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: ZVV9N

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2163473.18025
FMO2-HF: Nuclear repulsion 2080405.036706
FMO2-HF: Total energy -83068.143544
FMO2-MP2: Total energy -83310.830461


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.
0.2724.3670.177-1.823-2.450.001
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 : 0.047 / q_NPA : 0.024
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].
3C3LYS10.9310.9643.038-1.7872.1690.178-1.807-2.3270.001
4C4THR00.0240.0044.3781.0991.238-0.001-0.016-0.1230.000
5C5ARG10.9880.9876.9250.9290.9290.0000.0000.0000.000
6C6ALA00.0000.01110.0020.2000.2000.0000.0000.0000.000
7C7VAL00.0030.00512.774-0.014-0.0140.0000.0000.0000.000
8C8PRO00.000-0.01316.2420.0190.0190.0000.0000.0000.000
9C9GLY00.0410.03119.4250.0290.0290.0000.0000.0000.000
10C10ALA0-0.001-0.00316.4000.0180.0180.0000.0000.0000.000
11C11GLY00.0130.00218.2520.0180.0180.0000.0000.0000.000
12C12THR0-0.079-0.03620.0210.0440.0440.0000.0000.0000.000
13C13PHE00.0370.02522.8930.0010.0010.0000.0000.0000.000
14C14GLY00.0230.00925.430-0.010-0.0100.0000.0000.0000.000
15C15SER0-0.017-0.00827.1730.0090.0090.0000.0000.0000.000
16C16ALA00.0100.00229.5100.0130.0130.0000.0000.0000.000
17C17VAL0-0.039-0.00522.869-0.004-0.0040.0000.0000.0000.000
18C18ALA00.0110.00224.4280.0190.0190.0000.0000.0000.000
19C19GLY0-0.024-0.01220.993-0.021-0.0210.0000.0000.0000.000
20C20GLN0-0.016-0.01720.065-0.037-0.0370.0000.0000.0000.000
21C21GLU-1-0.906-0.95321.635-0.019-0.0190.0000.0000.0000.000
22C22LEU00.0060.01420.5160.0220.0220.0000.0000.0000.000
23C23PRO0-0.032-0.03121.088-0.010-0.0100.0000.0000.0000.000
24C24LEU00.0410.02424.2760.0150.0150.0000.0000.0000.000
25C25CYS0-0.034-0.03527.038-0.007-0.0070.0000.0000.0000.000
26C26GLY0-0.0160.00926.2900.0060.0060.0000.0000.0000.000
27C27VAL00.0060.01127.2640.0140.0140.0000.0000.0000.000
28C28ARG10.9700.98829.751-0.168-0.1680.0000.0000.0000.000
29C29ALA00.0110.00430.934-0.003-0.0030.0000.0000.0000.000
30C30TYR0-0.005-0.01634.0780.0000.0000.0000.0000.0000.000
31C31TYR0-0.0020.00736.949-0.003-0.0030.0000.0000.0000.000
32C32PRO00.0430.01539.6200.0010.0010.0000.0000.0000.000
33C33PRO00.009-0.00643.392-0.004-0.0040.0000.0000.0000.000
34C34ASN0-0.017-0.01442.357-0.005-0.0050.0000.0000.0000.000
35C35ALA00.0260.01446.574-0.003-0.0030.0000.0000.0000.000
36C36TYR0-0.027-0.00848.342-0.003-0.0030.0000.0000.0000.000
37C37ILE0-0.0140.00447.756-0.002-0.0020.0000.0000.0000.000
38C38PRO00.0000.00750.4670.0000.0000.0000.0000.0000.000
39C39ALA0-0.019-0.02251.774-0.001-0.0010.0000.0000.0000.000
40C40GLN00.0220.02344.470-0.002-0.0020.0000.0000.0000.000
41C41VAL0-0.0060.01246.769-0.001-0.0010.0000.0000.0000.000
42C42ARG10.8250.88643.543-0.010-0.0100.0000.0000.0000.000
43C43ASP-1-0.827-0.90643.494-0.030-0.0300.0000.0000.0000.000
44C44TRP00.0460.01142.9590.0030.0030.0000.0000.0000.000
45C45LEU0-0.032-0.02147.077-0.001-0.0010.0000.0000.0000.000
46C46GLU-1-0.786-0.89448.146-0.004-0.0040.0000.0000.0000.000
47C47PHE0-0.026-0.02548.0160.0020.0020.0000.0000.0000.000
48C48ALA0-0.011-0.00851.9760.0000.0000.0000.0000.0000.000
49C49HIS00.0300.02753.4400.0010.0010.0000.0000.0000.000
50C50ARG10.8820.96255.2710.0090.0090.0000.0000.0000.000
51C51PRO0-0.003-0.01357.546-0.002-0.0020.0000.0000.0000.000
52C52GLY00.053-0.00159.9060.0010.0010.0000.0000.0000.000
53C53LEU0-0.0600.00061.212-0.001-0.0010.0000.0000.0000.000
54C54MET0-0.031-0.01362.607-0.001-0.0010.0000.0000.0000.000
55C55ALA0-0.005-0.00164.087-0.001-0.0010.0000.0000.0000.000
56C56THR0-0.005-0.00167.7230.0010.0010.0000.0000.0000.000
57C57VAL0-0.022-0.01270.9800.0000.0000.0000.0000.0000.000
58C58PRO0-0.009-0.00473.5350.0010.0010.0000.0000.0000.000
59C59TRP00.0210.01277.2170.0000.0000.0000.0000.0000.000
60C60THR0-0.041-0.06480.0960.0010.0010.0000.0000.0000.000
61C61MET0-0.028-0.01083.8100.0000.0000.0000.0000.0000.000
62C62ALA0-0.057-0.01986.7730.0000.0000.0000.0000.0000.000
63C63ASP-1-0.793-0.86181.845-0.019-0.0190.0000.0000.0000.000
64C64GLU-1-0.912-0.95484.946-0.019-0.0190.0000.0000.0000.000
65C65PRO0-0.030-0.03484.1220.0000.0000.0000.0000.0000.000
66C66ALA0-0.077-0.05281.189-0.001-0.0010.0000.0000.0000.000
67C67GLU-1-0.828-0.88980.289-0.026-0.0260.0000.0000.0000.000
68C68ARG10.8910.94073.2730.0320.0320.0000.0000.0000.000
69C69LEU00.0000.00275.6810.0000.0000.0000.0000.0000.000
70C70GLY0-0.002-0.00971.7870.0000.0000.0000.0000.0000.000
71C71ILE0-0.046-0.03068.5420.0000.0000.0000.0000.0000.000
72C72PHE00.0080.01462.3620.0000.0000.0000.0000.0000.000
73C73PRO00.0340.02561.7630.0000.0000.0000.0000.0000.000
74C74VAL00.014-0.00758.6190.0000.0000.0000.0000.0000.000
75C75SER00.0450.01257.121-0.002-0.0020.0000.0000.0000.000
76C76PRO0-0.0070.00653.0480.0030.0030.0000.0000.0000.000
77C77SER0-0.024-0.00755.1130.0010.0010.0000.0000.0000.000
78C78ALA0-0.009-0.00857.7450.0020.0020.0000.0000.0000.000
79C79ILE0-0.018-0.01655.0810.0020.0020.0000.0000.0000.000
80C80ALA0-0.002-0.00653.1630.0010.0010.0000.0000.0000.000
81C81GLY00.009-0.00254.9240.0000.0000.0000.0000.0000.000
82C82THR0-0.0190.00157.5890.0010.0010.0000.0000.0000.000
83C83GLY00.0280.02458.2870.0020.0020.0000.0000.0000.000
84C84ALA0-0.0160.00758.5900.0020.0020.0000.0000.0000.000
85C85PRO00.0370.01854.866-0.002-0.0020.0000.0000.0000.000
86C86ILE00.0170.01053.426-0.002-0.0020.0000.0000.0000.000
87C87SER0-0.048-0.02253.219-0.003-0.0030.0000.0000.0000.000
88C88TYR00.0280.02046.949-0.004-0.0040.0000.0000.0000.000
89C89VAL00.0170.00448.203-0.003-0.0030.0000.0000.0000.000
90C90ILE0-0.025-0.01948.417-0.004-0.0040.0000.0000.0000.000
91C91SER0-0.045-0.02449.209-0.004-0.0040.0000.0000.0000.000
92C92LEU00.0220.02644.331-0.004-0.0040.0000.0000.0000.000
93C93PHE0-0.045-0.02041.662-0.006-0.0060.0000.0000.0000.000
94C94SER00.0340.01743.109-0.001-0.0010.0000.0000.0000.000
95C95GLN0-0.017-0.00644.5390.0000.0000.0000.0000.0000.000
96C96TRP00.0230.01447.2800.0030.0030.0000.0000.0000.000
97C97ARG10.8920.92847.3700.0520.0520.0000.0000.0000.000
98C98GLY00.0510.02952.1660.0020.0020.0000.0000.0000.000
99C99GLU-1-0.831-0.89654.702-0.039-0.0390.0000.0000.0000.000
100C100LEU0-0.042-0.01756.1680.0010.0010.0000.0000.0000.000
101C101ALA00.0120.00859.3790.0010.0010.0000.0000.0000.000
102C102ALA00.0140.01161.7510.0000.0000.0000.0000.0000.000
103C103HIS10.8010.86161.8500.0200.0200.0000.0000.0000.000
104C104LEU0-0.0040.01466.9910.0000.0000.0000.0000.0000.000
105C105LEU00.0060.00670.1960.0010.0010.0000.0000.0000.000
106C106PHE00.0730.02671.920-0.001-0.0010.0000.0000.0000.000
107C107THR0-0.112-0.05773.7270.0010.0010.0000.0000.0000.000
108C108GLY00.0150.01876.5880.0000.0000.0000.0000.0000.000
109C109SER0-0.006-0.01180.2610.0010.0010.0000.0000.0000.000
110C110ALA00.0380.00883.162-0.001-0.0010.0000.0000.0000.000
111C111GLN0-0.045-0.03184.1750.0000.0000.0000.0000.0000.000
112C112HIS0-0.020-0.00383.7110.0000.0000.0000.0000.0000.000
113C113TYR00.0290.02284.6400.0000.0000.0000.0000.0000.000
114C114GLY00.0590.02683.9490.0000.0000.0000.0000.0000.000
115C115ARG10.7940.89280.7270.0160.0160.0000.0000.0000.000
116C116LEU00.0350.04076.546-0.001-0.0010.0000.0000.0000.000
117C117VAL0-0.040-0.02975.6820.0000.0000.0000.0000.0000.000
118C118VAL00.0050.01770.015-0.001-0.0010.0000.0000.0000.000
119C119CYS0-0.036-0.01971.5180.0000.0000.0000.0000.0000.000
120C120TYR00.019-0.00762.3520.0000.0000.0000.0000.0000.000
121C121THR0-0.015-0.01267.4190.0000.0000.0000.0000.0000.000
122C122PRO00.015-0.00463.509-0.001-0.0010.0000.0000.0000.000
123C123ALA0-0.017-0.00360.9750.0000.0000.0000.0000.0000.000
124C124ALA00.0170.01163.1150.0000.0000.0000.0000.0000.000
125C125PRO00.004-0.00364.9460.0000.0000.0000.0000.0000.000
126C126GLN0-0.037-0.01965.9700.0010.0010.0000.0000.0000.000
127C127PRO0-0.0070.01267.9690.0000.0000.0000.0000.0000.000
128C128PRO0-0.021-0.00769.4420.0000.0000.0000.0000.0000.000
129C129SER0-0.044-0.04372.6560.0010.0010.0000.0000.0000.000
130C130THR00.008-0.00175.6740.0010.0010.0000.0000.0000.000
131C131MET00.0660.05176.707-0.001-0.0010.0000.0000.0000.000
132C132GLN00.005-0.01177.383-0.001-0.0010.0000.0000.0000.000
133C133GLU-1-0.863-0.91174.440-0.036-0.0360.0000.0000.0000.000
134C134ALA00.0390.01273.120-0.001-0.0010.0000.0000.0000.000
135C135MET0-0.049-0.00973.1450.0000.0000.0000.0000.0000.000
136C136ARG10.9050.97273.9100.0350.0350.0000.0000.0000.000
137C137GLY0-0.0170.00170.436-0.001-0.0010.0000.0000.0000.000
138C138THR0-0.028-0.01367.6960.0010.0010.0000.0000.0000.000
139C139TYR00.0250.01569.9970.0000.0000.0000.0000.0000.000
140C140THR0-0.009-0.01071.9590.0010.0010.0000.0000.0000.000
141C141VAL0-0.027-0.01474.0100.0000.0000.0000.0000.0000.000
142C142TRP00.0170.00474.5880.0000.0000.0000.0000.0000.000
143C143ASP-1-0.831-0.90977.139-0.014-0.0140.0000.0000.0000.000
144C144VAL0-0.005-0.01277.9220.0000.0000.0000.0000.0000.000
145C145ASN0-0.083-0.03779.2940.0010.0010.0000.0000.0000.000
146C146ALA00.0390.00678.4710.0000.0000.0000.0000.0000.000
147C147ALA0-0.0340.01074.5010.0010.0010.0000.0000.0000.000
148C148SER00.007-0.01573.185-0.001-0.0010.0000.0000.0000.000
149C149THR0-0.018-0.01368.657-0.001-0.0010.0000.0000.0000.000
150C150LEU0-0.0170.02170.8470.0000.0000.0000.0000.0000.000
151C151GLU-1-0.824-0.91065.757-0.017-0.0170.0000.0000.0000.000
152C152PHE0-0.003-0.00466.828-0.001-0.0010.0000.0000.0000.000
153C153THR00.006-0.00162.3890.0000.0000.0000.0000.0000.000
154C154ILE0-0.0010.00061.916-0.001-0.0010.0000.0000.0000.000
155C155PRO0-0.019-0.01561.206-0.001-0.0010.0000.0000.0000.000
156C156PHE00.0040.00853.251-0.002-0.0020.0000.0000.0000.000
157C157ILE0-0.033-0.00858.545-0.002-0.0020.0000.0000.0000.000
158C158SER0-0.045-0.03854.734-0.001-0.0010.0000.0000.0000.000
159C159ASN00.0010.00655.2130.0010.0010.0000.0000.0000.000
160C160SER0-0.025-0.01651.138-0.002-0.0020.0000.0000.0000.000
161C161TYR00.003-0.00649.1980.0030.0030.0000.0000.0000.000
162C162TRP0-0.004-0.01245.8220.0030.0030.0000.0000.0000.000
163C163LYS10.7820.92249.9040.0600.0600.0000.0000.0000.000
164C164THR00.003-0.02747.922-0.001-0.0010.0000.0000.0000.000
165C165VAL0-0.046-0.02448.5970.0030.0030.0000.0000.0000.000
166C166ASP-1-0.804-0.90449.015-0.082-0.0820.0000.0000.0000.000
167C167VAL0-0.010-0.01450.5290.0020.0020.0000.0000.0000.000
168C168ASN0-0.065-0.03849.6860.0030.0030.0000.0000.0000.000
169C169ASN0-0.0080.00552.4650.0030.0030.0000.0000.0000.000
170C170PRO0-0.009-0.00354.101-0.001-0.0010.0000.0000.0000.000
171C171ASP-1-0.897-0.96056.341-0.062-0.0620.0000.0000.0000.000
172C172ALA00.0400.03154.069-0.001-0.0010.0000.0000.0000.000
173C173LEU00.0660.01055.5310.0020.0020.0000.0000.0000.000
174C174LEU0-0.040-0.01349.9030.0020.0020.0000.0000.0000.000
175C175SER0-0.019-0.00152.0290.0000.0000.0000.0000.0000.000
176C176THR00.0840.04754.2130.0030.0030.0000.0000.0000.000
177C177THR0-0.012-0.00757.362-0.002-0.0020.0000.0000.0000.000
178C178GLY00.0330.01659.6450.0010.0010.0000.0000.0000.000
179C179TYR0-0.0250.00762.9820.0000.0000.0000.0000.0000.000
180C180VAL00.0410.02764.6310.0010.0010.0000.0000.0000.000
181C181SER0-0.030-0.01867.1800.0000.0000.0000.0000.0000.000
182C182ILE0-0.011-0.00170.3030.0010.0010.0000.0000.0000.000
183C183TRP00.016-0.01273.4690.0000.0000.0000.0000.0000.000
184C184VAL00.0230.02377.1910.0010.0010.0000.0000.0000.000
185C185GLN0-0.027-0.03879.7580.0000.0000.0000.0000.0000.000
186C186ASN0-0.047-0.03981.9570.0000.0000.0000.0000.0000.000
187C187PRO00.0890.03084.1040.0000.0000.0000.0000.0000.000
188C188LEU0-0.0160.02083.0320.0010.0010.0000.0000.0000.000
189C189VAL00.002-0.01485.5230.0000.0000.0000.0000.0000.000
190C190GLY00.0500.00687.8140.0000.0000.0000.0000.0000.000
191C191PRO0-0.040-0.00490.0530.0000.0000.0000.0000.0000.000
192C192HIS00.0600.02292.449-0.001-0.0010.0000.0000.0000.000
193C193THR0-0.059-0.03793.3330.0010.0010.0000.0000.0000.000
194C194ALA00.0120.03288.9430.0010.0010.0000.0000.0000.000
195C195PRO0-0.035-0.03285.1410.0000.0000.0000.0000.0000.000
196C196ALA00.0750.04287.0770.0000.0000.0000.0000.0000.000
197C197SER0-0.002-0.00182.023-0.001-0.0010.0000.0000.0000.000
198C198ALA0-0.026-0.02180.5330.0010.0010.0000.0000.0000.000
199C199LEU0-0.0100.00575.380-0.001-0.0010.0000.0000.0000.000
200C200VAL00.0250.02072.7010.0010.0010.0000.0000.0000.000
201C201GLN0-0.016-0.00169.706-0.002-0.0020.0000.0000.0000.000
202C202ALA00.0430.02667.7920.0010.0010.0000.0000.0000.000
203C203PHE0-0.015-0.01764.0470.0000.0000.0000.0000.0000.000
204C204ILE0-0.030-0.02159.981-0.001-0.0010.0000.0000.0000.000
205C205SER00.0130.01658.3380.0010.0010.0000.0000.0000.000
206C206ALA0-0.019-0.01454.398-0.002-0.0020.0000.0000.0000.000
207C207GLY00.0360.02556.4020.0020.0020.0000.0000.0000.000
208C208GLU-1-0.886-0.97255.221-0.019-0.0190.0000.0000.0000.000
209C209SER0-0.057-0.04053.2760.0000.0000.0000.0000.0000.000
210C210PHE0-0.043-0.00351.470-0.004-0.0040.0000.0000.0000.000
211C211ASN00.0010.00047.494-0.002-0.0020.0000.0000.0000.000
212C212VAL00.0420.01046.349-0.002-0.0020.0000.0000.0000.000
213C213ARG10.8450.93342.2670.0860.0860.0000.0000.0000.000
214C214LEU00.006-0.00639.011-0.001-0.0010.0000.0000.0000.000
215C215MET00.0300.02135.7840.0040.0040.0000.0000.0000.000
216C216GLN0-0.036-0.01540.334-0.013-0.0130.0000.0000.0000.000
217C217ASN0-0.0080.00442.2150.0060.0060.0000.0000.0000.000
218C218PRO0-0.018-0.02143.671-0.001-0.0010.0000.0000.0000.000
219C219ALA00.0070.00747.310-0.001-0.0010.0000.0000.0000.000
220C220LEU0-0.0160.01149.414-0.002-0.0020.0000.0000.0000.000