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: 5JY3Z

Calculation Name: 3G7K-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G7K

Chain ID: C

ChEMBL ID:

UniProt ID: Q0QLE6

Base Structure: X-ray

Registration Date: 2023-09-22

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2432098.496513
FMO2-HF: Nuclear repulsion 2348099.030979
FMO2-HF: Total energy -83999.465534
FMO2-MP2: Total energy -84241.805349


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:2:SER)


Summations of interaction energy for fragment #1(C:2: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.
-0.1082.5910.284-1.296-1.6890.003
Interaction energy analysis for fragmet #1(C:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.015
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].
3C4GLN0-0.033-0.0183.695-1.7850.238-0.005-1.022-0.9960.002
4C5MET0-0.067-0.0354.4762.6562.8250.000-0.030-0.1400.000
5C6ARG10.9460.9756.284-2.661-2.6610.0000.0000.0000.000
6C7ILE00.0150.0159.625-0.116-0.1160.0000.0000.0000.000
7C8PRO00.0010.01913.2880.0240.0240.0000.0000.0000.000
8C9CYS0-0.019-0.00116.164-0.062-0.0620.0000.0000.0000.000
9C10VAL00.0300.02018.6530.0170.0170.0000.0000.0000.000
10C11ILE0-0.0020.01620.678-0.024-0.0240.0000.0000.0000.000
11C12MET0-0.030-0.01524.065-0.001-0.0010.0000.0000.0000.000
12C13ARG10.8680.95727.844-0.124-0.1240.0000.0000.0000.000
13C14ALA00.0280.01931.0680.0010.0010.0000.0000.0000.000
14C15GLY00.0440.00733.066-0.007-0.0070.0000.0000.0000.000
15C16THR0-0.091-0.06935.8910.0030.0030.0000.0000.0000.000
16C17SER0-0.037-0.01732.051-0.005-0.0050.0000.0000.0000.000
17C18LYS10.9560.97226.830-0.150-0.1500.0000.0000.0000.000
18C19GLY00.0020.00727.404-0.011-0.0110.0000.0000.0000.000
19C20ILE00.0050.00520.6480.0200.0200.0000.0000.0000.000
20C21PHE0-0.001-0.01523.449-0.021-0.0210.0000.0000.0000.000
21C22LEU00.007-0.00218.5200.0360.0360.0000.0000.0000.000
22C23LYS10.9680.99821.200-0.312-0.3120.0000.0000.0000.000
23C24GLY00.001-0.00820.9820.0130.0130.0000.0000.0000.000
24C25ASN0-0.048-0.04320.451-0.022-0.0220.0000.0000.0000.000
25C26ASP-1-0.896-0.93816.8590.4040.4040.0000.0000.0000.000
26C27LEU0-0.032-0.02015.9990.0400.0400.0000.0000.0000.000
27C28PRO0-0.031-0.01015.412-0.017-0.0170.0000.0000.0000.000
28C29ALA00.0280.01317.8340.0000.0000.0000.0000.0000.000
29C30ASP-1-0.892-0.95419.806-0.078-0.0780.0000.0000.0000.000
30C31GLN00.0710.01220.7590.0110.0110.0000.0000.0000.000
31C32GLU-1-0.883-0.91521.073-0.146-0.1460.0000.0000.0000.000
32C33LEU0-0.026-0.01714.496-0.001-0.0010.0000.0000.0000.000
33C34ARG10.8730.92817.672-0.076-0.0760.0000.0000.0000.000
34C35ASP-1-0.801-0.90219.6140.0420.0420.0000.0000.0000.000
35C36LYS10.8710.93416.6920.2580.2580.0000.0000.0000.000
36C37VAL0-0.016-0.00913.8120.0080.0080.0000.0000.0000.000
37C38ILE00.0370.02016.3190.0570.0570.0000.0000.0000.000
38C39LEU0-0.011-0.00319.3550.0200.0200.0000.0000.0000.000
39C40ARG10.9090.95914.2660.0810.0810.0000.0000.0000.000
40C41ILE00.0090.02315.7270.0370.0370.0000.0000.0000.000
41C42PHE0-0.009-0.01317.0710.0220.0220.0000.0000.0000.000
42C43GLY00.0160.03219.0840.0040.0040.0000.0000.0000.000
43C44SER0-0.066-0.05819.980-0.013-0.0130.0000.0000.0000.000
44C45PRO0-0.063-0.03120.922-0.010-0.0100.0000.0000.0000.000
45C46ASP-1-0.823-0.94123.262-0.017-0.0170.0000.0000.0000.000
46C47VAL0-0.025-0.01625.1730.0160.0160.0000.0000.0000.000
47C48ARG10.8940.91925.2770.0060.0060.0000.0000.0000.000
48C49GLN0-0.030-0.00822.9640.0220.0220.0000.0000.0000.000
49C50ILE0-0.025-0.00620.4130.0210.0210.0000.0000.0000.000
50C51ASP-1-0.960-0.97915.6640.0290.0290.0000.0000.0000.000
51C52GLY0-0.004-0.01416.9590.0040.0040.0000.0000.0000.000
52C53LEU0-0.054-0.04217.6390.0030.0030.0000.0000.0000.000
53C54ALA0-0.071-0.00720.017-0.005-0.0050.0000.0000.0000.000
54C55GLY00.000-0.00423.537-0.001-0.0010.0000.0000.0000.000
55C56ALA00.0060.00626.202-0.009-0.0090.0000.0000.0000.000
56C57ASP-1-0.843-0.89927.9710.0510.0510.0000.0000.0000.000
57C58PRO00.0540.01230.1200.0080.0080.0000.0000.0000.000
58C59LEU0-0.074-0.05631.6320.0060.0060.0000.0000.0000.000
59C60THR0-0.099-0.06427.8000.0110.0110.0000.0000.0000.000
60C61SER00.0670.02626.1570.0180.0180.0000.0000.0000.000
61C62LYS10.8600.94127.188-0.090-0.0900.0000.0000.0000.000
62C63LEU00.0030.00122.5510.0190.0190.0000.0000.0000.000
63C64ALA0-0.0050.00125.772-0.017-0.0170.0000.0000.0000.000
64C65ILE0-0.012-0.00423.3510.0210.0210.0000.0000.0000.000
65C66ILE0-0.015-0.01125.332-0.018-0.0180.0000.0000.0000.000
66C67GLY00.0190.00225.6210.0200.0200.0000.0000.0000.000
67C68PRO00.006-0.00526.868-0.003-0.0030.0000.0000.0000.000
68C69SER00.0060.00830.098-0.006-0.0060.0000.0000.0000.000
69C70THR0-0.053-0.01932.925-0.003-0.0030.0000.0000.0000.000
70C71HIS0-0.007-0.00234.749-0.005-0.0050.0000.0000.0000.000
71C72PRO0-0.045-0.03138.2860.0040.0040.0000.0000.0000.000
72C73ASP-1-0.885-0.93240.7850.0510.0510.0000.0000.0000.000
73C74ALA0-0.068-0.03437.0740.0010.0010.0000.0000.0000.000
74C75ASP-1-0.837-0.91236.1500.0890.0890.0000.0000.0000.000
75C76VAL0-0.105-0.06730.9980.0080.0080.0000.0000.0000.000
76C77ASP-1-0.726-0.83230.8240.0710.0710.0000.0000.0000.000
77C78TYR0-0.025-0.02930.1670.0150.0150.0000.0000.0000.000
78C79THR0-0.020-0.00827.867-0.015-0.0150.0000.0000.0000.000
79C80PHE0-0.013-0.00728.4640.0130.0130.0000.0000.0000.000
80C81ALA00.0400.01926.759-0.011-0.0110.0000.0000.0000.000
81C82GLN00.0040.01628.5420.0160.0160.0000.0000.0000.000
82C83VAL0-0.0050.00423.477-0.012-0.0120.0000.0000.0000.000
83C84SER00.0100.03326.8730.0050.0050.0000.0000.0000.000
84C85ILE00.0410.06626.2830.0000.0000.0000.0000.0000.000
85C86THR00.005-0.00926.514-0.004-0.0040.0000.0000.0000.000
86C87ASP-1-0.893-0.93828.208-0.041-0.0410.0000.0000.0000.000
87C88ALA0-0.044-0.02024.1220.0100.0100.0000.0000.0000.000
88C89VAL0-0.015-0.02225.456-0.004-0.0040.0000.0000.0000.000
89C90VAL00.006-0.00123.3680.0130.0130.0000.0000.0000.000
90C91ASP-1-0.861-0.92726.7150.0170.0170.0000.0000.0000.000
91C92TYR0-0.039-0.02624.7350.0180.0180.0000.0000.0000.000
92C93ASN0-0.016-0.00731.2330.0020.0020.0000.0000.0000.000
93C94GLY00.0280.01834.9360.0000.0000.0000.0000.0000.000
94C95ASN00.0210.00634.9670.0100.0100.0000.0000.0000.000
95C96CYS0-0.034-0.00833.960-0.003-0.0030.0000.0000.0000.000
96C97GLY00.0760.03035.7920.0050.0050.0000.0000.0000.000
97C98ASN00.0210.00835.7530.0050.0050.0000.0000.0000.000
98C99ILE00.0700.02730.4060.0050.0050.0000.0000.0000.000
99C100SER0-0.005-0.00732.6320.0070.0070.0000.0000.0000.000
100C101ALA00.013-0.01634.8400.0010.0010.0000.0000.0000.000
101C102GLY00.0010.00931.5300.0040.0040.0000.0000.0000.000
102C103VAL0-0.020-0.00631.1360.0090.0090.0000.0000.0000.000
103C104GLY00.0620.04132.0420.0070.0070.0000.0000.0000.000
104C105PRO00.028-0.00132.5230.0060.0060.0000.0000.0000.000
105C106PHE00.004-0.00124.4400.0120.0120.0000.0000.0000.000
106C107ALA00.0200.00229.2170.0120.0120.0000.0000.0000.000
107C108ILE0-0.0060.00631.2150.0020.0020.0000.0000.0000.000
108C109ASP-1-0.841-0.92428.9310.1760.1760.0000.0000.0000.000
109C110GLU-1-0.923-0.97024.5160.2920.2920.0000.0000.0000.000
110C111SER0-0.117-0.05327.8900.0000.0000.0000.0000.0000.000
111C112PHE0-0.032-0.01626.194-0.001-0.0010.0000.0000.0000.000
112C113VAL00.0080.00831.401-0.011-0.0110.0000.0000.0000.000
113C114LYS10.9370.96834.615-0.093-0.0930.0000.0000.0000.000
114C115ALA00.0280.02136.326-0.004-0.0040.0000.0000.0000.000
115C116VAL0-0.084-0.04537.852-0.003-0.0030.0000.0000.0000.000
116C117GLU-1-0.831-0.94441.1950.1010.1010.0000.0000.0000.000
117C118PRO0-0.077-0.04043.073-0.004-0.0040.0000.0000.0000.000
118C119MET00.0060.02043.0690.0040.0040.0000.0000.0000.000
119C120THR00.0190.02038.397-0.001-0.0010.0000.0000.0000.000
120C121ARG10.8930.95841.027-0.064-0.0640.0000.0000.0000.000
121C122VAL0-0.0010.00035.7440.0030.0030.0000.0000.0000.000
122C123CYS0-0.074-0.02439.104-0.004-0.0040.0000.0000.0000.000
123C124ILE0-0.002-0.00534.6720.0040.0040.0000.0000.0000.000
124C125HIS00.019-0.00134.946-0.011-0.0110.0000.0000.0000.000
125C126ASN0-0.075-0.05034.009-0.002-0.0020.0000.0000.0000.000
126C127THR00.0530.00931.051-0.006-0.0060.0000.0000.0000.000
127C128ASN0-0.080-0.04631.5310.0010.0010.0000.0000.0000.000
128C129THR0-0.0520.00234.835-0.007-0.0070.0000.0000.0000.000
129C130GLY00.0200.01537.539-0.005-0.0050.0000.0000.0000.000
130C131LYS10.8850.93839.021-0.035-0.0350.0000.0000.0000.000
131C132LEU00.0460.01739.2440.0040.0040.0000.0000.0000.000
132C133LEU0-0.063-0.03137.223-0.003-0.0030.0000.0000.0000.000
133C134TYR00.0040.00440.4150.0040.0040.0000.0000.0000.000
134C135ALA00.0410.03138.670-0.001-0.0010.0000.0000.0000.000
135C136GLU-1-0.939-0.97340.5880.0660.0660.0000.0000.0000.000
136C137VAL0-0.014-0.02136.7310.0000.0000.0000.0000.0000.000
137C138GLU-1-0.823-0.91340.1700.0860.0860.0000.0000.0000.000
138C139VAL0-0.087-0.03837.2850.0080.0080.0000.0000.0000.000
139C140GLU-1-0.910-0.96338.0880.1050.1050.0000.0000.0000.000
140C141ASP-1-0.882-0.92636.6930.1290.1290.0000.0000.0000.000
141C142GLY0-0.100-0.06235.2450.0090.0090.0000.0000.0000.000
142C143LYS10.9010.95429.316-0.175-0.1750.0000.0000.0000.000
143C144ALA00.0110.00533.595-0.011-0.0110.0000.0000.0000.000
144C145LYS10.9020.96235.149-0.103-0.1030.0000.0000.0000.000
145C146VAL00.008-0.00233.3620.0010.0010.0000.0000.0000.000
146C147SER0-0.044-0.03436.768-0.002-0.0020.0000.0000.0000.000
147C148GLY00.0820.03539.803-0.001-0.0010.0000.0000.0000.000
148C149ASP-1-0.940-0.97643.3470.0780.0780.0000.0000.0000.000
149C150CYS0-0.0450.00643.488-0.005-0.0050.0000.0000.0000.000
150C151LYS10.9330.96942.854-0.066-0.0660.0000.0000.0000.000
151C152ILE0-0.0010.00038.800-0.003-0.0030.0000.0000.0000.000
152C153ASP-1-0.837-0.91942.4160.0600.0600.0000.0000.0000.000
153C154GLY00.000-0.01240.1060.0010.0010.0000.0000.0000.000
154C155VAL0-0.030-0.01536.7420.0050.0050.0000.0000.0000.000
155C156PRO0-0.053-0.03137.458-0.004-0.0040.0000.0000.0000.000
156C157GLY00.0040.00839.2410.0050.0050.0000.0000.0000.000
157C158THR0-0.0230.00241.550-0.003-0.0030.0000.0000.0000.000
158C159ASN0-0.041-0.03637.4650.0060.0060.0000.0000.0000.000
159C160ALA00.0330.02139.443-0.006-0.0060.0000.0000.0000.000
160C161PRO0-0.055-0.02340.3260.0020.0020.0000.0000.0000.000
161C162GLU-1-0.821-0.91237.4650.1050.1050.0000.0000.0000.000
162C163LEU0-0.054-0.01541.525-0.004-0.0040.0000.0000.0000.000
163C164MET0-0.0100.01137.8390.0040.0040.0000.0000.0000.000
164C165ASP-1-0.861-0.95842.5730.0480.0480.0000.0000.0000.000
165C166PHE0-0.019-0.01939.9810.0020.0020.0000.0000.0000.000
166C167SER0-0.0200.00944.833-0.002-0.0020.0000.0000.0000.000
167C168ASP-1-0.871-0.92445.1100.0420.0420.0000.0000.0000.000
168C169THR0-0.051-0.05242.8330.0000.0000.0000.0000.0000.000
169C170ALA0-0.033-0.01244.780-0.003-0.0030.0000.0000.0000.000
170C171GLY0-0.027-0.01447.4600.0000.0000.0000.0000.0000.000
171C172ALA0-0.033-0.02143.305-0.002-0.0020.0000.0000.0000.000
172C173ALA00.0310.02542.9190.0000.0000.0000.0000.0000.000
173C174THR0-0.029-0.02244.191-0.002-0.0020.0000.0000.0000.000
174C175GLY00.0290.02347.664-0.002-0.0020.0000.0000.0000.000
175C176LYS10.8770.92048.813-0.015-0.0150.0000.0000.0000.000
176C177VAL00.0330.04650.8890.0000.0000.0000.0000.0000.000
177C333ASP-1-0.876-0.94356.0400.0350.0350.0000.0000.0000.000
178C334THR0-0.085-0.04752.7680.0010.0010.0000.0000.0000.000
179C335VAL0-0.038-0.01353.157-0.002-0.0020.0000.0000.0000.000
180C336ARG10.9280.95752.510-0.033-0.0330.0000.0000.0000.000
181C337ILE00.0580.02148.378-0.002-0.0020.0000.0000.0000.000
182C338GLY0-0.0180.00650.0980.0020.0020.0000.0000.0000.000
183C339HIS00.0130.00442.809-0.003-0.0030.0000.0000.0000.000
184C340PRO00.022-0.01343.2850.0000.0000.0000.0000.0000.000
185C341ALA0-0.0080.00942.6640.0000.0000.0000.0000.0000.000
186C342GLY0-0.029-0.00544.7230.0030.0030.0000.0000.0000.000
187C343VAL0-0.059-0.04747.574-0.004-0.0040.0000.0000.0000.000
188C344ILE0-0.033-0.02044.4080.0030.0030.0000.0000.0000.000
189C345PRO0-0.0220.00448.189-0.003-0.0030.0000.0000.0000.000
190C346VAL00.001-0.00347.6470.0030.0030.0000.0000.0000.000
191C347VAL0-0.009-0.01250.035-0.003-0.0030.0000.0000.0000.000
192C348SER00.0070.00152.0890.0000.0000.0000.0000.0000.000
193C349ILE00.0520.02153.236-0.001-0.0010.0000.0000.0000.000
194C350VAL0-0.032-0.01155.8480.0000.0000.0000.0000.0000.000
195C351LYS10.8410.90057.602-0.031-0.0310.0000.0000.0000.000
196C352ASP-1-0.912-0.95959.4030.0190.0190.0000.0000.0000.000
197C353GLY00.0420.03056.4430.0000.0000.0000.0000.0000.000
198C354LYS10.8190.90154.232-0.033-0.0330.0000.0000.0000.000
199C355VAL00.0160.00750.3960.0000.0000.0000.0000.0000.000
200C356GLU-1-0.852-0.89152.3750.0350.0350.0000.0000.0000.000
201C357LYS11.0310.98750.581-0.048-0.0480.0000.0000.0000.000
202C358ALA00.0090.01547.903-0.002-0.0020.0000.0000.0000.000
203C359ALA00.0220.02846.6630.0020.0020.0000.0000.0000.000
204C360LEU0-0.014-0.00943.020-0.003-0.0030.0000.0000.0000.000
205C361ILE00.0390.03343.9290.0030.0030.0000.0000.0000.000
206C362ARG10.8330.90838.941-0.074-0.0740.0000.0000.0000.000
207C363THR00.0940.04137.6900.0030.0030.0000.0000.0000.000
208C364ALA00.0140.00933.2970.0010.0010.0000.0000.0000.000
209C365ARG10.9730.99129.947-0.168-0.1680.0000.0000.0000.000
210C366ARG10.9120.96224.713-0.254-0.2540.0000.0000.0000.000
211C367ILE0-0.127-0.05725.308-0.007-0.0070.0000.0000.0000.000
212C368MET0-0.009-0.01518.817-0.001-0.0010.0000.0000.0000.000
213C369GLU-1-0.839-0.90820.8900.3070.3070.0000.0000.0000.000
214C370GLY00.0110.00517.1920.0140.0140.0000.0000.0000.000
215C371TYR0-0.029-0.03212.2470.0280.0280.0000.0000.0000.000
216C372VAL00.0260.02213.4310.0490.0490.0000.0000.0000.000
217C373TYR0-0.041-0.0326.9390.3500.3500.0000.0000.0000.000
218C374VAL00.0600.0359.486-0.237-0.2370.0000.0000.0000.000
219C375GLU-1-0.847-0.9378.371-0.521-0.5210.0000.0000.0000.000
220C376LYS10.9180.9532.6800.4790.9860.289-0.244-0.5530.001
221C377ALA00.0330.0218.3730.1090.1090.0000.0000.0000.000
222C378LYS10.8800.95110.4990.4930.4930.0000.0000.0000.000
223C379LEU0-0.020-0.01210.8810.1390.1390.0000.0000.0000.000
224C380VAL0-0.0290.00413.7060.0360.0360.0000.0000.0000.000