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: G6811

Calculation Name: 1KU1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KU1

Chain ID: A

ChEMBL ID:

UniProt ID: P39993

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptAll
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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2456665.874475
FMO2-HF: Nuclear repulsion 2369821.178282
FMO2-HF: Total energy -86844.696193
FMO2-MP2: Total energy -87092.997475


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:-9:GLY)


Summations of interaction energy for fragment #1(A:-9:GLY)
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.
-3.971-1.3290.072-1.367-1.348-0.004
Interaction energy analysis for fragmet #1(A:-9:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.010
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].
3A-7VAL0-0.018-0.0092.919-0.9520.6830.018-0.784-0.8700.001
4A-6PRO0-0.027-0.0153.094-2.864-1.8570.054-0.583-0.478-0.005
5A-5ARG10.8410.9085.304-0.341-0.3410.0000.0000.0000.000
6A-4GLY00.0160.0106.964-0.082-0.0820.0000.0000.0000.000
7A-3SER-1-0.817-0.9038.129-0.657-0.6570.0000.0000.0000.000
8A-2HIS-1-0.928-0.98110.451-0.080-0.0800.0000.0000.0000.000
9A-1MET00.0120.0048.1380.0110.0110.0000.0000.0000.000
10A558ASP-1-0.788-0.8568.8120.7320.7320.0000.0000.0000.000
11A559ARG11.0161.00611.501-0.048-0.0480.0000.0000.0000.000
12A560LYS10.8620.92411.9140.1660.1660.0000.0000.0000.000
13A561THR0-0.009-0.01512.437-0.009-0.0090.0000.0000.0000.000
14A562GLU-1-0.803-0.90315.0810.2050.2050.0000.0000.0000.000
15A563PHE0-0.0070.00617.556-0.026-0.0260.0000.0000.0000.000
16A564ILE0-0.0200.00616.467-0.018-0.0180.0000.0000.0000.000
17A565GLU-1-0.925-0.95818.2270.2300.2300.0000.0000.0000.000
18A566CYS0-0.042-0.01921.133-0.012-0.0120.0000.0000.0000.000
19A567THR0-0.001-0.03322.341-0.012-0.0120.0000.0000.0000.000
20A568ASN0-0.044-0.00823.627-0.014-0.0140.0000.0000.0000.000
21A569ALA00.011-0.00625.309-0.006-0.0060.0000.0000.0000.000
22A570PHE00.010-0.00627.183-0.005-0.0050.0000.0000.0000.000
23A571ASN0-0.002-0.01526.362-0.010-0.0100.0000.0000.0000.000
24A572GLU-1-0.954-0.95229.2560.0490.0490.0000.0000.0000.000
25A573LYS10.9230.95231.218-0.062-0.0620.0000.0000.0000.000
26A574PRO00.1060.06731.9720.0060.0060.0000.0000.0000.000
27A575LYS10.9380.96932.701-0.041-0.0410.0000.0000.0000.000
28A576LYS10.9020.94730.215-0.078-0.0780.0000.0000.0000.000
29A577GLY00.0540.02527.9880.0060.0060.0000.0000.0000.000
30A578ILE00.0350.01828.0120.0030.0030.0000.0000.0000.000
31A579PRO00.0050.00129.4180.0010.0010.0000.0000.0000.000
32A580MET00.0090.01622.2350.0000.0000.0000.0000.0000.000
33A581LEU00.006-0.01224.0850.0070.0070.0000.0000.0000.000
34A582ILE0-0.0090.01125.481-0.001-0.0010.0000.0000.0000.000
35A583GLU-1-0.962-0.97523.8740.1460.1460.0000.0000.0000.000
36A584LYS10.8160.90820.264-0.182-0.1820.0000.0000.0000.000
37A585GLY0-0.0080.01121.601-0.001-0.0010.0000.0000.0000.000
38A586PHE0-0.095-0.05618.514-0.016-0.0160.0000.0000.0000.000
39A587ILE0-0.054-0.02324.116-0.012-0.0120.0000.0000.0000.000
40A588ALA00.0140.01127.9370.0060.0060.0000.0000.0000.000
41A589SER0-0.035-0.04129.6650.0030.0030.0000.0000.0000.000
42A590ASP-1-0.892-0.96432.4790.0410.0410.0000.0000.0000.000
43A591SER0-0.035-0.02134.698-0.003-0.0030.0000.0000.0000.000
44A592ASP-1-0.811-0.90335.8680.0190.0190.0000.0000.0000.000
45A593LYS10.8710.91533.259-0.008-0.0080.0000.0000.0000.000
46A594ASP-1-0.794-0.85631.9290.0160.0160.0000.0000.0000.000
47A595ILE0-0.012-0.00832.036-0.001-0.0010.0000.0000.0000.000
48A596ALA00.0060.00732.834-0.002-0.0020.0000.0000.0000.000
49A597GLU-1-0.823-0.90331.132-0.005-0.0050.0000.0000.0000.000
50A598PHE00.000-0.00824.738-0.004-0.0040.0000.0000.0000.000
51A599LEU0-0.015-0.02429.500-0.003-0.0030.0000.0000.0000.000
52A600PHE00.0580.03531.788-0.004-0.0040.0000.0000.0000.000
53A601ASN0-0.032-0.01128.518-0.010-0.0100.0000.0000.0000.000
54A602ASN0-0.064-0.03424.907-0.009-0.0090.0000.0000.0000.000
55A603ASN00.0530.03727.6710.0010.0010.0000.0000.0000.000
56A604ASN0-0.055-0.03027.6980.0060.0060.0000.0000.0000.000
57A605ARG10.8870.94619.8590.0430.0430.0000.0000.0000.000
58A606MET00.0150.02825.2660.0120.0120.0000.0000.0000.000
59A607ASN00.015-0.00128.047-0.010-0.0100.0000.0000.0000.000
60A608LYS10.9170.94831.0740.0250.0250.0000.0000.0000.000
61A609LYS10.9560.99933.895-0.014-0.0140.0000.0000.0000.000
62A610THR0-0.070-0.03733.044-0.001-0.0010.0000.0000.0000.000
63A611ILE00.0040.00531.2600.0020.0020.0000.0000.0000.000
64A612GLY00.0580.03735.2200.0010.0010.0000.0000.0000.000
65A613LEU0-0.036-0.04038.4530.0010.0010.0000.0000.0000.000
66A614LEU0-0.021-0.00534.8590.0020.0020.0000.0000.0000.000
67A615LEU00.0010.00537.6470.0010.0010.0000.0000.0000.000
68A616CYS0-0.0300.01140.4610.0000.0000.0000.0000.0000.000
69A617HIS0-0.060-0.03641.7790.0010.0010.0000.0000.0000.000
70A618PRO00.0320.01243.898-0.001-0.0010.0000.0000.0000.000
71A619ASP-1-0.834-0.88643.0100.0240.0240.0000.0000.0000.000
72A620LYS10.7960.87039.191-0.024-0.0240.0000.0000.0000.000
73A621VAL00.0860.05242.673-0.001-0.0010.0000.0000.0000.000
74A622SER0-0.042-0.03243.129-0.002-0.0020.0000.0000.0000.000
75A623LEU00.0180.01136.382-0.001-0.0010.0000.0000.0000.000
76A624LEU0-0.043-0.02140.090-0.002-0.0020.0000.0000.0000.000
77A625ASN0-0.019-0.01442.032-0.003-0.0030.0000.0000.0000.000
78A626GLU-1-0.845-0.91639.4310.0030.0030.0000.0000.0000.000
79A627TYR0-0.025-0.03434.884-0.003-0.0030.0000.0000.0000.000
80A628ILE0-0.059-0.03739.120-0.003-0.0030.0000.0000.0000.000
81A629ARG10.8990.93941.956-0.005-0.0050.0000.0000.0000.000
82A630LEU0-0.040-0.00135.334-0.001-0.0010.0000.0000.0000.000
83A631PHE0-0.100-0.04838.471-0.003-0.0030.0000.0000.0000.000
84A632ASP-1-0.829-0.87540.392-0.018-0.0180.0000.0000.0000.000
85A633PHE0-0.033-0.04342.776-0.002-0.0020.0000.0000.0000.000
86A634SER00.003-0.00245.8070.0000.0000.0000.0000.0000.000
87A635GLY0-0.035-0.01647.725-0.002-0.0020.0000.0000.0000.000
88A636LEU0-0.0360.00244.481-0.001-0.0010.0000.0000.0000.000
89A637ARG10.8200.89049.2040.0210.0210.0000.0000.0000.000
90A638VAL00.0460.02049.401-0.001-0.0010.0000.0000.0000.000
91A639ASP-1-0.745-0.84548.789-0.019-0.0190.0000.0000.0000.000
92A640GLU-1-0.836-0.90346.246-0.023-0.0230.0000.0000.0000.000
93A641ALA00.0360.02544.730-0.001-0.0010.0000.0000.0000.000
94A642ILE00.0170.00844.1780.0000.0000.0000.0000.0000.000
95A643ARG10.7220.84342.7390.0220.0220.0000.0000.0000.000
96A644ILE00.0050.01039.568-0.001-0.0010.0000.0000.0000.000
97A645LEU00.0010.02639.3010.0000.0000.0000.0000.0000.000
98A646LEU00.001-0.00739.2590.0010.0010.0000.0000.0000.000
99A647THR0-0.064-0.03335.556-0.001-0.0010.0000.0000.0000.000
100A648LYS10.8080.91232.6280.0220.0220.0000.0000.0000.000
101A649PHE0-0.013-0.02434.3830.0030.0030.0000.0000.0000.000
102A650ARG10.8910.94836.4740.0050.0050.0000.0000.0000.000
103A651LEU00.0620.03038.7660.0020.0020.0000.0000.0000.000
104A652PRO0-0.044-0.02041.8330.0010.0010.0000.0000.0000.000
105A653GLY00.003-0.00643.133-0.002-0.0020.0000.0000.0000.000
106A654GLU-1-0.865-0.91945.7080.0120.0120.0000.0000.0000.000
107A655SER00.0460.01848.805-0.001-0.0010.0000.0000.0000.000
108A656GLN00.033-0.00649.516-0.002-0.0020.0000.0000.0000.000
109A657GLN0-0.104-0.05645.4250.0000.0000.0000.0000.0000.000
110A658ILE00.002-0.01346.5900.0000.0000.0000.0000.0000.000
111A659GLU-1-0.885-0.93847.7430.0040.0040.0000.0000.0000.000
112A660ARG10.9560.97447.121-0.012-0.0120.0000.0000.0000.000
113A661ILE0-0.059-0.02242.5860.0000.0000.0000.0000.0000.000
114A662ILE0-0.0010.00946.054-0.001-0.0010.0000.0000.0000.000
115A663GLU-1-0.886-0.92848.9960.0040.0040.0000.0000.0000.000
116A664ALA0-0.0110.00445.886-0.001-0.0010.0000.0000.0000.000
117A665PHE0-0.015-0.01545.343-0.001-0.0010.0000.0000.0000.000
118A666SER00.008-0.01547.128-0.001-0.0010.0000.0000.0000.000
119A667SER0-0.052-0.03949.7300.0000.0000.0000.0000.0000.000
120A668ALA0-0.006-0.00545.9110.0000.0000.0000.0000.0000.000
121A669TYR0-0.036-0.04348.036-0.001-0.0010.0000.0000.0000.000
122A670CYS0-0.021-0.00749.311-0.001-0.0010.0000.0000.0000.000
123A671GLU-1-0.966-0.96948.206-0.007-0.0070.0000.0000.0000.000
124A672ASN0-0.007-0.01145.704-0.002-0.0020.0000.0000.0000.000
125A673GLN0-0.035-0.02649.167-0.003-0.0030.0000.0000.0000.000
126A674ASP-1-0.940-0.96252.496-0.011-0.0110.0000.0000.0000.000
127A675TYR0-0.046-0.03655.160-0.001-0.0010.0000.0000.0000.000
128A676ASP-1-0.760-0.84558.061-0.009-0.0090.0000.0000.0000.000
129A677PRO00.0080.00160.8980.0000.0000.0000.0000.0000.000
130A678SER0-0.136-0.09363.8340.0000.0000.0000.0000.0000.000
131A679LYS10.8670.92059.7310.0120.0120.0000.0000.0000.000
132A680ILE0-0.046-0.00162.8350.0000.0000.0000.0000.0000.000
133A681SER0-0.007-0.00963.9520.0000.0000.0000.0000.0000.000
134A682ASP-1-0.891-0.94464.220-0.010-0.0100.0000.0000.0000.000
135A683ASN0-0.095-0.06365.873-0.001-0.0010.0000.0000.0000.000
136A684ALA00.0150.01263.142-0.001-0.0010.0000.0000.0000.000
137A685GLU-1-0.839-0.94061.697-0.015-0.0150.0000.0000.0000.000
138A686ASP-1-0.823-0.88856.683-0.020-0.0200.0000.0000.0000.000
139A687ASP-1-0.851-0.88056.665-0.016-0.0160.0000.0000.0000.000
140A688ILE0-0.022-0.01852.6770.0010.0010.0000.0000.0000.000
141A689SER0-0.051-0.03856.0550.0010.0010.0000.0000.0000.000
142A690THR0-0.036-0.03457.5990.0010.0010.0000.0000.0000.000
143A691VAL0-0.035-0.01858.1900.0010.0010.0000.0000.0000.000
144A692GLN0-0.032-0.03457.6080.0000.0000.0000.0000.0000.000
145A693PRO0-0.0040.01655.8780.0010.0010.0000.0000.0000.000
146A694ASP-1-0.770-0.86556.850-0.004-0.0040.0000.0000.0000.000
147A695ALA00.0790.01454.5400.0000.0000.0000.0000.0000.000
148A696ASP-1-0.906-0.95255.326-0.001-0.0010.0000.0000.0000.000
149A697SER0-0.014-0.02857.7330.0000.0000.0000.0000.0000.000
150A698VAL0-0.010-0.00651.947-0.001-0.0010.0000.0000.0000.000
151A699PHE00.0130.03052.617-0.001-0.0010.0000.0000.0000.000
152A700ILE00.006-0.01154.1920.0000.0000.0000.0000.0000.000
153A701LEU00.0030.01154.6360.0000.0000.0000.0000.0000.000
154A702SER00.022-0.00550.240-0.001-0.0010.0000.0000.0000.000
155A703TYR0-0.026-0.01551.4500.0000.0000.0000.0000.0000.000
156A704SER0-0.039-0.02253.250-0.001-0.0010.0000.0000.0000.000
157A705ILE00.0560.02549.550-0.001-0.0010.0000.0000.0000.000
158A706ILE0-0.022-0.01147.816-0.001-0.0010.0000.0000.0000.000
159A707MET0-0.040-0.00450.226-0.001-0.0010.0000.0000.0000.000
160A708LEU00.0540.02353.3980.0000.0000.0000.0000.0000.000
161A709ASN0-0.006-0.01046.217-0.002-0.0020.0000.0000.0000.000
162A710THR0-0.076-0.04350.052-0.001-0.0010.0000.0000.0000.000
163A711ASP-1-0.841-0.92850.962-0.011-0.0110.0000.0000.0000.000
164A712LEU0-0.019-0.00752.8940.0000.0000.0000.0000.0000.000
165A713HIS10.8030.89048.3330.0180.0180.0000.0000.0000.000
166A714ASN00.0090.01550.146-0.001-0.0010.0000.0000.0000.000
167A715PRO00.008-0.00350.4930.0000.0000.0000.0000.0000.000
168A716GLN0-0.057-0.02853.2830.0010.0010.0000.0000.0000.000
169A717VAL0-0.034-0.00255.5190.0010.0010.0000.0000.0000.000
170A718LYS10.8010.88257.6860.0110.0110.0000.0000.0000.000
171A719GLU-1-0.859-0.91360.737-0.012-0.0120.0000.0000.0000.000
172A720HIS0-0.069-0.02554.8940.0000.0000.0000.0000.0000.000
173A721MET0-0.0030.00858.6800.0000.0000.0000.0000.0000.000
174A722SER00.008-0.00159.885-0.001-0.0010.0000.0000.0000.000
175A723PHE00.0430.01160.3750.0000.0000.0000.0000.0000.000
176A724GLU-1-0.874-0.93662.219-0.011-0.0110.0000.0000.0000.000
177A725ASP-1-0.843-0.88962.983-0.008-0.0080.0000.0000.0000.000
178A726TYR0-0.037-0.02955.9840.0000.0000.0000.0000.0000.000
179A727SER0-0.038-0.04261.3610.0010.0010.0000.0000.0000.000
180A728GLY00.0030.01063.4140.0000.0000.0000.0000.0000.000
181A729ASN0-0.086-0.07862.3970.0010.0010.0000.0000.0000.000
182A730LEU00.0040.01458.4480.0010.0010.0000.0000.0000.000
183A731LYS10.8170.90062.7680.0080.0080.0000.0000.0000.000
184A732GLY0-0.044-0.01765.9790.0010.0010.0000.0000.0000.000
185A733CYS0-0.091-0.03661.0600.0010.0010.0000.0000.0000.000
186A734CYS00.0270.00860.9570.0000.0000.0000.0000.0000.000
187A735ASN00.0050.00361.3490.0000.0000.0000.0000.0000.000
188A736HIS0-0.039-0.01663.8610.0000.0000.0000.0000.0000.000
189A737LYS10.8900.94465.8220.0050.0050.0000.0000.0000.000
190A738ASP-1-0.761-0.87265.295-0.007-0.0070.0000.0000.0000.000
191A739PHE00.0300.00858.0120.0000.0000.0000.0000.0000.000
192A740PRO00.0070.00961.4540.0000.0000.0000.0000.0000.000
193A741PHE0-0.0030.00761.9810.0000.0000.0000.0000.0000.000
194A742TRP00.0760.04355.893-0.001-0.0010.0000.0000.0000.000
195A743TYR00.0210.02754.116-0.001-0.0010.0000.0000.0000.000
196A744LEU00.014-0.00157.0090.0000.0000.0000.0000.0000.000
197A745ASP-1-0.819-0.88958.008-0.017-0.0170.0000.0000.0000.000
198A746ARG10.6920.80554.6750.0170.0170.0000.0000.0000.000
199A747VAL0-0.025-0.00253.238-0.001-0.0010.0000.0000.0000.000
200A748TYR0-0.053-0.05453.414-0.001-0.0010.0000.0000.0000.000
201A749CYS0-0.042-0.02454.744-0.001-0.0010.0000.0000.0000.000
202A750SER00.0000.00249.789-0.002-0.0020.0000.0000.0000.000
203A751ILE0-0.044-0.02649.053-0.001-0.0010.0000.0000.0000.000
204A752ARG10.8290.88450.5990.0190.0190.0000.0000.0000.000
205A753ASP-1-0.836-0.88250.973-0.023-0.0230.0000.0000.0000.000
206A754LYS10.8740.93441.5500.0320.0320.0000.0000.0000.000
207A755GLU-1-0.829-0.89044.956-0.020-0.0200.0000.0000.0000.000
208A756ILE0-0.033-0.01743.335-0.002-0.0020.0000.0000.0000.000
209A757VAL00.0160.00239.6360.0010.0010.0000.0000.0000.000
210A758MET00.007-0.00634.7030.0000.0000.0000.0000.0000.000
211A759PRO0-0.0120.02035.0110.0040.0040.0000.0000.0000.000