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: LQMZ9

Calculation Name: 4DOT-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DOT

Chain ID: A

ChEMBL ID:

UniProt ID: P53816

Base Structure: X-ray

Registration Date: 2025-07-11

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -816868.422504
FMO2-HF: Nuclear repulsion 776198.171147
FMO2-HF: Total energy -40670.251357
FMO2-MP2: Total energy -40790.500364


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-1.8080.5050.004-1.045-1.2720.001
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.030
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].
3A7GLU-1-0.899-0.7564.638-0.910-0.563-0.001-0.089-0.2580.000
4A8PRO0-0.074-0.1273.591-1.4660.5000.005-0.956-1.0140.001
5A9LYS00.038-0.0155.826-0.044-0.0440.0000.0000.0000.000
6A9LYS10.9181.0855.9100.5480.5480.0000.0000.0000.000
7A10PRO00.012-0.0848.3250.0690.0690.0000.0000.0000.000
8A11GLY0-0.030-0.03311.9210.0050.0050.0000.0000.0000.000
9A12ASP00.114-0.0019.7020.0490.0490.0000.0000.0000.000
10A12ASP-1-0.876-0.8037.807-0.378-0.3780.0000.0000.0000.000
11A13LEU00.059-0.09911.2440.0060.0060.0000.0000.0000.000
12A13LEU0-0.0840.11013.2570.0020.0020.0000.0000.0000.000
13A14ILE00.046-0.10310.3750.0050.0050.0000.0000.0000.000
14A14ILE0-0.0760.0988.4980.0110.0110.0000.0000.0000.000
15A15GLU00.147-0.10210.785-0.042-0.0420.0000.0000.0000.000
16A15GLU-1-0.911-0.76011.6310.1630.1630.0000.0000.0000.000
17A16ILE00.062-0.08911.3420.1060.1060.0000.0000.0000.000
18A16ILE0-0.0730.08112.535-0.005-0.0050.0000.0000.0000.000
19A17PHE00.048-0.08213.308-0.060-0.0600.0000.0000.0000.000
20A17PHE0-0.1480.05910.647-0.012-0.0120.0000.0000.0000.000
21A18ARG00.159-0.07315.1060.0150.0150.0000.0000.0000.000
22A18ARG10.8061.04917.383-0.127-0.1270.0000.0000.0000.000
23A19PRO00.004-0.10118.087-0.010-0.0100.0000.0000.0000.000
24A20PHE00.0020.00120.796-0.006-0.0060.0000.0000.0000.000
25A20PHE0-0.1090.08124.233-0.001-0.0010.0000.0000.0000.000
26A21TYR00.075-0.13720.949-0.012-0.0120.0000.0000.0000.000
27A21TYR0-0.0770.10321.3240.0000.0000.0000.0000.0000.000
28A22ARG00.178-0.04917.6220.0130.0130.0000.0000.0000.000
29A22ARG10.7911.03816.509-0.113-0.1130.0000.0000.0000.000
30A23HIS00.074-0.08416.878-0.024-0.0240.0000.0000.0000.000
31A23HIS0-0.1090.03617.2040.0040.0040.0000.0000.0000.000
32A24TRP00.049-0.10815.5920.0340.0340.0000.0000.0000.000
33A24TRP0-0.0890.09914.0920.0060.0060.0000.0000.0000.000
34A25ALA00.123-0.08814.837-0.014-0.0140.0000.0000.0000.000
35A25ALA0-0.0820.09714.2560.0010.0010.0000.0000.0000.000
36A26ILE00.006-0.08114.1780.0170.0170.0000.0000.0000.000
37A26ILE0-0.0830.07414.859-0.001-0.0010.0000.0000.0000.000
38A27TYR00.171-0.07810.8980.0270.0270.0000.0000.0000.000
39A27TYR0-0.1430.0459.1580.0280.0280.0000.0000.0000.000
40A28VAL0-0.077-0.15812.422-0.020-0.0200.0000.0000.0000.000
41A28VAL0-0.0510.12715.9160.0050.0050.0000.0000.0000.000
42A29GLY00.061-0.09611.803-0.002-0.0020.0000.0000.0000.000
43A30ASP00.022-0.01812.2830.0200.0200.0000.0000.0000.000
44A30ASP-1-0.997-0.85114.496-0.180-0.1800.0000.0000.0000.000
45A31GLY00.060-0.09310.5720.0370.0370.0000.0000.0000.000
46A32TYR00.0240.01011.5960.0610.0610.0000.0000.0000.000
47A32TYR0-0.0530.07715.4020.0040.0040.0000.0000.0000.000
48A33VAL00.049-0.08013.451-0.042-0.0420.0000.0000.0000.000
49A33VAL0-0.0520.08112.5110.0090.0090.0000.0000.0000.000
50A34VAL00.075-0.08614.9730.0040.0040.0000.0000.0000.000
51A34VAL0-0.0520.09018.285-0.001-0.0010.0000.0000.0000.000
52A35HIS0-0.020-0.08017.9020.0020.0020.0000.0000.0000.000
53A35HIS0-0.0750.05017.9340.0140.0140.0000.0000.0000.000
54A36LEU00.082-0.09219.958-0.007-0.0070.0000.0000.0000.000
55A36LEU0-0.0360.11023.2700.0010.0010.0000.0000.0000.000
56A37ALA00.104-0.09722.3060.0110.0110.0000.0000.0000.000
57A37ALA0-0.0660.10522.5830.0000.0000.0000.0000.0000.000
58A38PRO00.001-0.10624.114-0.005-0.0050.0000.0000.0000.000
59A39PRO00.0060.01226.9770.0020.0020.0000.0000.0000.000
60A58ALA00.1580.01828.2960.0010.0010.0000.0000.0000.000
61A58ALA0-0.0820.08327.3250.0010.0010.0000.0000.0000.000
62A59ILE00.004-0.11927.411-0.003-0.0030.0000.0000.0000.000
63A59ILE0-0.0810.07427.1590.0000.0000.0000.0000.0000.000
64A60VAL00.118-0.10724.3270.0070.0070.0000.0000.0000.000
65A60VAL0-0.0770.13723.1650.0000.0000.0000.0000.0000.000
66A61LYS00.017-0.10122.760-0.006-0.0060.0000.0000.0000.000
67A61LYS10.8591.06222.211-0.024-0.0240.0000.0000.0000.000
68A62LYS00.166-0.07719.4570.0040.0040.0000.0000.0000.000
69A62LYS10.7661.01118.0900.0690.0690.0000.0000.0000.000
70A63GLU00.003-0.12418.037-0.006-0.0060.0000.0000.0000.000
71A63GLU-1-0.918-0.80917.9610.0390.0390.0000.0000.0000.000
72A64LEU00.113-0.08414.723-0.013-0.0130.0000.0000.0000.000
73A64LEU0-0.0810.11214.001-0.001-0.0010.0000.0000.0000.000
74A65LEU00.137-0.10310.9790.0260.0260.0000.0000.0000.000
75A65LEU0-0.0860.0988.151-0.013-0.0130.0000.0000.0000.000
76A66TYR00.042-0.08411.6450.0710.0710.0000.0000.0000.000
77A66TYR0-0.1150.06911.292-0.004-0.0040.0000.0000.0000.000
78A67ASP00.101-0.09212.5180.0340.0340.0000.0000.0000.000
79A67ASP-1-0.949-0.85517.1000.0330.0330.0000.0000.0000.000
80A68VAL00.030-0.08515.3740.0070.0070.0000.0000.0000.000
81A68VAL0-0.1190.06114.6560.0010.0010.0000.0000.0000.000
82A69ALA00.055-0.12111.859-0.025-0.0250.0000.0000.0000.000
83A69ALA0-0.0660.09711.2660.0230.0230.0000.0000.0000.000
84A70GLY00.019-0.06713.319-0.010-0.0100.0000.0000.0000.000
85A71SER00.0060.01813.2640.0470.0470.0000.0000.0000.000
86A71SER0-0.0580.04816.090-0.017-0.0170.0000.0000.0000.000
87A72ASP00.022-0.12514.1010.0060.0060.0000.0000.0000.000
88A72ASP-1-0.950-0.83214.7080.1770.1770.0000.0000.0000.000
89A73LYS00.145-0.06210.4990.0790.0790.0000.0000.0000.000
90A73LYS10.8471.02610.943-0.275-0.2750.0000.0000.0000.000
91A74TYR00.020-0.0959.267-0.135-0.1350.0000.0000.0000.000
92A74TYR0-0.0490.0895.9770.0390.0390.0000.0000.0000.000
93A75GLN00.054-0.0986.5080.3460.3460.0000.0000.0000.000
94A75GLN0-0.1130.0707.3370.0010.0010.0000.0000.0000.000
95A76VAL00.121-0.0756.193-0.045-0.0450.0000.0000.0000.000
96A76VAL0-0.0500.1035.943-0.017-0.0170.0000.0000.0000.000
97A77ASN00.013-0.0887.8550.0110.0110.0000.0000.0000.000
98A77ASN0-0.1300.02311.243-0.025-0.0250.0000.0000.0000.000
99A78ASN00.166-0.04811.1310.0050.0050.0000.0000.0000.000
100A78ASN0-0.1590.07410.6730.0210.0210.0000.0000.0000.000
101A79LYS00.160-0.06913.145-0.013-0.0130.0000.0000.0000.000
102A79LYS10.7680.99215.516-0.069-0.0690.0000.0000.0000.000
103A80HIS00.041-0.07115.544-0.002-0.0020.0000.0000.0000.000
104A80HIS0-0.0940.07019.209-0.001-0.0010.0000.0000.0000.000
105A81ASP00.217-0.08316.2670.0010.0010.0000.0000.0000.000
106A81ASP-1-0.831-0.75514.670-0.064-0.0640.0000.0000.0000.000
107A82ASP00.002-0.06717.642-0.007-0.0070.0000.0000.0000.000
108A82ASP-1-0.942-0.86718.2330.0070.0070.0000.0000.0000.000
109A83LYS0-0.054-0.13119.346-0.002-0.0020.0000.0000.0000.000
110A83LYS10.8781.05422.102-0.001-0.0010.0000.0000.0000.000
111A84TYR00.039-0.09721.1660.0000.0000.0000.0000.0000.000
112A84TYR0-0.0750.08221.4410.0020.0020.0000.0000.0000.000
113A85SER00.053-0.09620.327-0.003-0.0030.0000.0000.0000.000
114A85SER0-0.0030.08622.1510.0000.0000.0000.0000.0000.000
115A86PRO0-0.063-0.08316.3390.0040.0040.0000.0000.0000.000
116A87LEU00.037-0.01419.048-0.001-0.0010.0000.0000.0000.000
117A87LEU0-0.0550.10220.7100.0000.0000.0000.0000.0000.000
118A88PRO0-0.021-0.12918.960-0.009-0.0090.0000.0000.0000.000
119A89CYS00.1520.01216.0850.0100.0100.0000.0000.0000.000
120A89CYS0-0.1080.10513.8690.0030.0030.0000.0000.0000.000
121A90SER00.079-0.03017.437-0.005-0.0050.0000.0000.0000.000
122A90SER0-0.0440.02520.4000.0020.0020.0000.0000.0000.000
123A91LYS00.085-0.05119.9770.0010.0010.0000.0000.0000.000
124A91LYS10.8811.03922.1570.0430.0430.0000.0000.0000.000
125A92ILE00.083-0.05618.1400.0100.0100.0000.0000.0000.000
126A92ILE0-0.1030.08416.482-0.003-0.0030.0000.0000.0000.000
127A93ILE00.056-0.09118.1820.0120.0120.0000.0000.0000.000
128A93ILE0-0.0480.10514.918-0.001-0.0010.0000.0000.0000.000
129A94GLN00.170-0.07018.8200.0050.0050.0000.0000.0000.000
130A94GLN0-0.1240.08923.087-0.001-0.0010.0000.0000.0000.000
131A95ARG00.092-0.09122.5270.0050.0050.0000.0000.0000.000
132A95ARG10.8331.07522.5490.0200.0200.0000.0000.0000.000
133A96ALA00.068-0.11219.7860.0090.0090.0000.0000.0000.000
134A96ALA0-0.0670.08019.423-0.001-0.0010.0000.0000.0000.000
135A97GLU00.081-0.09721.3360.0100.0100.0000.0000.0000.000
136A97GLU-1-0.918-0.81019.346-0.078-0.0780.0000.0000.0000.000
137A98GLU00.017-0.11322.4730.0030.0030.0000.0000.0000.000
138A98GLU-1-1.002-0.89025.729-0.030-0.0300.0000.0000.0000.000
139A99LEU00.067-0.11125.0040.0020.0020.0000.0000.0000.000
140A99LEU0-0.1040.08623.9320.0010.0010.0000.0000.0000.000
141A100VAL00.053-0.09124.2750.0070.0070.0000.0000.0000.000
142A100VAL0-0.0950.10922.3180.0000.0000.0000.0000.0000.000
143A101GLY0-0.075-0.14025.208-0.002-0.0020.0000.0000.0000.000
144A102GLN00.059-0.01828.1910.0030.0030.0000.0000.0000.000
145A102GLN0-0.0940.09728.7460.0010.0010.0000.0000.0000.000
146A103GLU00.091-0.11128.6180.0020.0020.0000.0000.0000.000
147A103GLU-1-1.013-0.84631.7860.0080.0080.0000.0000.0000.000
148A104VAL0-0.007-0.11228.977-0.003-0.0030.0000.0000.0000.000
149A104VAL0-0.0760.10427.7180.0000.0000.0000.0000.0000.000
150A105LEU00.106-0.09930.4150.0020.0020.0000.0000.0000.000
151A105LEU0-0.0800.08834.0860.0000.0000.0000.0000.0000.000
152A106TYR00.057-0.07330.9670.0000.0000.0000.0000.0000.000
153A106TYR0-0.0570.08426.6070.0010.0010.0000.0000.0000.000
154A107LYS00.118-0.06130.1440.0000.0000.0000.0000.0000.000
155A107LYS10.8821.04230.026-0.030-0.0300.0000.0000.0000.000
156A108LEU00.021-0.11226.327-0.002-0.0020.0000.0000.0000.000
157A108LEU00.0020.15324.2890.0010.0010.0000.0000.0000.000
158A109THR0-0.014-0.07625.6840.0020.0020.0000.0000.0000.000
159A109THR0-0.0190.05926.394-0.001-0.0010.0000.0000.0000.000
160A110SER00.104-0.07921.587-0.003-0.0030.0000.0000.0000.000
161A110SER0-0.0280.07020.6870.0000.0000.0000.0000.0000.000
162A111GLU00.024-0.08921.4660.0040.0040.0000.0000.0000.000
163A111GLU-1-0.889-0.83324.5900.0460.0460.0000.0000.0000.000
164A112ASN00.067-0.05723.812-0.003-0.0030.0000.0000.0000.000
165A112ASN0-0.1550.02825.932-0.002-0.0020.0000.0000.0000.000
166A113CYS00.166-0.06121.351-0.009-0.0090.0000.0000.0000.000
167A113CYS0-0.1390.08420.3830.0010.0010.0000.0000.0000.000
168A114GLU00.109-0.12319.190-0.004-0.0040.0000.0000.0000.000
169A114GLU-1-0.967-0.82918.3220.0610.0610.0000.0000.0000.000
170A115HIS00.037-0.10220.211-0.005-0.0050.0000.0000.0000.000
171A115HIS0-0.0960.08424.6390.0020.0020.0000.0000.0000.000
172A116PHE00.115-0.06222.993-0.007-0.0070.0000.0000.0000.000
173A116PHE0-0.0710.07721.101-0.001-0.0010.0000.0000.0000.000
174A117VAL00.064-0.08918.026-0.011-0.0110.0000.0000.0000.000
175A117VAL0-0.0710.09216.7220.0010.0010.0000.0000.0000.000
176A118ASN00.088-0.08719.153-0.013-0.0130.0000.0000.0000.000
177A118ASN0-0.0820.05118.7670.0000.0000.0000.0000.0000.000
178A119GLU00.096-0.09220.370-0.007-0.0070.0000.0000.0000.000
179A119GLU-1-0.994-0.83824.2050.0020.0020.0000.0000.0000.000
180A120LEU00.012-0.12020.483-0.004-0.0040.0000.0000.0000.000
181A120LEU0-0.0830.09919.722-0.002-0.0020.0000.0000.0000.000
182A121ARG00.103-0.08717.685-0.010-0.0100.0000.0000.0000.000
183A121ARG10.7030.97413.4880.0840.0840.0000.0000.0000.000
184A122TYR00.001-0.13418.793-0.010-0.0100.0000.0000.0000.000
185A122TYR0-0.1010.05916.6480.0050.0050.0000.0000.0000.000
186A123GLY00.011-0.07621.5790.0000.0000.0000.0000.0000.000
187A124VAL00.059-0.00824.8340.0030.0030.0000.0000.0000.000
188A124VAL0-0.1070.10027.5110.0000.0000.0000.0000.0000.000
189A125ALA0-0.085-0.15725.8590.0000.0000.0000.0000.0000.000
190A125ALA00.0610.04529.3810.0000.0000.0000.0000.0000.000