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: JQ579

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 OptH
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 -1819783.509592
FMO2-HF: Nuclear repulsion 1747968.625014
FMO2-HF: Total energy -71814.884578
FMO2-MP2: Total energy -72023.943869


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.
-0.9131.691.064-1.151-2.5150.007
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 : 0.036 / q_NPA : 0.005
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].
3A3GLY00.0040.0123.7160.1521.305-0.006-0.383-0.7630.003
4A4ARG10.9240.9456.1310.8200.8200.0000.0000.0000.000
5A5LEU00.0250.0407.973-0.130-0.1300.0000.0000.0000.000
6A6ARG10.8830.92910.7030.2980.2980.0000.0000.0000.000
7A7GLY00.0130.01313.953-0.024-0.0240.0000.0000.0000.000
8A8ILE00.0480.03816.0530.0140.0140.0000.0000.0000.000
9A9ILE0-0.0040.01418.401-0.003-0.0030.0000.0000.0000.000
10A10ILE00.0350.01918.7310.0090.0090.0000.0000.0000.000
11A11GLU-1-0.902-0.96620.858-0.042-0.0420.0000.0000.0000.000
12A12LYS10.7710.87721.3620.0670.0670.0000.0000.0000.000
13A13GLN0-0.024-0.01222.5090.0100.0100.0000.0000.0000.000
14A14PRO0-0.0320.04322.3170.0070.0070.0000.0000.0000.000
15A15PRO00.028-0.01419.3750.0030.0030.0000.0000.0000.000
16A16LEU0-0.004-0.01317.3080.0030.0030.0000.0000.0000.000
17A17VAL00.008-0.00317.033-0.010-0.0100.0000.0000.0000.000
18A18LEU00.0060.01615.7470.0040.0040.0000.0000.0000.000
19A19ILE0-0.036-0.02014.215-0.007-0.0070.0000.0000.0000.000
20A20GLU-1-0.916-0.95714.201-0.166-0.1660.0000.0000.0000.000
21A21VAL0-0.033-0.02510.574-0.009-0.0090.0000.0000.0000.000
22A22GLY0-0.032-0.01212.407-0.033-0.0330.0000.0000.0000.000
23A23GLY00.0600.02614.0920.0250.0250.0000.0000.0000.000
24A24VAL0-0.054-0.0219.6480.0120.0120.0000.0000.0000.000
25A25GLY00.0490.02612.883-0.010-0.0100.0000.0000.0000.000
26A26TYR0-0.034-0.0277.157-0.056-0.0560.0000.0000.0000.000
27A27GLU-1-0.878-0.93512.3280.0050.0050.0000.0000.0000.000
28A28VAL0-0.080-0.03812.2110.0490.0490.0000.0000.0000.000
29A29HIS00.0260.01113.421-0.028-0.0280.0000.0000.0000.000
30A30MET0-0.028-0.01614.3190.0050.0050.0000.0000.0000.000
31A31PRO00.0050.00616.0130.0060.0060.0000.0000.0000.000
32A32MET00.004-0.00919.175-0.009-0.0090.0000.0000.0000.000
33A33THR0-0.055-0.04022.253-0.008-0.0080.0000.0000.0000.000
34A34CYS0-0.038-0.01018.412-0.002-0.0020.0000.0000.0000.000
35A35PHE00.004-0.00520.316-0.008-0.0080.0000.0000.0000.000
36A36TYR0-0.034-0.02921.791-0.001-0.0010.0000.0000.0000.000
37A37GLU-1-0.907-0.94722.349-0.067-0.0670.0000.0000.0000.000
38A38LEU0-0.122-0.04118.668-0.010-0.0100.0000.0000.0000.000
39A39PRO00.0900.05021.5170.0060.0060.0000.0000.0000.000
40A40GLU-1-0.867-0.93024.453-0.077-0.0770.0000.0000.0000.000
41A41ALA0-0.008-0.01524.002-0.007-0.0070.0000.0000.0000.000
42A42GLY0-0.029-0.01323.5090.0050.0050.0000.0000.0000.000
43A43GLN0-0.035-0.01023.801-0.008-0.0080.0000.0000.0000.000
44A44GLU-1-0.908-0.96318.411-0.194-0.1940.0000.0000.0000.000
45A45ALA00.0250.02217.9020.0100.0100.0000.0000.0000.000
46A46ILE0-0.045-0.04614.491-0.036-0.0360.0000.0000.0000.000
47A47VAL00.0010.01412.0840.0240.0240.0000.0000.0000.000
48A48PHE0-0.022-0.03510.821-0.105-0.1050.0000.0000.0000.000
49A49THR00.020-0.0126.417-0.027-0.0270.0000.0000.0000.000
50A50HIS00.0130.0086.055-0.302-0.3020.0000.0000.0000.000
51A51PHE00.0180.0162.750-1.603-0.2321.071-0.767-1.6750.004
52A52VAL0-0.052-0.0355.341-0.324-0.245-0.001-0.001-0.0770.000
53A53VAL00.0090.0065.3040.0270.0270.0000.0000.0000.000
54A54ARG10.8590.9298.238-0.322-0.3220.0000.0000.0000.000
55A55GLU-1-0.940-0.96411.5050.1950.1950.0000.0000.0000.000
56A56ASP-1-0.876-0.94013.8450.1600.1600.0000.0000.0000.000
57A57ALA00.0040.00612.779-0.027-0.0270.0000.0000.0000.000
58A58GLN00.002-0.0136.365-0.012-0.0120.0000.0000.0000.000
59A59LEU00.0130.0149.582-0.109-0.1090.0000.0000.0000.000
60A60LEU00.0350.0256.7210.3190.3190.0000.0000.0000.000
61A61TYR0-0.0010.0099.212-0.142-0.1420.0000.0000.0000.000
62A62GLY00.023-0.00510.104-0.014-0.0140.0000.0000.0000.000
63A63PHE0-0.004-0.02210.8350.0110.0110.0000.0000.0000.000
64A64ASN00.0790.03514.531-0.024-0.0240.0000.0000.0000.000
65A65ASN0-0.005-0.00616.151-0.022-0.0220.0000.0000.0000.000
66A66LYS10.9500.95412.4100.3090.3090.0000.0000.0000.000
67A67GLN00.0300.03014.260-0.001-0.0010.0000.0000.0000.000
68A68GLU-1-0.722-0.86616.335-0.094-0.0940.0000.0000.0000.000
69A69ARG10.8470.9508.5570.5020.5020.0000.0000.0000.000
70A70THR0-0.035-0.01512.4470.0030.0030.0000.0000.0000.000
71A71LEU00.0470.04313.8160.0190.0190.0000.0000.0000.000
72A72PHE00.0130.01211.0410.0210.0210.0000.0000.0000.000
73A73LYS10.8230.8826.3430.4040.4040.0000.0000.0000.000
74A74GLU-1-0.876-0.95512.413-0.053-0.0530.0000.0000.0000.000
75A75LEU0-0.016-0.02015.8030.0150.0150.0000.0000.0000.000
76A76ILE0-0.055-0.03010.9040.0150.0150.0000.0000.0000.000
77A77LYS10.8610.95513.3000.0710.0710.0000.0000.0000.000
78A78THR0-0.078-0.01016.3240.0050.0050.0000.0000.0000.000
79A79ASN00.0620.02119.9620.0080.0080.0000.0000.0000.000
80A80GLY0-0.015-0.01521.358-0.006-0.0060.0000.0000.0000.000
81A81VAL0-0.017-0.00618.717-0.001-0.0010.0000.0000.0000.000
82A82GLY00.0550.03616.5560.0060.0060.0000.0000.0000.000
83A83PRO00.0130.00012.951-0.017-0.0170.0000.0000.0000.000
84A84LYS11.0151.00815.274-0.057-0.0570.0000.0000.0000.000
85A85LEU00.0020.00518.448-0.010-0.0100.0000.0000.0000.000
86A86ALA00.0440.01916.382-0.010-0.0100.0000.0000.0000.000
87A87LEU0-0.019-0.00515.898-0.011-0.0110.0000.0000.0000.000
88A88ALA00.0190.00918.492-0.010-0.0100.0000.0000.0000.000
89A89ILE0-0.007-0.00621.177-0.006-0.0060.0000.0000.0000.000
90A90LEU0-0.001-0.00717.356-0.005-0.0050.0000.0000.0000.000
91A91SER0-0.038-0.01221.316-0.007-0.0070.0000.0000.0000.000
92A92GLY0-0.041-0.00923.361-0.002-0.0020.0000.0000.0000.000
93A93MET0-0.027-0.00324.949-0.001-0.0010.0000.0000.0000.000
94A94SER00.0460.02823.857-0.001-0.0010.0000.0000.0000.000
95A95ALA00.0600.01720.4700.0030.0030.0000.0000.0000.000
96A96GLN00.0790.03022.4360.0070.0070.0000.0000.0000.000
97A97GLN0-0.0040.00325.6130.0040.0040.0000.0000.0000.000
98A98PHE00.0180.00722.2840.0050.0050.0000.0000.0000.000
99A99VAL00.0370.01122.9830.0030.0030.0000.0000.0000.000
100A100ASN0-0.015-0.00625.5180.0030.0030.0000.0000.0000.000
101A101ALA0-0.001-0.01028.4290.0020.0020.0000.0000.0000.000
102A102VAL0-0.048-0.01124.7680.0030.0030.0000.0000.0000.000
103A103GLU-1-0.801-0.92027.750-0.027-0.0270.0000.0000.0000.000
104A104ARG10.8200.91530.1540.0210.0210.0000.0000.0000.000
105A105GLU-1-0.909-0.95531.575-0.008-0.0080.0000.0000.0000.000
106A106GLU-1-0.895-0.95031.955-0.016-0.0160.0000.0000.0000.000
107A107VAL00.006-0.00131.5420.0000.0000.0000.0000.0000.000
108A108GLY0-0.018-0.02532.7610.0020.0020.0000.0000.0000.000
109A109ALA00.0200.01131.3280.0010.0010.0000.0000.0000.000
110A110LEU00.0520.01825.8310.0000.0000.0000.0000.0000.000
111A111VAL0-0.081-0.03229.1450.0020.0020.0000.0000.0000.000
112A112LYS10.8740.92631.7020.0060.0060.0000.0000.0000.000
113A113LEU00.0010.02025.7680.0010.0010.0000.0000.0000.000
114A114PRO00.0310.00826.8940.0020.0020.0000.0000.0000.000
115A115GLY0-0.003-0.01125.9340.0020.0020.0000.0000.0000.000
116A116ILE00.0240.03824.4830.0040.0040.0000.0000.0000.000
117A117GLY0-0.002-0.00927.1630.0010.0010.0000.0000.0000.000
118A118LYS10.9350.95430.817-0.010-0.0100.0000.0000.0000.000
119A119LYS11.0491.02131.576-0.011-0.0110.0000.0000.0000.000
120A120THR00.0280.01325.228-0.001-0.0010.0000.0000.0000.000
121A121ALA00.0220.02627.102-0.001-0.0010.0000.0000.0000.000
122A122GLU-1-0.887-0.95628.4560.0030.0030.0000.0000.0000.000
123A123ARG10.8770.95322.916-0.021-0.0210.0000.0000.0000.000
124A124LEU00.009-0.00721.734-0.001-0.0010.0000.0000.0000.000
125A125ILE00.0010.02524.968-0.004-0.0040.0000.0000.0000.000
126A126VAL00.0090.01127.257-0.003-0.0030.0000.0000.0000.000
127A127GLU-1-0.884-0.96723.1840.0090.0090.0000.0000.0000.000
128A128MET0-0.090-0.04219.304-0.002-0.0020.0000.0000.0000.000
129A129LYS10.8640.94423.4490.0120.0120.0000.0000.0000.000
130A130ASP-1-0.977-0.98025.111-0.015-0.0150.0000.0000.0000.000
131A131ARG10.8870.93718.8140.0100.0100.0000.0000.0000.000
132A132PHE00.002-0.01020.689-0.008-0.0080.0000.0000.0000.000
133A133LYS10.9140.98023.1820.0170.0170.0000.0000.0000.000
134A134GLY00.0010.00522.710-0.001-0.0010.0000.0000.0000.000
135A135LEU0-0.086-0.03617.175-0.009-0.0090.0000.0000.0000.000
136A136HIS00.010-0.01415.2670.0030.0030.0000.0000.0000.000
137A137GLY00.0330.01820.0440.0090.0090.0000.0000.0000.000
138A138ASP-1-0.915-0.94821.691-0.098-0.0980.0000.0000.0000.000
139A139LEU0-0.088-0.04220.1590.0010.0010.0000.0000.0000.000
140A140PHE00.0110.01618.0160.0080.0080.0000.0000.0000.000
141A158ASP-1-0.878-0.96122.181-0.065-0.0650.0000.0000.0000.000
142A159ALA00.0130.00622.624-0.004-0.0040.0000.0000.0000.000
143A160GLU-1-0.839-0.92922.995-0.040-0.0400.0000.0000.0000.000
144A161GLN00.0380.00521.8760.0060.0060.0000.0000.0000.000
145A162GLU-1-0.952-0.96117.782-0.148-0.1480.0000.0000.0000.000
146A163ALA00.018-0.00918.842-0.003-0.0030.0000.0000.0000.000
147A164VAL00.0020.00220.8510.0060.0060.0000.0000.0000.000
148A165ALA00.0120.00816.6780.0050.0050.0000.0000.0000.000
149A166ALA0-0.013-0.00515.946-0.001-0.0010.0000.0000.0000.000
150A167LEU0-0.004-0.00916.9640.0110.0110.0000.0000.0000.000
151A168VAL0-0.049-0.01817.4300.0110.0110.0000.0000.0000.000
152A169ALA0-0.056-0.02213.3510.0070.0070.0000.0000.0000.000
153A170LEU0-0.053-0.03215.1430.0150.0150.0000.0000.0000.000
154A171GLY0-0.0060.01017.1910.0170.0170.0000.0000.0000.000
155A172TYR0-0.0300.00219.3200.0060.0060.0000.0000.0000.000
156A173LYS10.9290.96621.269-0.006-0.0060.0000.0000.0000.000
157A174PRO00.0780.02121.6540.0000.0000.0000.0000.0000.000
158A175GLN00.0200.03323.739-0.001-0.0010.0000.0000.0000.000
159A176GLU-1-0.881-0.97425.6900.0020.0020.0000.0000.0000.000
160A177ALA00.0230.01522.9110.0010.0010.0000.0000.0000.000
161A178SER00.015-0.02424.893-0.004-0.0040.0000.0000.0000.000
162A179ARG10.9020.96227.0200.0090.0090.0000.0000.0000.000
163A180MET0-0.039-0.01925.5790.0010.0010.0000.0000.0000.000
164A181VAL0-0.068-0.01424.2390.0010.0010.0000.0000.0000.000
165A182SER00.0700.01627.672-0.001-0.0010.0000.0000.0000.000
166A183LYS10.8670.95231.2890.0080.0080.0000.0000.0000.000
167A184ILE0-0.007-0.00429.3070.0010.0010.0000.0000.0000.000
168A185ALA0-0.0020.01529.818-0.002-0.0020.0000.0000.0000.000
169A186ARG10.8900.94430.6110.0340.0340.0000.0000.0000.000
170A187PRO0-0.001-0.01031.058-0.003-0.0030.0000.0000.0000.000
171A188ASP-1-0.907-0.94430.636-0.041-0.0410.0000.0000.0000.000
172A189ALA00.0150.00328.8170.0020.0020.0000.0000.0000.000
173A190SER00.0310.02323.899-0.002-0.0020.0000.0000.0000.000
174A191SER00.0580.02019.6850.0100.0100.0000.0000.0000.000
175A192GLU-1-0.892-0.94419.017-0.073-0.0730.0000.0000.0000.000
176A193THR0-0.113-0.05921.7180.0110.0110.0000.0000.0000.000
177A194LEU00.0680.05124.4570.0060.0060.0000.0000.0000.000
178A195ILE00.0230.02018.6980.0060.0060.0000.0000.0000.000
179A196ARG10.8800.93822.8470.0330.0330.0000.0000.0000.000
180A197GLU-1-0.953-0.99124.670-0.009-0.0090.0000.0000.0000.000
181A198ALA0-0.032-0.02325.1460.0040.0040.0000.0000.0000.000
182A199LEU0-0.017-0.01221.1320.0040.0040.0000.0000.0000.000
183A200ARG10.9360.97725.6260.0060.0060.0000.0000.0000.000
184A201ALA0-0.045-0.01728.6610.0030.0030.0000.0000.0000.000
185A202ALA0-0.006-0.01227.782-0.002-0.0020.0000.0000.0000.000
186A203LEU0-0.0450.00425.1060.0040.0040.0000.0000.0000.000