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

tag_button

FMODB ID: 66QRZ

Calculation Name: 4Y66-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: C

ChEMBL ID:

UniProt ID: E2RTU1

Base Structure: X-ray

Registration Date: 2023-06-20

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1439301.553426
FMO2-HF: Nuclear repulsion 1359797.030585
FMO2-HF: Total energy -79504.522841
FMO2-MP2: Total energy -79736.293598


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:6:THR)


Summations of interaction energy for fragment #1(C:6:THR)
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.
-25.099-15.630.921-4.829-5.5610.003
Interaction energy analysis for fragmet #1(C:6:THR)
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 : 0.014
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].
3C8LEU0-0.063-0.0252.672-7.167-3.0570.456-2.142-2.4250.018
4C9ASP-1-0.806-0.9252.695-15.334-10.5460.464-2.576-2.675-0.015
5C10GLU-1-0.868-0.9243.722-3.041-2.4700.001-0.111-0.4610.000
6C11LYS10.8940.9395.902-0.030-0.0300.0000.0000.0000.000
7C12LYS10.7910.8826.3561.2311.2310.0000.0000.0000.000
8C13GLU-1-0.891-0.9348.122-1.094-1.0940.0000.0000.0000.000
9C14ARG10.8030.9049.8570.7600.7600.0000.0000.0000.000
10C15LEU0-0.020-0.03611.8780.1320.1320.0000.0000.0000.000
11C16LEU00.0590.02113.0710.1010.1010.0000.0000.0000.000
12C17GLU-1-0.914-0.94713.983-0.391-0.3910.0000.0000.0000.000
13C18GLU-1-0.826-0.90215.784-0.238-0.2380.0000.0000.0000.000
14C19MET0-0.084-0.03917.5390.0480.0480.0000.0000.0000.000
15C20LEU0-0.030-0.00417.0310.0390.0390.0000.0000.0000.000
16C21LYS10.9310.97619.9590.3110.3110.0000.0000.0000.000
17C22ARG10.7790.87320.8180.2350.2350.0000.0000.0000.000
18C23GLY00.0180.02823.1600.0200.0200.0000.0000.0000.000
19C24GLU-1-0.903-0.92124.385-0.112-0.1120.0000.0000.0000.000
20C25ILE0-0.011-0.01524.589-0.007-0.0070.0000.0000.0000.000
21C26TYR00.004-0.03522.1110.0010.0010.0000.0000.0000.000
22C27SER00.015-0.02324.8720.0110.0110.0000.0000.0000.000
23C28ASN00.0520.00723.025-0.007-0.0070.0000.0000.0000.000
24C29LYS11.0010.98422.605-0.008-0.0080.0000.0000.0000.000
25C30THR00.0220.04624.4100.0040.0040.0000.0000.0000.000
26C31ILE00.0780.06218.882-0.006-0.0060.0000.0000.0000.000
27C32GLU-1-0.823-0.88820.2080.0200.0200.0000.0000.0000.000
28C33THR0-0.036-0.01921.3750.0060.0060.0000.0000.0000.000
29C34LEU00.000-0.01218.476-0.004-0.0040.0000.0000.0000.000
30C35SER0-0.036-0.00417.450-0.032-0.0320.0000.0000.0000.000
31C36LYS10.9220.96118.0560.0440.0440.0000.0000.0000.000
32C37PRO00.0030.01818.899-0.009-0.0090.0000.0000.0000.000
33C38THR0-0.019-0.03014.076-0.031-0.0310.0000.0000.0000.000
34C39GLY00.0300.03413.671-0.062-0.0620.0000.0000.0000.000
35C40ILE0-0.041-0.01111.5650.0600.0600.0000.0000.0000.000
36C41SER00.0340.00614.151-0.013-0.0130.0000.0000.0000.000
37C42SER00.019-0.01016.1660.0230.0230.0000.0000.0000.000
38C43MET0-0.0120.00117.5670.0020.0020.0000.0000.0000.000
39C44VAL0-0.031-0.03711.4950.0310.0310.0000.0000.0000.000
40C45ILE00.0060.02814.0720.0220.0220.0000.0000.0000.000
41C46LYS10.9150.94014.917-0.066-0.0660.0000.0000.0000.000
42C47ASN0-0.023-0.00813.151-0.033-0.0330.0000.0000.0000.000
43C48VAL00.0040.0099.9630.0370.0370.0000.0000.0000.000
44C49LEU0-0.0070.00211.978-0.094-0.0940.0000.0000.0000.000
45C50GLN0-0.046-0.02314.865-0.041-0.0410.0000.0000.0000.000
46C51ALA0-0.003-0.0159.818-0.015-0.0150.0000.0000.0000.000
47C52LEU00.0390.01511.288-0.083-0.0830.0000.0000.0000.000
48C53VAL0-0.045-0.01713.212-0.027-0.0270.0000.0000.0000.000
49C54ASN0-0.018-0.00213.292-0.006-0.0060.0000.0000.0000.000
50C55GLU-1-0.867-0.9209.525-0.643-0.6430.0000.0000.0000.000
51C56ASP-1-0.834-0.90314.204-0.246-0.2460.0000.0000.0000.000
52C57LEU0-0.0040.00611.741-0.018-0.0180.0000.0000.0000.000
53C58VAL0-0.061-0.05116.295-0.004-0.0040.0000.0000.0000.000
54C59ASP-1-0.872-0.92518.730-0.156-0.1560.0000.0000.0000.000
55C60THR0-0.057-0.03621.2460.0140.0140.0000.0000.0000.000
56C61ASP-1-0.805-0.90623.203-0.061-0.0610.0000.0000.0000.000
57C62LYS10.7660.88026.6520.0110.0110.0000.0000.0000.000
58C63ILE00.0450.03029.155-0.001-0.0010.0000.0000.0000.000
59C64GLY0-0.0060.00232.3390.0040.0040.0000.0000.0000.000
60C65ALA00.0500.01232.6330.0020.0020.0000.0000.0000.000
61C66SER0-0.051-0.02328.9610.0090.0090.0000.0000.0000.000
62C67THR0-0.033-0.01224.0730.0010.0010.0000.0000.0000.000
63C68TYR0-0.014-0.01925.5920.0060.0060.0000.0000.0000.000
64C69TYR00.016-0.00320.2170.0050.0050.0000.0000.0000.000
65C70TRP0-0.014-0.00422.6310.0020.0020.0000.0000.0000.000
66C71CYS00.0130.01018.129-0.008-0.0080.0000.0000.0000.000
67C72PHE00.0680.04221.6920.0010.0010.0000.0000.0000.000
68C73ALA00.0510.02421.607-0.020-0.0200.0000.0000.0000.000
69C74SER0-0.039-0.03023.000-0.012-0.0120.0000.0000.0000.000
70C75LYS10.8400.93319.5010.2390.2390.0000.0000.0000.000
71C76ARG11.0581.00618.1490.3420.3420.0000.0000.0000.000
72C77SER00.0040.00722.6310.0220.0220.0000.0000.0000.000
73C78GLN00.0320.02425.8510.0160.0160.0000.0000.0000.000
74C79ALA00.0600.03924.3330.0130.0130.0000.0000.0000.000
75C80ALA00.0010.00525.4670.0120.0120.0000.0000.0000.000
76C81ARG10.8790.92927.1050.1520.1520.0000.0000.0000.000
77C82THR0-0.026-0.02229.6190.0110.0110.0000.0000.0000.000
78C83GLU-1-0.803-0.89027.881-0.083-0.0830.0000.0000.0000.000
79C84LEU0-0.036-0.00730.3760.0070.0070.0000.0000.0000.000
80C85ALA00.025-0.00432.5940.0070.0070.0000.0000.0000.000
81C86ARG10.8730.92230.3310.0820.0820.0000.0000.0000.000
82C87LEU0-0.025-0.00631.3160.0070.0070.0000.0000.0000.000
83C88GLN00.0000.00134.8590.0030.0030.0000.0000.0000.000
84C89LYS10.8280.92437.6650.0520.0520.0000.0000.0000.000
85C90ALA00.0190.00937.0260.0040.0040.0000.0000.0000.000
86C91LEU0-0.020-0.00738.5450.0040.0040.0000.0000.0000.000
87C92GLU-1-0.863-0.93040.251-0.046-0.0460.0000.0000.0000.000
88C93GLU-1-0.914-0.95942.616-0.040-0.0400.0000.0000.0000.000
89C94GLN00.010-0.00240.6460.0050.0050.0000.0000.0000.000
90C95THR0-0.025-0.01843.7320.0030.0030.0000.0000.0000.000
91C96ASN00.0810.03945.9170.0040.0040.0000.0000.0000.000
92C97PHE0-0.046-0.01445.7240.0020.0020.0000.0000.0000.000
93C98ILE00.0160.00345.5000.0020.0020.0000.0000.0000.000
94C99ASP-1-0.897-0.93848.556-0.030-0.0300.0000.0000.0000.000
95C100LYS10.8560.91251.3670.0280.0280.0000.0000.0000.000
96C101ALA0-0.0170.00650.7960.0020.0020.0000.0000.0000.000
97C102THR0-0.006-0.01651.5360.0020.0020.0000.0000.0000.000
98C103ALA00.0260.03554.1420.0010.0010.0000.0000.0000.000
99C104ARG10.8230.89256.1900.0170.0170.0000.0000.0000.000
100C105ILE0-0.007-0.02753.4960.0010.0010.0000.0000.0000.000
101C106GLU-1-0.820-0.89557.456-0.016-0.0160.0000.0000.0000.000
102C107GLU-1-0.836-0.90459.764-0.016-0.0160.0000.0000.0000.000
103C108LEU0-0.071-0.03559.3020.0010.0010.0000.0000.0000.000
104C109LYS10.8320.89858.6570.0160.0160.0000.0000.0000.000
105C110VAL00.0180.02962.8440.0010.0010.0000.0000.0000.000
106C111GLY0-0.036-0.00666.0720.0000.0000.0000.0000.0000.000
107C112ARG10.7770.87363.1280.0100.0100.0000.0000.0000.000
108C113GLU-1-0.832-0.90864.555-0.011-0.0110.0000.0000.0000.000
109C114GLU-1-0.990-0.99061.236-0.007-0.0070.0000.0000.0000.000
110C115THR00.0220.00065.8840.0000.0000.0000.0000.0000.000
111C116GLU-1-0.875-0.93668.979-0.003-0.0030.0000.0000.0000.000
112C117GLU-1-0.837-0.92071.666-0.006-0.0060.0000.0000.0000.000
113C118ARG10.9380.98768.0820.0070.0070.0000.0000.0000.000
114C119SER0-0.016-0.00667.8760.0010.0010.0000.0000.0000.000
115C120SER00.005-0.02369.3960.0010.0010.0000.0000.0000.000
116C121LEU00.0560.02273.0850.0000.0000.0000.0000.0000.000
117C122LEU0-0.092-0.03966.8370.0000.0000.0000.0000.0000.000
118C123LYS10.8680.92967.4620.0030.0030.0000.0000.0000.000
119C124GLU-1-0.911-0.94971.908-0.002-0.0020.0000.0000.0000.000
120C125LYS10.9740.98770.8440.0040.0040.0000.0000.0000.000
121C126LEU0-0.026-0.00768.8890.0000.0000.0000.0000.0000.000
122C127ALA00.0260.01372.8600.0000.0000.0000.0000.0000.000
123C128LEU00.0040.00175.6970.0000.0000.0000.0000.0000.000
124C129GLN0-0.042-0.02772.5770.0000.0000.0000.0000.0000.000
125C130VAL00.0550.03173.7870.0000.0000.0000.0000.0000.000
126C131LYS10.9250.96476.455-0.001-0.0010.0000.0000.0000.000
127C132LEU0-0.007-0.02479.5730.0000.0000.0000.0000.0000.000
128C133GLU-1-0.824-0.87275.4150.0010.0010.0000.0000.0000.000
129C134GLU-1-0.896-0.93978.9390.0030.0030.0000.0000.0000.000
130C135GLN0-0.030-0.00680.9990.0000.0000.0000.0000.0000.000
131C136ARG10.7990.86278.1270.0000.0000.0000.0000.0000.000
132C137GLY00.0270.01982.0410.0000.0000.0000.0000.0000.000
133C138THR0-0.003-0.00882.9330.0000.0000.0000.0000.0000.000
134C139PHE0-0.005-0.00886.3560.0000.0000.0000.0000.0000.000
135C140ARG10.9210.95381.969-0.003-0.0030.0000.0000.0000.000
136C141ASP-1-0.799-0.88785.3210.0040.0040.0000.0000.0000.000
137C142LEU0-0.048-0.01987.9060.0000.0000.0000.0000.0000.000
138C143LEU0-0.049-0.02089.3060.0000.0000.0000.0000.0000.000
139C144LYS10.8070.90185.061-0.004-0.0040.0000.0000.0000.000
140C145ASN0-0.095-0.05688.4560.0000.0000.0000.0000.0000.000
141C146ASP-1-0.824-0.91092.4990.0030.0030.0000.0000.0000.000
142C147PRO00.0310.01196.1610.0000.0000.0000.0000.0000.000
143C148ASP-1-0.901-0.95197.9400.0030.0030.0000.0000.0000.000
144C149VAL0-0.0030.00297.7010.0000.0000.0000.0000.0000.000
145C150ALA00.0210.01096.0800.0000.0000.0000.0000.0000.000
146C151GLN0-0.035-0.01497.9570.0000.0000.0000.0000.0000.000
147C152LYS10.9670.987101.378-0.004-0.0040.0000.0000.0000.000
148C153LEU00.0120.00796.1730.0000.0000.0000.0000.0000.000
149C154ARG10.9090.96597.646-0.003-0.0030.0000.0000.0000.000
150C155ASN00.0490.033101.0290.0000.0000.0000.0000.0000.000
151C156TYR00.017-0.010103.2690.0000.0000.0000.0000.0000.000
152C157THR0-0.026-0.01799.0410.0000.0000.0000.0000.0000.000
153C158ASP-1-0.896-0.946102.2890.0040.0040.0000.0000.0000.000
154C159ILE0-0.007-0.002104.3620.0000.0000.0000.0000.0000.000
155C160ALA0-0.0040.001103.6300.0000.0000.0000.0000.0000.000
156C161LYS10.8920.932100.073-0.005-0.0050.0000.0000.0000.000
157C162GLN0-0.054-0.020104.1300.0000.0000.0000.0000.0000.000
158C163GLU-1-0.863-0.938107.4440.0050.0050.0000.0000.0000.000
159C164ALA0-0.012-0.003104.3620.0000.0000.0000.0000.0000.000
160C165ASN00.0210.013104.0580.0000.0000.0000.0000.0000.000
161C166LEU00.0510.038106.9040.0000.0000.0000.0000.0000.000
162C167TRP0-0.020-0.016108.7280.0000.0000.0000.0000.0000.000
163C168THR0-0.0020.012105.2510.0000.0000.0000.0000.0000.000
164C169ASP-1-0.853-0.903108.0270.0050.0050.0000.0000.0000.000
165C170ASN0-0.040-0.035111.0370.0000.0000.0000.0000.0000.000
166C171ILE0-0.0060.003107.2640.0000.0000.0000.0000.0000.000
167C172PHE00.0600.019105.1550.0000.0000.0000.0000.0000.000
168C173CYS0-0.083-0.043111.2140.0000.0000.0000.0000.0000.000
169C174LEU00.0230.020113.2070.0000.0000.0000.0000.0000.000
170C175GLN00.0550.032109.1550.0000.0000.0000.0000.0000.000
171C176LYS10.9660.974113.015-0.005-0.0050.0000.0000.0000.000
172C177TYR0-0.0050.001115.4420.0000.0000.0000.0000.0000.000
173C178MET00.003-0.012113.4410.0000.0000.0000.0000.0000.000
174C179LEU0-0.047-0.003111.3730.0000.0000.0000.0000.0000.000
175C180THR0-0.032-0.030115.7980.0000.0000.0000.0000.0000.000
176C181LYS10.9120.944119.080-0.005-0.0050.0000.0000.0000.000
177C182LEU00.0030.002118.6280.0000.0000.0000.0000.0000.000
178C183GLN0-0.063-0.007118.5260.0000.0000.0000.0000.0000.000
179C184MET00.0180.029113.8920.0000.0000.0000.0000.0000.000
180C185ASP-1-0.786-0.883109.6210.0080.0080.0000.0000.0000.000
181C186LYS10.9660.986106.833-0.007-0.0070.0000.0000.0000.000
182C187LYS10.9750.991103.654-0.009-0.0090.0000.0000.0000.000
183C188THR0-0.027-0.035106.7810.0000.0000.0000.0000.0000.000
184C189VAL0-0.003-0.013109.3280.0000.0000.0000.0000.0000.000
185C190SER0-0.012-0.002104.6450.0000.0000.0000.0000.0000.000
186C191THR0-0.080-0.047102.8190.0000.0000.0000.0000.0000.000
187C192ALA0-0.0210.005105.2010.0000.0000.0000.0000.0000.000
188C193LEU0-0.057-0.041107.9420.0000.0000.0000.0000.0000.000
189C194GLY00.0070.026103.9770.0000.0000.0000.0000.0000.000
190C195ILE0-0.045-0.023103.5410.0000.0000.0000.0000.0000.000
191C196THR0-0.028-0.02898.3110.0000.0000.0000.0000.0000.000
192C197GLY0-0.023-0.02899.7800.0000.0000.0000.0000.0000.000
193C198GLU-1-0.922-0.95893.5930.0080.0080.0000.0000.0000.000
194C199PHE0-0.095-0.04098.1210.0000.0000.0000.0000.0000.000
195C200ASP-1-0.854-0.920100.2690.0060.0060.0000.0000.0000.000
196C201TYR0-0.140-0.097102.0410.0000.0000.0000.0000.0000.000
197C202LEU0-0.051-0.02999.0570.0000.0000.0000.0000.0000.000