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: 528ZZ

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1933306.470895
FMO2-HF: Nuclear repulsion 1855101.175994
FMO2-HF: Total energy -78205.294901
FMO2-MP2: Total energy -78428.559356


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.
-9.919-6.2072.095-2.027-3.782-0.008
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 : 0.029 / q_NPA : 0.011
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].
3D5VAL00.0010.0093.908-1.566-0.185-0.010-0.640-0.7310.003
4D6GLN0-0.004-0.0116.2980.5820.5820.0000.0000.0000.000
5D7SER0-0.047-0.0158.5240.0840.0840.0000.0000.0000.000
6D8PRO00.0670.03411.9870.0800.0800.0000.0000.0000.000
7D9GLN00.0570.02211.198-0.017-0.0170.0000.0000.0000.000
8D10ALA0-0.050-0.02513.181-0.012-0.0120.0000.0000.0000.000
9D11VAL00.0190.00316.6620.0160.0160.0000.0000.0000.000
10D12ILE0-0.024-0.01319.8880.0010.0010.0000.0000.0000.000
11D13LEU0-0.0270.00422.4830.0070.0070.0000.0000.0000.000
12D14ARG10.8030.87926.2820.1420.1420.0000.0000.0000.000
13D15GLU-1-0.805-0.90028.763-0.128-0.1280.0000.0000.0000.000
14D16GLY0-0.021-0.00730.0270.0090.0090.0000.0000.0000.000
15D17GLU-1-0.800-0.87627.704-0.147-0.1470.0000.0000.0000.000
16D18ASP-1-0.835-0.91025.663-0.118-0.1180.0000.0000.0000.000
17D19ALA0-0.017-0.01120.846-0.014-0.0140.0000.0000.0000.000
18D20ILE0-0.024-0.01718.5690.0150.0150.0000.0000.0000.000
19D21ILE0-0.0330.00514.005-0.032-0.0320.0000.0000.0000.000
20D22ASN0-0.055-0.03113.2790.0480.0480.0000.0000.0000.000
21D23CYS00.0120.0108.037-0.082-0.0820.0000.0000.0000.000
22D24SER0-0.0150.0058.1140.4010.4010.0000.0000.0000.000
23D25SER00.0400.0015.243-0.113-0.1130.0000.0000.0000.000
24D26SER0-0.018-0.0074.969-0.354-0.3540.0000.0000.0000.000
25D27LYS10.9320.9705.178-5.710-5.629-0.0010.000-0.0800.000
26D28ALA00.0630.0388.081-0.209-0.2090.0000.0000.0000.000
27D29LEU0-0.0220.0028.7940.5100.5100.0000.0000.0000.000
28D30TYR00.0090.0108.871-0.012-0.0120.0000.0000.0000.000
29D31SER0-0.001-0.01310.790-0.191-0.1910.0000.0000.0000.000
30D32VAL0-0.027-0.0159.2850.2490.2490.0000.0000.0000.000
31D33HIS0-0.008-0.00810.492-0.096-0.0960.0000.0000.0000.000
32D34TRP00.002-0.01811.004-0.237-0.2370.0000.0000.0000.000
33D35TYR00.0100.00311.4680.0720.0720.0000.0000.0000.000
34D36ARG10.8790.93914.4880.1560.1560.0000.0000.0000.000
35D37GLN0-0.037-0.02714.916-0.041-0.0410.0000.0000.0000.000
36D38LYS10.8900.94317.8850.2540.2540.0000.0000.0000.000
37D39HIS00.013-0.00420.108-0.047-0.0470.0000.0000.0000.000
38D40GLY00.0070.01320.6410.0230.0230.0000.0000.0000.000
39D41GLU-1-0.903-0.95021.186-0.238-0.2380.0000.0000.0000.000
40D42ALA00.0270.01118.226-0.042-0.0420.0000.0000.0000.000
41D43PRO0-0.027-0.02513.6800.0130.0130.0000.0000.0000.000
42D44ILE00.0120.02516.0440.0360.0360.0000.0000.0000.000
43D45PHE0-0.003-0.01115.655-0.033-0.0330.0000.0000.0000.000
44D46LEU0-0.061-0.01116.7970.0150.0150.0000.0000.0000.000
45D47MET0-0.0150.00616.7600.0540.0540.0000.0000.0000.000
46D48ILE00.0090.01614.400-0.037-0.0370.0000.0000.0000.000
47D49LEU0-0.074-0.03014.776-0.003-0.0030.0000.0000.0000.000
48D50LEU00.0700.02014.3680.0880.0880.0000.0000.0000.000
49D51LYS10.8980.94216.238-0.448-0.4480.0000.0000.0000.000
50D52GLY0-0.0060.01819.012-0.037-0.0370.0000.0000.0000.000
51D53GLY00.0250.00721.026-0.047-0.0470.0000.0000.0000.000
52D54GLU-1-0.891-0.93118.0440.3350.3350.0000.0000.0000.000
53D55GLN00.0820.03819.412-0.014-0.0140.0000.0000.0000.000
54D56LYS10.8390.93619.624-0.131-0.1310.0000.0000.0000.000
55D57GLY00.051-0.00621.923-0.015-0.0150.0000.0000.0000.000
56D58HIS0-0.0070.00621.5890.0190.0190.0000.0000.0000.000
57D59ASP-1-0.819-0.91223.572-0.148-0.1480.0000.0000.0000.000
58D60LYS10.9280.96225.5010.0950.0950.0000.0000.0000.000
59D61ILE0-0.0140.02319.897-0.004-0.0040.0000.0000.0000.000
60D62SER00.0190.00222.1450.0230.0230.0000.0000.0000.000
61D63ALA00.0100.00117.183-0.037-0.0370.0000.0000.0000.000
62D64SER0-0.017-0.02417.7570.0280.0280.0000.0000.0000.000
63D65PHE0-0.0210.00612.471-0.050-0.0500.0000.0000.0000.000
64D66ASN00.011-0.00514.9950.0550.0550.0000.0000.0000.000
65D67GLU-1-0.830-0.93714.4230.7200.7200.0000.0000.0000.000
66D68LYS10.9440.97514.452-0.405-0.4050.0000.0000.0000.000
67D69LYS10.9030.94014.883-0.119-0.1190.0000.0000.0000.000
68D70GLN0-0.0220.0079.6640.2190.2190.0000.0000.0000.000
69D71GLN00.0330.0199.8430.0320.0320.0000.0000.0000.000
70D72SER0-0.045-0.02611.7540.0600.0600.0000.0000.0000.000
71D73SER0-0.002-0.02213.381-0.124-0.1240.0000.0000.0000.000
72D74LEU00.0190.02715.5310.0550.0550.0000.0000.0000.000
73D75TYR0-0.005-0.03017.391-0.037-0.0370.0000.0000.0000.000
74D76LEU0-0.022-0.01618.4640.0140.0140.0000.0000.0000.000
75D77THR00.0420.02122.741-0.002-0.0020.0000.0000.0000.000
76D78ALA0-0.024-0.02026.360-0.002-0.0020.0000.0000.0000.000
77D79SER0-0.029-0.01225.293-0.006-0.0060.0000.0000.0000.000
78D80GLN00.0460.01826.7860.0120.0120.0000.0000.0000.000
79D81LEU00.0840.04426.668-0.018-0.0180.0000.0000.0000.000
80D82SER0-0.006-0.00426.333-0.021-0.0210.0000.0000.0000.000
81D83TYR0-0.024-0.01322.746-0.013-0.0130.0000.0000.0000.000
82D84SER00.0410.04421.560-0.036-0.0360.0000.0000.0000.000
83D85GLY00.0300.01619.9600.0240.0240.0000.0000.0000.000
84D86THR0-0.025-0.01013.598-0.007-0.0070.0000.0000.0000.000
85D87TYR0-0.017-0.02514.3250.0540.0540.0000.0000.0000.000
86D88PHE0-0.0130.0028.732-0.103-0.1030.0000.0000.0000.000
87D90GLY00.0410.0096.184-0.539-0.5390.0000.0000.0000.000
88D91LEU0-0.021-0.0193.388-0.0290.3330.015-0.065-0.3130.000
89D92GLY00.0060.0086.3920.0140.0140.0000.0000.0000.000
90D93ASP-1-0.786-0.9007.0041.3311.3310.0000.0000.0000.000
91D94ALA0-0.045-0.0248.504-0.392-0.3920.0000.0000.0000.000
92D95GLY0-0.015-0.00111.283-0.187-0.1870.0000.0000.0000.000
93D96ASN0-0.056-0.02511.380-0.121-0.1210.0000.0000.0000.000
94D97MET00.0040.0146.587-0.317-0.3170.0000.0000.0000.000
95D98LEU0-0.039-0.0137.8000.1980.1980.0000.0000.0000.000
96D99THR0-0.0120.0052.164-1.071-0.4602.025-0.665-1.971-0.006
97D100PHE00.016-0.0134.363-0.571-0.433-0.001-0.038-0.1000.000
98D101GLY00.0210.0113.178-3.069-2.0150.068-0.615-0.507-0.005
99D102GLY0-0.023-0.0204.8110.6920.777-0.001-0.004-0.0800.000
100D103GLY00.0240.0156.5170.3900.3900.0000.0000.0000.000
101D104THR0-0.083-0.0509.829-0.005-0.0050.0000.0000.0000.000
102D105ARG10.9050.95713.2730.7070.7070.0000.0000.0000.000
103D106LEU00.0050.00716.5370.0220.0220.0000.0000.0000.000
104D107MET0-0.019-0.01719.5850.0070.0070.0000.0000.0000.000
105D108VAL0-0.0150.00423.1320.0090.0090.0000.0000.0000.000
106D109LYS10.9150.97426.1040.1980.1980.0000.0000.0000.000
107D110PRO00.0570.01829.2490.0040.0040.0000.0000.0000.000
108D111HIS0-0.058-0.02532.6200.0000.0000.0000.0000.0000.000
109D112ILE00.0070.00335.6000.0010.0010.0000.0000.0000.000
110D113GLN00.0070.00238.879-0.001-0.0010.0000.0000.0000.000
111D114ASN0-0.033-0.02642.1580.0040.0040.0000.0000.0000.000
112D115PRO0-0.0230.00940.857-0.001-0.0010.0000.0000.0000.000
113D116ASP-1-0.869-0.92842.931-0.076-0.0760.0000.0000.0000.000
114D117PRO0-0.054-0.02042.229-0.003-0.0030.0000.0000.0000.000
115D118ALA00.0490.04243.7980.0040.0040.0000.0000.0000.000
116D119VAL0-0.050-0.02743.825-0.006-0.0060.0000.0000.0000.000
117D120TYR00.003-0.00145.3160.0060.0060.0000.0000.0000.000
118D121GLN0-0.001-0.02446.138-0.002-0.0020.0000.0000.0000.000
119D122LEU0-0.034-0.01343.5370.0030.0030.0000.0000.0000.000
120D123ARG10.9110.94447.5580.0690.0690.0000.0000.0000.000
121D124ASP-1-0.773-0.85649.046-0.085-0.0850.0000.0000.0000.000
122D125SER0-0.044-0.02048.8210.0040.0040.0000.0000.0000.000
123D126LYS10.9660.95350.3000.0800.0800.0000.0000.0000.000
124D127SER0-0.034-0.01349.7440.0030.0030.0000.0000.0000.000
125D128SER0-0.035-0.01747.451-0.004-0.0040.0000.0000.0000.000
126D129ASP-1-0.883-0.92748.268-0.085-0.0850.0000.0000.0000.000
127D130LYS10.7710.87847.5660.0860.0860.0000.0000.0000.000
128D131SER0-0.013-0.01347.055-0.003-0.0030.0000.0000.0000.000
129D132VAL0-0.047-0.00441.434-0.002-0.0020.0000.0000.0000.000
130D133CYS0-0.036-0.02143.3180.0060.0060.0000.0000.0000.000
131D134LEU0-0.010-0.00840.070-0.006-0.0060.0000.0000.0000.000
132D135PHE00.0140.01238.3550.0050.0050.0000.0000.0000.000
133D136THR0-0.022-0.06939.621-0.010-0.0100.0000.0000.0000.000
134D137ASP-1-0.754-0.85240.093-0.096-0.0960.0000.0000.0000.000
135D138PHE00.0060.02834.8040.0020.0020.0000.0000.0000.000
136D139ASP-1-0.736-0.87536.840-0.123-0.1230.0000.0000.0000.000
137D140SER0-0.019-0.01432.258-0.005-0.0050.0000.0000.0000.000
138D141GLN0-0.057-0.04232.237-0.022-0.0220.0000.0000.0000.000
139D142THR0-0.045-0.01733.706-0.003-0.0030.0000.0000.0000.000
140D143ASN0-0.049-0.04530.195-0.020-0.0200.0000.0000.0000.000
141D144VAL00.0240.01532.8320.0080.0080.0000.0000.0000.000
142D145SER0-0.009-0.01032.632-0.014-0.0140.0000.0000.0000.000
143D146GLN00.0310.01528.9410.0140.0140.0000.0000.0000.000
144D147SER00.0280.01133.9700.0070.0070.0000.0000.0000.000
145D148LYS10.8040.88334.1880.1420.1420.0000.0000.0000.000
146D149ASP-1-0.835-0.90237.959-0.106-0.1060.0000.0000.0000.000
147D150SER00.003-0.00338.010-0.005-0.0050.0000.0000.0000.000
148D151ASP-1-0.825-0.88539.040-0.106-0.1060.0000.0000.0000.000
149D152VAL0-0.0050.02640.5220.0030.0030.0000.0000.0000.000
150D153TYR0-0.050-0.01836.497-0.007-0.0070.0000.0000.0000.000
151D154ILE00.012-0.01135.8310.0060.0060.0000.0000.0000.000
152D155THR0-0.059-0.02032.760-0.006-0.0060.0000.0000.0000.000
153D156ASP-1-0.800-0.89028.256-0.208-0.2080.0000.0000.0000.000
154D157LYS10.8320.90228.3090.2150.2150.0000.0000.0000.000
155D158CYS0-0.044-0.02030.400-0.017-0.0170.0000.0000.0000.000
156D159VAL0-0.014-0.00230.5930.0090.0090.0000.0000.0000.000
157D160LEU0-0.0050.00332.883-0.004-0.0040.0000.0000.0000.000
158D161ASP-1-0.810-0.91234.497-0.113-0.1130.0000.0000.0000.000
159D162MET00.0130.01236.4460.0000.0000.0000.0000.0000.000
160D163ARG10.7880.87234.0250.1120.1120.0000.0000.0000.000
161D164SER0-0.042-0.02339.9420.0030.0030.0000.0000.0000.000
162D165MET0-0.036-0.02542.8740.0040.0040.0000.0000.0000.000
163D166ASP-1-0.917-0.95138.966-0.090-0.0900.0000.0000.0000.000
164D167PHE00.0120.02640.123-0.002-0.0020.0000.0000.0000.000
165D168LYS10.8440.91134.5690.1060.1060.0000.0000.0000.000
166D169SER0-0.031-0.00937.0640.0020.0020.0000.0000.0000.000
167D170ASN0-0.051-0.03333.627-0.017-0.0170.0000.0000.0000.000
168D171SER00.0080.00735.2900.0080.0080.0000.0000.0000.000
169D172ALA00.0270.00135.086-0.011-0.0110.0000.0000.0000.000
170D173VAL00.0080.00836.4200.0090.0090.0000.0000.0000.000
171D174ALA00.0170.01037.475-0.007-0.0070.0000.0000.0000.000
172D175TRP0-0.022-0.02135.6790.0050.0050.0000.0000.0000.000
173D176SER00.041-0.00941.497-0.003-0.0030.0000.0000.0000.000
174D177ASN00.0080.00543.8760.0000.0000.0000.0000.0000.000
175D178LYS10.7890.89945.0570.1040.1040.0000.0000.0000.000
176D179SER00.020-0.00747.9790.0000.0000.0000.0000.0000.000
177D180ASP-1-0.921-0.94950.357-0.077-0.0770.0000.0000.0000.000
178D181PHE00.0280.01143.700-0.003-0.0030.0000.0000.0000.000
179D182ALA00.011-0.00248.3650.0030.0030.0000.0000.0000.000
180D183CYS00.0360.02147.235-0.003-0.0030.0000.0000.0000.000
181D184ALA00.0370.03546.8860.0020.0020.0000.0000.0000.000
182D185ASN0-0.026-0.01645.944-0.006-0.0060.0000.0000.0000.000
183D186ALA00.0240.01843.193-0.003-0.0030.0000.0000.0000.000
184D187PHE00.0520.01739.001-0.005-0.0050.0000.0000.0000.000
185D188ASN0-0.030-0.01940.831-0.004-0.0040.0000.0000.0000.000
186D189ASN0-0.037-0.01937.895-0.005-0.0050.0000.0000.0000.000
187D190SER00.0100.02436.999-0.010-0.0100.0000.0000.0000.000
188D191ILE0-0.053-0.01434.4020.0050.0050.0000.0000.0000.000
189D192ILE0-0.016-0.00438.374-0.002-0.0020.0000.0000.0000.000
190D193PRO0-0.014-0.01740.5510.0020.0020.0000.0000.0000.000
191D194GLU-1-0.893-0.95043.170-0.071-0.0710.0000.0000.0000.000
192D195ASP-1-0.961-0.97345.832-0.071-0.0710.0000.0000.0000.000
193D196THR0-0.050-0.01745.257-0.003-0.0030.0000.0000.0000.000
194D197PHE00.0230.00746.8720.0040.0040.0000.0000.0000.000
195D198PHE0-0.016-0.03245.285-0.004-0.0040.0000.0000.0000.000
196D199PRO00.0100.00949.9200.0030.0030.0000.0000.0000.000
197D200SER0-0.034-0.00652.8600.0000.0000.0000.0000.0000.000