FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 8NN9Y

Calculation Name: 3TUP-A-Xray372

Preferred Name: Phenylalanyl-tRNA synthetase mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3TUP

Chain ID: A

ChEMBL ID: CHEMBL2511

UniProt ID: O95363

Base Structure: X-ray

Registration Date: 2023-09-27

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 404
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6980304.784446
FMO2-HF: Nuclear repulsion 6815329.756375
FMO2-HF: Total energy -164975.028071
FMO2-MP2: Total energy -165461.018724


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:12:GLY)


Summations of interaction energy for fragment #1(A:12:GLY)
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.
-2.2350.5110.047-1.327-1.4660.003
Interaction energy analysis for fragmet #1(A:12:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.027
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].
3A14VAL0-0.045-0.0223.245-0.2501.6280.021-1.012-0.8870.005
4A15VAL00.0200.0093.458-0.3400.2600.026-0.262-0.364-0.002
5A16GLU-1-0.946-0.9685.9700.0240.0240.0000.0000.0000.000
6A17LEU0-0.052-0.0249.3710.1520.1520.0000.0000.0000.000
7A18LEU00.005-0.01012.0120.0610.0610.0000.0000.0000.000
8A19GLY00.0250.02814.858-0.025-0.0250.0000.0000.0000.000
9A20LYS10.9510.96913.7350.1870.1870.0000.0000.0000.000
10A21SER00.0590.0358.7540.0840.0840.0000.0000.0000.000
11A22TYR0-0.053-0.0358.7010.0170.0170.0000.0000.0000.000
12A23PRO00.027-0.0017.363-0.328-0.3280.0000.0000.0000.000
13A24GLN00.0000.0273.730-0.303-0.0350.000-0.053-0.2150.000
14A25ASP-1-0.737-0.8847.190-0.858-0.8580.0000.0000.0000.000
15A26ASP-1-0.884-0.9298.410-0.792-0.7920.0000.0000.0000.000
16A27HIS0-0.051-0.03610.7850.2720.2720.0000.0000.0000.000
17A28SER0-0.033-0.0326.2500.3900.3900.0000.0000.0000.000
18A29ASN0-0.054-0.0328.481-0.037-0.0370.0000.0000.0000.000
19A30LEU00.0270.0138.8300.2090.2090.0000.0000.0000.000
20A31THR00.0120.0118.4030.2360.2360.0000.0000.0000.000
21A32ARG11.0391.01110.043-0.835-0.8350.0000.0000.0000.000
22A33LYS10.8980.94311.088-0.507-0.5070.0000.0000.0000.000
23A34VAL00.0290.03813.900-0.025-0.0250.0000.0000.0000.000
24A35LEU00.0740.0308.996-0.034-0.0340.0000.0000.0000.000
25A36THR0-0.093-0.05313.185-0.043-0.0430.0000.0000.0000.000
26A37ARG10.8760.93415.416-0.260-0.2600.0000.0000.0000.000
27A38VAL00.0630.03114.685-0.027-0.0270.0000.0000.0000.000
28A39GLY00.0270.02817.3840.0190.0190.0000.0000.0000.000
29A40ARG10.7600.88019.704-0.170-0.1700.0000.0000.0000.000
30A41ASN0-0.058-0.03521.843-0.002-0.0020.0000.0000.0000.000
31A42LEU00.0950.04324.290-0.001-0.0010.0000.0000.0000.000
32A43HIS00.0520.06225.0390.0090.0090.0000.0000.0000.000
33A44ASN0-0.049-0.07228.457-0.010-0.0100.0000.0000.0000.000
34A45GLN0-0.0230.02728.4270.0040.0040.0000.0000.0000.000
35A46GLN00.014-0.04330.6260.0020.0020.0000.0000.0000.000
36A47HIS0-0.0160.02834.242-0.002-0.0020.0000.0000.0000.000
37A48HIS00.0290.00629.513-0.004-0.0040.0000.0000.0000.000
38A49PRO00.0450.02533.432-0.007-0.0070.0000.0000.0000.000
39A50LEU0-0.023-0.01629.555-0.007-0.0070.0000.0000.0000.000
40A51TRP0-0.010-0.00332.593-0.006-0.0060.0000.0000.0000.000
41A52LEU00.0260.03233.809-0.007-0.0070.0000.0000.0000.000
42A53ILE00.014-0.00335.524-0.005-0.0050.0000.0000.0000.000
43A54LYS10.8060.90331.468-0.028-0.0280.0000.0000.0000.000
44A55GLU-1-0.711-0.87435.8710.0120.0120.0000.0000.0000.000
45A56ARG10.7480.91038.875-0.028-0.0280.0000.0000.0000.000
46A57VAL00.0410.01538.086-0.002-0.0020.0000.0000.0000.000
47A58LYS10.7970.89835.370-0.012-0.0120.0000.0000.0000.000
48A59GLU-1-0.878-0.91239.7730.0110.0110.0000.0000.0000.000
49A60HIS0-0.0080.00743.325-0.004-0.0040.0000.0000.0000.000
50A61PHE00.018-0.02040.152-0.002-0.0020.0000.0000.0000.000
51A62TYR0-0.052-0.00143.380-0.001-0.0010.0000.0000.0000.000
52A63LYS10.8430.89744.915-0.009-0.0090.0000.0000.0000.000
53A64GLN0-0.0110.00947.364-0.002-0.0020.0000.0000.0000.000
54A65TYR0-0.034-0.03145.993-0.001-0.0010.0000.0000.0000.000
55A66VAL00.0060.00047.1470.0010.0010.0000.0000.0000.000
56A67GLY00.0130.03747.4500.0000.0000.0000.0000.0000.000
57A68ARG10.9410.95948.5400.0260.0260.0000.0000.0000.000
58A69PHE0-0.017-0.02550.7230.0010.0010.0000.0000.0000.000
59A70GLY00.0700.04250.1180.0010.0010.0000.0000.0000.000
60A71THR0-0.058-0.02444.2600.0010.0010.0000.0000.0000.000
61A72PRO00.0370.01243.302-0.001-0.0010.0000.0000.0000.000
62A73LEU00.0030.00343.826-0.002-0.0020.0000.0000.0000.000
63A74PHE00.0180.01340.042-0.003-0.0030.0000.0000.0000.000
64A75SER0-0.025-0.00337.2300.0030.0030.0000.0000.0000.000
65A76VAL00.010-0.01135.204-0.003-0.0030.0000.0000.0000.000
66A77TYR00.0170.01530.5150.0000.0000.0000.0000.0000.000
67A78ASP-1-0.816-0.89130.2030.0080.0080.0000.0000.0000.000
68A79ASN0-0.032-0.01725.2380.0050.0050.0000.0000.0000.000
69A80LEU00.0790.03725.138-0.008-0.0080.0000.0000.0000.000
70A81SER0-0.032-0.01419.5960.0160.0160.0000.0000.0000.000
71A82PRO00.0220.00318.386-0.019-0.0190.0000.0000.0000.000
72A83VAL0-0.030-0.02014.574-0.019-0.0190.0000.0000.0000.000
73A84VAL0-0.0270.01817.403-0.003-0.0030.0000.0000.0000.000
74A85THR0-0.015-0.03218.376-0.041-0.0410.0000.0000.0000.000
75A86THR00.0330.01118.6950.0300.0300.0000.0000.0000.000
76A87TRP00.0280.01020.5040.0230.0230.0000.0000.0000.000
77A88GLN00.0030.01522.755-0.003-0.0030.0000.0000.0000.000
78A89ASN00.0310.00821.9380.0370.0370.0000.0000.0000.000
79A90PHE0-0.025-0.02419.9410.0140.0140.0000.0000.0000.000
80A91ASP-1-0.769-0.88725.056-0.215-0.2150.0000.0000.0000.000
81A92SER0-0.053-0.01327.2970.0170.0170.0000.0000.0000.000
82A93LEU0-0.007-0.01128.9390.0120.0120.0000.0000.0000.000
83A94LEU00.0190.00830.7700.0050.0050.0000.0000.0000.000
84A95ILE0-0.0300.01026.8100.0040.0040.0000.0000.0000.000
85A96PRO00.0310.02328.294-0.016-0.0160.0000.0000.0000.000
86A97ALA00.0160.00826.070-0.007-0.0070.0000.0000.0000.000
87A98ASP-1-0.897-0.94924.479-0.207-0.2070.0000.0000.0000.000
88A99HIS00.0260.03625.8530.0110.0110.0000.0000.0000.000
89A100PRO00.0560.00025.211-0.010-0.0100.0000.0000.0000.000
90A101SER0-0.039-0.02824.140-0.009-0.0090.0000.0000.0000.000
91A102ARG10.7990.89821.4770.2030.2030.0000.0000.0000.000
92A103LYS10.9570.99120.0810.0720.0720.0000.0000.0000.000
93A104LYS10.9750.99011.4200.3740.3740.0000.0000.0000.000
94A105GLY0-0.058-0.03316.2980.0190.0190.0000.0000.0000.000
95A106ASP-1-0.846-0.91317.672-0.049-0.0490.0000.0000.0000.000
96A107ASN0-0.047-0.03217.8210.0330.0330.0000.0000.0000.000
97A108TYR00.001-0.00113.2930.0180.0180.0000.0000.0000.000
98A109TYR00.002-0.00112.7550.0190.0190.0000.0000.0000.000
99A110LEU0-0.047-0.0269.564-0.019-0.0190.0000.0000.0000.000
100A111ASN00.013-0.0059.297-0.222-0.2220.0000.0000.0000.000
101A112ARG10.9640.97711.4260.6460.6460.0000.0000.0000.000
102A113THR0-0.084-0.05314.4610.1060.1060.0000.0000.0000.000
103A114HIS00.0530.03514.0930.0050.0050.0000.0000.0000.000
104A115MET0-0.042-0.00414.313-0.074-0.0740.0000.0000.0000.000
105A116LEU0-0.0070.00114.3620.0300.0300.0000.0000.0000.000
106A117ARG10.7770.87317.2020.0640.0640.0000.0000.0000.000
107A118ALA00.0620.03620.9630.0250.0250.0000.0000.0000.000
108A119HIS10.8100.90322.3560.1160.1160.0000.0000.0000.000
109A120THR00.0590.01625.615-0.012-0.0120.0000.0000.0000.000
110A121SER0-0.087-0.05827.412-0.007-0.0070.0000.0000.0000.000
111A122ALA0-0.059-0.03624.541-0.007-0.0070.0000.0000.0000.000
112A123HIS00.0170.00923.8890.0000.0000.0000.0000.0000.000
113A124GLN0-0.029-0.01128.315-0.001-0.0010.0000.0000.0000.000
114A125TRP00.0180.00629.9590.0000.0000.0000.0000.0000.000
115A126ASP-1-0.857-0.91427.386-0.132-0.1320.0000.0000.0000.000
116A127LEU0-0.038-0.02630.8300.0050.0050.0000.0000.0000.000
117A128LEU00.0120.00533.3660.0040.0040.0000.0000.0000.000
118A129HIS0-0.045-0.01033.4110.0020.0020.0000.0000.0000.000
119A130ALA0-0.064-0.02833.9070.0030.0030.0000.0000.0000.000
120A131GLY00.0550.02235.7990.0020.0020.0000.0000.0000.000
121A132LEU0-0.103-0.02835.6290.0040.0040.0000.0000.0000.000
122A133ASP-1-0.761-0.87838.979-0.050-0.0500.0000.0000.0000.000
123A134ALA0-0.021-0.03540.3700.0020.0020.0000.0000.0000.000
124A135PHE0-0.047-0.01733.6920.0010.0010.0000.0000.0000.000
125A136LEU00.0380.01735.4630.0010.0010.0000.0000.0000.000
126A137VAL0-0.040-0.01428.932-0.003-0.0030.0000.0000.0000.000
127A138VAL00.000-0.00430.5860.0030.0030.0000.0000.0000.000
128A139GLY00.0100.00126.4360.0000.0000.0000.0000.0000.000
129A140ASP-1-0.829-0.88821.2140.0290.0290.0000.0000.0000.000
130A141VAL0-0.039-0.00222.071-0.018-0.0180.0000.0000.0000.000
131A142TYR0-0.040-0.06918.1030.0420.0420.0000.0000.0000.000
132A143ARG10.9810.99620.1530.0080.0080.0000.0000.0000.000
133A144ARG10.7490.86715.4700.0100.0100.0000.0000.0000.000
134A145ASP-1-0.842-0.92118.6390.0120.0120.0000.0000.0000.000
135A146GLN0-0.036-0.02721.0120.0410.0410.0000.0000.0000.000
136A147ILE0-0.055-0.03320.4760.0080.0080.0000.0000.0000.000
137A148ASP-1-0.889-0.92224.7670.0730.0730.0000.0000.0000.000
138A149SER00.008-0.01228.5040.0010.0010.0000.0000.0000.000
139A150GLN00.0180.00131.259-0.003-0.0030.0000.0000.0000.000
140A151HIS10.8570.93426.265-0.053-0.0530.0000.0000.0000.000
141A152TYR00.0460.00523.0880.0320.0320.0000.0000.0000.000
142A153PRO0-0.054-0.01918.765-0.010-0.0100.0000.0000.0000.000
143A154ILE0-0.063-0.02220.240-0.012-0.0120.0000.0000.0000.000
144A155PHE00.0180.01622.1260.0070.0070.0000.0000.0000.000
145A156HIS10.8250.88224.868-0.064-0.0640.0000.0000.0000.000
146A157GLN00.0410.01427.447-0.008-0.0080.0000.0000.0000.000
147A158LEU00.0130.01129.760-0.001-0.0010.0000.0000.0000.000
148A159GLU-1-0.762-0.84131.164-0.057-0.0570.0000.0000.0000.000
149A160ALA0-0.038-0.02633.4450.0020.0020.0000.0000.0000.000
150A161VAL00.013-0.00335.376-0.003-0.0030.0000.0000.0000.000
151A162ARG10.8720.97138.2660.0290.0290.0000.0000.0000.000
152A163LEU00.0100.01739.425-0.002-0.0020.0000.0000.0000.000
153A164PHE0-0.036-0.02943.4190.0040.0040.0000.0000.0000.000
154A165SER00.0340.01947.166-0.004-0.0040.0000.0000.0000.000
155A166LYS10.9570.97549.6680.0360.0360.0000.0000.0000.000
156A167HIS0-0.016-0.02452.0540.0010.0010.0000.0000.0000.000
157A168GLU-1-0.879-0.95449.758-0.030-0.0300.0000.0000.0000.000
158A169LEU0-0.0560.00349.5530.0010.0010.0000.0000.0000.000
159A170PHE0-0.015-0.01552.3600.0010.0010.0000.0000.0000.000
160A171ALA00.0330.00556.0070.0010.0010.0000.0000.0000.000
161A172GLY00.0370.05557.9640.0010.0010.0000.0000.0000.000
162A173ILE0-0.052-0.05258.7260.0000.0000.0000.0000.0000.000
163A174LYS10.9330.96361.6920.0160.0160.0000.0000.0000.000
164A175ASP-1-0.909-0.95662.579-0.022-0.0220.0000.0000.0000.000
165A176GLY00.0350.03163.9270.0000.0000.0000.0000.0000.000
166A177GLU-1-0.977-0.98260.082-0.027-0.0270.0000.0000.0000.000
167A178SER0-0.075-0.03761.504-0.001-0.0010.0000.0000.0000.000
168A179LEU0-0.016-0.02557.3050.0000.0000.0000.0000.0000.000
169A180GLN00.0250.02154.8040.0000.0000.0000.0000.0000.000
170A181LEU0-0.011-0.01048.7140.0000.0000.0000.0000.0000.000
171A182PHE0-0.028-0.02147.1400.0000.0000.0000.0000.0000.000
172A183GLU-1-0.865-0.93051.202-0.042-0.0420.0000.0000.0000.000
173A184GLN0-0.005-0.01249.525-0.003-0.0030.0000.0000.0000.000
174A185SER0-0.0190.00651.638-0.001-0.0010.0000.0000.0000.000
175A186SER00.0240.00049.090-0.001-0.0010.0000.0000.0000.000
176A187ARG10.7310.86240.2670.0670.0670.0000.0000.0000.000
177A188SER00.0200.03346.9050.0000.0000.0000.0000.0000.000
178A189ALA0-0.049-0.03745.822-0.001-0.0010.0000.0000.0000.000
179A190HIS00.058-0.00346.2720.0000.0000.0000.0000.0000.000
180A191LYS10.8510.94846.6250.0440.0440.0000.0000.0000.000
181A192GLN00.0850.02841.480-0.003-0.0030.0000.0000.0000.000
182A193GLU-1-0.871-0.94943.379-0.062-0.0620.0000.0000.0000.000
183A194THR0-0.0280.00044.2290.0000.0000.0000.0000.0000.000
184A195HIS0-0.033-0.02343.8930.0020.0020.0000.0000.0000.000
185A196THR00.0270.00448.6950.0010.0010.0000.0000.0000.000
186A197MET0-0.005-0.00351.6100.0010.0010.0000.0000.0000.000
187A198GLU-1-0.823-0.90752.990-0.028-0.0280.0000.0000.0000.000
188A199ALA00.0490.02650.3350.0010.0010.0000.0000.0000.000
189A200VAL0-0.006-0.01947.4480.0010.0010.0000.0000.0000.000
190A201LYS10.8610.91249.2380.0270.0270.0000.0000.0000.000
191A202LEU00.0050.02151.6430.0020.0020.0000.0000.0000.000
192A203VAL00.0170.02845.1710.0020.0020.0000.0000.0000.000
193A204GLU-1-0.797-0.89546.282-0.026-0.0260.0000.0000.0000.000
194A205PHE00.0310.02647.4060.0030.0030.0000.0000.0000.000
195A206ASP-1-0.786-0.88846.730-0.021-0.0210.0000.0000.0000.000
196A207LEU00.0050.00141.3760.0020.0020.0000.0000.0000.000
197A208LYS10.8130.89044.9520.0250.0250.0000.0000.0000.000
198A209GLN0-0.0360.01646.6830.0030.0030.0000.0000.0000.000
199A210THR0-0.051-0.03643.7400.0030.0030.0000.0000.0000.000
200A211LEU00.0010.00640.3770.0030.0030.0000.0000.0000.000
201A212THR0-0.020-0.03344.4840.0030.0030.0000.0000.0000.000
202A213ARG10.8360.91147.5440.0120.0120.0000.0000.0000.000
203A214LEU0-0.005-0.01340.5490.0030.0030.0000.0000.0000.000
204A215MET0-0.017-0.01640.5730.0040.0040.0000.0000.0000.000
205A216ALA00.0580.04044.9070.0030.0030.0000.0000.0000.000
206A217HIS0-0.052-0.01244.7270.0000.0000.0000.0000.0000.000
207A218LEU0-0.063-0.02441.0120.0030.0030.0000.0000.0000.000
208A219PHE00.008-0.03240.8490.0040.0040.0000.0000.0000.000
209A220GLY0-0.068-0.03546.2250.0030.0030.0000.0000.0000.000
210A221ASP-1-0.911-0.96649.9320.0030.0030.0000.0000.0000.000
211A222GLU-1-0.953-0.95451.1230.0150.0150.0000.0000.0000.000
212A223LEU0-0.046-0.01446.0390.0020.0020.0000.0000.0000.000
213A224GLU-1-0.914-0.94948.2860.0050.0050.0000.0000.0000.000
214A225ILE00.015-0.01345.6620.0010.0010.0000.0000.0000.000
215A226ARG10.7920.88243.756-0.001-0.0010.0000.0000.0000.000
216A227TRP0-0.007-0.02142.429-0.001-0.0010.0000.0000.0000.000
217A228VAL00.0050.01241.1820.0000.0000.0000.0000.0000.000
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