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

tag_button

FMODB ID: 498RN

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1926689.500396
FMO2-HF: Nuclear repulsion 1848484.948384
FMO2-HF: Total energy -78204.552012
FMO2-MP2: Total energy -78427.738011


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.
-4.489-1.7152.228-1.74-3.259-0.003
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 : 0.035 / q_NPA : 0.020
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].
3D5VAL0-0.012-0.0103.943-1.738-0.315-0.010-0.761-0.6510.003
4D6GLN0-0.038-0.0506.3130.6450.6450.0000.0000.0000.000
5D7SER0-0.0220.0078.6050.0650.0650.0000.0000.0000.000
6D8PRO00.0430.02212.0220.0910.0910.0000.0000.0000.000
7D9GLN00.0610.01811.0270.0230.0230.0000.0000.0000.000
8D10ALA0-0.055-0.03413.1270.0290.0290.0000.0000.0000.000
9D11VAL00.0200.00816.7320.0030.0030.0000.0000.0000.000
10D12ILE0-0.012-0.00719.8980.0130.0130.0000.0000.0000.000
11D13LEU0-0.031-0.00722.310-0.004-0.0040.0000.0000.0000.000
12D14ARG10.8630.92626.1360.1410.1410.0000.0000.0000.000
13D15GLU-1-0.845-0.91928.988-0.082-0.0820.0000.0000.0000.000
14D16GLY00.0160.01429.6410.0070.0070.0000.0000.0000.000
15D17GLU-1-0.854-0.91427.599-0.136-0.1360.0000.0000.0000.000
16D18ASP-1-0.846-0.92325.610-0.093-0.0930.0000.0000.0000.000
17D19ALA0-0.031-0.02420.768-0.019-0.0190.0000.0000.0000.000
18D20ILE0-0.020-0.01018.6380.0180.0180.0000.0000.0000.000
19D21ILE0-0.0230.00014.523-0.044-0.0440.0000.0000.0000.000
20D22ASN0-0.050-0.01713.6370.0050.0050.0000.0000.0000.000
21D23CYS00.0140.0258.191-0.036-0.0360.0000.0000.0000.000
22D24SER0-0.015-0.0018.6340.3000.3000.0000.0000.0000.000
23D25SER00.002-0.0185.533-0.378-0.3780.0000.0000.0000.000
24D26SER0-0.034-0.0015.1570.0580.0580.0000.0000.0000.000
25D27LYS10.9940.9905.373-2.859-2.8590.0000.0000.0000.000
26D28ALA00.0620.0357.960-0.153-0.1530.0000.0000.0000.000
27D29LEU0-0.036-0.0088.5510.5100.5100.0000.0000.0000.000
28D30TYR00.0090.0178.928-0.077-0.0770.0000.0000.0000.000
29D31SER0-0.009-0.04110.784-0.179-0.1790.0000.0000.0000.000
30D32VAL0-0.026-0.0129.8280.2440.2440.0000.0000.0000.000
31D33HIS0-0.007-0.01110.472-0.196-0.1960.0000.0000.0000.000
32D34TRP00.0300.00011.311-0.197-0.1970.0000.0000.0000.000
33D35TYR00.0080.00711.9020.0470.0470.0000.0000.0000.000
34D36ARG10.9550.98914.4960.0000.0000.0000.0000.0000.000
35D37GLN0-0.027-0.02415.054-0.012-0.0120.0000.0000.0000.000
36D38LYS10.8880.94717.6480.0880.0880.0000.0000.0000.000
37D39HIS00.015-0.00920.249-0.020-0.0200.0000.0000.0000.000
38D40GLY00.0110.01520.6870.0160.0160.0000.0000.0000.000
39D41GLU-1-0.924-0.94821.078-0.059-0.0590.0000.0000.0000.000
40D42ALA00.0070.00418.765-0.020-0.0200.0000.0000.0000.000
41D43PRO0-0.034-0.02614.239-0.004-0.0040.0000.0000.0000.000
42D44ILE00.0210.01416.6220.0460.0460.0000.0000.0000.000
43D45PHE0-0.017-0.01916.160-0.030-0.0300.0000.0000.0000.000
44D46LEU0-0.061-0.01116.904-0.014-0.0140.0000.0000.0000.000
45D47MET0-0.0250.01317.2430.0240.0240.0000.0000.0000.000
46D48ILE00.0000.00314.5920.0000.0000.0000.0000.0000.000
47D49LEU0-0.090-0.03414.905-0.029-0.0290.0000.0000.0000.000
48D50LEU00.0590.01514.4800.1210.1210.0000.0000.0000.000
49D51LYS10.9320.96316.368-0.480-0.4800.0000.0000.0000.000
50D52GLY0-0.044-0.01018.812-0.050-0.0500.0000.0000.0000.000
51D53GLY00.0650.02320.244-0.047-0.0470.0000.0000.0000.000
52D54GLU-1-0.959-0.95318.7480.3360.3360.0000.0000.0000.000
53D55GLN00.0710.02719.577-0.018-0.0180.0000.0000.0000.000
54D56LYS10.8950.96119.859-0.228-0.2280.0000.0000.0000.000
55D57GLY00.065-0.00422.004-0.026-0.0260.0000.0000.0000.000
56D58HIS0-0.031-0.01121.8480.0280.0280.0000.0000.0000.000
57D59ASP-1-0.872-0.94223.727-0.014-0.0140.0000.0000.0000.000
58D60LYS10.9390.96626.4080.0260.0260.0000.0000.0000.000
59D61ILE0-0.0240.01320.131-0.010-0.0100.0000.0000.0000.000
60D62SER00.0380.01822.5600.0240.0240.0000.0000.0000.000
61D63ALA00.0090.00217.394-0.033-0.0330.0000.0000.0000.000
62D64SER0-0.009-0.03018.0130.0210.0210.0000.0000.0000.000
63D65PHE0-0.0100.00912.896-0.040-0.0400.0000.0000.0000.000
64D66ASN00.0050.00215.2090.0300.0300.0000.0000.0000.000
65D67GLU-1-0.837-0.93514.6820.6330.6330.0000.0000.0000.000
66D68LYS10.9470.97014.490-0.275-0.2750.0000.0000.0000.000
67D69LYS10.8990.93715.1500.0410.0410.0000.0000.0000.000
68D70GLN0-0.0100.0189.8610.1120.1120.0000.0000.0000.000
69D71GLN00.0260.01210.098-0.084-0.0840.0000.0000.0000.000
70D72SER0-0.039-0.01712.0570.1100.1100.0000.0000.0000.000
71D73SER00.009-0.01413.448-0.159-0.1590.0000.0000.0000.000
72D74LEU00.0080.01715.6350.0730.0730.0000.0000.0000.000
73D75TYR0-0.015-0.03617.405-0.054-0.0540.0000.0000.0000.000
74D76LEU0-0.016-0.01318.6680.0210.0210.0000.0000.0000.000
75D77THR00.0370.02822.789-0.008-0.0080.0000.0000.0000.000
76D78ALA0-0.029-0.02326.4180.0070.0070.0000.0000.0000.000
77D79SER0-0.049-0.02825.2310.0030.0030.0000.0000.0000.000
78D80GLN00.0490.02527.0790.0090.0090.0000.0000.0000.000
79D81LEU00.0900.03226.987-0.012-0.0120.0000.0000.0000.000
80D82SER0-0.030-0.00827.060-0.012-0.0120.0000.0000.0000.000
81D83TYR0-0.031-0.01322.8970.0010.0010.0000.0000.0000.000
82D84SER00.0960.08521.622-0.027-0.0270.0000.0000.0000.000
83D85GLY00.0240.01620.1190.0290.0290.0000.0000.0000.000
84D86THR0-0.004-0.01313.661-0.026-0.0260.0000.0000.0000.000
85D87TYR0-0.029-0.02314.3880.0610.0610.0000.0000.0000.000
86D88PHE0-0.0150.0088.897-0.111-0.1110.0000.0000.0000.000
87D90GLY00.0290.0086.883-0.462-0.4620.0000.0000.0000.000
88D91LEU0-0.018-0.0413.611-0.286-0.0140.006-0.045-0.2320.000
89D92GLY00.0080.0116.6950.1970.1970.0000.0000.0000.000
90D93ASP-1-0.767-0.8716.7732.4922.4920.0000.0000.0000.000
91D94ALA0-0.052-0.0338.126-0.539-0.5390.0000.0000.0000.000
92D95GLY0-0.0100.00110.970-0.293-0.2930.0000.0000.0000.000
93D96ASN0-0.063-0.01411.252-0.215-0.2150.0000.0000.0000.000
94D97MET0-0.0240.0067.260-0.402-0.4020.0000.0000.0000.000
95D98LEU00.0100.0087.7560.6840.6840.0000.0000.0000.000
96D99THR0-0.006-0.0052.276-0.525-0.0192.228-0.706-2.028-0.005
97D100PHE0-0.012-0.0244.726-0.620-0.522-0.001-0.013-0.0840.000
98D101GLY00.0180.0213.660-1.682-1.2750.006-0.213-0.199-0.001
99D102GLY0-0.015-0.0185.2130.5140.582-0.001-0.002-0.0650.000
100D103GLY00.0240.0196.9820.3380.3380.0000.0000.0000.000
101D104THR0-0.059-0.04010.265-0.065-0.0650.0000.0000.0000.000
102D105ARG10.9330.98513.5660.5950.5950.0000.0000.0000.000
103D106LEU0-0.023-0.02016.768-0.005-0.0050.0000.0000.0000.000
104D107MET0-0.009-0.01919.6620.0240.0240.0000.0000.0000.000
105D108VAL00.0000.00523.1930.0000.0000.0000.0000.0000.000
106D109LYS10.8940.96326.2530.1690.1690.0000.0000.0000.000
107D110PRO00.0610.02029.3800.0030.0030.0000.0000.0000.000
108D111HIS0-0.050-0.01632.692-0.006-0.0060.0000.0000.0000.000
109D112ILE00.0100.01235.7240.0040.0040.0000.0000.0000.000
110D113GLN00.0180.01138.787-0.003-0.0030.0000.0000.0000.000
111D114ASN0-0.036-0.02842.0870.0010.0010.0000.0000.0000.000
112D115PRO0-0.048-0.01341.2330.0000.0000.0000.0000.0000.000
113D116ASP-1-0.845-0.91843.267-0.055-0.0550.0000.0000.0000.000
114D117PRO0-0.058-0.02042.329-0.001-0.0010.0000.0000.0000.000
115D118ALA00.0730.04744.0910.0030.0030.0000.0000.0000.000
116D119VAL0-0.056-0.02344.013-0.003-0.0030.0000.0000.0000.000
117D120TYR00.0100.00745.5630.0050.0050.0000.0000.0000.000
118D121GLN0-0.020-0.03746.454-0.001-0.0010.0000.0000.0000.000
119D122LEU0-0.029-0.00744.2460.0030.0030.0000.0000.0000.000
120D123ARG10.9690.97248.1410.0390.0390.0000.0000.0000.000
121D124ASP-1-0.771-0.85649.009-0.052-0.0520.0000.0000.0000.000
122D125SER0-0.076-0.03448.9770.0030.0030.0000.0000.0000.000
123D126LYS10.9570.95050.6790.0390.0390.0000.0000.0000.000
124D127SER0-0.022-0.00450.2580.0010.0010.0000.0000.0000.000
125D128SER0-0.039-0.03147.888-0.002-0.0020.0000.0000.0000.000
126D129ASP-1-0.913-0.93148.760-0.052-0.0520.0000.0000.0000.000
127D130LYS10.8150.90847.7460.0590.0590.0000.0000.0000.000
128D131SER0-0.013-0.01547.609-0.001-0.0010.0000.0000.0000.000
129D132VAL0-0.052-0.02141.838-0.003-0.0030.0000.0000.0000.000
130D133CYS0-0.045-0.02443.4700.0040.0040.0000.0000.0000.000
131D134LEU0-0.005-0.00640.085-0.004-0.0040.0000.0000.0000.000
132D135PHE00.0160.01338.7020.0030.0030.0000.0000.0000.000
133D136THR0-0.019-0.05939.710-0.006-0.0060.0000.0000.0000.000
134D137ASP-1-0.789-0.88340.509-0.064-0.0640.0000.0000.0000.000
135D138PHE00.0020.02234.8620.0000.0000.0000.0000.0000.000
136D139ASP-1-0.748-0.88436.944-0.100-0.1000.0000.0000.0000.000
137D140SER0-0.020-0.03232.159-0.005-0.0050.0000.0000.0000.000
138D141GLN0-0.065-0.03732.345-0.021-0.0210.0000.0000.0000.000
139D142THR0-0.038-0.01333.590-0.006-0.0060.0000.0000.0000.000
140D143ASN0-0.023-0.02130.321-0.010-0.0100.0000.0000.0000.000
141D144VAL00.0360.01432.9690.0050.0050.0000.0000.0000.000
142D145SER0-0.039-0.02232.553-0.011-0.0110.0000.0000.0000.000
143D146GLN00.0360.01228.9440.0110.0110.0000.0000.0000.000
144D147SER00.0290.00134.0740.0020.0020.0000.0000.0000.000
145D148LYS10.8180.89234.2900.1270.1270.0000.0000.0000.000
146D149ASP-1-0.847-0.89937.779-0.088-0.0880.0000.0000.0000.000
147D150SER00.012-0.01137.761-0.003-0.0030.0000.0000.0000.000
148D151ASP-1-0.849-0.89038.802-0.080-0.0800.0000.0000.0000.000
149D152VAL0-0.0020.01140.4280.0050.0050.0000.0000.0000.000
150D153TYR0-0.026-0.00436.627-0.005-0.0050.0000.0000.0000.000
151D154ILE0-0.001-0.01335.7930.0050.0050.0000.0000.0000.000
152D155THR0-0.028-0.00933.093-0.006-0.0060.0000.0000.0000.000
153D156ASP-1-0.841-0.90528.256-0.163-0.1630.0000.0000.0000.000
154D157LYS10.8230.89528.2800.1720.1720.0000.0000.0000.000
155D158CYS0-0.032-0.02130.488-0.010-0.0100.0000.0000.0000.000
156D159VAL0-0.004-0.00131.0860.0050.0050.0000.0000.0000.000
157D160LEU0-0.0240.00433.0460.0010.0010.0000.0000.0000.000
158D161ASP-1-0.831-0.92934.449-0.060-0.0600.0000.0000.0000.000
159D162MET00.0230.02236.5110.0030.0030.0000.0000.0000.000
160D163ARG10.8380.92234.1340.0540.0540.0000.0000.0000.000
161D164SER0-0.036-0.03340.1610.0030.0030.0000.0000.0000.000
162D165MET0-0.047-0.03843.0890.0010.0010.0000.0000.0000.000
163D166ASP-1-0.971-0.97339.432-0.045-0.0450.0000.0000.0000.000
164D167PHE0-0.0130.01340.903-0.002-0.0020.0000.0000.0000.000
165D168LYS10.8790.92234.6490.0670.0670.0000.0000.0000.000
166D169SER00.0300.02137.3630.0000.0000.0000.0000.0000.000
167D170ASN0-0.071-0.03633.764-0.008-0.0080.0000.0000.0000.000
168D171SER00.002-0.00135.4300.0060.0060.0000.0000.0000.000
169D172ALA00.0290.00835.210-0.008-0.0080.0000.0000.0000.000
170D173VAL00.0180.01036.4900.0060.0060.0000.0000.0000.000
171D174ALA00.0040.00837.501-0.006-0.0060.0000.0000.0000.000
172D175TRP00.007-0.00135.9810.0040.0040.0000.0000.0000.000
173D176SER00.032-0.00341.526-0.003-0.0030.0000.0000.0000.000
174D177ASN00.0120.01144.0580.0010.0010.0000.0000.0000.000
175D178LYS10.8080.90445.2140.0810.0810.0000.0000.0000.000
176D179SER00.015-0.00948.2710.0000.0000.0000.0000.0000.000
177D180ASP-1-0.926-0.95650.712-0.059-0.0590.0000.0000.0000.000
178D181PHE00.019-0.00143.758-0.003-0.0030.0000.0000.0000.000
179D182ALA0-0.001-0.00248.6760.0030.0030.0000.0000.0000.000
180D183CYS00.0420.02547.383-0.002-0.0020.0000.0000.0000.000
181D184ALA00.0120.01847.1200.0010.0010.0000.0000.0000.000
182D185ASN0-0.026-0.01646.409-0.005-0.0050.0000.0000.0000.000
183D186ALA00.0100.02243.331-0.003-0.0030.0000.0000.0000.000
184D187PHE00.031-0.00338.905-0.004-0.0040.0000.0000.0000.000
185D188ASN0-0.033-0.02440.731-0.006-0.0060.0000.0000.0000.000
186D189ASN00.0190.01137.647-0.006-0.0060.0000.0000.0000.000
187D190SER0-0.0040.02036.895-0.007-0.0070.0000.0000.0000.000
188D191ILE0-0.038-0.01434.5710.0040.0040.0000.0000.0000.000
189D192ILE0-0.019-0.00138.490-0.001-0.0010.0000.0000.0000.000
190D193PRO0-0.020-0.01740.8540.0010.0010.0000.0000.0000.000
191D194GLU-1-0.921-0.96443.279-0.065-0.0650.0000.0000.0000.000
192D195ASP-1-0.945-0.97745.971-0.057-0.0570.0000.0000.0000.000
193D196THR0-0.049-0.01345.1220.0000.0000.0000.0000.0000.000
194D197PHE00.0230.01646.7630.0030.0030.0000.0000.0000.000
195D198PHE0-0.032-0.04345.591-0.002-0.0020.0000.0000.0000.000
196D199PRO00.0080.01050.1630.0020.0020.0000.0000.0000.000
197D200SER0-0.027-0.00453.247-0.001-0.0010.0000.0000.0000.000