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: R56Y8

Calculation Name: 3EUH-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EUH

Chain ID: C

ChEMBL ID:

UniProt ID: P22524

Base Structure: X-ray

Registration Date: 2023-06-19

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2401931.327529
FMO2-HF: Nuclear repulsion 2318275.710396
FMO2-HF: Total energy -83655.617133
FMO2-MP2: Total energy -83899.064732


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:19:MET)


Summations of interaction energy for fragment #1(C:19:MET)
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.
-7.429-0.3115.656-3.256-9.515-0.015
Interaction energy analysis for fragmet #1(C:19:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.020
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].
3C21VAL00.0600.0102.613-3.785-1.3100.680-1.302-1.853-0.013
4C22LYS11.0131.0085.1401.1151.312-0.001-0.007-0.1890.000
5C23LEU00.0260.0312.304-1.361-0.1762.470-0.652-3.002-0.006
6C24ALA00.0160.0003.2600.4922.0990.642-0.685-1.563-0.003
7C25GLN0-0.049-0.0164.0820.059-0.1260.0530.351-0.219-0.001
8C26ALA00.0090.0007.3950.1280.1280.0000.0000.0000.000
9C27LEU0-0.020-0.0373.199-0.895-0.1990.283-0.182-0.797-0.001
10C28ALA0-0.0440.0027.124-0.152-0.1520.0000.0000.0000.000
11C29ASN00.0000.0179.017-0.100-0.1000.0000.0000.0000.000
12C30PRO00.002-0.01911.9720.0300.0300.0000.0000.0000.000
13C31LEU0-0.0080.00014.6600.0030.0030.0000.0000.0000.000
14C32PHE00.0080.0118.5540.0290.0290.0000.0000.0000.000
15C33PRO00.0400.03011.400-0.003-0.0030.0000.0000.0000.000
16C34ALA00.0320.01013.090-0.001-0.0010.0000.0000.0000.000
17C35LEU00.0270.02414.641-0.001-0.0010.0000.0000.0000.000
18C36ASP-1-0.785-0.86211.2410.1650.1650.0000.0000.0000.000
19C37SER0-0.035-0.03013.710-0.005-0.0050.0000.0000.0000.000
20C38ALA0-0.0090.00216.383-0.003-0.0030.0000.0000.0000.000
21C39LEU00.0270.02914.286-0.003-0.0030.0000.0000.0000.000
22C40ARG10.8220.91710.030-0.143-0.1430.0000.0000.0000.000
23C41SER0-0.139-0.06717.120-0.005-0.0050.0000.0000.0000.000
24C42GLY0-0.008-0.01419.944-0.007-0.0070.0000.0000.0000.000
25C43ARG10.7480.87521.052-0.034-0.0340.0000.0000.0000.000
26C44HIS0-0.0330.00620.8170.0090.0090.0000.0000.0000.000
27C45ILE00.000-0.01018.961-0.004-0.0040.0000.0000.0000.000
28C46GLY00.0670.02721.9770.0000.0000.0000.0000.0000.000
29C47LEU0-0.025-0.02724.388-0.002-0.0020.0000.0000.0000.000
30C48ASP-1-0.918-0.95826.2250.0010.0010.0000.0000.0000.000
31C49GLU-1-0.870-0.91422.4690.0230.0230.0000.0000.0000.000
32C50LEU00.024-0.00422.8100.0010.0010.0000.0000.0000.000
33C51ASP-1-0.858-0.92120.422-0.036-0.0360.0000.0000.0000.000
34C52ASN0-0.024-0.02018.3030.0010.0010.0000.0000.0000.000
35C53HIS0-0.040-0.03218.108-0.002-0.0020.0000.0000.0000.000
36C54ALA00.0270.02419.550-0.005-0.0050.0000.0000.0000.000
37C55PHE0-0.026-0.01710.824-0.016-0.0160.0000.0000.0000.000
38C56LEU0-0.024-0.02814.293-0.007-0.0070.0000.0000.0000.000
39C57MET0-0.049-0.02415.129-0.002-0.0020.0000.0000.0000.000
40C58ASP-1-0.979-0.96714.214-0.228-0.2280.0000.0000.0000.000
41C59PHE0-0.029-0.0269.034-0.047-0.0470.0000.0000.0000.000
42C60GLN00.0090.01310.9300.0260.0260.0000.0000.0000.000
43C61GLU-1-0.883-0.95010.981-0.173-0.1730.0000.0000.0000.000
44C62TYR00.019-0.0056.048-0.107-0.1070.0000.0000.0000.000
45C63LEU0-0.006-0.0147.6010.1820.1820.0000.0000.0000.000
46C64GLU-1-0.924-0.9609.2830.1360.1360.0000.0000.0000.000
47C65GLU-1-0.928-0.9667.0610.2510.2510.0000.0000.0000.000
48C66PHE0-0.080-0.0403.977-0.0630.1310.000-0.016-0.1770.000
49C67TYR0-0.001-0.0706.6420.0020.0020.0000.0000.0000.000
50C68ALA00.0480.04410.081-0.021-0.0210.0000.0000.0000.000
51C69ARG10.8940.9592.049-2.539-1.5901.529-0.763-1.7150.009
52C70TYR0-0.031-0.0108.052-0.050-0.0500.0000.0000.0000.000
53C71ASN0-0.060-0.01712.198-0.016-0.0160.0000.0000.0000.000
54C72VAL0-0.018-0.02413.622-0.035-0.0350.0000.0000.0000.000
55C73GLU-1-0.878-0.91713.8510.1620.1620.0000.0000.0000.000
56C74LEU00.0060.01612.895-0.015-0.0150.0000.0000.0000.000
57C75ILE00.0060.00315.350-0.006-0.0060.0000.0000.0000.000
58C76ARG10.9540.98918.903-0.003-0.0030.0000.0000.0000.000
59C77ALA0-0.007-0.00320.7320.0000.0000.0000.0000.0000.000
60C78PRO00.0070.01124.396-0.006-0.0060.0000.0000.0000.000
61C79GLU-1-0.825-0.90227.0910.0190.0190.0000.0000.0000.000
62C80GLY0-0.049-0.02224.476-0.004-0.0040.0000.0000.0000.000
63C81PHE00.0130.04523.252-0.002-0.0020.0000.0000.0000.000
64C82PHE00.005-0.00917.4160.0070.0070.0000.0000.0000.000
65C83TYR0-0.038-0.08219.228-0.005-0.0050.0000.0000.0000.000
66C84LEU00.0000.02114.0630.0070.0070.0000.0000.0000.000
67C85ARG10.8330.88517.775-0.111-0.1110.0000.0000.0000.000
68C86PRO0-0.047-0.02618.0190.0110.0110.0000.0000.0000.000
69C87ARG10.9941.00016.655-0.200-0.2000.0000.0000.0000.000
70C88SER0-0.035-0.03020.204-0.001-0.0010.0000.0000.0000.000
71C89THR0-0.023-0.02317.910-0.005-0.0050.0000.0000.0000.000
72C90THR0-0.033-0.02417.1270.0220.0220.0000.0000.0000.000
73C91LEU00.0080.00713.364-0.011-0.0110.0000.0000.0000.000
74C92ILE0-0.040-0.01213.137-0.012-0.0120.0000.0000.0000.000
75C93PRO00.0100.01517.2720.0000.0000.0000.0000.0000.000
76C94ARG11.0000.99621.093-0.091-0.0910.0000.0000.0000.000
77C95SER0-0.059-0.03823.022-0.006-0.0060.0000.0000.0000.000
78C96VAL0-0.010-0.00826.3430.0030.0030.0000.0000.0000.000
79C97LEU0-0.038-0.00429.254-0.002-0.0020.0000.0000.0000.000
80C98SER00.000-0.01831.5490.0000.0000.0000.0000.0000.000
81C99GLU-1-0.813-0.93735.2050.0340.0340.0000.0000.0000.000
82C100LEU0-0.0030.00737.833-0.001-0.0010.0000.0000.0000.000
83C101ASP-1-0.782-0.86433.5520.0330.0330.0000.0000.0000.000
84C102MET00.0440.03132.816-0.001-0.0010.0000.0000.0000.000
85C103MET0-0.044-0.01035.754-0.002-0.0020.0000.0000.0000.000
86C104VAL00.0370.01036.639-0.002-0.0020.0000.0000.0000.000
87C105GLY00.018-0.01434.535-0.001-0.0010.0000.0000.0000.000
88C106LYS10.8080.86035.276-0.032-0.0320.0000.0000.0000.000
89C107ILE00.0190.04337.518-0.001-0.0010.0000.0000.0000.000
90C108LEU0-0.029-0.01134.234-0.002-0.0020.0000.0000.0000.000
91C109CYS0-0.015-0.03235.087-0.002-0.0020.0000.0000.0000.000
92C110TYR0-0.035-0.00236.588-0.001-0.0010.0000.0000.0000.000
93C111LEU0-0.014-0.01939.935-0.002-0.0020.0000.0000.0000.000
94C112TYR0-0.055-0.02233.469-0.002-0.0020.0000.0000.0000.000
95C113LEU0-0.027-0.01036.927-0.001-0.0010.0000.0000.0000.000
96C114SER00.0160.01840.326-0.001-0.0010.0000.0000.0000.000
97C115PRO00.0190.00643.786-0.001-0.0010.0000.0000.0000.000
98C116GLU-1-0.954-0.97945.5580.0030.0030.0000.0000.0000.000
99C117ARG10.8680.92543.934-0.008-0.0080.0000.0000.0000.000
100C118LEU0-0.0070.01342.657-0.001-0.0010.0000.0000.0000.000
101C119ALA00.0150.02044.187-0.001-0.0010.0000.0000.0000.000
102C120ASN0-0.056-0.03543.018-0.001-0.0010.0000.0000.0000.000
103C121GLU-1-0.953-0.95940.816-0.006-0.0060.0000.0000.0000.000
104C122GLY0-0.019-0.00938.1740.0000.0000.0000.0000.0000.000
105C123ILE0-0.083-0.05438.1830.0020.0020.0000.0000.0000.000
106C124PHE00.0600.02439.3870.0000.0000.0000.0000.0000.000
107C125THR00.003-0.01741.1930.0000.0000.0000.0000.0000.000
108C126GLN0-0.033-0.04139.9060.0020.0020.0000.0000.0000.000
109C127GLN0-0.061-0.02143.0690.0010.0010.0000.0000.0000.000
110C128GLU-1-0.817-0.91444.3120.0060.0060.0000.0000.0000.000
111C129LEU0-0.024-0.00639.4900.0010.0010.0000.0000.0000.000
112C130TYR0-0.013-0.02843.0880.0010.0010.0000.0000.0000.000
113C131ASP-1-0.838-0.92245.2820.0100.0100.0000.0000.0000.000
114C132GLU-1-0.866-0.94644.4390.0120.0120.0000.0000.0000.000
115C133LEU0-0.041-0.04242.6840.0010.0010.0000.0000.0000.000
116C134LEU0-0.051-0.04745.2190.0010.0010.0000.0000.0000.000
117C135THR0-0.0350.00248.6490.0000.0000.0000.0000.0000.000
118C136LEU0-0.026-0.00744.4290.0000.0000.0000.0000.0000.000
119C137ALA0-0.034-0.00145.2200.0010.0010.0000.0000.0000.000
120C138ASP-1-0.825-0.93847.2100.0190.0190.0000.0000.0000.000
121C139GLU-1-0.927-0.97049.3790.0150.0150.0000.0000.0000.000
122C140ALA00.0060.00850.3280.0000.0000.0000.0000.0000.000
123C141LYS10.9220.95346.056-0.026-0.0260.0000.0000.0000.000
124C142LEU00.0060.00743.8110.0010.0010.0000.0000.0000.000
125C143LEU00.009-0.00446.3600.0010.0010.0000.0000.0000.000
126C144LYS10.9260.97048.172-0.022-0.0220.0000.0000.0000.000
127C145LEU0-0.0320.00741.7540.0010.0010.0000.0000.0000.000
128C146VAL0-0.108-0.04644.4340.0010.0010.0000.0000.0000.000
129C147ASN0-0.024-0.01046.1300.0010.0010.0000.0000.0000.000
130C148ASN00.0000.00448.9510.0010.0010.0000.0000.0000.000
131C149ARG10.9130.95050.257-0.020-0.0200.0000.0000.0000.000
132C150SER00.0340.01752.291-0.001-0.0010.0000.0000.0000.000
133C151THR0-0.013-0.01153.8190.0010.0010.0000.0000.0000.000
134C152GLY00.0440.02555.004-0.001-0.0010.0000.0000.0000.000
135C153SER0-0.004-0.00654.841-0.001-0.0010.0000.0000.0000.000
136C154ASP-1-0.880-0.93154.3980.0120.0120.0000.0000.0000.000
137C155VAL00.0050.00752.9190.0000.0000.0000.0000.0000.000
138C156ASP-1-0.836-0.95250.7600.0180.0180.0000.0000.0000.000
139C157ARG10.9941.00449.475-0.012-0.0120.0000.0000.0000.000
140C158GLN00.0620.03849.0750.0000.0000.0000.0000.0000.000
141C159LYS10.8360.91345.905-0.017-0.0170.0000.0000.0000.000
142C160LEU0-0.018-0.00644.6980.0010.0010.0000.0000.0000.000
143C161GLN0-0.012-0.00644.3300.0010.0010.0000.0000.0000.000
144C162GLU-1-0.841-0.90443.5480.0160.0160.0000.0000.0000.000
145C163LYS10.9240.95940.715-0.024-0.0240.0000.0000.0000.000
146C164VAL00.0370.01939.6840.0010.0010.0000.0000.0000.000
147C165ARG10.9600.98739.224-0.012-0.0120.0000.0000.0000.000
148C166SER0-0.057-0.03937.0710.0000.0000.0000.0000.0000.000
149C167SER0-0.049-0.02835.3690.0010.0010.0000.0000.0000.000
150C168LEU00.0310.04134.3340.0020.0020.0000.0000.0000.000
151C169ASN00.0080.00033.6930.0020.0020.0000.0000.0000.000
152C170ARG10.8550.91230.116-0.033-0.0330.0000.0000.0000.000
153C171LEU00.0400.01029.5670.0030.0030.0000.0000.0000.000
154C172ARG10.9040.97829.165-0.021-0.0210.0000.0000.0000.000
155C173ARG10.9030.95826.780-0.034-0.0340.0000.0000.0000.000
156C174LEU00.015-0.00125.2020.0020.0020.0000.0000.0000.000
157C175GLY00.0060.00525.3600.0030.0030.0000.0000.0000.000
158C176MET0-0.073-0.00626.661-0.003-0.0030.0000.0000.0000.000
159C177VAL00.0090.00429.571-0.003-0.0030.0000.0000.0000.000
160C178TRP00.0160.01726.5100.0020.0020.0000.0000.0000.000
161C179PHE0-0.012-0.03432.1940.0000.0000.0000.0000.0000.000
162C180MET0-0.011-0.01534.623-0.002-0.0020.0000.0000.0000.000
163C181GLY00.0190.02137.196-0.002-0.0020.0000.0000.0000.000
164C182HIS0-0.018-0.01137.1990.0020.0020.0000.0000.0000.000
165C183ASP-1-0.836-0.91238.7990.0080.0080.0000.0000.0000.000
166C184SER0-0.032-0.01538.0060.0010.0010.0000.0000.0000.000
167C185SER0-0.084-0.03439.0720.0010.0010.0000.0000.0000.000
168C186LYS10.9800.98940.645-0.002-0.0020.0000.0000.0000.000
169C187PHE00.006-0.01435.7990.0000.0000.0000.0000.0000.000
170C188ARG11.0051.01833.5800.0010.0010.0000.0000.0000.000
171C189ILE0-0.034-0.00533.8540.0020.0020.0000.0000.0000.000
172C190THR00.0440.04027.897-0.003-0.0030.0000.0000.0000.000
173C191GLU-1-0.724-0.87427.1980.0110.0110.0000.0000.0000.000
174C192SER00.012-0.03025.8060.0020.0020.0000.0000.0000.000
175C193VAL00.0160.01627.9330.0050.0050.0000.0000.0000.000
176C194PHE00.026-0.01130.1390.0010.0010.0000.0000.0000.000
177C195ARG10.8430.92024.739-0.059-0.0590.0000.0000.0000.000
178C196PHE0-0.0320.00329.8000.0020.0020.0000.0000.0000.000
179C197GLY00.0150.01733.080-0.001-0.0010.0000.0000.0000.000
180C198ALA00.0140.00230.624-0.001-0.0010.0000.0000.0000.000
181C199ASP-1-0.937-0.96032.6390.0350.0350.0000.0000.0000.000
182C200VAL0-0.014-0.02435.483-0.001-0.0010.0000.0000.0000.000
183C201ARG10.7820.89531.535-0.024-0.0240.0000.0000.0000.000
184C202ALA0-0.031-0.01433.870-0.002-0.0020.0000.0000.0000.000
185C203GLY00.0240.00135.7810.0010.0010.0000.0000.0000.000
186C204ASP-1-0.892-0.94337.1650.0360.0360.0000.0000.0000.000
187C205ASP-1-0.879-0.92140.3130.0310.0310.0000.0000.0000.000
188C206PRO00.0870.02239.5960.0030.0030.0000.0000.0000.000
189C207ARG10.9230.95138.571-0.030-0.0300.0000.0000.0000.000
190C208GLU-1-0.923-0.94038.6300.0420.0420.0000.0000.0000.000
191C209ALA00.0210.00135.0760.0040.0040.0000.0000.0000.000
192C210GLN00.0150.00433.8230.0050.0050.0000.0000.0000.000
193C211ARG10.8950.95333.684-0.045-0.0450.0000.0000.0000.000
194C212ARG10.8470.90727.390-0.061-0.0610.0000.0000.0000.000
195C213LEU00.001-0.00829.4490.0060.0060.0000.0000.0000.000
196C214ILE0-0.050-0.02128.8290.0050.0050.0000.0000.0000.000
197C215ARG10.8790.94528.365-0.070-0.0700.0000.0000.0000.000
198C216ASP-1-0.823-0.90425.3910.0870.0870.0000.0000.0000.000
199C217GLY0-0.023-0.00424.2090.0060.0060.0000.0000.0000.000
200C218GLU-1-0.817-0.84424.4810.0690.0690.0000.0000.0000.000
201C219ALA0-0.019-0.01526.508-0.005-0.0050.0000.0000.0000.000
202C220MET00.0100.00829.3620.0080.0080.0000.0000.0000.000
203C221PRO0-0.0190.00631.389-0.003-0.0030.0000.0000.0000.000
204C222ILE0-0.014-0.00535.1530.0020.0020.0000.0000.0000.000
205C223GLU-1-0.916-0.94637.2630.0400.0400.0000.0000.0000.000
206C224ASN0-0.054-0.03240.184-0.001-0.0010.0000.0000.0000.000