Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QYK4Y

Calculation Name: 5T76-A-Xray372

Preferred Name: Alanyl-tRNA synthetase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5T76

Chain ID: A

ChEMBL ID: CHEMBL3574

UniProt ID: P49588

Base Structure: X-ray

Registration Date: 2023-06-22

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014915.623826
FMO2-HF: Nuclear repulsion 1934669.019878
FMO2-HF: Total energy -80246.603948
FMO2-MP2: Total energy -80476.518871


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-3.275-0.3040.098-1.244-1.8260.002
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.014
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].
3A4ALA00.0570.0263.689-1.1980.545-0.003-0.846-0.8950.002
4A5GLN00.0700.0372.967-2.301-1.5410.103-0.212-0.6520.000
5A6LYS10.8100.8874.0880.1850.594-0.001-0.185-0.2230.000
6A7ALA00.0220.0205.8950.1170.1170.0000.0000.0000.000
7A8LEU00.0170.0047.908-0.047-0.0470.0000.0000.0000.000
8A9ARG10.9240.9504.5910.1030.162-0.001-0.001-0.0560.000
9A10LYS10.8800.9479.9100.0760.0760.0000.0000.0000.000
10A11ALA00.0570.03411.985-0.018-0.0180.0000.0000.0000.000
11A12GLU-1-0.831-0.90313.1690.2250.2250.0000.0000.0000.000
12A13SER0-0.053-0.04513.127-0.031-0.0310.0000.0000.0000.000
13A14LEU0-0.016-0.00215.493-0.014-0.0140.0000.0000.0000.000
14A15LYS10.8980.93816.638-0.218-0.2180.0000.0000.0000.000
15A16LYS10.9591.00318.795-0.064-0.0640.0000.0000.0000.000
16A17CYS0-0.023-0.00919.857-0.008-0.0080.0000.0000.0000.000
17A18LEU00.0310.01021.558-0.004-0.0040.0000.0000.0000.000
18A19SER0-0.004-0.00723.322-0.001-0.0010.0000.0000.0000.000
19A20VAL0-0.045-0.02024.309-0.003-0.0030.0000.0000.0000.000
20A21MET00.002-0.00125.334-0.004-0.0040.0000.0000.0000.000
21A22GLU-1-0.871-0.92427.6560.0420.0420.0000.0000.0000.000
22A23ALA0-0.033-0.02129.537-0.002-0.0020.0000.0000.0000.000
23A24LYS10.8390.89929.4250.0010.0010.0000.0000.0000.000
24A25VAL00.0090.00031.069-0.003-0.0030.0000.0000.0000.000
25A26LYS10.8410.91132.477-0.037-0.0370.0000.0000.0000.000
26A27ALA0-0.0060.01035.4930.0000.0000.0000.0000.0000.000
27A28GLN0-0.064-0.02235.261-0.004-0.0040.0000.0000.0000.000
28A29THR0-0.002-0.01038.4700.0010.0010.0000.0000.0000.000
29A30ALA0-0.001-0.00240.9290.0000.0000.0000.0000.0000.000
30A31PRO00.006-0.00139.7230.0000.0000.0000.0000.0000.000
31A32ASN00.0120.00735.311-0.003-0.0030.0000.0000.0000.000
32A33LYS10.8830.91135.0070.0160.0160.0000.0000.0000.000
33A34ASP-1-0.890-0.93732.365-0.019-0.0190.0000.0000.0000.000
34A35VAL00.006-0.00130.713-0.001-0.0010.0000.0000.0000.000
35A36GLN0-0.052-0.05230.2740.0000.0000.0000.0000.0000.000
36A37ARG10.8510.92325.6930.0440.0440.0000.0000.0000.000
37A38GLU-1-0.797-0.88426.264-0.012-0.0120.0000.0000.0000.000
38A39ILE0-0.025-0.01925.3800.0000.0000.0000.0000.0000.000
39A40ALA0-0.010-0.00225.9280.0010.0010.0000.0000.0000.000
40A41ASP-1-0.836-0.90522.755-0.049-0.0490.0000.0000.0000.000
41A42LEU0-0.038-0.02620.575-0.007-0.0070.0000.0000.0000.000
42A43GLY00.021-0.00121.1100.0030.0030.0000.0000.0000.000
43A44GLU-1-0.862-0.92719.749-0.072-0.0720.0000.0000.0000.000
44A45ALA0-0.0270.00317.368-0.014-0.0140.0000.0000.0000.000
45A46LEU00.0090.00216.477-0.007-0.0070.0000.0000.0000.000
46A47ALA0-0.0060.00117.8210.0040.0040.0000.0000.0000.000
47A48THR0-0.001-0.01315.204-0.005-0.0050.0000.0000.0000.000
48A49ALA0-0.106-0.03913.289-0.042-0.0420.0000.0000.0000.000
49A50VAL00.0220.02010.4480.0390.0390.0000.0000.0000.000
50A51ILE0-0.015-0.01210.8380.0220.0220.0000.0000.0000.000
51A52PRO00.0170.00612.532-0.027-0.0270.0000.0000.0000.000
52A53GLN0-0.009-0.01915.492-0.020-0.0200.0000.0000.0000.000
53A54TRP00.0480.01716.903-0.013-0.0130.0000.0000.0000.000
54A55GLN00.0290.02615.3080.0140.0140.0000.0000.0000.000
55A56LYS10.7740.87316.503-0.009-0.0090.0000.0000.0000.000
56A57ASP-1-0.742-0.85519.1360.0400.0400.0000.0000.0000.000
57A58GLU-1-0.903-0.95520.8770.1490.1490.0000.0000.0000.000
58A59LEU0-0.051-0.02217.380-0.009-0.0090.0000.0000.0000.000
59A60ARG10.8550.91122.040-0.041-0.0410.0000.0000.0000.000
60A61GLU-1-0.803-0.88424.3730.0330.0330.0000.0000.0000.000
61A62THR00.0410.02325.309-0.005-0.0050.0000.0000.0000.000
62A63LEU00.0180.02423.884-0.006-0.0060.0000.0000.0000.000
63A64LYS10.8020.87826.787-0.039-0.0390.0000.0000.0000.000
64A65SER0-0.067-0.03829.985-0.003-0.0030.0000.0000.0000.000
65A66LEU00.0100.00627.229-0.003-0.0030.0000.0000.0000.000
66A67LYS10.8910.92830.1600.0020.0020.0000.0000.0000.000
67A68LYS10.7840.88232.083-0.015-0.0150.0000.0000.0000.000
68A69VAL00.0510.02134.991-0.002-0.0020.0000.0000.0000.000
69A70MET0-0.0020.01533.129-0.002-0.0020.0000.0000.0000.000
70A71ASP-1-0.754-0.87035.035-0.003-0.0030.0000.0000.0000.000
71A72ASP-1-0.828-0.88937.5540.0100.0100.0000.0000.0000.000
72A73LEU00.0040.01838.6830.0000.0000.0000.0000.0000.000
73A74ASP-1-0.831-0.91337.787-0.005-0.0050.0000.0000.0000.000
74A75ARG10.8010.88837.481-0.004-0.0040.0000.0000.0000.000
75A76ALA00.0050.00743.4070.0000.0000.0000.0000.0000.000
76A77SER00.0220.01844.2230.0000.0000.0000.0000.0000.000
77A78LYS10.8270.89143.3810.0080.0080.0000.0000.0000.000
78A79ALA0-0.038-0.01746.7800.0000.0000.0000.0000.0000.000
79A80ASP-1-0.851-0.91449.2530.0000.0000.0000.0000.0000.000
80A81VAL00.0060.01048.5280.0000.0000.0000.0000.0000.000
81A82GLN0-0.025-0.01851.171-0.001-0.0010.0000.0000.0000.000
82A83LYS10.8320.90553.058-0.001-0.0010.0000.0000.0000.000
83A84ARG10.8600.90050.8000.0030.0030.0000.0000.0000.000
84A85VAL0-0.0070.00253.7900.0000.0000.0000.0000.0000.000
85A86LEU0-0.0020.00556.6120.0000.0000.0000.0000.0000.000
86A87GLU-1-0.865-0.92559.1610.0010.0010.0000.0000.0000.000
87A88LYS10.9941.00059.3920.0050.0050.0000.0000.0000.000
88A89THR0-0.048-0.04160.0760.0000.0000.0000.0000.0000.000
89A90LYS10.8870.95561.3390.0000.0000.0000.0000.0000.000
90A91GLN00.0770.04263.2260.0000.0000.0000.0000.0000.000
91A92PHE0-0.0040.01065.0970.0000.0000.0000.0000.0000.000
92A93ILE00.010-0.00165.5610.0000.0000.0000.0000.0000.000
93A94ASP-1-0.923-0.97168.856-0.001-0.0010.0000.0000.0000.000
94A95SER0-0.073-0.04069.9530.0000.0000.0000.0000.0000.000
95A96ASN0-0.094-0.03769.4480.0000.0000.0000.0000.0000.000
96A97PRO00.0240.02071.9480.0000.0000.0000.0000.0000.000
97A98ASN0-0.032-0.04472.3500.0000.0000.0000.0000.0000.000
98A99GLN00.0260.02169.7630.0000.0000.0000.0000.0000.000
99A100PRO00.0410.00871.3060.0000.0000.0000.0000.0000.000
100A101LEU0-0.0210.00067.5400.0000.0000.0000.0000.0000.000
101A102VAL0-0.0200.00564.7450.0000.0000.0000.0000.0000.000
102A103ILE00.0110.01062.1910.0000.0000.0000.0000.0000.000
103A104LEU0-0.022-0.00261.1830.0000.0000.0000.0000.0000.000
104A105GLU-1-0.873-0.94154.055-0.011-0.0110.0000.0000.0000.000
105A106MET0-0.064-0.03155.4000.0010.0010.0000.0000.0000.000
106A107GLU-1-0.806-0.89452.046-0.005-0.0050.0000.0000.0000.000
107A108SER00.0430.01849.7880.0000.0000.0000.0000.0000.000
108A109GLY00.0240.03546.9480.0000.0000.0000.0000.0000.000
109A110ALA00.0040.00747.5380.0010.0010.0000.0000.0000.000
110A111THR0-0.013-0.00447.202-0.001-0.0010.0000.0000.0000.000
111A112ALA00.1060.03448.6990.0010.0010.0000.0000.0000.000
112A113LYS10.8380.91050.0190.0010.0010.0000.0000.0000.000
113A114ALA00.0340.01151.7450.0010.0010.0000.0000.0000.000
114A115LEU00.0490.03453.0160.0000.0000.0000.0000.0000.000
115A116ASN00.0060.00554.3760.0000.0000.0000.0000.0000.000
116A117GLU-1-0.827-0.89054.837-0.001-0.0010.0000.0000.0000.000
117A118ALA00.0500.02257.6770.0000.0000.0000.0000.0000.000
118A119LEU00.0110.00358.4950.0000.0000.0000.0000.0000.000
119A120LYS10.8210.89656.4700.0020.0020.0000.0000.0000.000
120A121LEU0-0.0180.00061.4750.0000.0000.0000.0000.0000.000
121A122PHE00.0630.01362.6380.0000.0000.0000.0000.0000.000
122A123LYS10.8330.92064.2710.0030.0030.0000.0000.0000.000
123A124MET0-0.040-0.01566.4950.0000.0000.0000.0000.0000.000
124A125HIS00.0110.00366.4640.0000.0000.0000.0000.0000.000
125A126SER00.0070.01668.9580.0000.0000.0000.0000.0000.000
126A127PRO00.0360.03570.1370.0000.0000.0000.0000.0000.000
127A128GLN0-0.053-0.03271.1990.0000.0000.0000.0000.0000.000
128A129THR0-0.040-0.02567.5510.0000.0000.0000.0000.0000.000
129A130SER0-0.019-0.01367.7390.0000.0000.0000.0000.0000.000
130A131ALA0-0.0010.00363.9370.0000.0000.0000.0000.0000.000
131A132MET0-0.031-0.01459.7590.0000.0000.0000.0000.0000.000
132A133LEU0-0.028-0.01157.8850.0000.0000.0000.0000.0000.000
133A134PHE00.0670.01354.9180.0000.0000.0000.0000.0000.000
134A135THR0-0.022-0.02950.4800.0010.0010.0000.0000.0000.000
135A136VAL00.0510.02648.095-0.001-0.0010.0000.0000.0000.000
136A137ASP-1-0.831-0.91043.591-0.012-0.0120.0000.0000.0000.000
137A138ASN00.019-0.01644.427-0.002-0.0020.0000.0000.0000.000
138A139GLU-1-0.839-0.87338.449-0.017-0.0170.0000.0000.0000.000
139A140ALA0-0.029-0.02439.333-0.002-0.0020.0000.0000.0000.000
140A141GLY0-0.0020.01140.868-0.002-0.0020.0000.0000.0000.000
141A142LYN0-0.034-0.01541.368-0.001-0.0010.0000.0000.0000.000
142A143ILE00.0220.01845.3440.0010.0010.0000.0000.0000.000
143A144THR0-0.032-0.03048.9920.0000.0000.0000.0000.0000.000
144A145CYS0-0.0040.00551.0270.0010.0010.0000.0000.0000.000
145A146LEU0-0.006-0.01152.8350.0000.0000.0000.0000.0000.000
146A147CYS0-0.060-0.00356.7030.0000.0000.0000.0000.0000.000
147A148GLN00.032-0.00560.4670.0000.0000.0000.0000.0000.000
148A149VAL00.0150.01963.4160.0000.0000.0000.0000.0000.000
149A150PRO00.0170.02367.0420.0000.0000.0000.0000.0000.000
150A151GLN00.018-0.00870.0400.0000.0000.0000.0000.0000.000
151A152ASN00.0190.00871.4970.0000.0000.0000.0000.0000.000
152A153ALA00.0450.02071.3380.0000.0000.0000.0000.0000.000
153A154ALA00.0550.03569.0390.0000.0000.0000.0000.0000.000
154A155ASN0-0.060-0.03270.7610.0000.0000.0000.0000.0000.000
155A156ARG10.9000.96874.0910.0040.0040.0000.0000.0000.000
156A157GLY00.0610.03772.6780.0000.0000.0000.0000.0000.000
157A158LEU0-0.0340.00667.2010.0000.0000.0000.0000.0000.000
158A159LYS10.8660.93565.7780.0070.0070.0000.0000.0000.000
159A160ALA00.019-0.00662.5440.0000.0000.0000.0000.0000.000
160A161SER0-0.042-0.02360.7670.0000.0000.0000.0000.0000.000
161A162GLU-1-0.780-0.89160.989-0.009-0.0090.0000.0000.0000.000
162A163TRP0-0.022-0.02362.5450.0000.0000.0000.0000.0000.000
163A164VAL00.011-0.00756.4770.0000.0000.0000.0000.0000.000
164A165GLN0-0.018-0.01057.9550.0000.0000.0000.0000.0000.000
165A166GLN0-0.072-0.02758.915-0.001-0.0010.0000.0000.0000.000
166A167VAL00.0150.00456.5200.0000.0000.0000.0000.0000.000
167A168SER00.010-0.01153.613-0.001-0.0010.0000.0000.0000.000
168A169GLY0-0.022-0.00452.571-0.001-0.0010.0000.0000.0000.000
169A170LEU00.0560.03252.456-0.001-0.0010.0000.0000.0000.000
170A171MET0-0.009-0.00950.8130.0000.0000.0000.0000.0000.000
171A172ASP-1-0.846-0.91545.434-0.024-0.0240.0000.0000.0000.000
172A173GLY0-0.0060.00447.455-0.001-0.0010.0000.0000.0000.000
173A174LYS10.7770.88645.5270.0210.0210.0000.0000.0000.000
174A175GLY00.029-0.01150.1920.0010.0010.0000.0000.0000.000
175A176GLY00.0020.01853.1750.0000.0000.0000.0000.0000.000
176A177GLY0-0.022-0.01856.3600.0000.0000.0000.0000.0000.000
177A178LYS10.8900.94658.7730.0050.0050.0000.0000.0000.000
178A179ASP-1-0.796-0.91662.430-0.007-0.0070.0000.0000.0000.000
179A180VAL00.0350.02464.7010.0000.0000.0000.0000.0000.000
180A181SER0-0.042-0.02860.4270.0010.0010.0000.0000.0000.000
181A182ALA00.0030.02458.3360.0000.0000.0000.0000.0000.000
182A183GLN0-0.0110.01153.0670.0010.0010.0000.0000.0000.000
183A184ALA00.0540.01252.2330.0000.0000.0000.0000.0000.000
184A185THR0-0.045-0.02046.4980.0010.0010.0000.0000.0000.000
185A186GLY00.0140.01546.9980.0000.0000.0000.0000.0000.000
186A187LYS10.9120.95840.4810.0240.0240.0000.0000.0000.000
187A188ASN00.0020.01445.567-0.001-0.0010.0000.0000.0000.000
188A189VAL00.030-0.00346.3510.0010.0010.0000.0000.0000.000
189A190GLY00.0110.00749.1120.0010.0010.0000.0000.0000.000
190A191CYS0-0.056-0.00551.3360.0010.0010.0000.0000.0000.000
191A192LEU00.0160.01053.5250.0010.0010.0000.0000.0000.000
192A193GLN00.0180.00455.2100.0010.0010.0000.0000.0000.000
193A194GLU-1-0.875-0.93157.832-0.014-0.0140.0000.0000.0000.000
194A195ALA00.006-0.00856.4600.0010.0010.0000.0000.0000.000
195A196LEU00.0060.00358.5210.0010.0010.0000.0000.0000.000
196A197GLN00.0030.01060.9340.0000.0000.0000.0000.0000.000
197A198LEU00.0100.00560.4730.0010.0010.0000.0000.0000.000
198A199ALA00.0060.00461.4530.0000.0000.0000.0000.0000.000
199A200THR00.003-0.02663.5050.0010.0010.0000.0000.0000.000
200A201SER0-0.056-0.02166.5400.0010.0010.0000.0000.0000.000
201A202PHE0-0.018-0.01765.8870.0000.0000.0000.0000.0000.000
202A203ALA00.007-0.00467.1970.0000.0000.0000.0000.0000.000
203A204GLN00.006-0.00668.9990.0010.0010.0000.0000.0000.000
204A205LEU0-0.0270.00371.7660.0000.0000.0000.0000.0000.000
205A206ARG10.8490.92168.7210.0090.0090.0000.0000.0000.000
206A207LEU0-0.0190.00071.2490.0000.0000.0000.0000.0000.000
207A208GLY0-0.046-0.04874.8750.0000.0000.0000.0000.0000.000
208A209ASP-1-0.962-0.96177.328-0.005-0.0050.0000.0000.0000.000