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: 2NR9R

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2183276.76873
FMO2-HF: Nuclear repulsion 2107077.12331
FMO2-HF: Total energy -76199.645419
FMO2-MP2: Total energy -76426.033406


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.
-1.5242.5020.025-1.949-2.1010.005
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 : 0.033 / q_NPA : 0.018
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].
3C3ASN00.006-0.0183.369-1.7961.3520.014-1.702-1.4600.005
4C4ASP-1-0.824-0.9185.9340.4600.4600.0000.0000.0000.000
5C5ASN0-0.0020.0098.3330.1000.1000.0000.0000.0000.000
6C6ILE0-0.023-0.0117.7130.0190.0190.0000.0000.0000.000
7C7LYS10.8920.9463.662-0.634-0.4760.000-0.026-0.1310.000
8C8ASP-1-0.844-0.9089.180-0.056-0.0560.0000.0000.0000.000
9C9LEU0-0.086-0.04412.4620.0540.0540.0000.0000.0000.000
10C10LEU0-0.007-0.0079.0360.0440.0440.0000.0000.0000.000
11C11ASP-1-0.876-0.91412.4640.0820.0820.0000.0000.0000.000
12C12TRP0-0.060-0.03214.5550.0460.0460.0000.0000.0000.000
13C13TYR0-0.062-0.05716.2490.0370.0370.0000.0000.0000.000
14C14SER0-0.036-0.01415.2010.0190.0190.0000.0000.0000.000
15C15SER0-0.063-0.02317.5550.0370.0370.0000.0000.0000.000
16C16GLY00.0000.01120.0390.0220.0220.0000.0000.0000.000
17C17SER0-0.057-0.04223.182-0.008-0.0080.0000.0000.0000.000
18C18ASP-1-0.801-0.87226.197-0.050-0.0500.0000.0000.0000.000
19C19THR0-0.008-0.01429.789-0.013-0.0130.0000.0000.0000.000
20C20PHE0-0.028-0.00432.7970.0090.0090.0000.0000.0000.000
21C21THR00.0050.00436.411-0.004-0.0040.0000.0000.0000.000
22C22ASN0-0.026-0.01539.4090.0030.0030.0000.0000.0000.000
23C23SER0-0.021-0.00839.0450.0050.0050.0000.0000.0000.000
24C24GLU-1-0.957-0.98441.949-0.035-0.0350.0000.0000.0000.000
25C25VAL0-0.0160.00342.5360.0020.0020.0000.0000.0000.000
26C26LEU0-0.038-0.03743.5910.0040.0040.0000.0000.0000.000
27C27ASP-1-0.943-0.99443.555-0.030-0.0300.0000.0000.0000.000
28C28ASN0-0.087-0.05442.258-0.004-0.0040.0000.0000.0000.000
29C29SER00.0260.03741.3560.0030.0030.0000.0000.0000.000
30C30LEU00.0260.00639.458-0.004-0.0040.0000.0000.0000.000
31C31GLY00.0150.00936.6650.0030.0030.0000.0000.0000.000
32C32SER0-0.072-0.04835.655-0.002-0.0020.0000.0000.0000.000
33C33MET00.0430.04437.425-0.002-0.0020.0000.0000.0000.000
34C34ARG10.9540.99738.0160.0200.0200.0000.0000.0000.000
35C35ILE00.019-0.00237.9840.0000.0000.0000.0000.0000.000
36C36LYS10.9310.97540.1890.0230.0230.0000.0000.0000.000
37C37ASN00.0330.01336.934-0.009-0.0090.0000.0000.0000.000
38C38THR00.0260.00340.8600.0050.0050.0000.0000.0000.000
39C39ASP-1-0.848-0.90937.985-0.022-0.0220.0000.0000.0000.000
40C40GLY0-0.003-0.00641.6310.0050.0050.0000.0000.0000.000
41C41SER0-0.079-0.02337.4970.0010.0010.0000.0000.0000.000
42C42ILE0-0.051-0.02838.749-0.003-0.0030.0000.0000.0000.000
43C43SER00.022-0.01534.6180.0040.0040.0000.0000.0000.000
44C44LEU0-0.023-0.00234.943-0.001-0.0010.0000.0000.0000.000
45C45ILE0-0.033-0.00432.452-0.001-0.0010.0000.0000.0000.000
46C46ILE00.0130.00529.0380.0030.0030.0000.0000.0000.000
47C47PHE00.011-0.01732.255-0.011-0.0110.0000.0000.0000.000
48C48PRO0-0.003-0.01229.2810.0050.0050.0000.0000.0000.000
49C49SER0-0.021-0.01131.9610.0000.0000.0000.0000.0000.000
50C50PRO0-0.005-0.00333.6390.0060.0060.0000.0000.0000.000
51C51TYR0-0.055-0.03033.7410.0010.0010.0000.0000.0000.000
52C52TYR0-0.034-0.02032.9780.0010.0010.0000.0000.0000.000
53C53SER00.0420.03036.1730.0020.0020.0000.0000.0000.000
54C54PRO0-0.027-0.01937.3500.0020.0020.0000.0000.0000.000
55C55ALA00.0380.01640.2590.0040.0040.0000.0000.0000.000
56C56PHE0-0.0280.00540.1440.0020.0020.0000.0000.0000.000
57C57THR0-0.011-0.00644.8020.0030.0030.0000.0000.0000.000
58C58LYS10.9860.96847.2530.0260.0260.0000.0000.0000.000
59C59GLY0-0.0150.00847.8010.0010.0010.0000.0000.0000.000
60C60GLU-1-0.856-0.91646.261-0.058-0.0580.0000.0000.0000.000
61C61LYS10.9160.95444.7280.0430.0430.0000.0000.0000.000
62C62VAL0-0.0040.00439.811-0.003-0.0030.0000.0000.0000.000
63C63ASP-1-0.823-0.91137.279-0.076-0.0760.0000.0000.0000.000
64C64LEU0-0.021-0.01533.998-0.003-0.0030.0000.0000.0000.000
65C65ASN00.0290.01830.9670.0070.0070.0000.0000.0000.000
66C66THR0-0.011-0.03129.178-0.011-0.0110.0000.0000.0000.000
67C67LYS10.9150.97220.6720.1820.1820.0000.0000.0000.000
68C68ARG10.9140.94925.3260.0410.0410.0000.0000.0000.000
69C69THR0-0.042-0.03724.775-0.002-0.0020.0000.0000.0000.000
70C70LYS10.9260.96324.8860.0080.0080.0000.0000.0000.000
71C71LYS10.9440.97525.160-0.092-0.0920.0000.0000.0000.000
72C72SER00.0310.02127.8980.0000.0000.0000.0000.0000.000
73C73GLN0-0.057-0.02031.5280.0100.0100.0000.0000.0000.000
74C74HIS00.0550.02834.319-0.008-0.0080.0000.0000.0000.000
75C75THR0-0.036-0.01437.7180.0050.0050.0000.0000.0000.000
76C76SER00.0320.00940.2190.0020.0020.0000.0000.0000.000
77C77GLU-1-0.894-0.94643.2720.0140.0140.0000.0000.0000.000
78C78GLY0-0.0020.00943.102-0.002-0.0020.0000.0000.0000.000
79C79THR0-0.080-0.04841.440-0.003-0.0030.0000.0000.0000.000
80C80TYR00.0160.01833.1050.0020.0020.0000.0000.0000.000
81C81ILE0-0.031-0.01935.529-0.006-0.0060.0000.0000.0000.000
82C82HIS00.0540.01832.1900.0060.0060.0000.0000.0000.000
83C83PHE0-0.007-0.01429.912-0.001-0.0010.0000.0000.0000.000
84C84GLN0-0.007-0.00729.0940.0000.0000.0000.0000.0000.000
85C85ILE0-0.046-0.02026.0820.0040.0040.0000.0000.0000.000
86C86SER0-0.010-0.01529.049-0.010-0.0100.0000.0000.0000.000
87C87GLY00.0300.02531.3900.0070.0070.0000.0000.0000.000
88C88VAL00.0190.01632.2990.0060.0060.0000.0000.0000.000
89C89THR0-0.0280.00735.684-0.005-0.0050.0000.0000.0000.000
90C90ASN00.0740.03438.3500.0040.0040.0000.0000.0000.000
91C91THR0-0.007-0.02240.641-0.004-0.0040.0000.0000.0000.000
92C92GLU-1-0.930-0.94942.705-0.080-0.0800.0000.0000.0000.000
93C93LYS10.8780.94339.4480.0780.0780.0000.0000.0000.000
94C94LEU0-0.011-0.00239.3770.0020.0020.0000.0000.0000.000
95C95PRO0-0.028-0.01943.2010.0030.0030.0000.0000.0000.000
96C96THR0-0.015-0.01142.9200.0040.0040.0000.0000.0000.000
97C97PRO00.0180.00838.353-0.005-0.0050.0000.0000.0000.000
98C98ILE00.0070.01436.4460.0000.0000.0000.0000.0000.000
99C99GLU-1-0.919-0.96331.958-0.180-0.1800.0000.0000.0000.000
100C100LEU00.0110.01331.1620.0010.0010.0000.0000.0000.000
101C101PRO00.0380.01631.117-0.012-0.0120.0000.0000.0000.000
102C102LEU00.0200.01723.991-0.010-0.0100.0000.0000.0000.000
103C103LYS10.8560.93426.6120.2580.2580.0000.0000.0000.000
104C104VAL00.0610.02420.000-0.017-0.0170.0000.0000.0000.000
105C105LYS10.9350.98521.4770.3910.3910.0000.0000.0000.000
106C106VAL00.003-0.00515.246-0.043-0.0430.0000.0000.0000.000
107C107HIS0-0.075-0.04112.0450.1500.1500.0000.0000.0000.000
108C108GLY00.0390.02917.4750.0360.0360.0000.0000.0000.000
109C109LYS10.8780.94919.7110.4540.4540.0000.0000.0000.000
110C110ASP-1-0.929-0.96621.271-0.361-0.3610.0000.0000.0000.000
111C111SER0-0.046-0.04919.3900.0140.0140.0000.0000.0000.000
112C112PRO00.002-0.01021.7420.0110.0110.0000.0000.0000.000
113C113LEU00.0230.02422.891-0.022-0.0220.0000.0000.0000.000
114C114LYS10.9280.95921.3760.2640.2640.0000.0000.0000.000
115C115TYR0-0.021-0.02123.695-0.014-0.0140.0000.0000.0000.000
116C116TRP0-0.0080.01025.508-0.011-0.0110.0000.0000.0000.000
117C117PRO00.0210.01327.6570.0110.0110.0000.0000.0000.000
118C118LYS10.9220.96830.7660.1270.1270.0000.0000.0000.000
119C119PHE00.012-0.01229.2050.0050.0050.0000.0000.0000.000
120C120ASP-1-0.867-0.94635.357-0.097-0.0970.0000.0000.0000.000
121C121LYS10.8090.91236.0440.1090.1090.0000.0000.0000.000
122C122LYS10.9000.96138.3830.0980.0980.0000.0000.0000.000
123C123GLN00.028-0.00637.773-0.002-0.0020.0000.0000.0000.000
124C124LEU0-0.0080.00031.6610.0040.0040.0000.0000.0000.000
125C125ALA00.0560.02831.812-0.003-0.0030.0000.0000.0000.000
126C126ILE00.0270.00528.312-0.011-0.0110.0000.0000.0000.000
127C127SER0-0.033-0.02426.694-0.016-0.0160.0000.0000.0000.000
128C128THR0-0.0150.00126.139-0.008-0.0080.0000.0000.0000.000
129C129LEU00.0410.01127.021-0.010-0.0100.0000.0000.0000.000
130C130ASP-1-0.753-0.86022.774-0.374-0.3740.0000.0000.0000.000
131C131PHE0-0.027-0.02322.192-0.029-0.0290.0000.0000.0000.000
132C132GLU-1-0.919-0.95022.528-0.205-0.2050.0000.0000.0000.000
133C133ILE0-0.009-0.01021.956-0.019-0.0190.0000.0000.0000.000
134C134ARG10.8130.87617.4190.4670.4670.0000.0000.0000.000
135C135ALA00.0520.05518.200-0.051-0.0510.0000.0000.0000.000
136C136GLN00.0420.00819.517-0.020-0.0200.0000.0000.0000.000
137C137LEU0-0.033-0.01717.042-0.024-0.0240.0000.0000.0000.000
138C138THR0-0.0120.00614.214-0.047-0.0470.0000.0000.0000.000
139C139GLN0-0.051-0.03415.010-0.034-0.0340.0000.0000.0000.000
140C140ILE0-0.063-0.01817.4600.0250.0250.0000.0000.0000.000
141C141HIS00.0150.01316.302-0.035-0.0350.0000.0000.0000.000
142C142GLY0-0.0010.00512.294-0.091-0.0910.0000.0000.0000.000
143C143LEU0-0.010-0.01210.932-0.251-0.2510.0000.0000.0000.000
144C144TYR0-0.063-0.0999.6180.2050.2050.0000.0000.0000.000
145C145ARG10.8690.9458.1540.4370.4370.0000.0000.0000.000
146C146SER0-0.011-0.0014.6180.0040.094-0.001-0.006-0.0820.000
147C147SER00.021-0.0143.282-0.734-0.2130.013-0.211-0.3240.000
148C148ASP-1-0.845-0.9155.054-1.593-1.484-0.001-0.004-0.1040.000
149C149LYS10.8630.9408.3321.8801.8800.0000.0000.0000.000
150C150THR0-0.013-0.0127.6700.1340.1340.0000.0000.0000.000
151C151GLY00.0790.04310.8620.1200.1200.0000.0000.0000.000
152C152GLY00.0110.01214.275-0.008-0.0080.0000.0000.0000.000
153C153TYR0-0.053-0.03517.7270.0140.0140.0000.0000.0000.000
154C154TRP00.004-0.00120.927-0.002-0.0020.0000.0000.0000.000
155C155LYS10.9420.95523.6320.2920.2920.0000.0000.0000.000
156C156ILE00.0000.00727.2710.0020.0020.0000.0000.0000.000
157C157THR0-0.016-0.01230.4030.0040.0040.0000.0000.0000.000
158C158MET00.0450.03133.6200.0000.0000.0000.0000.0000.000
159C159ASN0-0.001-0.02236.896-0.007-0.0070.0000.0000.0000.000
160C160ASP-1-0.872-0.92739.919-0.146-0.1460.0000.0000.0000.000
161C161GLY0-0.052-0.02338.0380.0020.0020.0000.0000.0000.000
162C162SER00.0060.01436.830-0.010-0.0100.0000.0000.0000.000
163C163THR0-0.095-0.05231.522-0.012-0.0120.0000.0000.0000.000
164C164TYR00.0210.01430.0190.0070.0070.0000.0000.0000.000
165C165GLN00.002-0.00324.4610.0150.0150.0000.0000.0000.000
166C166SER0-0.0070.00523.0130.0110.0110.0000.0000.0000.000
167C167ASP-1-0.763-0.86818.254-0.681-0.6810.0000.0000.0000.000
168C168LEU0-0.0150.00216.4100.0090.0090.0000.0000.0000.000
169C169SER0-0.0450.00713.983-0.072-0.0720.0000.0000.0000.000
170C170LYS10.9120.96214.8700.5870.5870.0000.0000.0000.000
171C171LYS10.9801.00217.3270.2050.2050.0000.0000.0000.000
172C172PHE0-0.0060.00419.1520.0090.0090.0000.0000.0000.000
173C173GLU-1-0.890-0.94922.564-0.232-0.2320.0000.0000.0000.000
174C174TYR00.031-0.01423.4680.0110.0110.0000.0000.0000.000
175C175ASN00.0140.00226.8390.0040.0040.0000.0000.0000.000
176C176THR0-0.0170.00028.6530.0110.0110.0000.0000.0000.000
177C177GLU-1-0.792-0.87829.794-0.169-0.1690.0000.0000.0000.000
178C178LYS10.9180.98131.1380.1900.1900.0000.0000.0000.000
179C179PRO00.019-0.00433.811-0.004-0.0040.0000.0000.0000.000
180C180PRO0-0.015-0.00234.956-0.009-0.0090.0000.0000.0000.000
181C181ILE00.0220.02733.3080.0040.0040.0000.0000.0000.000
182C182ASN00.0230.00036.9700.0060.0060.0000.0000.0000.000
183C183ILE00.004-0.01534.450-0.007-0.0070.0000.0000.0000.000
184C184ASP-1-0.858-0.93236.936-0.122-0.1220.0000.0000.0000.000
185C185GLU-1-0.942-0.97139.147-0.121-0.1210.0000.0000.0000.000
186C186ILE0-0.042-0.01332.775-0.007-0.0070.0000.0000.0000.000
187C187LYS10.9340.98335.9420.1770.1770.0000.0000.0000.000
188C188THR0-0.081-0.06031.7300.0010.0010.0000.0000.0000.000
189C189ILE00.0230.01726.866-0.002-0.0020.0000.0000.0000.000
190C190GLU-1-0.933-0.96826.149-0.303-0.3030.0000.0000.0000.000
191C191ALA00.012-0.00521.207-0.005-0.0050.0000.0000.0000.000
192C192GLU-1-0.936-0.95820.203-0.474-0.4740.0000.0000.0000.000
193C193ILE0-0.028-0.00913.727-0.048-0.0480.0000.0000.0000.000
194C194ASN00.0480.01311.3890.0380.0380.0000.0000.0000.000