Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7242K

Calculation Name: 1PKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PKQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q63345

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2203059.398066
FMO2-HF: Nuclear repulsion 2119527.126242
FMO2-HF: Total energy -83532.271824
FMO2-MP2: Total energy -83776.627585


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(A:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
5.85712.2052.466-3.537-5.2750.028
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.914 / q_NPA : -0.969
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].
3A3GLU-1-0.834-0.8673.86437.17739.093-0.015-0.872-1.0280.003
4A4LEU0-0.008-0.0235.774-3.216-3.2160.0000.0000.0000.000
5A5THR00.000-0.0059.417-0.955-0.9550.0000.0000.0000.000
6A6GLN0-0.003-0.01412.2640.0860.0860.0000.0000.0000.000
7A7SER0-0.0170.00915.269-0.403-0.4030.0000.0000.0000.000
8A8PRO00.020-0.00318.708-0.227-0.2270.0000.0000.0000.000
9A9SER00.0730.04918.9140.3690.3690.0000.0000.0000.000
10A10SER0-0.016-0.01219.8710.1890.1890.0000.0000.0000.000
11A11LEU0-0.055-0.02123.399-0.198-0.1980.0000.0000.0000.000
12A12ALA00.0400.02326.5510.0200.0200.0000.0000.0000.000
13A13VAL0-0.005-0.00329.605-0.152-0.1520.0000.0000.0000.000
14A14SER0-0.033-0.03632.286-0.058-0.0580.0000.0000.0000.000
15A15ALA0-0.0030.00134.9360.1660.1660.0000.0000.0000.000
16A16GLY00.0250.01535.936-0.260-0.2600.0000.0000.0000.000
17A17GLU-1-0.781-0.84133.7788.7808.7800.0000.0000.0000.000
18A18LYS10.9580.99429.608-9.882-9.8820.0000.0000.0000.000
19A19VAL0-0.0050.00326.3840.0070.0070.0000.0000.0000.000
20A20THR0-0.039-0.02624.123-0.161-0.1610.0000.0000.0000.000
21A21MET0-0.0270.00820.759-0.029-0.0290.0000.0000.0000.000
22A22SER00.0070.00318.1510.3610.3610.0000.0000.0000.000
23A23CYS0-0.031-0.01613.4510.3580.3580.0000.0000.0000.000
24A24LYS10.8420.93013.584-16.315-16.3150.0000.0000.0000.000
25A25SER00.016-0.0089.1401.8761.8760.0000.0000.0000.000
26A26SER0-0.018-0.0365.657-1.482-1.4820.0000.0000.0000.000
27A27GLN0-0.004-0.0033.425-5.521-4.7650.020-0.371-0.4040.001
28A28SER0-0.0100.0028.548-1.151-1.1510.0000.0000.0000.000
29A29LEU00.0370.0228.2130.9880.9880.0000.0000.0000.000
30A30LEU0-0.068-0.02211.396-1.189-1.1890.0000.0000.0000.000
31A30ASN00.0500.03014.0230.3050.3050.0000.0000.0000.000
32A30SER00.040-0.01015.651-0.687-0.6870.0000.0000.0000.000
33A30GLY00.0150.01818.367-0.811-0.8110.0000.0000.0000.000
34A30ASN0-0.059-0.02419.230-0.029-0.0290.0000.0000.0000.000
35A30GLN0-0.023-0.00520.365-0.502-0.5020.0000.0000.0000.000
36A30LYS10.9811.00418.760-13.805-13.8050.0000.0000.0000.000
37A31ASN00.0210.00914.229-0.163-0.1630.0000.0000.0000.000
38A32TYR0-0.030-0.02713.107-0.919-0.9190.0000.0000.0000.000
39A33LEU0-0.0080.01011.8131.7341.7340.0000.0000.0000.000
40A34ALA00.0110.00713.686-1.575-1.5750.0000.0000.0000.000
41A35TRP00.006-0.01815.1000.9180.9180.0000.0000.0000.000
42A36TYR0-0.019-0.02314.968-1.345-1.3450.0000.0000.0000.000
43A37GLN00.0150.00819.478-0.130-0.1300.0000.0000.0000.000
44A38GLN0-0.002-0.00519.8890.4710.4710.0000.0000.0000.000
45A39LYS10.8230.90022.784-10.989-10.9890.0000.0000.0000.000
46A40PRO00.049-0.00325.3700.3220.3220.0000.0000.0000.000
47A41GLY00.0160.01525.776-0.381-0.3810.0000.0000.0000.000
48A42LEU0-0.046-0.00125.375-0.175-0.1750.0000.0000.0000.000
49A43PRO00.0370.00321.4570.4350.4350.0000.0000.0000.000
50A44PRO00.0020.00317.566-0.568-0.5680.0000.0000.0000.000
51A45LYS10.9010.97020.633-11.579-11.5790.0000.0000.0000.000
52A46LEU00.0220.01318.3620.2260.2260.0000.0000.0000.000
53A47LEU0-0.062-0.03020.880-0.832-0.8320.0000.0000.0000.000
54A48ILE0-0.024-0.01719.526-0.689-0.6890.0000.0000.0000.000
55A49TYR00.0860.03417.7830.9310.9310.0000.0000.0000.000
56A50GLY0-0.0010.00017.171-0.714-0.7140.0000.0000.0000.000
57A51ALA00.0020.00916.960-0.635-0.6350.0000.0000.0000.000
58A52SER0-0.033-0.02218.333-0.314-0.3140.0000.0000.0000.000
59A53THR0-0.069-0.04021.842-0.594-0.5940.0000.0000.0000.000
60A54ARG10.8750.95422.616-10.044-10.0440.0000.0000.0000.000
61A55GLU-1-0.802-0.86623.34412.45112.4510.0000.0000.0000.000
62A56SER0-0.021-0.06025.257-0.573-0.5730.0000.0000.0000.000
63A57GLY0-0.043-0.01728.7520.0580.0580.0000.0000.0000.000
64A58VAL0-0.069-0.01625.530-0.161-0.1610.0000.0000.0000.000
65A59PRO0-0.011-0.01228.899-0.145-0.1450.0000.0000.0000.000
66A60ASP-1-0.878-0.95329.9939.4179.4170.0000.0000.0000.000
67A61ARG10.7710.85430.799-9.546-9.5460.0000.0000.0000.000
68A62PHE0-0.0140.00825.5870.1920.1920.0000.0000.0000.000
69A63THR0-0.042-0.02526.181-0.128-0.1280.0000.0000.0000.000
70A64GLY00.0490.02122.0220.2770.2770.0000.0000.0000.000
71A65SER0-0.035-0.01821.584-0.493-0.4930.0000.0000.0000.000
72A66GLY00.0590.02019.3690.4460.4460.0000.0000.0000.000
73A67SER0-0.043-0.02317.946-0.381-0.3810.0000.0000.0000.000
74A68GLY00.0040.00615.7730.0190.0190.0000.0000.0000.000
75A69THR00.023-0.01211.7130.9700.9700.0000.0000.0000.000
76A70ASP-1-0.856-0.89413.72817.78817.7880.0000.0000.0000.000
77A71PHE00.004-0.00713.308-0.911-0.9110.0000.0000.0000.000
78A72THR0-0.010-0.01317.9040.0090.0090.0000.0000.0000.000
79A73LEU0-0.0100.02220.540-0.215-0.2150.0000.0000.0000.000
80A74THR0-0.049-0.06022.131-0.156-0.1560.0000.0000.0000.000
81A75ILE00.0000.02025.946-0.023-0.0230.0000.0000.0000.000
82A76SER0-0.014-0.02428.828-0.122-0.1220.0000.0000.0000.000
83A77SER0-0.039-0.03732.093-0.259-0.2590.0000.0000.0000.000
84A78VAL00.0040.00829.9770.0620.0620.0000.0000.0000.000
85A79GLN0-0.0040.00232.503-0.583-0.5830.0000.0000.0000.000
86A80ALA00.0480.03232.9420.2600.2600.0000.0000.0000.000
87A81GLU-1-0.788-0.89232.6549.4039.4030.0000.0000.0000.000
88A82ASP-1-0.786-0.86929.00810.62810.6280.0000.0000.0000.000
89A83LEU00.0120.04127.9340.5020.5020.0000.0000.0000.000
90A84ALA0-0.042-0.02124.529-0.035-0.0350.0000.0000.0000.000
91A85VAL00.0160.02219.424-0.133-0.1330.0000.0000.0000.000
92A86TYR0-0.010-0.02720.2840.0160.0160.0000.0000.0000.000
93A87TYR00.0170.00714.9570.3630.3630.0000.0000.0000.000
94A89GLN0-0.006-0.02310.422-0.562-0.5620.0000.0000.0000.000
95A90ASN00.0410.0165.242-6.033-6.0330.0000.0000.0000.000
96A91ASP-1-0.899-0.9469.00922.64122.6410.0000.0000.0000.000
97A92HIS0-0.030-0.0089.284-0.247-0.2470.0000.0000.0000.000
98A93SER0-0.0120.0015.441-0.987-0.9870.0000.0000.0000.000
99A94TYR0-0.037-0.0126.1150.3560.3560.0000.0000.0000.000
100A95PRO00.0330.0162.660-7.649-4.4772.459-2.183-3.4480.024
101A96LEU0-0.0010.0064.3211.5061.578-0.001-0.021-0.0500.000
102A97THR0-0.026-0.0284.0080.0010.4330.003-0.090-0.3450.000
103A98PHE00.004-0.0117.072-3.901-3.9010.0000.0000.0000.000
104A99GLY00.0230.0189.1131.9151.9150.0000.0000.0000.000
105A100ALA0-0.050-0.03511.399-0.578-0.5780.0000.0000.0000.000
106A101GLY00.0010.01013.342-0.930-0.9300.0000.0000.0000.000
107A102THR0-0.051-0.03916.5850.0220.0220.0000.0000.0000.000
108A103LYS10.7540.87019.934-11.622-11.6220.0000.0000.0000.000
109A104LEU0-0.013-0.01223.131-0.156-0.1560.0000.0000.0000.000
110A105GLU-1-0.781-0.89226.28210.77810.7780.0000.0000.0000.000
111A106ILE0-0.020-0.00829.624-0.065-0.0650.0000.0000.0000.000
112A107LYS10.7870.89532.974-9.059-9.0590.0000.0000.0000.000
113A108ARG10.8420.90135.402-7.795-7.7950.0000.0000.0000.000
114A109THR00.0240.00839.0760.0110.0110.0000.0000.0000.000
115A110VAL0-0.0070.00842.1030.1050.1050.0000.0000.0000.000
116A111ALA0-0.027-0.00643.027-0.098-0.0980.0000.0000.0000.000
117A112ALA00.0300.01244.4570.1150.1150.0000.0000.0000.000
118A113PRO00.0090.00044.449-0.012-0.0120.0000.0000.0000.000
119A114SER00.0040.02046.399-0.230-0.2300.0000.0000.0000.000
120A115VAL0-0.019-0.00847.5880.0880.0880.0000.0000.0000.000
121A116PHE0-0.033-0.00747.975-0.209-0.2090.0000.0000.0000.000
122A117ILE0-0.009-0.00948.7590.1190.1190.0000.0000.0000.000
123A118PHE00.0010.00047.223-0.100-0.1000.0000.0000.0000.000
124A119PRO00.0240.00950.4920.0890.0890.0000.0000.0000.000
125A120PRO0-0.0120.00450.4360.0770.0770.0000.0000.0000.000
126A121SER00.009-0.00950.895-0.086-0.0860.0000.0000.0000.000
127A122ASP-1-0.819-0.92952.7865.6715.6710.0000.0000.0000.000
128A123GLU-1-0.867-0.89751.5695.8895.8890.0000.0000.0000.000
129A124GLN00.0430.02546.838-0.021-0.0210.0000.0000.0000.000
130A125LEU00.0050.00850.878-0.011-0.0110.0000.0000.0000.000
131A126LYS10.7770.85354.150-5.811-5.8110.0000.0000.0000.000
132A127SER0-0.031-0.00750.018-0.022-0.0220.0000.0000.0000.000
133A128GLY0-0.014-0.00150.6690.1140.1140.0000.0000.0000.000
134A129THR0-0.048-0.02347.4330.0390.0390.0000.0000.0000.000
135A130ALA00.0180.00349.678-0.089-0.0890.0000.0000.0000.000
136A131SER00.000-0.00345.4610.0500.0500.0000.0000.0000.000
137A132VAL0-0.043-0.00447.650-0.066-0.0660.0000.0000.0000.000
138A133VAL00.0270.01244.1640.1290.1290.0000.0000.0000.000
139A134CYS0-0.061-0.01445.554-0.117-0.1170.0000.0000.0000.000
140A135LEU0-0.0190.00042.5380.1910.1910.0000.0000.0000.000
141A136LEU00.0040.00342.867-0.209-0.2090.0000.0000.0000.000
142A137ASN00.000-0.01442.5350.2700.2700.0000.0000.0000.000
143A138ASN0-0.031-0.03841.545-0.163-0.1630.0000.0000.0000.000
144A139PHE0-0.0050.00639.659-0.169-0.1690.0000.0000.0000.000
145A140TYR00.1020.03035.1580.2200.2200.0000.0000.0000.000
146A141PRO00.011-0.00437.919-0.241-0.2410.0000.0000.0000.000
147A142ARG10.9991.01732.826-9.577-9.5770.0000.0000.0000.000
148A143GLU-1-0.913-0.96435.6388.7148.7140.0000.0000.0000.000
149A144ALA0-0.017-0.00538.864-0.224-0.2240.0000.0000.0000.000
150A145LYS10.8890.94941.467-6.720-6.7200.0000.0000.0000.000
151A146VAL00.0450.01543.228-0.152-0.1520.0000.0000.0000.000
152A147GLN0-0.003-0.00145.1040.1810.1810.0000.0000.0000.000
153A148TRP00.0130.00045.244-0.242-0.2420.0000.0000.0000.000
154A149LYS10.7910.87349.626-5.870-5.8700.0000.0000.0000.000
155A150VAL00.0120.00552.918-0.006-0.0060.0000.0000.0000.000
156A151ASP-1-0.774-0.88655.6335.3285.3280.0000.0000.0000.000
157A152ASN0-0.047-0.03257.4700.0000.0000.0000.0000.0000.000
158A153ALA00.0250.03356.2160.0340.0340.0000.0000.0000.000
159A154LEU00.0020.00051.4090.0840.0840.0000.0000.0000.000
160A155GLN0-0.0190.00549.2050.0240.0240.0000.0000.0000.000
161A156SER0-0.008-0.02446.2260.0930.0930.0000.0000.0000.000
162A157GLY0-0.0200.00243.154-0.070-0.0700.0000.0000.0000.000
163A158ASN00.011-0.00143.7100.1740.1740.0000.0000.0000.000
164A159SER00.0210.00843.807-0.134-0.1340.0000.0000.0000.000
165A160GLN0-0.049-0.00937.5210.1800.1800.0000.0000.0000.000
166A161GLU-1-0.839-0.91038.3917.6447.6440.0000.0000.0000.000
167A162SER0-0.0150.00534.5050.3330.3330.0000.0000.0000.000
168A163VAL0-0.007-0.01934.263-0.281-0.2810.0000.0000.0000.000
169A164THR0-0.037-0.01433.3670.1890.1890.0000.0000.0000.000
170A165GLU-1-0.802-0.88528.05911.00011.0000.0000.0000.0000.000
171A166GLN0-0.021-0.03231.724-0.080-0.0800.0000.0000.0000.000
172A167ASP-1-0.738-0.85733.2788.7338.7330.0000.0000.0000.000
173A168SER0-0.107-0.07433.702-0.001-0.0010.0000.0000.0000.000
174A169LYS10.8750.93434.882-8.492-8.4920.0000.0000.0000.000
175A170ASP-1-0.763-0.84738.4017.7807.7800.0000.0000.0000.000
176A171SER0-0.039-0.01135.365-0.101-0.1010.0000.0000.0000.000
177A172THR0-0.092-0.05536.8260.0620.0620.0000.0000.0000.000
178A173TYR00.003-0.00332.2480.1680.1680.0000.0000.0000.000
179A174SER00.0400.01837.488-0.372-0.3720.0000.0000.0000.000
180A175LEU0-0.0360.00137.8190.2530.2530.0000.0000.0000.000
181A176SER0-0.009-0.00739.295-0.200-0.2000.0000.0000.0000.000
182A177SER00.016-0.02040.2100.1380.1380.0000.0000.0000.000
183A178THR0-0.001-0.01041.895-0.203-0.2030.0000.0000.0000.000
184A179LEU0-0.0050.01243.6660.1030.1030.0000.0000.0000.000
185A180THR0-0.022-0.00944.747-0.024-0.0240.0000.0000.0000.000
186A181LEU0-0.0220.00046.817-0.014-0.0140.0000.0000.0000.000
187A182SER00.0660.02949.7520.0290.0290.0000.0000.0000.000
188A183LYS10.8670.90551.854-5.589-5.5890.0000.0000.0000.000
189A184ALA00.0240.01254.727-0.090-0.0900.0000.0000.0000.000
190A185ASP-1-0.805-0.91453.8295.7085.7080.0000.0000.0000.000
191A186TYR00.0310.03353.708-0.036-0.0360.0000.0000.0000.000
192A187GLU-1-0.804-0.90155.4165.4235.4230.0000.0000.0000.000
193A188LYS10.7710.89157.124-5.732-5.7320.0000.0000.0000.000
194A189HIS10.8530.92956.305-5.664-5.6640.0000.0000.0000.000
195A190LYS10.8920.94659.956-5.051-5.0510.0000.0000.0000.000
196A191VAL0-0.018-0.01558.4290.0060.0060.0000.0000.0000.000
197A192TYR0-0.004-0.01253.1570.0960.0960.0000.0000.0000.000
198A193ALA00.029-0.00253.843-0.049-0.0490.0000.0000.0000.000
199A195GLU-1-0.783-0.86549.9405.8105.8100.0000.0000.0000.000
200A196VAL00.0410.02546.1820.1520.1520.0000.0000.0000.000
201A197THR0-0.052-0.03546.763-0.176-0.1760.0000.0000.0000.000
202A198HIS00.0500.01841.718-0.028-0.0280.0000.0000.0000.000
203A199GLN00.0450.02242.823-0.021-0.0210.0000.0000.0000.000
204A200GLY00.003-0.00845.908-0.098-0.0980.0000.0000.0000.000
205A201LEU0-0.073-0.03147.643-0.114-0.1140.0000.0000.0000.000
206A202SER0-0.003-0.00850.4170.0030.0030.0000.0000.0000.000
207A203SER00.0000.00453.247-0.116-0.1160.0000.0000.0000.000
208A204PRO0-0.031-0.01551.3900.0780.0780.0000.0000.0000.000
209A205VAL00.0130.01351.279-0.136-0.1360.0000.0000.0000.000
210A206THR0-0.020-0.02951.7930.1050.1050.0000.0000.0000.000
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