FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 6G9KZ

Calculation Name: 3HJ5-A-Xray540

Preferred Name: Prion protein

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3HJ5

Chain ID: A

ChEMBL ID: CHEMBL4869

UniProt ID: P04156

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -670126.547835
FMO2-HF: Nuclear repulsion 626211.612142
FMO2-HF: Total energy -43914.935693
FMO2-MP2: Total energy -44037.109623


3D Structure Molmil
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:125:LEU)


Summations of interaction energy for fragment #1(A:125:LEU)
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.
-2.963-1.218-0.027-0.851-0.8710.002
Interaction energy analysis for fragmet #1(A:125:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.144 / q_NPA : 0.025
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].
4A127GLY0-0.006-0.0183.848-1.980-0.591-0.021-0.787-0.5820.002
5A128TYR00.042-0.0025.2660.4360.510-0.002-0.004-0.0690.000
6A128TYR0-0.1820.0314.098-0.0780.121-0.001-0.054-0.1450.000
7A129VAL00.159-0.0835.725-0.975-0.948-0.0020.001-0.0270.000
8A129VAL0-0.0960.1049.3900.0440.0440.0000.0000.0000.000
9A130LEU00.136-0.1148.4480.0040.0040.0000.0000.0000.000
10A130LEU0-0.1460.1068.529-0.022-0.0220.0000.0000.0000.000
11A131GLY0-0.070-0.1369.7920.1590.1590.0000.0000.0000.000
12A132SER00.0930.02013.367-0.040-0.0400.0000.0000.0000.000
13A132SER0-0.0330.08016.8630.0150.0150.0000.0000.0000.000
14A133ALA00.120-0.09016.1150.0030.0030.0000.0000.0000.000
15A133ALA0-0.1350.08517.7320.0060.0060.0000.0000.0000.000
16A134MET0-0.016-0.10617.9540.0320.0320.0000.0000.0000.000
17A134MET0-0.1080.08017.8710.0060.0060.0000.0000.0000.000
18A135SER00.118-0.08320.444-0.002-0.0020.0000.0000.0000.000
19A135SER0-0.0270.08524.7610.0080.0080.0000.0000.0000.000
20A136ARG0-0.008-0.14022.487-0.017-0.0170.0000.0000.0000.000
21A136ARG10.8371.05220.1040.2760.2760.0000.0000.0000.000
22A137PRO00.008-0.08521.8520.0160.0160.0000.0000.0000.000
23A138ILE00.1000.01724.8490.0000.0000.0000.0000.0000.000
24A138ILE0-0.0830.11128.7860.0010.0010.0000.0000.0000.000
25A139ILE00.021-0.12227.2710.0010.0010.0000.0000.0000.000
26A139ILE0-0.0660.09323.809-0.003-0.0030.0000.0000.0000.000
27A140HIS00.098-0.04228.5190.0010.0010.0000.0000.0000.000
28A140HIS0-0.1230.06231.4720.0050.0050.0000.0000.0000.000
29A141PHE00.031-0.11830.3060.0010.0010.0000.0000.0000.000
30A141PHE0-0.0690.08225.294-0.003-0.0030.0000.0000.0000.000
31A142GLY00.038-0.08130.9220.0040.0040.0000.0000.0000.000
32A143SER00.0290.04633.4250.0040.0040.0000.0000.0000.000
33A143SER0-0.127-0.02133.1520.0010.0010.0000.0000.0000.000
34A144ASP00.160-0.09134.430-0.006-0.0060.0000.0000.0000.000
35A144ASP-1-0.988-0.85237.804-0.071-0.0710.0000.0000.0000.000
36A145TYR00.100-0.07234.191-0.003-0.0030.0000.0000.0000.000
37A145TYR0-0.1040.07929.8940.0020.0020.0000.0000.0000.000
38A146GLU00.061-0.12130.235-0.004-0.0040.0000.0000.0000.000
39A146GLU-1-0.882-0.77729.544-0.088-0.0880.0000.0000.0000.000
40A147ASP00.094-0.10230.196-0.010-0.0100.0000.0000.0000.000
41A147ASP-1-0.892-0.77832.057-0.102-0.1020.0000.0000.0000.000
42A148ARG00.062-0.12531.949-0.008-0.0080.0000.0000.0000.000
43A148ARG10.7871.02034.2320.0800.0800.0000.0000.0000.000
44A149TYR00.056-0.11230.022-0.003-0.0030.0000.0000.0000.000
45A149TYR0-0.0810.09425.644-0.002-0.0020.0000.0000.0000.000
46A150TYR00.079-0.11727.131-0.006-0.0060.0000.0000.0000.000
47A150TYR0-0.0640.08723.880-0.008-0.0080.0000.0000.0000.000
48A151ARG00.098-0.08427.724-0.014-0.0140.0000.0000.0000.000
49A151ARG10.7631.02531.9250.0970.0970.0000.0000.0000.000
50A152GLU00.019-0.11029.802-0.008-0.0080.0000.0000.0000.000
51A152GLU-1-0.858-0.76530.976-0.088-0.0880.0000.0000.0000.000
52A153ASN00.026-0.07626.307-0.002-0.0020.0000.0000.0000.000
53A153ASN0-0.0980.05025.287-0.001-0.0010.0000.0000.0000.000
54A154MET00.211-0.06923.811-0.012-0.0120.0000.0000.0000.000
55A154MET0-0.0780.11424.410-0.004-0.0040.0000.0000.0000.000
56A155HIS0-0.024-0.13622.718-0.028-0.0280.0000.0000.0000.000
57A155HIS0-0.0250.11324.706-0.002-0.0020.0000.0000.0000.000
58A156ARG00.029-0.10921.610-0.019-0.0190.0000.0000.0000.000
59A156ARG10.8081.03321.7320.1510.1510.0000.0000.0000.000
60A157TYR00.013-0.10018.621-0.020-0.0200.0000.0000.0000.000
61A157TYR0-0.0580.10119.2730.0040.0040.0000.0000.0000.000
62A158PRO00.037-0.07714.5760.0090.0090.0000.0000.0000.000
63A159ASN00.0990.03916.6100.0240.0240.0000.0000.0000.000
64A159ASN0-0.0740.07116.870-0.023-0.0230.0000.0000.0000.000
65A160GLN00.037-0.10615.0650.0530.0530.0000.0000.0000.000
66A160GLN0-0.0550.10913.0010.0470.0470.0000.0000.0000.000
67A161VAL00.043-0.10512.539-0.027-0.0270.0000.0000.0000.000
68A161VAL0-0.0190.11713.0300.0100.0100.0000.0000.0000.000
69A162TYR00.152-0.0878.1500.0010.0010.0000.0000.0000.000
70A162TYR0-0.0680.1045.974-0.201-0.2010.0000.0000.0000.000
71A163TYR00.103-0.0559.3530.0970.0970.0000.0000.0000.000
72A163TYR0-0.0790.07711.6920.0450.0450.0000.0000.0000.000
73A164ARG00.142-0.1039.372-0.277-0.2770.0000.0000.0000.000
74A164ARG10.7851.0299.8310.3260.3260.0000.0000.0000.000
75A165PRO0-0.059-0.12310.4460.1170.1170.0000.0000.0000.000
76A166MET00.1180.01413.5790.0160.0160.0000.0000.0000.000
77A166MET0-0.1170.09317.610-0.005-0.0050.0000.0000.0000.000
78A167ASP00.061-0.07016.984-0.002-0.0020.0000.0000.0000.000
79A167ASP-1-0.831-0.80416.010-0.196-0.1960.0000.0000.0000.000
80A168GLU00.100-0.12918.549-0.014-0.0140.0000.0000.0000.000
81A168GLU-1-0.930-0.79721.560-0.066-0.0660.0000.0000.0000.000
82A169TYR00.049-0.07019.2510.0130.0130.0000.0000.0000.000
83A169TYR0-0.1420.05518.2110.0110.0110.0000.0000.0000.000
84A170SER0-0.022-0.11517.7370.0120.0120.0000.0000.0000.000
85A170SER0-0.0710.06217.067-0.024-0.0240.0000.0000.0000.000
86A171ASN00.139-0.04518.5960.0010.0010.0000.0000.0000.000
87A171ASN0-0.1100.06619.4800.0010.0010.0000.0000.0000.000
88A172GLN00.162-0.08918.865-0.017-0.0170.0000.0000.0000.000
89A172GLN0-0.0790.09520.6180.0120.0120.0000.0000.0000.000
90A173ASN00.085-0.05718.478-0.031-0.0310.0000.0000.0000.000
91A173ASN0-0.1140.05620.369-0.001-0.0010.0000.0000.0000.000
92A174ASN00.126-0.03516.454-0.005-0.0050.0000.0000.0000.000
93A174ASN0-0.0570.05115.843-0.017-0.0170.0000.0000.0000.000
94A175PHE00.147-0.06814.234-0.022-0.0220.0000.0000.0000.000
95A175PHE0-0.1370.08015.221-0.012-0.0120.0000.0000.0000.000
96A176VAL00.061-0.12313.637-0.081-0.0810.0000.0000.0000.000
97A176VAL0-0.0820.10217.1360.0020.0020.0000.0000.0000.000
98A177HIS00.151-0.06014.416-0.032-0.0320.0000.0000.0000.000
99A177HIS0-0.1410.07014.0320.0350.0350.0000.0000.0000.000
100A178ASP00.035-0.10110.8270.0360.0360.0000.0000.0000.000
101A178ASP-1-0.934-0.8249.931-0.395-0.3950.0000.0000.0000.000
102A179CYS00.222-0.06010.443-0.030-0.0300.0000.0000.0000.000
103A179CYS0-0.1970.08911.4870.0230.0230.0000.0000.0000.000
104A180VAL00.059-0.10911.188-0.089-0.0890.0000.0000.0000.000
105A180VAL0-0.0750.11114.5070.0070.0070.0000.0000.0000.000
106A181ASN00.115-0.07211.139-0.018-0.0180.0000.0000.0000.000
107A181ASN0-0.1120.05910.7660.0030.0030.0000.0000.0000.000
108A182ILE00.009-0.1227.0060.1570.1570.0000.0000.0000.000
109A182ILE0-0.0710.1025.048-0.028-0.0280.0000.0000.0000.000
110A183THR00.031-0.0987.772-0.100-0.1000.0000.0000.0000.000
111A183THR00.0010.07711.112-0.039-0.0390.0000.0000.0000.000
112A184ILE00.104-0.06410.107-0.032-0.0320.0000.0000.0000.000
113A184ILE0-0.0820.10912.4480.0100.0100.0000.0000.0000.000
114A185LYS00.134-0.0548.935-0.002-0.0020.0000.0000.0000.000
115A185LYS10.8791.0617.317-0.204-0.2040.0000.0000.0000.000
116A186GLN00.069-0.1357.7720.1690.1690.0000.0000.0000.000
117A186GLN0-0.0910.1044.2970.1970.253-0.001-0.007-0.0480.000
118A187HIS00.107-0.0798.508-0.039-0.0390.0000.0000.0000.000
119A187HIS0-0.0790.09012.657-0.045-0.0450.0000.0000.0000.000
120A188THR0-0.023-0.09012.0640.0300.0300.0000.0000.0000.000
121A188THR0-0.1090.01512.0340.0300.0300.0000.0000.0000.000
122A189VAL00.022-0.09510.5600.0480.0480.0000.0000.0000.000
123A189VAL0-0.1070.0788.4650.0210.0210.0000.0000.0000.000
124A190THR00.011-0.08411.9640.0300.0300.0000.0000.0000.000
125A190THR0-0.0490.07911.638-0.034-0.0340.0000.0000.0000.000
126A191THR00.008-0.08713.2120.0450.0450.0000.0000.0000.000
127A191THR0-0.0390.06614.5050.0060.0060.0000.0000.0000.000
128A192THR00.003-0.11716.366-0.026-0.0260.0000.0000.0000.000
129A192THR0-0.0450.06918.3760.0030.0030.0000.0000.0000.000
130A193THR00.003-0.07519.8070.0170.0170.0000.0000.0000.000
131A193THR0-0.0900.01523.6020.0070.0070.0000.0000.0000.000
132A194LYS00.068-0.10023.582-0.011-0.0110.0000.0000.0000.000
133A194LYS10.8961.05824.8570.0620.0620.0000.0000.0000.000
134A195GLY00.009-0.07925.3190.0000.0000.0000.0000.0000.000
135A196GLU00.091-0.00123.8460.0080.0080.0000.0000.0000.000
136A196GLU-1-0.803-0.72521.768-0.179-0.1790.0000.0000.0000.000
137A197ASN00.032-0.04423.984-0.015-0.0150.0000.0000.0000.000
138A197ASN0-0.0980.06220.823-0.001-0.0010.0000.0000.0000.000
139A198PHE00.005-0.12024.8840.0010.0010.0000.0000.0000.000
140A198PHE0-0.0980.08428.7090.0040.0040.0000.0000.0000.000
141A199THR00.087-0.06428.655-0.004-0.0040.0000.0000.0000.000
142A199THR0-0.0730.01328.7370.0020.0020.0000.0000.0000.000
143A200GLU00.206-0.05930.7240.0040.0040.0000.0000.0000.000
144A200GLU-1-0.986-0.84435.108-0.074-0.0740.0000.0000.0000.000
145A201THR0-0.054-0.11933.9100.0060.0060.0000.0000.0000.000
146A201THR0-0.0540.04533.4190.0010.0010.0000.0000.0000.000
147A202ASP00.088-0.09531.7540.0070.0070.0000.0000.0000.000
148A202ASP-1-0.868-0.78730.090-0.096-0.0960.0000.0000.0000.000
149A203VAL00.047-0.10033.1860.0060.0060.0000.0000.0000.000
150A203VAL0-0.0490.12633.4240.0000.0000.0000.0000.0000.000
151A204LYS00.038-0.10735.4390.0050.0050.0000.0000.0000.000
152A204LYS10.7701.00538.0600.0610.0610.0000.0000.0000.000
153A205MET00.087-0.10936.5230.0050.0050.0000.0000.0000.000
154A205MET0-0.1110.09635.5290.0000.0000.0000.0000.0000.000
155A206MET00.135-0.07835.2930.0060.0060.0000.0000.0000.000
156A206MET0-0.1400.08832.1480.0010.0010.0000.0000.0000.000
157A207GLU00.031-0.12236.4180.0050.0050.0000.0000.0000.000
158A207GLU-1-0.842-0.78938.922-0.055-0.0550.0000.0000.0000.000
159A208ARG00.107-0.05339.5420.0030.0030.0000.0000.0000.000
160A208ARG10.8471.04840.5130.0400.0400.0000.0000.0000.000
161A209VAL00.062-0.10538.9470.0040.0040.0000.0000.0000.000
162A209VAL0-0.1010.08937.8280.0000.0000.0000.0000.0000.000
163A210VAL00.100-0.10539.1990.0040.0040.0000.0000.0000.000
164A210VAL0-0.0840.08637.0520.0000.0000.0000.0000.0000.000
165A211GLU00.119-0.09040.2560.0020.0020.0000.0000.0000.000
166A211GLU-1-0.985-0.84343.792-0.033-0.0330.0000.0000.0000.000
167A212GLN00.081-0.08143.7210.0020.0020.0000.0000.0000.000
168A212GLN0-0.1060.07843.603-0.002-0.0020.0000.0000.0000.000
169A213MET00.097-0.09742.3140.0030.0030.0000.0000.0000.000
170A213MET0-0.1090.07738.465-0.001-0.0010.0000.0000.0000.000
171A214CYS00.096-0.09343.8230.0030.0030.0000.0000.0000.000
172A214CYS0-0.1300.08342.6720.0000.0000.0000.0000.0000.000
173A215ILE00.031-0.09045.2110.0020.0020.0000.0000.0000.000
174A215ILE0-0.0540.10847.5630.0000.0000.0000.0000.0000.000
175A216THR00.069-0.07847.1570.0010.0010.0000.0000.0000.000
176A216THR0-0.0690.04846.5040.0000.0000.0000.0000.0000.000
177A217GLN00.101-0.06746.3340.0020.0020.0000.0000.0000.000
178A217GLN0-0.1300.06944.6980.0010.0010.0000.0000.0000.000
179A218TYR00.116-0.05447.5990.0020.0020.0000.0000.0000.000
180A218TYR0-0.1120.06549.8220.0000.0000.0000.0000.0000.000
181A219GLU00.128-0.08650.4940.0010.0010.0000.0000.0000.000
182A219GLU-1-0.990-0.85351.501-0.015-0.0150.0000.0000.0000.000
183A220ARG00.097-0.09250.7030.0010.0010.0000.0000.0000.000
184A220ARG10.7671.00547.8950.0090.0090.0000.0000.0000.000
185A221GLU0-0.020-0.13451.0090.0020.0020.0000.0000.0000.000
186A221GLU-1-0.963-0.84848.886-0.010-0.0100.0000.0000.0000.000
187A222SER00.037-0.05751.9650.0010.0010.0000.0000.0000.000
188A222SER0-0.0860.04854.3450.0000.0000.0000.0000.0000.000
189A223GLN00.036-0.11955.1120.0000.0000.0000.0000.0000.000
190A223GLN0-0.1420.05754.2850.0000.0000.0000.0000.0000.000
191A224ALA00.066-0.09655.7700.0010.0010.0000.0000.0000.000
192A224ALA0-0.1120.09455.2810.0000.0000.0000.0000.0000.000
193A225TYR0-0.124-0.14556.4710.0000.0000.0000.0000.0000.000
194A225TYR00.0770.04057.3360.0000.0000.0000.0000.0000.000