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: 9G622

Calculation Name: 4Y66-D-Xray372

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: 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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1498182.948197
FMO2-HF: Nuclear repulsion 1414527.26501
FMO2-HF: Total energy -83655.683188
FMO2-MP2: Total energy -83895.531991


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:8:ALA)


Summations of interaction energy for fragment #1(D:8:ALA)
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.
-0.146-1.08113.761-6.073-6.752-0.02
Interaction energy analysis for fragmet #1(D:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.008
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].
3D10ALA00.0740.0183.090-0.9700.4680.023-0.594-0.8670.000
4D11ALA0-0.019-0.0051.7821.625-2.63710.980-3.753-2.964-0.007
5D12VAL0-0.0070.0033.441-0.3500.0110.0110.002-0.3740.000
6D13LYS10.8590.9425.8530.3590.3590.0000.0000.0000.000
7D14GLU-1-0.837-0.9257.0140.4600.4600.0000.0000.0000.000
8D15LEU0-0.0360.0448.1440.0390.0390.0000.0000.0000.000
9D16MET00.012-0.0179.8400.0360.0360.0000.0000.0000.000
10D17GLN0-0.0060.01211.6150.0480.0480.0000.0000.0000.000
11D18THR0-0.075-0.09211.6560.0060.0060.0000.0000.0000.000
12D19SER0-0.018-0.00514.1300.0260.0260.0000.0000.0000.000
13D20ASN00.0320.01915.523-0.043-0.0430.0000.0000.0000.000
14D21LYS10.9010.94717.8270.1080.1080.0000.0000.0000.000
15D22PRO00.0290.01416.614-0.024-0.0240.0000.0000.0000.000
16D23GLN0-0.056-0.04513.256-0.044-0.0440.0000.0000.0000.000
17D24ASN00.0830.04715.580-0.029-0.0290.0000.0000.0000.000
18D25VAL00.0640.02111.848-0.053-0.0530.0000.0000.0000.000
19D26GLN0-0.028-0.02512.426-0.064-0.0640.0000.0000.0000.000
20D27THR00.1240.02914.042-0.006-0.0060.0000.0000.0000.000
21D28ALA0-0.0330.0129.4690.0050.0050.0000.0000.0000.000
22D29ILE0-0.059-0.0058.507-0.043-0.0430.0000.0000.0000.000
23D30ASN0-0.031-0.01210.4520.0690.0690.0000.0000.0000.000
24D31ASN0-0.012-0.03011.5930.0280.0280.0000.0000.0000.000
25D32THR00.0830.0935.082-0.070-0.0700.0000.0000.0000.000
26D33GLY0-0.054-0.0408.1600.1170.1170.0000.0000.0000.000
27D34SER00.012-0.0248.968-0.011-0.0110.0000.0000.0000.000
28D35LYS10.9610.9895.1550.2960.2960.0000.0000.0000.000
29D36TYR00.0080.0012.716-2.297-0.7692.747-1.728-2.547-0.013
30D37GLY00.0440.0236.7490.1360.1360.0000.0000.0000.000
31D38LYS10.9380.9569.5820.2560.2560.0000.0000.0000.000
32D39THR00.0540.00711.165-0.073-0.0730.0000.0000.0000.000
33D40THR0-0.020-0.0105.2160.1130.1130.0000.0000.0000.000
34D41VAL00.0130.0136.680-0.237-0.2370.0000.0000.0000.000
35D42GLN00.0370.0077.750-0.016-0.0160.0000.0000.0000.000
36D43LYS10.9861.0086.1590.4130.4130.0000.0000.0000.000
37D44ALA0-0.0130.0006.1340.0470.0470.0000.0000.0000.000
38D45LEU00.030-0.0218.1350.1050.1050.0000.0000.0000.000
39D46ASP-1-0.895-0.93411.132-0.182-0.1820.0000.0000.0000.000
40D47GLU-1-0.954-0.9859.490-0.156-0.1560.0000.0000.0000.000
41D48LEU0-0.067-0.0279.5200.0510.0510.0000.0000.0000.000
42D49VAL00.0000.00212.5620.0610.0610.0000.0000.0000.000
43D50ALA0-0.0180.00115.1500.0350.0350.0000.0000.0000.000
44D51GLN0-0.038-0.02111.5680.0130.0130.0000.0000.0000.000
45D52ASN0-0.024-0.00516.3300.0080.0080.0000.0000.0000.000
46D53LEU00.011-0.00112.2150.0150.0150.0000.0000.0000.000
47D54CYS0-0.128-0.05513.621-0.063-0.0630.0000.0000.0000.000
48D55ILE00.0090.01616.1210.0260.0260.0000.0000.0000.000
49D56TYR00.0270.01818.323-0.017-0.0170.0000.0000.0000.000
50D65LEU0-0.074-0.04218.155-0.009-0.0090.0000.0000.0000.000
51D66TYR00.0220.00815.1210.0100.0100.0000.0000.0000.000
52D67LEU0-0.0140.01516.401-0.017-0.0170.0000.0000.0000.000
53D68TRP00.1260.05811.813-0.018-0.0180.0000.0000.0000.000
54D69ASN0-0.012-0.00216.4250.0240.0240.0000.0000.0000.000
55D70GLN00.0880.01819.2570.0200.0200.0000.0000.0000.000
56D71ASN0-0.069-0.02622.0030.0150.0150.0000.0000.0000.000
57D72LEU0-0.047-0.01917.7640.0090.0090.0000.0000.0000.000
58D73LEU0-0.077-0.02019.3910.0140.0140.0000.0000.0000.000
59D74GLU-1-0.920-0.95522.8900.0220.0220.0000.0000.0000.000
60D75VAL0-0.019-0.01226.172-0.003-0.0030.0000.0000.0000.000
61D76LEU0-0.036-0.00829.2170.0030.0030.0000.0000.0000.000
62D77SER00.0090.00231.872-0.004-0.0040.0000.0000.0000.000
63D78ASP-1-0.873-0.95835.530-0.011-0.0110.0000.0000.0000.000
64D79ALA0-0.0050.00237.7750.0000.0000.0000.0000.0000.000
65D80GLN00.0570.01433.715-0.001-0.0010.0000.0000.0000.000
66D81LEU00.0040.02232.4230.0020.0020.0000.0000.0000.000
67D82MET00.014-0.00335.164-0.001-0.0010.0000.0000.0000.000
68D83GLU-1-0.896-0.93536.9990.0110.0110.0000.0000.0000.000
69D84VAL0-0.008-0.00631.3140.0010.0010.0000.0000.0000.000
70D85ASN0-0.044-0.04434.6290.0000.0000.0000.0000.0000.000
71D86ALA00.0400.03736.127-0.001-0.0010.0000.0000.0000.000
72D87GLN0-0.005-0.00633.347-0.001-0.0010.0000.0000.0000.000
73D88ILE00.003-0.00431.2300.0010.0010.0000.0000.0000.000
74D89ASN0-0.104-0.05634.939-0.002-0.0020.0000.0000.0000.000
75D90ASP-1-0.893-0.94238.3500.0140.0140.0000.0000.0000.000
76D91LEU00.005-0.00832.7260.0010.0010.0000.0000.0000.000
77D92LYS10.9020.94634.2380.0080.0080.0000.0000.0000.000
78D93ALA00.0530.04137.060-0.001-0.0010.0000.0000.0000.000
79D94GLN0-0.065-0.02837.7330.0020.0020.0000.0000.0000.000
80D95VAL0-0.002-0.00733.9890.0000.0000.0000.0000.0000.000
81D96GLU-1-0.932-0.96537.3420.0010.0010.0000.0000.0000.000
82D97LYS10.9130.96339.997-0.014-0.0140.0000.0000.0000.000
83D98LEU0-0.021-0.03237.3980.0000.0000.0000.0000.0000.000
84D99THR0-0.0030.01237.3340.0010.0010.0000.0000.0000.000
85D100GLN00.0630.03740.0030.0010.0010.0000.0000.0000.000
86D101GLN00.0250.01543.1110.0000.0000.0000.0000.0000.000
87D102GLY00.0440.02841.0800.0010.0010.0000.0000.0000.000
88D103GLU-1-0.925-0.95642.1130.0050.0050.0000.0000.0000.000
89D104THR0-0.060-0.04244.2600.0000.0000.0000.0000.0000.000
90D105LEU0-0.010-0.01543.5630.0000.0000.0000.0000.0000.000
91D106ARG10.9100.96439.577-0.008-0.0080.0000.0000.0000.000
92D107ILE0-0.024-0.01145.2970.0000.0000.0000.0000.0000.000
93D108THR0-0.037-0.03349.0090.0000.0000.0000.0000.0000.000
94D109GLN00.0150.02544.2170.0000.0000.0000.0000.0000.000
95D110ARG10.9870.98945.589-0.006-0.0060.0000.0000.0000.000
96D111ASN0-0.037-0.02850.1000.0000.0000.0000.0000.0000.000
97D112LEU0-0.048-0.01551.6370.0000.0000.0000.0000.0000.000
98D113GLU-1-0.938-0.97647.3700.0140.0140.0000.0000.0000.000
99D114ALA0-0.081-0.02752.3300.0000.0000.0000.0000.0000.000
100D115ALA0-0.021-0.00255.024-0.001-0.0010.0000.0000.0000.000
101D116PRO00.0330.03356.1630.0010.0010.0000.0000.0000.000
102D117ILE00.0100.00355.5940.0000.0000.0000.0000.0000.000
103D118THR00.0780.00958.6810.0000.0000.0000.0000.0000.000
104D119GLU-1-0.890-0.96061.2080.0120.0120.0000.0000.0000.000
105D120VAL00.0400.02658.8520.0000.0000.0000.0000.0000.000
106D121LEU0-0.0010.01562.082-0.001-0.0010.0000.0000.0000.000
107D122LYS10.8630.92263.671-0.012-0.0120.0000.0000.0000.000
108D123GLN0-0.0080.00164.392-0.001-0.0010.0000.0000.0000.000
109D124GLU-1-0.887-0.94361.2680.0090.0090.0000.0000.0000.000
110D125VAL0-0.020-0.01766.020-0.001-0.0010.0000.0000.0000.000
111D126ASP-1-0.836-0.90669.0650.0080.0080.0000.0000.0000.000
112D127GLU-1-0.966-0.98766.8350.0090.0090.0000.0000.0000.000
113D128LEU00.0310.00767.4130.0000.0000.0000.0000.0000.000
114D129ARG10.7850.89570.941-0.008-0.0080.0000.0000.0000.000
115D130GLN0-0.053-0.03273.7350.0000.0000.0000.0000.0000.000
116D131GLN0-0.0210.00469.8730.0000.0000.0000.0000.0000.000
117D132VAL00.002-0.00474.0730.0000.0000.0000.0000.0000.000
118D133SER00.0620.02576.3420.0000.0000.0000.0000.0000.000
119D134ALA0-0.0070.00577.9140.0000.0000.0000.0000.0000.000
120D135ASN0-0.042-0.03575.4260.0000.0000.0000.0000.0000.000
121D136ASP-1-0.884-0.92879.1570.0040.0040.0000.0000.0000.000
122D137GLU-1-0.939-0.97982.0010.0040.0040.0000.0000.0000.000
123D138LYS10.8760.93877.951-0.005-0.0050.0000.0000.0000.000
124D139LEU00.0300.00580.9880.0000.0000.0000.0000.0000.000
125D140ARG10.9350.97984.140-0.004-0.0040.0000.0000.0000.000
126D141LEU00.020-0.00187.1520.0000.0000.0000.0000.0000.000
127D142VAL0-0.046-0.01584.6340.0000.0000.0000.0000.0000.000
128D143ARG10.9260.94984.377-0.003-0.0030.0000.0000.0000.000
129D144GLU-1-0.990-0.96089.6390.0030.0030.0000.0000.0000.000
130D145SER0-0.069-0.03191.8290.0000.0000.0000.0000.0000.000
131D146ASN0-0.029-0.01188.1450.0000.0000.0000.0000.0000.000
132D147ALA00.0400.01291.0150.0000.0000.0000.0000.0000.000
133D148ILE0-0.071-0.04184.1700.0000.0000.0000.0000.0000.000
134D149VAL00.0070.00986.9530.0000.0000.0000.0000.0000.000
135D150SER0-0.0020.00183.1680.0000.0000.0000.0000.0000.000
136D151ASP-1-0.802-0.91780.3980.0000.0000.0000.0000.0000.000
137D152ALA0-0.024-0.02983.5100.0000.0000.0000.0000.0000.000
138D153ASP-1-0.879-0.93285.1300.0010.0010.0000.0000.0000.000
139D154MET0-0.012-0.01486.9770.0000.0000.0000.0000.0000.000
140D155LEU00.0200.02184.3490.0000.0000.0000.0000.0000.000
141D156THR0-0.068-0.03288.3230.0000.0000.0000.0000.0000.000
142D157LEU0-0.0010.01491.1310.0000.0000.0000.0000.0000.000
143D158GLN00.0250.00389.6570.0000.0000.0000.0000.0000.000
144D159LYS10.8410.91792.1420.0010.0010.0000.0000.0000.000
145D160ASN00.0290.00393.9610.0000.0000.0000.0000.0000.000
146D161TYR0-0.013-0.02596.7230.0000.0000.0000.0000.0000.000
147D162LYS10.9260.97395.2590.0010.0010.0000.0000.0000.000
148D163ASP-1-0.806-0.88697.072-0.001-0.0010.0000.0000.0000.000
149D164ALA0-0.0080.00099.7940.0000.0000.0000.0000.0000.000
150D165MET0-0.002-0.003101.3870.0000.0000.0000.0000.0000.000
151D166THR0-0.061-0.047100.4130.0000.0000.0000.0000.0000.000
152D167ALA0-0.0110.000103.1060.0000.0000.0000.0000.0000.000
153D168TRP00.0310.018105.5590.0000.0000.0000.0000.0000.000
154D169ALA0-0.001-0.004106.2220.0000.0000.0000.0000.0000.000
155D170THR0-0.006-0.024106.0410.0000.0000.0000.0000.0000.000
156D171ARG10.9400.963106.8000.0010.0010.0000.0000.0000.000
157D172ARG10.8740.943111.0660.0010.0010.0000.0000.0000.000
158D173ALA0-0.0130.001111.1200.0000.0000.0000.0000.0000.000
159D174LYS10.9860.997112.6860.0020.0020.0000.0000.0000.000
160D175CYS0-0.047-0.021114.3850.0000.0000.0000.0000.0000.000
161D176ARG10.9690.962116.6280.0010.0010.0000.0000.0000.000
162D177GLU-1-0.894-0.932113.513-0.002-0.0020.0000.0000.0000.000
163D178VAL0-0.035-0.016118.0830.0000.0000.0000.0000.0000.000
164D179ILE0-0.015-0.014120.6240.0000.0000.0000.0000.0000.000
165D180ASP-1-0.884-0.927120.893-0.001-0.0010.0000.0000.0000.000
166D181THR0-0.028-0.004122.5710.0000.0000.0000.0000.0000.000
167D182LEU0-0.041-0.029124.6610.0000.0000.0000.0000.0000.000
168D183SER0-0.048-0.027125.8880.0000.0000.0000.0000.0000.000
169D184GLU-1-0.870-0.952126.654-0.001-0.0010.0000.0000.0000.000
170D185GLY0-0.069-0.025129.1470.0000.0000.0000.0000.0000.000
171D186MET0-0.093-0.039130.9960.0000.0000.0000.0000.0000.000
172D187GLY00.0160.019132.1380.0000.0000.0000.0000.0000.000
173D188VAL0-0.044-0.025131.4340.0000.0000.0000.0000.0000.000
174D189LYS10.9970.989128.7400.0010.0010.0000.0000.0000.000
175D190PRO00.0920.046124.0530.0000.0000.0000.0000.0000.000
176D191SER0-0.059-0.043125.1680.0000.0000.0000.0000.0000.000
177D192ALA00.0050.012126.1420.0000.0000.0000.0000.0000.000
178D193PHE00.0580.014125.5420.0000.0000.0000.0000.0000.000
179D194MET0-0.057-0.030121.4790.0000.0000.0000.0000.0000.000
180D195ASP-1-0.854-0.919125.9400.0000.0000.0000.0000.0000.000
181D196GLN0-0.126-0.047128.1030.0000.0000.0000.0000.0000.000
182D197LEU0-0.060-0.054126.0710.0000.0000.0000.0000.0000.000
183D198GLY00.0040.024126.2950.0000.0000.0000.0000.0000.000
184D199LEU0-0.081-0.038121.2260.0000.0000.0000.0000.0000.000
185D200GLU-1-0.900-0.943119.3030.0000.0000.0000.0000.0000.000
186D201GLU-1-0.886-0.952115.659-0.001-0.0010.0000.0000.0000.000
187D202GLY0-0.0060.007116.2340.0000.0000.0000.0000.0000.000
188D203LEU0-0.030-0.019110.4470.0000.0000.0000.0000.0000.000
189D204PRO00.0450.049113.6980.0000.0000.0000.0000.0000.000
190D205MET00.010-0.028109.8410.0000.0000.0000.0000.0000.000
191D206THR00.0350.014110.4810.0000.0000.0000.0000.0000.000
192D207THR00.0750.016109.5000.0000.0000.0000.0000.0000.000
193D208TYR00.0450.030104.4650.0000.0000.0000.0000.0000.000
194D209THR0-0.037-0.017105.7260.0000.0000.0000.0000.0000.000
195D210GLU-1-1.005-1.006105.1280.0000.0000.0000.0000.0000.000
196D211MET0-0.016-0.025103.7250.0000.0000.0000.0000.0000.000
197D212LYS10.9400.985101.0260.0010.0010.0000.0000.0000.000
198D213LYS10.9190.97799.9850.0000.0000.0000.0000.0000.000
199D214ALA0-0.031-0.02199.1160.0000.0000.0000.0000.0000.000
200D215LEU00.0390.01795.4420.0000.0000.0000.0000.0000.000
201D216PRO00.0220.05195.0720.0000.0000.0000.0000.0000.000
202D217PRO0-0.037-0.01595.7250.0000.0000.0000.0000.0000.000
203D218VAL00.0540.03690.0630.0000.0000.0000.0000.0000.000
204D219ASN0-0.051-0.04191.5990.0000.0000.0000.0000.0000.000
205D220VAL00.0430.04288.0370.0000.0000.0000.0000.0000.000
206D221SER0-0.017-0.02887.0530.0000.0000.0000.0000.0000.000
207D222LYS10.8730.97985.7930.0010.0010.0000.0000.0000.000
208D223ALA00.050-0.00283.6560.0000.0000.0000.0000.0000.000
209D224ASP-1-0.931-0.97379.861-0.001-0.0010.0000.0000.0000.000
210D225ILE00.0200.01879.3910.0000.0000.0000.0000.0000.000