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

tag_button

FMODB ID: Q1ZNY

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2404274.483171
FMO2-HF: Nuclear repulsion 2320617.268647
FMO2-HF: Total energy -83657.214524
FMO2-MP2: Total energy -83900.559852


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.
-9.393-2.423.931-3.207-7.6990
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 : 0.009 / q_NPA : 0.007
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].
3C21VAL00.0530.0082.925-2.6070.2280.179-1.409-1.605-0.004
4C22LYS10.8590.9285.5331.3321.3320.0000.0000.0000.000
5C23LEU00.0070.0202.445-0.1680.6043.029-0.786-3.014-0.001
6C24ALA00.0130.0033.5410.9722.0360.140-0.323-0.882-0.001
7C25GLN0-0.024-0.0094.617-0.184-0.0930.0130.021-0.1250.000
8C26ALA00.002-0.0047.5320.1470.1470.0000.0000.0000.000
9C27LEU0-0.022-0.0363.866-0.4120.0660.063-0.124-0.4170.000
10C28ALA0-0.0420.0047.277-0.183-0.1830.0000.0000.0000.000
11C29ASN0-0.0140.0029.418-0.176-0.1760.0000.0000.0000.000
12C30PRO00.002-0.01712.2940.0770.0770.0000.0000.0000.000
13C31LEU00.0020.01214.8880.0070.0070.0000.0000.0000.000
14C32PHE00.0080.0078.8650.0650.0650.0000.0000.0000.000
15C33PRO00.0550.04012.0770.0090.0090.0000.0000.0000.000
16C34ALA00.0330.00813.701-0.001-0.0010.0000.0000.0000.000
17C35LEU00.0160.01915.124-0.015-0.0150.0000.0000.0000.000
18C36ASP-1-0.746-0.83211.5550.9300.9300.0000.0000.0000.000
19C37SER0-0.053-0.03514.441-0.025-0.0250.0000.0000.0000.000
20C38ALA00.0050.00617.028-0.028-0.0280.0000.0000.0000.000
21C39LEU00.0250.02715.219-0.031-0.0310.0000.0000.0000.000
22C40ARG10.7630.85910.413-0.916-0.9160.0000.0000.0000.000
23C41SER0-0.135-0.06518.026-0.035-0.0350.0000.0000.0000.000
24C42GLY0-0.007-0.01320.985-0.034-0.0340.0000.0000.0000.000
25C43ARG10.7480.88121.831-0.219-0.2190.0000.0000.0000.000
26C44HIS0-0.034-0.00921.7000.0180.0180.0000.0000.0000.000
27C45ILE0-0.016-0.01819.263-0.012-0.0120.0000.0000.0000.000
28C46GLY00.0810.03422.514-0.003-0.0030.0000.0000.0000.000
29C47LEU0-0.036-0.03424.6450.0040.0040.0000.0000.0000.000
30C48ASP-1-0.851-0.90926.3700.0900.0900.0000.0000.0000.000
31C49GLU-1-0.840-0.89922.6020.1990.1990.0000.0000.0000.000
32C50LEU00.014-0.00322.8640.0130.0130.0000.0000.0000.000
33C51ASP-1-0.857-0.92720.5810.0830.0830.0000.0000.0000.000
34C52ASN0-0.016-0.02618.3060.0210.0210.0000.0000.0000.000
35C53HIS0-0.044-0.03018.1500.0140.0140.0000.0000.0000.000
36C54ALA00.0250.02019.495-0.010-0.0100.0000.0000.0000.000
37C55PHE0-0.018-0.01610.951-0.018-0.0180.0000.0000.0000.000
38C56LEU0-0.025-0.02514.3010.0140.0140.0000.0000.0000.000
39C57MET0-0.025-0.01315.030-0.005-0.0050.0000.0000.0000.000
40C58ASP-1-0.867-0.90214.276-0.215-0.2150.0000.0000.0000.000
41C59PHE0-0.045-0.0379.319-0.082-0.0820.0000.0000.0000.000
42C60GLN0-0.041-0.01610.8030.1030.1030.0000.0000.0000.000
43C61GLU-1-0.824-0.90410.307-0.374-0.3740.0000.0000.0000.000
44C62TYR0-0.040-0.0496.201-0.070-0.0700.0000.0000.0000.000
45C63LEU0-0.016-0.0157.7110.5320.5320.0000.0000.0000.000
46C64GLU-1-0.857-0.9219.7500.3620.3620.0000.0000.0000.000
47C65GLU-1-0.906-0.9546.4490.0280.0280.0000.0000.0000.000
48C66PHE0-0.075-0.0445.4730.1820.305-0.001-0.011-0.1120.000
49C67TYR00.012-0.0467.552-0.059-0.0590.0000.0000.0000.000
50C68ALA00.0490.04410.481-0.110-0.1100.0000.0000.0000.000
51C69ARG10.8980.9612.421-7.598-5.9880.508-0.575-1.5440.006
52C70TYR0-0.024-0.0078.505-0.193-0.1930.0000.0000.0000.000
53C71ASN0-0.072-0.02913.119-0.103-0.1030.0000.0000.0000.000
54C72VAL0-0.026-0.02614.581-0.096-0.0960.0000.0000.0000.000
55C73GLU-1-0.784-0.86414.6270.3410.3410.0000.0000.0000.000
56C74LEU00.0010.01412.974-0.022-0.0220.0000.0000.0000.000
57C75ILE0-0.009-0.00716.029-0.038-0.0380.0000.0000.0000.000
58C76ARG10.9570.99019.324-0.076-0.0760.0000.0000.0000.000
59C77ALA0-0.0030.00521.030-0.017-0.0170.0000.0000.0000.000
60C78PRO00.0120.00824.712-0.011-0.0110.0000.0000.0000.000
61C79GLU-1-0.833-0.89327.1620.0760.0760.0000.0000.0000.000
62C80GLY0-0.047-0.02624.398-0.005-0.0050.0000.0000.0000.000
63C81PHE00.0240.04723.4540.0040.0040.0000.0000.0000.000
64C82PHE0-0.001-0.01717.6570.0100.0100.0000.0000.0000.000
65C83TYR0-0.018-0.05320.052-0.008-0.0080.0000.0000.0000.000
66C84LEU0-0.0040.02215.1550.0080.0080.0000.0000.0000.000
67C85ARG10.8270.88718.938-0.265-0.2650.0000.0000.0000.000
68C86PRO0-0.044-0.02919.2070.0090.0090.0000.0000.0000.000
69C87ARG10.9000.95217.063-0.385-0.3850.0000.0000.0000.000
70C88SER0-0.015-0.02421.0710.0100.0100.0000.0000.0000.000
71C89THR0-0.019-0.01319.257-0.010-0.0100.0000.0000.0000.000
72C90THR0-0.027-0.01818.0240.0600.0600.0000.0000.0000.000
73C91LEU00.0030.00413.573-0.030-0.0300.0000.0000.0000.000
74C92ILE0-0.042-0.01213.9450.0040.0040.0000.0000.0000.000
75C93PRO00.0110.01018.159-0.025-0.0250.0000.0000.0000.000
76C94ARG11.0171.01621.973-0.233-0.2330.0000.0000.0000.000
77C95SER0-0.051-0.03424.167-0.017-0.0170.0000.0000.0000.000
78C96VAL0-0.015-0.01127.4810.0040.0040.0000.0000.0000.000
79C97LEU0-0.0220.00430.540-0.004-0.0040.0000.0000.0000.000
80C98SER00.008-0.01932.819-0.006-0.0060.0000.0000.0000.000
81C99GLU-1-0.782-0.92636.4240.0930.0930.0000.0000.0000.000
82C100LEU00.0220.01739.135-0.003-0.0030.0000.0000.0000.000
83C101ASP-1-0.753-0.81734.7190.1290.1290.0000.0000.0000.000
84C102MET00.0370.03133.8410.0010.0010.0000.0000.0000.000
85C103MET0-0.042-0.01036.924-0.005-0.0050.0000.0000.0000.000
86C104VAL00.0340.00537.628-0.004-0.0040.0000.0000.0000.000
87C105GLY00.018-0.00435.540-0.002-0.0020.0000.0000.0000.000
88C106LYS10.7970.85636.276-0.093-0.0930.0000.0000.0000.000
89C107ILE00.0080.01438.503-0.004-0.0040.0000.0000.0000.000
90C108LEU0-0.025-0.00834.883-0.004-0.0040.0000.0000.0000.000
91C109CYS0-0.012-0.01535.933-0.003-0.0030.0000.0000.0000.000
92C110TYR0-0.036-0.00637.375-0.005-0.0050.0000.0000.0000.000
93C111LEU0-0.006-0.01540.689-0.004-0.0040.0000.0000.0000.000
94C112TYR0-0.059-0.02733.466-0.004-0.0040.0000.0000.0000.000
95C113LEU0-0.025-0.00937.619-0.003-0.0030.0000.0000.0000.000
96C114SER0-0.0080.01140.892-0.005-0.0050.0000.0000.0000.000
97C115PRO00.0470.01244.3690.0000.0000.0000.0000.0000.000
98C116GLU-1-0.959-0.97445.9470.0280.0280.0000.0000.0000.000
99C117ARG10.8200.88744.452-0.047-0.0470.0000.0000.0000.000
100C118LEU0-0.0070.01142.7010.0010.0010.0000.0000.0000.000
101C119ALA00.0180.01944.4760.0000.0000.0000.0000.0000.000
102C120ASN0-0.080-0.05743.310-0.003-0.0030.0000.0000.0000.000
103C121GLU-1-0.931-0.94940.9710.0350.0350.0000.0000.0000.000
104C122GLY0-0.011-0.00838.5390.0030.0030.0000.0000.0000.000
105C123ILE0-0.078-0.04738.6360.0070.0070.0000.0000.0000.000
106C124PHE00.0550.02439.663-0.003-0.0030.0000.0000.0000.000
107C125THR0-0.023-0.04341.7720.0030.0030.0000.0000.0000.000
108C126GLN00.010-0.02540.5070.0040.0040.0000.0000.0000.000
109C127GLN0-0.078-0.03943.8430.0020.0020.0000.0000.0000.000
110C128GLU-1-0.737-0.85245.1480.0510.0510.0000.0000.0000.000
111C129LEU0-0.045-0.01540.0170.0000.0000.0000.0000.0000.000
112C130TYR0-0.005-0.02543.9100.0000.0000.0000.0000.0000.000
113C131ASP-1-0.815-0.90146.1960.0510.0510.0000.0000.0000.000
114C132GLU-1-0.819-0.90145.1880.0490.0490.0000.0000.0000.000
115C133LEU0-0.050-0.02743.3480.0010.0010.0000.0000.0000.000
116C134LEU0-0.043-0.03546.1950.0000.0000.0000.0000.0000.000
117C135THR0-0.062-0.01649.636-0.002-0.0020.0000.0000.0000.000
118C136LEU0-0.008-0.00145.379-0.001-0.0010.0000.0000.0000.000
119C137ALA0-0.031-0.00146.3110.0010.0010.0000.0000.0000.000
120C138ASP-1-0.807-0.92148.3050.0560.0560.0000.0000.0000.000
121C139GLU-1-0.828-0.91950.5870.0550.0550.0000.0000.0000.000
122C140ALA0-0.0040.00051.5350.0020.0020.0000.0000.0000.000
123C141LYS10.8680.92245.262-0.078-0.0780.0000.0000.0000.000
124C142LEU00.0000.00444.9540.0040.0040.0000.0000.0000.000
125C143LEU00.0220.00347.5490.0030.0030.0000.0000.0000.000
126C144LYS10.9180.97049.461-0.060-0.0600.0000.0000.0000.000
127C145LEU0-0.0470.00443.1480.0030.0030.0000.0000.0000.000
128C146VAL0-0.108-0.04945.4610.0050.0050.0000.0000.0000.000
129C147ASN0-0.013-0.01947.1210.0030.0030.0000.0000.0000.000
130C148ASN0-0.0040.00949.9090.0000.0000.0000.0000.0000.000
131C149ARG10.9220.95251.271-0.059-0.0590.0000.0000.0000.000
132C150SER00.013-0.01253.245-0.001-0.0010.0000.0000.0000.000
133C151THR0-0.031-0.01954.9380.0020.0020.0000.0000.0000.000
134C152GLY00.0370.02256.126-0.002-0.0020.0000.0000.0000.000
135C153SER0-0.010-0.03055.864-0.001-0.0010.0000.0000.0000.000
136C154ASP-1-0.837-0.91555.3400.0520.0520.0000.0000.0000.000
137C155VAL00.0060.00453.7140.0010.0010.0000.0000.0000.000
138C156ASP-1-0.780-0.88051.6310.0650.0650.0000.0000.0000.000
139C157ARG10.8780.94950.413-0.049-0.0490.0000.0000.0000.000
140C158GLN00.0470.03350.0290.0030.0030.0000.0000.0000.000
141C159LYS10.7970.88447.528-0.069-0.0690.0000.0000.0000.000
142C160LEU0-0.008-0.00645.7100.0050.0050.0000.0000.0000.000
143C161GLN00.0020.00045.3200.0040.0040.0000.0000.0000.000
144C162GLU-1-0.819-0.88544.2500.0780.0780.0000.0000.0000.000
145C163LYS10.8790.94941.886-0.085-0.0850.0000.0000.0000.000
146C164VAL00.0320.01340.6380.0060.0060.0000.0000.0000.000
147C165ARG10.9070.96140.241-0.073-0.0730.0000.0000.0000.000
148C166SER0-0.057-0.03837.8830.0060.0060.0000.0000.0000.000
149C167SER0-0.042-0.04736.2430.0070.0070.0000.0000.0000.000
150C168LEU00.0220.03435.3670.0080.0080.0000.0000.0000.000
151C169ASN00.0010.00133.8600.0150.0150.0000.0000.0000.000
152C170ARG10.8360.89531.353-0.129-0.1290.0000.0000.0000.000
153C171LEU00.0480.01430.5510.0130.0130.0000.0000.0000.000
154C172ARG10.8770.96430.467-0.131-0.1310.0000.0000.0000.000
155C173ARG10.8940.95527.561-0.157-0.1570.0000.0000.0000.000
156C174LEU00.0240.00426.1860.0130.0130.0000.0000.0000.000
157C175GLY00.0030.00226.2390.0090.0090.0000.0000.0000.000
158C176MET0-0.073-0.01227.409-0.012-0.0120.0000.0000.0000.000
159C177VAL00.001-0.00530.354-0.012-0.0120.0000.0000.0000.000
160C178TRP0-0.0230.00326.5530.0120.0120.0000.0000.0000.000
161C179PHE00.004-0.03632.735-0.005-0.0050.0000.0000.0000.000
162C180MET0-0.010-0.00635.093-0.001-0.0010.0000.0000.0000.000
163C181GLY00.0270.02237.605-0.003-0.0030.0000.0000.0000.000
164C182HIS0-0.022-0.01237.8560.0080.0080.0000.0000.0000.000
165C183ASP-1-0.797-0.88139.4690.0720.0720.0000.0000.0000.000
166C184SER0-0.032-0.02438.5770.0040.0040.0000.0000.0000.000
167C185SER0-0.094-0.03939.7840.0010.0010.0000.0000.0000.000
168C186LYS10.9650.99041.239-0.053-0.0530.0000.0000.0000.000
169C187PHE0-0.017-0.03336.5770.0050.0050.0000.0000.0000.000
170C188ARG10.9791.00234.352-0.064-0.0640.0000.0000.0000.000
171C189ILE0-0.054-0.01334.4470.0090.0090.0000.0000.0000.000
172C190THR0-0.0020.00928.360-0.004-0.0040.0000.0000.0000.000
173C191GLU-1-0.698-0.86727.5500.1070.1070.0000.0000.0000.000
174C192SER00.033-0.00926.7900.0010.0010.0000.0000.0000.000
175C193VAL0-0.020-0.00628.6470.0080.0080.0000.0000.0000.000
176C194PHE00.044-0.00530.956-0.005-0.0050.0000.0000.0000.000
177C195ARG10.8180.91926.120-0.195-0.1950.0000.0000.0000.000
178C196PHE0-0.038-0.01230.6480.0010.0010.0000.0000.0000.000
179C197GLY00.0250.01533.874-0.006-0.0060.0000.0000.0000.000
180C198ALA00.0170.00231.255-0.006-0.0060.0000.0000.0000.000
181C199ASP-1-0.902-0.93633.2090.0880.0880.0000.0000.0000.000
182C200VAL0-0.027-0.03036.045-0.005-0.0050.0000.0000.0000.000
183C201ARG10.7940.89831.447-0.077-0.0770.0000.0000.0000.000
184C202ALA0-0.035-0.01633.857-0.006-0.0060.0000.0000.0000.000
185C203GLY00.0300.00535.8390.0010.0010.0000.0000.0000.000
186C204ASP-1-0.891-0.94537.1530.0560.0560.0000.0000.0000.000
187C205ASP-1-0.823-0.88540.4370.0570.0570.0000.0000.0000.000
188C206PRO00.1070.04140.0160.0050.0050.0000.0000.0000.000
189C207ARG10.8390.89539.076-0.055-0.0550.0000.0000.0000.000
190C208GLU-1-0.901-0.90638.3520.0740.0740.0000.0000.0000.000
191C209ALA00.0440.01735.4460.0060.0060.0000.0000.0000.000
192C210GLN0-0.012-0.00834.2200.0080.0080.0000.0000.0000.000
193C211ARG10.8440.90334.256-0.071-0.0710.0000.0000.0000.000
194C212ARG10.8480.90327.467-0.106-0.1060.0000.0000.0000.000
195C213LEU0-0.007-0.01430.0880.0110.0110.0000.0000.0000.000
196C214ILE0-0.044-0.01829.4450.0150.0150.0000.0000.0000.000
197C215ARG10.8150.89728.714-0.107-0.1070.0000.0000.0000.000
198C216ASP-1-0.766-0.86025.8330.1480.1480.0000.0000.0000.000
199C217GLY0-0.0150.00324.7840.0180.0180.0000.0000.0000.000
200C218GLU-1-0.808-0.84725.1780.2010.2010.0000.0000.0000.000
201C219ALA0-0.014-0.01327.325-0.002-0.0020.0000.0000.0000.000
202C220MET0-0.021-0.01830.2980.0130.0130.0000.0000.0000.000
203C221PRO0-0.0060.01632.470-0.004-0.0040.0000.0000.0000.000
204C222ILE0-0.024-0.01536.2640.0050.0050.0000.0000.0000.000
205C223GLU-1-0.900-0.94038.5280.0910.0910.0000.0000.0000.000
206C224ASN0-0.050-0.02941.416-0.001-0.0010.0000.0000.0000.000