FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 16LYZ

Calculation Name: 3Q4H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q4H

Chain ID: A

ChEMBL ID:

UniProt ID: A0QQ43

Base Structure: X-ray

Registration Date: 2025-07-09

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 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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -449323.052452
FMO2-HF: Nuclear repulsion 416658.97478
FMO2-HF: Total energy -32664.077672
FMO2-MP2: Total energy -32758.029496


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:5:ASP)


Summations of interaction energy for fragment #1(A:5:ASP)
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.
-12.615-7.1170.822-3.136-3.1820.029
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.106 / q_NPA : 0.027
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].
4A6ALA0-0.0860.1144.709-0.1650.009-0.001-0.079-0.0930.000
5A7HIS00.015-0.1052.789-5.926-3.2790.406-1.499-1.5540.014
6A7HIS0-0.0740.0853.106-2.221-0.4990.362-1.202-0.8820.013
7A8ILE0-0.007-0.1153.768-1.948-1.5310.006-0.152-0.2710.001
8A8ILE0-0.0090.1223.357-0.4140.0160.050-0.186-0.2940.001
9A9PRO00.071-0.0915.019-0.951-0.843-0.001-0.018-0.0880.000
10A10GLN00.0860.0067.493-0.473-0.4730.0000.0000.0000.000
11A10GLN0-0.0740.1077.7730.0850.0850.0000.0000.0000.000
12A11LEU00.101-0.1078.251-0.576-0.5760.0000.0000.0000.000
13A11LEU0-0.0870.1288.5060.1750.1750.0000.0000.0000.000
14A12ILE00.124-0.0929.577-0.259-0.2590.0000.0000.0000.000
15A12ILE0-0.0760.1038.741-0.040-0.0400.0000.0000.0000.000
16A13ALA00.113-0.08111.484-0.191-0.1910.0000.0000.0000.000
17A13ALA0-0.1080.10412.625-0.023-0.0230.0000.0000.0000.000
18A14SER0-0.051-0.14312.841-0.191-0.1910.0000.0000.0000.000
19A14SER0-0.0580.07312.723-0.022-0.0220.0000.0000.0000.000
20A15GLU00.091-0.12714.078-0.137-0.1370.0000.0000.0000.000
21A15GLU-1-1.004-0.81413.8051.2321.2320.0000.0000.0000.000
22A16ALA00.142-0.08615.511-0.090-0.0900.0000.0000.0000.000
23A16ALA0-0.0500.12716.197-0.012-0.0120.0000.0000.0000.000
24A17ASN00.074-0.08317.390-0.083-0.0830.0000.0000.0000.000
25A17ASN0-0.1500.05317.624-0.045-0.0450.0000.0000.0000.000
26A18PHE00.025-0.13218.693-0.082-0.0820.0000.0000.0000.000
27A18PHE0-0.0500.11819.2350.0000.0000.0000.0000.0000.000
28A19GLY00.039-0.08919.885-0.049-0.0490.0000.0000.0000.000
29A20ALA00.154-0.00421.603-0.044-0.0440.0000.0000.0000.000
30A20ALA0-0.0910.12822.426-0.004-0.0040.0000.0000.0000.000
31A21LYS00.021-0.12023.510-0.041-0.0410.0000.0000.0000.000
32A21LYS10.9021.06522.962-0.375-0.3750.0000.0000.0000.000
33A22ALA00.122-0.09324.595-0.030-0.0300.0000.0000.0000.000
34A22ALA0-0.0830.12324.8160.0040.0040.0000.0000.0000.000
35A23ALA00.098-0.14625.907-0.020-0.0200.0000.0000.0000.000
36A23ALA0-0.0670.15226.487-0.002-0.0020.0000.0000.0000.000
37A24LEU00.039-0.12727.628-0.024-0.0240.0000.0000.0000.000
38A24LEU0-0.0960.11127.352-0.001-0.0010.0000.0000.0000.000
39A25MET00.154-0.07629.295-0.024-0.0240.0000.0000.0000.000
40A25MET0-0.1120.11129.845-0.003-0.0030.0000.0000.0000.000
41A26ARG00.053-0.13530.686-0.015-0.0150.0000.0000.0000.000
42A26ARG10.7481.00527.150-0.251-0.2510.0000.0000.0000.000
43A27SER00.059-0.04332.045-0.013-0.0130.0000.0000.0000.000
44A27SER0-0.0580.05532.296-0.004-0.0040.0000.0000.0000.000
45A28THR00.046-0.11233.595-0.015-0.0150.0000.0000.0000.000
46A28THR0-0.0750.07133.184-0.001-0.0010.0000.0000.0000.000
47A29ILE00.033-0.08835.207-0.011-0.0110.0000.0000.0000.000
48A29ILE0-0.0730.08534.5030.0020.0020.0000.0000.0000.000
49A30ALA00.120-0.10136.660-0.008-0.0080.0000.0000.0000.000
50A30ALA0-0.0850.12937.1230.0000.0000.0000.0000.0000.000
51A31GLN00.052-0.12638.007-0.009-0.0090.0000.0000.0000.000
52A31GLN0-0.0760.09936.069-0.008-0.0080.0000.0000.0000.000
53A32ALA00.106-0.10839.563-0.010-0.0100.0000.0000.0000.000
54A32ALA0-0.0930.11539.9870.0010.0010.0000.0000.0000.000
55A33GLU00.093-0.10341.203-0.006-0.0060.0000.0000.0000.000
56A33GLU-1-0.959-0.81841.7540.1130.1130.0000.0000.0000.000
57A34GLN00.036-0.12042.746-0.006-0.0060.0000.0000.0000.000
58A34GLN0-0.0890.08641.4080.0040.0040.0000.0000.0000.000
59A35ALA00.117-0.10144.207-0.007-0.0070.0000.0000.0000.000
60A35ALA0-0.0700.12444.7080.0000.0000.0000.0000.0000.000
61A36ALA00.079-0.10745.631-0.005-0.0050.0000.0000.0000.000
62A36ALA0-0.0910.11145.8960.0010.0010.0000.0000.0000.000
63A37MET00.044-0.11847.189-0.004-0.0040.0000.0000.0000.000
64A37MET0-0.0960.09246.7790.0010.0010.0000.0000.0000.000
65A38SER0-0.037-0.11348.856-0.004-0.0040.0000.0000.0000.000
66A38SER0-0.0540.08448.507-0.001-0.0010.0000.0000.0000.000
67A39SER0-0.026-0.10550.779-0.005-0.0050.0000.0000.0000.000
68A39SER0-0.0200.08350.8970.0020.0020.0000.0000.0000.000
69A40GLN00.152-0.08252.4360.0000.0000.0000.0000.0000.000
70A40GLN0-0.1250.06852.9560.0010.0010.0000.0000.0000.000
71A41ALA00.109-0.09754.052-0.001-0.0010.0000.0000.0000.000
72A41ALA0-0.0830.09056.3070.0000.0000.0000.0000.0000.000
73A42PHE00.015-0.10056.867-0.002-0.0020.0000.0000.0000.000
74A42PHE0-0.1150.07854.3960.0000.0000.0000.0000.0000.000
75A43HIS00.087-0.04757.988-0.003-0.0030.0000.0000.0000.000
76A43HIS0-0.1240.06854.497-0.002-0.0020.0000.0000.0000.000
77A44MET00.165-0.10359.4820.0000.0000.0000.0000.0000.000
78A44MET0-0.0740.11663.415-0.001-0.0010.0000.0000.0000.000
79A45GLY0-0.048-0.13161.7460.0010.0010.0000.0000.0000.000
80A46GLU00.1230.00660.7540.0020.0020.0000.0000.0000.000
81A46GLU-1-0.994-0.84061.0820.0640.0640.0000.0000.0000.000
82A47ALA00.113-0.11758.6910.0030.0030.0000.0000.0000.000
83A47ALA0-0.0610.12658.7890.0000.0000.0000.0000.0000.000
84A48SER00.079-0.07556.9200.0040.0040.0000.0000.0000.000
85A48SER0-0.0280.09957.9350.0000.0000.0000.0000.0000.000
86A49ALA00.057-0.10455.9060.0030.0030.0000.0000.0000.000
87A49ALA0-0.0660.11858.2130.0000.0000.0000.0000.0000.000
88A50ALA00.090-0.12655.0650.0030.0030.0000.0000.0000.000
89A50ALA0-0.0700.13355.1250.0000.0000.0000.0000.0000.000
90A51PHE00.067-0.10052.4460.0050.0050.0000.0000.0000.000
91A51PHE0-0.0720.11350.1640.0000.0000.0000.0000.0000.000
92A52GLN00.089-0.09351.2760.0050.0050.0000.0000.0000.000
93A52GLN0-0.0840.08053.724-0.003-0.0030.0000.0000.0000.000
94A53ALA00.081-0.10051.1290.0030.0030.0000.0000.0000.000
95A53ALA0-0.0760.11052.4650.0000.0000.0000.0000.0000.000
96A54ALA00.057-0.15548.8760.0050.0050.0000.0000.0000.000
97A54ALA0-0.0720.13748.8040.0000.0000.0000.0000.0000.000
98A55HIS00.029-0.10847.1390.0080.0080.0000.0000.0000.000
99A55HIS0-0.1230.07445.915-0.004-0.0040.0000.0000.0000.000
100A56ALA00.144-0.10046.2810.0060.0060.0000.0000.0000.000
101A56ALA0-0.0650.11348.928-0.001-0.0010.0000.0000.0000.000
102A57ARG00.087-0.10845.8320.0040.0040.0000.0000.0000.000
103A57ARG10.8121.07642.957-0.137-0.1370.0000.0000.0000.000
104A58PHE00.089-0.12242.8160.0090.0090.0000.0000.0000.000
105A58PHE0-0.0720.12840.1930.0010.0010.0000.0000.0000.000
106A59VAL00.041-0.11441.5420.0110.0110.0000.0000.0000.000
107A59VAL0-0.0260.13042.757-0.001-0.0010.0000.0000.0000.000
108A60GLU00.110-0.09841.3810.0060.0060.0000.0000.0000.000
109A60GLU-1-0.972-0.84042.1120.1350.1350.0000.0000.0000.000
110A61VAL00.033-0.14739.5350.0080.0080.0000.0000.0000.000
111A61VAL0-0.0910.11338.1580.0000.0000.0000.0000.0000.000
112A62SER00.069-0.10937.1160.0150.0150.0000.0000.0000.000
113A62SER0-0.0100.10637.8130.0000.0000.0000.0000.0000.000
114A63ALA00.101-0.06236.0000.0140.0140.0000.0000.0000.000
115A63ALA0-0.0580.12638.553-0.002-0.0020.0000.0000.0000.000
116A64LYS00.072-0.08835.6000.0090.0090.0000.0000.0000.000
117A64LYS10.7991.01336.323-0.157-0.1570.0000.0000.0000.000
118A65VAL00.020-0.11833.1280.0160.0160.0000.0000.0000.000
119A65VAL0-0.0570.11732.1740.0000.0000.0000.0000.0000.000
120A66ASN00.077-0.06931.5600.0220.0220.0000.0000.0000.000
121A66ASN0-0.0950.05932.8850.0050.0050.0000.0000.0000.000
122A67ALA00.192-0.07330.8440.0150.0150.0000.0000.0000.000
123A67ALA0-0.0940.10133.153-0.003-0.0030.0000.0000.0000.000
124A68LEU00.013-0.13229.8700.0140.0140.0000.0000.0000.000
125A68LEU0-0.1130.09129.8680.0000.0000.0000.0000.0000.000
126A69LEU00.086-0.11127.1800.0330.0330.0000.0000.0000.000
127A69LEU0-0.1170.09327.2080.0000.0000.0000.0000.0000.000
128A70ASP00.103-0.10725.9820.0370.0370.0000.0000.0000.000
129A70ASP-1-0.904-0.79828.3020.2460.2460.0000.0000.0000.000
130A71ILE00.057-0.09425.5860.0170.0170.0000.0000.0000.000
131A71ILE0-0.0960.08825.1560.0000.0000.0000.0000.0000.000
132A72ALA00.106-0.10823.1940.0400.0400.0000.0000.0000.000
133A72ALA0-0.1000.09723.383-0.003-0.0030.0000.0000.0000.000
134A73GLN00.067-0.09621.4780.0680.0680.0000.0000.0000.000
135A73GLN0-0.0700.09422.3490.0310.0310.0000.0000.0000.000
136A74LEU00.034-0.11920.3330.0480.0480.0000.0000.0000.000
137A74LEU0-0.0590.10222.118-0.006-0.0060.0000.0000.0000.000
138A75ASN00.075-0.05519.1520.0340.0340.0000.0000.0000.000
139A75ASN0-0.1750.03219.8080.0180.0180.0000.0000.0000.000
140A76ILE00.089-0.07616.8960.0950.0950.0000.0000.0000.000
141A76ILE0-0.0980.07116.940-0.007-0.0070.0000.0000.0000.000
142A77GLY00.004-0.09717.9280.0180.0180.0000.0000.0000.000
143A78ASP00.1640.01717.8020.0740.0740.0000.0000.0000.000
144A78ASP-1-1.023-0.87320.8490.3370.3370.0000.0000.0000.000
145A79ALA00.075-0.07918.3920.0070.0070.0000.0000.0000.000
146A79ALA0-0.0750.09420.405-0.009-0.0090.0000.0000.0000.000
147A80ALA00.088-0.13016.535-0.036-0.0360.0000.0000.0000.000
148A80ALA0-0.0770.14615.7200.0070.0070.0000.0000.0000.000
149A81SER00.111-0.07613.5390.0950.0950.0000.0000.0000.000
150A81SER0-0.0800.06614.418-0.036-0.0360.0000.0000.0000.000
151A82SER00.074-0.05913.3980.0480.0480.0000.0000.0000.000
152A82SER0-0.0710.07017.384-0.022-0.0220.0000.0000.0000.000
153A83TYR00.069-0.09414.605-0.063-0.0630.0000.0000.0000.000
154A83TYR0-0.0840.09513.360-0.055-0.0550.0000.0000.0000.000
155A84VAL00.066-0.11310.681-0.106-0.1060.0000.0000.0000.000
156A84VAL0-0.0730.1128.6670.0710.0710.0000.0000.0000.000
157A85ALA00.094-0.0749.8090.0870.0870.0000.0000.0000.000
158A85ALA0-0.0940.08812.461-0.025-0.0250.0000.0000.0000.000
159A86GLN00.039-0.10211.384-0.121-0.1210.0000.0000.0000.000
160A86GLN0-0.1310.04815.120-0.052-0.0520.0000.0000.0000.000
161A87ASP00.034-0.13911.728-0.184-0.1840.0000.0000.0000.000
162A87ASP-1-0.978-0.85010.2950.7520.7520.0000.0000.0000.000
163A88ALA00.148-0.0907.957-0.086-0.0860.0000.0000.0000.000
164A88ALA0-0.0890.1207.2110.0320.0320.0000.0000.0000.000
165A89ALA00.083-0.0348.686-0.317-0.3170.0000.0000.0000.000
166A89ALA0-0.0640.11012.3300.0000.0000.0000.0000.0000.000
167A90ALA00.079-0.11211.474-0.149-0.1490.0000.0000.0000.000
168A90ALA0-0.0530.11513.4830.0120.0120.0000.0000.0000.000
169A91ALA00.039-0.1419.750-0.085-0.0850.0000.0000.0000.000
170A91ALA0-0.0490.1338.9540.0310.0310.0000.0000.0000.000
171A92SER0-0.035-0.1059.309-0.111-0.1110.0000.0000.0000.000
172A92SER0-0.148-0.0398.487-0.077-0.0770.0000.0000.0000.000
173A93THR0-0.045-0.08410.008-0.135-0.1350.0000.0000.0000.000
174A93THR0-0.0740.03813.7170.0000.0000.0000.0000.0000.000
175A94TYR0-0.083-0.11113.595-0.043-0.0430.0000.0000.0000.000
176A94TYR00.0300.02214.1320.0240.0240.0000.0000.0000.000