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: Z67GN

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2003947.696113
FMO2-HF: Nuclear repulsion 1923702.702637
FMO2-HF: Total energy -80244.993476
FMO2-MP2: Total energy -80474.781539


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.
-1.990.9710.412-1.305-2.0670.003
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 : 0.048 / q_NPA : 0.019
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].
3A4ALA00.0320.0103.800-2.617-0.961-0.008-0.798-0.8500.003
4A5GLN00.0350.0182.609-1.754-0.8190.420-0.349-1.0060.000
5A6LYS10.9260.9523.9730.7341.1040.000-0.158-0.2110.000
6A7ALA00.0270.0195.7190.2100.2100.0000.0000.0000.000
7A8LEU00.0370.0217.7570.0390.0390.0000.0000.0000.000
8A9ARG10.9540.9795.0650.9860.9860.0000.0000.0000.000
9A10LYS10.9340.9659.6040.3590.3590.0000.0000.0000.000
10A11ALA00.0650.03811.5910.0320.0320.0000.0000.0000.000
11A12GLU-1-0.916-0.95513.165-0.086-0.0860.0000.0000.0000.000
12A13SER0-0.061-0.04312.9930.0070.0070.0000.0000.0000.000
13A14LEU0-0.024-0.01615.2590.0150.0150.0000.0000.0000.000
14A15LYS10.9720.99416.8590.0620.0620.0000.0000.0000.000
15A16LYS10.9801.00718.5990.1280.1280.0000.0000.0000.000
16A17CYS0-0.034-0.01719.6590.0100.0100.0000.0000.0000.000
17A18LEU00.0300.00220.7400.0070.0070.0000.0000.0000.000
18A19SER00.0420.03423.2380.0080.0080.0000.0000.0000.000
19A20VAL0-0.067-0.03123.9630.0040.0040.0000.0000.0000.000
20A21MET0-0.006-0.00924.9960.0030.0030.0000.0000.0000.000
21A22GLU-1-0.918-0.94727.425-0.027-0.0270.0000.0000.0000.000
22A23ALA0-0.019-0.01029.3200.0040.0040.0000.0000.0000.000
23A24LYS10.8700.93428.4710.0600.0600.0000.0000.0000.000
24A25VAL00.007-0.01030.4060.0020.0020.0000.0000.0000.000
25A26LYS10.9350.96832.9950.0320.0320.0000.0000.0000.000
26A27ALA0-0.034-0.01135.1630.0020.0020.0000.0000.0000.000
27A28GLN0-0.0430.00234.9860.0010.0010.0000.0000.0000.000
28A29THR0-0.005-0.00638.1080.0010.0010.0000.0000.0000.000
29A30ALA00.0120.00940.6060.0020.0020.0000.0000.0000.000
30A31PRO00.0220.00939.121-0.001-0.0010.0000.0000.0000.000
31A32ASN00.023-0.00535.218-0.002-0.0020.0000.0000.0000.000
32A33LYS11.0190.99834.7200.0280.0280.0000.0000.0000.000
33A34ASP-1-0.871-0.92832.191-0.043-0.0430.0000.0000.0000.000
34A35VAL0-0.033-0.01330.464-0.004-0.0040.0000.0000.0000.000
35A36GLN0-0.033-0.03129.830-0.004-0.0040.0000.0000.0000.000
36A37ARG10.8740.93625.5230.0600.0600.0000.0000.0000.000
37A38GLU-1-0.846-0.93225.954-0.062-0.0620.0000.0000.0000.000
38A39ILE0-0.046-0.02425.014-0.005-0.0050.0000.0000.0000.000
39A40ALA0-0.023-0.00725.4290.0000.0000.0000.0000.0000.000
40A41ASP-1-0.846-0.91222.326-0.067-0.0670.0000.0000.0000.000
41A42LEU0-0.040-0.02220.118-0.008-0.0080.0000.0000.0000.000
42A43GLY00.007-0.02120.552-0.003-0.0030.0000.0000.0000.000
43A44GLU-1-0.890-0.93319.501-0.039-0.0390.0000.0000.0000.000
44A45ALA0-0.021-0.01316.619-0.004-0.0040.0000.0000.0000.000
45A46LEU0-0.055-0.03116.214-0.008-0.0080.0000.0000.0000.000
46A47ALA0-0.022-0.02317.6650.0120.0120.0000.0000.0000.000
47A48THR00.0120.01815.3220.0070.0070.0000.0000.0000.000
48A49ALA0-0.077-0.02612.891-0.011-0.0110.0000.0000.0000.000
49A50VAL00.0180.01110.5960.0270.0270.0000.0000.0000.000
50A51ILE0-0.039-0.01811.039-0.019-0.0190.0000.0000.0000.000
51A52PRO00.0290.01412.7690.0180.0180.0000.0000.0000.000
52A53GLN00.001-0.00215.679-0.016-0.0160.0000.0000.0000.000
53A54TRP00.0590.02316.426-0.019-0.0190.0000.0000.0000.000
54A55GLN00.0460.02914.993-0.010-0.0100.0000.0000.0000.000
55A56LYS10.7800.87716.570-0.025-0.0250.0000.0000.0000.000
56A57ASP-1-0.862-0.94819.2430.0310.0310.0000.0000.0000.000
57A58GLU-1-0.917-0.95121.7210.0140.0140.0000.0000.0000.000
58A59LEU0-0.040-0.02317.528-0.009-0.0090.0000.0000.0000.000
59A60ARG10.9530.97121.998-0.018-0.0180.0000.0000.0000.000
60A61GLU-1-0.844-0.91924.2520.0060.0060.0000.0000.0000.000
61A62THR00.0280.02125.037-0.002-0.0020.0000.0000.0000.000
62A63LEU0-0.0170.00023.643-0.002-0.0020.0000.0000.0000.000
63A64LYS10.8500.91626.665-0.009-0.0090.0000.0000.0000.000
64A65SER0-0.0320.00029.721-0.001-0.0010.0000.0000.0000.000
65A66LEU00.0230.01027.1270.0000.0000.0000.0000.0000.000
66A67LYS10.9460.97029.1920.0180.0180.0000.0000.0000.000
67A68LYS10.8280.90331.7620.0080.0080.0000.0000.0000.000
68A69VAL00.0220.01234.5710.0010.0010.0000.0000.0000.000
69A70MET0-0.0080.00532.587-0.001-0.0010.0000.0000.0000.000
70A71ASP-1-0.823-0.93034.665-0.015-0.0150.0000.0000.0000.000
71A72ASP-1-0.885-0.92337.172-0.008-0.0080.0000.0000.0000.000
72A73LEU0-0.0020.00638.0520.0010.0010.0000.0000.0000.000
73A74ASP-1-0.828-0.90537.419-0.020-0.0200.0000.0000.0000.000
74A75ARG10.8250.90038.0490.0090.0090.0000.0000.0000.000
75A76ALA00.0090.00743.1370.0010.0010.0000.0000.0000.000
76A77SER00.0490.03743.7060.0010.0010.0000.0000.0000.000
77A78LYS10.9370.95742.4980.0140.0140.0000.0000.0000.000
78A79ALA0-0.049-0.01846.5030.0010.0010.0000.0000.0000.000
79A80ASP-1-0.880-0.93648.896-0.011-0.0110.0000.0000.0000.000
80A81VAL0-0.034-0.00948.1960.0000.0000.0000.0000.0000.000
81A82GLN0-0.004-0.00750.8360.0000.0000.0000.0000.0000.000
82A83LYS10.9180.96252.7260.0090.0090.0000.0000.0000.000
83A84ARG10.9300.95749.9250.0120.0120.0000.0000.0000.000
84A85VAL0-0.014-0.00553.6240.0000.0000.0000.0000.0000.000
85A86LEU0-0.029-0.02556.4150.0000.0000.0000.0000.0000.000
86A87GLU-1-0.941-0.96858.877-0.007-0.0070.0000.0000.0000.000
87A88LYS10.9941.00159.0100.0090.0090.0000.0000.0000.000
88A89THR0-0.032-0.01959.7820.0000.0000.0000.0000.0000.000
89A90LYS10.9210.95761.2660.0050.0050.0000.0000.0000.000
90A91GLN00.0480.03163.7130.0000.0000.0000.0000.0000.000
91A92PHE0-0.008-0.00164.8630.0000.0000.0000.0000.0000.000
92A93ILE0-0.010-0.02265.3460.0000.0000.0000.0000.0000.000
93A94ASP-1-0.932-0.95868.495-0.004-0.0040.0000.0000.0000.000
94A95SER0-0.079-0.04070.0050.0000.0000.0000.0000.0000.000
95A96ASN0-0.090-0.02969.2320.0000.0000.0000.0000.0000.000
96A97PRO00.0460.03171.5280.0000.0000.0000.0000.0000.000
97A98ASN0-0.012-0.02272.0480.0000.0000.0000.0000.0000.000
98A99GLN00.0150.01669.1750.0000.0000.0000.0000.0000.000
99A100PRO00.0430.02470.9020.0000.0000.0000.0000.0000.000
100A101LEU00.0130.00767.1720.0000.0000.0000.0000.0000.000
101A102VAL0-0.0240.01264.1590.0000.0000.0000.0000.0000.000
102A103ILE00.0180.00861.5710.0000.0000.0000.0000.0000.000
103A104LEU0-0.025-0.00660.7340.0000.0000.0000.0000.0000.000
104A105GLU-1-0.900-0.94854.086-0.011-0.0110.0000.0000.0000.000
105A106MET0-0.062-0.02854.6840.0000.0000.0000.0000.0000.000
106A107GLU-1-0.812-0.90551.282-0.012-0.0120.0000.0000.0000.000
107A108SER00.0270.00048.8530.0000.0000.0000.0000.0000.000
108A109GLY00.0190.01846.2910.0000.0000.0000.0000.0000.000
109A110ALA0-0.0110.00446.9840.0000.0000.0000.0000.0000.000
110A111THR0-0.035-0.01146.7120.0000.0000.0000.0000.0000.000
111A112ALA00.1140.03948.3050.0000.0000.0000.0000.0000.000
112A113LYS10.9310.95848.8770.0040.0040.0000.0000.0000.000
113A114ALA00.0490.01651.0500.0000.0000.0000.0000.0000.000
114A115LEU00.0570.02952.7200.0000.0000.0000.0000.0000.000
115A116ASN0-0.028-0.01554.0870.0010.0010.0000.0000.0000.000
116A117GLU-1-0.927-0.96954.585-0.002-0.0020.0000.0000.0000.000
117A118ALA00.0280.01857.1260.0000.0000.0000.0000.0000.000
118A119LEU00.0150.00758.2940.0000.0000.0000.0000.0000.000
119A120LYS10.8520.93256.6550.0020.0020.0000.0000.0000.000
120A121LEU0-0.0140.00061.1840.0000.0000.0000.0000.0000.000
121A122PHE00.0790.02862.3410.0000.0000.0000.0000.0000.000
122A123LYS10.8990.96164.2350.0010.0010.0000.0000.0000.000
123A124MET0-0.054-0.02266.1590.0000.0000.0000.0000.0000.000
124A125HIS00.007-0.00666.2910.0000.0000.0000.0000.0000.000
125A126SER0-0.033-0.01368.4130.0000.0000.0000.0000.0000.000
126A127PRO00.0280.00969.7680.0000.0000.0000.0000.0000.000
127A128GLN0-0.056-0.03770.8850.0000.0000.0000.0000.0000.000
128A129THR0-0.041-0.01267.1370.0000.0000.0000.0000.0000.000
129A130SER0-0.031-0.00967.0980.0000.0000.0000.0000.0000.000
130A131ALA00.007-0.00363.2320.0000.0000.0000.0000.0000.000
131A132MET0-0.026-0.00859.1850.0000.0000.0000.0000.0000.000
132A133LEU0-0.025-0.01357.3980.0000.0000.0000.0000.0000.000
133A134PHE00.0610.00854.5790.0000.0000.0000.0000.0000.000
134A135THR0-0.042-0.02650.1310.0000.0000.0000.0000.0000.000
135A136VAL00.0680.03047.6940.0000.0000.0000.0000.0000.000
136A137ASP-1-0.878-0.94443.396-0.015-0.0150.0000.0000.0000.000
137A138ASN0-0.001-0.03044.0230.0000.0000.0000.0000.0000.000
138A139GLU-1-0.987-0.96637.947-0.023-0.0230.0000.0000.0000.000
139A140ALA0-0.031-0.01738.957-0.001-0.0010.0000.0000.0000.000
140A141GLY0-0.0110.00940.2450.0000.0000.0000.0000.0000.000
141A142LYN0-0.017-0.01940.2800.0010.0010.0000.0000.0000.000
142A143ILE00.0040.01744.9300.0000.0000.0000.0000.0000.000
143A144THR0-0.041-0.02848.3280.0010.0010.0000.0000.0000.000
144A145CYS0-0.0040.00650.6180.0000.0000.0000.0000.0000.000
145A146LEU00.001-0.00352.5520.0010.0010.0000.0000.0000.000
146A147CYS0-0.0520.00356.2950.0000.0000.0000.0000.0000.000
147A148GLN0-0.007-0.03760.0480.0010.0010.0000.0000.0000.000
148A149VAL00.0020.00962.8690.0000.0000.0000.0000.0000.000
149A150PRO00.0070.01566.4380.0000.0000.0000.0000.0000.000
150A151GLN00.0280.00569.5010.0000.0000.0000.0000.0000.000
151A152ASN00.0220.00671.1020.0000.0000.0000.0000.0000.000
152A153ALA00.0320.01370.6860.0000.0000.0000.0000.0000.000
153A154ALA00.0830.04968.6570.0000.0000.0000.0000.0000.000
154A155ASN0-0.106-0.05470.4450.0000.0000.0000.0000.0000.000
155A156ARG10.9240.97173.9190.0010.0010.0000.0000.0000.000
156A157GLY00.0490.03872.1800.0000.0000.0000.0000.0000.000
157A158LEU0-0.0210.00766.4450.0000.0000.0000.0000.0000.000
158A159LYS10.9170.94365.3540.0000.0000.0000.0000.0000.000
159A160ALA00.010-0.00361.8640.0000.0000.0000.0000.0000.000
160A161SER0-0.021-0.01560.0110.0000.0000.0000.0000.0000.000
161A162GLU-1-0.885-0.94160.311-0.001-0.0010.0000.0000.0000.000
162A163TRP0-0.041-0.03662.2890.0000.0000.0000.0000.0000.000
163A164VAL00.005-0.01956.0420.0000.0000.0000.0000.0000.000
164A165GLN0-0.035-0.01957.5650.0000.0000.0000.0000.0000.000
165A166GLN0-0.053-0.01158.551-0.001-0.0010.0000.0000.0000.000
166A167VAL00.0270.01456.4170.0000.0000.0000.0000.0000.000
167A168SER0-0.016-0.02253.2800.0000.0000.0000.0000.0000.000
168A169GLY0-0.033-0.01052.4800.0000.0000.0000.0000.0000.000
169A170LEU00.0460.02152.4180.0000.0000.0000.0000.0000.000
170A171MET0-0.0140.00050.491-0.001-0.0010.0000.0000.0000.000
171A172ASP-1-0.928-0.95245.129-0.010-0.0100.0000.0000.0000.000
172A173GLY00.001-0.02346.6720.0000.0000.0000.0000.0000.000
173A174LYS10.9180.97643.8290.0040.0040.0000.0000.0000.000
174A175GLY00.0740.01649.9360.0000.0000.0000.0000.0000.000
175A176GLY0-0.046-0.01053.0880.0010.0010.0000.0000.0000.000
176A177GLY00.000-0.00755.4890.0000.0000.0000.0000.0000.000
177A178LYS10.8650.95558.124-0.001-0.0010.0000.0000.0000.000
178A179ASP-1-0.778-0.91161.6630.0000.0000.0000.0000.0000.000
179A180VAL00.0240.01363.7910.0000.0000.0000.0000.0000.000
180A181SER0-0.022-0.01758.8650.0000.0000.0000.0000.0000.000
181A182ALA0-0.0010.00757.6300.0010.0010.0000.0000.0000.000
182A183GLN0-0.0130.00851.8580.0000.0000.0000.0000.0000.000
183A184ALA00.0500.00851.9020.0010.0010.0000.0000.0000.000
184A185THR0-0.034-0.01646.1300.0000.0000.0000.0000.0000.000
185A186GLY0-0.0010.00646.6780.0010.0010.0000.0000.0000.000
186A187LYS10.9370.97539.7960.0110.0110.0000.0000.0000.000
187A188ASN0-0.0100.00444.831-0.002-0.0020.0000.0000.0000.000
188A189VAL00.016-0.01045.6170.0010.0010.0000.0000.0000.000
189A190GLY0-0.006-0.00348.4130.0000.0000.0000.0000.0000.000
190A191CYS0-0.0310.01250.6270.0000.0000.0000.0000.0000.000
191A192LEU00.0100.00753.0370.0010.0010.0000.0000.0000.000
192A193GLN00.024-0.00154.7720.0010.0010.0000.0000.0000.000
193A194GLU-1-0.887-0.94557.462-0.007-0.0070.0000.0000.0000.000
194A195ALA00.002-0.00356.0200.0010.0010.0000.0000.0000.000
195A196LEU00.0180.00558.1340.0010.0010.0000.0000.0000.000
196A197GLN0-0.0080.00660.5020.0000.0000.0000.0000.0000.000
197A198LEU00.0280.01460.2580.0000.0000.0000.0000.0000.000
198A199ALA0-0.0010.01061.1630.0010.0010.0000.0000.0000.000
199A200THR0-0.014-0.03063.1740.0000.0000.0000.0000.0000.000
200A201SER0-0.040-0.02066.2140.0000.0000.0000.0000.0000.000
201A202PHE00.0020.00365.5100.0000.0000.0000.0000.0000.000
202A203ALA00.024-0.00266.9360.0000.0000.0000.0000.0000.000
203A204GLN00.005-0.00668.6740.0000.0000.0000.0000.0000.000
204A205LEU0-0.0270.00271.4280.0000.0000.0000.0000.0000.000
205A206ARG10.8940.95069.1210.0030.0030.0000.0000.0000.000
206A207LEU0-0.026-0.00570.7330.0000.0000.0000.0000.0000.000
207A208GLY0-0.065-0.04374.1040.0000.0000.0000.0000.0000.000
208A209ASP-1-0.951-0.95177.406-0.003-0.0030.0000.0000.0000.000