Manual

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: 2NN4R

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 OptAll
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 -1927552.98881
FMO2-HF: Nuclear repulsion 1854253.035432
FMO2-HF: Total energy -73299.953378
FMO2-MP2: Total energy -73508.635438


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.
-0.3610.749-0.005-0.439-0.6670.001
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 : -0.023 / 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].
3A247LYS10.9670.9803.8630.7321.842-0.005-0.439-0.6670.001
4A248GLU-1-0.771-0.8406.2170.3220.3220.0000.0000.0000.000
5A249SER0-0.066-0.0539.098-0.150-0.1500.0000.0000.0000.000
6A250PHE00.0360.01512.4780.0800.0800.0000.0000.0000.000
7A251GLU-1-0.816-0.87816.193-0.047-0.0470.0000.0000.0000.000
8A252GLY00.0090.00818.6780.0050.0050.0000.0000.0000.000
9A253ASP-1-0.928-0.95921.797-0.024-0.0240.0000.0000.0000.000
10A254GLY00.0210.01724.613-0.007-0.0070.0000.0000.0000.000
11A255TYR0-0.064-0.07326.5410.0070.0070.0000.0000.0000.000
12A256HIS10.8200.91221.9140.0120.0120.0000.0000.0000.000
13A257LYS10.8200.90126.238-0.003-0.0030.0000.0000.0000.000
14A258GLY0-0.0030.00626.703-0.008-0.0080.0000.0000.0000.000
15A259PRO0-0.029-0.01823.3750.0060.0060.0000.0000.0000.000
16A260LYS10.8370.91915.705-0.021-0.0210.0000.0000.0000.000
17A261GLN0-0.039-0.03117.4370.0320.0320.0000.0000.0000.000
18A262VAL0-0.024-0.00914.331-0.024-0.0240.0000.0000.0000.000
19A263VAL00.0480.02911.507-0.013-0.0130.0000.0000.0000.000
20A264ALA00.0110.00412.9920.0740.0740.0000.0000.0000.000
21A265LEU00.0140.0138.4970.0490.0490.0000.0000.0000.000
22A266LYS10.9000.92011.730-0.846-0.8460.0000.0000.0000.000
23A267ALA00.0280.02315.041-0.019-0.0190.0000.0000.0000.000
24A268THR0-0.0160.00018.3760.0120.0120.0000.0000.0000.000
25A269LYS10.8830.93521.106-0.195-0.1950.0000.0000.0000.000
26A270LEU00.0170.02024.620-0.001-0.0010.0000.0000.0000.000
27A271PHE0-0.030-0.01124.477-0.006-0.0060.0000.0000.0000.000
28A272THR0-0.003-0.02328.999-0.007-0.0070.0000.0000.0000.000
29A273TYR00.0690.03328.854-0.002-0.0020.0000.0000.0000.000
30A274ASP-1-0.864-0.92830.7860.0490.0490.0000.0000.0000.000
31A275SER00.0430.01834.526-0.003-0.0030.0000.0000.0000.000
32A276ILE0-0.0020.00336.947-0.003-0.0030.0000.0000.0000.000
33A277LYS10.8560.92537.622-0.047-0.0470.0000.0000.0000.000
34A278SER00.0010.00037.5580.0000.0000.0000.0000.0000.000
35A279LYS10.9480.99833.702-0.052-0.0520.0000.0000.0000.000
36A280LYS10.7800.88431.002-0.085-0.0850.0000.0000.0000.000
37A281MET0-0.0010.01424.399-0.012-0.0120.0000.0000.0000.000
38A282PHE0-0.0090.00621.6020.0030.0030.0000.0000.0000.000
39A283HIS00.0380.02219.326-0.006-0.0060.0000.0000.0000.000
40A284ALA00.015-0.00217.4620.0210.0210.0000.0000.0000.000
41A285THR0-0.029-0.00711.096-0.029-0.0290.0000.0000.0000.000
42A286VAL0-0.008-0.00713.2440.0640.0640.0000.0000.0000.000
43A287ALA0-0.002-0.0028.8100.0070.0070.0000.0000.0000.000
44A288THR00.0390.00810.398-0.027-0.0270.0000.0000.0000.000
45A289ASP-1-0.929-0.9697.3990.3770.3770.0000.0000.0000.000
46A290THR0-0.071-0.0686.660-0.331-0.3310.0000.0000.0000.000
47A291GLU-1-0.868-0.8926.912-1.029-1.0290.0000.0000.0000.000
48A292PHE0-0.016-0.0046.3760.3620.3620.0000.0000.0000.000
49A293PHE00.0700.0469.906-0.145-0.1450.0000.0000.0000.000
50A294ARG10.8320.88913.115-0.140-0.1400.0000.0000.0000.000
51A295VAL0-0.020-0.01215.567-0.056-0.0560.0000.0000.0000.000
52A296MET00.0110.01319.0980.0220.0220.0000.0000.0000.000
53A297VAL00.0010.00122.114-0.018-0.0180.0000.0000.0000.000
54A298PHE0-0.015-0.02924.8270.0030.0030.0000.0000.0000.000
55A299GLU-1-0.841-0.90528.1500.0790.0790.0000.0000.0000.000
56A300GLU-1-0.775-0.90028.2700.0990.0990.0000.0000.0000.000
57A301ASN0-0.020-0.02229.4490.0130.0130.0000.0000.0000.000
58A302LEU00.0470.01824.9640.0010.0010.0000.0000.0000.000
59A303GLU-1-0.880-0.92024.0620.1550.1550.0000.0000.0000.000
60A304LYS10.7850.87223.450-0.102-0.1020.0000.0000.0000.000
61A305LYS10.9020.97222.953-0.119-0.1190.0000.0000.0000.000
62A306PHE0-0.023-0.01918.5250.0100.0100.0000.0000.0000.000
63A307ILE00.0070.01318.8740.0370.0370.0000.0000.0000.000
64A308PRO0-0.060-0.03515.5150.0180.0180.0000.0000.0000.000
65A309GLY00.0130.00214.4890.0140.0140.0000.0000.0000.000
66A310ASN0-0.052-0.02215.535-0.009-0.0090.0000.0000.0000.000
67A311THR00.0050.01415.4750.0300.0300.0000.0000.0000.000
68A312ILE0-0.011-0.00217.365-0.030-0.0300.0000.0000.0000.000
69A313ALA0-0.018-0.02618.831-0.007-0.0070.0000.0000.0000.000
70A314LEU0-0.0020.01918.919-0.001-0.0010.0000.0000.0000.000
71A315SER0-0.006-0.01222.211-0.019-0.0190.0000.0000.0000.000
72A316ASP-1-0.761-0.84825.3870.0250.0250.0000.0000.0000.000
73A317TYR0-0.030-0.00520.7650.0060.0060.0000.0000.0000.000
74A318PHE00.016-0.00525.637-0.014-0.0140.0000.0000.0000.000
75A319GLY00.0370.02422.8710.0140.0140.0000.0000.0000.000
76A320MET0-0.007-0.02122.804-0.007-0.0070.0000.0000.0000.000
77A321TYR00.0010.00022.4350.0120.0120.0000.0000.0000.000
78A322GLY00.0840.06318.7650.0030.0030.0000.0000.0000.000
79A323SER0-0.063-0.04117.4570.0300.0300.0000.0000.0000.000
80A324LEU0-0.025-0.01018.260-0.018-0.0180.0000.0000.0000.000
81A325ALA0-0.023-0.00620.9830.0180.0180.0000.0000.0000.000
82A326ILE00.0150.00021.320-0.011-0.0110.0000.0000.0000.000
83A327HIS0-0.011-0.02725.6740.0130.0130.0000.0000.0000.000
84A328GLU-1-0.840-0.88729.2270.0460.0460.0000.0000.0000.000
85A329TYR0-0.021-0.01928.0730.0070.0070.0000.0000.0000.000
86A330SER0-0.025-0.05429.0040.0050.0050.0000.0000.0000.000
87A331SER0-0.056-0.01526.2750.0000.0000.0000.0000.0000.000
88A332VAL0-0.0010.00022.600-0.001-0.0010.0000.0000.0000.000
89A333SER00.0100.00524.668-0.001-0.0010.0000.0000.0000.000
90A334GLU-1-0.836-0.93622.2790.1820.1820.0000.0000.0000.000
91A335VAL0-0.0320.00420.310-0.011-0.0110.0000.0000.0000.000
92A354LEU0-0.045-0.0309.5230.0210.0210.0000.0000.0000.000
93A355LYS10.8120.88011.068-0.165-0.1650.0000.0000.0000.000
94A356ILE00.003-0.01713.611-0.027-0.0270.0000.0000.0000.000
95A357CYS0-0.062-0.02415.446-0.015-0.0150.0000.0000.0000.000
96A358ASP-1-0.770-0.89911.2820.0010.0010.0000.0000.0000.000
97A359LEU0-0.046-0.02214.448-0.020-0.0200.0000.0000.0000.000
98A360HIS0-0.021-0.01816.932-0.015-0.0150.0000.0000.0000.000
99A361LEU0-0.055-0.01215.667-0.008-0.0080.0000.0000.0000.000
100A362GLN0-0.091-0.03713.680-0.034-0.0340.0000.0000.0000.000
101A363THR0-0.007-0.01218.0990.0020.0020.0000.0000.0000.000
102A364GLU-1-0.974-0.98019.388-0.105-0.1050.0000.0000.0000.000
103A365GLU-1-0.853-0.89519.694-0.022-0.0220.0000.0000.0000.000
104A366ARG10.8090.86911.7040.0980.0980.0000.0000.0000.000
105A367LEU00.0160.01717.9140.0180.0180.0000.0000.0000.000
106A368VAL0-0.019-0.00915.8940.0150.0150.0000.0000.0000.000
107A369ASP-1-0.796-0.88814.4450.3050.3050.0000.0000.0000.000
108A370GLY00.0130.01714.5750.0210.0210.0000.0000.0000.000
109A371GLU-1-0.873-0.92815.5210.4160.4160.0000.0000.0000.000
110A372PHE00.0340.02115.461-0.001-0.0010.0000.0000.0000.000
111A373LYS10.8750.94419.896-0.152-0.1520.0000.0000.0000.000
112A374VAL00.0140.01223.143-0.009-0.0090.0000.0000.0000.000
113A375TYR0-0.005-0.01026.137-0.004-0.0040.0000.0000.0000.000
114A376ARG10.7620.81228.740-0.060-0.0600.0000.0000.0000.000
115A377LYS10.8520.90530.160-0.072-0.0720.0000.0000.0000.000
116A378SER0-0.038-0.00532.820-0.005-0.0050.0000.0000.0000.000
117A379SER00.0290.01935.0350.0030.0030.0000.0000.0000.000
118A380GLY00.014-0.00636.250-0.002-0.0020.0000.0000.0000.000
119A381ASN0-0.038-0.02137.2430.0020.0020.0000.0000.0000.000
120A382ASN00.0310.00737.6080.0000.0000.0000.0000.0000.000
121A383CYS0-0.060-0.01033.4960.0010.0010.0000.0000.0000.000
122A384ILE00.0090.01332.534-0.002-0.0020.0000.0000.0000.000
123A385CYM-1-0.808-0.80331.0980.0540.0540.0000.0000.0000.000
124A386TYR00.0710.01027.905-0.001-0.0010.0000.0000.0000.000
125A387GLY0-0.019-0.01626.759-0.006-0.0060.0000.0000.0000.000
126A388ILE0-0.021-0.00520.2620.0040.0040.0000.0000.0000.000
127A389TRP0-0.002-0.01321.597-0.011-0.0110.0000.0000.0000.000
128A390ASP-1-0.737-0.87816.6460.1720.1720.0000.0000.0000.000
129A391ASP-1-0.876-0.92217.0270.1440.1440.0000.0000.0000.000
130A392THR0-0.051-0.02915.541-0.019-0.0190.0000.0000.0000.000
131A393GLY00.0120.01318.865-0.016-0.0160.0000.0000.0000.000
132A394ALA0-0.009-0.00221.3580.0130.0130.0000.0000.0000.000
133A395MET00.0160.02320.580-0.003-0.0030.0000.0000.0000.000
134A396LYS10.9971.00523.681-0.024-0.0240.0000.0000.0000.000
135A397VAL00.021-0.00323.5530.0020.0020.0000.0000.0000.000
136A398VAL00.0080.01426.2060.0000.0000.0000.0000.0000.000
137A399VAL00.0100.00627.8810.0030.0030.0000.0000.0000.000
138A400SER00.009-0.02630.047-0.007-0.0070.0000.0000.0000.000
139A401GLY00.0280.01831.7650.0050.0050.0000.0000.0000.000
140A402GLN00.0500.01732.7170.0020.0020.0000.0000.0000.000
141A403LEU00.0390.03326.6850.0010.0010.0000.0000.0000.000
142A404THR0-0.039-0.02230.8980.0030.0030.0000.0000.0000.000
143A405SER0-0.040-0.02433.598-0.003-0.0030.0000.0000.0000.000
144A406VAL0-0.065-0.02228.1380.0010.0010.0000.0000.0000.000
145A407ASN0-0.069-0.04131.5720.0010.0010.0000.0000.0000.000
146A408CYS00.0260.02127.4280.0110.0110.0000.0000.0000.000
147A409GLU-1-0.804-0.87830.8000.0690.0690.0000.0000.0000.000
148A410ILE00.0160.00330.1430.0080.0080.0000.0000.0000.000
149A411GLY00.0160.01928.841-0.002-0.0020.0000.0000.0000.000
150A412ASN0-0.029-0.01027.6050.0090.0090.0000.0000.0000.000
151A413THR00.023-0.00221.173-0.007-0.0070.0000.0000.0000.000
152A414ILE00.0220.01122.5260.0010.0010.0000.0000.0000.000
153A415ARG10.7940.89114.003-0.437-0.4370.0000.0000.0000.000
154A416LEU00.0140.00119.204-0.025-0.0250.0000.0000.0000.000
155A417VAL0-0.017-0.01317.9880.0430.0430.0000.0000.0000.000
156A418CYS00.0190.00618.540-0.036-0.0360.0000.0000.0000.000
157A419PHE00.0070.02820.025-0.022-0.0220.0000.0000.0000.000
158A420GLU-1-0.832-0.89820.4680.0370.0370.0000.0000.0000.000
159A421LEU0-0.016-0.00718.0650.0030.0030.0000.0000.0000.000
160A422THR0-0.043-0.03221.509-0.010-0.0100.0000.0000.0000.000
161A423SER00.030-0.01125.0240.0010.0010.0000.0000.0000.000
162A424ASN0-0.090-0.07426.2460.0030.0030.0000.0000.0000.000
163A425ALA0-0.025-0.01728.625-0.005-0.0050.0000.0000.0000.000
164A426ASP-1-0.945-0.96431.0020.0110.0110.0000.0000.0000.000
165A427GLU-1-0.925-0.95026.3660.0210.0210.0000.0000.0000.000
166A428TRP00.0140.01721.8780.0030.0030.0000.0000.0000.000
167A429PHE0-0.037-0.01924.1870.0060.0060.0000.0000.0000.000
168A430LEU00.0200.02219.396-0.001-0.0010.0000.0000.0000.000
169A431ARG10.8490.90323.414-0.039-0.0390.0000.0000.0000.000
170A432ALA00.0010.01125.0750.0070.0070.0000.0000.0000.000
171A433THR00.006-0.00825.383-0.011-0.0110.0000.0000.0000.000
172A434ARG10.7690.85427.900-0.055-0.0550.0000.0000.0000.000
173A435TYR00.0340.00325.302-0.001-0.0010.0000.0000.0000.000
174A436SER0-0.0100.00223.6020.0080.0080.0000.0000.0000.000
175A437TYR0-0.069-0.06922.727-0.014-0.0140.0000.0000.0000.000
176A438MET0-0.0060.00123.0030.0080.0080.0000.0000.0000.000
177A439GLU-1-0.814-0.86622.8830.2050.2050.0000.0000.0000.000
178A440VAL00.0100.00623.8060.0060.0060.0000.0000.0000.000
179A441ILE0-0.005-0.00720.3060.0050.0050.0000.0000.0000.000
180A442MET0-0.002-0.00123.002-0.011-0.0110.0000.0000.0000.000