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: JL2R9

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 OptAll
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 -2667440.570296
FMO2-HF: Nuclear repulsion 2578979.610799
FMO2-HF: Total energy -88460.959497
FMO2-MP2: Total energy -88721.217512


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.
-0.0572.3211.185-1.446-2.117-0.005
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 : -0.028 / q_NPA : -0.030
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].
3D6PHE0-0.032-0.0132.5640.9903.3681.185-1.446-2.117-0.005
4D7TYR00.0680.0246.267-0.639-0.6390.0000.0000.0000.000
5D8ASP-1-1.010-0.98610.5640.3660.3660.0000.0000.0000.000
6D16GLY00.0600.03321.3650.0030.0030.0000.0000.0000.000
7D17PHE0-0.035-0.02823.197-0.002-0.0020.0000.0000.0000.000
8D18ASP-1-0.834-0.91425.4970.1250.1250.0000.0000.0000.000
9D19PRO00.002-0.00829.0620.0010.0010.0000.0000.0000.000
10D20ASP-1-0.769-0.85531.4620.0960.0960.0000.0000.0000.000
11D21ALA00.0030.00329.816-0.004-0.0040.0000.0000.0000.000
12D22GLY0-0.010-0.00929.9210.0010.0010.0000.0000.0000.000
13D23TYR0-0.090-0.07530.6070.0000.0000.0000.0000.0000.000
14D24MET00.0200.01034.192-0.006-0.0060.0000.0000.0000.000
15D25ASP-1-0.766-0.85829.5170.1530.1530.0000.0000.0000.000
16D26PHE00.002-0.00632.387-0.004-0.0040.0000.0000.0000.000
17D27CYS00.0150.00133.560-0.004-0.0040.0000.0000.0000.000
18D28VAL00.0080.01334.957-0.005-0.0050.0000.0000.0000.000
19D29LYS10.7740.87928.572-0.156-0.1560.0000.0000.0000.000
20D30ASN0-0.049-0.03733.799-0.003-0.0030.0000.0000.0000.000
21D31ALA00.0110.00237.628-0.004-0.0040.0000.0000.0000.000
22D32GLU-1-0.906-0.93440.4290.0630.0630.0000.0000.0000.000
23D33SER0-0.066-0.04040.066-0.002-0.0020.0000.0000.0000.000
24D34LEU0-0.071-0.02038.836-0.001-0.0010.0000.0000.0000.000
25D35ASN00.0520.01942.532-0.005-0.0050.0000.0000.0000.000
26D36LEU00.0890.03745.3080.0020.0020.0000.0000.0000.000
27D37ALA00.0280.02047.1350.0010.0010.0000.0000.0000.000
28D38ALA00.0140.00642.4620.0010.0010.0000.0000.0000.000
29D39VAL00.0110.00841.5860.0030.0030.0000.0000.0000.000
30D40ARG10.8810.94443.279-0.050-0.0500.0000.0000.0000.000
31D41ILE0-0.023-0.01342.6650.0010.0010.0000.0000.0000.000
32D42PHE0-0.0020.00735.5330.0030.0030.0000.0000.0000.000
33D43PHE00.0330.00539.9160.0020.0020.0000.0000.0000.000
34D44LEU0-0.0310.00042.2410.0000.0000.0000.0000.0000.000
35D45ASN0-0.075-0.04940.262-0.003-0.0030.0000.0000.0000.000
36D46ALA00.0490.04037.4210.0040.0040.0000.0000.0000.000
37D47ALA0-0.029-0.02136.5430.0060.0060.0000.0000.0000.000
38D48LYS10.9440.95736.763-0.063-0.0630.0000.0000.0000.000
39D49ALA00.0560.02834.5650.0020.0020.0000.0000.0000.000
40D50LYS10.9290.97532.255-0.099-0.0990.0000.0000.0000.000
41D51ALA00.0090.01232.1500.0050.0050.0000.0000.0000.000
42D52ALA00.0140.01833.3940.0010.0010.0000.0000.0000.000
43D53LEU00.0340.01428.9160.0010.0010.0000.0000.0000.000
44D54SER0-0.077-0.05528.4490.0050.0050.0000.0000.0000.000
45D55ARG10.9090.93828.836-0.085-0.0850.0000.0000.0000.000
46D56LYS10.8650.93828.139-0.110-0.1100.0000.0000.0000.000
47D57PRO00.0460.02223.8710.0100.0100.0000.0000.0000.000
48D58GLU-1-0.804-0.88622.9990.1420.1420.0000.0000.0000.000
49D59ARG10.9780.97615.270-0.325-0.3250.0000.0000.0000.000
50D60LYS10.8550.92222.474-0.195-0.1950.0000.0000.0000.000
51D61ALA0-0.030-0.00625.316-0.010-0.0100.0000.0000.0000.000
52D62ASN00.0450.02029.1030.0120.0120.0000.0000.0000.000
53D63PRO0-0.042-0.00832.129-0.008-0.0080.0000.0000.0000.000
54D64LYS10.8610.90035.022-0.065-0.0650.0000.0000.0000.000
55D65PHE0-0.026-0.00535.521-0.002-0.0020.0000.0000.0000.000
56D66GLY00.0370.01640.694-0.002-0.0020.0000.0000.0000.000
57D67GLU-1-0.832-0.90843.4480.0580.0580.0000.0000.0000.000
58D68TRP00.0360.02336.1710.0010.0010.0000.0000.0000.000
59D69GLN0-0.026-0.01634.7680.0050.0050.0000.0000.0000.000
60D70VAL00.0130.01732.4320.0010.0010.0000.0000.0000.000
61D71GLU-1-0.840-0.90026.4390.1760.1760.0000.0000.0000.000
62D72VAL0-0.055-0.03028.5230.0030.0030.0000.0000.0000.000
63D73ILE00.0340.00821.4390.0010.0010.0000.0000.0000.000
64D74ASN0-0.075-0.04124.478-0.012-0.0120.0000.0000.0000.000
65D75ASN0-0.010-0.01422.2120.0000.0000.0000.0000.0000.000
66D76HIS00.0540.02023.7780.0010.0010.0000.0000.0000.000
67D77PHE00.0040.00922.242-0.008-0.0080.0000.0000.0000.000
68D78PRO0-0.017-0.02123.6870.0170.0170.0000.0000.0000.000
69D79GLY00.0290.02120.3240.0080.0080.0000.0000.0000.000
70D80ASN00.0140.00018.8990.0480.0480.0000.0000.0000.000
71D81ARG10.8210.92320.131-0.133-0.1330.0000.0000.0000.000
72D82ASN00.0070.00216.784-0.014-0.0140.0000.0000.0000.000
73D83ASN0-0.028-0.00416.4990.0810.0810.0000.0000.0000.000
74D84PRO00.0050.00913.997-0.043-0.0430.0000.0000.0000.000
75D85ILE0-0.039-0.02417.288-0.024-0.0240.0000.0000.0000.000
76D86GLY00.0630.04520.3690.0090.0090.0000.0000.0000.000
77D87ASN0-0.020-0.04421.326-0.010-0.0100.0000.0000.0000.000
78D88ASN0-0.021-0.01924.487-0.003-0.0030.0000.0000.0000.000
79D89ASP-1-0.856-0.90922.1160.2530.2530.0000.0000.0000.000
80D90LEU00.0100.01825.557-0.008-0.0080.0000.0000.0000.000
81D91THR00.0430.00725.8870.0010.0010.0000.0000.0000.000
82D92ILE00.015-0.00228.793-0.007-0.0070.0000.0000.0000.000
83D93HIS0-0.083-0.05030.280-0.008-0.0080.0000.0000.0000.000
84D94ARG10.8290.90724.348-0.217-0.2170.0000.0000.0000.000
85D95LEU00.0210.02031.583-0.006-0.0060.0000.0000.0000.000
86D96SER0-0.015-0.02234.133-0.008-0.0080.0000.0000.0000.000
87D97GLY00.0200.01235.260-0.005-0.0050.0000.0000.0000.000
88D98TYR0-0.004-0.01429.955-0.002-0.0020.0000.0000.0000.000
89D99LEU00.0190.00836.540-0.005-0.0050.0000.0000.0000.000
90D100ALA0-0.0090.00639.416-0.005-0.0050.0000.0000.0000.000
91D101ARG10.7850.87437.589-0.097-0.0970.0000.0000.0000.000
92D102TRP00.0490.02540.437-0.003-0.0030.0000.0000.0000.000
93D103VAL00.005-0.00542.187-0.004-0.0040.0000.0000.0000.000
94D104LEU0-0.028-0.01044.281-0.003-0.0030.0000.0000.0000.000
95D105ASP-1-0.845-0.90942.4180.0740.0740.0000.0000.0000.000
96D106GLN0-0.040-0.04845.872-0.002-0.0020.0000.0000.0000.000
97D107TYR0-0.086-0.04948.087-0.002-0.0020.0000.0000.0000.000
98D108ASN0-0.058-0.04247.572-0.004-0.0040.0000.0000.0000.000
99D109GLU-1-0.865-0.88849.3080.0550.0550.0000.0000.0000.000
100D110ASN0-0.046-0.02851.216-0.003-0.0030.0000.0000.0000.000
101D111ASP-1-0.910-0.94755.0570.0420.0420.0000.0000.0000.000
102D112ASP-1-0.836-0.89057.4470.0380.0380.0000.0000.0000.000
103D113GLU-1-0.769-0.87957.7890.0400.0400.0000.0000.0000.000
104D114SER0-0.081-0.05559.3610.0000.0000.0000.0000.0000.000
105D115GLN0-0.001-0.01152.2040.0000.0000.0000.0000.0000.000
106D116HIS00.0130.00354.5220.0010.0010.0000.0000.0000.000
107D117GLU-1-0.821-0.90154.9080.0420.0420.0000.0000.0000.000
108D118LEU0-0.0260.00353.6800.0010.0010.0000.0000.0000.000
109D119ILE0-0.0110.00049.6080.0020.0020.0000.0000.0000.000
110D120ARG10.7510.83951.506-0.040-0.0400.0000.0000.0000.000
111D121THR0-0.0250.00453.699-0.001-0.0010.0000.0000.0000.000
112D122THR0-0.102-0.06849.6390.0000.0000.0000.0000.0000.000
113D123ILE0-0.037-0.01646.0100.0020.0020.0000.0000.0000.000
114D124ILE00.0370.02847.696-0.002-0.0020.0000.0000.0000.000
115D125ASN00.028-0.00544.0830.0040.0040.0000.0000.0000.000
116D126PRO00.0100.00245.108-0.002-0.0020.0000.0000.0000.000
117D127ILE0-0.052-0.00540.925-0.001-0.0010.0000.0000.0000.000
118D128ALA00.0410.03245.3130.0000.0000.0000.0000.0000.000
119D129GLU-1-0.759-0.86648.1880.0480.0480.0000.0000.0000.000
120D130SER0-0.122-0.07747.477-0.002-0.0020.0000.0000.0000.000
121D131ASN0-0.037-0.02847.7370.0020.0020.0000.0000.0000.000
122D132GLY00.0200.02750.906-0.001-0.0010.0000.0000.0000.000
123D133VAL0-0.043-0.02050.547-0.001-0.0010.0000.0000.0000.000
124D134GLY00.0880.03751.5340.0020.0020.0000.0000.0000.000
125D135TRP00.025-0.02148.5440.0010.0010.0000.0000.0000.000
126D136ASP-1-0.812-0.88353.5950.0420.0420.0000.0000.0000.000
127D137SER0-0.057-0.03353.211-0.001-0.0010.0000.0000.0000.000
128D138GLY00.0280.02552.9010.0000.0000.0000.0000.0000.000
129D139PRO00.0320.01349.9520.0020.0020.0000.0000.0000.000
130D140GLU-1-0.799-0.88746.5900.0580.0580.0000.0000.0000.000
131D141ILE0-0.0070.01546.2130.0040.0040.0000.0000.0000.000
132D142TYR0-0.020-0.01847.4370.0030.0030.0000.0000.0000.000
133D143LEU00.0250.00144.1530.0030.0030.0000.0000.0000.000
134D144SER0-0.032-0.04742.5880.0050.0050.0000.0000.0000.000
135D145PHE0-0.036-0.00842.3740.0030.0030.0000.0000.0000.000
136D146PHE0-0.0480.00039.9900.0020.0020.0000.0000.0000.000
137D147PRO0-0.040-0.01335.5700.0030.0030.0000.0000.0000.000
138D148GLY00.0030.00234.2270.0010.0010.0000.0000.0000.000
139D149THR00.0460.00335.1830.0030.0030.0000.0000.0000.000
140D150GLU-1-0.809-0.90333.3810.1170.1170.0000.0000.0000.000
141D151MET0-0.128-0.04831.8510.0070.0070.0000.0000.0000.000
142D152PHE00.0340.01634.4190.0020.0020.0000.0000.0000.000
143D153LEU00.0070.00836.985-0.007-0.0070.0000.0000.0000.000
144D154GLU-1-0.846-0.89839.6060.0670.0670.0000.0000.0000.000
145D155THR00.0020.00140.642-0.002-0.0020.0000.0000.0000.000
146D156PHE00.0130.01039.817-0.002-0.0020.0000.0000.0000.000
147D157LYS10.9030.93843.614-0.057-0.0570.0000.0000.0000.000
148D158PHE00.026-0.01240.270-0.003-0.0030.0000.0000.0000.000
149D159TYR0-0.023-0.01143.1310.0010.0010.0000.0000.0000.000
150D160PRO0-0.0050.01139.696-0.001-0.0010.0000.0000.0000.000
151D161LEU0-0.040-0.01538.1500.0010.0010.0000.0000.0000.000
152D162THR0-0.008-0.01740.709-0.001-0.0010.0000.0000.0000.000
153D163ILE00.0420.02843.797-0.003-0.0030.0000.0000.0000.000
154D164GLY00.0100.00040.917-0.001-0.0010.0000.0000.0000.000
155D165ILE0-0.003-0.01541.608-0.002-0.0020.0000.0000.0000.000
156D166HIS00.0170.01443.434-0.002-0.0020.0000.0000.0000.000
157D167ARG10.8870.92942.444-0.067-0.0670.0000.0000.0000.000
158D168VAL0-0.047-0.02040.573-0.001-0.0010.0000.0000.0000.000
159D169LYS10.8410.92343.758-0.049-0.0490.0000.0000.0000.000
160D170GLN0-0.036-0.00547.230-0.004-0.0040.0000.0000.0000.000
161D171GLY00.0040.00745.266-0.001-0.0010.0000.0000.0000.000
162D172MET0-0.065-0.03045.1770.0010.0010.0000.0000.0000.000
163D173MET0-0.071-0.03038.9220.0040.0040.0000.0000.0000.000
164D174ASP-1-0.806-0.88236.5700.0760.0760.0000.0000.0000.000
165D175PRO00.0760.01037.5770.0040.0040.0000.0000.0000.000
166D176GLN0-0.064-0.03732.3910.0090.0090.0000.0000.0000.000
167D177TYR0-0.041-0.02033.0710.0110.0110.0000.0000.0000.000
168D178LEU00.0250.01534.5740.0050.0050.0000.0000.0000.000
169D179LYS10.9560.99127.327-0.127-0.1270.0000.0000.0000.000
170D180LYS10.8960.95929.877-0.126-0.1260.0000.0000.0000.000
171D181ALA00.0850.03131.9550.0030.0030.0000.0000.0000.000
172D182LEU0-0.004-0.01134.250-0.001-0.0010.0000.0000.0000.000
173D183ARG10.8740.92826.039-0.158-0.1580.0000.0000.0000.000
174D184GLN0-0.0020.02331.0440.0100.0100.0000.0000.0000.000
175D185ARG10.9300.96629.816-0.137-0.1370.0000.0000.0000.000
176D186TYR0-0.042-0.03934.631-0.004-0.0040.0000.0000.0000.000
177D187GLY00.1010.04638.182-0.002-0.0020.0000.0000.0000.000
178D188THR0-0.021-0.01235.9730.0060.0060.0000.0000.0000.000
179D189LEU0-0.066-0.02436.2700.0000.0000.0000.0000.0000.000
180D190THR00.0590.00431.6750.0030.0030.0000.0000.0000.000
181D191ALA00.0570.03333.392-0.007-0.0070.0000.0000.0000.000
182D192ASP-1-0.883-0.95332.5760.0950.0950.0000.0000.0000.000
183D193LYS10.9140.97935.546-0.086-0.0860.0000.0000.0000.000
184D194TRP0-0.026-0.01935.983-0.009-0.0090.0000.0000.0000.000
185D195MET0-0.019-0.01735.393-0.004-0.0040.0000.0000.0000.000
186D196SER0-0.0260.00540.356-0.004-0.0040.0000.0000.0000.000
187D197GLN00.020-0.02141.4240.0010.0010.0000.0000.0000.000
188D198LYS10.8860.95442.635-0.064-0.0640.0000.0000.0000.000
189D199VAL00.0340.03144.4850.0000.0000.0000.0000.0000.000
190D200ALA00.0410.01946.2160.0000.0000.0000.0000.0000.000
191D201ALA00.0020.00346.772-0.001-0.0010.0000.0000.0000.000
192D202ILE0-0.0050.00342.3950.0000.0000.0000.0000.0000.000
193D203ALA00.001-0.00246.2610.0000.0000.0000.0000.0000.000
194D204LYS10.9430.97449.343-0.046-0.0460.0000.0000.0000.000
195D205SER00.0060.00346.6120.0000.0000.0000.0000.0000.000
196D206LEU0-0.006-0.01746.6380.0000.0000.0000.0000.0000.000
197D207LYS10.8830.93748.952-0.042-0.0420.0000.0000.0000.000
198D208ASP-1-0.826-0.89851.1280.0460.0460.0000.0000.0000.000
199D209VAL0-0.0160.00047.3030.0000.0000.0000.0000.0000.000
200D210GLU-1-0.840-0.92950.6590.0430.0430.0000.0000.0000.000
201D211GLN0-0.077-0.04052.752-0.003-0.0030.0000.0000.0000.000
202D212LEU0-0.0020.02050.574-0.001-0.0010.0000.0000.0000.000
203D213LYS10.8200.89054.609-0.042-0.0420.0000.0000.0000.000
204D214TRP0-0.015-0.03047.8260.0010.0010.0000.0000.0000.000
205D215GLY0-0.0060.01752.6180.0010.0010.0000.0000.0000.000
206D216LYS10.9540.98055.081-0.035-0.0350.0000.0000.0000.000
207D217GLY00.0370.02454.3470.0010.0010.0000.0000.0000.000
208D218GLY00.0090.00651.9740.0010.0010.0000.0000.0000.000
209D219LEU0-0.070-0.03452.033-0.002-0.0020.0000.0000.0000.000
210D220SER00.0630.02553.8580.0000.0000.0000.0000.0000.000
211D221ASP-1-0.825-0.91657.1720.0360.0360.0000.0000.0000.000
212D222THR00.0060.00258.4280.0000.0000.0000.0000.0000.000
213D223ALA00.0290.02056.724-0.001-0.0010.0000.0000.0000.000
214D224LYS10.9310.96650.686-0.044-0.0440.0000.0000.0000.000
215D225THR0-0.001-0.01555.5180.0000.0000.0000.0000.0000.000
216D226PHE0-0.033-0.01858.044-0.001-0.0010.0000.0000.0000.000
217D227LEU00.0240.00452.5060.0000.0000.0000.0000.0000.000
218D228GLN00.0030.01352.5140.0010.0010.0000.0000.0000.000
219D229LYS10.9240.96055.200-0.027-0.0270.0000.0000.0000.000
220D230PHE0-0.0150.00756.439-0.001-0.0010.0000.0000.0000.000
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