000.000
58A617ASP-1-0.837-0.90814.1070.5390.5390.0000.0000.0000.000
59A618MET0-0.0010.01515.7220.0350.0350.0000.0000.0000.000
60A619GLN0-0.021-0.0209.928-0.132-0.1320.0000.0000.0000.000
61A620ALA00.0020.00410.9030.1150.1150.0000.0000.0000.000
62A621ASP-1-0.796-0.88111.7990.6110.6110.0000.0000.0000.000
63A622PHE0-0.0050.00112.413-0.004-0.0040.0000.0000.0000.000
64A623GLN00.013-0.0076.592-0.142-0.1420.0000.0000.0000.000
65A624ARG10.7960.8969.810-0.501-0.5010.0000.0000.0000.000
66A625GLU-1-0.846-0.94011.2650.2670.2670.0000.0000.0000.000
67A626ALA0-0.0060.00010.533-0.088-0.0880.0000.0000.0000.000
68A627ALA0-0.035-0.0258.548-0.114-0.1140.0000.0000.0000.000
69A628LEU0-0.044-0.01410.263-0.146-0.1460.0000.0000.0000.000
70A629MET00.0090.01013.793-0.078-0.0780.0000.0000.0000.000
71A630ALA0-0.0030.00611.631-0.061-0.0610.0000.0000.0000.000
72A631GLU-1-0.867-0.92811.349-0.198-0.1980.0000.0000.0000.000
73A632PHE0-0.062-0.01915.171-0.029-0.0290.0000.0000.0000.000
74A633ASP-1-0.825-0.90518.695-0.035-0.0350.0000.0000.0000.000
75A634ASN00.0170.00020.864-0.004-0.0040.0000.0000.0000.000
76A635PRO00.0300.01124.5290.0070.0070.0000.0000.0000.000
77A636ASN0-0.048-0.03327.416-0.002-0.0020.0000.0000.0000.000
78A637ILE0-0.034-0.00622.0190.0080.0080.0000.0000.0000.000
79A638VAL0-0.042-0.00921.991-0.008-0.0080.0000.0000.0000.000
80A639LYS10.8630.91018.8200.0340.0340.0000.0000.0000.000
81A640LEU0-0.041-0.01613.0950.0110.0110.0000.0000.0000.000
82A641LEU0-0.027-0.03216.675-0.025-0.0250.0000.0000.0000.000
83A642GLY00.0530.02514.342-0.034-0.0340.0000.0000.0000.000
84A643VAL0-0.064-0.02810.1630.0590.0590.0000.0000.0000.000
85A644CYS0-0.0380.01212.199-0.056-0.0560.0000.0000.0000.000
86A645ALA00.000-0.0287.6390.0630.0630.0000.0000.0000.000
87A646VAL0-0.0140.0086.5010.1380.1380.0000.0000.0000.000
88A647GLY0-0.0060.0039.039-0.076-0.0760.0000.0000.0000.000
89A648LYS10.8350.95111.961-0.356-0.3560.0000.0000.0000.000
90A649PRO00.1120.04614.683-0.033-0.0330.0000.0000.0000.000
91A650MET0-0.027-0.0038.949-0.009-0.0090.0000.0000.0000.000
92A651CYS0-0.066-0.03213.668-0.034-0.0340.0000.0000.0000.000
93A652LEU00.0070.01112.4220.0230.0230.0000.0000.0000.000
94A653LEU00.0080.00015.864-0.016-0.0160.0000.0000.0000.000
95A654PHE00.0360.01017.066-0.006-0.0060.0000.0000.0000.000
96A655GLU-1-0.750-0.84420.5350.0380.0380.0000.0000.0000.000
97A656TYR0-0.0080.00123.4770.0120.0120.0000.0000.0000.000
98A657MET0-0.033-0.00626.673-0.010-0.0100.0000.0000.0000.000
99A658ALA0-0.018-0.04029.4440.0040.0040.0000.0000.0000.000
100A659TYR0-0.074-0.05332.5210.0000.0000.0000.0000.0000.000
101A660GLY00.0220.04132.0320.0000.0000.0000.0000.0000.000
102A661ASP-1-0.770-0.87631.4350.0810.0810.0000.0000.0000.000
103A662LEU0-0.003-0.02632.586-0.005-0.0050.0000.0000.0000.000
104A663ASN0-0.076-0.02934.782-0.005-0.0050.0000.0000.0000.000
105A664GLU-1-0.905-0.95936.2090.0610.0610.0000.0000.0000.000
106A665PHE00.0350.01636.996-0.005-0.0050.0000.0000.0000.000
107A666LEU0-0.035-0.01738.261-0.004-0.0040.0000.0000.0000.000
108A667ARG10.8820.93839.682-0.068-0.0680.0000.0000.0000.000
109A668SER0-0.091-0.03541.586-0.003-0.0030.0000.0000.0000.000
110A669MET0-0.030-0.01142.562-0.003-0.0030.0000.0000.0000.000
111A670SER0-0.012-0.00544.940-0.001-0.0010.0000.0000.0000.000
112A671PRO0-0.055-0.01647.1140.0000.0000.0000.0000.0000.000
113A694PRO0-0.022-0.03249.2910.0000.0000.0000.0000.0000.000
114A695PRO00.0030.01947.8990.0010.0010.0000.0000.0000.000
115A696LEU00.0120.01741.997-0.001-0.0010.0000.0000.0000.000
116A697SER0-0.026-0.04846.3420.0000.0000.0000.0000.0000.000
117A698CYS00.0440.00346.2370.0010.0010.0000.0000.0000.000
118A699ALA00.0010.00145.6560.0010.0010.0000.0000.0000.000
119A700GLU-1-0.775-0.85743.0320.0250.0250.0000.0000.0000.000
120A701GLN00.0110.01341.4940.0000.0000.0000.0000.0000.000
121A702LEU00.0210.00140.8960.0030.0030.0000.0000.0000.000
122A703CYS0-0.0210.00439.5100.0000.0000.0000.0000.0000.000
123A704ILE00.0310.01636.3150.0010.0010.0000.0000.0000.000
124A705ALA00.0250.01235.9690.0030.0030.0000.0000.0000.000
125A706ARG10.9240.96136.144-0.019-0.0190.0000.0000.0000.000
126A707GLN0-0.019-0.01033.062-0.001-0.0010.0000.0000.0000.000
127A708VAL00.0580.03431.4440.0020.0020.0000.0000.0000.000
128A709ALA0-0.007-0.00131.2000.0040.0040.0000.0000.0000.000
129A710ALA0-0.024-0.01431.7210.0000.0000.0000.0000.0000.000
130A711GLY00.0210.01427.814-0.002-0.0020.0000.0000.0000.000
131A712MET00.0090.00326.9740.0060.0060.0000.0000.0000.000
132A713ALA0-0.027-0.01427.9460.0020.0020.0000.0000.0000.000
133A714TYR00.0240.02521.2520.0000.0000.0000.0000.0000.000
134A715LEU00.0140.00221.968-0.001-0.0010.0000.0000.0000.000
135A716SER0-0.010-0.00323.6180.0020.0020.0000.0000.0000.000
136A717GLU-1-0.935-0.94524.0390.0050.0050.0000.0000.0000.000
137A718ARG10.8880.95016.686-0.043-0.0430.0000.0000.0000.000
138A719LYS10.7420.85120.614-0.019-0.0190.0000.0000.0000.000
139A720PHE0-0.008-0.00418.0850.0190.0190.0000.0000.0000.000
140A721VAL0-0.034-0.01821.762-0.013-0.0130.0000.0000.0000.000
141A722HIS0-0.036-0.02622.8860.0200.0200.0000.0000.0000.000
142A723ARG10.8910.93323.067-0.176-0.1760.0000.0000.0000.000
143A724ASP-1-0.762-0.84226.5720.1400.1400.0000.0000.0000.000
144A725LEU00.0080.02128.069-0.003-0.0030.0000.0000.0000.000
145A726ALA00.0690.01129.821-0.004-0.0040.0000.0000.0000.000
146A727THR0-0.057-0.05931.6360.0030.0030.0000.0000.0000.000
147A728ARG10.8380.91431.022-0.108-0.1080.0000.0000.0000.000
148A729ASN0-0.050-0.01227.4240.0050.0050.0000.0000.0000.000
149A730CYS0-0.084-0.02827.8560.0020.0020.0000.0000.0000.000
150A731LEU0-0.002-0.00126.5610.0000.0000.0000.0000.0000.000
151A732VAL00.0170.00430.395-0.005-0.0050.0000.0000.0000.000
152A733GLY00.008-0.00332.3380.0020.0020.0000.0000.0000.000
153A734GLU-1-0.802-0.88433.0410.0260.0260.0000.0000.0000.000
154A735ASN0-0.071-0.05235.567-0.002-0.0020.0000.0000.0000.000
155A736MET0-0.0210.00737.207-0.001-0.0010.0000.0000.0000.000
156A737VAL00.0150.03231.3220.0010.0010.0000.0000.0000.000
157A738VAL0-0.007-0.00932.1020.0040.0040.0000.0000.0000.000
158A739LYS10.8080.89726.077-0.042-0.0420.0000.0000.0000.000
159A740ILE0-0.008-0.00525.4590.0050.0050.0000.0000.0000.000
160A741ALA00.007-0.00423.5370.0000.0000.0000.0000.0000.000
161A742ASP-1-0.789-0.90322.2540.1850.1850.0000.0000.0000.000
162A743PHE0-0.038-0.02021.6510.0240.0240.0000.0000.0000.000
163A744GLY00.0020.01422.7990.0140.0140.0000.0000.0000.000
164A745LEU0-0.014-0.01323.9440.0020.0020.0000.0000.0000.000
165A746SER00.025-0.00627.014-0.011-0.0110.0000.0000.0000.000
166A747ARG10.8440.93426.782-0.178-0.1780.0000.0000.0000.000
167A748ASN0-0.098-0.04829.271-0.011-0.0110.0000.0000.0000.000
168A749ILE00.0270.00330.376-0.007-0.0070.0000.0000.0000.000
169A750TYR0-0.026-0.04632.443-0.008-0.0080.0000.0000.0000.000
170A751SER00.0110.01633.793-0.001-0.0010.0000.0000.0000.000
171A752ALA0-0.017-0.01734.7280.0010.0010.0000.0000.0000.000
172A753ASP-1-0.810-0.89434.5050.0820.0820.0000.0000.0000.000
173A754TYR0-0.084-0.08029.0940.0020.0020.0000.0000.0000.000
174A755TYR0-0.100-0.07334.327-0.003-0.0030.0000.0000.0000.000
175A756LYS10.8840.94033.297-0.105-0.1050.0000.0000.0000.000
176A757ALA00.0580.04135.131-0.002-0.0020.0000.0000.0000.000
177A758ASP-1-0.888-0.96635.2690.1080.1080.0000.0000.0000.000
178A759GLY0-0.048-0.01633.7010.0050.0050.0000.0000.0000.000
179A760ASN0-0.106-0.04730.9960.0130.0130.0000.0000.0000.000
180A761ASP-1-0.866-0.94627.0200.2050.2050.0000.0000.0000.000
181A762ALA0-0.064-0.02129.605-0.010-0.0100.0000.0000.0000.000
182A763ILE00.0540.02729.7230.0090.0090.0000.0000.0000.000
183A764PRO00.0320.03930.260-0.009-0.0090.0000.0000.0000.000
184A765ILE00.020-0.00833.217-0.005-0.0050.0000.0000.0000.000
185A766ARG10.8010.89736.271-0.075-0.0750.0000.0000.0000.000
186A767TRP0-0.025-0.03733.882-0.003-0.0030.0000.0000.0000.000
187A768MET0-0.058-0.01631.6700.0020.0020.0000.0000.0000.000
188A769PRO00.0250.04033.300-0.005-0.0050.0000.0000.0000.000
189A770PRO00.0690.01135.5750.0050.0050.0000.0000.0000.000
190A771GLU-1-0.753-0.84232.8310.0820.0820.0000.0000.0000.000
191A772SER0-0.028-0.03131.1650.0040.0040.0000.0000.0000.000
192A773ILE0-0.032-0.01632.5700.0070.0070.0000.0000.0000.000
193A774PHE0-0.043-0.03035.1370.0010.0010.0000.0000.0000.000
194A775TYR0-0.059-0.02933.918-0.003-0.0030.0000.0000.0000.000
195A776ASN0-0.0060.01727.1250.0080.0080.0000.0000.0000.000
196A777ARG10.9330.97228.787-0.075-0.0750.0000.0000.0000.000
197A778TYR00.0130.01026.071-0.002-0.0020.0000.0000.0000.000
198A779THR0-0.042-0.04626.2990.0080.0080.0000.0000.0000.000
199A780THR00.0780.03327.2640.0030.0030.0000.0000.0000.000
200A781GLU-1-0.797-0.89728.5080.0720.0720.0000.0000.0000.000
201A782SER0-0.023-0.01729.885-0.002-0.0020.0000.0000.0000.000
202A783ASP-1-0.761-0.88227.1250.1180.1180.0000.0000.0000.000
203A784VAL0-0.040-0.01630.721-0.004-0.0040.0000.0000.0000.000
204A785TRP00.0170.03033.801-0.006-0.0060.0000.0000.0000.000
205A786ALA00.0150.00932.314-0.004-0.0040.0000.0000.0000.000
206A787TYR0-0.011-0.03833.445-0.003-0.0030.0000.0000.0000.000
207A788GLY00.0340.01635.020-0.004-0.0040.0000.0000.0000.000
208A789VAL0-0.043-0.01736.935-0.003-0.0030.0000.0000.0000.000
209A790VAL00.0000.01933.565-0.002-0.0020.0000.0000.0000.000
210A791LEU0-0.040-0.01637.012-0.003-0.0030.0000.0000.0000.000
211A792TRP00.031-0.00539.923-0.002-0.0020.0000.0000.0000.000
212A793GLU-1-0.722-0.83436.2500.0730.0730.0000.0000.0000.000
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