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: YVRQ2

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 OptAll
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 -2403580.520247
FMO2-HF: Nuclear repulsion 2317639.141725
FMO2-HF: Total energy -85941.378522
FMO2-MP2: Total energy -86188.700627


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.
-3.611-1.0950.04-1.267-1.2880.003
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 : 0.056 / 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].
3C25THR00.0390.0123.302-3.892-1.3760.040-1.267-1.2880.003
4C26ASN00.0400.0055.8320.7040.7040.0000.0000.0000.000
5C27LEU00.0250.0287.9450.1030.1030.0000.0000.0000.000
6C28ALA00.0190.0067.1850.0110.0110.0000.0000.0000.000
7C29ALA0-0.032-0.0195.8280.1980.1980.0000.0000.0000.000
8C30ASN0-0.046-0.0287.659-0.422-0.4220.0000.0000.0000.000
9C31LEU0-0.0190.00910.942-0.242-0.2420.0000.0000.0000.000
10C32SER0-0.021-0.01712.8710.0000.0000.0000.0000.0000.000
11C33ALA0-0.026-0.01515.513-0.053-0.0530.0000.0000.0000.000
12C34VAL00.0070.00515.9890.0150.0150.0000.0000.0000.000
13C35ARG10.9060.95918.751-0.262-0.2620.0000.0000.0000.000
14C36GLU-1-0.878-0.92622.5850.2050.2050.0000.0000.0000.000
15C37SER0-0.036-0.05225.7690.0000.0000.0000.0000.0000.000
16C38ALA00.0380.02628.618-0.005-0.0050.0000.0000.0000.000
17C39THR00.0040.00231.430-0.011-0.0110.0000.0000.0000.000
18C40ALA0-0.069-0.01928.055-0.004-0.0040.0000.0000.0000.000
19C41THR00.0190.00530.1200.0020.0020.0000.0000.0000.000
20C42LEU00.0030.00629.0260.0000.0000.0000.0000.0000.000
21C43SER00.0030.00032.920-0.002-0.0020.0000.0000.0000.000
22C44GLY00.0020.01036.094-0.002-0.0020.0000.0000.0000.000
23C52GLU-1-0.934-0.98146.7130.0300.0300.0000.0000.0000.000
24C53ASP-1-0.840-0.91549.6980.0230.0230.0000.0000.0000.000
25C54PHE00.0350.00746.9100.0000.0000.0000.0000.0000.000
26C55PRO0-0.016-0.01350.621-0.001-0.0010.0000.0000.0000.000
27C56ALA0-0.0030.00250.942-0.001-0.0010.0000.0000.0000.000
28C57LEU00.0220.01944.0700.0000.0000.0000.0000.0000.000
29C58ILE0-0.019-0.01347.507-0.001-0.0010.0000.0000.0000.000
30C59LYS10.9220.95349.680-0.018-0.0180.0000.0000.0000.000
31C60GLN0-0.020-0.01142.8870.0000.0000.0000.0000.0000.000
32C61ALA00.0290.01745.1600.0000.0000.0000.0000.0000.000
33C62SER0-0.043-0.02746.177-0.002-0.0020.0000.0000.0000.000
34C63LEU0-0.0140.00148.485-0.001-0.0010.0000.0000.0000.000
35C64ASP-1-0.775-0.86642.9380.0290.0290.0000.0000.0000.000
36C65ALA0-0.042-0.01244.077-0.001-0.0010.0000.0000.0000.000
37C66LEU00.0070.02645.534-0.002-0.0020.0000.0000.0000.000
38C67PHE00.0710.00145.313-0.001-0.0010.0000.0000.0000.000
39C68LYS10.8320.91440.712-0.012-0.0120.0000.0000.0000.000
40C69CYS0-0.068-0.02141.618-0.001-0.0010.0000.0000.0000.000
41C70GLY00.0280.02644.242-0.001-0.0010.0000.0000.0000.000
42C71LYS10.8930.92641.950-0.021-0.0210.0000.0000.0000.000
43C72ASP-1-0.793-0.88840.7410.0420.0420.0000.0000.0000.000
44C73ALA00.0200.00440.985-0.001-0.0010.0000.0000.0000.000
45C74GLU-1-0.943-0.96738.3880.0480.0480.0000.0000.0000.000
46C75ALA00.0370.01542.650-0.001-0.0010.0000.0000.0000.000
47C76LEU0-0.059-0.02145.132-0.002-0.0020.0000.0000.0000.000
48C77LYS10.8530.91341.532-0.035-0.0350.0000.0000.0000.000
49C78GLU-1-0.902-0.90946.1520.0350.0350.0000.0000.0000.000
50C79VAL00.0430.01248.068-0.001-0.0010.0000.0000.0000.000
51C80PHE0-0.024-0.02350.407-0.002-0.0020.0000.0000.0000.000
52C81THR0-0.067-0.05949.487-0.001-0.0010.0000.0000.0000.000
53C82ASN0-0.043-0.04150.329-0.001-0.0010.0000.0000.0000.000
54C83SER0-0.077-0.02253.845-0.001-0.0010.0000.0000.0000.000
55C84ASN00.023-0.00356.4680.0000.0000.0000.0000.0000.000
56C85ASN0-0.0060.01859.592-0.001-0.0010.0000.0000.0000.000
57C86VAL00.0410.00960.3460.0000.0000.0000.0000.0000.000
58C87ALA00.0160.02661.6360.0000.0000.0000.0000.0000.000
59C88GLY00.0720.01859.679-0.001-0.0010.0000.0000.0000.000
60C89LYS10.8200.90755.031-0.023-0.0230.0000.0000.0000.000
61C90LYS10.9170.97157.370-0.011-0.0110.0000.0000.0000.000
62C91ALA00.0500.02158.961-0.001-0.0010.0000.0000.0000.000
63C92ILE0-0.0110.00152.982-0.001-0.0010.0000.0000.0000.000
64C93MET0-0.023-0.00753.0860.0000.0000.0000.0000.0000.000
65C94GLU-1-0.860-0.90855.2740.0090.0090.0000.0000.0000.000
66C95PHE00.0140.00252.012-0.001-0.0010.0000.0000.0000.000
67C96ALA00.0110.00850.964-0.001-0.0010.0000.0000.0000.000
68C97GLY0-0.0010.00751.795-0.001-0.0010.0000.0000.0000.000
69C98LEU00.0180.01154.093-0.001-0.0010.0000.0000.0000.000
70C99PHE00.013-0.00246.530-0.001-0.0010.0000.0000.0000.000
71C100ARG10.9510.96948.962-0.011-0.0110.0000.0000.0000.000
72C101SER0-0.043-0.03750.451-0.001-0.0010.0000.0000.0000.000
73C102ALA00.0600.02652.167-0.001-0.0010.0000.0000.0000.000
74C103LEU0-0.044-0.00644.645-0.001-0.0010.0000.0000.0000.000
75C104ASN0-0.049-0.02748.114-0.001-0.0010.0000.0000.0000.000
76C105ALA0-0.0110.00449.949-0.001-0.0010.0000.0000.0000.000
77C106THR0-0.006-0.02149.738-0.001-0.0010.0000.0000.0000.000
78C107SER0-0.071-0.05144.8040.0000.0000.0000.0000.0000.000
79C108ASP-1-0.919-0.94945.135-0.009-0.0090.0000.0000.0000.000
80C109SER00.0040.01947.053-0.001-0.0010.0000.0000.0000.000
81C110PRO00.004-0.00344.4650.0020.0020.0000.0000.0000.000
82C111GLU-1-0.807-0.86646.206-0.009-0.0090.0000.0000.0000.000
83C112ALA00.0590.02249.5810.0020.0020.0000.0000.0000.000
84C113LYS10.9620.99641.7830.0020.0020.0000.0000.0000.000
85C114THR0-0.034-0.03546.0450.0020.0020.0000.0000.0000.000
86C115LEU0-0.025-0.01647.2190.0020.0020.0000.0000.0000.000
87C116LEU00.0120.02448.2320.0010.0010.0000.0000.0000.000
88C117MET0-0.069-0.04243.6830.0020.0020.0000.0000.0000.000
89C118LYS10.8420.91646.811-0.003-0.0030.0000.0000.0000.000
90C119VAL00.0020.00749.0880.0010.0010.0000.0000.0000.000
91C120GLY00.0400.01348.8390.0010.0010.0000.0000.0000.000
92C121ALA0-0.0070.02146.4470.0020.0020.0000.0000.0000.000
93C122GLU-1-0.850-0.91148.0860.0080.0080.0000.0000.0000.000
94C123TYR00.0390.01651.6060.0010.0010.0000.0000.0000.000
95C124THR0-0.021-0.04647.9150.0010.0010.0000.0000.0000.000
96C125ALA0-0.014-0.01048.9150.0020.0020.0000.0000.0000.000
97C126GLN00.0260.01250.0280.0020.0020.0000.0000.0000.000
98C127ILE00.0030.00351.3180.0010.0010.0000.0000.0000.000
99C128ILE0-0.018-0.00447.5730.0010.0010.0000.0000.0000.000
100C129LYS10.8010.89450.998-0.016-0.0160.0000.0000.0000.000
101C130ASP-1-0.799-0.85453.6810.0170.0170.0000.0000.0000.000
102C131GLY00.004-0.00453.8460.0000.0000.0000.0000.0000.000
103C132LEU0-0.0260.00453.8810.0010.0010.0000.0000.0000.000
104C133LYS10.9070.96454.856-0.024-0.0240.0000.0000.0000.000
105C134GLU-1-0.891-0.94960.1320.0170.0170.0000.0000.0000.000
106C135LYS10.9580.98563.786-0.016-0.0160.0000.0000.0000.000
107C136SER0-0.059-0.06359.1560.0010.0010.0000.0000.0000.000
108C137ALA00.0190.00559.718-0.001-0.0010.0000.0000.0000.000
109C138PHE0-0.044-0.02355.260-0.001-0.0010.0000.0000.0000.000
110C139GLY00.0390.00260.3120.0010.0010.0000.0000.0000.000
111C140PRO0-0.027-0.01363.368-0.001-0.0010.0000.0000.0000.000
112C141TRP00.0600.03163.546-0.001-0.0010.0000.0000.0000.000
113C142LEU0-0.0010.01962.174-0.001-0.0010.0000.0000.0000.000
114C143PRO00.0200.02965.4800.0000.0000.0000.0000.0000.000
115C144GLU-1-0.744-0.86968.0770.0110.0110.0000.0000.0000.000
116C145THR0-0.003-0.01370.4440.0000.0000.0000.0000.0000.000
117C146LYS11.0361.00771.537-0.007-0.0070.0000.0000.0000.000
118C147LYS10.9440.98672.734-0.006-0.0060.0000.0000.0000.000
119C148ALA00.0090.00871.3670.0000.0000.0000.0000.0000.000
120C149GLU-1-0.897-0.96067.4310.0080.0080.0000.0000.0000.000
121C150ALA00.0650.03969.0310.0000.0000.0000.0000.0000.000
122C151LYS10.9220.95471.304-0.004-0.0040.0000.0000.0000.000
123C152LEU00.0150.02364.5720.0000.0000.0000.0000.0000.000
124C153GLU-1-0.877-0.94165.9820.0050.0050.0000.0000.0000.000
125C154ASN0-0.100-0.06567.564-0.001-0.0010.0000.0000.0000.000
126C155LEU00.0090.01367.435-0.001-0.0010.0000.0000.0000.000
127C156GLU-1-0.792-0.90063.4130.0050.0050.0000.0000.0000.000
128C157LYS10.8330.90865.657-0.001-0.0010.0000.0000.0000.000
129C158GLN0-0.026-0.02467.521-0.001-0.0010.0000.0000.0000.000
130C159LEU0-0.0040.00365.178-0.001-0.0010.0000.0000.0000.000
131C160LEU00.0140.01362.290-0.001-0.0010.0000.0000.0000.000
132C161ASP-1-0.836-0.90365.399-0.002-0.0020.0000.0000.0000.000
133C162ILE0-0.030-0.00868.756-0.001-0.0010.0000.0000.0000.000
134C163ILE0-0.016-0.01362.533-0.001-0.0010.0000.0000.0000.000
135C164LYS10.8590.92765.0380.0020.0020.0000.0000.0000.000
136C165ASN0-0.066-0.03765.949-0.001-0.0010.0000.0000.0000.000
137C166ASN0-0.0140.01765.4110.0000.0000.0000.0000.0000.000
138C167THR0-0.002-0.00966.9420.0000.0000.0000.0000.0000.000
139C168GLY0-0.021-0.01164.1980.0000.0000.0000.0000.0000.000
140C169GLY00.0100.00463.249-0.001-0.0010.0000.0000.0000.000
141C170GLU-1-0.943-0.96663.669-0.004-0.0040.0000.0000.0000.000
142C171LEU0-0.030-0.00864.5390.0000.0000.0000.0000.0000.000
143C172SER00.0210.00866.8650.0000.0000.0000.0000.0000.000
144C173LYS10.9960.97270.4130.0030.0030.0000.0000.0000.000
145C174LEU00.0120.02373.1160.0000.0000.0000.0000.0000.000
146C175SER00.027-0.00169.1520.0000.0000.0000.0000.0000.000
147C176THR00.0160.00769.0560.0010.0010.0000.0000.0000.000
148C177ASN0-0.042-0.02470.3720.0010.0010.0000.0000.0000.000
149C178LEU0-0.005-0.00572.4520.0000.0000.0000.0000.0000.000
150C179VAL00.0260.01466.7650.0000.0000.0000.0000.0000.000
151C180MET0-0.032-0.01269.9570.0010.0010.0000.0000.0000.000
152C181GLN0-0.023-0.01671.9140.0000.0000.0000.0000.0000.000
153C182GLU-1-0.863-0.92370.7250.0020.0020.0000.0000.0000.000
154C183VAL0-0.014-0.00667.2540.0010.0010.0000.0000.0000.000
155C184MET0-0.006-0.00170.1630.0000.0000.0000.0000.0000.000
156C185PRO00.0060.00072.8460.0010.0010.0000.0000.0000.000
157C186TYR0-0.0100.00466.8860.0000.0000.0000.0000.0000.000
158C187ILE00.0340.01667.5630.0010.0010.0000.0000.0000.000
159C188ALA00.0270.00870.8800.0000.0000.0000.0000.0000.000
160C189SER0-0.036-0.03273.4760.0000.0000.0000.0000.0000.000
161C190CYS0-0.073-0.02369.6130.0000.0000.0000.0000.0000.000
162C191ILE0-0.021-0.01271.9040.0010.0010.0000.0000.0000.000
163C192GLU-1-0.927-0.94573.8910.0060.0060.0000.0000.0000.000
164C193HIS0-0.112-0.07275.0090.0000.0000.0000.0000.0000.000
165C194ASN0-0.079-0.02769.1750.0000.0000.0000.0000.0000.000
166C195PHE0-0.028-0.03771.6690.0000.0000.0000.0000.0000.000
167C196GLY0-0.010-0.00567.5680.0010.0010.0000.0000.0000.000
168C197CYS0-0.055-0.02267.4030.0010.0010.0000.0000.0000.000
169C198THR00.0170.01467.3400.0000.0000.0000.0000.0000.000
170C199LEU0-0.040-0.01970.1770.0000.0000.0000.0000.0000.000
171C200ASP-1-0.789-0.87872.9620.0110.0110.0000.0000.0000.000
172C201PRO00.014-0.00676.7950.0000.0000.0000.0000.0000.000
173C202LEU00.0190.01378.9390.0000.0000.0000.0000.0000.000
174C203THR0-0.009-0.01575.349-0.001-0.0010.0000.0000.0000.000
175C204ARG10.7850.87273.755-0.010-0.0100.0000.0000.0000.000
176C205SER0-0.028-0.01776.4750.0000.0000.0000.0000.0000.000
177C206ASN0-0.050-0.02976.689-0.001-0.0010.0000.0000.0000.000
178C207LEU0-0.026-0.00472.0560.0000.0000.0000.0000.0000.000
179C208THR00.0320.01674.0780.0000.0000.0000.0000.0000.000
180C209HIS00.0580.01572.8460.0000.0000.0000.0000.0000.000
181C210LEU0-0.042-0.00468.6820.0000.0000.0000.0000.0000.000
182C211VAL00.0400.01669.7500.0000.0000.0000.0000.0000.000
183C212ASP-1-0.853-0.93270.9270.0040.0040.0000.0000.0000.000
184C213LYS10.8670.92767.846-0.006-0.0060.0000.0000.0000.000
185C214ALA00.0140.01365.9340.0000.0000.0000.0000.0000.000
186C215ALA00.0230.01066.0400.0000.0000.0000.0000.0000.000
187C216ALA00.0230.00467.3750.0000.0000.0000.0000.0000.000
188C217LYS10.8400.88861.091-0.004-0.0040.0000.0000.0000.000
189C218ALA00.0140.01562.4900.0000.0000.0000.0000.0000.000
190C219VAL00.0120.00163.4600.0000.0000.0000.0000.0000.000
191C220GLU-1-0.846-0.89761.2260.0020.0020.0000.0000.0000.000
192C221ALA0-0.026-0.01158.958-0.001-0.0010.0000.0000.0000.000
193C222LEU00.003-0.00458.9950.0000.0000.0000.0000.0000.000
194C223ASP-1-0.779-0.88761.118-0.003-0.0030.0000.0000.0000.000
195C224MET0-0.0210.00055.823-0.001-0.0010.0000.0000.0000.000
196C225CYS0-0.021-0.01256.333-0.001-0.0010.0000.0000.0000.000
197C226HIS0-0.017-0.00457.114-0.001-0.0010.0000.0000.0000.000
198C227GLN0-0.060-0.03358.422-0.001-0.0010.0000.0000.0000.000
199C228LYS10.8770.94752.1970.0050.0050.0000.0000.0000.000
200C229LEU0-0.034-0.00853.595-0.002-0.0020.0000.0000.0000.000
201C240GLU-1-0.943-0.97559.796-0.007-0.0070.0000.0000.0000.000
202C241ALA00.0490.01154.7080.0010.0010.0000.0000.0000.000
203C242ARG10.8210.86952.0180.0080.0080.0000.0000.0000.000
204C243HIS0-0.001-0.00957.4850.0000.0000.0000.0000.0000.000
205C244LEU00.0510.03755.8190.0010.0010.0000.0000.0000.000
206C245GLU-1-0.788-0.89852.185-0.005-0.0050.0000.0000.0000.000
207C246MET0-0.019-0.01055.7370.0010.0010.0000.0000.0000.000
208C247GLN0-0.027-0.01158.7150.0000.0000.0000.0000.0000.000
209C248THR0-0.044-0.02955.2980.0010.0010.0000.0000.0000.000
210C249LEU00.0230.01052.4940.0010.0010.0000.0000.0000.000
211C250ILE0-0.0090.00456.4480.0010.0010.0000.0000.0000.000
212C251PRO00.0100.01059.0020.0010.0010.0000.0000.0000.000
213C252LEU0-0.028-0.00353.1990.0010.0010.0000.0000.0000.000
214C253LEU0-0.009-0.01555.9110.0010.0010.0000.0000.0000.000
215C254LEU0-0.0090.00758.3270.0000.0000.0000.0000.0000.000
216C255ARG10.7670.84058.576-0.007-0.0070.0000.0000.0000.000
217C256ASN00.0040.00054.8840.0020.0020.0000.0000.0000.000
218C257VAL0-0.011-0.00757.5360.0010.0010.0000.0000.0000.000
219C258PHE0-0.009-0.02760.6290.0000.0000.0000.0000.0000.000
220C259ALA00.0130.01957.6830.0000.0000.0000.0000.0000.000
221C260GLN0-0.063-0.02854.8790.0010.0010.0000.0000.0000.000
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