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: 497JN

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 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 279
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4055714.191305
FMO2-HF: Nuclear repulsion 3940205.186575
FMO2-HF: Total energy -115509.004731
FMO2-MP2: Total energy -115833.326386


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.
-0.4011.5742.635-1.231-3.379-0.004
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 : 0.009 / q_NPA : -0.009
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].
3A562PRO00.040-0.0013.626-0.8781.197-0.016-0.780-1.2790.001
4A563LYS10.9951.0295.3550.3860.510-0.001-0.004-0.1190.000
5A564LEU00.0180.0036.3190.1430.1430.0000.0000.0000.000
6A565LEU0-0.006-0.0022.140-0.446-0.6702.652-0.447-1.981-0.005
7A566SER0-0.108-0.0656.3140.0760.0760.0000.0000.0000.000
8A567LEU0-0.016-0.0109.3370.0390.0390.0000.0000.0000.000
9A568GLU-1-0.856-0.9229.2090.2520.2520.0000.0000.0000.000
10A569TYR00.012-0.01911.142-0.035-0.0350.0000.0000.0000.000
11A570PRO00.0080.00114.7890.0360.0360.0000.0000.0000.000
12A571ARG10.9400.93912.975-0.262-0.2620.0000.0000.0000.000
13A572ASN0-0.058-0.04117.4280.0090.0090.0000.0000.0000.000
14A573ASN0-0.0260.00419.769-0.002-0.0020.0000.0000.0000.000
15A574ILE0-0.045-0.01918.334-0.005-0.0050.0000.0000.0000.000
16A575GLU-1-0.859-0.90422.4060.0470.0470.0000.0000.0000.000
17A576TYR0-0.079-0.06326.185-0.002-0.0020.0000.0000.0000.000
18A577VAL0-0.041-0.00827.511-0.008-0.0080.0000.0000.0000.000
19A578ARG10.9150.93629.731-0.078-0.0780.0000.0000.0000.000
20A579ASP-1-0.799-0.89628.5810.1190.1190.0000.0000.0000.000
21A580ILE0-0.089-0.03826.664-0.008-0.0080.0000.0000.0000.000
22A581GLY00.0430.01328.078-0.006-0.0060.0000.0000.0000.000
23A582GLU-1-0.964-0.97626.3850.1480.1480.0000.0000.0000.000
24A583GLY00.0240.00224.301-0.007-0.0070.0000.0000.0000.000
25A584ALA0-0.042-0.02322.7330.0010.0010.0000.0000.0000.000
26A585PHE00.000-0.00917.118-0.001-0.0010.0000.0000.0000.000
27A586GLY00.0450.02020.4370.0140.0140.0000.0000.0000.000
28A587ARG10.9261.01022.435-0.160-0.1600.0000.0000.0000.000
29A588VAL00.0300.01522.3600.0180.0180.0000.0000.0000.000
30A589PHE0-0.021-0.01422.267-0.012-0.0120.0000.0000.0000.000
31A590GLN00.0600.03124.9200.0060.0060.0000.0000.0000.000
32A591ALA0-0.011-0.01524.0720.0010.0010.0000.0000.0000.000
33A592ARG10.8820.93025.925-0.045-0.0450.0000.0000.0000.000
34A593ALA00.0360.02321.2030.0060.0060.0000.0000.0000.000
35A594PRO0-0.001-0.00823.261-0.010-0.0100.0000.0000.0000.000
36A595GLY00.0100.00522.4460.0000.0000.0000.0000.0000.000
37A596LEU0-0.0400.00117.843-0.009-0.0090.0000.0000.0000.000
38A597LEU0-0.0140.00119.910-0.015-0.0150.0000.0000.0000.000
39A598PRO0-0.010-0.02821.0550.0030.0030.0000.0000.0000.000
40A599TYR0-0.034-0.01623.890-0.002-0.0020.0000.0000.0000.000
41A600GLU-1-0.804-0.86026.3960.0070.0070.0000.0000.0000.000
42A601PRO0-0.047-0.01226.778-0.001-0.0010.0000.0000.0000.000
43A602PHE0-0.015-0.02925.8930.0020.0020.0000.0000.0000.000
44A603THR00.003-0.01423.425-0.003-0.0030.0000.0000.0000.000
45A604MET0-0.0550.00024.8080.0090.0090.0000.0000.0000.000
46A605VAL00.004-0.00921.188-0.002-0.0020.0000.0000.0000.000
47A606ALA0-0.0080.00023.2790.0000.0000.0000.0000.0000.000
48A607VAL0-0.003-0.01619.4520.0110.0110.0000.0000.0000.000
49A608LYS10.9230.98618.027-0.300-0.3000.0000.0000.0000.000
50A609MET0-0.035-0.03117.8550.0220.0220.0000.0000.0000.000
51A610LEU0-0.040-0.01114.232-0.005-0.0050.0000.0000.0000.000
52A611LYS10.9220.94417.852-0.241-0.2410.0000.0000.0000.000
53A612GLU-1-0.902-0.95017.7620.2670.2670.0000.0000.0000.000
54A613GLU-1-0.929-0.97618.0040.2650.2650.0000.0000.0000.000
55A614ALA0-0.037-0.01817.332-0.009-0.0090.0000.0000.0000.000
56A615SER00.015-0.00117.8900.0300.0300.0000.0000.0000.000
57A616ALA00.036-0.00314.5110.0380.0380.0000.0000.0000.000
58A617ASP-1-0.895-0.95114.1710.5940.5940.0000.0000.0000.000
59A618MET0-0.0050.01215.7490.0270.0270.0000.0000.0000.000
60A619GLN0-0.018-0.0119.988-0.138-0.1380.0000.0000.0000.000
61A620ALA00.0050.00610.9290.1150.1150.0000.0000.0000.000
62A621ASP-1-0.888-0.94311.8240.6190.6190.0000.0000.0000.000
63A622PHE0-0.0050.00312.491-0.010-0.0100.0000.0000.0000.000
64A623GLN00.005-0.0186.924-0.046-0.0460.0000.0000.0000.000
65A624ARG10.8810.9599.824-0.520-0.5200.0000.0000.0000.000
66A625GLU-1-0.888-0.96811.2860.2610.2610.0000.0000.0000.000
67A626ALA00.0070.00510.535-0.090-0.0900.0000.0000.0000.000
68A627ALA0-0.042-0.0308.612-0.115-0.1150.0000.0000.0000.000
69A628LEU0-0.036-0.01010.271-0.149-0.1490.0000.0000.0000.000
70A629MET0-0.0040.00213.802-0.077-0.0770.0000.0000.0000.000
71A630ALA0-0.024-0.01411.660-0.058-0.0580.0000.0000.0000.000
72A631GLU-1-0.962-0.98711.499-0.222-0.2220.0000.0000.0000.000
73A632PHE0-0.083-0.03215.171-0.021-0.0210.0000.0000.0000.000
74A633ASP-1-0.945-0.97418.691-0.048-0.0480.0000.0000.0000.000
75A634ASN00.021-0.00421.076-0.002-0.0020.0000.0000.0000.000
76A635PRO00.0200.00424.6290.0070.0070.0000.0000.0000.000
77A636ASN0-0.046-0.02727.545-0.001-0.0010.0000.0000.0000.000
78A637ILE0-0.029-0.00421.9570.0080.0080.0000.0000.0000.000
79A638VAL0-0.030-0.00722.195-0.008-0.0080.0000.0000.0000.000
80A639LYS10.9750.97718.8060.0420.0420.0000.0000.0000.000
81A640LEU0-0.035-0.00913.0250.0120.0120.0000.0000.0000.000
82A641LEU0-0.035-0.04016.755-0.028-0.0280.0000.0000.0000.000
83A642GLY00.0520.02514.342-0.034-0.0340.0000.0000.0000.000
84A643VAL0-0.049-0.02310.3810.0550.0550.0000.0000.0000.000
85A644CYS0-0.0390.01912.534-0.056-0.0560.0000.0000.0000.000
86A645ALA00.002-0.0178.2140.0590.0590.0000.0000.0000.000
87A646VAL0-0.0150.0196.7410.1520.1520.0000.0000.0000.000
88A647GLY00.0030.0039.201-0.082-0.0820.0000.0000.0000.000
89A648LYS10.8960.97412.127-0.394-0.3940.0000.0000.0000.000
90A649PRO00.0970.03714.999-0.034-0.0340.0000.0000.0000.000
91A650MET00.0010.0059.246-0.007-0.0070.0000.0000.0000.000
92A651CYS0-0.050-0.02414.152-0.039-0.0390.0000.0000.0000.000
93A652LEU00.0090.01512.6410.0230.0230.0000.0000.0000.000
94A653LEU00.005-0.00315.860-0.016-0.0160.0000.0000.0000.000
95A654PHE00.0320.01417.287-0.008-0.0080.0000.0000.0000.000
96A655GLU-1-0.740-0.83820.5280.0340.0340.0000.0000.0000.000
97A656TYR0-0.0080.00423.4830.0120.0120.0000.0000.0000.000
98A657MET0-0.0270.00026.641-0.010-0.0100.0000.0000.0000.000
99A658ALA0-0.015-0.04029.4380.0040.0040.0000.0000.0000.000
100A659TYR0-0.046-0.01532.5140.0000.0000.0000.0000.0000.000
101A660GLY00.0230.04332.0320.0000.0000.0000.0000.0000.000
102A661ASP-1-0.779-0.86331.4440.0780.0780.0000.0000.0000.000
103A662LEU0-0.006-0.02432.589-0.005-0.0050.0000.0000.0000.000
104A663ASN0-0.075-0.02634.806-0.005-0.0050.0000.0000.0000.000
105A664GLU-1-0.895-0.96336.2150.0610.0610.0000.0000.0000.000
106A665PHE00.0300.01637.033-0.005-0.0050.0000.0000.0000.000
107A666LEU0-0.036-0.01538.394-0.004-0.0040.0000.0000.0000.000
108A667ARG10.9060.95440.529-0.065-0.0650.0000.0000.0000.000
109A668SER0-0.091-0.03741.555-0.002-0.0020.0000.0000.0000.000
110A669MET0-0.030-0.00942.563-0.003-0.0030.0000.0000.0000.000
111A670SER0-0.048-0.02744.941-0.002-0.0020.0000.0000.0000.000
112A671PRO0-0.041-0.01247.1170.0000.0000.0000.0000.0000.000
113A694PRO0-0.022-0.02749.3270.0000.0000.0000.0000.0000.000
114A695PRO0-0.0050.01247.9110.0010.0010.0000.0000.0000.000
115A696LEU00.0160.01441.922-0.001-0.0010.0000.0000.0000.000
116A697SER0-0.020-0.02446.342-0.001-0.0010.0000.0000.0000.000
117A698CYS00.0500.00546.2370.0010.0010.0000.0000.0000.000
118A699ALA0-0.007-0.00545.6570.0010.0010.0000.0000.0000.000
119A700GLU-1-0.816-0.89343.0380.0230.0230.0000.0000.0000.000
120A701GLN00.0460.03041.4930.0000.0000.0000.0000.0000.000
121A702LEU00.009-0.00240.8970.0020.0020.0000.0000.0000.000
122A703CYS0-0.039-0.00239.3080.0000.0000.0000.0000.0000.000
123A704ILE00.0300.01536.2030.0010.0010.0000.0000.0000.000
124A705ALA00.0290.01435.9710.0030.0030.0000.0000.0000.000
125A706ARG10.9620.99336.122-0.014-0.0140.0000.0000.0000.000
126A707GLN0-0.050-0.03033.064-0.001-0.0010.0000.0000.0000.000
127A708VAL00.0680.04331.4940.0010.0010.0000.0000.0000.000
128A709ALA0-0.006-0.00531.2040.0030.0030.0000.0000.0000.000
129A710ALA0-0.028-0.01231.652-0.001-0.0010.0000.0000.0000.000
130A711GLY00.0250.01427.814-0.003-0.0030.0000.0000.0000.000
131A712MET00.0110.00526.9770.0040.0040.0000.0000.0000.000
132A713ALA0-0.027-0.01427.8540.0010.0010.0000.0000.0000.000
133A714TYR00.0160.02420.9270.0000.0000.0000.0000.0000.000
134A715LEU00.013-0.00222.047-0.003-0.0030.0000.0000.0000.000
135A716SER00.0300.00623.5270.0050.0050.0000.0000.0000.000
136A717GLU-1-1.011-0.97724.293-0.017-0.0170.0000.0000.0000.000
137A718ARG10.9270.96916.481-0.020-0.0200.0000.0000.0000.000
138A719LYS10.7960.89420.5260.0050.0050.0000.0000.0000.000
139A720PHE0-0.011-0.00518.2910.0160.0160.0000.0000.0000.000
140A721VAL0-0.029-0.01621.671-0.010-0.0100.0000.0000.0000.000
141A722HIS0-0.024-0.01822.8210.0200.0200.0000.0000.0000.000
142A723ARG10.8920.93022.954-0.169-0.1690.0000.0000.0000.000
143A724ASP-1-0.771-0.85326.5720.1350.1350.0000.0000.0000.000
144A725LEU0-0.0020.02028.085-0.002-0.0020.0000.0000.0000.000
145A726ALA00.0670.00929.833-0.004-0.0040.0000.0000.0000.000
146A727THR0-0.052-0.04631.6440.0030.0030.0000.0000.0000.000
147A728ARG10.8710.94031.109-0.105-0.1050.0000.0000.0000.000
148A729ASN0-0.060-0.02427.3560.0060.0060.0000.0000.0000.000
149A730CYS0-0.075-0.02627.8620.0010.0010.0000.0000.0000.000
150A731LEU0-0.005-0.00326.2600.0010.0010.0000.0000.0000.000
151A732VAL00.0270.01030.395-0.006-0.0060.0000.0000.0000.000
152A733GLY0-0.004-0.00932.3440.0030.0030.0000.0000.0000.000
153A734GLU-1-0.838-0.94133.0340.0230.0230.0000.0000.0000.000
154A735ASN0-0.065-0.04035.640-0.001-0.0010.0000.0000.0000.000
155A736MET0-0.0030.01837.262-0.001-0.0010.0000.0000.0000.000
156A737VAL00.0090.02531.3750.0000.0000.0000.0000.0000.000
157A738VAL0-0.005-0.00732.0430.0050.0050.0000.0000.0000.000
158A739LYS10.7950.88426.678-0.036-0.0360.0000.0000.0000.000
159A740ILE0-0.005-0.00225.5880.0060.0060.0000.0000.0000.000
160A741ALA00.013-0.00223.546-0.001-0.0010.0000.0000.0000.000
161A742ASP-1-0.822-0.91622.0690.1800.1800.0000.0000.0000.000
162A743PHE0-0.030-0.01721.6600.0250.0250.0000.0000.0000.000
163A744GLY00.0020.01422.8080.0150.0150.0000.0000.0000.000
164A745LEU00.000-0.00923.9570.0030.0030.0000.0000.0000.000
165A746SER00.0370.00727.024-0.011-0.0110.0000.0000.0000.000
166A747ARG10.8900.96826.661-0.179-0.1790.0000.0000.0000.000
167A748ASN0-0.071-0.02329.471-0.011-0.0110.0000.0000.0000.000
168A749ILE00.0490.01230.278-0.006-0.0060.0000.0000.0000.000
169A750TYR0-0.027-0.05032.147-0.008-0.0080.0000.0000.0000.000
170A751SER00.0050.01133.807-0.001-0.0010.0000.0000.0000.000
171A752ALA0-0.020-0.02134.7440.0010.0010.0000.0000.0000.000
172A753ASP-1-0.829-0.90834.4720.0810.0810.0000.0000.0000.000
173A754TYR0-0.095-0.08629.1200.0020.0020.0000.0000.0000.000
174A755TYR0-0.059-0.03834.346-0.003-0.0030.0000.0000.0000.000
175A756LYS10.8780.94533.329-0.105-0.1050.0000.0000.0000.000
176A757ALA00.0610.03935.155-0.003-0.0030.0000.0000.0000.000
177A758ASP-1-0.876-0.96035.2890.1090.1090.0000.0000.0000.000
178A759GLY0-0.049-0.01833.6430.0060.0060.0000.0000.0000.000
179A760ASN0-0.123-0.05631.1970.0140.0140.0000.0000.0000.000
180A761ASP-1-0.857-0.93827.0720.2030.2030.0000.0000.0000.000
181A762ALA0-0.060-0.02529.605-0.010-0.0100.0000.0000.0000.000
182A763ILE00.0410.02429.8540.0080.0080.0000.0000.0000.000
183A764PRO00.0380.03730.289-0.009-0.0090.0000.0000.0000.000
184A765ILE00.034-0.00333.236-0.006-0.0060.0000.0000.0000.000
185A766ARG10.8050.91236.273-0.074-0.0740.0000.0000.0000.000
186A767TRP0-0.020-0.03033.868-0.003-0.0030.0000.0000.0000.000
187A768MET0-0.060-0.01731.3030.0010.0010.0000.0000.0000.000
188A769PRO00.0210.04233.232-0.005-0.0050.0000.0000.0000.000
189A770PRO00.0820.01335.5160.0050.0050.0000.0000.0000.000
190A771GLU-1-0.760-0.86832.8700.0730.0730.0000.0000.0000.000
191A772SER0-0.048-0.05030.9630.0040.0040.0000.0000.0000.000
192A773ILE0-0.027-0.01032.5290.0070.0070.0000.0000.0000.000
193A774PHE0-0.050-0.03435.1370.0020.0020.0000.0000.0000.000
194A775TYR0-0.061-0.02733.754-0.003-0.0030.0000.0000.0000.000
195A776ASN00.0060.02426.9080.0060.0060.0000.0000.0000.000
196A777ARG10.9500.97428.706-0.069-0.0690.0000.0000.0000.000
197A778TYR00.0200.02525.915-0.002-0.0020.0000.0000.0000.000
198A779THR0-0.014-0.01526.2120.0070.0070.0000.0000.0000.000
199A780THR00.0780.02526.8050.0060.0060.0000.0000.0000.000
200A781GLU-1-0.867-0.93828.4170.0520.0520.0000.0000.0000.000
201A782SER0-0.025-0.00429.736-0.001-0.0010.0000.0000.0000.000
202A783ASP-1-0.759-0.88427.0790.1060.1060.0000.0000.0000.000
203A784VAL0-0.046-0.02030.628-0.003-0.0030.0000.0000.0000.000
204A785TRP00.0280.03133.708-0.005-0.0050.0000.0000.0000.000
205A786ALA00.0160.01032.339-0.003-0.0030.0000.0000.0000.000
206A787TYR0-0.012-0.04233.482-0.003-0.0030.0000.0000.0000.000
207A788GLY00.0330.01435.031-0.004-0.0040.0000.0000.0000.000
208A789VAL0-0.039-0.01536.888-0.003-0.0030.0000.0000.0000.000
209A790VAL0-0.0030.01633.613-0.001-0.0010.0000.0000.0000.000
210A791LEU0-0.031-0.01937.022-0.003-0.0030.0000.0000.0000.000
211A792TRP00.0430.01039.931-0.002-0.0020.0000.0000.0000.000
212A793GLU-1-0.757-0.87136.4390.0690.0690.0000.0000.0000.000
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