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: M9G4Z

Calculation Name: 3HJ5-B-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: B

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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -676925.585571
FMO2-HF: Nuclear repulsion 632371.295094
FMO2-HF: Total energy -44554.290477
FMO2-MP2: Total energy -44678.273356


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(B:126:GLY)


Summations of interaction energy for fragment #1(B:126:GLY)
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.
0.6864.1120.257-1.457-2.225-0.003
Interaction energy analysis for fragmet #1(B:126:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / 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].
3B128TYR00.0640.0022.868-1.1121.2850.033-1.181-1.250-0.003
4B128TYR0-0.1390.0282.595-1.125-0.4200.227-0.159-0.7730.000
5B129VAL00.050-0.1154.4671.6291.722-0.001-0.014-0.0770.000
6B129VAL0-0.0560.1267.2830.0010.0010.0000.0000.0000.000
7B130LEU00.095-0.1016.911-0.315-0.3150.0000.0000.0000.000
8B130LEU0-0.1050.1048.2040.0200.0200.0000.0000.0000.000
9B131GLY0-0.051-0.1168.9550.0570.0570.0000.0000.0000.000
10B132SER00.0970.03312.4760.0220.0220.0000.0000.0000.000
11B132SER0-0.0470.06316.7200.0010.0010.0000.0000.0000.000
12B133ALA00.114-0.09015.744-0.026-0.0260.0000.0000.0000.000
13B133ALA0-0.1330.08817.9250.0010.0010.0000.0000.0000.000
14B134MET00.008-0.11317.8090.0080.0080.0000.0000.0000.000
15B134MET0-0.0800.10016.021-0.003-0.0030.0000.0000.0000.000
16B135SER00.045-0.09419.7950.0050.0050.0000.0000.0000.000
17B135SER0-0.0040.08224.4800.0000.0000.0000.0000.0000.000
18B136ARG00.032-0.12122.433-0.009-0.0090.0000.0000.0000.000
19B136ARG10.8161.05919.6910.0160.0160.0000.0000.0000.000
20B137PRO0-0.011-0.08522.8410.0060.0060.0000.0000.0000.000
21B138ILE00.1230.01225.858-0.002-0.0020.0000.0000.0000.000
22B138ILE0-0.0790.11129.7710.0010.0010.0000.0000.0000.000
23B139ILE00.048-0.11627.9700.0010.0010.0000.0000.0000.000
24B139ILE0-0.0850.09324.616-0.001-0.0010.0000.0000.0000.000
25B140HIS00.061-0.06229.2350.0000.0000.0000.0000.0000.000
26B140HIS0-0.1180.07033.8570.0000.0000.0000.0000.0000.000
27B141PHE00.085-0.08631.485-0.002-0.0020.0000.0000.0000.000
28B141PHE0-0.0850.06826.265-0.002-0.0020.0000.0000.0000.000
29B142GLY00.027-0.09332.0820.0030.0030.0000.0000.0000.000
30B143SER00.0420.04534.6940.0030.0030.0000.0000.0000.000
31B143SER0-0.099-0.01334.5790.0010.0010.0000.0000.0000.000
32B144ASP00.126-0.10235.612-0.001-0.0010.0000.0000.0000.000
33B144ASP-1-0.956-0.83839.043-0.026-0.0260.0000.0000.0000.000
34B145TYR00.070-0.09535.5650.0020.0020.0000.0000.0000.000
35B145TYR0-0.0950.08631.1870.0010.0010.0000.0000.0000.000
36B146GLU00.062-0.13731.5910.0020.0020.0000.0000.0000.000
37B146GLU-1-0.906-0.77630.763-0.053-0.0530.0000.0000.0000.000
38B147ASP00.124-0.09231.114-0.002-0.0020.0000.0000.0000.000
39B147ASP-1-0.949-0.80633.119-0.034-0.0340.0000.0000.0000.000
40B148ARG00.000-0.13432.4590.0020.0020.0000.0000.0000.000
41B148ARG10.7720.97735.1590.0190.0190.0000.0000.0000.000
42B149TYR00.102-0.06230.8800.0040.0040.0000.0000.0000.000
43B149TYR0-0.0910.09226.470-0.002-0.0020.0000.0000.0000.000
44B150TYR00.122-0.08527.7360.0020.0020.0000.0000.0000.000
45B150TYR0-0.0770.08724.316-0.003-0.0030.0000.0000.0000.000
46B151ARG00.091-0.06928.1250.0010.0010.0000.0000.0000.000
47B151ARG10.8221.05332.1770.0210.0210.0000.0000.0000.000
48B152GLU00.067-0.11830.1050.0040.0040.0000.0000.0000.000
49B152GLU-1-0.886-0.77931.152-0.018-0.0180.0000.0000.0000.000
50B153ASN00.058-0.08826.7450.0050.0050.0000.0000.0000.000
51B153ASN0-0.1070.07025.734-0.001-0.0010.0000.0000.0000.000
52B154MET00.112-0.08324.354-0.003-0.0030.0000.0000.0000.000
53B154MET0-0.0440.10824.8510.0000.0000.0000.0000.0000.000
54B155HIS0-0.031-0.14722.839-0.006-0.0060.0000.0000.0000.000
55B155HIS0-0.0470.10824.2970.0030.0030.0000.0000.0000.000
56B156ARG00.053-0.11021.5900.0090.0090.0000.0000.0000.000
57B156ARG10.7991.03422.0530.0310.0310.0000.0000.0000.000
58B157TYR00.024-0.11918.596-0.005-0.0050.0000.0000.0000.000
59B157TYR0-0.0490.11319.018-0.002-0.0020.0000.0000.0000.000
60B158PRO00.029-0.07814.1700.0170.0170.0000.0000.0000.000
61B159ASN00.0670.03516.314-0.013-0.0130.0000.0000.0000.000
62B159ASN0-0.0730.07617.4430.0030.0030.0000.0000.0000.000
63B160GLN00.083-0.11914.257-0.002-0.0020.0000.0000.0000.000
64B160GLN0-0.0340.12113.3780.0090.0090.0000.0000.0000.000
65B161VAL00.082-0.09011.410-0.003-0.0030.0000.0000.0000.000
66B161VAL0-0.0690.09911.020-0.001-0.0010.0000.0000.0000.000
67B162TYR00.074-0.1146.7560.1690.1690.0000.0000.0000.000
68B162TYR0-0.0450.1105.093-0.140-0.1400.0000.0000.0000.000
69B163TYR00.070-0.0897.805-0.200-0.2000.0000.0000.0000.000
70B163TYR0-0.0550.1009.9810.0140.0140.0000.0000.0000.000
71B164ARG00.135-0.0837.6320.1670.1670.0000.0000.0000.000
72B164ARG10.8401.0764.2942.4412.609-0.001-0.092-0.0740.000
73B165PRO0-0.041-0.1328.1280.0310.0310.0000.0000.0000.000
74B166MET00.0850.01111.311-0.071-0.0710.0000.0000.0000.000
75B166MET0-0.1220.08714.9700.0060.0060.0000.0000.0000.000
76B167ASP00.087-0.08113.6730.0580.0580.0000.0000.0000.000
77B167ASP-1-1.021-0.87912.005-0.253-0.2530.0000.0000.0000.000
78B168GLU00.106-0.14415.1790.0280.0280.0000.0000.0000.000
79B168GLU-1-1.007-0.85117.933-0.124-0.1240.0000.0000.0000.000
80B169TYR00.045-0.09216.2920.0140.0140.0000.0000.0000.000
81B169TYR0-0.0920.09315.563-0.014-0.0140.0000.0000.0000.000
82B170SER0-0.010-0.09015.1540.0030.0030.0000.0000.0000.000
83B170SER0-0.0500.07613.213-0.012-0.0120.0000.0000.0000.000
84B171ASN00.121-0.02416.3770.0280.0280.0000.0000.0000.000
85B171ASN0-0.0680.05719.4790.0040.0040.0000.0000.0000.000
86B172GLN00.228-0.04317.624-0.031-0.0310.0000.0000.0000.000
87B172GLN0-0.0960.08619.5210.0100.0100.0000.0000.0000.000
88B173ASN00.114-0.03917.259-0.022-0.0220.0000.0000.0000.000
89B173ASN0-0.0890.06019.458-0.002-0.0020.0000.0000.0000.000
90B174ASN00.106-0.07815.702-0.018-0.0180.0000.0000.0000.000
91B174ASN0-0.0830.05715.1270.0220.0220.0000.0000.0000.000
92B175PHE00.186-0.02413.248-0.084-0.0840.0000.0000.0000.000
93B175PHE0-0.1310.06312.394-0.003-0.0030.0000.0000.0000.000
94B176VAL00.022-0.11013.081-0.062-0.0620.0000.0000.0000.000
95B176VAL0-0.0620.09516.6130.0070.0070.0000.0000.0000.000
96B177HIS00.084-0.06214.568-0.004-0.0040.0000.0000.0000.000
97B177HIS0-0.0960.07814.894-0.019-0.0190.0000.0000.0000.000
98B178ASP00.109-0.10611.2720.0190.0190.0000.0000.0000.000
99B178ASP-1-0.916-0.8078.975-1.015-1.0150.0000.0000.0000.000
100B179CYS00.104-0.0909.738-0.109-0.1090.0000.0000.0000.000
101B179CYS0-0.1530.09510.8390.0380.0380.0000.0000.0000.000
102B180VAL00.103-0.10810.628-0.020-0.0200.0000.0000.0000.000
103B180VAL0-0.0910.09014.5620.0090.0090.0000.0000.0000.000
104B181ASN00.079-0.07311.5590.0300.0300.0000.0000.0000.000
105B181ASN0-0.1490.03710.5470.0100.0100.0000.0000.0000.000
106B182ILE00.068-0.0897.2260.1270.1270.0000.0000.0000.000
107B182ILE0-0.0900.0994.235-0.125-0.062-0.001-0.011-0.0510.000
108B183THR00.062-0.0888.6580.0460.0460.0000.0000.0000.000
109B183THR0-0.0120.09010.0790.0210.0210.0000.0000.0000.000
110B184ILE00.118-0.0829.9960.0550.0550.0000.0000.0000.000
111B184ILE0-0.0590.10913.5850.0050.0050.0000.0000.0000.000
112B185LYS00.116-0.03711.1160.0760.0760.0000.0000.0000.000
113B185LYS10.8721.06310.0730.3880.3880.0000.0000.0000.000
114B186GLN00.082-0.1198.2260.0210.0210.0000.0000.0000.000
115B186GLN0-0.1190.0946.872-0.168-0.1680.0000.0000.0000.000
116B187HIS00.094-0.0729.3780.0670.0670.0000.0000.0000.000
117B187HIS0-0.1160.06512.934-0.002-0.0020.0000.0000.0000.000
118B188THR00.014-0.08112.7560.0380.0380.0000.0000.0000.000
119B188THR0-0.0980.00113.9210.0030.0030.0000.0000.0000.000
120B189VAL00.017-0.09112.3990.0280.0280.0000.0000.0000.000
121B189VAL0-0.0810.09010.250-0.003-0.0030.0000.0000.0000.000
122B190THR00.015-0.10713.4410.0220.0220.0000.0000.0000.000
123B190THR0-0.0540.08612.4840.0150.0150.0000.0000.0000.000
124B191THR00.018-0.07814.061-0.010-0.0100.0000.0000.0000.000
125B191THR0-0.0550.06216.1000.0030.0030.0000.0000.0000.000
126B192THR00.071-0.02817.2410.0170.0170.0000.0000.0000.000
127B192THR0-0.1130.00719.396-0.004-0.0040.0000.0000.0000.000
128B193THR0-0.095-0.13120.2610.0020.0020.0000.0000.0000.000
129B193THR0-0.0090.07823.697-0.001-0.0010.0000.0000.0000.000
130B194LYS00.162-0.03823.984-0.003-0.0030.0000.0000.0000.000
131B194LYS10.8621.04826.0380.0160.0160.0000.0000.0000.000
132B195GLY0-0.004-0.12026.453-0.002-0.0020.0000.0000.0000.000
133B196GLU00.1590.02224.956-0.002-0.0020.0000.0000.0000.000
134B196GLU-1-0.919-0.79122.3070.0290.0290.0000.0000.0000.000
135B197ASN00.078-0.06524.8360.0010.0010.0000.0000.0000.000
136B197ASN0-0.1190.05721.682-0.010-0.0100.0000.0000.0000.000
137B198PHE00.030-0.09125.489-0.005-0.0050.0000.0000.0000.000
138B198PHE0-0.1310.06729.4170.0000.0000.0000.0000.0000.000
139B199THR00.073-0.05029.1420.0040.0040.0000.0000.0000.000
140B199THR0-0.0420.02728.5170.0000.0000.0000.0000.0000.000
141B200GLU00.120-0.12130.7040.0010.0010.0000.0000.0000.000
142B200GLU-1-0.992-0.83533.891-0.002-0.0020.0000.0000.0000.000
143B201THR0-0.012-0.06433.5430.0010.0010.0000.0000.0000.000
144B201THR0-0.0890.04333.6980.0000.0000.0000.0000.0000.000
145B202ASP00.110-0.08932.4570.0010.0010.0000.0000.0000.000
146B202ASP-1-0.852-0.80730.880-0.020-0.0200.0000.0000.0000.000
147B203VAL00.054-0.07433.9020.0000.0000.0000.0000.0000.000
148B203VAL0-0.0540.11633.2140.0000.0000.0000.0000.0000.000
149B204LYS00.212-0.05535.5080.0010.0010.0000.0000.0000.000
150B204LYS10.8381.06138.4080.0060.0060.0000.0000.0000.000
151B205MET00.016-0.13837.1570.0010.0010.0000.0000.0000.000
152B205MET0-0.1260.08936.332-0.001-0.0010.0000.0000.0000.000
153B206MET00.073-0.12136.209-0.001-0.0010.0000.0000.0000.000
154B206MET0-0.1040.09032.1990.0000.0000.0000.0000.0000.000
155B207GLU00.034-0.10137.5660.0000.0000.0000.0000.0000.000
156B207GLU-1-0.931-0.83439.754-0.002-0.0020.0000.0000.0000.000
157B208ARG00.113-0.06440.2180.0010.0010.0000.0000.0000.000
158B208ARG10.8721.05841.9390.0100.0100.0000.0000.0000.000
159B209VAL00.047-0.11639.5620.0000.0000.0000.0000.0000.000
160B209VAL0-0.0980.08738.3360.0000.0000.0000.0000.0000.000
161B210VAL00.073-0.11340.274-0.001-0.0010.0000.0000.0000.000
162B210VAL0-0.0830.09338.1680.0000.0000.0000.0000.0000.000
163B211GLU00.163-0.09041.2370.0010.0010.0000.0000.0000.000
164B211GLU-1-0.968-0.82044.839-0.006-0.0060.0000.0000.0000.000
165B212GLN00.054-0.10644.6290.0010.0010.0000.0000.0000.000
166B212GLN0-0.1320.07844.525-0.001-0.0010.0000.0000.0000.000
167B213MET00.096-0.10742.6270.0000.0000.0000.0000.0000.000
168B213MET0-0.0950.08438.866-0.001-0.0010.0000.0000.0000.000
169B214CYS00.071-0.11944.1430.0000.0000.0000.0000.0000.000
170B214CYS0-0.1410.08543.2750.0010.0010.0000.0000.0000.000
171B215ILE00.067-0.08745.8260.0010.0010.0000.0000.0000.000
172B215ILE0-0.0500.12448.8290.0000.0000.0000.0000.0000.000
173B216THR00.041-0.10147.7590.0010.0010.0000.0000.0000.000
174B216THR0-0.0830.05346.807-0.001-0.0010.0000.0000.0000.000
175B217GLN00.059-0.08846.9280.0000.0000.0000.0000.0000.000
176B217GLN0-0.0670.11944.0080.0000.0000.0000.0000.0000.000
177B218TYR00.137-0.05648.1550.0000.0000.0000.0000.0000.000
178B218TYR0-0.0680.09850.9580.0000.0000.0000.0000.0000.000
179B219GLU00.068-0.11351.2090.0010.0010.0000.0000.0000.000
180B219GLU-1-0.998-0.83252.406-0.006-0.0060.0000.0000.0000.000
181B220ARG00.078-0.07750.4170.0000.0000.0000.0000.0000.000
182B220ARG10.8101.01945.2680.0080.0080.0000.0000.0000.000
183B221GLU00.059-0.11551.2820.0000.0000.0000.0000.0000.000
184B221GLU-1-1.040-0.87250.099-0.001-0.0010.0000.0000.0000.000
185B222SER00.068-0.10352.2520.0000.0000.0000.0000.0000.000
186B222SER0-0.0890.04554.8690.0000.0000.0000.0000.0000.000
187B223GLN00.085-0.08855.3810.0000.0000.0000.0000.0000.000
188B223GLN0-0.1460.07055.2330.0000.0000.0000.0000.0000.000
189B224ALA00.084-0.11755.5150.0000.0000.0000.0000.0000.000
190B224ALA0-0.0730.10754.8270.0000.0000.0000.0000.0000.000
191B225TYR00.057-0.09656.5080.0000.0000.0000.0000.0000.000
192B225TYR0-0.1380.07856.1720.0000.0000.0000.0000.0000.000
193B226TYR0-0.042-0.11457.8550.0010.0010.0000.0000.0000.000
194B226TYR0-0.1260.07159.1940.0000.0000.0000.0000.0000.000
195B227GLN0-0.020-0.12261.3520.0000.0000.0000.0000.0000.000
196B227GLN00.0580.03558.4490.0000.0000.0000.0000.0000.000