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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 766YK

Calculation Name: 4L5T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L5T

Chain ID: A

ChEMBL ID:

UniProt ID: Q9R002

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1924157.787565
FMO2-HF: Nuclear repulsion 1850858.540347
FMO2-HF: Total energy -73299.247218
FMO2-MP2: Total energy -73507.837901


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:245:LEU)


Summations of interaction energy for fragment #1(A:245: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.
-0.6190.784-0.016-0.613-0.7740.001
Interaction energy analysis for fragmet #1(A:245:LEU)
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 : -0.028
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].
3A247LYS10.9630.9813.7880.2511.654-0.016-0.613-0.7740.001
4A248GLU-1-0.798-0.8656.6650.3400.3400.0000.0000.0000.000
5A249SER0-0.049-0.0529.395-0.144-0.1440.0000.0000.0000.000
6A250PHE00.0330.02112.6550.0730.0730.0000.0000.0000.000
7A251GLU-1-0.820-0.87516.3690.0080.0080.0000.0000.0000.000
8A252GLY00.0080.00918.5030.0040.0040.0000.0000.0000.000
9A253ASP-1-0.915-0.94921.7070.0110.0110.0000.0000.0000.000
10A254GLY00.0140.01424.502-0.010-0.0100.0000.0000.0000.000
11A255TYR0-0.072-0.08226.2250.0090.0090.0000.0000.0000.000
12A256HIS10.8530.92822.150-0.021-0.0210.0000.0000.0000.000
13A257LYS10.8220.90125.855-0.019-0.0190.0000.0000.0000.000
14A258GLY0-0.009-0.00125.794-0.005-0.0050.0000.0000.0000.000
15A259PRO0-0.021-0.01123.3210.0080.0080.0000.0000.0000.000
16A260LYS10.8610.92815.397-0.087-0.0870.0000.0000.0000.000
17A261GLN0-0.026-0.02017.1580.0300.0300.0000.0000.0000.000
18A262VAL0-0.058-0.02914.098-0.013-0.0130.0000.0000.0000.000
19A263VAL00.0580.02511.114-0.024-0.0240.0000.0000.0000.000
20A264ALA00.0130.02012.4160.1040.1040.0000.0000.0000.000
21A265LEU00.0410.0288.184-0.004-0.0040.0000.0000.0000.000
22A266LYS10.9060.92511.260-0.862-0.8620.0000.0000.0000.000
23A267ALA00.0220.01614.676-0.022-0.0220.0000.0000.0000.000
24A268THR00.0220.02218.0280.0030.0030.0000.0000.0000.000
25A269LYS10.8750.93920.940-0.207-0.2070.0000.0000.0000.000
26A270LEU00.0250.02124.464-0.002-0.0020.0000.0000.0000.000
27A271PHE0-0.0120.00124.191-0.010-0.0100.0000.0000.0000.000
28A272THR0-0.006-0.01728.672-0.007-0.0070.0000.0000.0000.000
29A273TYR00.0310.01028.634-0.002-0.0020.0000.0000.0000.000
30A274ASP-1-0.887-0.94030.4550.0650.0650.0000.0000.0000.000
31A275SER00.039-0.01034.104-0.003-0.0030.0000.0000.0000.000
32A276ILE0-0.043-0.01436.632-0.004-0.0040.0000.0000.0000.000
33A277LYS10.8810.93037.677-0.056-0.0560.0000.0000.0000.000
34A278SER00.0080.00637.1660.0000.0000.0000.0000.0000.000
35A279LYS10.9500.99433.573-0.066-0.0660.0000.0000.0000.000
36A280LYS10.8190.90030.758-0.097-0.0970.0000.0000.0000.000
37A281MET0-0.0250.00624.271-0.012-0.0120.0000.0000.0000.000
38A282PHE0-0.025-0.00721.2510.0020.0020.0000.0000.0000.000
39A283HIS00.0310.01519.1630.0010.0010.0000.0000.0000.000
40A284ALA00.034-0.00217.0910.0210.0210.0000.0000.0000.000
41A285THR0-0.0310.00910.901-0.031-0.0310.0000.0000.0000.000
42A286VAL0-0.023-0.01713.1370.0620.0620.0000.0000.0000.000
43A287ALA00.005-0.0058.3820.0810.0810.0000.0000.0000.000
44A288THR00.0490.02810.281-0.044-0.0440.0000.0000.0000.000
45A289ASP-1-0.914-0.9637.3340.4250.4250.0000.0000.0000.000
46A290THR0-0.087-0.0696.704-0.333-0.3330.0000.0000.0000.000
47A291GLU-1-0.873-0.9006.990-0.792-0.7920.0000.0000.0000.000
48A292PHE0-0.013-0.0086.4060.3440.3440.0000.0000.0000.000
49A293PHE00.0480.0329.574-0.139-0.1390.0000.0000.0000.000
50A294ARG10.8880.92812.952-0.238-0.2380.0000.0000.0000.000
51A295VAL0-0.026-0.02815.356-0.063-0.0630.0000.0000.0000.000
52A296MET0-0.004-0.01418.6740.0150.0150.0000.0000.0000.000
53A297VAL0-0.0060.01221.687-0.020-0.0200.0000.0000.0000.000
54A298PHE0-0.057-0.05624.248-0.002-0.0020.0000.0000.0000.000
55A299GLU-1-0.879-0.92827.5160.0880.0880.0000.0000.0000.000
56A300GLU-1-0.790-0.90628.0610.1100.1100.0000.0000.0000.000
57A301ASN0-0.041-0.03528.9960.0130.0130.0000.0000.0000.000
58A302LEU00.0340.01024.957-0.006-0.0060.0000.0000.0000.000
59A303GLU-1-0.887-0.93323.9360.1680.1680.0000.0000.0000.000
60A304LYS10.8060.89223.443-0.114-0.1140.0000.0000.0000.000
61A305LYS10.9280.97722.839-0.116-0.1160.0000.0000.0000.000
62A306PHE0-0.022-0.00618.3820.0070.0070.0000.0000.0000.000
63A307ILE0-0.0070.01118.5730.0400.0400.0000.0000.0000.000
64A308PRO0-0.036-0.02115.4750.0190.0190.0000.0000.0000.000
65A309GLY0-0.012-0.00814.348-0.025-0.0250.0000.0000.0000.000
66A310ASN0-0.048-0.02815.332-0.011-0.0110.0000.0000.0000.000
67A311THR00.0020.00614.6820.0220.0220.0000.0000.0000.000
68A312ILE00.0160.01516.788-0.031-0.0310.0000.0000.0000.000
69A313ALA0-0.020-0.01318.336-0.002-0.0020.0000.0000.0000.000
70A314LEU0-0.023-0.00418.2280.0020.0020.0000.0000.0000.000
71A315SER00.007-0.00721.636-0.020-0.0200.0000.0000.0000.000
72A316ASP-1-0.787-0.87624.8570.0440.0440.0000.0000.0000.000
73A317TYR0-0.028-0.01020.5040.0060.0060.0000.0000.0000.000
74A318PHE00.011-0.01124.797-0.015-0.0150.0000.0000.0000.000
75A319GLY00.0490.05222.7510.0170.0170.0000.0000.0000.000
76A320MET0-0.001-0.02322.971-0.011-0.0110.0000.0000.0000.000
77A321TYR00.003-0.00222.7880.0140.0140.0000.0000.0000.000
78A322GLY00.0660.05519.0470.0070.0070.0000.0000.0000.000
79A323SER0-0.069-0.03917.7330.0370.0370.0000.0000.0000.000
80A324LEU0-0.017-0.01317.610-0.023-0.0230.0000.0000.0000.000
81A325ALA0-0.008-0.00920.8130.0190.0190.0000.0000.0000.000
82A326ILE0-0.0060.00620.834-0.013-0.0130.0000.0000.0000.000
83A327HIS00.020-0.00224.9700.0140.0140.0000.0000.0000.000
84A328GLU-1-0.829-0.89428.6120.0590.0590.0000.0000.0000.000
85A329TYR00.000-0.01428.1190.0060.0060.0000.0000.0000.000
86A330SER0-0.045-0.05628.8470.0040.0040.0000.0000.0000.000
87A331SER0-0.0310.00126.0210.0000.0000.0000.0000.0000.000
88A332VAL00.0100.02122.4180.0030.0030.0000.0000.0000.000
89A333SER0-0.008-0.00624.215-0.008-0.0080.0000.0000.0000.000
90A334GLU-1-0.850-0.95522.3420.1800.1800.0000.0000.0000.000
91A335VAL0-0.064-0.00120.191-0.014-0.0140.0000.0000.0000.000
92A354LEU0-0.042-0.0359.5550.0190.0190.0000.0000.0000.000
93A355LYS10.8540.92611.015-0.196-0.1960.0000.0000.0000.000
94A356ILE00.0350.01113.275-0.020-0.0200.0000.0000.0000.000
95A357CYS0-0.063-0.02315.727-0.015-0.0150.0000.0000.0000.000
96A358ASP-1-0.815-0.93311.5690.0490.0490.0000.0000.0000.000
97A359LEU0-0.036-0.03114.637-0.017-0.0170.0000.0000.0000.000
98A360HIS0-0.034-0.01616.960-0.011-0.0110.0000.0000.0000.000
99A361LEU0-0.071-0.02415.523-0.011-0.0110.0000.0000.0000.000
100A362GLN0-0.064-0.02113.562-0.024-0.0240.0000.0000.0000.000
101A363THR00.0090.00118.061-0.001-0.0010.0000.0000.0000.000
102A364GLU-1-0.966-0.97919.212-0.058-0.0580.0000.0000.0000.000
103A365GLU-1-0.894-0.90419.4050.0130.0130.0000.0000.0000.000
104A366ARG10.8470.88711.619-0.009-0.0090.0000.0000.0000.000
105A367LEU0-0.013-0.01317.1060.0090.0090.0000.0000.0000.000
106A368VAL0-0.049-0.03015.4840.0190.0190.0000.0000.0000.000
107A369ASP-1-0.802-0.90313.9630.3830.3830.0000.0000.0000.000
108A370GLY00.0120.00114.5280.0100.0100.0000.0000.0000.000
109A371GLU-1-0.886-0.93015.4590.4450.4450.0000.0000.0000.000
110A372PHE00.0360.02415.5730.0000.0000.0000.0000.0000.000
111A373LYS10.8930.94919.895-0.154-0.1540.0000.0000.0000.000
112A374VAL00.0350.02623.122-0.007-0.0070.0000.0000.0000.000
113A375TYR0-0.002-0.01626.054-0.006-0.0060.0000.0000.0000.000
114A376ARG10.7810.81528.639-0.075-0.0750.0000.0000.0000.000
115A377LYS10.8570.91130.172-0.080-0.0800.0000.0000.0000.000
116A378SER0-0.038-0.01032.686-0.007-0.0070.0000.0000.0000.000
117A379SER00.0400.02434.9130.0030.0030.0000.0000.0000.000
118A380GLY00.0190.00136.098-0.002-0.0020.0000.0000.0000.000
119A381ASN0-0.048-0.01137.0770.0000.0000.0000.0000.0000.000
120A382ASN00.015-0.02637.399-0.001-0.0010.0000.0000.0000.000
121A383CYS0-0.077-0.01933.2620.0020.0020.0000.0000.0000.000
122A384ILE00.0140.00832.333-0.003-0.0030.0000.0000.0000.000
123A385CYM-1-0.823-0.81230.9100.0720.0720.0000.0000.0000.000
124A386TYR00.039-0.01327.513-0.001-0.0010.0000.0000.0000.000
125A387GLY0-0.002-0.00426.870-0.005-0.0050.0000.0000.0000.000
126A388ILE0-0.034-0.01520.3090.0030.0030.0000.0000.0000.000
127A389TRP0-0.003-0.01321.709-0.007-0.0070.0000.0000.0000.000
128A390ASP-1-0.716-0.88816.7480.1940.1940.0000.0000.0000.000
129A391ASP-1-0.934-0.95317.4190.1450.1450.0000.0000.0000.000
130A392THR0-0.058-0.02815.586-0.020-0.0200.0000.0000.0000.000
131A393GLY00.0150.01618.462-0.014-0.0140.0000.0000.0000.000
132A394ALA0-0.018-0.01321.4030.0130.0130.0000.0000.0000.000
133A395MET00.0150.02320.541-0.003-0.0030.0000.0000.0000.000
134A396LYS10.9880.99623.736-0.043-0.0430.0000.0000.0000.000
135A397VAL00.0150.00323.7340.0060.0060.0000.0000.0000.000
136A398VAL0-0.0190.01126.334-0.006-0.0060.0000.0000.0000.000
137A399VAL00.0350.01227.5930.0060.0060.0000.0000.0000.000
138A400SER00.0210.00430.028-0.006-0.0060.0000.0000.0000.000
139A401GLY00.0180.00731.7100.0060.0060.0000.0000.0000.000
140A402GLN00.0820.04832.3080.0020.0020.0000.0000.0000.000
141A403LEU00.0370.02726.2180.0020.0020.0000.0000.0000.000
142A404THR0-0.037-0.00430.6100.0040.0040.0000.0000.0000.000
143A405SER0-0.032-0.02533.211-0.004-0.0040.0000.0000.0000.000
144A406VAL0-0.077-0.01528.2290.0000.0000.0000.0000.0000.000
145A407ASN0-0.048-0.03031.6200.0000.0000.0000.0000.0000.000
146A408CYS00.0310.00927.4590.0110.0110.0000.0000.0000.000
147A409GLU-1-0.808-0.87730.6200.0760.0760.0000.0000.0000.000
148A410ILE00.0070.00430.0600.0090.0090.0000.0000.0000.000
149A411GLY00.0070.01728.811-0.003-0.0030.0000.0000.0000.000
150A412ASN0-0.025-0.00627.2670.0070.0070.0000.0000.0000.000
151A413THR00.0340.00420.794-0.010-0.0100.0000.0000.0000.000
152A414ILE00.0230.02022.4090.0020.0020.0000.0000.0000.000
153A415ARG10.8140.91113.901-0.491-0.4910.0000.0000.0000.000
154A416LEU0-0.016-0.01618.977-0.025-0.0250.0000.0000.0000.000
155A417VAL0-0.023-0.01917.4870.0470.0470.0000.0000.0000.000
156A418CYS00.0000.00818.427-0.039-0.0390.0000.0000.0000.000
157A419PHE00.0110.02719.734-0.026-0.0260.0000.0000.0000.000
158A420GLU-1-0.807-0.89520.3120.0730.0730.0000.0000.0000.000
159A421LEU0-0.030-0.00718.126-0.002-0.0020.0000.0000.0000.000
160A422THR0-0.060-0.03621.567-0.009-0.0090.0000.0000.0000.000
161A423SER00.0530.01224.9380.0000.0000.0000.0000.0000.000
162A424ASN0-0.110-0.08726.6270.0020.0020.0000.0000.0000.000
163A425ALA0-0.054-0.01628.835-0.003-0.0030.0000.0000.0000.000
164A426ASP-1-0.997-0.98530.3770.0240.0240.0000.0000.0000.000
165A427GLU-1-0.864-0.92926.3830.0380.0380.0000.0000.0000.000
166A428TRP00.0400.02621.7930.0020.0020.0000.0000.0000.000
167A429PHE0-0.038-0.02924.3870.0060.0060.0000.0000.0000.000
168A430LEU00.0340.01319.385-0.001-0.0010.0000.0000.0000.000
169A431ARG10.8870.93623.530-0.061-0.0610.0000.0000.0000.000
170A432ALA00.0000.00624.9330.0110.0110.0000.0000.0000.000
171A433THR0-0.046-0.01625.062-0.009-0.0090.0000.0000.0000.000
172A434ARG10.8720.91327.661-0.072-0.0720.0000.0000.0000.000
173A435TYR00.001-0.00924.961-0.001-0.0010.0000.0000.0000.000
174A436SER00.0440.02723.6360.0110.0110.0000.0000.0000.000
175A437TYR0-0.080-0.07622.465-0.018-0.0180.0000.0000.0000.000
176A438MET00.0030.00622.8730.0130.0130.0000.0000.0000.000
177A439GLU-1-0.807-0.87722.8570.2300.2300.0000.0000.0000.000
178A440VAL0-0.0050.00923.4970.0130.0130.0000.0000.0000.000
179A441ILE00.008-0.00320.3020.0020.0020.0000.0000.0000.000
180A442MET0-0.017-0.00822.597-0.013-0.0130.0000.0000.0000.000