Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4JY3N

Calculation Name: 2FM8-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FM8

Chain ID: C

ChEMBL ID:

UniProt ID: P0CL52

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2391217.888782
FMO2-HF: Nuclear repulsion 2305278.113845
FMO2-HF: Total energy -85939.774937
FMO2-MP2: Total energy -86187.103365


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:23:GLN)


Summations of interaction energy for fragment #1(C:23:GLN)
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.
-1.9340.8930.016-1.417-1.4260.004
Interaction energy analysis for fragmet #1(C:23:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.012
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].
3C25THR00.0410.0193.339-2.4590.3680.016-1.417-1.4260.004
4C26ASN00.0690.0176.0221.5631.5630.0000.0000.0000.000
5C27LEU00.0170.0168.0110.1850.1850.0000.0000.0000.000
6C28ALA0-0.002-0.0087.111-0.057-0.0570.0000.0000.0000.000
7C29ALA0-0.029-0.0135.3780.0030.0030.0000.0000.0000.000
8C30ASN0-0.049-0.0337.140-0.613-0.6130.0000.0000.0000.000
9C31LEU0-0.0470.00410.557-0.417-0.4170.0000.0000.0000.000
10C32SER00.0000.00412.5660.0280.0280.0000.0000.0000.000
11C33ALA00.002-0.02015.241-0.083-0.0830.0000.0000.0000.000
12C34VAL0-0.0040.00816.3010.0180.0180.0000.0000.0000.000
13C35ARG10.9420.97518.944-0.382-0.3820.0000.0000.0000.000
14C36GLU-1-0.895-0.94122.7210.1760.1760.0000.0000.0000.000
15C37SER0-0.066-0.04225.889-0.002-0.0020.0000.0000.0000.000
16C38ALA00.0650.03328.675-0.006-0.0060.0000.0000.0000.000
17C39THR0-0.035-0.00530.783-0.004-0.0040.0000.0000.0000.000
18C40ALA0-0.052-0.03928.271-0.002-0.0020.0000.0000.0000.000
19C41THR00.0120.00930.221-0.006-0.0060.0000.0000.0000.000
20C42LEU00.0270.01429.3500.0060.0060.0000.0000.0000.000
21C43SER0-0.004-0.01032.664-0.004-0.0040.0000.0000.0000.000
22C44GLY0-0.0040.01236.1110.0000.0000.0000.0000.0000.000
23C52GLU-1-0.943-0.99147.4400.0490.0490.0000.0000.0000.000
24C53ASP-1-0.856-0.92049.5270.0500.0500.0000.0000.0000.000
25C54PHE00.0370.00347.4360.0030.0030.0000.0000.0000.000
26C55PRO0-0.002-0.00850.9430.0010.0010.0000.0000.0000.000
27C56ALA0-0.0040.01050.8580.0010.0010.0000.0000.0000.000
28C57LEU00.0260.01544.6020.0030.0030.0000.0000.0000.000
29C58ILE0-0.035-0.01247.7170.0020.0020.0000.0000.0000.000
30C59LYS10.9280.94949.968-0.052-0.0520.0000.0000.0000.000
31C60GLN0-0.053-0.03142.984-0.001-0.0010.0000.0000.0000.000
32C61ALA00.0410.02145.5690.0030.0030.0000.0000.0000.000
33C62SER0-0.034-0.01846.5630.0000.0000.0000.0000.0000.000
34C63LEU0-0.026-0.01648.5640.0010.0010.0000.0000.0000.000
35C64ASP-1-0.787-0.88143.1810.0930.0930.0000.0000.0000.000
36C65ALA0-0.065-0.02544.1670.0040.0040.0000.0000.0000.000
37C66LEU00.0130.01245.6390.0010.0010.0000.0000.0000.000
38C67PHE00.033-0.01345.2040.0020.0020.0000.0000.0000.000
39C68LYS10.9300.97440.655-0.088-0.0880.0000.0000.0000.000
40C69CYS0-0.092-0.03541.8350.0040.0040.0000.0000.0000.000
41C70GLY00.0210.02244.375-0.001-0.0010.0000.0000.0000.000
42C71LYS10.8910.93342.001-0.104-0.1040.0000.0000.0000.000
43C72ASP-1-0.797-0.90240.5650.1350.1350.0000.0000.0000.000
44C73ALA00.0150.00141.092-0.006-0.0060.0000.0000.0000.000
45C74GLU-1-0.945-0.97138.5210.1280.1280.0000.0000.0000.000
46C75ALA00.0480.02642.605-0.006-0.0060.0000.0000.0000.000
47C76LEU0-0.064-0.02345.041-0.006-0.0060.0000.0000.0000.000
48C77LYS10.8810.94141.422-0.106-0.1060.0000.0000.0000.000
49C78GLU-1-0.916-0.95346.3220.0910.0910.0000.0000.0000.000
50C79VAL0-0.0080.00048.304-0.004-0.0040.0000.0000.0000.000
51C80PHE0-0.035-0.03050.685-0.005-0.0050.0000.0000.0000.000
52C81THR0-0.059-0.04249.620-0.005-0.0050.0000.0000.0000.000
53C82ASN0-0.0050.00650.515-0.004-0.0040.0000.0000.0000.000
54C83SER0-0.073-0.01353.977-0.003-0.0030.0000.0000.0000.000
55C84ASN0-0.004-0.01756.758-0.001-0.0010.0000.0000.0000.000
56C85ASN0-0.021-0.01159.659-0.004-0.0040.0000.0000.0000.000
57C86VAL00.0290.00760.3570.0010.0010.0000.0000.0000.000
58C87ALA00.0330.01061.4970.0010.0010.0000.0000.0000.000
59C88GLY00.0770.03260.0310.0000.0000.0000.0000.0000.000
60C89LYS10.9120.95855.407-0.059-0.0590.0000.0000.0000.000
61C90LYS10.9470.97557.226-0.042-0.0420.0000.0000.0000.000
62C91ALA00.0190.00659.1180.0000.0000.0000.0000.0000.000
63C92ILE00.0210.02052.9990.0010.0010.0000.0000.0000.000
64C93MET0-0.049-0.02353.0510.0010.0010.0000.0000.0000.000
65C94GLU-1-0.854-0.91255.3240.0480.0480.0000.0000.0000.000
66C95PHE00.0310.01952.2240.0000.0000.0000.0000.0000.000
67C96ALA0-0.004-0.00350.9480.0010.0010.0000.0000.0000.000
68C97GLY0-0.012-0.00151.8110.0010.0010.0000.0000.0000.000
69C98LEU00.018-0.00153.947-0.001-0.0010.0000.0000.0000.000
70C99PHE0-0.009-0.01046.6140.0000.0000.0000.0000.0000.000
71C100ARG10.9620.97849.315-0.055-0.0550.0000.0000.0000.000
72C101SER0-0.017-0.01350.489-0.001-0.0010.0000.0000.0000.000
73C102ALA00.0690.03152.063-0.001-0.0010.0000.0000.0000.000
74C103LEU0-0.029-0.00544.4960.0020.0020.0000.0000.0000.000
75C104ASN0-0.061-0.01648.3330.0020.0020.0000.0000.0000.000
76C105ALA0-0.0020.00850.056-0.001-0.0010.0000.0000.0000.000
77C106THR0-0.027-0.03049.5670.0000.0000.0000.0000.0000.000
78C107SER0-0.084-0.07245.1660.0040.0040.0000.0000.0000.000
79C108ASP-1-0.907-0.93645.2140.0590.0590.0000.0000.0000.000
80C109SER00.0050.03147.288-0.001-0.0010.0000.0000.0000.000
81C110PRO00.0140.00144.6930.0020.0020.0000.0000.0000.000
82C111GLU-1-0.857-0.92846.4170.0640.0640.0000.0000.0000.000
83C112ALA00.0630.03349.5610.0010.0010.0000.0000.0000.000
84C113LYS10.9751.00041.332-0.088-0.0880.0000.0000.0000.000
85C114THR0-0.049-0.04545.9870.0050.0050.0000.0000.0000.000
86C115LEU0-0.016-0.01547.1330.0020.0020.0000.0000.0000.000
87C116LEU00.0050.02147.8820.0010.0010.0000.0000.0000.000
88C117MET0-0.079-0.03843.8660.0030.0030.0000.0000.0000.000
89C118LYS10.8770.94646.848-0.069-0.0690.0000.0000.0000.000
90C119VAL00.0030.00448.9350.0000.0000.0000.0000.0000.000
91C120GLY00.0530.02048.539-0.001-0.0010.0000.0000.0000.000
92C121ALA0-0.0090.00646.3080.0010.0010.0000.0000.0000.000
93C122GLU-1-0.889-0.93647.9420.0720.0720.0000.0000.0000.000
94C123TYR00.0590.02851.4040.0000.0000.0000.0000.0000.000
95C124THR0-0.034-0.04747.5930.0010.0010.0000.0000.0000.000
96C125ALA0-0.008-0.00249.0270.0010.0010.0000.0000.0000.000
97C126GLN00.0070.00050.1620.0020.0020.0000.0000.0000.000
98C127ILE00.0010.00451.141-0.002-0.0020.0000.0000.0000.000
99C128ILE0-0.043-0.01347.692-0.001-0.0010.0000.0000.0000.000
100C129LYS10.8880.95251.159-0.069-0.0690.0000.0000.0000.000
101C130ASP-1-0.822-0.87153.7440.0600.0600.0000.0000.0000.000
102C131GLY00.0130.00354.258-0.001-0.0010.0000.0000.0000.000
103C132LEU0-0.067-0.02454.2770.0000.0000.0000.0000.0000.000
104C133LYS10.9790.99556.294-0.068-0.0680.0000.0000.0000.000
105C134GLU-1-0.903-0.94360.2350.0460.0460.0000.0000.0000.000
106C135LYS10.9490.97663.879-0.052-0.0520.0000.0000.0000.000
107C136SER0-0.063-0.06459.3270.0020.0020.0000.0000.0000.000
108C137ALA00.0000.00059.656-0.002-0.0020.0000.0000.0000.000
109C138PHE0-0.041-0.02255.393-0.001-0.0010.0000.0000.0000.000
110C139GLY00.0290.00060.6150.0000.0000.0000.0000.0000.000
111C140PRO0-0.023-0.01363.434-0.002-0.0020.0000.0000.0000.000
112C141TRP00.0320.01763.958-0.002-0.0020.0000.0000.0000.000
113C142LEU0-0.0020.01562.0530.0000.0000.0000.0000.0000.000
114C143PRO00.0450.03665.841-0.001-0.0010.0000.0000.0000.000
115C144GLU-1-0.738-0.86568.5130.0390.0390.0000.0000.0000.000
116C145THR0-0.026-0.01470.865-0.001-0.0010.0000.0000.0000.000
117C146LYS11.0470.99872.014-0.029-0.0290.0000.0000.0000.000
118C147LYS10.9400.98072.917-0.029-0.0290.0000.0000.0000.000
119C148ALA00.0000.00271.7530.0000.0000.0000.0000.0000.000
120C149GLU-1-0.890-0.95367.9060.0370.0370.0000.0000.0000.000
121C150ALA00.0380.02569.2820.0000.0000.0000.0000.0000.000
122C151LYS10.8760.93071.559-0.030-0.0300.0000.0000.0000.000
123C152LEU00.0300.02664.7920.0000.0000.0000.0000.0000.000
124C153GLU-1-0.875-0.93565.9640.0360.0360.0000.0000.0000.000
125C154ASN0-0.066-0.04667.7990.0000.0000.0000.0000.0000.000
126C155LEU0-0.0120.00867.4060.0000.0000.0000.0000.0000.000
127C156GLU-1-0.820-0.91763.4920.0440.0440.0000.0000.0000.000
128C157LYS10.8210.90265.948-0.031-0.0310.0000.0000.0000.000
129C158GLN00.002-0.00467.7000.0000.0000.0000.0000.0000.000
130C159LEU0-0.0010.00765.2670.0000.0000.0000.0000.0000.000
131C160LEU0-0.0010.01062.4800.0000.0000.0000.0000.0000.000
132C161ASP-1-0.871-0.92765.5620.0320.0320.0000.0000.0000.000
133C162ILE0-0.028-0.01668.738-0.001-0.0010.0000.0000.0000.000
134C163ILE0-0.013-0.01162.7730.0000.0000.0000.0000.0000.000
135C164LYS10.9080.96164.944-0.034-0.0340.0000.0000.0000.000
136C165ASN0-0.010-0.00766.167-0.001-0.0010.0000.0000.0000.000
137C166ASN0-0.0010.02566.327-0.002-0.0020.0000.0000.0000.000
138C167THR0-0.014-0.02767.1500.0000.0000.0000.0000.0000.000
139C168GLY0-0.014-0.00764.5650.0000.0000.0000.0000.0000.000
140C169GLY0-0.0050.00162.9110.0010.0010.0000.0000.0000.000
141C170GLU-1-0.966-0.96963.5900.0430.0430.0000.0000.0000.000
142C171LEU0-0.037-0.01564.423-0.002-0.0020.0000.0000.0000.000
143C172SER00.0190.02067.031-0.001-0.0010.0000.0000.0000.000
144C173LYS10.9910.96170.625-0.032-0.0320.0000.0000.0000.000
145C174LEU00.0110.01573.2860.0000.0000.0000.0000.0000.000
146C175SER00.0400.00169.287-0.001-0.0010.0000.0000.0000.000
147C176THR00.0050.01669.5460.0010.0010.0000.0000.0000.000
148C177ASN0-0.033-0.03370.6700.0010.0010.0000.0000.0000.000
149C178LEU0-0.035-0.01172.5040.0000.0000.0000.0000.0000.000
150C179VAL00.0670.03267.1060.0000.0000.0000.0000.0000.000
151C180MET0-0.038-0.01470.2590.0010.0010.0000.0000.0000.000
152C181GLN0-0.028-0.01772.1050.0000.0000.0000.0000.0000.000
153C182GLU-1-0.890-0.94370.7060.0330.0330.0000.0000.0000.000
154C183VAL0-0.022-0.01267.4160.0000.0000.0000.0000.0000.000
155C184MET0-0.018-0.00770.3520.0000.0000.0000.0000.0000.000
156C185PRO00.0060.00172.9670.0000.0000.0000.0000.0000.000
157C186TYR0-0.026-0.01367.284-0.001-0.0010.0000.0000.0000.000
158C187ILE00.0190.00567.8610.0000.0000.0000.0000.0000.000
159C188ALA00.0350.00071.0300.0000.0000.0000.0000.0000.000
160C189SER0-0.023-0.00873.645-0.001-0.0010.0000.0000.0000.000
161C190CYS0-0.063-0.00869.8190.0000.0000.0000.0000.0000.000
162C191ILE0-0.032-0.00972.1560.0000.0000.0000.0000.0000.000
163C192GLU-1-0.984-0.98173.8490.0300.0300.0000.0000.0000.000
164C193HIS0-0.044-0.02574.989-0.001-0.0010.0000.0000.0000.000
165C194ASN0-0.073-0.02469.436-0.001-0.0010.0000.0000.0000.000
166C195PHE0-0.023-0.03272.2580.0000.0000.0000.0000.0000.000
167C196GLY0-0.027-0.00867.9700.0010.0010.0000.0000.0000.000
168C197CYS0-0.081-0.02967.5260.0020.0020.0000.0000.0000.000
169C198THR00.0420.01467.768-0.001-0.0010.0000.0000.0000.000
170C199LEU0-0.048-0.02170.6580.0000.0000.0000.0000.0000.000
171C200ASP-1-0.841-0.91572.9910.0360.0360.0000.0000.0000.000
172C201PRO00.034-0.00676.7260.0000.0000.0000.0000.0000.000
173C202LEU00.0440.01978.8650.0000.0000.0000.0000.0000.000
174C203THR00.0120.02175.3090.0000.0000.0000.0000.0000.000
175C204ARG10.7790.87373.351-0.037-0.0370.0000.0000.0000.000
176C205SER0-0.060-0.04276.6050.0000.0000.0000.0000.0000.000
177C206ASN0-0.012-0.00177.060-0.001-0.0010.0000.0000.0000.000
178C207LEU0-0.038-0.01772.3050.0010.0010.0000.0000.0000.000
179C208THR00.0830.03474.3540.0000.0000.0000.0000.0000.000
180C209HIS00.022-0.00173.1760.0010.0010.0000.0000.0000.000
181C210LEU0-0.056-0.01268.9570.0010.0010.0000.0000.0000.000
182C211VAL00.0390.01269.9690.0010.0010.0000.0000.0000.000
183C212ASP-1-0.863-0.92271.1350.0370.0370.0000.0000.0000.000
184C213LYS10.9100.94167.969-0.044-0.0440.0000.0000.0000.000
185C214ALA0-0.0010.00966.2070.0010.0010.0000.0000.0000.000
186C215ALA00.0230.00866.2770.0010.0010.0000.0000.0000.000
187C216ALA00.0370.00867.6700.0000.0000.0000.0000.0000.000
188C217LYS10.9600.98159.602-0.056-0.0560.0000.0000.0000.000
189C218ALA00.0040.00862.7620.0010.0010.0000.0000.0000.000
190C219VAL00.0140.01163.5350.0000.0000.0000.0000.0000.000
191C220GLU-1-0.938-0.97561.7300.0510.0510.0000.0000.0000.000
192C221ALA0-0.056-0.02459.0160.0010.0010.0000.0000.0000.000
193C222LEU0-0.018-0.02159.2810.0010.0010.0000.0000.0000.000
194C223ASP-1-0.787-0.88761.1320.0450.0450.0000.0000.0000.000
195C224MET0-0.019-0.01055.9290.0010.0010.0000.0000.0000.000
196C225CYS0-0.054-0.03256.2460.0010.0010.0000.0000.0000.000
197C226HIS0-0.010-0.01457.0540.0000.0000.0000.0000.0000.000
198C227GLN0-0.051-0.01758.3080.0010.0010.0000.0000.0000.000
199C228LYS10.8690.94251.441-0.065-0.0650.0000.0000.0000.000
200C229LEU00.0040.01553.5400.0000.0000.0000.0000.0000.000
201C240GLU-1-0.939-0.97359.3090.0320.0320.0000.0000.0000.000
202C241ALA00.0460.00854.4470.0010.0010.0000.0000.0000.000
203C242ARG10.8400.90252.019-0.051-0.0510.0000.0000.0000.000
204C243HIS0-0.009-0.01857.2790.0000.0000.0000.0000.0000.000
205C244LEU00.0290.02855.6510.0000.0000.0000.0000.0000.000
206C245GLU-1-0.783-0.90052.2240.0540.0540.0000.0000.0000.000
207C246MET0-0.013-0.01255.7310.0010.0010.0000.0000.0000.000
208C247GLN0-0.0010.00358.6260.0010.0010.0000.0000.0000.000
209C248THR0-0.058-0.01655.1160.0010.0010.0000.0000.0000.000
210C249LEU00.0280.00252.6250.0020.0020.0000.0000.0000.000
211C250ILE0-0.0140.00456.5470.0010.0010.0000.0000.0000.000
212C251PRO00.0300.01658.9050.0010.0010.0000.0000.0000.000
213C252LEU0-0.015-0.00553.0800.0010.0010.0000.0000.0000.000
214C253LEU0-0.004-0.01055.7030.0020.0020.0000.0000.0000.000
215C254LEU00.0080.01158.2480.0000.0000.0000.0000.0000.000
216C255ARG10.7680.85858.707-0.047-0.0470.0000.0000.0000.000
217C256ASN0-0.004-0.00855.1420.0020.0020.0000.0000.0000.000
218C257VAL0-0.001-0.00257.8600.0010.0010.0000.0000.0000.000
219C258PHE0-0.020-0.02560.9330.0000.0000.0000.0000.0000.000
220C259ALA00.0070.02058.0560.0000.0000.0000.0000.0000.000
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