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

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FMODB ID: ZN3KN

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 OptAll
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 -671375.148431
FMO2-HF: Nuclear repulsion 627459.757075
FMO2-HF: Total energy -43915.391356
FMO2-MP2: Total energy -44037.497255


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.
-2.342-0.949-0.021-0.694-0.6760.002
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 : 0.135 / q_NPA : 0.023
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].
4A127GLY0-0.010-0.0203.874-1.829-0.740-0.015-0.654-0.4180.002
5A128TYR00.0510.0025.2940.4680.536-0.002-0.004-0.0620.000
6A128TYR0-0.1890.0324.503-0.0270.106-0.001-0.030-0.1020.000
7A129VAL00.166-0.1015.768-0.996-0.974-0.0020.001-0.0210.000
8A129VAL0-0.0890.1229.4760.0430.0430.0000.0000.0000.000
9A130LEU00.108-0.1098.4670.0270.0270.0000.0000.0000.000
10A130LEU0-0.1190.1128.249-0.017-0.0170.0000.0000.0000.000
11A131GLY0-0.048-0.1289.5360.1660.1660.0000.0000.0000.000
12A132SER00.0770.01313.231-0.051-0.0510.0000.0000.0000.000
13A132SER0-0.0310.08417.1750.0120.0120.0000.0000.0000.000
14A133ALA00.125-0.08816.186-0.016-0.0160.0000.0000.0000.000
15A133ALA0-0.1160.09318.3420.0070.0070.0000.0000.0000.000
16A134MET0-0.019-0.11818.2720.0240.0240.0000.0000.0000.000
17A134MET0-0.0850.09417.4050.0040.0040.0000.0000.0000.000
18A135SER00.086-0.08420.791-0.003-0.0030.0000.0000.0000.000
19A135SER0-0.0210.08324.9360.0090.0090.0000.0000.0000.000
20A136ARG00.008-0.11422.487-0.020-0.0200.0000.0000.0000.000
21A136ARG10.8161.04319.8520.2910.2910.0000.0000.0000.000
22A137PRO0-0.002-0.10121.9070.0160.0160.0000.0000.0000.000
23A138ILE00.1230.03524.9720.0000.0000.0000.0000.0000.000
24A138ILE0-0.0690.10229.0580.0020.0020.0000.0000.0000.000
25A139ILE0-0.006-0.12127.584-0.002-0.0020.0000.0000.0000.000
26A139ILE0-0.0580.08924.130-0.002-0.0020.0000.0000.0000.000
27A140HIS00.057-0.06028.7900.0010.0010.0000.0000.0000.000
28A140HIS0-0.1060.06231.7510.0050.0050.0000.0000.0000.000
29A141PHE00.028-0.09730.717-0.001-0.0010.0000.0000.0000.000
30A141PHE0-0.1100.07125.629-0.003-0.0030.0000.0000.0000.000
31A142GLY00.064-0.08731.3770.0050.0050.0000.0000.0000.000
32A143SER00.0040.00733.7410.0060.0060.0000.0000.0000.000
33A143SER0-0.0900.00933.8000.0010.0010.0000.0000.0000.000
34A144ASP00.125-0.07934.352-0.007-0.0070.0000.0000.0000.000
35A144ASP-1-0.994-0.86037.996-0.079-0.0790.0000.0000.0000.000
36A145TYR00.114-0.07334.478-0.005-0.0050.0000.0000.0000.000
37A145TYR0-0.0980.08430.1540.0020.0020.0000.0000.0000.000
38A146GLU00.031-0.12530.481-0.004-0.0040.0000.0000.0000.000
39A146GLU-1-0.871-0.78330.011-0.100-0.1000.0000.0000.0000.000
40A147ASP00.121-0.09230.144-0.011-0.0110.0000.0000.0000.000
41A147ASP-1-0.899-0.79332.255-0.111-0.1110.0000.0000.0000.000
42A148ARG00.063-0.10531.660-0.009-0.0090.0000.0000.0000.000
43A148ARG10.7790.99034.1480.0880.0880.0000.0000.0000.000
44A149TYR00.054-0.10629.962-0.003-0.0030.0000.0000.0000.000
45A149TYR0-0.0710.09725.547-0.003-0.0030.0000.0000.0000.000
46A150TYR00.112-0.07827.061-0.007-0.0070.0000.0000.0000.000
47A150TYR0-0.0830.07123.817-0.008-0.0080.0000.0000.0000.000
48A151ARG00.089-0.10227.848-0.013-0.0130.0000.0000.0000.000
49A151ARG10.7671.01132.1080.1020.1020.0000.0000.0000.000
50A152GLU00.024-0.09730.269-0.006-0.0060.0000.0000.0000.000
51A152GLU-1-0.830-0.73331.198-0.094-0.0940.0000.0000.0000.000
52A153ASN00.060-0.08326.4060.0020.0020.0000.0000.0000.000
53A153ASN0-0.1030.05125.4000.0000.0000.0000.0000.0000.000
54A154MET00.148-0.08224.044-0.014-0.0140.0000.0000.0000.000
55A154MET0-0.0740.10324.668-0.004-0.0040.0000.0000.0000.000
56A155HIS00.012-0.12722.750-0.028-0.0280.0000.0000.0000.000
57A155HIS0-0.0520.10524.360-0.002-0.0020.0000.0000.0000.000
58A156ARG00.006-0.10121.495-0.024-0.0240.0000.0000.0000.000
59A156ARG10.8131.03521.7830.1580.1580.0000.0000.0000.000
60A157TYR00.039-0.09118.459-0.016-0.0160.0000.0000.0000.000
61A157TYR0-0.0360.11019.1850.0030.0030.0000.0000.0000.000
62A158PRO00.046-0.07414.3640.0090.0090.0000.0000.0000.000
63A159ASN00.0720.03316.4370.0360.0360.0000.0000.0000.000
64A159ASN0-0.0850.05816.627-0.020-0.0200.0000.0000.0000.000
65A160GLN00.060-0.10814.9700.0600.0600.0000.0000.0000.000
66A160GLN0-0.0220.12212.6090.0670.0670.0000.0000.0000.000
67A161VAL00.002-0.11512.440-0.009-0.0090.0000.0000.0000.000
68A161VAL0-0.0030.11713.0510.0120.0120.0000.0000.0000.000
69A162TYR00.132-0.0878.0110.0530.0530.0000.0000.0000.000
70A162TYR0-0.0710.0995.819-0.207-0.2070.0000.0000.0000.000
71A163TYR00.084-0.0679.2470.1060.1060.0000.0000.0000.000
72A163TYR0-0.0670.08811.7840.0540.0540.0000.0000.0000.000
73A164ARG00.133-0.1049.664-0.236-0.2360.0000.0000.0000.000
74A164ARG10.7811.02210.6330.2950.2950.0000.0000.0000.000
75A165PRO0-0.056-0.12910.3940.1010.1010.0000.0000.0000.000
76A166MET00.1190.01113.5620.0160.0160.0000.0000.0000.000
77A166MET0-0.1070.10117.420-0.008-0.0080.0000.0000.0000.000
78A167ASP00.048-0.06917.0700.0060.0060.0000.0000.0000.000
79A167ASP-1-0.804-0.76916.388-0.171-0.1710.0000.0000.0000.000
80A168GLU00.083-0.13118.743-0.018-0.0180.0000.0000.0000.000
81A168GLU-1-0.923-0.79021.815-0.044-0.0440.0000.0000.0000.000
82A169TYR00.055-0.07819.3520.0100.0100.0000.0000.0000.000
83A169TYR0-0.1400.04418.2830.0090.0090.0000.0000.0000.000
84A170SER00.009-0.10617.7600.0050.0050.0000.0000.0000.000
85A170SER0-0.0870.03916.802-0.027-0.0270.0000.0000.0000.000
86A171ASN00.077-0.06018.5150.0060.0060.0000.0000.0000.000
87A171ASN0-0.1030.06519.773-0.001-0.0010.0000.0000.0000.000
88A172GLN00.153-0.09219.117-0.025-0.0250.0000.0000.0000.000
89A172GLN0-0.0760.10321.2940.0150.0150.0000.0000.0000.000
90A173ASN00.121-0.04319.192-0.029-0.0290.0000.0000.0000.000
91A173ASN0-0.1180.05620.651-0.004-0.0040.0000.0000.0000.000
92A174ASN00.112-0.05216.618-0.016-0.0160.0000.0000.0000.000
93A174ASN0-0.0470.06515.994-0.013-0.0130.0000.0000.0000.000
94A175PHE00.154-0.07114.745-0.042-0.0420.0000.0000.0000.000
95A175PHE0-0.1310.08415.498-0.008-0.0080.0000.0000.0000.000
96A176VAL00.056-0.11814.269-0.088-0.0880.0000.0000.0000.000
97A176VAL0-0.0800.10017.5650.0030.0030.0000.0000.0000.000
98A177HIS00.135-0.07014.896-0.040-0.0400.0000.0000.0000.000
99A177HIS0-0.1490.06214.3610.0390.0390.0000.0000.0000.000
100A178ASP00.056-0.10711.1480.0370.0370.0000.0000.0000.000
101A178ASP-1-0.915-0.80010.366-0.455-0.4550.0000.0000.0000.000
102A179CYS00.154-0.07910.525-0.092-0.0920.0000.0000.0000.000
103A179CYS0-0.1960.08112.1760.0340.0340.0000.0000.0000.000
104A180VAL00.074-0.10211.417-0.113-0.1130.0000.0000.0000.000
105A180VAL0-0.0700.10814.8220.0080.0080.0000.0000.0000.000
106A181ASN00.126-0.06211.421-0.023-0.0230.0000.0000.0000.000
107A181ASN0-0.1100.06210.9600.0150.0150.0000.0000.0000.000
108A182ILE00.025-0.1197.2770.1660.1660.0000.0000.0000.000
109A182ILE0-0.0660.1115.272-0.049-0.0490.0000.0000.0000.000
110A183THR00.019-0.1077.940-0.114-0.1140.0000.0000.0000.000
111A183THR0-0.0100.07611.218-0.037-0.0370.0000.0000.0000.000
112A184ILE00.102-0.06510.249-0.021-0.0210.0000.0000.0000.000
113A184ILE0-0.0650.11012.8600.0090.0090.0000.0000.0000.000
114A185LYS00.114-0.0498.8870.0410.0410.0000.0000.0000.000
115A185LYS10.8741.0557.087-0.094-0.0940.0000.0000.0000.000
116A186GLN00.094-0.1157.8140.1800.1800.0000.0000.0000.000
117A186GLN0-0.1110.0964.1280.4220.503-0.001-0.007-0.0730.000
118A187HIS00.119-0.0768.4770.0090.0090.0000.0000.0000.000
119A187HIS0-0.0980.07912.806-0.048-0.0480.0000.0000.0000.000
120A188THR00.009-0.08912.0970.0340.0340.0000.0000.0000.000
121A188THR0-0.1080.01712.1880.0260.0260.0000.0000.0000.000
122A189VAL00.013-0.08310.5110.0630.0630.0000.0000.0000.000
123A189VAL0-0.1140.0738.3910.0190.0190.0000.0000.0000.000
124A190THR00.028-0.09811.7910.0190.0190.0000.0000.0000.000
125A190THR0-0.0610.07711.680-0.035-0.0350.0000.0000.0000.000
126A191THR00.007-0.09813.2130.0430.0430.0000.0000.0000.000
127A191THR0-0.0620.06514.4600.0050.0050.0000.0000.0000.000
128A192THR00.029-0.08216.270-0.024-0.0240.0000.0000.0000.000
129A192THR0-0.0690.05018.0740.0000.0000.0000.0000.0000.000
130A193THR0-0.033-0.08819.5420.0160.0160.0000.0000.0000.000
131A193THR0-0.0820.01023.3980.0080.0080.0000.0000.0000.000
132A194LYS00.107-0.08123.266-0.012-0.0120.0000.0000.0000.000
133A194LYS10.8771.05424.8390.0790.0790.0000.0000.0000.000
134A195GLY00.002-0.09625.3610.0000.0000.0000.0000.0000.000
135A196GLU00.047-0.02023.4400.0090.0090.0000.0000.0000.000
136A196GLU-1-0.772-0.70721.932-0.171-0.1710.0000.0000.0000.000
137A197ASN00.040-0.04024.011-0.014-0.0140.0000.0000.0000.000
138A197ASN0-0.1040.05420.773-0.001-0.0010.0000.0000.0000.000
139A198PHE00.056-0.11824.9240.0020.0020.0000.0000.0000.000
140A198PHE0-0.0890.08828.8990.0030.0030.0000.0000.0000.000
141A199THR00.076-0.06828.763-0.004-0.0040.0000.0000.0000.000
142A199THR0-0.0750.02528.8360.0030.0030.0000.0000.0000.000
143A200GLU00.162-0.06930.8440.0040.0040.0000.0000.0000.000
144A200GLU-1-0.935-0.82535.309-0.077-0.0770.0000.0000.0000.000
145A201THR0-0.015-0.09134.0030.0070.0070.0000.0000.0000.000
146A201THR0-0.0670.03333.2890.0010.0010.0000.0000.0000.000
147A202ASP00.081-0.09831.4370.0070.0070.0000.0000.0000.000
148A202ASP-1-0.855-0.79029.884-0.109-0.1090.0000.0000.0000.000
149A203VAL00.052-0.08632.8720.0060.0060.0000.0000.0000.000
150A203VAL0-0.0690.11333.0920.0000.0000.0000.0000.0000.000
151A204LYS00.034-0.12735.1120.0050.0050.0000.0000.0000.000
152A204LYS10.7491.02437.9210.0680.0680.0000.0000.0000.000
153A205MET00.083-0.09936.3500.0050.0050.0000.0000.0000.000
154A205MET0-0.1190.08435.3470.0000.0000.0000.0000.0000.000
155A206MET00.112-0.08635.0970.0060.0060.0000.0000.0000.000
156A206MET0-0.1360.08131.9570.0000.0000.0000.0000.0000.000
157A207GLU00.071-0.10336.2310.0040.0040.0000.0000.0000.000
158A207GLU-1-0.887-0.81338.850-0.061-0.0610.0000.0000.0000.000
159A208ARG00.101-0.08239.3830.0040.0040.0000.0000.0000.000
160A208ARG10.8621.06540.5380.0450.0450.0000.0000.0000.000
161A209VAL00.091-0.09638.8880.0040.0040.0000.0000.0000.000
162A209VAL0-0.0860.09637.7760.0000.0000.0000.0000.0000.000
163A210VAL00.091-0.09439.2350.0040.0040.0000.0000.0000.000
164A210VAL0-0.0780.09537.1300.0000.0000.0000.0000.0000.000
165A211GLU00.140-0.09240.1770.0030.0030.0000.0000.0000.000
166A211GLU-1-1.011-0.84943.718-0.039-0.0390.0000.0000.0000.000
167A212GLN00.084-0.06743.7510.0030.0030.0000.0000.0000.000
168A212GLN0-0.0920.08043.257-0.002-0.0020.0000.0000.0000.000
169A213MET00.090-0.09342.0640.0030.0030.0000.0000.0000.000
170A213MET0-0.1050.07738.455-0.001-0.0010.0000.0000.0000.000
171A214CYS00.096-0.11043.5600.0030.0030.0000.0000.0000.000
172A214CYS0-0.1560.07442.4640.0000.0000.0000.0000.0000.000
173A215ILE00.037-0.09545.1230.0020.0020.0000.0000.0000.000
174A215ILE0-0.0750.09747.6820.0000.0000.0000.0000.0000.000
175A216THR00.078-0.08147.2520.0020.0020.0000.0000.0000.000
176A216THR0-0.0810.04246.3590.0000.0000.0000.0000.0000.000
177A217GLN00.089-0.06946.5710.0020.0020.0000.0000.0000.000
178A217GLN0-0.1440.06544.8890.0010.0010.0000.0000.0000.000
179A218TYR00.127-0.06947.7980.0020.0020.0000.0000.0000.000
180A218TYR0-0.1060.07849.7600.0000.0000.0000.0000.0000.000
181A219GLU00.092-0.09650.5410.0010.0010.0000.0000.0000.000
182A219GLU-1-0.999-0.85251.409-0.019-0.0190.0000.0000.0000.000
183A220ARG00.097-0.08750.9010.0010.0010.0000.0000.0000.000
184A220ARG10.7371.00647.6600.0140.0140.0000.0000.0000.000
185A221GLU00.025-0.12751.4360.0020.0020.0000.0000.0000.000
186A221GLU-1-0.917-0.82249.259-0.014-0.0140.0000.0000.0000.000
187A222SER00.044-0.07352.4550.0010.0010.0000.0000.0000.000
188A222SER0-0.0850.04954.4690.0000.0000.0000.0000.0000.000
189A223GLN00.017-0.14355.4330.0010.0010.0000.0000.0000.000
190A223GLN0-0.1080.08654.3630.0010.0010.0000.0000.0000.000
191A224ALA00.071-0.07755.9300.0010.0010.0000.0000.0000.000
192A224ALA0-0.0830.10055.1230.0000.0000.0000.0000.0000.000
193A225TYR0-0.134-0.14457.1810.0010.0010.0000.0000.0000.000
194A225TYR00.0320.00757.1390.0000.0000.0000.0000.0000.000