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: 6YY5Z

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2162552.502109
FMO2-HF: Nuclear repulsion 2079484.837064
FMO2-HF: Total energy -83067.665046
FMO2-MP2: Total energy -83310.321819


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.
2.1365.5520.116-1.47-2.061-0.001
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 : 0.043 / 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].
3C3LYS10.9320.9653.189-0.0123.2660.116-1.452-1.941-0.001
4C4THR00.0200.0054.2091.1541.2920.000-0.018-0.1200.000
5C5ARG10.9890.9857.0060.9180.9180.0000.0000.0000.000
6C6ALA00.0020.01010.0850.1890.1890.0000.0000.0000.000
7C7VAL00.0010.00812.974-0.030-0.0300.0000.0000.0000.000
8C8PRO0-0.008-0.01716.3950.0240.0240.0000.0000.0000.000
9C9GLY00.0480.03219.6150.0280.0280.0000.0000.0000.000
10C10ALA00.0010.00016.7580.0220.0220.0000.0000.0000.000
11C11GLY00.0120.00218.5860.0130.0130.0000.0000.0000.000
12C12THR0-0.076-0.03420.3300.0380.0380.0000.0000.0000.000
13C13PHE00.0410.02523.0710.0040.0040.0000.0000.0000.000
14C14GLY00.0190.00525.499-0.013-0.0130.0000.0000.0000.000
15C15SER0-0.016-0.00427.2260.0110.0110.0000.0000.0000.000
16C16ALA00.0220.01029.5460.0130.0130.0000.0000.0000.000
17C17VAL0-0.035-0.00222.816-0.002-0.0020.0000.0000.0000.000
18C18ALA00.0240.01224.3770.0180.0180.0000.0000.0000.000
19C19GLY0-0.019-0.01220.977-0.016-0.0160.0000.0000.0000.000
20C20GLN0-0.015-0.03020.120-0.025-0.0250.0000.0000.0000.000
21C21GLU-1-0.947-0.97021.7090.0560.0560.0000.0000.0000.000
22C22LEU00.0100.02220.6280.0280.0280.0000.0000.0000.000
23C23PRO0-0.039-0.03521.042-0.016-0.0160.0000.0000.0000.000
24C24LEU00.0490.02724.2520.0140.0140.0000.0000.0000.000
25C25CYS0-0.040-0.03927.013-0.013-0.0130.0000.0000.0000.000
26C26GLY0-0.0120.00926.2730.0090.0090.0000.0000.0000.000
27C27VAL00.0050.01227.2520.0160.0160.0000.0000.0000.000
28C28ARG10.9680.98629.830-0.221-0.2210.0000.0000.0000.000
29C29ALA00.0110.00530.928-0.005-0.0050.0000.0000.0000.000
30C30TYR0-0.002-0.01434.0690.0020.0020.0000.0000.0000.000
31C31TYR0-0.018-0.00137.145-0.005-0.0050.0000.0000.0000.000
32C32PRO00.0370.01139.6120.0010.0010.0000.0000.0000.000
33C33PRO00.005-0.00543.385-0.003-0.0030.0000.0000.0000.000
34C34ASN00.0120.00042.344-0.005-0.0050.0000.0000.0000.000
35C35ALA00.0300.01446.568-0.004-0.0040.0000.0000.0000.000
36C36TYR0-0.032-0.01148.340-0.002-0.0020.0000.0000.0000.000
37C37ILE0-0.0200.00247.654-0.003-0.0030.0000.0000.0000.000
38C38PRO00.0040.00750.4620.0000.0000.0000.0000.0000.000
39C39ALA0-0.018-0.01951.766-0.001-0.0010.0000.0000.0000.000
40C40GLN00.0020.00444.125-0.001-0.0010.0000.0000.0000.000
41C41VAL00.0130.02546.738-0.001-0.0010.0000.0000.0000.000
42C42ARG10.8590.91543.567-0.038-0.0380.0000.0000.0000.000
43C43ASP-1-0.845-0.91843.487-0.001-0.0010.0000.0000.0000.000
44C44TRP00.0490.00742.8710.0010.0010.0000.0000.0000.000
45C45LEU0-0.014-0.00447.065-0.002-0.0020.0000.0000.0000.000
46C46GLU-1-0.816-0.91848.4550.0190.0190.0000.0000.0000.000
47C47PHE0-0.029-0.02448.3690.0010.0010.0000.0000.0000.000
48C48ALA0-0.008-0.00851.966-0.001-0.0010.0000.0000.0000.000
49C49HIS00.0430.03052.6910.0000.0000.0000.0000.0000.000
50C50ARG10.8780.96055.377-0.009-0.0090.0000.0000.0000.000
51C51PRO00.000-0.01157.535-0.002-0.0020.0000.0000.0000.000
52C52GLY00.0530.00059.8910.0010.0010.0000.0000.0000.000
53C53LEU0-0.0610.00061.219-0.001-0.0010.0000.0000.0000.000
54C54MET0-0.031-0.01462.731-0.001-0.0010.0000.0000.0000.000
55C55ALA0-0.003-0.00264.106-0.001-0.0010.0000.0000.0000.000
56C56THR0-0.0150.00567.7410.0010.0010.0000.0000.0000.000
57C57VAL0-0.015-0.00671.004-0.001-0.0010.0000.0000.0000.000
58C58PRO0-0.008-0.00773.5510.0010.0010.0000.0000.0000.000
59C59TRP00.0340.02477.2350.0000.0000.0000.0000.0000.000
60C60THR0-0.025-0.02680.1110.0010.0010.0000.0000.0000.000
61C61MET0-0.035-0.01783.8270.0000.0000.0000.0000.0000.000
62C62ALA0-0.058-0.02186.8020.0000.0000.0000.0000.0000.000
63C63ASP-1-0.798-0.88881.986-0.012-0.0120.0000.0000.0000.000
64C64GLU-1-0.932-0.97184.979-0.013-0.0130.0000.0000.0000.000
65C65PRO0-0.032-0.03484.2300.0000.0000.0000.0000.0000.000
66C66ALA0-0.060-0.04581.408-0.001-0.0010.0000.0000.0000.000
67C67GLU-1-0.868-0.91080.437-0.018-0.0180.0000.0000.0000.000
68C68ARG10.9050.94673.2180.0230.0230.0000.0000.0000.000
69C69LEU00.0120.01175.8020.0000.0000.0000.0000.0000.000
70C70GLY0-0.008-0.01271.8530.0000.0000.0000.0000.0000.000
71C71ILE0-0.047-0.03268.7810.0000.0000.0000.0000.0000.000
72C72PHE00.0020.01162.4360.0000.0000.0000.0000.0000.000
73C73PRO00.0470.03262.1070.0000.0000.0000.0000.0000.000
74C74VAL00.007-0.00658.8040.0010.0010.0000.0000.0000.000
75C75SER00.019-0.00357.365-0.003-0.0030.0000.0000.0000.000
76C76PRO0-0.0150.00253.3310.0030.0030.0000.0000.0000.000
77C77SER00.0010.00655.3800.0010.0010.0000.0000.0000.000
78C78ALA0-0.009-0.00458.0280.0020.0020.0000.0000.0000.000
79C79ILE0-0.017-0.01755.0660.0020.0020.0000.0000.0000.000
80C80ALA0-0.005-0.00653.2700.0020.0020.0000.0000.0000.000
81C81GLY00.011-0.00354.9330.0000.0000.0000.0000.0000.000
82C82THR0-0.0160.00257.6060.0010.0010.0000.0000.0000.000
83C83GLY00.0300.02458.3080.0010.0010.0000.0000.0000.000
84C84ALA0-0.0110.00758.6280.0020.0020.0000.0000.0000.000
85C85PRO00.0380.02354.912-0.002-0.0020.0000.0000.0000.000
86C86ILE00.0340.01653.456-0.001-0.0010.0000.0000.0000.000
87C87SER0-0.056-0.03053.235-0.003-0.0030.0000.0000.0000.000
88C88TYR00.0380.02547.054-0.003-0.0030.0000.0000.0000.000
89C89VAL00.0040.00148.138-0.002-0.0020.0000.0000.0000.000
90C90ILE0-0.026-0.01848.430-0.003-0.0030.0000.0000.0000.000
91C91SER0-0.046-0.02649.251-0.004-0.0040.0000.0000.0000.000
92C92LEU00.0170.02344.580-0.003-0.0030.0000.0000.0000.000
93C93PHE0-0.054-0.02241.733-0.004-0.0040.0000.0000.0000.000
94C94SER00.0430.02143.471-0.002-0.0020.0000.0000.0000.000
95C95GLN0-0.016-0.00444.3760.0000.0000.0000.0000.0000.000
96C96TRP00.0290.01547.5110.0040.0040.0000.0000.0000.000
97C97ARG10.9160.95646.9570.0320.0320.0000.0000.0000.000
98C98GLY00.0530.02952.2440.0030.0030.0000.0000.0000.000
99C99GLU-1-0.861-0.92754.697-0.023-0.0230.0000.0000.0000.000
100C100LEU0-0.036-0.01056.4280.0010.0010.0000.0000.0000.000
101C101ALA00.0080.00459.3710.0000.0000.0000.0000.0000.000
102C102ALA00.0160.01461.7430.0000.0000.0000.0000.0000.000
103C103HIS10.8290.88761.9230.0060.0060.0000.0000.0000.000
104C104LEU00.0060.01766.9810.0000.0000.0000.0000.0000.000
105C105LEU0-0.0010.00570.1180.0010.0010.0000.0000.0000.000
106C106PHE00.0710.02471.908-0.001-0.0010.0000.0000.0000.000
107C107THR0-0.115-0.05873.7100.0010.0010.0000.0000.0000.000
108C108GLY00.0220.02176.5740.0000.0000.0000.0000.0000.000
109C109SER0-0.005-0.00680.2470.0010.0010.0000.0000.0000.000
110C110ALA00.0400.01183.1510.0000.0000.0000.0000.0000.000
111C111GLN0-0.048-0.03784.1650.0000.0000.0000.0000.0000.000
112C112HIS0-0.030-0.01583.7340.0000.0000.0000.0000.0000.000
113C113TYR00.0390.02084.6460.0000.0000.0000.0000.0000.000
114C114GLY00.0560.02183.9640.0000.0000.0000.0000.0000.000
115C115ARG10.9120.96280.7180.0080.0080.0000.0000.0000.000
116C116LEU00.0390.04376.463-0.001-0.0010.0000.0000.0000.000
117C117VAL0-0.054-0.03175.7430.0000.0000.0000.0000.0000.000
118C118VAL00.0120.01869.999-0.001-0.0010.0000.0000.0000.000
119C119CYS0-0.033-0.02171.6590.0000.0000.0000.0000.0000.000
120C120TYR00.0630.01961.8620.0000.0000.0000.0000.0000.000
121C121THR0-0.015-0.01467.7170.0000.0000.0000.0000.0000.000
122C122PRO00.018-0.00263.735-0.001-0.0010.0000.0000.0000.000
123C123ALA0-0.0100.00061.1470.0000.0000.0000.0000.0000.000
124C124ALA00.0060.00263.2940.0000.0000.0000.0000.0000.000
125C125PRO0-0.023-0.01565.1280.0000.0000.0000.0000.0000.000
126C126GLN00.0040.00166.1480.0010.0010.0000.0000.0000.000
127C127PRO0-0.0270.00267.9440.0010.0010.0000.0000.0000.000
128C128PRO0-0.0170.00269.6560.0000.0000.0000.0000.0000.000
129C129SER0-0.030-0.03372.8680.0010.0010.0000.0000.0000.000
130C130THR00.0090.00275.8960.0010.0010.0000.0000.0000.000
131C131MET00.0590.05276.9260.0000.0000.0000.0000.0000.000
132C132GLN0-0.001-0.01877.597-0.001-0.0010.0000.0000.0000.000
133C133GLU-1-0.854-0.90974.740-0.028-0.0280.0000.0000.0000.000
134C134ALA00.0370.01173.325-0.001-0.0010.0000.0000.0000.000
135C135MET0-0.058-0.02273.3480.0000.0000.0000.0000.0000.000
136C136ARG10.9040.97074.2990.0270.0270.0000.0000.0000.000
137C137GLY0-0.0120.00370.619-0.001-0.0010.0000.0000.0000.000
138C138THR0-0.038-0.01767.7510.0010.0010.0000.0000.0000.000
139C139TYR00.0270.01370.1350.0010.0010.0000.0000.0000.000
140C140THR00.002-0.00471.8880.0010.0010.0000.0000.0000.000
141C141VAL0-0.029-0.01574.0040.0000.0000.0000.0000.0000.000
142C142TRP00.0170.00275.0020.0000.0000.0000.0000.0000.000
143C143ASP-1-0.921-0.96577.131-0.005-0.0050.0000.0000.0000.000
144C144VAL0-0.021-0.01877.9150.0010.0010.0000.0000.0000.000
145C145ASN0-0.067-0.01979.2860.0010.0010.0000.0000.0000.000
146C146ALA00.0540.01678.3420.0000.0000.0000.0000.0000.000
147C147ALA0-0.0350.00774.4600.0010.0010.0000.0000.0000.000
148C148SER00.004-0.01873.314-0.001-0.0010.0000.0000.0000.000
149C149THR0-0.020-0.01468.717-0.001-0.0010.0000.0000.0000.000
150C150LEU0-0.0170.01970.7270.0000.0000.0000.0000.0000.000
151C151GLU-1-0.859-0.94166.156-0.003-0.0030.0000.0000.0000.000
152C152PHE0-0.012-0.00566.805-0.001-0.0010.0000.0000.0000.000
153C153THR00.004-0.00562.4270.0000.0000.0000.0000.0000.000
154C154ILE0-0.0030.00261.867-0.001-0.0010.0000.0000.0000.000
155C155PRO0-0.014-0.01461.1990.0000.0000.0000.0000.0000.000
156C156PHE00.0160.01053.535-0.002-0.0020.0000.0000.0000.000
157C157ILE0-0.027-0.00258.710-0.002-0.0020.0000.0000.0000.000
158C158SER0-0.045-0.04454.932-0.002-0.0020.0000.0000.0000.000
159C159ASN00.0010.00756.0790.0010.0010.0000.0000.0000.000
160C160SER0-0.032-0.02151.232-0.002-0.0020.0000.0000.0000.000
161C161TYR00.005-0.00149.3610.0030.0030.0000.0000.0000.000
162C162TRP0-0.002-0.00645.8510.0030.0030.0000.0000.0000.000
163C163LYS10.8360.96750.0810.0460.0460.0000.0000.0000.000
164C164THR0-0.013-0.04548.0030.0010.0010.0000.0000.0000.000
165C165VAL0-0.038-0.02148.7980.0030.0030.0000.0000.0000.000
166C166ASP-1-0.856-0.93849.283-0.067-0.0670.0000.0000.0000.000
167C167VAL0-0.006-0.01150.7860.0010.0010.0000.0000.0000.000
168C168ASN0-0.014-0.00550.0090.0040.0040.0000.0000.0000.000
169C169ASN0-0.023-0.00852.7220.0020.0020.0000.0000.0000.000
170C170PRO0-0.007-0.00354.3280.0000.0000.0000.0000.0000.000
171C171ASP-1-0.899-0.95556.580-0.050-0.0500.0000.0000.0000.000
172C172ALA00.0330.02954.323-0.001-0.0010.0000.0000.0000.000
173C173LEU00.0650.00955.6950.0020.0020.0000.0000.0000.000
174C174LEU0-0.058-0.04149.9560.0020.0020.0000.0000.0000.000
175C175SER0-0.0140.01352.2200.0000.0000.0000.0000.0000.000
176C176THR00.0760.04554.4190.0040.0040.0000.0000.0000.000
177C177THR0-0.043-0.02657.443-0.001-0.0010.0000.0000.0000.000
178C178GLY00.0250.01159.8430.0010.0010.0000.0000.0000.000
179C179TYR0-0.0240.00763.2070.0000.0000.0000.0000.0000.000
180C180VAL00.0370.02664.6580.0010.0010.0000.0000.0000.000
181C181SER0-0.032-0.01767.3440.0000.0000.0000.0000.0000.000
182C182ILE0-0.0080.00170.3440.0010.0010.0000.0000.0000.000
183C183TRP00.014-0.01673.6300.0000.0000.0000.0000.0000.000
184C184VAL00.0210.02277.2950.0010.0010.0000.0000.0000.000
185C185GLN0-0.038-0.03279.919-0.001-0.0010.0000.0000.0000.000
186C186ASN0-0.051-0.03782.0050.0000.0000.0000.0000.0000.000
187C187PRO00.0910.02984.1100.0000.0000.0000.0000.0000.000
188C188LEU0-0.0120.01882.9060.0010.0010.0000.0000.0000.000
189C189VAL0-0.001-0.01385.5370.0000.0000.0000.0000.0000.000
190C190GLY00.0470.00087.8010.0000.0000.0000.0000.0000.000
191C191PRO0-0.040-0.00290.0400.0000.0000.0000.0000.0000.000
192C192HIS00.0600.02292.4430.0000.0000.0000.0000.0000.000
193C193THR0-0.046-0.03193.5010.0010.0010.0000.0000.0000.000
194C194ALA00.0070.02988.8500.0010.0010.0000.0000.0000.000
195C195PRO0-0.045-0.03585.2110.0000.0000.0000.0000.0000.000
196C196ALA00.0760.04387.1070.0000.0000.0000.0000.0000.000
197C197SER0-0.030-0.01482.035-0.001-0.0010.0000.0000.0000.000
198C198ALA00.008-0.00280.4880.0010.0010.0000.0000.0000.000
199C199LEU0-0.0030.00375.399-0.001-0.0010.0000.0000.0000.000
200C200VAL00.0200.02372.6810.0010.0010.0000.0000.0000.000
201C201GLN0-0.020-0.01869.692-0.001-0.0010.0000.0000.0000.000
202C202ALA00.0450.02867.7600.0010.0010.0000.0000.0000.000
203C203PHE0-0.016-0.01664.0830.0000.0000.0000.0000.0000.000
204C204ILE0-0.028-0.01859.892-0.001-0.0010.0000.0000.0000.000
205C205SER00.0120.01858.3240.0010.0010.0000.0000.0000.000
206C206ALA0-0.018-0.02154.412-0.002-0.0020.0000.0000.0000.000
207C207GLY00.0260.02556.3940.0020.0020.0000.0000.0000.000
208C208GLU-1-0.914-0.98655.2180.0000.0000.0000.0000.0000.000
209C209SER0-0.046-0.02253.2440.0000.0000.0000.0000.0000.000
210C210PHE0-0.046-0.00251.348-0.004-0.0040.0000.0000.0000.000
211C211ASN0-0.018-0.01847.5050.0000.0000.0000.0000.0000.000
212C212VAL00.0350.00846.643-0.003-0.0030.0000.0000.0000.000
213C213ARG10.8530.93242.2950.0640.0640.0000.0000.0000.000
214C214LEU00.001-0.01039.271-0.002-0.0020.0000.0000.0000.000
215C215MET00.0380.01836.0550.0030.0030.0000.0000.0000.000
216C216GLN0-0.032-0.00940.486-0.012-0.0120.0000.0000.0000.000
217C217ASN00.0060.00942.3490.0080.0080.0000.0000.0000.000
218C218PRO0-0.020-0.02143.762-0.002-0.0020.0000.0000.0000.000
219C219ALA00.0060.00847.334-0.001-0.0010.0000.0000.0000.000
220C220LEU0-0.0270.00549.590-0.002-0.0020.0000.0000.0000.000