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: 663RZ

Calculation Name: 4Y66-D-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y66

Chain ID: D

ChEMBL ID:

UniProt ID: E2RTU1

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1511985.868257
FMO2-HF: Nuclear repulsion 1427988.855972
FMO2-HF: Total energy -83997.012285
FMO2-MP2: Total energy -84237.949166


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(D:7:ACE )


Summations of interaction energy for fragment #1(D:7:ACE )
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.
0.3240.472.94-1.562-1.524-0.003
Interaction energy analysis for fragmet #1(D:7:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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].
3D9PHE 00.0560.0503.8161.0041.864-0.007-0.411-0.443-0.001
4D10ALA 00.0800.0215.6850.2800.2800.0000.0000.0000.000
5D11ALA 0-0.053-0.0172.4901.3600.2672.879-1.010-0.775-0.002
6D12VAL 00.0050.0124.4310.0680.1850.001-0.028-0.0890.000
7D13LYS 10.8580.9437.3080.1580.1580.0000.0000.0000.000
8D14GLU -1-0.835-0.9257.4710.1280.1280.0000.0000.0000.000
9D15LEU 0-0.0350.0458.7210.0450.0450.0000.0000.0000.000
10D16MET 00.013-0.01710.417-0.035-0.0350.0000.0000.0000.000
11D17GLN 0-0.0040.01212.745-0.041-0.0410.0000.0000.0000.000
12D18THR 0-0.079-0.09312.0310.0000.0000.0000.0000.0000.000
13D19SER 0-0.015-0.00414.791-0.003-0.0030.0000.0000.0000.000
14D20ASN 00.0360.02016.362-0.019-0.0190.0000.0000.0000.000
15D21LYS 10.8980.94718.371-0.107-0.1070.0000.0000.0000.000
16D22PRO 00.0270.01317.5010.0020.0020.0000.0000.0000.000
17D23GLN 0-0.054-0.04414.0860.0090.0090.0000.0000.0000.000
18D24ASN 00.0840.04816.990-0.037-0.0370.0000.0000.0000.000
19D25VAL 00.0510.01514.147-0.007-0.0070.0000.0000.0000.000
20D26GLN 0-0.027-0.02713.665-0.025-0.0250.0000.0000.0000.000
21D27THR 00.1220.02914.4420.0100.0100.0000.0000.0000.000
22D28ALA 0-0.0260.01410.5620.0370.0370.0000.0000.0000.000
23D29ILE 0-0.064-0.0068.7950.0610.0610.0000.0000.0000.000
24D30ASN 0-0.029-0.01110.7390.0430.0430.0000.0000.0000.000
25D31ASN 0-0.013-0.03010.8950.0880.0880.0000.0000.0000.000
26D32THR 00.0740.0914.919-0.070-0.0700.0000.0000.0000.000
27D33GLY 0-0.050-0.0417.5920.1860.1860.0000.0000.0000.000
28D34SER 00.010-0.0247.6010.1480.1480.0000.0000.0000.000
29D35LYS 10.9570.9873.163-3.226-2.9640.067-0.113-0.2170.000
30D36TYR 00.0200.0095.618-0.430-0.4300.0000.0000.0000.000
31D37GLY 00.0440.0227.7740.1620.1620.0000.0000.0000.000
32D38LYS 10.9390.96011.3900.1200.1200.0000.0000.0000.000
33D39THR 00.0500.00513.813-0.031-0.0310.0000.0000.0000.000
34D40THR 0-0.022-0.0128.8370.0130.0130.0000.0000.0000.000
35D41VAL 00.0200.0158.812-0.123-0.1230.0000.0000.0000.000
36D42GLN 00.0360.00610.7350.0040.0040.0000.0000.0000.000
37D43LYS 10.9851.00711.0060.7560.7560.0000.0000.0000.000
38D44ALA 0-0.0080.0029.9260.0120.0120.0000.0000.0000.000
39D45LEU 00.026-0.02311.6710.0510.0510.0000.0000.0000.000
40D46ASP -1-0.906-0.93814.203-0.166-0.1660.0000.0000.0000.000
41D47GLU -1-0.947-0.98314.686-0.385-0.3850.0000.0000.0000.000
42D48LEU 0-0.070-0.02812.0160.0260.0260.0000.0000.0000.000
43D49VAL 00.0010.00315.9810.0370.0370.0000.0000.0000.000
44D50ALA 0-0.0210.00019.3530.0190.0190.0000.0000.0000.000
45D51GLN 0-0.037-0.02115.8960.0130.0130.0000.0000.0000.000
46D52ASN 0-0.024-0.00420.1800.0150.0150.0000.0000.0000.000
47D53LEU 00.011-0.00114.8700.0150.0150.0000.0000.0000.000
48D54CYS 0-0.128-0.05415.8460.0070.0070.0000.0000.0000.000
49D55ILE 00.0040.01418.4900.0000.0000.0000.0000.0000.000
50D56TYR 00.0370.00920.4930.0010.0010.0000.0000.0000.000
51D57NME 0-0.0130.00522.6650.0090.0090.0000.0000.0000.000
52D64ACE 00.0250.00423.117-0.001-0.0010.0000.0000.0000.000
53D65LEU 0-0.090-0.05019.6150.0050.0050.0000.0000.0000.000
54D66TYR 00.0260.01717.0850.0010.0010.0000.0000.0000.000
55D67LEU 0-0.0050.02117.8970.0160.0160.0000.0000.0000.000
56D68TRP 00.1240.05713.483-0.023-0.0230.0000.0000.0000.000
57D69ASN 0-0.011-0.00118.0460.0190.0190.0000.0000.0000.000
58D70GLN 00.0860.01721.1630.0030.0030.0000.0000.0000.000
59D71ASN 0-0.068-0.02623.5920.0100.0100.0000.0000.0000.000
60D72LEU 0-0.048-0.01919.863-0.001-0.0010.0000.0000.0000.000
61D73LEU 0-0.078-0.02020.6760.0060.0060.0000.0000.0000.000
62D74GLU -1-0.918-0.95524.2100.0040.0040.0000.0000.0000.000
63D75VAL 0-0.018-0.01227.3160.0050.0050.0000.0000.0000.000
64D76LEU 0-0.036-0.00930.227-0.001-0.0010.0000.0000.0000.000
65D77SER 00.0090.00232.882-0.001-0.0010.0000.0000.0000.000
66D78ASP -1-0.872-0.95736.5830.0100.0100.0000.0000.0000.000
67D79ALA 0-0.0050.00238.8850.0020.0020.0000.0000.0000.000
68D80GLN 00.0560.01334.5360.0010.0010.0000.0000.0000.000
69D81LEU 00.0060.02333.3100.0040.0040.0000.0000.0000.000
70D82MET 00.014-0.00335.9850.0030.0030.0000.0000.0000.000
71D83GLU -1-0.901-0.93737.4700.0240.0240.0000.0000.0000.000
72D84VAL 0-0.002-0.00331.8360.0030.0030.0000.0000.0000.000
73D85ASN 0-0.045-0.04535.0710.0060.0060.0000.0000.0000.000
74D86ALA 00.0410.03836.6460.0010.0010.0000.0000.0000.000
75D87GLN 0-0.004-0.00533.403-0.001-0.0010.0000.0000.0000.000
76D88ILE 00.004-0.00431.6450.0030.0030.0000.0000.0000.000
77D89ASN 0-0.107-0.05735.1520.0020.0020.0000.0000.0000.000
78D90ASP -1-0.891-0.94238.5300.0380.0380.0000.0000.0000.000
79D91LEU 00.005-0.00932.5100.0020.0020.0000.0000.0000.000
80D92LYS 10.9000.94534.199-0.043-0.0430.0000.0000.0000.000
81D93ALA 00.0530.04236.8910.0000.0000.0000.0000.0000.000
82D94GLN 0-0.066-0.02837.3340.0020.0020.0000.0000.0000.000
83D95VAL 00.000-0.00633.5730.0010.0010.0000.0000.0000.000
84D96GLU -1-0.934-0.96536.8660.0490.0490.0000.0000.0000.000
85D97LYS 10.9150.96239.518-0.043-0.0430.0000.0000.0000.000
86D98LEU 0-0.022-0.03336.5870.0000.0000.0000.0000.0000.000
87D99THR 0-0.0010.01236.5570.0000.0000.0000.0000.0000.000
88D100GLN 00.0620.03639.208-0.001-0.0010.0000.0000.0000.000
89D101GLN 00.0250.01642.271-0.001-0.0010.0000.0000.0000.000
90D102GLY 00.0460.03040.0750.0000.0000.0000.0000.0000.000
91D103GLU -1-0.927-0.95641.1010.0500.0500.0000.0000.0000.000
92D104THR 0-0.061-0.04343.211-0.002-0.0020.0000.0000.0000.000
93D105LEU 0-0.011-0.01542.436-0.001-0.0010.0000.0000.0000.000
94D106ARG 10.9130.96438.398-0.059-0.0590.0000.0000.0000.000
95D107ILE 0-0.026-0.01244.036-0.001-0.0010.0000.0000.0000.000
96D108THR 0-0.038-0.03447.760-0.001-0.0010.0000.0000.0000.000
97D109GLN 00.0150.02542.7330.0000.0000.0000.0000.0000.000
98D110ARG 10.9890.99044.215-0.048-0.0480.0000.0000.0000.000
99D111ASN 0-0.039-0.02848.645-0.001-0.0010.0000.0000.0000.000
100D112LEU 0-0.048-0.01550.197-0.002-0.0020.0000.0000.0000.000
101D113GLU -1-0.938-0.97645.8080.0490.0490.0000.0000.0000.000
102D114ALA 0-0.081-0.02750.7540.0000.0000.0000.0000.0000.000
103D115ALA 0-0.021-0.00253.440-0.001-0.0010.0000.0000.0000.000
104D116PRO 00.0330.03254.5490.0010.0010.0000.0000.0000.000
105D117ILE 00.0100.00353.694-0.001-0.0010.0000.0000.0000.000
106D118THR 00.0780.00956.9110.0000.0000.0000.0000.0000.000
107D119GLU -1-0.891-0.95959.3030.0250.0250.0000.0000.0000.000
108D120VAL 00.0410.02556.9230.0000.0000.0000.0000.0000.000
109D121LEU 00.0000.01560.188-0.001-0.0010.0000.0000.0000.000
110D122LYS 10.8630.92261.895-0.025-0.0250.0000.0000.0000.000
111D123GLN 0-0.0070.00262.461-0.001-0.0010.0000.0000.0000.000
112D124GLU -1-0.888-0.94359.4550.0290.0290.0000.0000.0000.000
113D125VAL 0-0.019-0.01764.194-0.001-0.0010.0000.0000.0000.000
114D126ASP -1-0.837-0.90667.2990.0210.0210.0000.0000.0000.000
115D127GLU -1-0.963-0.98764.8590.0250.0250.0000.0000.0000.000
116D128LEU 00.0280.00665.597-0.001-0.0010.0000.0000.0000.000
117D129ARG 10.7880.89769.089-0.021-0.0210.0000.0000.0000.000
118D130GLN 0-0.054-0.03271.824-0.001-0.0010.0000.0000.0000.000
119D131GLN 0-0.0210.00367.9290.0000.0000.0000.0000.0000.000
120D132VAL 00.002-0.00472.219-0.001-0.0010.0000.0000.0000.000
121D133SER 00.0610.02674.467-0.001-0.0010.0000.0000.0000.000
122D134ALA 0-0.0060.00575.951-0.001-0.0010.0000.0000.0000.000
123D135ASN 0-0.043-0.03573.4720.0000.0000.0000.0000.0000.000
124D136ASP -1-0.882-0.92877.2090.0170.0170.0000.0000.0000.000
125D137GLU -1-0.939-0.97980.0970.0150.0150.0000.0000.0000.000
126D138LYS 10.8760.93975.905-0.019-0.0190.0000.0000.0000.000
127D139LEU 00.0280.00479.0730.0000.0000.0000.0000.0000.000
128D140ARG 10.9360.97982.184-0.015-0.0150.0000.0000.0000.000
129D141LEU 00.0210.00085.1460.0000.0000.0000.0000.0000.000
130D142VAL 0-0.050-0.01682.6170.0000.0000.0000.0000.0000.000
131D143ARG 10.9260.94982.513-0.016-0.0160.0000.0000.0000.000
132D144GLU -1-0.990-0.96087.6830.0130.0130.0000.0000.0000.000
133D145SER 0-0.069-0.03189.7760.0000.0000.0000.0000.0000.000
134D146ASN 0-0.029-0.01186.1150.0000.0000.0000.0000.0000.000
135D147ALA 00.0400.01189.0720.0000.0000.0000.0000.0000.000
136D148ILE 0-0.073-0.04282.2340.0000.0000.0000.0000.0000.000
137D149VAL 00.0040.00885.0490.0000.0000.0000.0000.0000.000
138D150SER 0-0.0010.00181.3710.0000.0000.0000.0000.0000.000
139D151ASP -1-0.802-0.91578.5250.0160.0160.0000.0000.0000.000
140D152ALA 0-0.024-0.02881.6500.0000.0000.0000.0000.0000.000
141D153ASP -1-0.887-0.93783.3350.0140.0140.0000.0000.0000.000
142D154MET 0-0.017-0.01385.093-0.001-0.0010.0000.0000.0000.000
143D155LEU 00.0220.02682.5290.0000.0000.0000.0000.0000.000
144D156THR 0-0.014-0.04786.5010.0000.0000.0000.0000.0000.000
145D157LEU 0-0.0440.01289.3470.0000.0000.0000.0000.0000.000
146D158GLN 00.0190.01587.7410.0000.0000.0000.0000.0000.000
147D159LYS 10.7660.97790.370-0.012-0.0120.0000.0000.0000.000
148D160ASN 00.022-0.00292.1720.0000.0000.0000.0000.0000.000
149D161TYR 0-0.009-0.02294.8880.0000.0000.0000.0000.0000.000
150D162LYS 10.9260.97493.484-0.011-0.0110.0000.0000.0000.000
151D163ASP -1-0.798-0.88195.3470.0110.0110.0000.0000.0000.000
152D164ALA 0-0.013-0.00198.0310.0000.0000.0000.0000.0000.000
153D165MET 0-0.002-0.00399.5130.0000.0000.0000.0000.0000.000
154D166THR 0-0.058-0.04698.6390.0000.0000.0000.0000.0000.000
155D167ALA 0-0.0100.000101.3290.0000.0000.0000.0000.0000.000
156D168TRP 00.0320.020103.8080.0000.0000.0000.0000.0000.000
157D169ALA 0-0.002-0.004104.4300.0000.0000.0000.0000.0000.000
158D170THR 0-0.006-0.024104.2970.0000.0000.0000.0000.0000.000
159D171ARG 10.9390.962105.130-0.009-0.0090.0000.0000.0000.000
160D172ARG 10.8770.944109.330-0.008-0.0080.0000.0000.0000.000
161D173ALA 0-0.0130.002109.3740.0000.0000.0000.0000.0000.000
162D174LYS 10.9870.997110.957-0.008-0.0080.0000.0000.0000.000
163D175CYS 0-0.049-0.022112.6740.0000.0000.0000.0000.0000.000
164D176ARG 10.9680.962114.868-0.007-0.0070.0000.0000.0000.000
165D177GLU -1-0.892-0.930111.8070.0080.0080.0000.0000.0000.000
166D178VAL 0-0.034-0.016116.3580.0000.0000.0000.0000.0000.000
167D179ILE 0-0.019-0.015118.8960.0000.0000.0000.0000.0000.000
168D180ASP -1-0.883-0.927119.1130.0070.0070.0000.0000.0000.000
169D181THR 0-0.025-0.003120.8750.0000.0000.0000.0000.0000.000
170D182LEU 0-0.042-0.030122.9750.0000.0000.0000.0000.0000.000
171D183SER 0-0.049-0.027124.1280.0000.0000.0000.0000.0000.000
172D184GLU -1-0.874-0.954124.8970.0060.0060.0000.0000.0000.000
173D185GLY 0-0.066-0.023127.4320.0000.0000.0000.0000.0000.000
174D186MET 0-0.093-0.040129.2940.0000.0000.0000.0000.0000.000
175D187GLY 00.0160.019130.3980.0000.0000.0000.0000.0000.000
176D188VAL 0-0.043-0.026129.6460.0000.0000.0000.0000.0000.000
177D189LYS 10.9980.989126.890-0.006-0.0060.0000.0000.0000.000
178D190PRO 00.0900.046122.2370.0000.0000.0000.0000.0000.000
179D191SER 0-0.058-0.042123.2980.0000.0000.0000.0000.0000.000
180D192ALA 00.0050.011124.2920.0000.0000.0000.0000.0000.000
181D193PHE 00.0580.014123.8020.0000.0000.0000.0000.0000.000
182D194MET 0-0.057-0.030119.6360.0000.0000.0000.0000.0000.000
183D195ASP -1-0.852-0.918124.1360.0070.0070.0000.0000.0000.000
184D196GLN 0-0.126-0.047126.2750.0000.0000.0000.0000.0000.000
185D197LEU 0-0.066-0.056124.3560.0000.0000.0000.0000.0000.000
186D198GLY 00.0090.026124.5140.0000.0000.0000.0000.0000.000
187D199LEU 0-0.083-0.038119.4610.0000.0000.0000.0000.0000.000
188D200GLU -1-0.899-0.942117.4760.0070.0070.0000.0000.0000.000
189D201GLU -1-0.886-0.952113.7890.0080.0080.0000.0000.0000.000
190D202GLY 0-0.0070.007114.3500.0000.0000.0000.0000.0000.000
191D203LEU 0-0.031-0.019108.5260.0000.0000.0000.0000.0000.000
192D204PRO 00.0460.049111.7580.0000.0000.0000.0000.0000.000
193D205MET 00.007-0.029107.9880.0000.0000.0000.0000.0000.000
194D206THR 00.0400.016108.5570.0000.0000.0000.0000.0000.000
195D207THR 00.0760.017107.5510.0000.0000.0000.0000.0000.000
196D208TYR 00.0420.028102.6190.0000.0000.0000.0000.0000.000
197D209THR 0-0.037-0.016103.7970.0000.0000.0000.0000.0000.000
198D210GLU -1-1.002-1.005103.1680.0090.0090.0000.0000.0000.000
199D211MET 0-0.015-0.025101.8070.0000.0000.0000.0000.0000.000
200D212LYS 10.9360.98399.121-0.010-0.0100.0000.0000.0000.000
201D213LYS 10.9230.97998.033-0.009-0.0090.0000.0000.0000.000
202D214ALA 0-0.032-0.02097.1250.0000.0000.0000.0000.0000.000
203D215LEU 00.0390.01793.4790.0000.0000.0000.0000.0000.000
204D216PRO 00.0240.05293.1440.0000.0000.0000.0000.0000.000
205D217PRO 0-0.036-0.01693.8140.0000.0000.0000.0000.0000.000
206D218VAL 00.0530.03788.1920.0000.0000.0000.0000.0000.000
207D219ASN 0-0.058-0.04289.8210.0000.0000.0000.0000.0000.000
208D220VAL 0-0.015-0.00486.4240.0000.0000.0000.0000.0000.000
209D221SER 00.030-0.03587.9870.0000.0000.0000.0000.0000.000
210D222LYS 11.0240.97984.983-0.014-0.0140.0000.0000.0000.000
211D223ALA 0-0.017-0.00981.9570.0000.0000.0000.0000.0000.000
212D224ASP -1-0.912-0.96478.1730.0160.0160.0000.0000.0000.000
213D225ILE 0-0.011-0.01577.5980.0000.0000.0000.0000.0000.000
214D226NME 00.0200.02278.2160.0000.0000.0000.0000.0000.000