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: 85N6Y

Calculation Name: 4BHH-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BHH

Chain ID: D

ChEMBL ID:

UniProt ID: P04873

Base Structure: X-ray

Registration Date: 2023-06-22

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2657449.933558
FMO2-HF: Nuclear repulsion 2568991.337439
FMO2-HF: Total energy -88458.596119
FMO2-MP2: Total energy -88718.863931


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:4:LEU)


Summations of interaction energy for fragment #1(D:4:LEU)
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.
-0.6661.750.067-1.136-1.347-0.001
Interaction energy analysis for fragmet #1(D:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.027
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].
3D6PHE0-0.036-0.0183.2910.1812.5970.067-1.136-1.347-0.001
4D7TYR00.0210.0026.895-0.416-0.4160.0000.0000.0000.000
5D8ASP-1-0.963-0.96110.6770.3500.3500.0000.0000.0000.000
6D16GLY00.002-0.01221.7240.0090.0090.0000.0000.0000.000
7D17PHE0-0.048-0.02323.271-0.001-0.0010.0000.0000.0000.000
8D18ASP-1-0.873-0.94625.2550.1240.1240.0000.0000.0000.000
9D19PRO0-0.002-0.00728.837-0.002-0.0020.0000.0000.0000.000
10D20ASP-1-0.854-0.93631.1470.0950.0950.0000.0000.0000.000
11D21ALA00.0060.01129.640-0.004-0.0040.0000.0000.0000.000
12D22GLY0-0.013-0.01429.860-0.001-0.0010.0000.0000.0000.000
13D23TYR0-0.048-0.03030.524-0.001-0.0010.0000.0000.0000.000
14D24MET00.0100.01333.903-0.006-0.0060.0000.0000.0000.000
15D25ASP-1-0.852-0.93229.6340.1450.1450.0000.0000.0000.000
16D26PHE0-0.020-0.01932.442-0.004-0.0040.0000.0000.0000.000
17D27CYS00.001-0.02833.543-0.005-0.0050.0000.0000.0000.000
18D28VAL00.0210.02634.750-0.005-0.0050.0000.0000.0000.000
19D29LYS10.8430.92828.670-0.151-0.1510.0000.0000.0000.000
20D30ASN0-0.046-0.03633.897-0.004-0.0040.0000.0000.0000.000
21D31ALA00.0030.02437.620-0.003-0.0030.0000.0000.0000.000
22D32GLU-1-0.938-0.97040.2000.0640.0640.0000.0000.0000.000
23D33SER0-0.033-0.01839.492-0.001-0.0010.0000.0000.0000.000
24D34LEU0-0.052-0.00639.2150.0000.0000.0000.0000.0000.000
25D35ASN00.0590.03142.695-0.004-0.0040.0000.0000.0000.000
26D36LEU00.0970.03245.1650.0030.0030.0000.0000.0000.000
27D37ALA00.0140.01246.6780.0010.0010.0000.0000.0000.000
28D38ALA0-0.006-0.00342.4170.0010.0010.0000.0000.0000.000
29D39VAL00.0360.01841.6320.0020.0020.0000.0000.0000.000
30D40ARG10.9030.93642.892-0.049-0.0490.0000.0000.0000.000
31D41ILE0-0.034-0.01642.4770.0000.0000.0000.0000.0000.000
32D42PHE0-0.028-0.01135.4620.0030.0030.0000.0000.0000.000
33D43PHE00.012-0.01339.6510.0020.0020.0000.0000.0000.000
34D44LEU0-0.0480.00741.876-0.001-0.0010.0000.0000.0000.000
35D45ASN0-0.063-0.04540.263-0.001-0.0010.0000.0000.0000.000
36D46ALA00.0680.04837.3100.0040.0040.0000.0000.0000.000
37D47ALA0-0.030-0.02136.4140.0050.0050.0000.0000.0000.000
38D48LYS10.9860.97536.898-0.059-0.0590.0000.0000.0000.000
39D49ALA00.0630.03134.2020.0010.0010.0000.0000.0000.000
40D50LYS10.9460.98432.436-0.097-0.0970.0000.0000.0000.000
41D51ALA00.0040.01232.2400.0040.0040.0000.0000.0000.000
42D52ALA00.0170.02732.9320.0040.0040.0000.0000.0000.000
43D53LEU00.0160.00128.9690.0010.0010.0000.0000.0000.000
44D54SER0-0.072-0.05328.4860.0060.0060.0000.0000.0000.000
45D55ARG10.9230.95228.977-0.081-0.0810.0000.0000.0000.000
46D56LYS10.9340.97728.554-0.098-0.0980.0000.0000.0000.000
47D57PRO00.0490.02524.5570.0080.0080.0000.0000.0000.000
48D58GLU-1-0.908-0.96123.3710.1370.1370.0000.0000.0000.000
49D59ARG10.9600.96515.027-0.309-0.3090.0000.0000.0000.000
50D60LYS10.9030.96521.727-0.198-0.1980.0000.0000.0000.000
51D61ALA0-0.018-0.01224.904-0.010-0.0100.0000.0000.0000.000
52D62ASN00.0710.04128.6770.0120.0120.0000.0000.0000.000
53D63PRO0-0.051-0.00431.675-0.009-0.0090.0000.0000.0000.000
54D64LYS10.9690.98134.529-0.065-0.0650.0000.0000.0000.000
55D65PHE0-0.027-0.00235.443-0.002-0.0020.0000.0000.0000.000
56D66GLY00.0450.01940.450-0.001-0.0010.0000.0000.0000.000
57D67GLU-1-0.981-1.01342.9100.0540.0540.0000.0000.0000.000
58D68TRP00.0450.03436.1800.0000.0000.0000.0000.0000.000
59D69GLN0-0.070-0.04534.6430.0060.0060.0000.0000.0000.000
60D70VAL00.0400.02332.2180.0010.0010.0000.0000.0000.000
61D71GLU-1-0.887-0.93926.5400.1680.1680.0000.0000.0000.000
62D72VAL0-0.064-0.02028.4940.0040.0040.0000.0000.0000.000
63D73ILE00.012-0.01321.5630.0010.0010.0000.0000.0000.000
64D74ASN0-0.035-0.01724.663-0.005-0.0050.0000.0000.0000.000
65D75ASN00.016-0.01520.989-0.004-0.0040.0000.0000.0000.000
66D76HIS0-0.007-0.00623.8620.0020.0020.0000.0000.0000.000
67D77PHE0-0.0080.01422.830-0.011-0.0110.0000.0000.0000.000
68D78PRO0-0.039-0.03424.2630.0150.0150.0000.0000.0000.000
69D79GLY00.0180.00820.8900.0090.0090.0000.0000.0000.000
70D80ASN00.0110.02219.4630.0230.0230.0000.0000.0000.000
71D81ARG10.8950.95819.958-0.123-0.1230.0000.0000.0000.000
72D82ASN0-0.0030.00016.852-0.003-0.0030.0000.0000.0000.000
73D83ASN0-0.021-0.00616.2480.0670.0670.0000.0000.0000.000
74D84PRO00.0110.01213.849-0.047-0.0470.0000.0000.0000.000
75D85ILE0-0.039-0.02417.163-0.015-0.0150.0000.0000.0000.000
76D86GLY00.0380.03020.1280.0040.0040.0000.0000.0000.000
77D87ASN0-0.027-0.05221.214-0.008-0.0080.0000.0000.0000.000
78D88ASN00.0480.02824.403-0.018-0.0180.0000.0000.0000.000
79D89ASP-1-0.886-0.90921.8410.2540.2540.0000.0000.0000.000
80D90LEU00.0200.00525.444-0.007-0.0070.0000.0000.0000.000
81D91THR00.0360.01326.0280.0020.0020.0000.0000.0000.000
82D92ILE00.0510.00828.517-0.007-0.0070.0000.0000.0000.000
83D93HIS0-0.076-0.02730.171-0.006-0.0060.0000.0000.0000.000
84D94ARG10.9290.96024.271-0.212-0.2120.0000.0000.0000.000
85D95LEU00.0340.03931.423-0.004-0.0040.0000.0000.0000.000
86D96SER0-0.002-0.01133.982-0.007-0.0070.0000.0000.0000.000
87D97GLY00.0010.00334.958-0.005-0.0050.0000.0000.0000.000
88D98TYR00.0070.00429.621-0.003-0.0030.0000.0000.0000.000
89D99LEU0-0.001-0.01636.304-0.005-0.0050.0000.0000.0000.000
90D100ALA0-0.0080.00639.030-0.005-0.0050.0000.0000.0000.000
91D101ARG10.8890.94837.455-0.092-0.0920.0000.0000.0000.000
92D102TRP00.0420.01940.462-0.003-0.0030.0000.0000.0000.000
93D103VAL00.0010.00042.094-0.004-0.0040.0000.0000.0000.000
94D104LEU0-0.021-0.00544.143-0.003-0.0030.0000.0000.0000.000
95D105ASP-1-0.862-0.94042.7300.0710.0710.0000.0000.0000.000
96D106GLN0-0.033-0.02245.851-0.004-0.0040.0000.0000.0000.000
97D107TYR0-0.052-0.02148.076-0.003-0.0030.0000.0000.0000.000
98D108ASN0-0.022-0.04048.140-0.004-0.0040.0000.0000.0000.000
99D109GLU-1-0.977-0.97348.6680.0550.0550.0000.0000.0000.000
100D110ASN0-0.045-0.01751.020-0.002-0.0020.0000.0000.0000.000
101D111ASP-1-0.883-0.93654.7260.0410.0410.0000.0000.0000.000
102D112ASP-1-0.988-0.98357.1780.0380.0380.0000.0000.0000.000
103D113GLU-1-0.848-0.93357.8700.0380.0380.0000.0000.0000.000
104D114SER0-0.035-0.02259.3840.0010.0010.0000.0000.0000.000
105D115GLN00.0270.00652.3590.0000.0000.0000.0000.0000.000
106D116HIS00.0110.00154.4400.0010.0010.0000.0000.0000.000
107D117GLU-1-0.838-0.92154.9250.0400.0400.0000.0000.0000.000
108D118LEU00.0160.07653.6550.0000.0000.0000.0000.0000.000
109D119ILE0-0.0080.01749.6260.0020.0020.0000.0000.0000.000
110D120ARG10.8890.94551.531-0.040-0.0400.0000.0000.0000.000
111D121THR0-0.065-0.07053.617-0.001-0.0010.0000.0000.0000.000
112D122THR0-0.117-0.08649.4980.0000.0000.0000.0000.0000.000
113D123ILE0-0.045-0.01545.8060.0020.0020.0000.0000.0000.000
114D124ILE00.0400.02047.549-0.001-0.0010.0000.0000.0000.000
115D125ASN00.036-0.00744.0980.0040.0040.0000.0000.0000.000
116D126PRO00.0030.00444.499-0.002-0.0020.0000.0000.0000.000
117D127ILE0-0.014-0.00340.583-0.001-0.0010.0000.0000.0000.000
118D128ALA00.0300.02745.074-0.001-0.0010.0000.0000.0000.000
119D129GLU-1-0.761-0.89747.6660.0450.0450.0000.0000.0000.000
120D130SER0-0.192-0.09247.468-0.002-0.0020.0000.0000.0000.000
121D131ASN0-0.093-0.06646.498-0.002-0.0020.0000.0000.0000.000
122D132GLY00.0080.00650.562-0.001-0.0010.0000.0000.0000.000
123D133VAL0-0.060-0.02050.077-0.001-0.0010.0000.0000.0000.000
124D134GLY00.1230.04751.4700.0020.0020.0000.0000.0000.000
125D135TRP0-0.001-0.02148.5890.0010.0010.0000.0000.0000.000
126D136ASP-1-0.945-0.96653.3790.0410.0410.0000.0000.0000.000
127D137SER0-0.044-0.02252.810-0.001-0.0010.0000.0000.0000.000
128D138GLY00.0160.00652.4710.0000.0000.0000.0000.0000.000
129D139PRO00.0490.02349.9010.0020.0020.0000.0000.0000.000
130D140GLU-1-0.884-0.94646.7830.0570.0570.0000.0000.0000.000
131D141ILE00.0020.00546.4750.0030.0030.0000.0000.0000.000
132D142TYR0-0.0100.01547.3560.0030.0030.0000.0000.0000.000
133D143LEU00.012-0.00644.0880.0020.0020.0000.0000.0000.000
134D144SER0-0.044-0.03142.5970.0050.0050.0000.0000.0000.000
135D145PHE0-0.045-0.01542.0330.0030.0030.0000.0000.0000.000
136D146PHE0-0.0520.00639.9190.0020.0020.0000.0000.0000.000
137D147PRO0-0.067-0.03335.5700.0030.0030.0000.0000.0000.000
138D148GLY00.008-0.02134.0260.0020.0020.0000.0000.0000.000
139D149THR00.0570.02334.9710.0030.0030.0000.0000.0000.000
140D150GLU-1-0.823-0.92433.6280.1060.1060.0000.0000.0000.000
141D151MET0-0.121-0.04231.7600.0060.0060.0000.0000.0000.000
142D152PHE00.0230.01134.2790.0020.0020.0000.0000.0000.000
143D153LEU00.0090.01736.930-0.006-0.0060.0000.0000.0000.000
144D154GLU-1-0.926-0.98239.5400.0680.0680.0000.0000.0000.000
145D155THR00.0100.00740.388-0.003-0.0030.0000.0000.0000.000
146D156PHE0-0.0080.00539.844-0.003-0.0030.0000.0000.0000.000
147D157LYS11.0171.01043.461-0.055-0.0550.0000.0000.0000.000
148D158PHE00.012-0.00740.425-0.003-0.0030.0000.0000.0000.000
149D159TYR0-0.0120.01743.3030.0000.0000.0000.0000.0000.000
150D160PRO0-0.0040.01639.489-0.001-0.0010.0000.0000.0000.000
151D161LEU0-0.057-0.02338.7560.0020.0020.0000.0000.0000.000
152D162THR00.016-0.01940.757-0.001-0.0010.0000.0000.0000.000
153D163ILE00.0320.03443.416-0.003-0.0030.0000.0000.0000.000
154D164GLY00.0300.00840.941-0.002-0.0020.0000.0000.0000.000
155D165ILE0-0.025-0.02241.937-0.001-0.0010.0000.0000.0000.000
156D166HIS00.0270.01143.500-0.002-0.0020.0000.0000.0000.000
157D167ARG10.9730.96541.934-0.067-0.0670.0000.0000.0000.000
158D168VAL0-0.054-0.01540.397-0.001-0.0010.0000.0000.0000.000
159D169LYS10.9310.96343.610-0.046-0.0460.0000.0000.0000.000
160D170GLN0-0.0330.00346.927-0.003-0.0030.0000.0000.0000.000
161D171GLY0-0.0060.00145.198-0.001-0.0010.0000.0000.0000.000
162D172MET0-0.057-0.01945.4240.0000.0000.0000.0000.0000.000
163D173MET0-0.071-0.02338.5520.0030.0030.0000.0000.0000.000
164D174ASP-1-0.828-0.91436.1670.0710.0710.0000.0000.0000.000
165D175PRO00.0920.01937.5020.0050.0050.0000.0000.0000.000
166D176GLN0-0.043-0.00232.5750.0030.0030.0000.0000.0000.000
167D177TYR0-0.071-0.03832.9960.0090.0090.0000.0000.0000.000
168D178LEU00.014-0.00435.0090.0040.0040.0000.0000.0000.000
169D179LYS10.9340.97727.184-0.123-0.1230.0000.0000.0000.000
170D180LYS10.8970.94229.954-0.122-0.1220.0000.0000.0000.000
171D181ALA00.0790.02831.8460.0040.0040.0000.0000.0000.000
172D182LEU0-0.0040.00134.091-0.001-0.0010.0000.0000.0000.000
173D183ARG10.9270.96626.218-0.155-0.1550.0000.0000.0000.000
174D184GLN0-0.0110.01230.2310.0050.0050.0000.0000.0000.000
175D185ARG11.0151.00829.527-0.130-0.1300.0000.0000.0000.000
176D186TYR0-0.0040.01634.790-0.002-0.0020.0000.0000.0000.000
177D187GLY00.1100.05438.011-0.004-0.0040.0000.0000.0000.000
178D188THR0-0.033-0.01336.0450.0060.0060.0000.0000.0000.000
179D189LEU0-0.050-0.01536.893-0.002-0.0020.0000.0000.0000.000
180D190THR00.013-0.01331.6720.0040.0040.0000.0000.0000.000
181D191ALA00.0650.03533.065-0.006-0.0060.0000.0000.0000.000
182D192ASP-1-0.884-0.95633.2230.0830.0830.0000.0000.0000.000
183D193LYS10.8970.96135.686-0.078-0.0780.0000.0000.0000.000
184D194TRP0-0.003-0.01136.033-0.009-0.0090.0000.0000.0000.000
185D195MET0-0.017-0.00835.238-0.004-0.0040.0000.0000.0000.000
186D196SER0-0.0020.01040.399-0.005-0.0050.0000.0000.0000.000
187D197GLN00.002-0.01641.4250.0010.0010.0000.0000.0000.000
188D198LYS10.9090.96342.852-0.060-0.0600.0000.0000.0000.000
189D199VAL00.0600.04644.7760.0000.0000.0000.0000.0000.000
190D200ALA00.0370.01346.4880.0000.0000.0000.0000.0000.000
191D201ALA0-0.003-0.00446.781-0.001-0.0010.0000.0000.0000.000
192D202ILE00.0140.00842.3420.0000.0000.0000.0000.0000.000
193D203ALA00.004-0.00446.4930.0000.0000.0000.0000.0000.000
194D204LYS10.9220.96149.543-0.044-0.0440.0000.0000.0000.000
195D205SER00.002-0.01546.768-0.001-0.0010.0000.0000.0000.000
196D206LEU00.0080.01047.2590.0010.0010.0000.0000.0000.000
197D207LYS10.9790.99449.315-0.038-0.0380.0000.0000.0000.000
198D208ASP-1-0.886-0.93051.1410.0440.0440.0000.0000.0000.000
199D209VAL0-0.012-0.00547.3750.0000.0000.0000.0000.0000.000
200D210GLU-1-0.970-1.00450.7340.0410.0410.0000.0000.0000.000
201D211GLN0-0.097-0.05452.953-0.003-0.0030.0000.0000.0000.000
202D212LEU0-0.0130.01250.807-0.001-0.0010.0000.0000.0000.000
203D213LYS10.9310.95454.897-0.037-0.0370.0000.0000.0000.000
204D214TRP00.0380.00947.5980.0020.0020.0000.0000.0000.000
205D215GLY0-0.0280.00653.1360.0010.0010.0000.0000.0000.000
206D216LYS10.9710.96954.981-0.032-0.0320.0000.0000.0000.000
207D217GLY00.0590.04854.2640.0010.0010.0000.0000.0000.000
208D218GLY00.0290.02652.0440.0010.0010.0000.0000.0000.000
209D219LEU0-0.073-0.03352.215-0.001-0.0010.0000.0000.0000.000
210D220SER00.0230.00854.195-0.001-0.0010.0000.0000.0000.000
211D221ASP-1-0.812-0.91857.5170.0340.0340.0000.0000.0000.000
212D222THR00.024-0.00358.8130.0000.0000.0000.0000.0000.000
213D223ALA0-0.0020.00457.072-0.001-0.0010.0000.0000.0000.000
214D224LYS10.9310.96851.042-0.040-0.0400.0000.0000.0000.000
215D225THR00.0070.00455.8150.0000.0000.0000.0000.0000.000
216D226PHE0-0.023-0.01358.352-0.001-0.0010.0000.0000.0000.000
217D227LEU00.0330.00253.213-0.001-0.0010.0000.0000.0000.000
218D228GLN0-0.0100.00953.2320.0010.0010.0000.0000.0000.000
219D229LYS10.9120.95555.703-0.025-0.0250.0000.0000.0000.000
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