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: 175RZ

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2452756.811067
FMO2-HF: Nuclear repulsion 2365912.808632
FMO2-HF: Total energy -86844.002435
FMO2-MP2: Total energy -87092.395265


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.
-2.057-0.095-0.008-0.963-0.992-0.001
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 : -0.013
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-7VAL0-0.001-0.0093.597-1.683-0.012-0.009-0.842-0.8210.000
4A-6PRO0-0.019-0.0023.793-0.395-0.1040.001-0.121-0.171-0.001
5A-5ARG10.7900.9035.746-0.578-0.5780.0000.0000.0000.000
6A-4GLY00.0610.0237.646-0.112-0.1120.0000.0000.0000.000
7A-3SER-1-0.863-0.9019.208-0.306-0.3060.0000.0000.0000.000
8A-2HIS-1-0.962-1.02711.3410.0700.0700.0000.0000.0000.000
9A-1MET00.0140.0078.813-0.053-0.0530.0000.0000.0000.000
10A558ASP-1-0.799-0.8799.7260.9560.9560.0000.0000.0000.000
11A559ARG11.0091.00612.267-0.155-0.1550.0000.0000.0000.000
12A560LYS10.9670.97513.906-0.015-0.0150.0000.0000.0000.000
13A561THR0-0.007-0.01913.051-0.029-0.0290.0000.0000.0000.000
14A562GLU-1-0.780-0.87415.7400.2720.2720.0000.0000.0000.000
15A563PHE0-0.0020.01418.286-0.035-0.0350.0000.0000.0000.000
16A564ILE0-0.035-0.01017.173-0.026-0.0260.0000.0000.0000.000
17A565GLU-1-0.930-0.95719.1180.2640.2640.0000.0000.0000.000
18A566CYS0-0.048-0.02721.727-0.016-0.0160.0000.0000.0000.000
19A567THR0-0.011-0.04023.163-0.017-0.0170.0000.0000.0000.000
20A568ASN0-0.045-0.00324.352-0.017-0.0170.0000.0000.0000.000
21A569ALA00.0250.00726.114-0.008-0.0080.0000.0000.0000.000
22A570PHE00.006-0.00627.971-0.008-0.0080.0000.0000.0000.000
23A571ASN0-0.008-0.01527.449-0.011-0.0110.0000.0000.0000.000
24A572GLU-1-0.943-0.94929.9060.0600.0600.0000.0000.0000.000
25A573LYS10.9120.94032.082-0.072-0.0720.0000.0000.0000.000
26A574PRO00.1110.08233.0530.0070.0070.0000.0000.0000.000
27A575LYS10.9270.96233.840-0.053-0.0530.0000.0000.0000.000
28A576LYS10.9150.94731.389-0.093-0.0930.0000.0000.0000.000
29A577GLY00.0490.00729.1890.0070.0070.0000.0000.0000.000
30A578ILE00.0320.01929.0810.0050.0050.0000.0000.0000.000
31A579PRO00.0230.00730.3250.0030.0030.0000.0000.0000.000
32A580MET00.0020.02223.2750.0010.0010.0000.0000.0000.000
33A581LEU00.010-0.00924.9590.0110.0110.0000.0000.0000.000
34A582ILE0-0.0180.00426.3050.0030.0030.0000.0000.0000.000
35A583GLU-1-0.980-0.98225.6850.1630.1630.0000.0000.0000.000
36A584LYS10.8150.88720.502-0.231-0.2310.0000.0000.0000.000
37A585GLY00.0030.01522.4370.0090.0090.0000.0000.0000.000
38A586PHE0-0.104-0.05719.239-0.012-0.0120.0000.0000.0000.000
39A587ILE0-0.058-0.02024.795-0.013-0.0130.0000.0000.0000.000
40A588ALA00.0070.00328.5790.0060.0060.0000.0000.0000.000
41A589SER0-0.016-0.03730.1390.0030.0030.0000.0000.0000.000
42A590ASP-1-0.911-0.97233.0000.0610.0610.0000.0000.0000.000
43A591SER0-0.0120.00335.361-0.005-0.0050.0000.0000.0000.000
44A592ASP-1-0.800-0.90936.6370.0370.0370.0000.0000.0000.000
45A593LYS10.8790.93234.374-0.033-0.0330.0000.0000.0000.000
46A594ASP-1-0.805-0.87232.7380.0430.0430.0000.0000.0000.000
47A595ILE0-0.026-0.01032.8840.0010.0010.0000.0000.0000.000
48A596ALA0-0.0020.00033.739-0.001-0.0010.0000.0000.0000.000
49A597GLU-1-0.826-0.91232.0380.0240.0240.0000.0000.0000.000
50A598PHE0-0.007-0.00925.611-0.002-0.0020.0000.0000.0000.000
51A599LEU0-0.020-0.02030.293-0.002-0.0020.0000.0000.0000.000
52A600PHE00.0370.02832.472-0.003-0.0030.0000.0000.0000.000
53A601ASN0-0.0030.00429.335-0.010-0.0100.0000.0000.0000.000
54A602ASN0-0.092-0.04425.858-0.005-0.0050.0000.0000.0000.000
55A603ASN00.0660.03928.6850.0030.0030.0000.0000.0000.000
56A604ASN0-0.032-0.02328.4600.0030.0030.0000.0000.0000.000
57A605ARG10.8840.95020.679-0.013-0.0130.0000.0000.0000.000
58A606MET00.0070.02626.0620.0120.0120.0000.0000.0000.000
59A607ASN00.010-0.00328.736-0.012-0.0120.0000.0000.0000.000
60A608LYS10.9240.94931.6690.0020.0020.0000.0000.0000.000
61A609LYS10.9440.99134.565-0.025-0.0250.0000.0000.0000.000
62A610THR0-0.070-0.03433.736-0.002-0.0020.0000.0000.0000.000
63A611ILE00.0290.01631.9350.0020.0020.0000.0000.0000.000
64A612GLY00.0500.03535.9990.0000.0000.0000.0000.0000.000
65A613LEU0-0.035-0.04739.0380.0000.0000.0000.0000.0000.000
66A614LEU0-0.052-0.01735.6610.0010.0010.0000.0000.0000.000
67A615LEU00.0120.00038.3290.0000.0000.0000.0000.0000.000
68A616CYS0-0.0150.03341.218-0.001-0.0010.0000.0000.0000.000
69A617HIS0-0.055-0.04342.7320.0000.0000.0000.0000.0000.000
70A618PRO00.0370.01744.8180.0000.0000.0000.0000.0000.000
71A619ASP-1-0.847-0.89244.2680.0360.0360.0000.0000.0000.000
72A620LYS10.8340.89040.102-0.038-0.0380.0000.0000.0000.000
73A621VAL00.0670.04043.6610.0000.0000.0000.0000.0000.000
74A622SER0-0.023-0.02143.862-0.002-0.0020.0000.0000.0000.000
75A623LEU00.0120.01637.404-0.001-0.0010.0000.0000.0000.000
76A624LEU0-0.050-0.02141.209-0.001-0.0010.0000.0000.0000.000
77A625ASN0-0.031-0.03542.921-0.003-0.0030.0000.0000.0000.000
78A626GLU-1-0.862-0.92140.3870.0210.0210.0000.0000.0000.000
79A627TYR0-0.037-0.04635.755-0.003-0.0030.0000.0000.0000.000
80A628ILE0-0.056-0.03340.059-0.002-0.0020.0000.0000.0000.000
81A629ARG10.9360.96142.793-0.019-0.0190.0000.0000.0000.000
82A630LEU0-0.057-0.00836.272-0.001-0.0010.0000.0000.0000.000
83A631PHE0-0.095-0.04439.184-0.002-0.0020.0000.0000.0000.000
84A632ASP-1-0.805-0.86141.401-0.004-0.0040.0000.0000.0000.000
85A633PHE0-0.056-0.05643.460-0.002-0.0020.0000.0000.0000.000
86A634SER0-0.003-0.00946.438-0.001-0.0010.0000.0000.0000.000
87A635GLY0-0.019-0.00548.168-0.001-0.0010.0000.0000.0000.000
88A636LEU0-0.0390.00145.171-0.001-0.0010.0000.0000.0000.000
89A637ARG10.8390.91149.9200.0110.0110.0000.0000.0000.000
90A638VAL00.0400.01350.3380.0000.0000.0000.0000.0000.000
91A639ASP-1-0.759-0.87849.754-0.008-0.0080.0000.0000.0000.000
92A640GLU-1-0.858-0.91647.352-0.011-0.0110.0000.0000.0000.000
93A641ALA00.0260.01945.6770.0000.0000.0000.0000.0000.000
94A642ILE00.0290.01644.9230.0010.0010.0000.0000.0000.000
95A643ARG10.7590.87443.5280.0120.0120.0000.0000.0000.000
96A644ILE00.0040.01240.0970.0000.0000.0000.0000.0000.000
97A645LEU00.0380.04040.0910.0010.0010.0000.0000.0000.000
98A646LEU0-0.031-0.01440.2430.0020.0020.0000.0000.0000.000
99A647THR0-0.046-0.02836.708-0.001-0.0010.0000.0000.0000.000
100A648LYS10.7990.89233.220-0.003-0.0030.0000.0000.0000.000
101A649PHE0-0.025-0.02535.3250.0040.0040.0000.0000.0000.000
102A650ARG10.9290.98037.515-0.008-0.0080.0000.0000.0000.000
103A651LEU00.0500.02439.6280.0030.0030.0000.0000.0000.000
104A652PRO0-0.037-0.01843.0720.0000.0000.0000.0000.0000.000
105A653GLY00.014-0.00744.109-0.002-0.0020.0000.0000.0000.000
106A654GLU-1-0.877-0.92046.8470.0200.0200.0000.0000.0000.000
107A655SER00.0580.02049.537-0.001-0.0010.0000.0000.0000.000
108A656GLN00.027-0.00750.028-0.002-0.0020.0000.0000.0000.000
109A657GLN0-0.092-0.05346.3320.0000.0000.0000.0000.0000.000
110A658ILE00.0050.00147.8000.0000.0000.0000.0000.0000.000
111A659GLU-1-0.899-0.94048.8980.0120.0120.0000.0000.0000.000
112A660ARG10.9560.97547.938-0.021-0.0210.0000.0000.0000.000
113A661ILE0-0.064-0.02943.4410.0000.0000.0000.0000.0000.000
114A662ILE00.003-0.00246.973-0.001-0.0010.0000.0000.0000.000
115A663GLU-1-0.890-0.91949.6790.0120.0120.0000.0000.0000.000
116A664ALA0-0.025-0.01246.7980.0000.0000.0000.0000.0000.000
117A665PHE0-0.026-0.02546.206-0.001-0.0010.0000.0000.0000.000
118A666SER00.016-0.01048.036-0.001-0.0010.0000.0000.0000.000
119A667SER0-0.033-0.02150.852-0.001-0.0010.0000.0000.0000.000
120A668ALA0-0.016-0.00846.7610.0000.0000.0000.0000.0000.000
121A669TYR0-0.039-0.05048.902-0.001-0.0010.0000.0000.0000.000
122A670CYS0-0.021-0.00950.049-0.001-0.0010.0000.0000.0000.000
123A671GLU-1-0.986-0.97549.0150.0060.0060.0000.0000.0000.000
124A672ASN00.003-0.00146.520-0.001-0.0010.0000.0000.0000.000
125A673GLN0-0.064-0.03549.882-0.002-0.0020.0000.0000.0000.000
126A674ASP-1-0.950-0.96253.042-0.001-0.0010.0000.0000.0000.000
127A675TYR0-0.052-0.06055.677-0.001-0.0010.0000.0000.0000.000
128A676ASP-1-0.733-0.81658.727-0.002-0.0020.0000.0000.0000.000
129A677PRO00.032-0.00161.583-0.001-0.0010.0000.0000.0000.000
130A678SER0-0.145-0.08564.5600.0000.0000.0000.0000.0000.000
131A679LYS10.8680.91160.7870.0040.0040.0000.0000.0000.000
132A680ILE0-0.057-0.00763.4880.0000.0000.0000.0000.0000.000
133A681SER0-0.004-0.00764.7450.0000.0000.0000.0000.0000.000
134A682ASP-1-0.910-0.95265.079-0.004-0.0040.0000.0000.0000.000
135A683ASN0-0.095-0.06466.514-0.001-0.0010.0000.0000.0000.000
136A684ALA00.0240.03363.5870.0000.0000.0000.0000.0000.000
137A685GLU-1-0.872-0.96762.203-0.008-0.0080.0000.0000.0000.000
138A686ASP-1-0.828-0.89357.492-0.012-0.0120.0000.0000.0000.000
139A687ASP-1-0.841-0.87657.520-0.008-0.0080.0000.0000.0000.000
140A688ILE0-0.001-0.02153.2560.0010.0010.0000.0000.0000.000
141A689SER0-0.067-0.04256.6430.0010.0010.0000.0000.0000.000
142A690THR0-0.027-0.02358.1670.0010.0010.0000.0000.0000.000
143A691VAL0-0.028-0.01058.9190.0000.0000.0000.0000.0000.000
144A692GLN0-0.045-0.04958.4990.0010.0010.0000.0000.0000.000
145A693PRO0-0.0030.02356.7840.0010.0010.0000.0000.0000.000
146A694ASP-1-0.784-0.86657.7580.0040.0040.0000.0000.0000.000
147A695ALA00.0860.00855.3980.0000.0000.0000.0000.0000.000
148A696ASP-1-0.904-0.95156.2630.0070.0070.0000.0000.0000.000
149A697SER0-0.019-0.03058.7160.0000.0000.0000.0000.0000.000
150A698VAL0-0.031-0.01452.720-0.001-0.0010.0000.0000.0000.000
151A699PHE00.0210.04253.2920.0000.0000.0000.0000.0000.000
152A700ILE00.008-0.00755.0670.0000.0000.0000.0000.0000.000
153A701LEU0-0.020-0.00655.5460.0000.0000.0000.0000.0000.000
154A702SER00.014-0.02751.178-0.001-0.0010.0000.0000.0000.000
155A703TYR0-0.034-0.01652.3670.0000.0000.0000.0000.0000.000
156A704SER00.0210.01354.159-0.001-0.0010.0000.0000.0000.000
157A705ILE00.0450.02350.455-0.001-0.0010.0000.0000.0000.000
158A706ILE0-0.030-0.01448.661-0.001-0.0010.0000.0000.0000.000
159A707MET0-0.051-0.02051.061-0.001-0.0010.0000.0000.0000.000
160A708LEU00.0510.02254.187-0.001-0.0010.0000.0000.0000.000
161A709ASN00.0020.00547.078-0.002-0.0020.0000.0000.0000.000
162A710THR0-0.072-0.04150.760-0.001-0.0010.0000.0000.0000.000
163A711ASP-1-0.844-0.91951.690-0.005-0.0050.0000.0000.0000.000
164A712LEU00.0150.00653.550-0.001-0.0010.0000.0000.0000.000
165A713HIS10.8050.91249.4460.0100.0100.0000.0000.0000.000
166A714ASN00.0310.03350.591-0.001-0.0010.0000.0000.0000.000
167A715PRO0-0.005-0.01250.9690.0000.0000.0000.0000.0000.000
168A716GLN0-0.073-0.04553.7950.0000.0000.0000.0000.0000.000
169A717VAL0-0.041-0.00556.2650.0010.0010.0000.0000.0000.000
170A718LYS10.8300.92458.4350.0060.0060.0000.0000.0000.000
171A719GLU-1-0.875-0.94861.597-0.008-0.0080.0000.0000.0000.000
172A720HIS0-0.070-0.02755.4800.0000.0000.0000.0000.0000.000
173A721MET00.0110.01659.2710.0000.0000.0000.0000.0000.000
174A722SER00.0100.00460.446-0.001-0.0010.0000.0000.0000.000
175A723PHE00.0510.01060.9180.0010.0010.0000.0000.0000.000
176A724GLU-1-0.871-0.94062.751-0.006-0.0060.0000.0000.0000.000
177A725ASP-1-0.865-0.89863.968-0.003-0.0030.0000.0000.0000.000
178A726TYR0-0.034-0.03256.5830.0000.0000.0000.0000.0000.000
179A727SER0-0.053-0.04861.9420.0010.0010.0000.0000.0000.000
180A728GLY0-0.012-0.00463.7660.0000.0000.0000.0000.0000.000
181A729ASN0-0.079-0.06563.3760.0010.0010.0000.0000.0000.000
182A730LEU0-0.0200.00259.3550.0010.0010.0000.0000.0000.000
183A731LYS10.8430.91463.6370.0020.0020.0000.0000.0000.000
184A732GLY0-0.032-0.02267.0250.0000.0000.0000.0000.0000.000
185A733CYS0-0.061-0.01961.9730.0010.0010.0000.0000.0000.000
186A734CYS00.0060.00762.0480.0000.0000.0000.0000.0000.000
187A735ASN00.011-0.00262.1960.0000.0000.0000.0000.0000.000
188A736HIS0-0.037-0.01964.6780.0000.0000.0000.0000.0000.000
189A737LYS10.9080.95966.596-0.001-0.0010.0000.0000.0000.000
190A738ASP-1-0.777-0.86866.217-0.001-0.0010.0000.0000.0000.000
191A739PHE00.0230.00958.9610.0000.0000.0000.0000.0000.000
192A740PRO00.0150.01162.0590.0000.0000.0000.0000.0000.000
193A741PHE00.0130.00262.8690.0000.0000.0000.0000.0000.000
194A742TRP00.0790.04356.9550.0000.0000.0000.0000.0000.000
195A743TYR00.0210.02555.188-0.001-0.0010.0000.0000.0000.000
196A744LEU00.015-0.00157.8590.0000.0000.0000.0000.0000.000
197A745ASP-1-0.848-0.90858.673-0.010-0.0100.0000.0000.0000.000
198A746ARG10.7170.81955.4630.0090.0090.0000.0000.0000.000
199A747VAL0-0.032-0.00453.899-0.001-0.0010.0000.0000.0000.000
200A748TYR0-0.047-0.05354.016-0.001-0.0010.0000.0000.0000.000
201A749CYS0-0.024-0.01855.295-0.001-0.0010.0000.0000.0000.000
202A750SER00.0050.02350.552-0.002-0.0020.0000.0000.0000.000
203A751ILE0-0.038-0.02249.782-0.001-0.0010.0000.0000.0000.000
204A752ARG10.8440.89651.0010.0120.0120.0000.0000.0000.000
205A753ASP-1-0.849-0.89151.432-0.016-0.0160.0000.0000.0000.000
206A754LYS10.8800.94341.9400.0200.0200.0000.0000.0000.000
207A755GLU-1-0.872-0.92145.857-0.010-0.0100.0000.0000.0000.000
208A756ILE0-0.015-0.01544.196-0.001-0.0010.0000.0000.0000.000
209A757VAL0-0.024-0.03540.4480.0010.0010.0000.0000.0000.000
210A758MET0-0.012-0.02135.5640.0010.0010.0000.0000.0000.000
211A759PRO0-0.0100.02935.5200.0040.0040.0000.0000.0000.000