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: 7MLQK

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 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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -678398.352638
FMO2-HF: Nuclear repulsion 633843.569431
FMO2-HF: Total energy -44554.783207
FMO2-MP2: Total energy -44678.70348


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.
-0.7921.9382.026-1.791-2.9650.002
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 : 0.035 / q_NPA : 0.004
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].
3B128TYR00.0600.0152.811-3.108-0.6690.134-1.266-1.3060.001
4B128TYR0-0.1380.0261.980-0.799-0.9671.892-0.362-1.3620.001
5B129VAL00.060-0.1224.4651.5101.615-0.001-0.011-0.0930.000
6B129VAL0-0.0590.1287.854-0.015-0.0150.0000.0000.0000.000
7B130LEU00.112-0.0977.451-0.289-0.2890.0000.0000.0000.000
8B130LEU0-0.1110.1108.8840.0240.0240.0000.0000.0000.000
9B131GLY0-0.058-0.1269.5550.0120.0120.0000.0000.0000.000
10B132SER00.0890.00513.0310.0230.0230.0000.0000.0000.000
11B132SER0-0.0420.07917.407-0.003-0.0030.0000.0000.0000.000
12B133ALA00.120-0.08116.338-0.024-0.0240.0000.0000.0000.000
13B133ALA0-0.1280.09018.4380.0010.0010.0000.0000.0000.000
14B134MET00.024-0.11918.2070.0020.0020.0000.0000.0000.000
15B134MET0-0.0680.11215.801-0.003-0.0030.0000.0000.0000.000
16B135SER00.036-0.10520.1320.0060.0060.0000.0000.0000.000
17B135SER0-0.0050.08724.727-0.001-0.0010.0000.0000.0000.000
18B136ARG00.029-0.10322.577-0.008-0.0080.0000.0000.0000.000
19B136ARG10.8321.06919.916-0.031-0.0310.0000.0000.0000.000
20B137PRO0-0.021-0.09222.8530.0030.0030.0000.0000.0000.000
21B138ILE00.1240.02025.878-0.001-0.0010.0000.0000.0000.000
22B138ILE0-0.0630.10829.9550.0010.0010.0000.0000.0000.000
23B139ILE00.033-0.12128.1020.0000.0000.0000.0000.0000.000
24B139ILE0-0.0780.09924.808-0.001-0.0010.0000.0000.0000.000
25B140HIS00.084-0.06529.3910.0010.0010.0000.0000.0000.000
26B140HIS0-0.1110.07133.8540.0000.0000.0000.0000.0000.000
27B141PHE00.052-0.07631.705-0.003-0.0030.0000.0000.0000.000
28B141PHE0-0.1140.06326.412-0.001-0.0010.0000.0000.0000.000
29B142GLY00.031-0.10332.3790.0020.0020.0000.0000.0000.000
30B143SER00.0250.01434.7320.0020.0020.0000.0000.0000.000
31B143SER0-0.0790.01435.0180.0010.0010.0000.0000.0000.000
32B144ASP00.089-0.11335.346-0.001-0.0010.0000.0000.0000.000
33B144ASP-1-0.916-0.82239.114-0.017-0.0170.0000.0000.0000.000
34B145TYR00.056-0.08835.6110.0030.0030.0000.0000.0000.000
35B145TYR0-0.0860.08631.4570.0010.0010.0000.0000.0000.000
36B146GLU00.052-0.13231.5100.0020.0020.0000.0000.0000.000
37B146GLU-1-0.853-0.77431.078-0.039-0.0390.0000.0000.0000.000
38B147ASP00.111-0.05931.1200.0000.0000.0000.0000.0000.000
39B147ASP-1-0.868-0.76933.672-0.017-0.0170.0000.0000.0000.000
40B148ARG00.013-0.12932.6890.0030.0030.0000.0000.0000.000
41B148ARG10.7810.97034.9720.0070.0070.0000.0000.0000.000
42B149TYR00.097-0.06230.8770.0040.0040.0000.0000.0000.000
43B149TYR0-0.0830.09525.8930.0010.0010.0000.0000.0000.000
44B150TYR00.135-0.08327.6750.0030.0030.0000.0000.0000.000
45B150TYR0-0.0950.07424.341-0.002-0.0020.0000.0000.0000.000
46B151ARG00.086-0.07628.1780.0030.0030.0000.0000.0000.000
47B151ARG10.7170.98332.3140.0090.0090.0000.0000.0000.000
48B152GLU00.071-0.12230.4410.0050.0050.0000.0000.0000.000
49B152GLU-1-0.870-0.74531.536-0.005-0.0050.0000.0000.0000.000
50B153ASN00.035-0.08526.9780.0060.0060.0000.0000.0000.000
51B153ASN0-0.0940.05726.0110.0010.0010.0000.0000.0000.000
52B154MET00.116-0.07324.237-0.001-0.0010.0000.0000.0000.000
53B154MET0-0.0560.10524.7310.0020.0020.0000.0000.0000.000
54B155HIS00.055-0.13022.724-0.002-0.0020.0000.0000.0000.000
55B155HIS0-0.0740.09124.5540.0040.0040.0000.0000.0000.000
56B156ARG00.010-0.11121.8830.0120.0120.0000.0000.0000.000
57B156ARG10.8031.02922.4060.0020.0020.0000.0000.0000.000
58B157TYR00.017-0.10518.819-0.002-0.0020.0000.0000.0000.000
59B157TYR0-0.0470.11019.342-0.004-0.0040.0000.0000.0000.000
60B158PRO00.020-0.08714.4400.0150.0150.0000.0000.0000.000
61B159ASN00.0440.03416.544-0.019-0.0190.0000.0000.0000.000
62B159ASN0-0.1090.05718.7610.0050.0050.0000.0000.0000.000
63B160GLN00.121-0.10714.605-0.006-0.0060.0000.0000.0000.000
64B160GLN0-0.0300.11613.6320.0030.0030.0000.0000.0000.000
65B161VAL00.062-0.09911.7140.0010.0010.0000.0000.0000.000
66B161VAL0-0.0590.10911.330-0.004-0.0040.0000.0000.0000.000
67B162TYR00.101-0.1047.0880.1350.1350.0000.0000.0000.000
68B162TYR0-0.0800.0955.696-0.101-0.1010.0000.0000.0000.000
69B163TYR00.095-0.0848.040-0.204-0.2040.0000.0000.0000.000
70B163TYR0-0.0620.09010.1030.0060.0060.0000.0000.0000.000
71B164ARG00.124-0.0927.5070.1920.1920.0000.0000.0000.000
72B164ARG10.8351.0793.8092.9623.1960.000-0.116-0.1180.000
73B165PRO0-0.037-0.1318.3030.0560.0560.0000.0000.0000.000
74B166MET00.0650.00711.318-0.111-0.1110.0000.0000.0000.000
75B166MET0-0.1020.08514.9840.0090.0090.0000.0000.0000.000
76B167ASP00.082-0.08013.0950.0670.0670.0000.0000.0000.000
77B167ASP-1-1.017-0.88311.312-0.390-0.3900.0000.0000.0000.000
78B168GLU00.120-0.11414.5670.0350.0350.0000.0000.0000.000
79B168GLU-1-0.981-0.83117.340-0.159-0.1590.0000.0000.0000.000
80B169TYR00.032-0.10616.1310.0210.0210.0000.0000.0000.000
81B169TYR0-0.1180.06615.124-0.016-0.0160.0000.0000.0000.000
82B170SER0-0.035-0.08714.6080.0020.0020.0000.0000.0000.000
83B170SER0-0.0430.07612.751-0.015-0.0150.0000.0000.0000.000
84B171ASN00.158-0.02815.6540.0290.0290.0000.0000.0000.000
85B171ASN0-0.0830.04918.7290.0080.0080.0000.0000.0000.000
86B172GLN00.173-0.07417.298-0.034-0.0340.0000.0000.0000.000
87B172GLN0-0.0660.10019.5090.0110.0110.0000.0000.0000.000
88B173ASN00.091-0.05717.553-0.010-0.0100.0000.0000.0000.000
89B173ASN0-0.0890.06319.6170.0060.0060.0000.0000.0000.000
90B174ASN00.113-0.05915.417-0.008-0.0080.0000.0000.0000.000
91B174ASN0-0.0880.06214.5270.0310.0310.0000.0000.0000.000
92B175PHE00.182-0.05113.059-0.084-0.0840.0000.0000.0000.000
93B175PHE0-0.1170.09112.8420.0000.0000.0000.0000.0000.000
94B176VAL00.049-0.11512.812-0.047-0.0470.0000.0000.0000.000
95B176VAL0-0.0850.08816.6430.0070.0070.0000.0000.0000.000
96B177HIS00.138-0.06914.2620.0040.0040.0000.0000.0000.000
97B177HIS0-0.1110.08213.523-0.022-0.0220.0000.0000.0000.000
98B178ASP00.083-0.08710.6510.0210.0210.0000.0000.0000.000
99B178ASP-1-0.925-0.8008.459-1.102-1.1020.0000.0000.0000.000
100B179CYS00.135-0.0929.308-0.107-0.1070.0000.0000.0000.000
101B179CYS0-0.1330.10610.6840.0330.0330.0000.0000.0000.000
102B180VAL00.064-0.10110.3870.0190.0190.0000.0000.0000.000
103B180VAL0-0.0680.10214.2870.0080.0080.0000.0000.0000.000
104B181ASN00.098-0.07611.2610.0540.0540.0000.0000.0000.000
105B181ASN0-0.1550.03410.5400.0130.0130.0000.0000.0000.000
106B182ILE00.064-0.1006.7310.1100.1100.0000.0000.0000.000
107B182ILE0-0.1020.1103.743-0.205-0.0850.001-0.036-0.0860.000
108B183THR00.018-0.1098.0990.0530.0530.0000.0000.0000.000
109B183THR0-0.0160.08010.0590.0380.0380.0000.0000.0000.000
110B184ILE00.114-0.07010.1120.0610.0610.0000.0000.0000.000
111B184ILE0-0.0640.11013.5720.0030.0030.0000.0000.0000.000
112B185LYS00.106-0.04910.7850.0710.0710.0000.0000.0000.000
113B185LYS10.8731.0629.7270.3610.3610.0000.0000.0000.000
114B186GLN00.087-0.1208.4700.0080.0080.0000.0000.0000.000
115B186GLN0-0.1020.1007.415-0.103-0.1030.0000.0000.0000.000
116B187HIS00.112-0.0849.5500.0710.0710.0000.0000.0000.000
117B187HIS0-0.0950.08213.2060.0070.0070.0000.0000.0000.000
118B188THR00.014-0.08713.0320.0340.0340.0000.0000.0000.000
119B188THR0-0.1100.01413.766-0.001-0.0010.0000.0000.0000.000
120B189VAL00.009-0.08812.2810.0140.0140.0000.0000.0000.000
121B189VAL0-0.0980.08310.128-0.005-0.0050.0000.0000.0000.000
122B190THR00.015-0.10913.4650.0250.0250.0000.0000.0000.000
123B190THR0-0.0670.08312.5680.0210.0210.0000.0000.0000.000
124B191THR00.036-0.07114.263-0.016-0.0160.0000.0000.0000.000
125B191THR0-0.0470.05416.1130.0020.0020.0000.0000.0000.000
126B192THR00.011-0.07017.3720.0190.0190.0000.0000.0000.000
127B192THR0-0.0790.03319.589-0.005-0.0050.0000.0000.0000.000
128B193THR0-0.051-0.10420.614-0.005-0.0050.0000.0000.0000.000
129B193THR0-0.0290.07224.088-0.002-0.0020.0000.0000.0000.000
130B194LYS00.136-0.06224.407-0.002-0.0020.0000.0000.0000.000
131B194LYS10.8651.04526.435-0.003-0.0030.0000.0000.0000.000
132B195GLY0-0.010-0.11326.811-0.003-0.0030.0000.0000.0000.000
133B196GLU00.1840.02625.356-0.004-0.0040.0000.0000.0000.000
134B196GLU-1-0.946-0.78822.6460.0650.0650.0000.0000.0000.000
135B197ASN00.073-0.04624.8280.0030.0030.0000.0000.0000.000
136B197ASN0-0.1160.05321.543-0.009-0.0090.0000.0000.0000.000
137B198PHE00.037-0.10425.622-0.006-0.0060.0000.0000.0000.000
138B198PHE0-0.1050.07329.3940.0000.0000.0000.0000.0000.000
139B199THR00.082-0.05929.3080.0050.0050.0000.0000.0000.000
140B199THR0-0.0670.02129.067-0.001-0.0010.0000.0000.0000.000
141B200GLU00.115-0.11831.0770.0000.0000.0000.0000.0000.000
142B200GLU-1-0.991-0.83934.2210.0130.0130.0000.0000.0000.000
143B201THR0-0.009-0.07434.1850.0000.0000.0000.0000.0000.000
144B201THR0-0.0790.03833.8150.0000.0000.0000.0000.0000.000
145B202ASP00.081-0.10032.201-0.002-0.0020.0000.0000.0000.000
146B202ASP-1-0.856-0.80130.602-0.003-0.0030.0000.0000.0000.000
147B203VAL00.051-0.07833.636-0.001-0.0010.0000.0000.0000.000
148B203VAL0-0.0610.10633.4470.0000.0000.0000.0000.0000.000
149B204LYS00.142-0.06835.6880.0000.0000.0000.0000.0000.000
150B204LYS10.7991.02438.641-0.005-0.0050.0000.0000.0000.000
151B205MET00.069-0.11737.2990.0000.0000.0000.0000.0000.000
152B205MET0-0.1200.09636.468-0.001-0.0010.0000.0000.0000.000
153B206MET00.069-0.12336.396-0.001-0.0010.0000.0000.0000.000
154B206MET0-0.1150.09732.3700.0010.0010.0000.0000.0000.000
155B207GLU00.062-0.10637.7230.0000.0000.0000.0000.0000.000
156B207GLU-1-0.907-0.80440.1390.0080.0080.0000.0000.0000.000
157B208ARG00.109-0.08040.6000.0000.0000.0000.0000.0000.000
158B208ARG10.8751.07042.4310.0020.0020.0000.0000.0000.000
159B209VAL00.070-0.10339.8840.0000.0000.0000.0000.0000.000
160B209VAL0-0.0890.08738.6160.0000.0000.0000.0000.0000.000
161B210VAL00.090-0.09340.690-0.001-0.0010.0000.0000.0000.000
162B210VAL0-0.0750.10038.6950.0000.0000.0000.0000.0000.000
163B211GLU00.160-0.07541.6130.0000.0000.0000.0000.0000.000
164B211GLU-1-0.975-0.82745.1750.0010.0010.0000.0000.0000.000
165B212GLN00.056-0.11144.9870.0010.0010.0000.0000.0000.000
166B212GLN0-0.1210.07144.849-0.001-0.0010.0000.0000.0000.000
167B213MET00.101-0.07542.883-0.001-0.0010.0000.0000.0000.000
168B213MET0-0.1140.07439.0440.0000.0000.0000.0000.0000.000
169B214CYS00.096-0.11144.3880.0000.0000.0000.0000.0000.000
170B214CYS0-0.1590.07243.7900.0010.0010.0000.0000.0000.000
171B215ILE00.081-0.08046.2560.0010.0010.0000.0000.0000.000
172B215ILE0-0.0660.11349.1710.0000.0000.0000.0000.0000.000
173B216THR00.048-0.09547.7180.0000.0000.0000.0000.0000.000
174B216THR0-0.0940.03746.773-0.001-0.0010.0000.0000.0000.000
175B217GLN00.083-0.07247.011-0.001-0.0010.0000.0000.0000.000
176B217GLN0-0.0910.10444.094-0.001-0.0010.0000.0000.0000.000
177B218TYR00.124-0.07448.1640.0000.0000.0000.0000.0000.000
178B218TYR0-0.0810.09051.1800.0000.0000.0000.0000.0000.000
179B219GLU00.069-0.11651.4340.0010.0010.0000.0000.0000.000
180B219GLU-1-0.993-0.83252.348-0.001-0.0010.0000.0000.0000.000
181B220ARG00.068-0.07350.6120.0000.0000.0000.0000.0000.000
182B220ARG10.8131.02145.8980.0020.0020.0000.0000.0000.000
183B221GLU00.089-0.10951.5780.0000.0000.0000.0000.0000.000
184B221GLU-1-1.039-0.86850.4430.0040.0040.0000.0000.0000.000
185B222SER00.056-0.10652.6800.0000.0000.0000.0000.0000.000
186B222SER0-0.0780.04955.1340.0000.0000.0000.0000.0000.000
187B223GLN00.086-0.10355.7220.0000.0000.0000.0000.0000.000
188B223GLN0-0.1680.07555.211-0.001-0.0010.0000.0000.0000.000
189B224ALA00.095-0.10155.4830.0000.0000.0000.0000.0000.000
190B224ALA0-0.0770.10854.9080.0000.0000.0000.0000.0000.000
191B225TYR00.070-0.10156.6210.0000.0000.0000.0000.0000.000
192B225TYR0-0.1290.08156.4400.0000.0000.0000.0000.0000.000
193B226TYR0-0.026-0.10158.1710.0000.0000.0000.0000.0000.000
194B226TYR0-0.1010.07559.6430.0000.0000.0000.0000.0000.000
195B227GLN0-0.050-0.14660.7880.0000.0000.0000.0000.0000.000
196B227GLN00.0260.03158.3390.0000.0000.0000.0000.0000.000