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: N927Q

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 OptHSide
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 -2659215.562142
FMO2-HF: Nuclear repulsion 2570755.485376
FMO2-HF: Total energy -88460.076766
FMO2-MP2: Total energy -88720.371323


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.
-0.8191.8060.276-1.279-1.622-0.003
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 : -0.025 / q_NPA : -0.029
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].
3D6PHE0-0.039-0.0202.9260.0782.7030.276-1.279-1.622-0.003
4D7TYR00.0270.0076.709-0.468-0.4680.0000.0000.0000.000
5D8ASP-1-0.964-0.96210.6770.3400.3400.0000.0000.0000.000
6D16GLY00.004-0.00821.6720.0090.0090.0000.0000.0000.000
7D17PHE0-0.013-0.01023.271-0.002-0.0020.0000.0000.0000.000
8D18ASP-1-0.871-0.94725.2550.1220.1220.0000.0000.0000.000
9D19PRO00.0130.00228.837-0.003-0.0030.0000.0000.0000.000
10D20ASP-1-0.781-0.87231.1470.0930.0930.0000.0000.0000.000
11D21ALA00.0240.01829.661-0.004-0.0040.0000.0000.0000.000
12D22GLY0-0.023-0.02029.858-0.001-0.0010.0000.0000.0000.000
13D23TYR0-0.069-0.05830.5240.0010.0010.0000.0000.0000.000
14D24MET00.0160.01633.975-0.006-0.0060.0000.0000.0000.000
15D25ASP-1-0.786-0.87029.7440.1470.1470.0000.0000.0000.000
16D26PHE00.007-0.00532.448-0.003-0.0030.0000.0000.0000.000
17D27CYS00.008-0.01733.586-0.004-0.0040.0000.0000.0000.000
18D28VAL00.0160.02234.976-0.005-0.0050.0000.0000.0000.000
19D29LYS10.7910.88528.780-0.150-0.1500.0000.0000.0000.000
20D30ASN0-0.061-0.04633.773-0.003-0.0030.0000.0000.0000.000
21D31ALA0-0.0060.01237.659-0.003-0.0030.0000.0000.0000.000
22D32GLU-1-0.926-0.96540.1960.0630.0630.0000.0000.0000.000
23D33SER0-0.050-0.02039.701-0.001-0.0010.0000.0000.0000.000
24D34LEU0-0.054-0.00839.0540.0000.0000.0000.0000.0000.000
25D35ASN00.0570.02142.738-0.004-0.0040.0000.0000.0000.000
26D36LEU00.0940.03245.2130.0030.0030.0000.0000.0000.000
27D37ALA00.0170.01346.7290.0010.0010.0000.0000.0000.000
28D38ALA0-0.0050.00342.5150.0010.0010.0000.0000.0000.000
29D39VAL00.0450.02341.4250.0020.0020.0000.0000.0000.000
30D40ARG10.9050.94142.946-0.050-0.0500.0000.0000.0000.000
31D41ILE0-0.021-0.01442.6280.0010.0010.0000.0000.0000.000
32D42PHE0-0.020-0.00435.3630.0030.0030.0000.0000.0000.000
33D43PHE00.019-0.00739.7900.0030.0030.0000.0000.0000.000
34D44LEU0-0.0390.00741.9350.0000.0000.0000.0000.0000.000
35D45ASN0-0.077-0.04440.192-0.002-0.0020.0000.0000.0000.000
36D46ALA00.0670.04637.3690.0050.0050.0000.0000.0000.000
37D47ALA0-0.029-0.02236.4750.0060.0060.0000.0000.0000.000
38D48LYS10.9490.95536.960-0.062-0.0620.0000.0000.0000.000
39D49ALA00.0590.03134.3020.0010.0010.0000.0000.0000.000
40D50LYS10.9430.98132.497-0.099-0.0990.0000.0000.0000.000
41D51ALA00.0010.01232.3010.0050.0050.0000.0000.0000.000
42D52ALA00.0300.03032.9580.0040.0040.0000.0000.0000.000
43D53LEU00.0210.00529.0660.0010.0010.0000.0000.0000.000
44D54SER0-0.076-0.05928.5410.0060.0060.0000.0000.0000.000
45D55ARG10.9120.94628.775-0.085-0.0850.0000.0000.0000.000
46D56LYS10.8690.93928.409-0.108-0.1080.0000.0000.0000.000
47D57PRO00.0460.01724.2770.0090.0090.0000.0000.0000.000
48D58GLU-1-0.834-0.91223.3750.1430.1430.0000.0000.0000.000
49D59ARG10.9820.97415.120-0.331-0.3310.0000.0000.0000.000
50D60LYS10.8490.91922.201-0.195-0.1950.0000.0000.0000.000
51D61ALA0-0.023-0.01124.947-0.010-0.0100.0000.0000.0000.000
52D62ASN00.0540.03128.7200.0110.0110.0000.0000.0000.000
53D63PRO0-0.043-0.00731.709-0.008-0.0080.0000.0000.0000.000
54D64LYS10.8810.92234.574-0.065-0.0650.0000.0000.0000.000
55D65PHE0-0.026-0.00635.360-0.002-0.0020.0000.0000.0000.000
56D66GLY00.0350.01440.498-0.001-0.0010.0000.0000.0000.000
57D67GLU-1-0.873-0.93943.0670.0580.0580.0000.0000.0000.000
58D68TRP00.0540.03336.1640.0000.0000.0000.0000.0000.000
59D69GLN0-0.052-0.03134.7070.0060.0060.0000.0000.0000.000
60D70VAL00.0380.02232.2990.0010.0010.0000.0000.0000.000
61D71GLU-1-0.841-0.89726.3800.1760.1760.0000.0000.0000.000
62D72VAL0-0.056-0.02028.5420.0040.0040.0000.0000.0000.000
63D73ILE00.020-0.00921.5640.0010.0010.0000.0000.0000.000
64D74ASN0-0.036-0.01224.737-0.009-0.0090.0000.0000.0000.000
65D75ASN0-0.007-0.01921.320-0.002-0.0020.0000.0000.0000.000
66D76HIS00.0440.01823.9230.0030.0030.0000.0000.0000.000
67D77PHE00.0070.01622.164-0.010-0.0100.0000.0000.0000.000
68D78PRO0-0.027-0.02924.1660.0160.0160.0000.0000.0000.000
69D79GLY00.0200.01220.6730.0090.0090.0000.0000.0000.000
70D80ASN00.0230.02119.2270.0470.0470.0000.0000.0000.000
71D81ARG10.8420.93620.023-0.131-0.1310.0000.0000.0000.000
72D82ASN0-0.0040.00217.070-0.013-0.0130.0000.0000.0000.000
73D83ASN0-0.042-0.01616.3110.0780.0780.0000.0000.0000.000
74D84PRO00.0100.01113.891-0.050-0.0500.0000.0000.0000.000
75D85ILE0-0.041-0.02617.225-0.016-0.0160.0000.0000.0000.000
76D86GLY00.0620.04620.1840.0030.0030.0000.0000.0000.000
77D87ASN0-0.014-0.03221.239-0.010-0.0100.0000.0000.0000.000
78D88ASN0-0.006-0.01924.403-0.006-0.0060.0000.0000.0000.000
79D89ASP-1-0.878-0.91121.9340.2520.2520.0000.0000.0000.000
80D90LEU00.0230.02625.492-0.007-0.0070.0000.0000.0000.000
81D91THR00.0400.01125.9510.0020.0020.0000.0000.0000.000
82D92ILE00.0450.00828.574-0.008-0.0080.0000.0000.0000.000
83D93HIS0-0.090-0.05430.289-0.007-0.0070.0000.0000.0000.000
84D94ARG10.8560.91324.083-0.217-0.2170.0000.0000.0000.000
85D95LEU00.0270.03231.482-0.004-0.0040.0000.0000.0000.000
86D96SER0-0.014-0.02634.038-0.008-0.0080.0000.0000.0000.000
87D97GLY00.0070.00935.015-0.005-0.0050.0000.0000.0000.000
88D98TYR00.020-0.00129.707-0.003-0.0030.0000.0000.0000.000
89D99LEU00.007-0.01136.359-0.005-0.0050.0000.0000.0000.000
90D100ALA0-0.0120.00339.088-0.005-0.0050.0000.0000.0000.000
91D101ARG10.7930.87137.331-0.094-0.0940.0000.0000.0000.000
92D102TRP00.0310.01640.458-0.003-0.0030.0000.0000.0000.000
93D103VAL00.0100.00442.146-0.004-0.0040.0000.0000.0000.000
94D104LEU0-0.017-0.00444.355-0.003-0.0030.0000.0000.0000.000
95D105ASP-1-0.837-0.89842.4570.0710.0710.0000.0000.0000.000
96D106GLN0-0.052-0.04145.919-0.003-0.0030.0000.0000.0000.000
97D107TYR0-0.077-0.03348.122-0.002-0.0020.0000.0000.0000.000
98D108ASN0-0.021-0.03947.801-0.004-0.0040.0000.0000.0000.000
99D109GLU-1-0.913-0.92749.3470.0530.0530.0000.0000.0000.000
100D110ASN0-0.066-0.02951.020-0.003-0.0030.0000.0000.0000.000
101D111ASP-1-0.873-0.93654.7260.0400.0400.0000.0000.0000.000
102D112ASP-1-0.878-0.91257.7130.0370.0370.0000.0000.0000.000
103D113GLU-1-0.773-0.87757.9220.0390.0390.0000.0000.0000.000
104D114SER0-0.094-0.07159.4380.0010.0010.0000.0000.0000.000
105D115GLN0-0.012-0.01452.3710.0000.0000.0000.0000.0000.000
106D116HIS00.021-0.00154.5060.0010.0010.0000.0000.0000.000
107D117GLU-1-0.814-0.89354.9810.0410.0410.0000.0000.0000.000
108D118LEU0-0.0180.01153.6240.0010.0010.0000.0000.0000.000
109D119ILE0-0.0230.00049.5480.0020.0020.0000.0000.0000.000
110D120ARG10.7640.84651.587-0.040-0.0400.0000.0000.0000.000
111D121THR0-0.0310.00753.674-0.001-0.0010.0000.0000.0000.000
112D122THR0-0.108-0.07349.5740.0010.0010.0000.0000.0000.000
113D123ILE0-0.058-0.02246.0390.0020.0020.0000.0000.0000.000
114D124ILE00.0510.02747.599-0.001-0.0010.0000.0000.0000.000
115D125ASN00.0290.00344.1380.0040.0040.0000.0000.0000.000
116D126PRO00.0110.00644.589-0.002-0.0020.0000.0000.0000.000
117D127ILE0-0.026-0.00940.601-0.001-0.0010.0000.0000.0000.000
118D128ALA00.0310.03145.141-0.001-0.0010.0000.0000.0000.000
119D129GLU-1-0.749-0.86047.7330.0470.0470.0000.0000.0000.000
120D130SER0-0.162-0.08447.450-0.002-0.0020.0000.0000.0000.000
121D131ASN0-0.045-0.03947.4570.0010.0010.0000.0000.0000.000
122D132GLY00.0370.02550.631-0.001-0.0010.0000.0000.0000.000
123D133VAL0-0.063-0.02150.215-0.001-0.0010.0000.0000.0000.000
124D134GLY00.1030.04151.5360.0020.0020.0000.0000.0000.000
125D135TRP00.023-0.01448.3140.0010.0010.0000.0000.0000.000
126D136ASP-1-0.884-0.94453.4410.0420.0420.0000.0000.0000.000
127D137SER0-0.070-0.03352.774-0.001-0.0010.0000.0000.0000.000
128D138GLY00.0320.01352.4700.0000.0000.0000.0000.0000.000
129D139PRO00.0510.02549.9330.0020.0020.0000.0000.0000.000
130D140GLU-1-0.807-0.89246.7910.0570.0570.0000.0000.0000.000
131D141ILE0-0.0030.01146.4750.0030.0030.0000.0000.0000.000
132D142TYR0-0.048-0.03247.3870.0030.0030.0000.0000.0000.000
133D143LEU00.022-0.00344.1170.0030.0030.0000.0000.0000.000
134D144SER0-0.057-0.04942.6150.0050.0050.0000.0000.0000.000
135D145PHE0-0.044-0.01342.0770.0030.0030.0000.0000.0000.000
136D146PHE0-0.0380.01040.0120.0030.0030.0000.0000.0000.000
137D147PRO0-0.049-0.02135.6360.0030.0030.0000.0000.0000.000
138D148GLY00.0110.00334.0820.0020.0020.0000.0000.0000.000
139D149THR00.0570.01635.0350.0030.0030.0000.0000.0000.000
140D150GLU-1-0.820-0.91033.3960.1130.1130.0000.0000.0000.000
141D151MET0-0.123-0.04431.5700.0070.0070.0000.0000.0000.000
142D152PHE00.0250.01334.2790.0010.0010.0000.0000.0000.000
143D153LEU00.0140.01937.021-0.006-0.0060.0000.0000.0000.000
144D154GLU-1-0.856-0.92939.5390.0650.0650.0000.0000.0000.000
145D155THR00.0010.00040.584-0.002-0.0020.0000.0000.0000.000
146D156PHE0-0.007-0.00139.891-0.003-0.0030.0000.0000.0000.000
147D157LYS10.9270.95043.461-0.055-0.0550.0000.0000.0000.000
148D158PHE00.003-0.01440.243-0.003-0.0030.0000.0000.0000.000
149D159TYR0-0.023-0.01243.3030.0010.0010.0000.0000.0000.000
150D160PRO00.0010.01439.4730.0000.0000.0000.0000.0000.000
151D161LEU0-0.062-0.02238.3420.0020.0020.0000.0000.0000.000
152D162THR00.016-0.00140.7570.0000.0000.0000.0000.0000.000
153D163ILE00.0370.03043.517-0.003-0.0030.0000.0000.0000.000
154D164GLY00.0350.00940.902-0.002-0.0020.0000.0000.0000.000
155D165ILE0-0.027-0.02741.901-0.001-0.0010.0000.0000.0000.000
156D166HIS00.0390.02043.465-0.002-0.0020.0000.0000.0000.000
157D167ARG10.9100.93442.075-0.067-0.0670.0000.0000.0000.000
158D168VAL0-0.050-0.01740.372-0.001-0.0010.0000.0000.0000.000
159D169LYS10.8410.92143.578-0.048-0.0480.0000.0000.0000.000
160D170GLN0-0.053-0.00946.896-0.004-0.0040.0000.0000.0000.000
161D171GLY00.0010.00245.168-0.001-0.0010.0000.0000.0000.000
162D172MET0-0.059-0.02345.3920.0000.0000.0000.0000.0000.000
163D173MET0-0.072-0.03138.8140.0040.0040.0000.0000.0000.000
164D174ASP-1-0.815-0.88636.4810.0740.0740.0000.0000.0000.000
165D175PRO00.1070.02637.4760.0050.0050.0000.0000.0000.000
166D176GLN0-0.079-0.03732.5550.0080.0080.0000.0000.0000.000
167D177TYR0-0.057-0.03032.9630.0120.0120.0000.0000.0000.000
168D178LEU00.011-0.00234.9750.0040.0040.0000.0000.0000.000
169D179LYS10.9590.98227.419-0.125-0.1250.0000.0000.0000.000
170D180LYS10.9080.95429.918-0.126-0.1260.0000.0000.0000.000
171D181ALA00.0740.02631.8320.0040.0040.0000.0000.0000.000
172D182LEU0-0.0080.00234.050-0.001-0.0010.0000.0000.0000.000
173D183ARG10.8950.94726.050-0.156-0.1560.0000.0000.0000.000
174D184GLN00.0060.02330.7170.0060.0060.0000.0000.0000.000
175D185ARG10.9660.99229.901-0.131-0.1310.0000.0000.0000.000
176D186TYR0-0.049-0.03534.790-0.002-0.0020.0000.0000.0000.000
177D187GLY00.0980.05138.021-0.004-0.0040.0000.0000.0000.000
178D188THR0-0.044-0.02136.0430.0060.0060.0000.0000.0000.000
179D189LEU0-0.046-0.01036.908-0.002-0.0020.0000.0000.0000.000
180D190THR00.025-0.01331.6290.0040.0040.0000.0000.0000.000
181D191ALA00.0640.03633.000-0.006-0.0060.0000.0000.0000.000
182D192ASP-1-0.886-0.95532.6240.0880.0880.0000.0000.0000.000
183D193LYS10.9030.96435.564-0.079-0.0790.0000.0000.0000.000
184D194TRP0-0.012-0.01836.064-0.009-0.0090.0000.0000.0000.000
185D195MET0-0.010-0.00435.341-0.004-0.0040.0000.0000.0000.000
186D196SER0-0.0070.00740.366-0.004-0.0040.0000.0000.0000.000
187D197GLN00.002-0.01241.4060.0000.0000.0000.0000.0000.000
188D198LYS10.8950.96342.654-0.062-0.0620.0000.0000.0000.000
189D199VAL00.0570.04444.8420.0000.0000.0000.0000.0000.000
190D200ALA00.0310.00946.4880.0000.0000.0000.0000.0000.000
191D201ALA00.0070.00146.824-0.001-0.0010.0000.0000.0000.000
192D202ILE00.0120.00742.4700.0000.0000.0000.0000.0000.000
193D203ALA00.006-0.00246.4930.0000.0000.0000.0000.0000.000
194D204LYS10.9270.96149.539-0.044-0.0440.0000.0000.0000.000
195D205SER00.012-0.00646.653-0.001-0.0010.0000.0000.0000.000
196D206LEU00.0010.00346.9930.0010.0010.0000.0000.0000.000
197D207LYS10.9830.99549.315-0.039-0.0390.0000.0000.0000.000
198D208ASP-1-0.863-0.91051.0930.0450.0450.0000.0000.0000.000
199D209VAL0-0.007-0.00347.3220.0000.0000.0000.0000.0000.000
200D210GLU-1-0.909-0.96650.7340.0430.0430.0000.0000.0000.000
201D211GLN0-0.080-0.04652.916-0.002-0.0020.0000.0000.0000.000
202D212LEU0-0.0160.01450.835-0.001-0.0010.0000.0000.0000.000
203D213LYS10.8860.93654.919-0.041-0.0410.0000.0000.0000.000
204D214TRP00.0180.00447.9170.0020.0020.0000.0000.0000.000
205D215GLY0-0.0270.00653.1970.0010.0010.0000.0000.0000.000
206D216LYS10.9730.96955.052-0.033-0.0330.0000.0000.0000.000
207D217GLY00.0570.04554.3330.0010.0010.0000.0000.0000.000
208D218GLY00.0180.02152.1120.0010.0010.0000.0000.0000.000
209D219LEU0-0.073-0.02952.337-0.001-0.0010.0000.0000.0000.000
210D220SER00.0420.01254.2650.0000.0000.0000.0000.0000.000
211D221ASP-1-0.823-0.91757.5070.0350.0350.0000.0000.0000.000
212D222THR00.010-0.00858.8230.0000.0000.0000.0000.0000.000
213D223ALA00.0170.01356.971-0.001-0.0010.0000.0000.0000.000
214D224LYS10.9360.96851.030-0.042-0.0420.0000.0000.0000.000
215D225THR00.004-0.00355.6230.0000.0000.0000.0000.0000.000
216D226PHE0-0.020-0.01258.198-0.001-0.0010.0000.0000.0000.000
217D227LEU00.0240.00053.010-0.001-0.0010.0000.0000.0000.000
218D228GLN0-0.0100.00553.1060.0010.0010.0000.0000.0000.000
219D229LYS10.9230.96455.527-0.027-0.0270.0000.0000.0000.000
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