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: 3J18L

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1817929.099989
FMO2-HF: Nuclear repulsion 1746112.780136
FMO2-HF: Total energy -71816.319853
FMO2-MP2: Total energy -72025.329012


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.
-1.2141.6261.306-1.275-2.870.007
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 : 0.033 / q_NPA : 0.002
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].
3A3GLY00.0080.0153.7780.0241.188-0.007-0.401-0.7560.002
4A4ARG10.9200.9436.1310.8920.8920.0000.0000.0000.000
5A5LEU00.0240.0458.056-0.108-0.1080.0000.0000.0000.000
6A6ARG10.8430.89410.8180.2810.2810.0000.0000.0000.000
7A7GLY00.0160.01014.101-0.015-0.0150.0000.0000.0000.000
8A8ILE00.0360.02916.1610.0100.0100.0000.0000.0000.000
9A9ILE0-0.0030.01518.467-0.004-0.0040.0000.0000.0000.000
10A10ILE00.0250.01518.7950.0110.0110.0000.0000.0000.000
11A11GLU-1-0.873-0.93320.843-0.049-0.0490.0000.0000.0000.000
12A12LYS10.7870.89721.3250.0830.0830.0000.0000.0000.000
13A13GLN0-0.046-0.03522.4020.0100.0100.0000.0000.0000.000
14A14PRO0-0.0290.04722.2080.0050.0050.0000.0000.0000.000
15A15PRO00.016-0.02419.3390.0050.0050.0000.0000.0000.000
16A16LEU0-0.013-0.02016.878-0.003-0.0030.0000.0000.0000.000
17A17VAL0-0.006-0.01017.234-0.006-0.0060.0000.0000.0000.000
18A18LEU00.0270.02815.8780.0010.0010.0000.0000.0000.000
19A19ILE0-0.027-0.01814.226-0.006-0.0060.0000.0000.0000.000
20A20GLU-1-0.912-0.95214.224-0.155-0.1550.0000.0000.0000.000
21A21VAL0-0.040-0.02910.926-0.010-0.0100.0000.0000.0000.000
22A22GLY0-0.028-0.00812.528-0.024-0.0240.0000.0000.0000.000
23A23GLY00.0540.02014.2070.0210.0210.0000.0000.0000.000
24A24VAL0-0.052-0.0189.6230.0120.0120.0000.0000.0000.000
25A25GLY00.0570.02712.915-0.014-0.0140.0000.0000.0000.000
26A26TYR0-0.045-0.0346.869-0.059-0.0590.0000.0000.0000.000
27A27GLU-1-0.875-0.93412.273-0.009-0.0090.0000.0000.0000.000
28A28VAL0-0.080-0.04012.0090.0360.0360.0000.0000.0000.000
29A29HIS00.0110.01013.321-0.015-0.0150.0000.0000.0000.000
30A30MET0-0.029-0.00914.229-0.008-0.0080.0000.0000.0000.000
31A31PRO00.0250.01115.8830.0110.0110.0000.0000.0000.000
32A32MET00.010-0.00719.098-0.008-0.0080.0000.0000.0000.000
33A33THR0-0.057-0.04122.218-0.007-0.0070.0000.0000.0000.000
34A34CYS0-0.067-0.02518.403-0.003-0.0030.0000.0000.0000.000
35A35PHE00.020-0.00320.078-0.006-0.0060.0000.0000.0000.000
36A36TYR0-0.030-0.02121.6970.0010.0010.0000.0000.0000.000
37A37GLU-1-0.918-0.95622.236-0.087-0.0870.0000.0000.0000.000
38A38LEU0-0.113-0.03818.505-0.009-0.0090.0000.0000.0000.000
39A39PRO00.0710.03721.5740.0080.0080.0000.0000.0000.000
40A40GLU-1-0.873-0.94224.493-0.086-0.0860.0000.0000.0000.000
41A41ALA0-0.010-0.01324.027-0.007-0.0070.0000.0000.0000.000
42A42GLY0-0.015-0.00823.5700.0060.0060.0000.0000.0000.000
43A43GLN0-0.030-0.01023.895-0.007-0.0070.0000.0000.0000.000
44A44GLU-1-0.874-0.92518.593-0.206-0.2060.0000.0000.0000.000
45A45ALA00.0220.01618.0930.0080.0080.0000.0000.0000.000
46A46ILE0-0.041-0.03814.691-0.035-0.0350.0000.0000.0000.000
47A47VAL00.0190.02312.2200.0220.0220.0000.0000.0000.000
48A48PHE0-0.036-0.03810.738-0.110-0.1100.0000.0000.0000.000
49A49THR00.021-0.0066.3540.0310.0310.0000.0000.0000.000
50A50HIS00.0070.0056.007-0.395-0.3950.0000.0000.0000.000
51A51PHE00.0110.0112.702-2.121-0.5261.314-0.873-2.0350.005
52A52VAL0-0.064-0.0365.267-0.303-0.222-0.001-0.001-0.0790.000
53A53VAL00.0140.0055.2950.0470.0470.0000.0000.0000.000
54A54ARG10.7710.8508.267-0.301-0.3010.0000.0000.0000.000
55A55GLU-1-0.942-0.95711.1930.2140.2140.0000.0000.0000.000
56A56ASP-1-0.783-0.86413.5460.1560.1560.0000.0000.0000.000
57A57ALA0-0.0010.00012.510-0.030-0.0300.0000.0000.0000.000
58A58GLN0-0.004-0.0146.104-0.003-0.0030.0000.0000.0000.000
59A59LEU00.0180.0179.441-0.105-0.1050.0000.0000.0000.000
60A60LEU00.0450.0346.6670.2690.2690.0000.0000.0000.000
61A61TYR00.0010.0049.126-0.095-0.0950.0000.0000.0000.000
62A62GLY00.029-0.00510.015-0.045-0.0450.0000.0000.0000.000
63A63PHE0-0.022-0.03210.8060.0200.0200.0000.0000.0000.000
64A64ASN00.1020.04914.448-0.038-0.0380.0000.0000.0000.000
65A65ASN0-0.015-0.01116.083-0.024-0.0240.0000.0000.0000.000
66A66LYS10.9530.95412.5540.3490.3490.0000.0000.0000.000
67A67GLN00.0060.00914.233-0.007-0.0070.0000.0000.0000.000
68A68GLU-1-0.751-0.87716.200-0.140-0.1400.0000.0000.0000.000
69A69ARG10.8350.9218.3000.6570.6570.0000.0000.0000.000
70A70THR0-0.022-0.00912.424-0.012-0.0120.0000.0000.0000.000
71A71LEU00.0460.04213.8070.0220.0220.0000.0000.0000.000
72A72PHE00.0100.00711.4000.0220.0220.0000.0000.0000.000
73A73LYS10.8500.9076.7360.5300.5300.0000.0000.0000.000
74A74GLU-1-0.845-0.92312.412-0.099-0.0990.0000.0000.0000.000
75A75LEU0-0.031-0.01915.8160.0200.0200.0000.0000.0000.000
76A76ILE0-0.040-0.02710.8380.0180.0180.0000.0000.0000.000
77A77LYS10.8150.91713.4130.1180.1180.0000.0000.0000.000
78A78THR0-0.094-0.04316.3530.0090.0090.0000.0000.0000.000
79A79ASN00.0790.03219.9850.0080.0080.0000.0000.0000.000
80A80GLY0-0.012-0.00321.379-0.005-0.0050.0000.0000.0000.000
81A81VAL0-0.025-0.01018.8640.0000.0000.0000.0000.0000.000
82A82GLY00.0690.04216.5460.0030.0030.0000.0000.0000.000
83A83PRO00.0270.00612.855-0.016-0.0160.0000.0000.0000.000
84A84LYS11.0021.00015.237-0.036-0.0360.0000.0000.0000.000
85A85LEU0-0.0030.00418.399-0.009-0.0090.0000.0000.0000.000
86A86ALA00.0470.02016.367-0.008-0.0080.0000.0000.0000.000
87A87LEU0-0.0110.00115.968-0.011-0.0110.0000.0000.0000.000
88A88ALA00.0180.02218.433-0.008-0.0080.0000.0000.0000.000
89A89ILE0-0.004-0.00821.201-0.004-0.0040.0000.0000.0000.000
90A90LEU00.0100.00317.502-0.003-0.0030.0000.0000.0000.000
91A91SER0-0.054-0.03721.261-0.007-0.0070.0000.0000.0000.000
92A92GLY0-0.037-0.00723.2930.0000.0000.0000.0000.0000.000
93A93MET0-0.055-0.01324.8920.0010.0010.0000.0000.0000.000
94A94SER00.0690.02923.794-0.004-0.0040.0000.0000.0000.000
95A95ALA00.0580.01920.4940.0040.0040.0000.0000.0000.000
96A96GLN00.0930.03122.3930.0080.0080.0000.0000.0000.000
97A97GLN00.0140.03125.5770.0030.0030.0000.0000.0000.000
98A98PHE00.0250.00722.2050.0060.0060.0000.0000.0000.000
99A99VAL00.0160.00423.0560.0040.0040.0000.0000.0000.000
100A100ASN0-0.059-0.03825.5000.0080.0080.0000.0000.0000.000
101A101ALA00.001-0.00128.3090.0030.0030.0000.0000.0000.000
102A102VAL0-0.056-0.01824.6990.0040.0040.0000.0000.0000.000
103A103GLU-1-0.812-0.93527.674-0.043-0.0430.0000.0000.0000.000
104A104ARG10.7970.90530.1530.0370.0370.0000.0000.0000.000
105A105GLU-1-0.873-0.91931.563-0.022-0.0220.0000.0000.0000.000
106A106GLU-1-0.830-0.90631.951-0.030-0.0300.0000.0000.0000.000
107A107VAL00.002-0.00131.251-0.001-0.0010.0000.0000.0000.000
108A108GLY0-0.013-0.02332.7480.0030.0030.0000.0000.0000.000
109A109ALA0-0.026-0.01931.3520.0010.0010.0000.0000.0000.000
110A110LEU00.0570.02025.8320.0000.0000.0000.0000.0000.000
111A111VAL0-0.050-0.01829.1140.0020.0020.0000.0000.0000.000
112A112LYS10.8970.94231.6750.0200.0200.0000.0000.0000.000
113A113LEU00.0070.02525.9200.0020.0020.0000.0000.0000.000
114A114PRO00.0270.00926.6560.0020.0020.0000.0000.0000.000
115A115GLY00.004-0.01125.9000.0000.0000.0000.0000.0000.000
116A116ILE00.0190.03824.8300.0030.0030.0000.0000.0000.000
117A117GLY0-0.002-0.00927.1430.0020.0020.0000.0000.0000.000
118A118LYS10.9320.95630.8010.0020.0020.0000.0000.0000.000
119A119LYS10.9070.93031.8650.0020.0020.0000.0000.0000.000
120A120THR00.0290.01625.350-0.001-0.0010.0000.0000.0000.000
121A121ALA00.0050.01827.104-0.003-0.0030.0000.0000.0000.000
122A122GLU-1-0.758-0.87028.455-0.009-0.0090.0000.0000.0000.000
123A123ARG10.7830.87123.1000.0000.0000.0000.0000.0000.000
124A124LEU00.0190.00221.609-0.002-0.0020.0000.0000.0000.000
125A125ILE0-0.0020.01824.977-0.005-0.0050.0000.0000.0000.000
126A126VAL00.0200.01427.270-0.003-0.0030.0000.0000.0000.000
127A127GLU-1-0.765-0.85323.052-0.014-0.0140.0000.0000.0000.000
128A128MET0-0.056-0.01918.958-0.004-0.0040.0000.0000.0000.000
129A129LYS10.8450.91523.4650.0280.0280.0000.0000.0000.000
130A130ASP-1-0.967-0.98425.296-0.034-0.0340.0000.0000.0000.000
131A131ARG10.8600.91118.8510.0380.0380.0000.0000.0000.000
132A132PHE0-0.006-0.01320.458-0.011-0.0110.0000.0000.0000.000
133A133LYS10.8690.95723.2040.0340.0340.0000.0000.0000.000
134A134GLY00.0030.00622.7590.0000.0000.0000.0000.0000.000
135A135LEU0-0.091-0.03316.878-0.013-0.0130.0000.0000.0000.000
136A136HIS00.013-0.02114.943-0.001-0.0010.0000.0000.0000.000
137A137GLY00.0380.02320.0640.0110.0110.0000.0000.0000.000
138A138ASP-1-0.899-0.93021.686-0.125-0.1250.0000.0000.0000.000
139A139LEU0-0.062-0.01719.8760.0010.0010.0000.0000.0000.000
140A140PHE00.0110.00318.0150.0090.0090.0000.0000.0000.000
141A158ASP-1-0.803-0.91522.372-0.082-0.0820.0000.0000.0000.000
142A159ALA0-0.027-0.01922.623-0.006-0.0060.0000.0000.0000.000
143A160GLU-1-0.859-0.94822.996-0.054-0.0540.0000.0000.0000.000
144A161GLN00.0190.00421.5580.0050.0050.0000.0000.0000.000
145A162GLU-1-0.958-0.94417.548-0.172-0.1720.0000.0000.0000.000
146A163ALA00.013-0.00818.840-0.005-0.0050.0000.0000.0000.000
147A164VAL00.0020.00420.8490.0060.0060.0000.0000.0000.000
148A165ALA00.0110.00416.6610.0040.0040.0000.0000.0000.000
149A166ALA0-0.017-0.00615.944-0.003-0.0030.0000.0000.0000.000
150A167LEU00.023-0.00116.9610.0110.0110.0000.0000.0000.000
151A168VAL0-0.050-0.01917.6400.0120.0120.0000.0000.0000.000
152A169ALA0-0.058-0.02313.3160.0070.0070.0000.0000.0000.000
153A170LEU0-0.048-0.02715.1360.0160.0160.0000.0000.0000.000
154A171GLY0-0.0080.00717.1870.0190.0190.0000.0000.0000.000
155A172TYR0-0.039-0.00219.3120.0070.0070.0000.0000.0000.000
156A173LYS10.9000.94721.2590.0040.0040.0000.0000.0000.000
157A174PRO00.0830.02421.5390.0000.0000.0000.0000.0000.000
158A175GLN00.0350.02223.727-0.002-0.0020.0000.0000.0000.000
159A176GLU-1-0.875-0.95025.644-0.010-0.0100.0000.0000.0000.000
160A177ALA00.0360.01622.8730.0020.0020.0000.0000.0000.000
161A178SER00.013-0.01124.887-0.004-0.0040.0000.0000.0000.000
162A179ARG10.8810.95327.0130.0190.0190.0000.0000.0000.000
163A180MET0-0.029-0.01725.7040.0020.0020.0000.0000.0000.000
164A181VAL0-0.0300.00324.2070.0020.0020.0000.0000.0000.000
165A182SER00.041-0.00227.669-0.002-0.0020.0000.0000.0000.000
166A183LYS10.8640.95731.2860.0150.0150.0000.0000.0000.000
167A184ILE0-0.017-0.01329.3610.0020.0020.0000.0000.0000.000
168A185ALA0-0.0070.01529.801-0.002-0.0020.0000.0000.0000.000
169A186ARG10.8710.93230.5980.0420.0420.0000.0000.0000.000
170A187PRO00.022-0.00331.061-0.003-0.0030.0000.0000.0000.000
171A188ASP-1-0.904-0.94730.627-0.048-0.0480.0000.0000.0000.000
172A189ALA00.0160.01728.8230.0030.0030.0000.0000.0000.000
173A190SER0-0.003-0.00523.794-0.005-0.0050.0000.0000.0000.000
174A191SER00.049-0.01519.9270.0120.0120.0000.0000.0000.000
175A192GLU-1-0.847-0.90319.640-0.061-0.0610.0000.0000.0000.000
176A193THR0-0.0060.00221.7250.0100.0100.0000.0000.0000.000
177A194LEU00.0040.03124.4170.0070.0070.0000.0000.0000.000
178A195ILE00.0250.02118.6240.0060.0060.0000.0000.0000.000
179A196ARG10.8060.88622.8500.0430.0430.0000.0000.0000.000
180A197GLU-1-0.861-0.94324.677-0.012-0.0120.0000.0000.0000.000
181A198ALA0-0.029-0.01725.1520.0050.0050.0000.0000.0000.000
182A199LEU0-0.020-0.00621.6050.0040.0040.0000.0000.0000.000
183A200ARG10.8770.93325.6290.0140.0140.0000.0000.0000.000
184A201ALA0-0.037-0.01128.6660.0040.0040.0000.0000.0000.000
185A202ALA0-0.030-0.03427.761-0.002-0.0020.0000.0000.0000.000
186A203LEU0-0.0310.01125.0800.0040.0040.0000.0000.0000.000