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: LNK99

Calculation Name: 1HJP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HJP

Chain ID: A

ChEMBL ID:

UniProt ID: P0A809

Base Structure: X-ray

Registration Date: 2023-09-24

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1819771.215722
FMO2-HF: Nuclear repulsion 1747954.050085
FMO2-HF: Total energy -71817.165637
FMO2-MP2: Total energy -72026.155803


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-1.7661.5581.336-1.477-3.1830.005
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.004
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].
3A3GLY00.0190.0323.7480.0501.2440.000-0.418-0.7760.002
4A4ARG10.9080.9555.6421.0001.0000.0000.0000.0000.000
5A5LEU00.0180.0347.660-0.135-0.1350.0000.0000.0000.000
6A6ARG10.8350.88210.4820.2630.2630.0000.0000.0000.000
7A7GLY00.0210.01813.800-0.015-0.0150.0000.0000.0000.000
8A8ILE00.0330.02615.9150.0080.0080.0000.0000.0000.000
9A9ILE00.0000.00418.215-0.005-0.0050.0000.0000.0000.000
10A10ILE00.0090.00618.6470.0110.0110.0000.0000.0000.000
11A11GLU-1-0.873-0.93120.391-0.050-0.0500.0000.0000.0000.000
12A12LYS10.8020.89520.8820.0810.0810.0000.0000.0000.000
13A13GLN0-0.045-0.02722.2340.0100.0100.0000.0000.0000.000
14A14PRO0-0.0060.02022.1290.0050.0050.0000.0000.0000.000
15A15PRO0-0.010-0.02119.0790.0060.0060.0000.0000.0000.000
16A16LEU0-0.020-0.00516.649-0.002-0.0020.0000.0000.0000.000
17A17VAL0-0.010-0.01016.977-0.007-0.0070.0000.0000.0000.000
18A18LEU00.0170.02215.6030.0030.0030.0000.0000.0000.000
19A19ILE0-0.017-0.01914.034-0.003-0.0030.0000.0000.0000.000
20A20GLU-1-0.915-0.95613.797-0.166-0.1660.0000.0000.0000.000
21A21VAL0-0.045-0.03110.603-0.006-0.0060.0000.0000.0000.000
22A22GLY0-0.035-0.01612.667-0.018-0.0180.0000.0000.0000.000
23A23GLY00.0190.00314.0300.0270.0270.0000.0000.0000.000
24A24VAL0-0.0180.0009.5800.0040.0040.0000.0000.0000.000
25A25GLY00.0540.02912.710-0.019-0.0190.0000.0000.0000.000
26A26TYR0-0.017-0.0176.430-0.084-0.0840.0000.0000.0000.000
27A27GLU-1-0.832-0.90711.8900.0070.0070.0000.0000.0000.000
28A28VAL0-0.078-0.04311.7020.0250.0250.0000.0000.0000.000
29A29HIS0-0.031-0.01313.063-0.008-0.0080.0000.0000.0000.000
30A30MET0-0.028-0.01313.996-0.004-0.0040.0000.0000.0000.000
31A31PRO00.009-0.00115.5300.0090.0090.0000.0000.0000.000
32A32MET00.0060.00018.770-0.010-0.0100.0000.0000.0000.000
33A33THR0-0.059-0.04521.840-0.007-0.0070.0000.0000.0000.000
34A34CYS0-0.055-0.02217.919-0.004-0.0040.0000.0000.0000.000
35A35PHE00.004-0.00519.797-0.007-0.0070.0000.0000.0000.000
36A36TYR0-0.022-0.01621.2990.0010.0010.0000.0000.0000.000
37A37GLU-1-0.906-0.95122.337-0.083-0.0830.0000.0000.0000.000
38A38LEU0-0.057-0.01218.114-0.009-0.0090.0000.0000.0000.000
39A39PRO00.0360.01821.3770.0090.0090.0000.0000.0000.000
40A40GLU-1-0.840-0.91724.007-0.083-0.0830.0000.0000.0000.000
41A41ALA0-0.020-0.01723.886-0.007-0.0070.0000.0000.0000.000
42A42GLY0-0.0040.00023.4820.0070.0070.0000.0000.0000.000
43A43GLN0-0.039-0.01523.747-0.007-0.0070.0000.0000.0000.000
44A44GLU-1-0.881-0.92518.468-0.197-0.1970.0000.0000.0000.000
45A45ALA00.0160.01218.0800.0100.0100.0000.0000.0000.000
46A46ILE0-0.040-0.03814.389-0.033-0.0330.0000.0000.0000.000
47A47VAL00.0420.03112.0760.0240.0240.0000.0000.0000.000
48A48PHE0-0.032-0.02410.441-0.110-0.1100.0000.0000.0000.000
49A49THR00.019-0.0226.3710.0390.0390.0000.0000.0000.000
50A50HIS00.0000.0015.805-0.451-0.4510.0000.0000.0000.000
51A51PHE00.0180.0122.762-2.418-0.3911.337-1.056-2.3080.003
52A52VAL0-0.057-0.0375.079-0.465-0.362-0.001-0.003-0.0990.000
53A53VAL00.0250.0175.464-0.086-0.0860.0000.0000.0000.000
54A54ARG10.7590.8398.213-0.300-0.3000.0000.0000.0000.000
55A55GLU-1-0.932-0.95910.9550.1870.1870.0000.0000.0000.000
56A56ASP-1-0.793-0.85713.5560.1470.1470.0000.0000.0000.000
57A57ALA00.0060.00012.275-0.033-0.0330.0000.0000.0000.000
58A58GLN0-0.013-0.0145.706-0.033-0.0330.0000.0000.0000.000
59A59LEU00.0140.0169.119-0.117-0.1170.0000.0000.0000.000
60A60LEU00.0040.0026.6080.3670.3670.0000.0000.0000.000
61A61TYR00.0230.0189.011-0.127-0.1270.0000.0000.0000.000
62A62GLY00.022-0.0059.583-0.034-0.0340.0000.0000.0000.000
63A63PHE0-0.012-0.01910.5360.0240.0240.0000.0000.0000.000
64A64ASN00.0660.02614.154-0.050-0.0500.0000.0000.0000.000
65A65ASN0-0.035-0.02915.616-0.020-0.0200.0000.0000.0000.000
66A66LYS10.9490.95612.6030.3350.3350.0000.0000.0000.000
67A67GLN00.0040.00313.627-0.010-0.0100.0000.0000.0000.000
68A68GLU-1-0.741-0.85915.870-0.139-0.1390.0000.0000.0000.000
69A69ARG10.8390.9147.8510.6890.6890.0000.0000.0000.000
70A70THR0-0.044-0.02911.834-0.020-0.0200.0000.0000.0000.000
71A71LEU00.0160.02313.4070.0220.0220.0000.0000.0000.000
72A72PHE00.010-0.00211.1270.0230.0230.0000.0000.0000.000
73A73LYS10.8750.9256.3580.5290.5290.0000.0000.0000.000
74A74GLU-1-0.795-0.89712.137-0.096-0.0960.0000.0000.0000.000
75A75LEU0-0.043-0.00915.5260.0200.0200.0000.0000.0000.000
76A76ILE00.0050.00010.6440.0200.0200.0000.0000.0000.000
77A77LYS10.7560.88612.9450.1150.1150.0000.0000.0000.000
78A78THR0-0.051-0.05815.9950.0030.0030.0000.0000.0000.000
79A79ASN00.0460.02119.5170.0090.0090.0000.0000.0000.000
80A80GLY00.0110.00821.158-0.006-0.0060.0000.0000.0000.000
81A81VAL0-0.029-0.00518.3930.0010.0010.0000.0000.0000.000
82A82GLY00.0660.04516.4570.0030.0030.0000.0000.0000.000
83A83PRO00.025-0.00812.555-0.017-0.0170.0000.0000.0000.000
84A84LYS11.0021.00314.910-0.042-0.0420.0000.0000.0000.000
85A85LEU0-0.0050.00318.155-0.010-0.0100.0000.0000.0000.000
86A86ALA00.0540.02215.943-0.009-0.0090.0000.0000.0000.000
87A87LEU0-0.0110.00715.831-0.012-0.0120.0000.0000.0000.000
88A88ALA00.0200.02017.972-0.009-0.0090.0000.0000.0000.000
89A89ILE0-0.011-0.01020.888-0.005-0.0050.0000.0000.0000.000
90A90LEU00.0100.00316.860-0.003-0.0030.0000.0000.0000.000
91A91SER0-0.032-0.02020.735-0.008-0.0080.0000.0000.0000.000
92A92GLY0-0.030-0.00322.8710.0000.0000.0000.0000.0000.000
93A93MET0-0.058-0.01824.5540.0010.0010.0000.0000.0000.000
94A94SER00.0530.01023.254-0.004-0.0040.0000.0000.0000.000
95A95ALA00.027-0.00819.9200.0040.0040.0000.0000.0000.000
96A96GLN00.1070.04021.8150.0080.0080.0000.0000.0000.000
97A97GLN00.0300.05225.0170.0020.0020.0000.0000.0000.000
98A98PHE00.0250.00621.9040.0060.0060.0000.0000.0000.000
99A99VAL00.0130.00722.6380.0050.0050.0000.0000.0000.000
100A100ASN0-0.034-0.02625.1230.0080.0080.0000.0000.0000.000
101A101ALA00.0080.00727.6820.0040.0040.0000.0000.0000.000
102A102VAL0-0.062-0.01824.3600.0050.0050.0000.0000.0000.000
103A103GLU-1-0.804-0.93827.301-0.043-0.0430.0000.0000.0000.000
104A104ARG10.8040.89029.9090.0360.0360.0000.0000.0000.000
105A105GLU-1-0.847-0.89831.238-0.022-0.0220.0000.0000.0000.000
106A106GLU-1-0.822-0.87731.702-0.029-0.0290.0000.0000.0000.000
107A107VAL00.015-0.01530.9830.0000.0000.0000.0000.0000.000
108A108GLY0-0.020-0.01632.0470.0020.0020.0000.0000.0000.000
109A109ALA0-0.021-0.01830.6250.0010.0010.0000.0000.0000.000
110A110LEU00.0470.01625.6450.0010.0010.0000.0000.0000.000
111A111VAL0-0.070-0.02729.0660.0030.0030.0000.0000.0000.000
112A112LYS10.9030.94231.1920.0200.0200.0000.0000.0000.000
113A113LEU00.0270.03225.3320.0000.0000.0000.0000.0000.000
114A114PRO0-0.012-0.01026.1400.0030.0030.0000.0000.0000.000
115A115GLY00.0320.00225.3850.0020.0020.0000.0000.0000.000
116A116ILE00.0010.02824.7460.0030.0030.0000.0000.0000.000
117A117GLY00.0150.01126.7580.0020.0020.0000.0000.0000.000
118A118LYS10.9030.93230.5170.0020.0020.0000.0000.0000.000
119A119LYS10.9010.92331.1490.0010.0010.0000.0000.0000.000
120A120THR0-0.007-0.00425.209-0.001-0.0010.0000.0000.0000.000
121A121ALA00.0360.01726.905-0.002-0.0020.0000.0000.0000.000
122A122GLU-1-0.789-0.86828.154-0.008-0.0080.0000.0000.0000.000
123A123ARG10.8080.87822.949-0.003-0.0030.0000.0000.0000.000
124A124LEU0-0.0140.00521.568-0.002-0.0020.0000.0000.0000.000
125A125ILE00.0250.01524.527-0.005-0.0050.0000.0000.0000.000
126A126VAL00.0210.01626.654-0.004-0.0040.0000.0000.0000.000
127A127GLU-1-0.736-0.82522.704-0.011-0.0110.0000.0000.0000.000
128A128MET0-0.074-0.01818.560-0.005-0.0050.0000.0000.0000.000
129A129LYS10.8270.91323.0710.0270.0270.0000.0000.0000.000
130A130ASP-1-0.911-0.92924.848-0.031-0.0310.0000.0000.0000.000
131A131ARG10.8360.89718.3740.0340.0340.0000.0000.0000.000
132A132PHE00.008-0.02019.977-0.011-0.0110.0000.0000.0000.000
133A133LYS10.8180.89822.7490.0330.0330.0000.0000.0000.000
134A134GLY0-0.0140.00822.2860.0030.0030.0000.0000.0000.000
135A135LEU0-0.089-0.03116.377-0.014-0.0140.0000.0000.0000.000
136A136HIS0-0.013-0.02014.6680.0010.0010.0000.0000.0000.000
137A137GLY00.0510.02419.8470.0080.0080.0000.0000.0000.000
138A138ASP-1-0.894-0.92721.703-0.123-0.1230.0000.0000.0000.000
139A139LEU0-0.0320.00619.0280.0080.0080.0000.0000.0000.000
140A140PHE0-0.018-0.02217.7590.0100.0100.0000.0000.0000.000
141A158ASP-1-0.791-0.90422.103-0.082-0.0820.0000.0000.0000.000
142A159ALA0-0.029-0.01922.156-0.009-0.0090.0000.0000.0000.000
143A160GLU-1-0.857-0.94623.009-0.051-0.0510.0000.0000.0000.000
144A161GLN00.016-0.00521.4100.0040.0040.0000.0000.0000.000
145A162GLU-1-0.942-0.93917.420-0.174-0.1740.0000.0000.0000.000
146A163ALA00.0190.00518.878-0.005-0.0050.0000.0000.0000.000
147A164VAL0-0.0100.00020.8720.0060.0060.0000.0000.0000.000
148A165ALA0-0.001-0.00716.9600.0030.0030.0000.0000.0000.000
149A166ALA0-0.009-0.00616.122-0.007-0.0070.0000.0000.0000.000
150A167LEU00.015-0.00517.2020.0120.0120.0000.0000.0000.000
151A168VAL0-0.042-0.02017.5380.0110.0110.0000.0000.0000.000
152A169ALA0-0.061-0.02313.3220.0060.0060.0000.0000.0000.000
153A170LEU0-0.042-0.02414.9170.0150.0150.0000.0000.0000.000
154A171GLY0-0.0170.00717.3010.0190.0190.0000.0000.0000.000
155A172TYR0-0.041-0.00919.0330.0080.0080.0000.0000.0000.000
156A173LYS10.9200.95521.2110.0030.0030.0000.0000.0000.000
157A174PRO00.0700.01721.6800.0010.0010.0000.0000.0000.000
158A175GLN00.0100.02423.895-0.002-0.0020.0000.0000.0000.000
159A176GLU-1-0.840-0.94025.775-0.013-0.0130.0000.0000.0000.000
160A177ALA00.0200.02022.8120.0010.0010.0000.0000.0000.000
161A178SER00.026-0.00624.787-0.003-0.0030.0000.0000.0000.000
162A179ARG10.9030.95927.0860.0180.0180.0000.0000.0000.000
163A180MET0-0.025-0.00825.1840.0030.0030.0000.0000.0000.000
164A181VAL0-0.020-0.00924.1750.0020.0020.0000.0000.0000.000
165A182SER00.003-0.01227.639-0.003-0.0030.0000.0000.0000.000
166A183LYS10.8170.91231.2750.0130.0130.0000.0000.0000.000
167A184ILE0-0.025-0.01029.5460.0020.0020.0000.0000.0000.000
168A185ALA00.0040.03229.971-0.002-0.0020.0000.0000.0000.000
169A186ARG10.8220.88930.3090.0430.0430.0000.0000.0000.000
170A187PRO00.0430.01230.541-0.004-0.0040.0000.0000.0000.000
171A188ASP-1-0.868-0.92330.736-0.044-0.0440.0000.0000.0000.000
172A189ALA0-0.0040.01828.7190.0030.0030.0000.0000.0000.000
173A190SER00.009-0.00123.561-0.006-0.0060.0000.0000.0000.000
174A191SER00.059-0.00319.7530.0130.0130.0000.0000.0000.000
175A192GLU-1-0.826-0.88619.887-0.047-0.0470.0000.0000.0000.000
176A193THR0-0.037-0.02421.6490.0100.0100.0000.0000.0000.000
177A194LEU00.0140.01824.5840.0070.0070.0000.0000.0000.000
178A195ILE00.0050.00218.7510.0060.0060.0000.0000.0000.000
179A196ARG10.7770.87923.0180.0390.0390.0000.0000.0000.000
180A197GLU-1-0.805-0.90824.765-0.010-0.0100.0000.0000.0000.000
181A198ALA0-0.0070.00325.6600.0050.0050.0000.0000.0000.000
182A199LEU0-0.002-0.00121.9470.0040.0040.0000.0000.0000.000
183A200ARG10.8550.91525.9150.0130.0130.0000.0000.0000.000
184A201ALA0-0.044-0.01328.7900.0040.0040.0000.0000.0000.000
185A202ALA0-0.041-0.02827.582-0.001-0.0010.0000.0000.0000.000
186A203LEU0-0.0250.01025.1580.0040.0040.0000.0000.0000.000