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: R9QK8

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005224.061568
FMO2-HF: Nuclear repulsion 1924977.929358
FMO2-HF: Total energy -80246.13221
FMO2-MP2: Total energy -80475.906817


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.
-4.393-0.8370.268-1.536-2.2870.004
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 : 0.035 / 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].
3A4ALA00.0500.0183.800-1.6050.239-0.010-0.875-0.9600.003
4A5GLN00.0330.0112.710-2.901-1.6590.279-0.481-1.0400.000
5A6LYS10.7980.8823.9530.1030.5150.000-0.179-0.2320.001
6A7ALA00.0260.0245.7150.0170.0170.0000.0000.0000.000
7A8LEU00.0320.0197.823-0.070-0.0700.0000.0000.0000.000
8A9ARG10.9700.9824.6620.1910.249-0.001-0.001-0.0550.000
9A10LYS10.9410.9779.5870.0910.0910.0000.0000.0000.000
10A11ALA00.0710.04211.588-0.026-0.0260.0000.0000.0000.000
11A12GLU-1-0.834-0.89813.1500.2120.2120.0000.0000.0000.000
12A13SER0-0.063-0.05212.813-0.039-0.0390.0000.0000.0000.000
13A14LEU0-0.020-0.01415.070-0.016-0.0160.0000.0000.0000.000
14A15LYS10.8950.93716.564-0.215-0.2150.0000.0000.0000.000
15A16LYS10.9691.00318.592-0.046-0.0460.0000.0000.0000.000
16A17CYS0-0.036-0.01519.659-0.008-0.0080.0000.0000.0000.000
17A18LEU00.0380.00821.048-0.005-0.0050.0000.0000.0000.000
18A19SER00.0090.01223.2280.0010.0010.0000.0000.0000.000
19A20VAL0-0.057-0.02924.103-0.003-0.0030.0000.0000.0000.000
20A21MET00.008-0.00225.058-0.004-0.0040.0000.0000.0000.000
21A22GLU-1-0.925-0.95227.4370.0440.0440.0000.0000.0000.000
22A23ALA0-0.033-0.01529.317-0.002-0.0020.0000.0000.0000.000
23A24LYS10.8370.89328.7640.0040.0040.0000.0000.0000.000
24A25VAL00.012-0.00230.817-0.002-0.0020.0000.0000.0000.000
25A26LYS10.9220.96432.997-0.030-0.0300.0000.0000.0000.000
26A27ALA0-0.024-0.00335.1650.0000.0000.0000.0000.0000.000
27A28GLN0-0.064-0.02034.936-0.004-0.0040.0000.0000.0000.000
28A29THR00.004-0.00438.1130.0010.0010.0000.0000.0000.000
29A30ALA0-0.0030.00440.6870.0000.0000.0000.0000.0000.000
30A31PRO00.0150.00239.2230.0000.0000.0000.0000.0000.000
31A32ASN00.0280.00835.113-0.003-0.0030.0000.0000.0000.000
32A33LYS10.8800.91234.8140.0170.0170.0000.0000.0000.000
33A34ASP-1-0.882-0.93932.280-0.021-0.0210.0000.0000.0000.000
34A35VAL0-0.019-0.00630.551-0.001-0.0010.0000.0000.0000.000
35A36GLN0-0.045-0.04029.9260.0000.0000.0000.0000.0000.000
36A37ARG10.8620.92925.5390.0450.0450.0000.0000.0000.000
37A38GLU-1-0.800-0.88226.045-0.015-0.0150.0000.0000.0000.000
38A39ILE0-0.042-0.02625.1100.0000.0000.0000.0000.0000.000
39A40ALA0-0.0130.00125.5360.0010.0010.0000.0000.0000.000
40A41ASP-1-0.823-0.90122.458-0.049-0.0490.0000.0000.0000.000
41A42LEU0-0.048-0.02220.316-0.006-0.0060.0000.0000.0000.000
42A43GLY00.021-0.01320.6620.0010.0010.0000.0000.0000.000
43A44GLU-1-0.881-0.92919.760-0.061-0.0610.0000.0000.0000.000
44A45ALA0-0.025-0.00816.805-0.011-0.0110.0000.0000.0000.000
45A46LEU0-0.048-0.03416.331-0.003-0.0030.0000.0000.0000.000
46A47ALA0-0.013-0.00917.7890.0100.0100.0000.0000.0000.000
47A48THR00.0200.01315.311-0.002-0.0020.0000.0000.0000.000
48A49ALA0-0.101-0.03913.011-0.033-0.0330.0000.0000.0000.000
49A50VAL00.0200.01810.7200.0340.0340.0000.0000.0000.000
50A51ILE0-0.027-0.01311.0390.0330.0330.0000.0000.0000.000
51A52PRO00.0290.01412.735-0.028-0.0280.0000.0000.0000.000
52A53GLN0-0.025-0.03215.679-0.021-0.0210.0000.0000.0000.000
53A54TRP00.0390.00916.878-0.014-0.0140.0000.0000.0000.000
54A55GLN00.0320.02715.0260.0130.0130.0000.0000.0000.000
55A56LYS10.7950.87916.600-0.037-0.0370.0000.0000.0000.000
56A57ASP-1-0.754-0.87119.2430.0560.0560.0000.0000.0000.000
57A58GLU-1-0.907-0.94421.5200.1450.1450.0000.0000.0000.000
58A59LEU0-0.036-0.01917.459-0.011-0.0110.0000.0000.0000.000
59A60ARG10.8610.91622.080-0.054-0.0540.0000.0000.0000.000
60A61GLU-1-0.820-0.88424.2440.0390.0390.0000.0000.0000.000
61A62THR00.0530.02925.045-0.004-0.0040.0000.0000.0000.000
62A63LEU0-0.0070.00323.703-0.006-0.0060.0000.0000.0000.000
63A64LYS10.8200.88326.662-0.047-0.0470.0000.0000.0000.000
64A65SER0-0.053-0.01429.717-0.004-0.0040.0000.0000.0000.000
65A66LEU00.0140.00727.388-0.004-0.0040.0000.0000.0000.000
66A67LYS10.8870.92329.808-0.002-0.0020.0000.0000.0000.000
67A68LYS10.8060.89731.874-0.018-0.0180.0000.0000.0000.000
68A69VAL00.0310.01334.609-0.002-0.0020.0000.0000.0000.000
69A70MET0-0.0030.01132.708-0.002-0.0020.0000.0000.0000.000
70A71ASP-1-0.778-0.89234.7750.0000.0000.0000.0000.0000.000
71A72ASP-1-0.839-0.89437.2840.0110.0110.0000.0000.0000.000
72A73LEU00.0050.01138.104-0.001-0.0010.0000.0000.0000.000
73A74ASP-1-0.847-0.91937.443-0.005-0.0050.0000.0000.0000.000
74A75ARG10.8060.88737.600-0.007-0.0070.0000.0000.0000.000
75A76ALA00.0110.01043.2500.0000.0000.0000.0000.0000.000
76A77SER00.0370.02843.7860.0000.0000.0000.0000.0000.000
77A78LYS10.8420.89843.0730.0070.0070.0000.0000.0000.000
78A79ALA0-0.043-0.01546.6130.0000.0000.0000.0000.0000.000
79A80ASP-1-0.864-0.92948.9940.0010.0010.0000.0000.0000.000
80A81VAL0-0.058-0.02148.1720.0000.0000.0000.0000.0000.000
81A82GLN0-0.009-0.01250.9470.0000.0000.0000.0000.0000.000
82A83LYS10.8520.90552.837-0.001-0.0010.0000.0000.0000.000
83A84ARG10.9160.93550.1580.0030.0030.0000.0000.0000.000
84A85VAL0-0.023-0.01253.7350.0000.0000.0000.0000.0000.000
85A86LEU0-0.013-0.00756.4310.0000.0000.0000.0000.0000.000
86A87GLU-1-0.876-0.91358.9880.0010.0010.0000.0000.0000.000
87A88LYS11.0021.00459.2120.0050.0050.0000.0000.0000.000
88A89THR0-0.044-0.03459.8720.0000.0000.0000.0000.0000.000
89A90LYS10.9210.95961.412-0.001-0.0010.0000.0000.0000.000
90A91GLN00.0550.03463.3560.0000.0000.0000.0000.0000.000
91A92PHE0-0.0070.00164.9600.0000.0000.0000.0000.0000.000
92A93ILE0-0.001-0.01765.3240.0000.0000.0000.0000.0000.000
93A94ASP-1-0.931-0.95668.606-0.001-0.0010.0000.0000.0000.000
94A95SER0-0.081-0.04370.0180.0000.0000.0000.0000.0000.000
95A96ASN0-0.093-0.03569.3240.0000.0000.0000.0000.0000.000
96A97PRO00.0370.02571.6380.0000.0000.0000.0000.0000.000
97A98ASN0-0.044-0.04072.1700.0000.0000.0000.0000.0000.000
98A99GLN00.0340.02969.3280.0000.0000.0000.0000.0000.000
99A100PRO00.0480.01171.0130.0000.0000.0000.0000.0000.000
100A101LEU0-0.003-0.00167.2090.0000.0000.0000.0000.0000.000
101A102VAL0-0.0270.00464.3580.0000.0000.0000.0000.0000.000
102A103ILE00.0180.00761.6960.0000.0000.0000.0000.0000.000
103A104LEU0-0.0160.00060.9050.0000.0000.0000.0000.0000.000
104A105GLU-1-0.887-0.94353.965-0.011-0.0110.0000.0000.0000.000
105A106MET0-0.063-0.02954.8850.0010.0010.0000.0000.0000.000
106A107GLU-1-0.809-0.88651.667-0.005-0.0050.0000.0000.0000.000
107A108SER00.0460.01149.0550.0000.0000.0000.0000.0000.000
108A109GLY00.0050.01946.3990.0000.0000.0000.0000.0000.000
109A110ALA00.0190.02747.0920.0010.0010.0000.0000.0000.000
110A111THR0-0.022-0.01846.876-0.001-0.0010.0000.0000.0000.000
111A112ALA00.1080.03848.4210.0000.0000.0000.0000.0000.000
112A113LYS10.8530.92449.4170.0000.0000.0000.0000.0000.000
113A114ALA00.0440.01551.1230.0010.0010.0000.0000.0000.000
114A115LEU00.0620.03452.7540.0000.0000.0000.0000.0000.000
115A116ASN0-0.022-0.01454.2600.0000.0000.0000.0000.0000.000
116A117GLU-1-0.846-0.90254.4570.0010.0010.0000.0000.0000.000
117A118ALA00.0380.02257.2430.0000.0000.0000.0000.0000.000
118A119LEU00.0090.00158.2340.0000.0000.0000.0000.0000.000
119A120LYS10.8200.89856.2600.0000.0000.0000.0000.0000.000
120A121LEU0-0.0100.00161.3650.0000.0000.0000.0000.0000.000
121A122PHE00.0710.02362.3930.0000.0000.0000.0000.0000.000
122A123LYS10.8480.93964.0430.0020.0020.0000.0000.0000.000
123A124MET0-0.039-0.01566.2840.0000.0000.0000.0000.0000.000
124A125HIS00.011-0.00266.3210.0000.0000.0000.0000.0000.000
125A126SER0-0.018-0.00368.6210.0000.0000.0000.0000.0000.000
126A127PRO00.0370.02469.8830.0000.0000.0000.0000.0000.000
127A128GLN0-0.049-0.03271.0030.0000.0000.0000.0000.0000.000
128A129THR0-0.040-0.00467.2570.0000.0000.0000.0000.0000.000
129A130SER0-0.015-0.00867.2260.0000.0000.0000.0000.0000.000
130A131ALA0-0.005-0.00863.3870.0000.0000.0000.0000.0000.000
131A132MET0-0.027-0.00959.3390.0000.0000.0000.0000.0000.000
132A133LEU0-0.033-0.01357.6260.0000.0000.0000.0000.0000.000
133A134PHE00.0690.00854.5980.0000.0000.0000.0000.0000.000
134A135THR0-0.036-0.02450.1900.0000.0000.0000.0000.0000.000
135A136VAL00.0770.03947.951-0.001-0.0010.0000.0000.0000.000
136A137ASP-1-0.831-0.92643.360-0.012-0.0120.0000.0000.0000.000
137A138ASN00.013-0.02244.119-0.002-0.0020.0000.0000.0000.000
138A139GLU-1-0.855-0.88037.937-0.017-0.0170.0000.0000.0000.000
139A140ALA0-0.024-0.01839.057-0.001-0.0010.0000.0000.0000.000
140A141GLY0-0.0010.01340.348-0.002-0.0020.0000.0000.0000.000
141A142LYN0-0.023-0.01440.831-0.001-0.0010.0000.0000.0000.000
142A143ILE00.0100.01845.0340.0010.0010.0000.0000.0000.000
143A144THR0-0.043-0.02748.7020.0000.0000.0000.0000.0000.000
144A145CYS0-0.0070.00950.7270.0010.0010.0000.0000.0000.000
145A146LEU00.003-0.00552.5910.0000.0000.0000.0000.0000.000
146A147CYS0-0.0510.00356.4090.0000.0000.0000.0000.0000.000
147A148GLN00.020-0.02160.1620.0010.0010.0000.0000.0000.000
148A149VAL00.0010.01162.9860.0000.0000.0000.0000.0000.000
149A150PRO00.0180.01966.5540.0000.0000.0000.0000.0000.000
150A151GLN00.016-0.00769.6190.0000.0000.0000.0000.0000.000
151A152ASN00.0170.00671.2220.0000.0000.0000.0000.0000.000
152A153ALA00.0530.02770.7480.0000.0000.0000.0000.0000.000
153A154ALA00.0710.04368.7710.0000.0000.0000.0000.0000.000
154A155ASN0-0.090-0.05070.5610.0000.0000.0000.0000.0000.000
155A156ARG10.9030.96874.0360.0040.0040.0000.0000.0000.000
156A157GLY00.0510.03972.2910.0000.0000.0000.0000.0000.000
157A158LEU0-0.0270.00666.7880.0000.0000.0000.0000.0000.000
158A159LYS10.9070.95465.4260.0060.0060.0000.0000.0000.000
159A160ALA00.001-0.01062.0500.0000.0000.0000.0000.0000.000
160A161SER0-0.020-0.01160.1200.0000.0000.0000.0000.0000.000
161A162GLU-1-0.846-0.92860.423-0.008-0.0080.0000.0000.0000.000
162A163TRP0-0.037-0.03162.3980.0000.0000.0000.0000.0000.000
163A164VAL00.007-0.02056.2000.0000.0000.0000.0000.0000.000
164A165GLN0-0.029-0.01757.6730.0000.0000.0000.0000.0000.000
165A166GLN0-0.074-0.02558.657-0.001-0.0010.0000.0000.0000.000
166A167VAL00.0210.00856.4190.0000.0000.0000.0000.0000.000
167A168SER0-0.010-0.01853.3860.0000.0000.0000.0000.0000.000
168A169GLY0-0.038-0.01152.584-0.001-0.0010.0000.0000.0000.000
169A170LEU00.0360.01752.517-0.001-0.0010.0000.0000.0000.000
170A171MET0-0.010-0.00150.5700.0000.0000.0000.0000.0000.000
171A172ASP-1-0.935-0.95745.256-0.023-0.0230.0000.0000.0000.000
172A173GLY0-0.006-0.02646.775-0.001-0.0010.0000.0000.0000.000
173A174LYS10.9220.97944.4610.0200.0200.0000.0000.0000.000
174A175GLY00.0750.01650.0470.0000.0000.0000.0000.0000.000
175A176GLY0-0.033-0.00453.2010.0000.0000.0000.0000.0000.000
176A177GLY0-0.015-0.01655.6040.0000.0000.0000.0000.0000.000
177A178LYS10.8580.93558.2420.0040.0040.0000.0000.0000.000
178A179ASP-1-0.778-0.90761.782-0.005-0.0050.0000.0000.0000.000
179A180VAL00.0390.02463.9620.0000.0000.0000.0000.0000.000
180A181SER0-0.0010.00359.4480.0000.0000.0000.0000.0000.000
181A182ALA0-0.0130.00357.7580.0000.0000.0000.0000.0000.000
182A183GLN0-0.0170.00652.4720.0010.0010.0000.0000.0000.000
183A184ALA00.0640.01652.0140.0000.0000.0000.0000.0000.000
184A185THR0-0.059-0.03546.1360.0010.0010.0000.0000.0000.000
185A186GLY00.0090.01546.7830.0000.0000.0000.0000.0000.000
186A187LYS10.9370.96739.8860.0230.0230.0000.0000.0000.000
187A188ASN0-0.0040.01544.932-0.001-0.0010.0000.0000.0000.000
188A189VAL00.026-0.00245.7720.0010.0010.0000.0000.0000.000
189A190GLY0-0.0020.00048.5080.0010.0010.0000.0000.0000.000
190A191CYS0-0.0400.00050.7170.0000.0000.0000.0000.0000.000
191A192LEU00.0080.00453.1400.0010.0010.0000.0000.0000.000
192A193GLN00.016-0.00554.8680.0010.0010.0000.0000.0000.000
193A194GLU-1-0.879-0.93757.488-0.014-0.0140.0000.0000.0000.000
194A195ALA0-0.001-0.00756.1210.0010.0010.0000.0000.0000.000
195A196LEU00.0110.00358.2590.0010.0010.0000.0000.0000.000
196A197GLN00.0000.00760.6020.0000.0000.0000.0000.0000.000
197A198LEU00.0290.01460.0280.0010.0010.0000.0000.0000.000
198A199ALA00.0020.01261.2480.0000.0000.0000.0000.0000.000
199A200THR0-0.010-0.03063.2780.0010.0010.0000.0000.0000.000
200A201SER0-0.036-0.01966.3170.0010.0010.0000.0000.0000.000
201A202PHE0-0.015-0.00165.5850.0000.0000.0000.0000.0000.000
202A203ALA00.018-0.00467.0030.0000.0000.0000.0000.0000.000
203A204GLN00.004-0.00768.7810.0000.0000.0000.0000.0000.000
204A205LEU0-0.0220.00671.5330.0000.0000.0000.0000.0000.000
205A206ARG10.8900.94869.2440.0080.0080.0000.0000.0000.000
206A207LEU0-0.024-0.00470.6810.0000.0000.0000.0000.0000.000
207A208GLY0-0.048-0.04674.2140.0000.0000.0000.0000.0000.000
208A209ASP-1-0.963-0.95777.232-0.005-0.0050.0000.0000.0000.000