FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 2215R

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:

Apendix: None


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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1439465.416511
FMO2-HF: Nuclear repulsion 1359962.579019
FMO2-HF: Total energy -79502.837492
FMO2-MP2: Total energy -79734.832249


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.
-21.202-12.3610.433-4.287-4.9870.002
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 : 0.049 / q_NPA : 0.026
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].
3C8LEU0-0.057-0.0243.032-5.286-1.5680.086-1.810-1.9940.011
4C9ASP-1-0.828-0.9312.607-11.574-7.1460.345-2.324-2.449-0.009
5C10GLU-1-0.910-0.9423.645-4.300-3.6050.002-0.153-0.5440.000
6C11LYS10.8900.9405.9530.2230.2230.0000.0000.0000.000
7C12LYS10.8380.8927.311-0.114-0.1140.0000.0000.0000.000
8C13GLU-1-0.885-0.9247.999-1.067-1.0670.0000.0000.0000.000
9C14ARG10.8140.9139.7970.7690.7690.0000.0000.0000.000
10C15LEU0-0.024-0.03411.9280.1220.1220.0000.0000.0000.000
11C16LEU00.0700.02313.0160.0900.0900.0000.0000.0000.000
12C17GLU-1-0.918-0.94613.917-0.404-0.4040.0000.0000.0000.000
13C18GLU-1-0.907-0.97215.761-0.265-0.2650.0000.0000.0000.000
14C19MET0-0.083-0.04417.4840.0500.0500.0000.0000.0000.000
15C20LEU0-0.028-0.00316.7240.0390.0390.0000.0000.0000.000
16C21LYS10.9420.98419.9100.2830.2830.0000.0000.0000.000
17C22ARG10.8730.92621.9030.2220.2220.0000.0000.0000.000
18C23GLY00.0220.03823.1030.0180.0180.0000.0000.0000.000
19C24GLU-1-0.921-0.93424.336-0.094-0.0940.0000.0000.0000.000
20C25ILE0-0.020-0.02224.539-0.003-0.0030.0000.0000.0000.000
21C26TYR0-0.013-0.02522.549-0.004-0.0040.0000.0000.0000.000
22C27SER00.0420.00525.1050.0130.0130.0000.0000.0000.000
23C28ASN00.0470.00623.116-0.006-0.0060.0000.0000.0000.000
24C29LYS10.9670.96122.890-0.023-0.0230.0000.0000.0000.000
25C30THR00.0690.05324.7140.0020.0020.0000.0000.0000.000
26C31ILE00.0870.10519.099-0.013-0.0130.0000.0000.0000.000
27C32GLU-1-0.885-0.94220.4800.0250.0250.0000.0000.0000.000
28C33THR0-0.055-0.08121.691-0.001-0.0010.0000.0000.0000.000
29C34LEU0-0.011-0.01918.463-0.011-0.0110.0000.0000.0000.000
30C35SER0-0.029-0.00717.618-0.037-0.0370.0000.0000.0000.000
31C36LYS10.9260.96618.0560.0630.0630.0000.0000.0000.000
32C37PRO0-0.0160.00718.961-0.014-0.0140.0000.0000.0000.000
33C38THR0-0.009-0.01014.065-0.039-0.0390.0000.0000.0000.000
34C39GLY00.0320.03113.707-0.076-0.0760.0000.0000.0000.000
35C40ILE0-0.030-0.00411.8360.0360.0360.0000.0000.0000.000
36C41SER00.0340.00813.8910.0100.0100.0000.0000.0000.000
37C42SER00.0460.01215.9170.0290.0290.0000.0000.0000.000
38C43MET0-0.0120.00017.4690.0100.0100.0000.0000.0000.000
39C44VAL0-0.028-0.03111.5770.0390.0390.0000.0000.0000.000
40C45ILE00.0170.02914.4330.0430.0430.0000.0000.0000.000
41C46LYS10.9300.95615.211-0.066-0.0660.0000.0000.0000.000
42C47ASN0-0.021-0.00813.312-0.008-0.0080.0000.0000.0000.000
43C48VAL0-0.0100.00410.3700.0730.0730.0000.0000.0000.000
44C49LEU0-0.0050.00312.237-0.056-0.0560.0000.0000.0000.000
45C50GLN0-0.025-0.00714.927-0.040-0.0400.0000.0000.0000.000
46C51ALA0-0.017-0.02810.1850.0000.0000.0000.0000.0000.000
47C52LEU00.0510.02111.531-0.054-0.0540.0000.0000.0000.000
48C53VAL0-0.053-0.00913.608-0.037-0.0370.0000.0000.0000.000
49C54ASN0-0.020-0.01613.797-0.048-0.0480.0000.0000.0000.000
50C55GLU-1-0.879-0.91410.1480.0150.0150.0000.0000.0000.000
51C56ASP-1-0.848-0.91314.459-0.136-0.1360.0000.0000.0000.000
52C57LEU0-0.020-0.00112.228-0.036-0.0360.0000.0000.0000.000
53C58VAL0-0.082-0.05316.446-0.022-0.0220.0000.0000.0000.000
54C59ASP-1-0.866-0.92218.921-0.071-0.0710.0000.0000.0000.000
55C60THR0-0.071-0.04021.6620.0100.0100.0000.0000.0000.000
56C61ASP-1-0.814-0.90723.593-0.012-0.0120.0000.0000.0000.000
57C62LYS10.8110.90427.025-0.035-0.0350.0000.0000.0000.000
58C63ILE00.0410.03529.482-0.003-0.0030.0000.0000.0000.000
59C64GLY0-0.012-0.00432.6530.0030.0030.0000.0000.0000.000
60C65ALA00.0450.00332.8560.0040.0040.0000.0000.0000.000
61C66SER0-0.085-0.04029.1750.0060.0060.0000.0000.0000.000
62C67THR00.0040.00424.340-0.002-0.0020.0000.0000.0000.000
63C68TYR0-0.025-0.02525.8430.0020.0020.0000.0000.0000.000
64C69TYR00.0170.00120.3610.0060.0060.0000.0000.0000.000
65C70TRP0-0.008-0.00322.807-0.008-0.0080.0000.0000.0000.000
66C71CYS00.0490.02719.384-0.005-0.0050.0000.0000.0000.000
67C72PHE00.0400.03121.649-0.006-0.0060.0000.0000.0000.000
68C73ALA00.0460.01721.565-0.013-0.0130.0000.0000.0000.000
69C74SER0-0.048-0.03222.961-0.008-0.0080.0000.0000.0000.000
70C75LYS10.8780.95119.3880.1380.1380.0000.0000.0000.000
71C76ARG11.0501.00418.3910.2530.2530.0000.0000.0000.000
72C77SER0-0.0060.00822.6090.0190.0190.0000.0000.0000.000
73C78GLN00.0130.01825.8250.0100.0100.0000.0000.0000.000
74C79ALA00.0630.02924.3680.0100.0100.0000.0000.0000.000
75C80ALA0-0.0080.00325.4990.0110.0110.0000.0000.0000.000
76C81ARG10.9110.93327.0930.1150.1150.0000.0000.0000.000
77C82THR0-0.010-0.00229.5980.0090.0090.0000.0000.0000.000
78C83GLU-1-0.813-0.89827.911-0.031-0.0310.0000.0000.0000.000
79C84LEU0-0.037-0.00630.4380.0050.0050.0000.0000.0000.000
80C85ALA00.019-0.00932.5900.0050.0050.0000.0000.0000.000
81C86ARG10.8960.93729.9110.0290.0290.0000.0000.0000.000
82C87LEU0-0.047-0.01731.3110.0060.0060.0000.0000.0000.000
83C88GLN00.0150.00634.8920.0010.0010.0000.0000.0000.000
84C89LYS10.8840.95537.6640.0280.0280.0000.0000.0000.000
85C90ALA00.0190.00937.1460.0030.0030.0000.0000.0000.000
86C91LEU0-0.018-0.00738.5940.0030.0030.0000.0000.0000.000
87C92GLU-1-0.893-0.95240.250-0.026-0.0260.0000.0000.0000.000
88C93GLU-1-0.968-0.98142.658-0.013-0.0130.0000.0000.0000.000
89C94GLN00.001-0.01240.7700.0030.0030.0000.0000.0000.000
90C95THR0-0.031-0.02243.7310.0020.0020.0000.0000.0000.000
91C96ASN00.0440.03645.9010.0010.0010.0000.0000.0000.000
92C97PHE0-0.037-0.02045.9830.0020.0020.0000.0000.0000.000
93C98ILE00.0290.00445.3000.0020.0020.0000.0000.0000.000
94C99ASP-1-0.895-0.93548.552-0.011-0.0110.0000.0000.0000.000
95C100LYS10.9110.94651.3460.0070.0070.0000.0000.0000.000
96C101ALA0-0.0170.00550.8420.0010.0010.0000.0000.0000.000
97C102THR0-0.002-0.01351.6290.0010.0010.0000.0000.0000.000
98C103ALA00.0310.03654.1120.0000.0000.0000.0000.0000.000
99C104ARG10.8210.89256.2610.0020.0020.0000.0000.0000.000
100C105ILE0-0.010-0.02853.4010.0010.0010.0000.0000.0000.000
101C106GLU-1-0.884-0.94657.307-0.002-0.0020.0000.0000.0000.000
102C107GLU-1-0.842-0.90259.723-0.002-0.0020.0000.0000.0000.000
103C108LEU0-0.091-0.04959.9260.0010.0010.0000.0000.0000.000
104C109LYS10.8850.93558.2370.0010.0010.0000.0000.0000.000
105C110VAL00.0240.03462.8020.0000.0000.0000.0000.0000.000
106C111GLY0-0.046-0.01466.0290.0000.0000.0000.0000.0000.000
107C112ARG10.8030.89563.558-0.003-0.0030.0000.0000.0000.000
108C113GLU-1-0.842-0.91664.6920.0010.0010.0000.0000.0000.000
109C114GLU-1-0.991-0.99461.0850.0060.0060.0000.0000.0000.000
110C115THR00.0340.01665.8040.0000.0000.0000.0000.0000.000
111C116GLU-1-0.870-0.92468.8820.0070.0070.0000.0000.0000.000
112C117GLU-1-0.826-0.91571.5720.0040.0040.0000.0000.0000.000
113C118ARG10.9670.99666.230-0.004-0.0040.0000.0000.0000.000
114C119SER0-0.065-0.03767.6390.0010.0010.0000.0000.0000.000
115C120SER0-0.009-0.02669.3450.0010.0010.0000.0000.0000.000
116C121LEU00.0500.01673.0370.0000.0000.0000.0000.0000.000
117C122LEU0-0.113-0.04766.7010.0000.0000.0000.0000.0000.000
118C123LYS10.9090.94966.724-0.009-0.0090.0000.0000.0000.000
119C124GLU-1-0.894-0.94271.9000.0070.0070.0000.0000.0000.000
120C125LYS11.0051.00270.925-0.007-0.0070.0000.0000.0000.000
121C126LEU0-0.026-0.00868.9750.0000.0000.0000.0000.0000.000
122C127ALA00.0230.01172.9010.0000.0000.0000.0000.0000.000
123C128LEU00.0020.00075.7270.0000.0000.0000.0000.0000.000
124C129GLN0-0.073-0.04172.5640.0000.0000.0000.0000.0000.000
125C130VAL00.0530.03273.9750.0000.0000.0000.0000.0000.000
126C131LYS10.9580.99476.527-0.009-0.0090.0000.0000.0000.000
127C132LEU0-0.003-0.02679.8860.0000.0000.0000.0000.0000.000
128C133GLU-1-0.875-0.92275.4800.0100.0100.0000.0000.0000.000
129C134GLU-1-0.907-0.94379.0500.0120.0120.0000.0000.0000.000
130C135GLN0-0.065-0.03981.0990.0000.0000.0000.0000.0000.000
131C136ARG10.8440.91178.053-0.009-0.0090.0000.0000.0000.000
132C137GLY00.0220.01382.1710.0000.0000.0000.0000.0000.000
133C138THR00.0240.01483.0690.0000.0000.0000.0000.0000.000
134C139PHE0-0.011-0.01486.4800.0000.0000.0000.0000.0000.000
135C140ARG10.9100.94882.689-0.011-0.0110.0000.0000.0000.000
136C141ASP-1-0.920-0.95385.5360.0110.0110.0000.0000.0000.000
137C142LEU0-0.070-0.03588.0620.0000.0000.0000.0000.0000.000
138C143LEU0-0.049-0.02189.7870.0000.0000.0000.0000.0000.000
139C144LYS10.9020.95884.467-0.012-0.0120.0000.0000.0000.000
140C145ASN0-0.033-0.01688.7150.0000.0000.0000.0000.0000.000
141C146ASP-1-0.827-0.91992.6740.0080.0080.0000.0000.0000.000
142C147PRO00.0340.00996.0930.0000.0000.0000.0000.0000.000
143C148ASP-1-0.910-0.95398.0930.0080.0080.0000.0000.0000.000
144C149VAL00.0130.01497.5690.0000.0000.0000.0000.0000.000
145C150ALA00.0030.00096.2500.0000.0000.0000.0000.0000.000
146C151GLN0-0.057-0.04398.1140.0000.0000.0000.0000.0000.000
147C152LYS10.9640.987101.523-0.009-0.0090.0000.0000.0000.000
148C153LEU00.005-0.00696.3370.0000.0000.0000.0000.0000.000
149C154ARG10.9310.97297.897-0.009-0.0090.0000.0000.0000.000
150C155ASN00.0630.055101.2600.0000.0000.0000.0000.0000.000
151C156TYR00.015-0.012103.4800.0000.0000.0000.0000.0000.000
152C157THR0-0.0350.00099.5140.0000.0000.0000.0000.0000.000
153C158ASP-1-0.932-0.975102.5880.0090.0090.0000.0000.0000.000
154C159ILE0-0.025-0.011104.6640.0000.0000.0000.0000.0000.000
155C160ALA0-0.0030.000103.9130.0000.0000.0000.0000.0000.000
156C161LYS10.9580.97299.652-0.010-0.0100.0000.0000.0000.000
157C162GLN0-0.0120.001104.4170.0000.0000.0000.0000.0000.000
158C163GLU-1-0.885-0.952107.7330.0090.0090.0000.0000.0000.000
159C164ALA0-0.013-0.007104.6440.0000.0000.0000.0000.0000.000
160C165ASN00.0260.018104.4780.0000.0000.0000.0000.0000.000
161C166LEU00.0520.040107.1790.0000.0000.0000.0000.0000.000
162C167TRP0-0.011-0.017108.9770.0000.0000.0000.0000.0000.000
163C168THR0-0.0100.004105.6870.0000.0000.0000.0000.0000.000
164C169ASP-1-0.848-0.898108.2880.0090.0090.0000.0000.0000.000
165C170ASN0-0.048-0.033111.3010.0000.0000.0000.0000.0000.000
166C171ILE0-0.0120.011107.5020.0000.0000.0000.0000.0000.000
167C172PHE00.0740.025105.6250.0000.0000.0000.0000.0000.000
168C173CYS0-0.080-0.045111.4620.0000.0000.0000.0000.0000.000
169C174LEU00.0160.018113.5250.0000.0000.0000.0000.0000.000
170C175GLN00.0550.029109.2190.0000.0000.0000.0000.0000.000
171C176LYS10.9560.972113.250-0.009-0.0090.0000.0000.0000.000
172C177TYR0-0.005-0.008115.6790.0000.0000.0000.0000.0000.000
173C178MET0-0.006-0.013113.5570.0000.0000.0000.0000.0000.000
174C179LEU0-0.0260.002111.6870.0000.0000.0000.0000.0000.000
175C180THR0-0.045-0.027116.0200.0000.0000.0000.0000.0000.000
176C181LYS10.9220.950119.304-0.008-0.0080.0000.0000.0000.000
177C182LEU00.0090.004119.0160.0000.0000.0000.0000.0000.000
178C183GLN0-0.063-0.007118.7600.0000.0000.0000.0000.0000.000
179C184MET00.0110.023114.6480.0000.0000.0000.0000.0000.000
180C185ASP-1-0.804-0.921109.7900.0110.0110.0000.0000.0000.000
181C186LYS10.9630.997107.015-0.011-0.0110.0000.0000.0000.000
182C187LYS10.9800.987103.608-0.012-0.0120.0000.0000.0000.000
183C188THR0-0.004-0.009106.9860.0000.0000.0000.0000.0000.000
184C189VAL00.004-0.010109.5360.0000.0000.0000.0000.0000.000
185C190SER0-0.080-0.023105.5290.0000.0000.0000.0000.0000.000
186C191THR0-0.038-0.021103.2560.0000.0000.0000.0000.0000.000
187C192ALA0-0.0150.005105.4140.0000.0000.0000.0000.0000.000
188C193LEU0-0.064-0.044108.1620.0000.0000.0000.0000.0000.000
189C194GLY00.0120.028104.2010.0000.0000.0000.0000.0000.000
190C195ILE0-0.051-0.024103.7750.0000.0000.0000.0000.0000.000
191C196THR0-0.015-0.01198.5610.0000.0000.0000.0000.0000.000
192C197GLY0-0.019-0.02999.9910.0000.0000.0000.0000.0000.000
193C198GLU-1-0.935-0.97393.6860.0130.0130.0000.0000.0000.000
194C199PHE0-0.087-0.03798.3680.0000.0000.0000.0000.0000.000
195C200ASP-1-0.842-0.903100.6360.0110.0110.0000.0000.0000.000
196C201TYR0-0.133-0.106102.3030.0000.0000.0000.0000.0000.000
197C202LEU0-0.093-0.05399.5360.0000.0000.0000.0000.0000.000