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: V5VM1

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2453008.301985
FMO2-HF: Nuclear repulsion 2366165.294039
FMO2-HF: Total energy -86843.007945
FMO2-MP2: Total energy -87091.442518


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.
-2.046-0.085-0.006-0.961-0.993-0.001
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 : -0.001 / q_NPA : -0.014
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-7VAL00.000-0.0033.572-1.668-0.002-0.008-0.833-0.8250.000
4A-6PRO0-0.015-0.0023.780-0.411-0.1160.002-0.128-0.168-0.001
5A-5ARG10.8840.9595.740-0.638-0.6380.0000.0000.0000.000
6A-4GLY00.0490.0137.637-0.119-0.1190.0000.0000.0000.000
7A-3SER-1-0.880-0.9079.363-0.221-0.2210.0000.0000.0000.000
8A-2HIS-1-0.938-1.01311.3300.0490.0490.0000.0000.0000.000
9A-1MET00.0180.0098.780-0.038-0.0380.0000.0000.0000.000
10A558ASP-1-0.887-0.9429.9600.9410.9410.0000.0000.0000.000
11A559ARG10.9961.00212.255-0.150-0.1500.0000.0000.0000.000
12A560LYS10.9670.97214.198-0.021-0.0210.0000.0000.0000.000
13A561THR0-0.004-0.00812.998-0.033-0.0330.0000.0000.0000.000
14A562GLU-1-0.799-0.90215.7230.2780.2780.0000.0000.0000.000
15A563PHE0-0.0220.00218.273-0.037-0.0370.0000.0000.0000.000
16A564ILE0-0.034-0.00917.205-0.027-0.0270.0000.0000.0000.000
17A565GLU-1-0.929-0.96218.8230.2730.2730.0000.0000.0000.000
18A566CYS0-0.038-0.02121.709-0.017-0.0170.0000.0000.0000.000
19A567THR0-0.018-0.03823.103-0.017-0.0170.0000.0000.0000.000
20A568ASN0-0.0250.00624.403-0.021-0.0210.0000.0000.0000.000
21A569ALA00.0170.00626.097-0.008-0.0080.0000.0000.0000.000
22A570PHE00.008-0.01027.954-0.008-0.0080.0000.0000.0000.000
23A571ASN00.005-0.01027.658-0.010-0.0100.0000.0000.0000.000
24A572GLU-1-0.942-0.94429.7470.0600.0600.0000.0000.0000.000
25A573LYS10.9100.93632.064-0.072-0.0720.0000.0000.0000.000
26A574PRO00.1170.08933.0430.0070.0070.0000.0000.0000.000
27A575LYS10.9150.95333.825-0.057-0.0570.0000.0000.0000.000
28A576LYS10.8980.93831.400-0.092-0.0920.0000.0000.0000.000
29A577GLY00.0650.01329.1740.0070.0070.0000.0000.0000.000
30A578ILE00.0310.02229.0670.0050.0050.0000.0000.0000.000
31A579PRO00.0090.00330.3120.0030.0030.0000.0000.0000.000
32A580MET00.0150.02723.2160.0010.0010.0000.0000.0000.000
33A581LEU00.009-0.01124.9730.0110.0110.0000.0000.0000.000
34A582ILE0-0.0140.00926.2940.0030.0030.0000.0000.0000.000
35A583GLU-1-0.997-0.98925.7310.1570.1570.0000.0000.0000.000
36A584LYS10.8420.91520.759-0.226-0.2260.0000.0000.0000.000
37A585GLY00.0070.01622.4280.0100.0100.0000.0000.0000.000
38A586PHE0-0.103-0.05519.129-0.011-0.0110.0000.0000.0000.000
39A587ILE0-0.063-0.02024.785-0.013-0.0130.0000.0000.0000.000
40A588ALA00.0130.00928.5690.0070.0070.0000.0000.0000.000
41A589SER0-0.031-0.06230.1310.0030.0030.0000.0000.0000.000
42A590ASP-1-0.947-0.98732.9910.0600.0600.0000.0000.0000.000
43A591SER00.0140.02135.351-0.005-0.0050.0000.0000.0000.000
44A592ASP-1-0.815-0.90036.6270.0370.0370.0000.0000.0000.000
45A593LYS11.0111.00936.717-0.028-0.0280.0000.0000.0000.000
46A594ASP-1-0.807-0.86732.7400.0450.0450.0000.0000.0000.000
47A595ILE0-0.044-0.02232.8740.0010.0010.0000.0000.0000.000
48A596ALA0-0.005-0.00533.727-0.001-0.0010.0000.0000.0000.000
49A597GLU-1-0.889-0.94831.8650.0230.0230.0000.0000.0000.000
50A598PHE0-0.012-0.01425.707-0.002-0.0020.0000.0000.0000.000
51A599LEU0-0.033-0.02830.280-0.002-0.0020.0000.0000.0000.000
52A600PHE00.0370.02332.458-0.004-0.0040.0000.0000.0000.000
53A601ASN00.0080.00629.300-0.010-0.0100.0000.0000.0000.000
54A602ASN0-0.096-0.04725.895-0.006-0.0060.0000.0000.0000.000
55A603ASN00.0680.04228.6710.0040.0040.0000.0000.0000.000
56A604ASN0-0.025-0.02828.3810.0040.0040.0000.0000.0000.000
57A605ARG10.8670.93820.757-0.013-0.0130.0000.0000.0000.000
58A606MET00.0140.02826.0440.0120.0120.0000.0000.0000.000
59A607ASN00.0050.00528.719-0.011-0.0110.0000.0000.0000.000
60A608LYS10.9770.98531.6510.0040.0040.0000.0000.0000.000
61A609LYS10.9440.98834.547-0.024-0.0240.0000.0000.0000.000
62A610THR0-0.069-0.03333.628-0.002-0.0020.0000.0000.0000.000
63A611ILE00.0250.01332.0160.0020.0020.0000.0000.0000.000
64A612GLY00.0530.03635.9820.0000.0000.0000.0000.0000.000
65A613LEU0-0.039-0.04839.0670.0000.0000.0000.0000.0000.000
66A614LEU0-0.062-0.02135.6660.0010.0010.0000.0000.0000.000
67A615LEU00.0170.00038.5270.0010.0010.0000.0000.0000.000
68A616CYS0-0.0050.03841.202-0.001-0.0010.0000.0000.0000.000
69A617HIS0-0.028-0.01442.734-0.001-0.0010.0000.0000.0000.000
70A618PRO00.0110.00144.8020.0000.0000.0000.0000.0000.000
71A619ASP-1-0.906-0.95144.2870.0360.0360.0000.0000.0000.000
72A620LYS10.9050.94739.557-0.041-0.0410.0000.0000.0000.000
73A621VAL00.0460.03143.6470.0000.0000.0000.0000.0000.000
74A622SER0-0.048-0.05243.652-0.002-0.0020.0000.0000.0000.000
75A623LEU00.0240.01637.413-0.001-0.0010.0000.0000.0000.000
76A624LEU0-0.040-0.01541.197-0.001-0.0010.0000.0000.0000.000
77A625ASN00.013-0.01242.907-0.003-0.0030.0000.0000.0000.000
78A626GLU-1-0.925-0.96340.3320.0220.0220.0000.0000.0000.000
79A627TYR0-0.025-0.03835.862-0.003-0.0030.0000.0000.0000.000
80A628ILE0-0.069-0.03440.047-0.002-0.0020.0000.0000.0000.000
81A629ARG10.9680.98442.749-0.019-0.0190.0000.0000.0000.000
82A630LEU0-0.049-0.00236.253-0.001-0.0010.0000.0000.0000.000
83A631PHE0-0.095-0.04139.326-0.002-0.0020.0000.0000.0000.000
84A632ASP-1-0.816-0.86041.389-0.004-0.0040.0000.0000.0000.000
85A633PHE0-0.050-0.06543.449-0.002-0.0020.0000.0000.0000.000
86A634SER0-0.008-0.01746.426-0.001-0.0010.0000.0000.0000.000
87A635GLY0-0.020-0.00448.157-0.001-0.0010.0000.0000.0000.000
88A636LEU0-0.0370.00545.198-0.001-0.0010.0000.0000.0000.000
89A637ARG10.8490.92149.9070.0120.0120.0000.0000.0000.000
90A638VAL00.0470.01650.3250.0000.0000.0000.0000.0000.000
91A639ASP-1-0.754-0.88549.740-0.008-0.0080.0000.0000.0000.000
92A640GLU-1-0.912-0.95247.345-0.012-0.0120.0000.0000.0000.000
93A641ALA00.0380.02545.6630.0000.0000.0000.0000.0000.000
94A642ILE00.0310.01544.9090.0010.0010.0000.0000.0000.000
95A643ARG10.7650.87743.4660.0130.0130.0000.0000.0000.000
96A644ILE00.0110.01640.1580.0000.0000.0000.0000.0000.000
97A645LEU00.0430.04540.0760.0010.0010.0000.0000.0000.000
98A646LEU0-0.032-0.01540.2280.0020.0020.0000.0000.0000.000
99A647THR0-0.069-0.04836.802-0.001-0.0010.0000.0000.0000.000
100A648LYS10.7950.89833.413-0.001-0.0010.0000.0000.0000.000
101A649PHE0-0.036-0.02935.3090.0040.0040.0000.0000.0000.000
102A650ARG10.9370.98137.498-0.008-0.0080.0000.0000.0000.000
103A651LEU00.0480.02039.6100.0030.0030.0000.0000.0000.000
104A652PRO0-0.043-0.01943.0540.0000.0000.0000.0000.0000.000
105A653GLY00.015-0.00644.091-0.002-0.0020.0000.0000.0000.000
106A654GLU-1-0.926-0.96146.8280.0200.0200.0000.0000.0000.000
107A655SER00.0200.00749.5180.0000.0000.0000.0000.0000.000
108A656GLN00.0930.03249.813-0.002-0.0020.0000.0000.0000.000
109A657GLN0-0.048-0.03445.3500.0000.0000.0000.0000.0000.000
110A658ILE00.0020.00347.7830.0000.0000.0000.0000.0000.000
111A659GLU-1-0.898-0.93648.8800.0120.0120.0000.0000.0000.000
112A660ARG10.9360.96347.852-0.020-0.0200.0000.0000.0000.000
113A661ILE0-0.066-0.02643.5790.0000.0000.0000.0000.0000.000
114A662ILE0-0.012-0.00846.957-0.001-0.0010.0000.0000.0000.000
115A663GLU-1-0.885-0.92849.6630.0120.0120.0000.0000.0000.000
116A664ALA0-0.009-0.00646.7620.0000.0000.0000.0000.0000.000
117A665PHE0-0.036-0.03046.320-0.001-0.0010.0000.0000.0000.000
118A666SER00.017-0.00548.022-0.001-0.0010.0000.0000.0000.000
119A667SER0-0.015-0.00850.914-0.001-0.0010.0000.0000.0000.000
120A668ALA0-0.021-0.01046.7750.0000.0000.0000.0000.0000.000
121A669TYR0-0.060-0.05748.890-0.001-0.0010.0000.0000.0000.000
122A670CYS0-0.020-0.01150.037-0.001-0.0010.0000.0000.0000.000
123A671GLU-1-1.002-0.99249.7400.0050.0050.0000.0000.0000.000
124A672ASN0-0.0050.01146.430-0.001-0.0010.0000.0000.0000.000
125A673GLN0-0.037-0.01949.872-0.003-0.0030.0000.0000.0000.000
126A674ASP-1-0.960-0.96053.031-0.001-0.0010.0000.0000.0000.000
127A675TYR0-0.039-0.04555.668-0.001-0.0010.0000.0000.0000.000
128A676ASP-1-0.821-0.90558.717-0.002-0.0020.0000.0000.0000.000
129A677PRO00.0210.00061.574-0.001-0.0010.0000.0000.0000.000
130A678SER0-0.118-0.05364.5500.0000.0000.0000.0000.0000.000
131A679LYS10.9410.96460.6790.0040.0040.0000.0000.0000.000
132A680ILE0-0.0440.00163.6190.0000.0000.0000.0000.0000.000
133A681SER0-0.014-0.01264.7320.0000.0000.0000.0000.0000.000
134A682ASP-1-0.952-0.98165.067-0.004-0.0040.0000.0000.0000.000
135A683ASN0-0.037-0.02266.4440.0000.0000.0000.0000.0000.000
136A684ALA00.0020.02463.442-0.001-0.0010.0000.0000.0000.000
137A685GLU-1-0.905-0.99862.191-0.008-0.0080.0000.0000.0000.000
138A686ASP-1-0.846-0.91657.616-0.012-0.0120.0000.0000.0000.000
139A687ASP-1-0.858-0.89757.509-0.009-0.0090.0000.0000.0000.000
140A688ILE00.017-0.01353.3770.0010.0010.0000.0000.0000.000
141A689SER0-0.074-0.03556.6320.0010.0010.0000.0000.0000.000
142A690THR0-0.024-0.02458.1560.0010.0010.0000.0000.0000.000
143A691VAL0-0.026-0.00758.8660.0000.0000.0000.0000.0000.000
144A692GLN0-0.042-0.04958.4870.0010.0010.0000.0000.0000.000
145A693PRO0-0.0230.01956.7970.0010.0010.0000.0000.0000.000
146A694ASP-1-0.770-0.88457.7450.0040.0040.0000.0000.0000.000
147A695ALA00.0710.00055.3850.0000.0000.0000.0000.0000.000
148A696ASP-1-0.890-0.94556.2490.0070.0070.0000.0000.0000.000
149A697SER0-0.014-0.00958.7010.0000.0000.0000.0000.0000.000
150A698VAL0-0.036-0.01452.672-0.001-0.0010.0000.0000.0000.000
151A699PHE00.0290.03953.404-0.001-0.0010.0000.0000.0000.000
152A700ILE00.016-0.00455.0510.0000.0000.0000.0000.0000.000
153A701LEU0-0.0020.00855.3740.0000.0000.0000.0000.0000.000
154A702SER00.023-0.00351.208-0.001-0.0010.0000.0000.0000.000
155A703TYR0-0.019-0.00852.3510.0000.0000.0000.0000.0000.000
156A704SER0-0.044-0.02854.142-0.001-0.0010.0000.0000.0000.000
157A705ILE00.0600.02650.392-0.001-0.0010.0000.0000.0000.000
158A706ILE0-0.036-0.01748.729-0.001-0.0010.0000.0000.0000.000
159A707MET0-0.058-0.01851.044-0.001-0.0010.0000.0000.0000.000
160A708LEU00.0580.01754.169-0.001-0.0010.0000.0000.0000.000
161A709ASN0-0.0050.00047.043-0.002-0.0020.0000.0000.0000.000
162A710THR0-0.055-0.02850.744-0.001-0.0010.0000.0000.0000.000
163A711ASP-1-0.846-0.92151.671-0.006-0.0060.0000.0000.0000.000
164A712LEU00.0250.00953.531-0.001-0.0010.0000.0000.0000.000
165A713HIS10.7890.90249.4330.0110.0110.0000.0000.0000.000
166A714ASN00.0320.04150.572-0.001-0.0010.0000.0000.0000.000
167A715PRO0-0.001-0.01451.0720.0000.0000.0000.0000.0000.000
168A716GLN0-0.069-0.04753.7760.0010.0010.0000.0000.0000.000
169A717VAL0-0.039-0.00356.2450.0010.0010.0000.0000.0000.000
170A718LYS10.8880.95058.4150.0070.0070.0000.0000.0000.000
171A719GLU-1-0.934-0.97861.577-0.008-0.0080.0000.0000.0000.000
172A720HIS0-0.070-0.02455.5500.0000.0000.0000.0000.0000.000
173A721MET00.0200.01959.3150.0000.0000.0000.0000.0000.000
174A722SER00.0560.04960.429-0.001-0.0010.0000.0000.0000.000
175A723PHE00.0550.01660.8580.0010.0010.0000.0000.0000.000
176A724GLU-1-0.886-0.94362.734-0.006-0.0060.0000.0000.0000.000
177A725ASP-1-0.909-0.94464.201-0.003-0.0030.0000.0000.0000.000
178A726TYR0-0.073-0.05556.6340.0000.0000.0000.0000.0000.000
179A727SER0-0.045-0.05061.9250.0010.0010.0000.0000.0000.000
180A728GLY0-0.051-0.02963.7500.0010.0010.0000.0000.0000.000
181A729ASN0-0.017-0.01962.9060.0010.0010.0000.0000.0000.000
182A730LEU0-0.022-0.00459.2650.0010.0010.0000.0000.0000.000
183A731LYS10.9140.96063.6210.0030.0030.0000.0000.0000.000
184A732GLY0-0.022-0.01967.0090.0010.0010.0000.0000.0000.000
185A733CYS0-0.060-0.01861.9230.0010.0010.0000.0000.0000.000
186A734CYS0-0.0180.00562.0330.0000.0000.0000.0000.0000.000
187A735ASN00.020-0.01262.1970.0000.0000.0000.0000.0000.000
188A736HIS0-0.038-0.01964.6640.0000.0000.0000.0000.0000.000
189A737LYS10.9090.95966.5820.0000.0000.0000.0000.0000.000
190A738ASP-1-0.835-0.90866.202-0.001-0.0010.0000.0000.0000.000
191A739PHE00.011-0.00359.0440.0000.0000.0000.0000.0000.000
192A740PRO00.0200.01362.1260.0000.0000.0000.0000.0000.000
193A741PHE00.0220.01162.8550.0000.0000.0000.0000.0000.000
194A742TRP00.0710.04457.047-0.001-0.0010.0000.0000.0000.000
195A743TYR00.0340.03154.9890.0000.0000.0000.0000.0000.000
196A744LEU00.0280.00457.8450.0000.0000.0000.0000.0000.000
197A745ASP-1-0.869-0.92458.657-0.011-0.0110.0000.0000.0000.000
198A746ARG10.7770.86355.3660.0100.0100.0000.0000.0000.000
199A747VAL0-0.0350.00153.867-0.001-0.0010.0000.0000.0000.000
200A748TYR0-0.054-0.06154.000-0.001-0.0010.0000.0000.0000.000
201A749CYS0-0.026-0.02255.279-0.001-0.0010.0000.0000.0000.000
202A750SER00.0230.03250.210-0.002-0.0020.0000.0000.0000.000
203A751ILE0-0.038-0.01649.981-0.001-0.0010.0000.0000.0000.000
204A752ARG10.9010.96250.9840.0130.0130.0000.0000.0000.000
205A753ASP-1-0.881-0.94051.255-0.017-0.0170.0000.0000.0000.000
206A754LYS10.8740.94341.8890.0200.0200.0000.0000.0000.000
207A755GLU-1-0.880-0.92845.910-0.011-0.0110.0000.0000.0000.000
208A756ILE0-0.028-0.01944.299-0.002-0.0020.0000.0000.0000.000
209A757VAL0-0.004-0.02240.4060.0010.0010.0000.0000.0000.000
210A758MET0-0.027-0.01935.0910.0020.0020.0000.0000.0000.000
211A759PRO0-0.0380.01035.5160.0040.0040.0000.0000.0000.000