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: 6Y7KZ

Calculation Name: 1QIL-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QIL

Chain ID: C

ChEMBL ID:

UniProt ID: P06886

Base Structure: X-ray

Registration Date: 2023-09-23

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2184078.335309
FMO2-HF: Nuclear repulsion 2107877.606732
FMO2-HF: Total energy -76200.728577
FMO2-MP2: Total energy -76427.166607


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:SER)


Summations of interaction energy for fragment #1(C:1:SER)
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.
-1.1292.1980.487-1.717-2.0970
Interaction energy analysis for fragmet #1(C:1:SER)
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 : 0.002
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].
3C3ASN00.017-0.0093.413-1.2940.5810.012-0.902-0.9840.001
4C4ASP-1-0.807-0.9045.9980.2440.2440.0000.0000.0000.000
5C5ASN00.0010.0148.3550.1580.1580.0000.0000.0000.000
6C6ILE0-0.015-0.0137.7300.0840.0840.0000.0000.0000.000
7C7LYS10.8560.9184.4260.1090.174-0.001-0.002-0.0620.000
8C8ASP-1-0.852-0.9119.1960.1080.1080.0000.0000.0000.000
9C9LEU0-0.093-0.04712.4610.0430.0430.0000.0000.0000.000
10C10LEU0-0.004-0.0018.8110.0420.0420.0000.0000.0000.000
11C11ASP-1-0.868-0.90912.4700.3930.3930.0000.0000.0000.000
12C12TRP0-0.020-0.01314.564-0.008-0.0080.0000.0000.0000.000
13C13TYR0-0.081-0.07816.312-0.006-0.0060.0000.0000.0000.000
14C14SER0-0.036-0.01815.1540.0110.0110.0000.0000.0000.000
15C15SER0-0.061-0.03417.5560.0000.0000.0000.0000.0000.000
16C16GLY0-0.0140.00420.043-0.012-0.0120.0000.0000.0000.000
17C17SER0-0.027-0.02123.184-0.006-0.0060.0000.0000.0000.000
18C18ASP-1-0.802-0.87226.2010.0930.0930.0000.0000.0000.000
19C19THR00.011-0.00529.795-0.009-0.0090.0000.0000.0000.000
20C20PHE0-0.019-0.00432.8010.0030.0030.0000.0000.0000.000
21C21THR00.0060.01136.416-0.003-0.0030.0000.0000.0000.000
22C22ASN0-0.061-0.03439.413-0.001-0.0010.0000.0000.0000.000
23C23SER00.003-0.00139.0820.0010.0010.0000.0000.0000.000
24C24GLU-1-0.868-0.92041.9560.0230.0230.0000.0000.0000.000
25C25VAL0-0.020-0.00342.4550.0020.0020.0000.0000.0000.000
26C26LEU0-0.047-0.04243.6260.0000.0000.0000.0000.0000.000
27C27ASP-1-0.916-0.98243.6290.0140.0140.0000.0000.0000.000
28C28ASN0-0.084-0.05941.9450.0010.0010.0000.0000.0000.000
29C29SER00.0280.03941.544-0.002-0.0020.0000.0000.0000.000
30C30LEU00.0220.00439.614-0.001-0.0010.0000.0000.0000.000
31C31GLY00.0240.01336.6940.0010.0010.0000.0000.0000.000
32C32SER0-0.083-0.04935.6760.0030.0030.0000.0000.0000.000
33C33MET00.0270.03837.441-0.001-0.0010.0000.0000.0000.000
34C34ARG10.9500.99038.030-0.028-0.0280.0000.0000.0000.000
35C35ILE00.022-0.00237.860-0.002-0.0020.0000.0000.0000.000
36C36LYS10.9040.96640.201-0.038-0.0380.0000.0000.0000.000
37C37ASN00.0150.01536.907-0.005-0.0050.0000.0000.0000.000
38C38THR00.0370.00940.8680.0010.0010.0000.0000.0000.000
39C39ASP-1-0.820-0.87337.9870.0600.0600.0000.0000.0000.000
40C40GLY0-0.003-0.00641.6370.0010.0010.0000.0000.0000.000
41C41SER0-0.079-0.05337.480-0.001-0.0010.0000.0000.0000.000
42C42ILE0-0.044-0.03038.772-0.004-0.0040.0000.0000.0000.000
43C43SER00.024-0.00634.7190.0060.0060.0000.0000.0000.000
44C44LEU0-0.031-0.00535.042-0.004-0.0040.0000.0000.0000.000
45C45ILE0-0.027-0.00732.3920.0040.0040.0000.0000.0000.000
46C46ILE00.0240.01329.038-0.003-0.0030.0000.0000.0000.000
47C47PHE00.028-0.01132.2700.0010.0010.0000.0000.0000.000
48C48PRO0-0.008-0.01129.272-0.001-0.0010.0000.0000.0000.000
49C49SER0-0.013-0.00932.084-0.006-0.0060.0000.0000.0000.000
50C50PRO0-0.017-0.00733.6840.0040.0040.0000.0000.0000.000
51C51TYR0-0.051-0.03133.7990.0000.0000.0000.0000.0000.000
52C52TYR0-0.020-0.02132.9680.0030.0030.0000.0000.0000.000
53C53SER00.0440.02836.1890.0020.0020.0000.0000.0000.000
54C54PRO0-0.032-0.01937.373-0.001-0.0010.0000.0000.0000.000
55C55ALA00.0270.01540.2710.0000.0000.0000.0000.0000.000
56C56PHE0-0.0280.00239.7670.0000.0000.0000.0000.0000.000
57C57THR0-0.025-0.02544.8130.0000.0000.0000.0000.0000.000
58C58LYS10.9790.96947.254-0.017-0.0170.0000.0000.0000.000
59C59GLY00.0020.01547.802-0.001-0.0010.0000.0000.0000.000
60C60GLU-1-0.821-0.88346.2720.0110.0110.0000.0000.0000.000
61C61LYS10.8110.88244.705-0.022-0.0220.0000.0000.0000.000
62C62VAL0-0.0040.00439.868-0.002-0.0020.0000.0000.0000.000
63C63ASP-1-0.800-0.89137.2740.0350.0350.0000.0000.0000.000
64C64LEU0-0.022-0.01433.935-0.003-0.0030.0000.0000.0000.000
65C65ASN0-0.0050.00131.0270.0010.0010.0000.0000.0000.000
66C66THR0-0.018-0.03329.164-0.004-0.0040.0000.0000.0000.000
67C67LYS10.9010.96420.644-0.100-0.1000.0000.0000.0000.000
68C68ARG10.9090.93525.413-0.124-0.1240.0000.0000.0000.000
69C69THR0-0.036-0.02924.7880.0070.0070.0000.0000.0000.000
70C70LYS10.8730.93824.893-0.058-0.0580.0000.0000.0000.000
71C71LYS10.9500.97325.748-0.150-0.1500.0000.0000.0000.000
72C72SER00.0110.01227.912-0.004-0.0040.0000.0000.0000.000
73C73GLN0-0.035-0.00831.5410.0050.0050.0000.0000.0000.000
74C74HIS00.0560.03134.334-0.006-0.0060.0000.0000.0000.000
75C75THR0-0.051-0.05337.7310.0020.0020.0000.0000.0000.000
76C76SER00.022-0.00540.2350.0020.0020.0000.0000.0000.000
77C77GLU-1-0.874-0.90643.2880.0450.0450.0000.0000.0000.000
78C78GLY00.0070.01143.115-0.001-0.0010.0000.0000.0000.000
79C79THR0-0.088-0.03941.7080.0000.0000.0000.0000.0000.000
80C80TYR00.0230.02132.4270.0040.0040.0000.0000.0000.000
81C81ILE0-0.038-0.02035.322-0.004-0.0040.0000.0000.0000.000
82C82HIS00.0620.02332.1960.0110.0110.0000.0000.0000.000
83C83PHE00.006-0.01230.018-0.006-0.0060.0000.0000.0000.000
84C84GLN0-0.001-0.00629.1070.0020.0020.0000.0000.0000.000
85C85ILE0-0.041-0.01726.084-0.006-0.0060.0000.0000.0000.000
86C86SER0-0.002-0.02029.0610.0020.0020.0000.0000.0000.000
87C87GLY00.0230.02631.4020.0070.0070.0000.0000.0000.000
88C88VAL00.0030.00732.3070.0040.0040.0000.0000.0000.000
89C89THR0-0.0220.00335.764-0.004-0.0040.0000.0000.0000.000
90C90ASN00.019-0.00938.3560.0040.0040.0000.0000.0000.000
91C91THR0-0.007-0.02340.6460.0010.0010.0000.0000.0000.000
92C92GLU-1-0.890-0.91442.7090.0110.0110.0000.0000.0000.000
93C93LYS10.8490.92339.550-0.031-0.0310.0000.0000.0000.000
94C94LEU0-0.008-0.00639.770-0.003-0.0030.0000.0000.0000.000
95C95PRO0-0.021-0.01843.1990.0020.0020.0000.0000.0000.000
96C96THR0-0.007-0.00943.2850.0030.0030.0000.0000.0000.000
97C97PRO00.0020.00638.332-0.002-0.0020.0000.0000.0000.000
98C98ILE00.0130.01436.7160.0000.0000.0000.0000.0000.000
99C99GLU-1-0.873-0.91532.9110.0450.0450.0000.0000.0000.000
100C100LEU00.0070.00831.110-0.005-0.0050.0000.0000.0000.000
101C101PRO00.0370.01831.5910.0050.0050.0000.0000.0000.000
102C102LEU00.0050.01424.525-0.007-0.0070.0000.0000.0000.000
103C103LYS10.7990.88427.3000.0250.0250.0000.0000.0000.000
104C104VAL00.0560.01820.876-0.010-0.0100.0000.0000.0000.000
105C105LYS10.8820.94421.9780.0530.0530.0000.0000.0000.000
106C106VAL0-0.007-0.01215.787-0.009-0.0090.0000.0000.0000.000
107C107HIS0-0.056-0.03712.5370.0280.0280.0000.0000.0000.000
108C108GLY00.0310.02717.657-0.007-0.0070.0000.0000.0000.000
109C109LYS10.8580.92920.205-0.025-0.0250.0000.0000.0000.000
110C110ASP-1-0.838-0.90821.793-0.010-0.0100.0000.0000.0000.000
111C111SER0-0.047-0.03420.2570.0140.0140.0000.0000.0000.000
112C112PRO00.014-0.00422.580-0.004-0.0040.0000.0000.0000.000
113C113LEU00.0060.01723.8070.0150.0150.0000.0000.0000.000
114C114LYS10.9100.94722.608-0.167-0.1670.0000.0000.0000.000
115C115TYR00.004-0.00223.8710.0120.0120.0000.0000.0000.000
116C116TRP00.0070.01325.6280.0060.0060.0000.0000.0000.000
117C117PRO00.0200.01327.953-0.004-0.0040.0000.0000.0000.000
118C118LYS10.8530.91030.942-0.046-0.0460.0000.0000.0000.000
119C119PHE00.009-0.01529.1540.0030.0030.0000.0000.0000.000
120C120ASP-1-0.846-0.93735.3530.0330.0330.0000.0000.0000.000
121C121LYS10.8280.93536.055-0.027-0.0270.0000.0000.0000.000
122C122LYS10.8130.91038.383-0.004-0.0040.0000.0000.0000.000
123C123GLN00.0530.01137.786-0.002-0.0020.0000.0000.0000.000
124C124LEU0-0.014-0.00131.9990.0050.0050.0000.0000.0000.000
125C125ALA00.0460.02431.829-0.005-0.0050.0000.0000.0000.000
126C126ILE00.0390.00728.3290.0020.0020.0000.0000.0000.000
127C127SER0-0.036-0.04426.6970.0030.0030.0000.0000.0000.000
128C128THR0-0.022-0.00626.1440.0040.0040.0000.0000.0000.000
129C129LEU00.0420.02027.0240.0070.0070.0000.0000.0000.000
130C130ASP-1-0.723-0.83322.445-0.025-0.0250.0000.0000.0000.000
131C131PHE0-0.023-0.02522.1890.0030.0030.0000.0000.0000.000
132C132GLU-1-0.910-0.94722.5280.0870.0870.0000.0000.0000.000
133C133ILE0-0.016-0.01522.1480.0110.0110.0000.0000.0000.000
134C134ARG10.7990.86817.2990.0740.0740.0000.0000.0000.000
135C135ALA00.0510.05318.1970.0230.0230.0000.0000.0000.000
136C136GLN00.027-0.00219.5180.0310.0310.0000.0000.0000.000
137C137LEU0-0.023-0.00917.4320.0180.0180.0000.0000.0000.000
138C138THR00.0050.01414.0610.0280.0280.0000.0000.0000.000
139C139GLN0-0.061-0.02915.2280.0970.0970.0000.0000.0000.000
140C140ILE0-0.062-0.02217.7630.0290.0290.0000.0000.0000.000
141C141HIS00.0100.01317.1510.0050.0050.0000.0000.0000.000
142C142GLY00.0000.01213.1170.0010.0010.0000.0000.0000.000
143C143LEU0-0.020-0.01911.5210.0580.0580.0000.0000.0000.000
144C144TYR0-0.049-0.0659.6120.0760.0760.0000.0000.0000.000
145C145ARG10.8610.9318.152-0.483-0.4830.0000.0000.0000.000
146C146SER0-0.028-0.0335.4950.5930.5930.0000.0000.0000.000
147C147SER00.012-0.0392.427-0.8760.4130.477-0.810-0.957-0.001
148C148ASP-1-0.810-0.8545.270-0.0980.000-0.001-0.003-0.0940.000
149C149LYS10.8250.9048.533-0.300-0.3000.0000.0000.0000.000
150C150THR0-0.004-0.0057.6420.1240.1240.0000.0000.0000.000
151C151GLY00.0740.04210.974-0.050-0.0500.0000.0000.0000.000
152C152GLY0-0.0040.00814.4870.0470.0470.0000.0000.0000.000
153C153TYR0-0.129-0.09417.939-0.010-0.0100.0000.0000.0000.000
154C154TRP0-0.002-0.00721.0640.0130.0130.0000.0000.0000.000
155C155LYS10.9080.93123.8280.0560.0560.0000.0000.0000.000
156C156ILE0-0.0070.00727.4430.0080.0080.0000.0000.0000.000
157C157THR00.0120.00530.588-0.008-0.0080.0000.0000.0000.000
158C158MET00.0380.03433.8630.0060.0060.0000.0000.0000.000
159C159ASN00.015-0.02937.085-0.004-0.0040.0000.0000.0000.000
160C160ASP-1-0.815-0.88239.786-0.031-0.0310.0000.0000.0000.000
161C161GLY0-0.054-0.01938.253-0.002-0.0020.0000.0000.0000.000
162C162SER0-0.031-0.02336.952-0.007-0.0070.0000.0000.0000.000
163C163THR0-0.069-0.05131.6070.0000.0000.0000.0000.0000.000
164C164TYR00.0140.01530.087-0.002-0.0020.0000.0000.0000.000
165C165GLN0-0.009-0.00724.8170.0070.0070.0000.0000.0000.000
166C166SER0-0.0160.00822.814-0.006-0.0060.0000.0000.0000.000
167C167ASP-1-0.712-0.80818.202-0.272-0.2720.0000.0000.0000.000
168C168LEU0-0.013-0.00216.3980.0060.0060.0000.0000.0000.000
169C169SER0-0.030-0.02114.117-0.007-0.0070.0000.0000.0000.000
170C170LYS10.8500.91014.9410.2670.2670.0000.0000.0000.000
171C171LYS10.9460.99217.3910.0190.0190.0000.0000.0000.000
172C172PHE0-0.0080.00619.198-0.010-0.0100.0000.0000.0000.000
173C173GLU-1-0.805-0.88322.575-0.084-0.0840.0000.0000.0000.000
174C174TYR00.039-0.01023.3130.0080.0080.0000.0000.0000.000
175C175ASN0-0.027-0.02226.7530.0060.0060.0000.0000.0000.000
176C176THR0-0.050-0.03028.7290.0040.0040.0000.0000.0000.000
177C177GLU-1-0.767-0.83129.681-0.009-0.0090.0000.0000.0000.000
178C178LYS10.8930.94931.1490.0540.0540.0000.0000.0000.000
179C179PRO00.0410.00833.8200.0030.0030.0000.0000.0000.000
180C180PRO0-0.040-0.01234.960-0.002-0.0020.0000.0000.0000.000
181C181ILE0-0.0040.01233.171-0.002-0.0020.0000.0000.0000.000
182C182ASN0-0.030-0.03036.9730.0060.0060.0000.0000.0000.000
183C183ILE00.007-0.01534.599-0.003-0.0030.0000.0000.0000.000
184C184ASP-1-0.795-0.88536.9350.0030.0030.0000.0000.0000.000
185C185GLU-1-0.879-0.93939.198-0.008-0.0080.0000.0000.0000.000
186C186ILE0-0.022-0.01132.831-0.005-0.0050.0000.0000.0000.000
187C187LYS10.8530.95936.3060.0310.0310.0000.0000.0000.000
188C188THR0-0.105-0.08332.1090.0030.0030.0000.0000.0000.000
189C189ILE00.0430.02627.256-0.005-0.0050.0000.0000.0000.000
190C190GLU-1-0.811-0.86826.296-0.035-0.0350.0000.0000.0000.000
191C191ALA00.0240.00021.765-0.005-0.0050.0000.0000.0000.000
192C192GLU-1-0.877-0.90520.551-0.092-0.0920.0000.0000.0000.000
193C193ILE0-0.0040.00014.248-0.020-0.0200.0000.0000.0000.000
194C194ASN00.0410.00711.5830.0090.0090.0000.0000.0000.000