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: K9M73

Calculation Name: 5WKF-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WKF

Chain ID: D

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2023-06-26

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1925235.821767
FMO2-HF: Nuclear repulsion 1847032.992552
FMO2-HF: Total energy -78202.829215
FMO2-MP2: Total energy -78426.009019


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:3:GLN)


Summations of interaction energy for fragment #1(D:3:GLN)
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.
4.6857.3762.065-1.742-3.0150.007
Interaction energy analysis for fragmet #1(D:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : -0.009
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].
3D5VAL0-0.005-0.0093.943-0.4660.554-0.008-0.481-0.5310.002
4D6GLN0-0.026-0.0466.2700.9300.9300.0000.0000.0000.000
5D7SER0-0.0340.0058.536-0.086-0.0860.0000.0000.0000.000
6D8PRO00.0480.02511.9670.0850.0850.0000.0000.0000.000
7D9GLN00.0590.02010.9920.0940.0940.0000.0000.0000.000
8D10ALA0-0.053-0.03113.0820.0930.0930.0000.0000.0000.000
9D11VAL00.0250.01016.680-0.037-0.0370.0000.0000.0000.000
10D12ILE0-0.008-0.00719.8390.0350.0350.0000.0000.0000.000
11D13LEU0-0.042-0.01122.312-0.019-0.0190.0000.0000.0000.000
12D14ARG10.9410.97726.0690.0940.0940.0000.0000.0000.000
13D15GLU-1-0.906-0.96128.9120.0230.0230.0000.0000.0000.000
14D16GLY00.0140.01129.576-0.003-0.0030.0000.0000.0000.000
15D17GLU-1-0.874-0.92127.605-0.084-0.0840.0000.0000.0000.000
16D18ASP-1-0.846-0.93425.549-0.020-0.0200.0000.0000.0000.000
17D19ALA0-0.025-0.01720.596-0.024-0.0240.0000.0000.0000.000
18D20ILE0-0.025-0.01618.6390.0270.0270.0000.0000.0000.000
19D21ILE0-0.0180.00314.487-0.057-0.0570.0000.0000.0000.000
20D22ASN0-0.027-0.00713.621-0.020-0.0200.0000.0000.0000.000
21D23CYS0-0.0020.0278.370-0.107-0.1070.0000.0000.0000.000
22D24SER0-0.003-0.0048.6340.1100.1100.0000.0000.0000.000
23D25SER0-0.013-0.0205.429-0.673-0.6730.0000.0000.0000.000
24D26SER0-0.0330.0005.1710.1160.1160.0000.0000.0000.000
25D27LYS10.9980.9944.8921.6071.6070.0000.0000.0000.000
26D28ALA00.0470.0217.9740.0630.0630.0000.0000.0000.000
27D29LEU0-0.028-0.0038.3120.2830.2830.0000.0000.0000.000
28D30TYR00.0150.0249.381-0.078-0.0780.0000.0000.0000.000
29D31SER0-0.005-0.03110.950-0.127-0.1270.0000.0000.0000.000
30D32VAL0-0.014-0.00910.0430.2680.2680.0000.0000.0000.000
31D33HIS00.0020.01610.738-0.276-0.2760.0000.0000.0000.000
32D34TRP00.031-0.00111.8230.0170.0170.0000.0000.0000.000
33D35TYR00.000-0.00412.398-0.053-0.0530.0000.0000.0000.000
34D36ARG10.9520.99115.007-0.332-0.3320.0000.0000.0000.000
35D37GLN0-0.027-0.02215.7200.0390.0390.0000.0000.0000.000
36D38LYS10.9470.98018.021-0.265-0.2650.0000.0000.0000.000
37D39HIS00.023-0.00520.4660.0260.0260.0000.0000.0000.000
38D40GLY00.0110.01620.9120.0010.0010.0000.0000.0000.000
39D41GLU-1-0.938-0.95221.3900.2960.2960.0000.0000.0000.000
40D42ALA00.0180.00619.4670.0380.0380.0000.0000.0000.000
41D43PRO0-0.034-0.02715.111-0.043-0.0430.0000.0000.0000.000
42D44ILE00.0260.00817.3660.0330.0330.0000.0000.0000.000
43D45PHE0-0.017-0.02116.312-0.005-0.0050.0000.0000.0000.000
44D46LEU0-0.061-0.01017.282-0.078-0.0780.0000.0000.0000.000
45D47MET0-0.0130.00217.784-0.050-0.0500.0000.0000.0000.000
46D48ILE0-0.008-0.00214.8500.0780.0780.0000.0000.0000.000
47D49LEU0-0.092-0.02715.207-0.099-0.0990.0000.0000.0000.000
48D50LEU00.0440.00614.6710.1290.1290.0000.0000.0000.000
49D51LYS10.9980.98516.402-0.350-0.3500.0000.0000.0000.000
50D52GLY0-0.075-0.01418.608-0.044-0.0440.0000.0000.0000.000
51D53GLY00.0870.03320.232-0.047-0.0470.0000.0000.0000.000
52D54GLU-1-0.994-0.98118.7660.2660.2660.0000.0000.0000.000
53D55GLN00.023-0.01919.458-0.023-0.0230.0000.0000.0000.000
54D56LYS10.8870.95119.835-0.336-0.3360.0000.0000.0000.000
55D57GLY00.0500.00322.245-0.032-0.0320.0000.0000.0000.000
56D58HIS0-0.0100.00322.4970.0410.0410.0000.0000.0000.000
57D59ASP-1-0.899-0.95824.3740.2010.2010.0000.0000.0000.000
58D60LYS10.9390.96326.880-0.100-0.1000.0000.0000.0000.000
59D61ILE0-0.0250.01720.466-0.018-0.0180.0000.0000.0000.000
60D62SER00.0280.01423.0150.0240.0240.0000.0000.0000.000
61D63ALA00.0210.00617.585-0.015-0.0150.0000.0000.0000.000
62D64SER00.0340.01517.9820.0160.0160.0000.0000.0000.000
63D65PHE00.0050.03112.847-0.008-0.0080.0000.0000.0000.000
64D66ASN00.012-0.00314.961-0.033-0.0330.0000.0000.0000.000
65D67GLU-1-0.834-0.93414.4690.2000.2000.0000.0000.0000.000
66D68LYS10.9390.96514.3380.0670.0670.0000.0000.0000.000
67D69LYS10.9170.95315.0360.3090.3090.0000.0000.0000.000
68D70GLN00.0040.0249.674-0.226-0.2260.0000.0000.0000.000
69D71GLN0-0.010-0.0089.944-0.230-0.2300.0000.0000.0000.000
70D72SER0-0.036-0.01411.9720.1760.1760.0000.0000.0000.000
71D73SER0-0.026-0.02813.398-0.131-0.1310.0000.0000.0000.000
72D74LEU00.0280.02015.8540.0690.0690.0000.0000.0000.000
73D75TYR0-0.017-0.03017.614-0.059-0.0590.0000.0000.0000.000
74D76LEU0-0.002-0.00218.8630.0340.0340.0000.0000.0000.000
75D77THR00.0150.01822.836-0.022-0.0220.0000.0000.0000.000
76D78ALA0-0.020-0.00926.4240.0170.0170.0000.0000.0000.000
77D79SER0-0.041-0.02525.1230.0190.0190.0000.0000.0000.000
78D80GLN00.0450.02527.0860.0000.0000.0000.0000.0000.000
79D81LEU00.0900.02126.9770.0050.0050.0000.0000.0000.000
80D82SER0-0.034-0.00427.1790.0020.0020.0000.0000.0000.000
81D83TYR0-0.002-0.00422.8990.0290.0290.0000.0000.0000.000
82D84SER00.0580.11621.6740.0060.0060.0000.0000.0000.000
83D85GLY00.0130.00920.0390.0190.0190.0000.0000.0000.000
84D86THR0-0.002-0.01413.695-0.072-0.0720.0000.0000.0000.000
85D87TYR0-0.076-0.09914.5480.0860.0860.0000.0000.0000.000
86D88PHE0-0.0220.0109.323-0.083-0.0830.0000.0000.0000.000
87D90GLY00.0450.0167.5260.2610.2610.0000.0000.0000.000
88D91LEU0-0.022-0.0453.817-0.956-0.7810.001-0.024-0.1520.000
89D92GLY0-0.0070.0086.9580.4230.4230.0000.0000.0000.000
90D93ASP-1-0.824-0.8847.2674.1194.1190.0000.0000.0000.000
91D94ALA0-0.030-0.0348.365-0.531-0.5310.0000.0000.0000.000
92D95GLY0-0.0100.00411.019-0.309-0.3090.0000.0000.0000.000
93D96ASN0-0.052-0.03111.445-0.102-0.1020.0000.0000.0000.000
94D97MET0-0.0140.0086.979-0.437-0.4370.0000.0000.0000.000
95D98LEU00.0260.0067.5410.9980.9980.0000.0000.0000.000
96D99THR0-0.0190.0002.194-0.9290.2722.074-1.198-2.0770.005
97D100PHE0-0.013-0.0255.044-0.539-0.499-0.001-0.005-0.0340.000
98D101GLY00.0180.0204.2551.2131.4090.000-0.033-0.1640.000
99D102GLY0-0.015-0.0165.2950.0110.070-0.001-0.001-0.0570.000
100D103GLY00.0270.0116.9260.2130.2130.0000.0000.0000.000
101D104THR0-0.057-0.04010.190-0.181-0.1810.0000.0000.0000.000
102D105ARG10.9480.99013.4930.2560.2560.0000.0000.0000.000
103D106LEU0-0.013-0.01816.701-0.046-0.0460.0000.0000.0000.000
104D107MET00.000-0.01419.5880.0330.0330.0000.0000.0000.000
105D108VAL0-0.006-0.00123.124-0.017-0.0170.0000.0000.0000.000
106D109LYS10.8870.95126.1770.0850.0850.0000.0000.0000.000
107D110PRO00.0600.01229.310-0.002-0.0020.0000.0000.0000.000
108D111HIS0-0.0350.00932.618-0.016-0.0160.0000.0000.0000.000
109D112ILE00.0070.01435.6510.0070.0070.0000.0000.0000.000
110D113GLN00.012-0.00438.716-0.007-0.0070.0000.0000.0000.000
111D114ASN0-0.028-0.02142.013-0.002-0.0020.0000.0000.0000.000
112D115PRO0-0.047-0.01841.1240.0030.0030.0000.0000.0000.000
113D116ASP-1-0.849-0.91643.203-0.006-0.0060.0000.0000.0000.000
114D117PRO0-0.045-0.01242.2630.0020.0020.0000.0000.0000.000
115D118ALA00.0790.05044.038-0.001-0.0010.0000.0000.0000.000
116D119VAL0-0.061-0.02743.9560.0010.0010.0000.0000.0000.000
117D120TYR00.0200.01045.6870.0010.0010.0000.0000.0000.000
118D121GLN0-0.020-0.03246.4070.0020.0020.0000.0000.0000.000
119D122LEU0-0.026-0.00644.5090.0020.0020.0000.0000.0000.000
120D123ARG10.9690.97548.090-0.021-0.0210.0000.0000.0000.000
121D124ASP-1-0.803-0.89448.9790.0220.0220.0000.0000.0000.000
122D125SER0-0.074-0.03848.7970.0010.0010.0000.0000.0000.000
123D126LYS10.9530.95850.507-0.044-0.0440.0000.0000.0000.000
124D127SER0-0.033-0.01650.192-0.002-0.0020.0000.0000.0000.000
125D128SER0-0.030-0.02747.6060.0030.0030.0000.0000.0000.000
126D129ASP-1-0.915-0.92848.8290.0160.0160.0000.0000.0000.000
127D130LYS10.8780.94947.629-0.002-0.0020.0000.0000.0000.000
128D131SER00.0170.01947.5740.0020.0020.0000.0000.0000.000
129D132VAL0-0.053-0.01541.803-0.002-0.0020.0000.0000.0000.000
130D133CYS0-0.026-0.01543.4420.0000.0000.0000.0000.0000.000
131D134LEU00.0030.00039.9360.0010.0010.0000.0000.0000.000
132D135PHE00.0150.02138.714-0.001-0.0010.0000.0000.0000.000
133D136THR0-0.016-0.03639.6570.0030.0030.0000.0000.0000.000
134D137ASP-1-0.818-0.91240.5710.0060.0060.0000.0000.0000.000
135D138PHE0-0.0210.00934.981-0.003-0.0030.0000.0000.0000.000
136D139ASP-1-0.817-0.93837.328-0.037-0.0370.0000.0000.0000.000
137D140SER0-0.024-0.03632.047-0.003-0.0030.0000.0000.0000.000
138D141GLN0-0.099-0.04232.291-0.008-0.0080.0000.0000.0000.000
139D142THR0-0.039-0.01233.545-0.007-0.0070.0000.0000.0000.000
140D143ASN0-0.028-0.02430.5480.0060.0060.0000.0000.0000.000
141D144VAL00.0420.01032.897-0.001-0.0010.0000.0000.0000.000
142D145SER0-0.033-0.02032.521-0.009-0.0090.0000.0000.0000.000
143D146GLN00.006-0.00229.5560.0080.0080.0000.0000.0000.000
144D147SER00.0330.00734.054-0.006-0.0060.0000.0000.0000.000
145D148LYS10.8910.93933.5820.0870.0870.0000.0000.0000.000
146D149ASP-1-0.899-0.92837.774-0.038-0.0380.0000.0000.0000.000
147D150SER0-0.001-0.01637.5810.0020.0020.0000.0000.0000.000
148D151ASP-1-0.838-0.90138.798-0.022-0.0220.0000.0000.0000.000
149D152VAL0-0.0300.00240.4080.0060.0060.0000.0000.0000.000
150D153TYR0-0.022-0.00536.600-0.004-0.0040.0000.0000.0000.000
151D154ILE00.002-0.01435.5870.0040.0040.0000.0000.0000.000
152D155THR0-0.097-0.04433.050-0.002-0.0020.0000.0000.0000.000
153D156ASP-1-0.884-0.95128.177-0.041-0.0410.0000.0000.0000.000
154D157LYS10.9200.96928.8360.0550.0550.0000.0000.0000.000
155D158CYS0-0.045-0.02830.4340.0070.0070.0000.0000.0000.000
156D159VAL0-0.012-0.01030.953-0.004-0.0040.0000.0000.0000.000
157D160LEU0-0.0060.01532.9730.0120.0120.0000.0000.0000.000
158D161ASP-1-0.907-0.98234.3650.0610.0610.0000.0000.0000.000
159D162MET00.0320.02036.5160.0060.0060.0000.0000.0000.000
160D163ARG10.9340.98733.871-0.073-0.0730.0000.0000.0000.000
161D164SER0-0.025-0.03440.315-0.002-0.0020.0000.0000.0000.000
162D165MET0-0.051-0.03643.200-0.004-0.0040.0000.0000.0000.000
163D166ASP-1-0.994-0.98339.9220.0390.0390.0000.0000.0000.000
164D167PHE0-0.0050.02140.846-0.003-0.0030.0000.0000.0000.000
165D168LYS10.9130.95234.351-0.035-0.0350.0000.0000.0000.000
166D169SER00.0490.02637.292-0.004-0.0040.0000.0000.0000.000
167D170ASN0-0.052-0.01833.6230.0070.0070.0000.0000.0000.000
168D171SER0-0.003-0.01035.3710.0020.0020.0000.0000.0000.000
169D172ALA00.0490.02835.1560.0000.0000.0000.0000.0000.000
170D173VAL00.0010.00336.4460.0000.0000.0000.0000.0000.000
171D174ALA00.0230.01637.462-0.004-0.0040.0000.0000.0000.000
172D175TRP00.0170.00736.0150.0030.0030.0000.0000.0000.000
173D176SER00.0370.00141.500-0.003-0.0030.0000.0000.0000.000
174D177ASN00.0180.01444.0340.0010.0010.0000.0000.0000.000
175D178LYS10.8740.94046.3590.0240.0240.0000.0000.0000.000
176D179SER0-0.042-0.04348.2540.0010.0010.0000.0000.0000.000
177D180ASP-1-0.944-0.96150.652-0.020-0.0200.0000.0000.0000.000
178D181PHE00.0440.01243.713-0.002-0.0020.0000.0000.0000.000
179D182ALA00.0000.00248.6550.0030.0030.0000.0000.0000.000
180D183CYS00.013-0.00847.349-0.001-0.0010.0000.0000.0000.000
181D184ALA00.0100.02147.090-0.001-0.0010.0000.0000.0000.000
182D185ASN0-0.035-0.02146.378-0.004-0.0040.0000.0000.0000.000
183D186ALA00.0100.02143.246-0.003-0.0030.0000.0000.0000.000
184D187PHE00.035-0.00138.693-0.002-0.0020.0000.0000.0000.000
185D188ASN0-0.036-0.02540.702-0.008-0.0080.0000.0000.0000.000
186D189ASN0-0.011-0.01037.527-0.002-0.0020.0000.0000.0000.000
187D190SER0-0.0050.01836.672-0.007-0.0070.0000.0000.0000.000
188D191ILE0-0.046-0.01434.6030.0010.0010.0000.0000.0000.000
189D192ILE0-0.028-0.00438.4600.0020.0020.0000.0000.0000.000
190D193PRO0-0.022-0.01540.946-0.003-0.0030.0000.0000.0000.000
191D194GLU-1-0.924-0.97143.238-0.041-0.0410.0000.0000.0000.000
192D195ASP-1-0.951-0.97845.849-0.020-0.0200.0000.0000.0000.000
193D196THR0-0.039-0.00745.0040.0040.0040.0000.0000.0000.000
194D197PHE00.0240.01546.7170.0000.0000.0000.0000.0000.000
195D198PHE0-0.030-0.04445.6210.0010.0010.0000.0000.0000.000
196D199PRO00.0060.01249.9880.0000.0000.0000.0000.0000.000
197D200SER0-0.029-0.00853.206-0.001-0.0010.0000.0000.0000.000