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: 5J53Z

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2392344.919603
FMO2-HF: Nuclear repulsion 2306403.986752
FMO2-HF: Total energy -85940.932851
FMO2-MP2: Total energy -86188.206841


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.
-3.487-0.7470.01-1.363-1.3870.005
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 : 0.044 / q_NPA : 0.013
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].
3C25THR00.0430.0183.408-3.783-1.0430.010-1.363-1.3870.005
4C26ASN00.0610.0166.0961.0121.0120.0000.0000.0000.000
5C27LEU00.0240.0218.0710.1610.1610.0000.0000.0000.000
6C28ALA00.001-0.0067.100-0.017-0.0170.0000.0000.0000.000
7C29ALA0-0.031-0.0135.7240.0670.0670.0000.0000.0000.000
8C30ASN0-0.053-0.0387.426-0.545-0.5450.0000.0000.0000.000
9C31LEU0-0.0430.01210.749-0.314-0.3140.0000.0000.0000.000
10C32SER00.0030.00812.7150.0180.0180.0000.0000.0000.000
11C33ALA0-0.011-0.03215.407-0.052-0.0520.0000.0000.0000.000
12C34VAL00.0020.01016.1850.0070.0070.0000.0000.0000.000
13C35ARG10.9400.97118.897-0.312-0.3120.0000.0000.0000.000
14C36GLU-1-0.900-0.94222.6730.2150.2150.0000.0000.0000.000
15C37SER0-0.061-0.04825.833-0.007-0.0070.0000.0000.0000.000
16C38ALA00.0600.03328.678-0.003-0.0030.0000.0000.0000.000
17C39THR0-0.043-0.00930.961-0.007-0.0070.0000.0000.0000.000
18C40ALA0-0.043-0.03128.330-0.005-0.0050.0000.0000.0000.000
19C41THR00.0290.01530.3060.0010.0010.0000.0000.0000.000
20C42LEU00.0150.01529.0480.0000.0000.0000.0000.0000.000
21C43SER00.002-0.00832.732-0.003-0.0030.0000.0000.0000.000
22C44GLY0-0.0050.01036.180-0.002-0.0020.0000.0000.0000.000
23C52GLU-1-0.948-0.98747.1320.0390.0390.0000.0000.0000.000
24C53ASP-1-0.850-0.92049.6020.0330.0330.0000.0000.0000.000
25C54PHE00.0320.00247.3330.0000.0000.0000.0000.0000.000
26C55PRO00.003-0.00951.0170.0000.0000.0000.0000.0000.000
27C56ALA00.0030.01050.9930.0000.0000.0000.0000.0000.000
28C57LEU00.0200.01744.3910.0010.0010.0000.0000.0000.000
29C58ILE0-0.026-0.01547.7870.0000.0000.0000.0000.0000.000
30C59LYS10.9280.95250.037-0.030-0.0300.0000.0000.0000.000
31C60GLN0-0.032-0.01743.0650.0000.0000.0000.0000.0000.000
32C61ALA00.0360.01945.6210.0010.0010.0000.0000.0000.000
33C62SER0-0.032-0.01846.631-0.001-0.0010.0000.0000.0000.000
34C63LEU0-0.030-0.01448.6580.0000.0000.0000.0000.0000.000
35C64ASP-1-0.762-0.85343.2600.0510.0510.0000.0000.0000.000
36C65ALA0-0.046-0.00744.2290.0010.0010.0000.0000.0000.000
37C66LEU00.0360.02245.702-0.001-0.0010.0000.0000.0000.000
38C67PHE00.0530.00045.3720.0000.0000.0000.0000.0000.000
39C68LYS10.8470.92740.923-0.035-0.0350.0000.0000.0000.000
40C69CYS0-0.093-0.03441.8900.0000.0000.0000.0000.0000.000
41C70GLY00.0230.02344.430-0.001-0.0010.0000.0000.0000.000
42C71LYS10.8980.93742.048-0.047-0.0470.0000.0000.0000.000
43C72ASP-1-0.795-0.89940.6170.0720.0720.0000.0000.0000.000
44C73ALA00.0100.00041.119-0.003-0.0030.0000.0000.0000.000
45C74GLU-1-0.928-0.96338.4490.0760.0760.0000.0000.0000.000
46C75ALA00.0290.01642.665-0.002-0.0020.0000.0000.0000.000
47C76LEU0-0.070-0.02645.098-0.003-0.0030.0000.0000.0000.000
48C77LYS10.8500.90141.896-0.058-0.0580.0000.0000.0000.000
49C78GLU-1-0.901-0.93246.4890.0550.0550.0000.0000.0000.000
50C79VAL00.0020.00248.364-0.002-0.0020.0000.0000.0000.000
51C80PHE0-0.028-0.02450.741-0.003-0.0030.0000.0000.0000.000
52C81THR0-0.058-0.06149.608-0.002-0.0020.0000.0000.0000.000
53C82ASN0-0.0220.00250.607-0.002-0.0020.0000.0000.0000.000
54C83SER0-0.074-0.01654.038-0.002-0.0020.0000.0000.0000.000
55C84ASN00.015-0.00456.8190.0000.0000.0000.0000.0000.000
56C85ASN0-0.0040.01359.726-0.002-0.0020.0000.0000.0000.000
57C86VAL00.0390.00860.4180.0000.0000.0000.0000.0000.000
58C87ALA00.0340.01361.5600.0000.0000.0000.0000.0000.000
59C88GLY00.0730.02660.0900.0000.0000.0000.0000.0000.000
60C89LYS10.8370.91755.427-0.036-0.0360.0000.0000.0000.000
61C90LYS10.9590.98357.289-0.022-0.0220.0000.0000.0000.000
62C91ALA00.003-0.00359.181-0.001-0.0010.0000.0000.0000.000
63C92ILE00.0270.02353.0470.0000.0000.0000.0000.0000.000
64C93MET0-0.031-0.01653.1390.0000.0000.0000.0000.0000.000
65C94GLU-1-0.867-0.90755.3870.0210.0210.0000.0000.0000.000
66C95PHE00.0440.02252.188-0.001-0.0010.0000.0000.0000.000
67C96ALA0-0.011-0.00851.0250.0000.0000.0000.0000.0000.000
68C97GLY0-0.0120.00051.8730.0000.0000.0000.0000.0000.000
69C98LEU00.0240.00254.009-0.001-0.0010.0000.0000.0000.000
70C99PHE0-0.005-0.01246.819-0.001-0.0010.0000.0000.0000.000
71C100ARG10.9460.97349.158-0.025-0.0250.0000.0000.0000.000
72C101SER0-0.016-0.01550.551-0.001-0.0010.0000.0000.0000.000
73C102ALA00.0720.03552.170-0.001-0.0010.0000.0000.0000.000
74C103LEU0-0.037-0.00744.6320.0000.0000.0000.0000.0000.000
75C104ASN0-0.052-0.02148.3910.0000.0000.0000.0000.0000.000
76C105ALA00.0010.01250.116-0.001-0.0010.0000.0000.0000.000
77C106THR0-0.025-0.03049.695-0.001-0.0010.0000.0000.0000.000
78C107SER0-0.075-0.06145.1880.0010.0010.0000.0000.0000.000
79C108ASP-1-0.915-0.94345.2660.0100.0100.0000.0000.0000.000
80C109SER00.0060.03047.339-0.001-0.0010.0000.0000.0000.000
81C110PRO0-0.005-0.00944.7390.0020.0020.0000.0000.0000.000
82C111GLU-1-0.805-0.88046.4610.0120.0120.0000.0000.0000.000
83C112ALA00.0630.02849.6040.0020.0020.0000.0000.0000.000
84C113LYS10.9660.98741.900-0.026-0.0260.0000.0000.0000.000
85C114THR0-0.051-0.04746.1070.0030.0030.0000.0000.0000.000
86C115LEU0-0.014-0.01447.1790.0020.0020.0000.0000.0000.000
87C116LEU00.0010.02148.2780.0010.0010.0000.0000.0000.000
88C117MET0-0.066-0.02843.7370.0030.0030.0000.0000.0000.000
89C118LYS10.8830.93646.898-0.022-0.0220.0000.0000.0000.000
90C119VAL00.0050.00448.9820.0010.0010.0000.0000.0000.000
91C120GLY00.0450.01748.5910.0010.0010.0000.0000.0000.000
92C121ALA0-0.0090.01146.3490.0020.0020.0000.0000.0000.000
93C122GLU-1-0.875-0.91747.9920.0270.0270.0000.0000.0000.000
94C123TYR00.0520.01851.4530.0010.0010.0000.0000.0000.000
95C124THR0-0.027-0.04547.5670.0010.0010.0000.0000.0000.000
96C125ALA0-0.007-0.00249.0340.0020.0020.0000.0000.0000.000
97C126GLN00.0310.02050.2110.0020.0020.0000.0000.0000.000
98C127ILE00.0020.00151.4020.0000.0000.0000.0000.0000.000
99C128ILE0-0.047-0.01747.7370.0000.0000.0000.0000.0000.000
100C129LYS10.8470.91751.211-0.032-0.0320.0000.0000.0000.000
101C130ASP-1-0.829-0.87153.7920.0310.0310.0000.0000.0000.000
102C131GLY00.0290.01554.3110.0000.0000.0000.0000.0000.000
103C132LEU0-0.037-0.01054.2860.0010.0010.0000.0000.0000.000
104C133LYS10.9150.96255.019-0.040-0.0400.0000.0000.0000.000
105C134GLU-1-0.892-0.94660.2910.0270.0270.0000.0000.0000.000
106C135LYS10.9500.98063.959-0.028-0.0280.0000.0000.0000.000
107C136SER0-0.072-0.06759.4330.0010.0010.0000.0000.0000.000
108C137ALA00.010-0.00159.759-0.001-0.0010.0000.0000.0000.000
109C138PHE0-0.049-0.02555.415-0.001-0.0010.0000.0000.0000.000
110C139GLY00.0320.00160.6710.0000.0000.0000.0000.0000.000
111C140PRO0-0.019-0.01063.493-0.001-0.0010.0000.0000.0000.000
112C141TRP00.0400.02463.768-0.001-0.0010.0000.0000.0000.000
113C142LEU0-0.0020.01962.1900.0000.0000.0000.0000.0000.000
114C143PRO00.0410.03765.9040.0000.0000.0000.0000.0000.000
115C144GLU-1-0.743-0.87168.5750.0200.0200.0000.0000.0000.000
116C145THR0-0.028-0.02270.927-0.001-0.0010.0000.0000.0000.000
117C146LYS11.0411.00672.083-0.014-0.0140.0000.0000.0000.000
118C147LYS10.9400.98072.980-0.013-0.0130.0000.0000.0000.000
119C148ALA00.0000.00671.8640.0000.0000.0000.0000.0000.000
120C149GLU-1-0.868-0.94767.7600.0170.0170.0000.0000.0000.000
121C150ALA00.0490.02969.3430.0000.0000.0000.0000.0000.000
122C151LYS10.9100.95171.618-0.012-0.0120.0000.0000.0000.000
123C152LEU00.0310.03064.8430.0000.0000.0000.0000.0000.000
124C153GLU-1-0.887-0.94366.1440.0140.0140.0000.0000.0000.000
125C154ASN0-0.109-0.07767.858-0.001-0.0010.0000.0000.0000.000
126C155LEU0-0.0050.01067.5390.0000.0000.0000.0000.0000.000
127C156GLU-1-0.799-0.90263.5320.0170.0170.0000.0000.0000.000
128C157LYS10.8600.92666.002-0.009-0.0090.0000.0000.0000.000
129C158GLN00.001-0.00767.755-0.001-0.0010.0000.0000.0000.000
130C159LEU0-0.0110.00565.2740.0000.0000.0000.0000.0000.000
131C160LEU00.0100.01662.4210.0000.0000.0000.0000.0000.000
132C161ASP-1-0.845-0.91065.6130.0080.0080.0000.0000.0000.000
133C162ILE0-0.0060.00068.924-0.001-0.0010.0000.0000.0000.000
134C163ILE0-0.021-0.01362.7580.0000.0000.0000.0000.0000.000
135C164LYS10.8720.93565.125-0.008-0.0080.0000.0000.0000.000
136C165ASN0-0.068-0.04166.214-0.001-0.0010.0000.0000.0000.000
137C166ASN0-0.0190.02465.9890.0000.0000.0000.0000.0000.000
138C167THR0-0.001-0.01567.1910.0000.0000.0000.0000.0000.000
139C168GLY0-0.022-0.00964.4810.0000.0000.0000.0000.0000.000
140C169GLY00.0060.00263.3740.0000.0000.0000.0000.0000.000
141C170GLU-1-0.947-0.96763.6290.0090.0090.0000.0000.0000.000
142C171LEU0-0.048-0.01664.461-0.001-0.0010.0000.0000.0000.000
143C172SER00.0280.02667.0720.0000.0000.0000.0000.0000.000
144C173LYS10.9980.96670.664-0.007-0.0070.0000.0000.0000.000
145C174LEU00.0180.01873.3250.0000.0000.0000.0000.0000.000
146C175SER00.041-0.00869.4530.0000.0000.0000.0000.0000.000
147C176THR0-0.0020.00969.6160.0010.0010.0000.0000.0000.000
148C177ASN0-0.037-0.02870.7130.0010.0010.0000.0000.0000.000
149C178LEU0-0.026-0.00872.6260.0000.0000.0000.0000.0000.000
150C179VAL00.0640.02967.1510.0000.0000.0000.0000.0000.000
151C180MET0-0.039-0.01670.3060.0010.0010.0000.0000.0000.000
152C181GLN0-0.027-0.01772.1530.0000.0000.0000.0000.0000.000
153C182GLU-1-0.890-0.94570.8080.0110.0110.0000.0000.0000.000
154C183VAL0-0.026-0.01467.5390.0010.0010.0000.0000.0000.000
155C184MET0-0.0070.00070.4030.0000.0000.0000.0000.0000.000
156C185PRO00.0140.00673.0180.0000.0000.0000.0000.0000.000
157C186TYR0-0.019-0.00267.3080.0000.0000.0000.0000.0000.000
158C187ILE00.0260.00967.7560.0010.0010.0000.0000.0000.000
159C188ALA00.024-0.00271.0830.0000.0000.0000.0000.0000.000
160C189SER0-0.038-0.02873.6720.0000.0000.0000.0000.0000.000
161C190CYS0-0.054-0.01369.9960.0000.0000.0000.0000.0000.000
162C191ILE0-0.033-0.01172.2120.0000.0000.0000.0000.0000.000
163C192GLU-1-0.932-0.95973.9040.0140.0140.0000.0000.0000.000
164C193HIS0-0.104-0.05975.2330.0000.0000.0000.0000.0000.000
165C194ASN0-0.084-0.02369.4090.0000.0000.0000.0000.0000.000
166C195PHE0-0.023-0.02972.3070.0000.0000.0000.0000.0000.000
167C196GLY0-0.019-0.00468.0300.0010.0010.0000.0000.0000.000
168C197CYS0-0.084-0.02967.5840.0010.0010.0000.0000.0000.000
169C198THR00.0440.01167.9450.0000.0000.0000.0000.0000.000
170C199LEU0-0.055-0.01970.7140.0000.0000.0000.0000.0000.000
171C200ASP-1-0.836-0.91673.0450.0190.0190.0000.0000.0000.000
172C201PRO00.0450.00176.7800.0000.0000.0000.0000.0000.000
173C202LEU00.0350.01478.9190.0000.0000.0000.0000.0000.000
174C203THR00.0080.01175.557-0.001-0.0010.0000.0000.0000.000
175C204ARG10.8040.87773.628-0.019-0.0190.0000.0000.0000.000
176C205SER0-0.059-0.03176.6570.0000.0000.0000.0000.0000.000
177C206ASN0-0.037-0.00877.054-0.001-0.0010.0000.0000.0000.000
178C207LEU0-0.035-0.01472.3640.0000.0000.0000.0000.0000.000
179C208THR00.0710.02674.4020.0000.0000.0000.0000.0000.000
180C209HIS00.0140.00073.2050.0000.0000.0000.0000.0000.000
181C210LEU0-0.049-0.01168.9030.0000.0000.0000.0000.0000.000
182C211VAL00.0400.01670.0160.0000.0000.0000.0000.0000.000
183C212ASP-1-0.865-0.92571.1830.0140.0140.0000.0000.0000.000
184C213LYS10.9220.94768.018-0.017-0.0170.0000.0000.0000.000
185C214ALA00.0020.01066.2550.0000.0000.0000.0000.0000.000
186C215ALA00.0220.00766.3240.0000.0000.0000.0000.0000.000
187C216ALA00.0280.00467.7160.0000.0000.0000.0000.0000.000
188C217LYS10.8550.90560.925-0.019-0.0190.0000.0000.0000.000
189C218ALA00.0040.00962.8080.0000.0000.0000.0000.0000.000
190C219VAL00.0100.00663.5820.0000.0000.0000.0000.0000.000
191C220GLU-1-0.842-0.90161.6830.0170.0170.0000.0000.0000.000
192C221ALA0-0.043-0.01859.1440.0000.0000.0000.0000.0000.000
193C222LEU0-0.011-0.01459.3260.0000.0000.0000.0000.0000.000
194C223ASP-1-0.785-0.88861.1770.0110.0110.0000.0000.0000.000
195C224MET0-0.015-0.00556.0160.0000.0000.0000.0000.0000.000
196C225CYS0-0.027-0.01756.2870.0000.0000.0000.0000.0000.000
197C226HIS0-0.032-0.01657.097-0.001-0.0010.0000.0000.0000.000
198C227GLN0-0.020-0.00858.3330.0000.0000.0000.0000.0000.000
199C228LYS10.8670.94751.795-0.016-0.0160.0000.0000.0000.000
200C229LEU0-0.045-0.01453.516-0.001-0.0010.0000.0000.0000.000
201C240GLU-1-0.958-0.98159.5830.0050.0050.0000.0000.0000.000
202C241ALA00.0550.01154.5030.0010.0010.0000.0000.0000.000
203C242ARG10.8210.87652.127-0.009-0.0090.0000.0000.0000.000
204C243HIS0-0.010-0.01457.3270.0000.0000.0000.0000.0000.000
205C244LEU00.0390.02955.7840.0010.0010.0000.0000.0000.000
206C245GLU-1-0.784-0.90152.1110.0120.0120.0000.0000.0000.000
207C246MET0-0.024-0.01855.7830.0010.0010.0000.0000.0000.000
208C247GLN00.0010.00358.6770.0010.0010.0000.0000.0000.000
209C248THR0-0.062-0.02155.1610.0010.0010.0000.0000.0000.000
210C249LEU00.0250.00352.6880.0010.0010.0000.0000.0000.000
211C250ILE0-0.0030.00556.6000.0010.0010.0000.0000.0000.000
212C251PRO00.0200.01558.9700.0010.0010.0000.0000.0000.000
213C252LEU0-0.020-0.00753.1320.0010.0010.0000.0000.0000.000
214C253LEU0-0.004-0.01055.8420.0010.0010.0000.0000.0000.000
215C254LEU00.0010.00858.3000.0000.0000.0000.0000.0000.000
216C255ARG10.7630.84158.766-0.019-0.0190.0000.0000.0000.000
217C256ASN0-0.032-0.02255.2190.0020.0020.0000.0000.0000.000
218C257VAL0-0.002-0.00757.9120.0010.0010.0000.0000.0000.000
219C258PHE0-0.020-0.02460.9830.0000.0000.0000.0000.0000.000
220C259ALA00.0050.02058.0960.0000.0000.0000.0000.0000.000
221C260GLN0-0.0060.00555.4240.0010.0010.0000.0000.0000.000
222C261ILE0-0.0300.00160.2440.0000.0000.0000.0000.0000.000
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