Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R8848

Calculation Name: 5AOO-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5AOO

Chain ID: C

ChEMBL ID:

UniProt ID: O91464

Base Structure: X-ray

Registration Date: 2023-09-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167026.704819
FMO2-HF: Nuclear repulsion 2083958.149805
FMO2-HF: Total energy -83068.555014
FMO2-MP2: Total energy -83311.326284


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(C:1:HIS)


Summations of interaction energy for fragment #1(C:1:HIS)
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.
-0.0993.4990.067-1.435-2.230.005
Interaction energy analysis for fragmet #1(C:1:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.034
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].
3C3LYS10.9300.9693.385-1.8481.5600.067-1.407-2.0670.005
4C4THR00.0300.0174.5680.9271.1170.000-0.028-0.1630.000
5C5ARG10.9370.9667.0040.8300.8300.0000.0000.0000.000
6C6ALA00.0350.03310.0440.2360.2360.0000.0000.0000.000
7C7VAL00.010-0.00712.740-0.003-0.0030.0000.0000.0000.000
8C8PRO0-0.002-0.00716.4110.0060.0060.0000.0000.0000.000
9C9GLY00.0870.04219.7860.0350.0350.0000.0000.0000.000
10C10ALA0-0.038-0.00815.9520.0340.0340.0000.0000.0000.000
11C11GLY00.0130.00817.7840.0070.0070.0000.0000.0000.000
12C12THR0-0.085-0.04419.6140.0580.0580.0000.0000.0000.000
13C13PHE00.0250.01022.183-0.002-0.0020.0000.0000.0000.000
14C14GLY00.007-0.00524.917-0.003-0.0030.0000.0000.0000.000
15C15SER0-0.012-0.00827.2490.0050.0050.0000.0000.0000.000
16C16ALA0-0.0090.00029.2970.0160.0160.0000.0000.0000.000
17C17VAL0-0.039-0.00822.928-0.007-0.0070.0000.0000.0000.000
18C18ALA00.0060.00024.3710.0200.0200.0000.0000.0000.000
19C19GLY0-0.031-0.01320.895-0.018-0.0180.0000.0000.0000.000
20C20GLN0-0.026-0.01519.859-0.057-0.0570.0000.0000.0000.000
21C21GLU-1-0.850-0.92021.914-0.137-0.1370.0000.0000.0000.000
22C22LEU00.0120.00321.0480.0110.0110.0000.0000.0000.000
23C23PRO0-0.012-0.01321.393-0.001-0.0010.0000.0000.0000.000
24C24LEU0-0.0020.00324.5150.0140.0140.0000.0000.0000.000
25C25CYS0-0.015-0.01227.1810.0050.0050.0000.0000.0000.000
26C26GLY00.0160.01726.4430.0030.0030.0000.0000.0000.000
27C27VAL0-0.016-0.00927.3680.0190.0190.0000.0000.0000.000
28C28ARG10.9470.97230.155-0.122-0.1220.0000.0000.0000.000
29C29ALA00.0290.01931.3640.0010.0010.0000.0000.0000.000
30C30TYR0-0.008-0.02134.5470.0040.0040.0000.0000.0000.000
31C31TYR00.0080.01637.409-0.002-0.0020.0000.0000.0000.000
32C32PRO00.0400.00940.0900.0040.0040.0000.0000.0000.000
33C33PRO00.009-0.00243.856-0.004-0.0040.0000.0000.0000.000
34C34ASN0-0.020-0.01442.742-0.004-0.0040.0000.0000.0000.000
35C35ALA00.0210.00646.921-0.003-0.0030.0000.0000.0000.000
36C36TYR0-0.0050.00948.433-0.002-0.0020.0000.0000.0000.000
37C37ILE0-0.020-0.00247.862-0.002-0.0020.0000.0000.0000.000
38C38PRO0-0.0020.00450.835-0.001-0.0010.0000.0000.0000.000
39C39ALA0-0.013-0.02452.020-0.001-0.0010.0000.0000.0000.000
40C40GLN00.0280.02545.181-0.003-0.0030.0000.0000.0000.000
41C41VAL0-0.0160.00847.4950.0010.0010.0000.0000.0000.000
42C42ARG10.8110.88343.9700.0100.0100.0000.0000.0000.000
43C43ASP-1-0.806-0.90043.737-0.051-0.0510.0000.0000.0000.000
44C44TRP00.019-0.00143.1740.0030.0030.0000.0000.0000.000
45C45LEU0-0.018-0.01147.4250.0000.0000.0000.0000.0000.000
46C46GLU-1-0.792-0.89748.259-0.021-0.0210.0000.0000.0000.000
47C47PHE0-0.028-0.02547.9700.0020.0020.0000.0000.0000.000
48C48ALA0-0.007-0.00451.8750.0010.0010.0000.0000.0000.000
49C49HIS00.0330.01853.7070.0010.0010.0000.0000.0000.000
50C50ARG10.8710.95255.2350.0250.0250.0000.0000.0000.000
51C51PRO00.0140.00457.653-0.002-0.0020.0000.0000.0000.000
52C52GLY0-0.008-0.01160.4060.0000.0000.0000.0000.0000.000
53C53LEU0-0.050-0.01561.304-0.001-0.0010.0000.0000.0000.000
54C54MET0-0.024-0.00962.474-0.002-0.0020.0000.0000.0000.000
55C55ALA0-0.0030.00164.066-0.001-0.0010.0000.0000.0000.000
56C56THR0-0.007-0.00667.7710.0010.0010.0000.0000.0000.000
57C57VAL0-0.023-0.00271.097-0.001-0.0010.0000.0000.0000.000
58C58PRO00.002-0.00573.5660.0010.0010.0000.0000.0000.000
59C59TRP0-0.0040.00177.3260.0000.0000.0000.0000.0000.000
60C60THR0-0.024-0.06680.2180.0010.0010.0000.0000.0000.000
61C61MET0-0.041-0.02183.9950.0000.0000.0000.0000.0000.000
62C62ALA0-0.045-0.00886.8030.0000.0000.0000.0000.0000.000
63C63ASP-1-0.794-0.86081.827-0.027-0.0270.0000.0000.0000.000
64C64GLU-1-0.899-0.96084.847-0.025-0.0250.0000.0000.0000.000
65C65PRO0-0.031-0.03584.114-0.001-0.0010.0000.0000.0000.000
66C66ALA0-0.068-0.04781.100-0.001-0.0010.0000.0000.0000.000
67C67GLU-1-0.807-0.87379.926-0.034-0.0340.0000.0000.0000.000
68C68ARG10.8780.92573.2860.0400.0400.0000.0000.0000.000
69C69LEU0-0.007-0.00175.665-0.001-0.0010.0000.0000.0000.000
70C70GLY00.0100.00271.7340.0000.0000.0000.0000.0000.000
71C71ILE0-0.042-0.03568.3730.0000.0000.0000.0000.0000.000
72C72PHE0-0.0030.01362.252-0.001-0.0010.0000.0000.0000.000
73C73PRO00.0490.02961.3270.0010.0010.0000.0000.0000.000
74C74VAL0-0.002-0.00958.8220.0000.0000.0000.0000.0000.000
75C75SER00.0330.00756.790-0.002-0.0020.0000.0000.0000.000
76C76PRO00.0220.00952.8770.0030.0030.0000.0000.0000.000
77C77SER0-0.031-0.01155.0260.0010.0010.0000.0000.0000.000
78C78ALA0-0.0020.00557.8260.0020.0020.0000.0000.0000.000
79C79ILE0-0.021-0.01354.8870.0010.0010.0000.0000.0000.000
80C80ALA0-0.013-0.00852.6760.0010.0010.0000.0000.0000.000
81C81GLY00.021-0.00554.294-0.001-0.0010.0000.0000.0000.000
82C82THR0-0.038-0.00957.0350.0010.0010.0000.0000.0000.000
83C83GLY00.0420.03158.0960.0020.0020.0000.0000.0000.000
84C84ALA0-0.0120.01058.5010.0020.0020.0000.0000.0000.000
85C85PRO00.0260.01754.789-0.003-0.0030.0000.0000.0000.000
86C86ILE00.0180.01453.610-0.003-0.0030.0000.0000.0000.000
87C87SER0-0.047-0.01453.346-0.004-0.0040.0000.0000.0000.000
88C88TYR00.0340.02247.107-0.005-0.0050.0000.0000.0000.000
89C89VAL00.0030.00348.534-0.004-0.0040.0000.0000.0000.000
90C90ILE0-0.017-0.01748.596-0.004-0.0040.0000.0000.0000.000
91C91SER0-0.045-0.03248.932-0.005-0.0050.0000.0000.0000.000
92C92LEU00.0130.02444.539-0.005-0.0050.0000.0000.0000.000
93C93PHE0-0.052-0.02341.836-0.006-0.0060.0000.0000.0000.000
94C94SER00.0350.01942.6090.0000.0000.0000.0000.0000.000
95C95GLN0-0.027-0.02144.8010.0020.0020.0000.0000.0000.000
96C96TRP00.0330.02247.1060.0020.0020.0000.0000.0000.000
97C97ARG10.8760.92047.7390.0610.0610.0000.0000.0000.000
98C98GLY00.0420.02952.0320.0010.0010.0000.0000.0000.000
99C99GLU-1-0.826-0.88754.819-0.045-0.0450.0000.0000.0000.000
100C100LEU0-0.037-0.00555.9590.0000.0000.0000.0000.0000.000
101C101ALA00.002-0.00159.3420.0010.0010.0000.0000.0000.000
102C102ALA00.0140.00562.1050.0000.0000.0000.0000.0000.000
103C103HIS10.7950.86061.9590.0300.0300.0000.0000.0000.000
104C104LEU0-0.0110.00067.0910.0000.0000.0000.0000.0000.000
105C105LEU00.0100.01470.3070.0010.0010.0000.0000.0000.000
106C106PHE00.0370.00771.956-0.001-0.0010.0000.0000.0000.000
107C107THR0-0.076-0.04274.0840.0010.0010.0000.0000.0000.000
108C108GLY00.0570.01476.892-0.001-0.0010.0000.0000.0000.000
109C109SER0-0.024-0.00580.6850.0010.0010.0000.0000.0000.000
110C110ALA00.0420.01683.7640.0000.0000.0000.0000.0000.000
111C111GLN0-0.055-0.03784.5720.0010.0010.0000.0000.0000.000
112C112HIS00.0000.00283.8540.0000.0000.0000.0000.0000.000
113C113TYR0-0.017-0.00484.9030.0000.0000.0000.0000.0000.000
114C114GLY00.0730.03284.3720.0000.0000.0000.0000.0000.000
115C115ARG10.7520.86281.1760.0210.0210.0000.0000.0000.000
116C116LEU00.0460.05176.413-0.001-0.0010.0000.0000.0000.000
117C117VAL0-0.036-0.03575.3880.0010.0010.0000.0000.0000.000
118C118VAL00.0110.02369.616-0.001-0.0010.0000.0000.0000.000
119C119CYS0-0.033-0.01871.3390.0010.0010.0000.0000.0000.000
120C120TYR00.003-0.02062.038-0.001-0.0010.0000.0000.0000.000
121C121THR00.0200.01167.5600.0010.0010.0000.0000.0000.000
122C122PRO00.010-0.00763.748-0.001-0.0010.0000.0000.0000.000
123C123ALA0-0.022-0.00260.8680.0000.0000.0000.0000.0000.000
124C124ALA00.0480.02762.9740.0000.0000.0000.0000.0000.000
125C125PRO0-0.008-0.01564.8400.0000.0000.0000.0000.0000.000
126C126GLN0-0.031-0.01165.8620.0010.0010.0000.0000.0000.000
127C127PRO00.0010.01467.9190.0000.0000.0000.0000.0000.000
128C128PRO0-0.031-0.00869.3810.0010.0010.0000.0000.0000.000
129C129SER0-0.024-0.03772.6510.0010.0010.0000.0000.0000.000
130C130THR00.001-0.01475.7030.0010.0010.0000.0000.0000.000
131C131MET00.0450.05076.796-0.001-0.0010.0000.0000.0000.000
132C132GLN00.006-0.01277.387-0.001-0.0010.0000.0000.0000.000
133C133GLU-1-0.874-0.91074.279-0.042-0.0420.0000.0000.0000.000
134C134ALA00.0290.00272.955-0.001-0.0010.0000.0000.0000.000
135C135MET0-0.0230.00672.9860.0000.0000.0000.0000.0000.000
136C136ARG10.8970.96473.7620.0400.0400.0000.0000.0000.000
137C137GLY0-0.0210.00070.241-0.001-0.0010.0000.0000.0000.000
138C138THR0-0.025-0.01067.3030.0020.0020.0000.0000.0000.000
139C139TYR00.0070.00069.7400.0000.0000.0000.0000.0000.000
140C140THR0-0.022-0.02072.1560.0010.0010.0000.0000.0000.000
141C141VAL0-0.0170.00074.0770.0000.0000.0000.0000.0000.000
142C142TRP00.005-0.00674.5900.0000.0000.0000.0000.0000.000
143C143ASP-1-0.815-0.90077.582-0.019-0.0190.0000.0000.0000.000
144C144VAL00.0140.00778.0070.0000.0000.0000.0000.0000.000
145C145ASN0-0.080-0.03579.6800.0010.0010.0000.0000.0000.000
146C146ALA00.0250.00478.6270.0010.0010.0000.0000.0000.000
147C147ALA0-0.0160.00474.3780.0010.0010.0000.0000.0000.000
148C148SER00.005-0.00173.789-0.001-0.0010.0000.0000.0000.000
149C149THR00.008-0.00669.106-0.001-0.0010.0000.0000.0000.000
150C150LEU0-0.0280.01371.1340.0010.0010.0000.0000.0000.000
151C151GLU-1-0.817-0.89265.819-0.027-0.0270.0000.0000.0000.000
152C152PHE0-0.009-0.01766.6600.0000.0000.0000.0000.0000.000
153C153THR0-0.012-0.00762.305-0.001-0.0010.0000.0000.0000.000
154C154ILE00.0020.00161.7380.0000.0000.0000.0000.0000.000
155C155PRO00.0100.00161.053-0.001-0.0010.0000.0000.0000.000
156C156PHE0-0.0010.00653.064-0.002-0.0020.0000.0000.0000.000
157C157ILE0-0.042-0.02258.280-0.002-0.0020.0000.0000.0000.000
158C158SER00.018-0.00154.684-0.002-0.0020.0000.0000.0000.000
159C159ASN0-0.029-0.01255.2040.0020.0020.0000.0000.0000.000
160C160SER0-0.027-0.03651.367-0.003-0.0030.0000.0000.0000.000
161C161TYR00.0010.00049.4450.0030.0030.0000.0000.0000.000
162C162TRP00.000-0.00745.8880.0010.0010.0000.0000.0000.000
163C163LYS10.7840.92250.0810.0710.0710.0000.0000.0000.000
164C164THR00.010-0.01647.842-0.001-0.0010.0000.0000.0000.000
165C165VAL0-0.053-0.02348.2860.0050.0050.0000.0000.0000.000
166C166ASP-1-0.798-0.89848.830-0.101-0.1010.0000.0000.0000.000
167C167VAL00.006-0.00250.5270.0030.0030.0000.0000.0000.000
168C168ASN0-0.073-0.04849.9980.0030.0030.0000.0000.0000.000
169C169ASN00.0080.01552.4210.0040.0040.0000.0000.0000.000
170C170PRO00.0010.02154.0990.0000.0000.0000.0000.0000.000
171C171ASP-1-0.890-0.95856.376-0.073-0.0730.0000.0000.0000.000
172C172ALA00.0400.02954.1850.0010.0010.0000.0000.0000.000
173C173LEU00.0370.00255.7800.0020.0020.0000.0000.0000.000
174C174LEU0-0.019-0.00549.8110.0020.0020.0000.0000.0000.000
175C175SER0-0.028-0.01252.136-0.001-0.0010.0000.0000.0000.000
176C176THR00.0510.02654.0570.0030.0030.0000.0000.0000.000
177C177THR0-0.005-0.00157.253-0.002-0.0020.0000.0000.0000.000
178C178GLY00.0190.01859.5080.0020.0020.0000.0000.0000.000
179C179TYR0-0.044-0.00862.788-0.001-0.0010.0000.0000.0000.000
180C180VAL00.0170.01264.5430.0010.0010.0000.0000.0000.000
181C181SER0-0.015-0.00567.0080.0000.0000.0000.0000.0000.000
182C182ILE0-0.006-0.00170.2930.0010.0010.0000.0000.0000.000
183C183TRP0-0.006-0.01473.3160.0000.0000.0000.0000.0000.000
184C184VAL00.0270.02477.1450.0010.0010.0000.0000.0000.000
185C185GLN0-0.020-0.03879.4990.0000.0000.0000.0000.0000.000
186C186ASN0-0.049-0.04281.9560.0010.0010.0000.0000.0000.000
187C187PRO00.0880.03884.0770.0000.0000.0000.0000.0000.000
188C188LEU0-0.0310.01782.9380.0010.0010.0000.0000.0000.000
189C189VAL00.010-0.00685.4630.0000.0000.0000.0000.0000.000
190C190GLY00.0560.01287.8300.0000.0000.0000.0000.0000.000
191C191PRO0-0.0320.00490.2390.0000.0000.0000.0000.0000.000
192C192HIS00.0730.01892.652-0.001-0.0010.0000.0000.0000.000
193C193THR0-0.068-0.04293.2260.0010.0010.0000.0000.0000.000
194C194ALA00.0010.02788.8240.0000.0000.0000.0000.0000.000
195C195PRO0-0.012-0.01585.3680.0000.0000.0000.0000.0000.000
196C196ALA00.0440.02387.2430.0000.0000.0000.0000.0000.000
197C197SER00.0060.00082.288-0.001-0.0010.0000.0000.0000.000
198C198ALA0-0.039-0.01380.2250.0010.0010.0000.0000.0000.000
199C199LEU0-0.0050.00875.414-0.001-0.0010.0000.0000.0000.000
200C200VAL00.0030.01372.3180.0010.0010.0000.0000.0000.000
201C201GLN00.0060.01369.644-0.003-0.0030.0000.0000.0000.000
202C202ALA00.0340.00967.6540.0010.0010.0000.0000.0000.000
203C203PHE00.003-0.00564.049-0.001-0.0010.0000.0000.0000.000
204C204ILE0-0.030-0.01959.9500.0000.0000.0000.0000.0000.000
205C205SER00.0060.00458.4270.0010.0010.0000.0000.0000.000
206C206ALA00.0010.00054.645-0.002-0.0020.0000.0000.0000.000
207C207GLY00.0640.03856.6690.0030.0030.0000.0000.0000.000
208C208GLU-1-0.893-0.96755.246-0.031-0.0310.0000.0000.0000.000
209C209SER0-0.045-0.04453.474-0.001-0.0010.0000.0000.0000.000
210C210PHE0-0.031-0.00151.627-0.004-0.0040.0000.0000.0000.000
211C211ASN0-0.001-0.00547.595-0.002-0.0020.0000.0000.0000.000
212C212VAL00.0480.01746.035-0.002-0.0020.0000.0000.0000.000
213C213ARG10.8440.92442.2650.0980.0980.0000.0000.0000.000
214C214LEU00.007-0.01038.699-0.001-0.0010.0000.0000.0000.000
215C215MET00.0320.02935.8050.0040.0040.0000.0000.0000.000
216C216GLN0-0.043-0.02140.137-0.014-0.0140.0000.0000.0000.000
217C217ASN0-0.009-0.00442.0800.0040.0040.0000.0000.0000.000
218C218PRO0-0.002-0.01243.5300.0000.0000.0000.0000.0000.000
219C219ALA0-0.012-0.00247.166-0.001-0.0010.0000.0000.0000.000
220C220LEU0-0.0350.00549.1230.0000.0000.0000.0000.0000.000