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: GYY51

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 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 404
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6984300.216806
FMO2-HF: Nuclear repulsion 6819330.708007
FMO2-HF: Total energy -164969.508799
FMO2-MP2: Total energy -165456.258053


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.
-1.4150.5230.053-0.817-1.175-0.001
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 : 0.023 / q_NPA : -0.001
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].
3A14VAL0-0.029-0.0083.2250.3691.4820.024-0.508-0.6290.001
4A15VAL00.0100.0023.449-0.723-0.1400.030-0.268-0.345-0.002
5A16GLU-1-0.927-0.9655.961-0.129-0.1290.0000.0000.0000.000
6A17LEU0-0.061-0.0269.3670.0760.0760.0000.0000.0000.000
7A18LEU00.010-0.01412.0070.0790.0790.0000.0000.0000.000
8A19GLY00.0310.03114.8640.0090.0090.0000.0000.0000.000
9A20LYS10.9340.96113.7270.3540.3540.0000.0000.0000.000
10A21SER00.0550.0398.6680.0100.0100.0000.0000.0000.000
11A22TYR0-0.045-0.0358.7010.1250.1250.0000.0000.0000.000
12A23PRO00.015-0.0057.345-0.404-0.4040.0000.0000.0000.000
13A24GLN00.0040.0153.832-0.973-0.731-0.001-0.041-0.2010.000
14A25ASP-1-0.754-0.8857.129-0.818-0.8180.0000.0000.0000.000
15A26ASP-1-0.904-0.9478.392-0.768-0.7680.0000.0000.0000.000
16A27HIS0-0.046-0.02210.7220.2020.2020.0000.0000.0000.000
17A28SER0-0.060-0.0396.3930.2910.2910.0000.0000.0000.000
18A29ASN0-0.028-0.0218.690-0.030-0.0300.0000.0000.0000.000
19A30LEU00.0160.0169.1650.2360.2360.0000.0000.0000.000
20A31THR00.0040.0108.270-0.063-0.0630.0000.0000.0000.000
21A32ARG11.0671.0229.585-0.084-0.0840.0000.0000.0000.000
22A33LYS10.9120.95110.5800.0560.0560.0000.0000.0000.000
23A34VAL00.0370.04513.5790.0250.0250.0000.0000.0000.000
24A35LEU00.0880.0318.9100.0250.0250.0000.0000.0000.000
25A36THR0-0.127-0.07513.1840.0290.0290.0000.0000.0000.000
26A37ARG10.8460.92515.4200.0980.0980.0000.0000.0000.000
27A38VAL00.0940.04415.0340.0130.0130.0000.0000.0000.000
28A39GLY00.0210.02917.3830.0060.0060.0000.0000.0000.000
29A40ARG10.8470.94719.7020.0830.0830.0000.0000.0000.000
30A41ASN0-0.033-0.02721.8440.0030.0030.0000.0000.0000.000
31A42LEU00.0900.03424.2880.0080.0080.0000.0000.0000.000
32A43HIS00.0250.04225.3400.0140.0140.0000.0000.0000.000
33A44ASN0-0.055-0.06427.8630.0040.0040.0000.0000.0000.000
34A45GLN0-0.0160.01628.2760.0040.0040.0000.0000.0000.000
35A46GLN00.004-0.05130.6270.0090.0090.0000.0000.0000.000
36A47HIS0-0.0240.02834.2420.0010.0010.0000.0000.0000.000
37A48HIS00.0270.02329.4800.0010.0010.0000.0000.0000.000
38A49PRO00.0240.00933.197-0.005-0.0050.0000.0000.0000.000
39A50LEU0-0.023-0.02329.629-0.002-0.0020.0000.0000.0000.000
40A51TRP0-0.0030.00932.578-0.003-0.0030.0000.0000.0000.000
41A52LEU00.0380.03533.806-0.001-0.0010.0000.0000.0000.000
42A53ILE0-0.004-0.01135.3920.0000.0000.0000.0000.0000.000
43A54LYS10.8980.96031.4170.0850.0850.0000.0000.0000.000
44A55GLU-1-0.806-0.94335.866-0.065-0.0650.0000.0000.0000.000
45A56ARG10.8310.95738.8700.0470.0470.0000.0000.0000.000
46A57VAL00.0270.01637.8980.0020.0020.0000.0000.0000.000
47A58LYS10.8740.95135.8490.0720.0720.0000.0000.0000.000
48A59GLU-1-0.956-0.97739.766-0.044-0.0440.0000.0000.0000.000
49A60HIS00.0040.00643.319-0.001-0.0010.0000.0000.0000.000
50A61PHE0-0.004-0.02941.4560.0010.0010.0000.0000.0000.000
51A62TYR0-0.0460.00343.4640.0010.0010.0000.0000.0000.000
52A63LYS10.9110.94744.9070.0430.0430.0000.0000.0000.000
53A64GLN0-0.032-0.01947.2800.0010.0010.0000.0000.0000.000
54A65TYR0-0.0230.00046.0230.0010.0010.0000.0000.0000.000
55A66VAL00.0150.00147.138-0.001-0.0010.0000.0000.0000.000
56A67GLY00.0090.03647.4570.0020.0020.0000.0000.0000.000
57A68ARG10.9510.97048.5280.0560.0560.0000.0000.0000.000
58A69PHE0-0.031-0.04350.7110.0010.0010.0000.0000.0000.000
59A70GLY00.0710.04450.1100.0000.0000.0000.0000.0000.000
60A71THR0-0.047-0.02044.1000.0000.0000.0000.0000.0000.000
61A72PRO00.0230.00643.3040.0000.0000.0000.0000.0000.000
62A73LEU00.0120.00643.816-0.002-0.0020.0000.0000.0000.000
63A74PHE00.0150.01440.227-0.003-0.0030.0000.0000.0000.000
64A75SER0-0.0040.00637.7280.0020.0020.0000.0000.0000.000
65A76VAL00.004-0.01135.219-0.005-0.0050.0000.0000.0000.000
66A77TYR00.0130.01230.5150.0000.0000.0000.0000.0000.000
67A78ASP-1-0.874-0.94030.262-0.102-0.1020.0000.0000.0000.000
68A79ASN0-0.025-0.00425.341-0.013-0.0130.0000.0000.0000.000
69A80LEU00.0630.02825.130-0.002-0.0020.0000.0000.0000.000
70A81SER0-0.024-0.01419.548-0.005-0.0050.0000.0000.0000.000
71A82PRO00.0280.01018.333-0.012-0.0120.0000.0000.0000.000
72A83VAL0-0.023-0.01714.696-0.022-0.0220.0000.0000.0000.000
73A84VAL0-0.0230.02117.3900.0190.0190.0000.0000.0000.000
74A85THR00.000-0.01118.359-0.049-0.0490.0000.0000.0000.000
75A86THR00.0570.02218.9990.0170.0170.0000.0000.0000.000
76A87TRP00.0050.00220.6500.0170.0170.0000.0000.0000.000
77A88GLN00.0150.01422.7800.0000.0000.0000.0000.0000.000
78A89ASN00.0920.03022.1260.0180.0180.0000.0000.0000.000
79A90PHE0-0.059-0.04320.3780.0130.0130.0000.0000.0000.000
80A91ASP-1-0.787-0.89625.030-0.247-0.2470.0000.0000.0000.000
81A92SER0-0.045-0.01527.4490.0180.0180.0000.0000.0000.000
82A93LEU0-0.042-0.02128.3080.0120.0120.0000.0000.0000.000
83A94LEU00.0310.00930.9960.0050.0050.0000.0000.0000.000
84A95ILE0-0.0390.00327.0580.0060.0060.0000.0000.0000.000
85A96PRO00.0250.01828.436-0.013-0.0130.0000.0000.0000.000
86A97ALA00.0230.02026.091-0.015-0.0150.0000.0000.0000.000
87A98ASP-1-0.895-0.94624.839-0.204-0.2040.0000.0000.0000.000
88A99HIS00.0360.05925.9270.0030.0030.0000.0000.0000.000
89A100PRO00.0650.00125.377-0.017-0.0170.0000.0000.0000.000
90A101SER0-0.024-0.04624.353-0.017-0.0170.0000.0000.0000.000
91A102ARG10.8210.93121.6990.2440.2440.0000.0000.0000.000
92A103LYS10.9360.98720.2520.1540.1540.0000.0000.0000.000
93A104LYS10.9920.99111.9520.5630.5630.0000.0000.0000.000
94A105GLY0-0.116-0.08116.587-0.020-0.0200.0000.0000.0000.000
95A106ASP-1-0.820-0.91217.954-0.181-0.1810.0000.0000.0000.000
96A107ASN0-0.064-0.03018.0960.0280.0280.0000.0000.0000.000
97A108TYR00.002-0.01013.496-0.020-0.0200.0000.0000.0000.000
98A109TYR00.0020.00213.0040.0380.0380.0000.0000.0000.000
99A110LEU0-0.040-0.0269.832-0.110-0.1100.0000.0000.0000.000
100A111ASN00.0300.0169.505-0.215-0.2150.0000.0000.0000.000
101A112ARG10.9910.98211.5340.5830.5830.0000.0000.0000.000
102A113THR0-0.040-0.05214.5080.0840.0840.0000.0000.0000.000
103A114HIS00.0030.02814.0740.0300.0300.0000.0000.0000.000
104A115MET0-0.0110.00514.373-0.099-0.0990.0000.0000.0000.000
105A116LEU0-0.029-0.00114.5500.0320.0320.0000.0000.0000.000
106A117ARG10.7790.86717.1890.2340.2340.0000.0000.0000.000
107A118ALA00.0490.02720.9490.0140.0140.0000.0000.0000.000
108A119HIS10.8060.90322.5950.2260.2260.0000.0000.0000.000
109A120THR00.0860.02325.601-0.014-0.0140.0000.0000.0000.000
110A121SER0-0.088-0.06427.400-0.003-0.0030.0000.0000.0000.000
111A122ALA0-0.064-0.03924.5440.0000.0000.0000.0000.0000.000
112A123HIS00.0250.02024.120-0.006-0.0060.0000.0000.0000.000
113A124GLN0-0.0090.00428.3000.0090.0090.0000.0000.0000.000
114A125TRP00.0160.00229.8970.0040.0040.0000.0000.0000.000
115A126ASP-1-0.886-0.94127.317-0.197-0.1970.0000.0000.0000.000
116A127LEU0-0.037-0.02630.8150.0090.0090.0000.0000.0000.000
117A128LEU0-0.0020.00533.3510.0070.0070.0000.0000.0000.000
118A129HIS0-0.030-0.00433.4060.0030.0030.0000.0000.0000.000
119A130ALA0-0.080-0.03334.0490.0060.0060.0000.0000.0000.000
120A131GLY00.0510.01635.7840.0050.0050.0000.0000.0000.000
121A132LEU0-0.113-0.02335.5910.0040.0040.0000.0000.0000.000
122A133ASP-1-0.854-0.91538.966-0.085-0.0850.0000.0000.0000.000
123A134ALA0-0.045-0.05640.3590.0020.0020.0000.0000.0000.000
124A135PHE0-0.048-0.01233.746-0.001-0.0010.0000.0000.0000.000
125A136LEU00.0360.01535.4610.0000.0000.0000.0000.0000.000
126A137VAL0-0.036-0.01028.954-0.004-0.0040.0000.0000.0000.000
127A138VAL00.0010.00230.2630.0010.0010.0000.0000.0000.000
128A139GLY00.012-0.01226.438-0.002-0.0020.0000.0000.0000.000
129A140ASP-1-0.845-0.91421.597-0.182-0.1820.0000.0000.0000.000
130A141VAL0-0.0480.00022.032-0.018-0.0180.0000.0000.0000.000
131A142TYR0-0.018-0.04218.4540.0090.0090.0000.0000.0000.000
132A143ARG10.9780.99220.4120.1680.1680.0000.0000.0000.000
133A144ARG10.7810.91715.0730.2750.2750.0000.0000.0000.000
134A145ASP-1-0.816-0.90918.804-0.130-0.1300.0000.0000.0000.000
135A146GLN0-0.066-0.03720.9550.0030.0030.0000.0000.0000.000
136A147ILE0-0.079-0.04320.434-0.009-0.0090.0000.0000.0000.000
137A148ASP-1-0.889-0.93424.523-0.057-0.0570.0000.0000.0000.000
138A149SER0-0.004-0.01328.237-0.003-0.0030.0000.0000.0000.000
139A150GLN00.0660.02330.997-0.006-0.0060.0000.0000.0000.000
140A151HIS10.8660.95426.4000.0750.0750.0000.0000.0000.000
141A152TYR00.0610.00322.5230.0090.0090.0000.0000.0000.000
142A153PRO0-0.033-0.00618.692-0.012-0.0120.0000.0000.0000.000
143A154ILE0-0.075-0.02820.254-0.021-0.0210.0000.0000.0000.000
144A155PHE00.0550.03022.0050.0140.0140.0000.0000.0000.000
145A156HIS10.8190.86324.8610.1010.1010.0000.0000.0000.000
146A157GLN00.0320.01727.440-0.003-0.0030.0000.0000.0000.000
147A158LEU00.0010.01029.751-0.004-0.0040.0000.0000.0000.000
148A159GLU-1-0.748-0.83831.372-0.140-0.1400.0000.0000.0000.000
149A160ALA0-0.049-0.04333.4340.0020.0020.0000.0000.0000.000
150A161VAL00.0270.00935.613-0.002-0.0020.0000.0000.0000.000
151A162ARG10.8990.98638.2530.0680.0680.0000.0000.0000.000
152A163LEU0-0.0040.01239.678-0.001-0.0010.0000.0000.0000.000
153A164PHE0-0.027-0.02743.4040.0030.0030.0000.0000.0000.000
154A165SER00.0430.01147.151-0.002-0.0020.0000.0000.0000.000
155A166LYS11.0181.00349.6520.0550.0550.0000.0000.0000.000
156A167HIS0-0.071-0.04952.0370.0020.0020.0000.0000.0000.000
157A168GLU-1-0.931-0.97149.684-0.060-0.0600.0000.0000.0000.000
158A169LEU0-0.0530.01549.8890.0010.0010.0000.0000.0000.000
159A170PHE0-0.026-0.02252.3450.0010.0010.0000.0000.0000.000
160A171ALA00.0410.01055.9910.0010.0010.0000.0000.0000.000
161A172GLY00.0370.05457.9480.0020.0020.0000.0000.0000.000
162A173ILE0-0.047-0.04658.2300.0000.0000.0000.0000.0000.000
163A174LYS10.9250.95661.6770.0340.0340.0000.0000.0000.000
164A175ASP-1-0.912-0.95962.198-0.041-0.0410.0000.0000.0000.000
165A176GLY00.0350.03363.9150.0010.0010.0000.0000.0000.000
166A177GLU-1-0.962-0.97660.314-0.043-0.0430.0000.0000.0000.000
167A178SER0-0.081-0.03861.4870.0000.0000.0000.0000.0000.000
168A179LEU00.004-0.01057.3410.0000.0000.0000.0000.0000.000
169A180GLN0-0.011-0.00254.9280.0000.0000.0000.0000.0000.000
170A181LEU00.0180.00348.8770.0000.0000.0000.0000.0000.000
171A182PHE0-0.038-0.04847.078-0.001-0.0010.0000.0000.0000.000
172A183GLU-1-0.856-0.92951.365-0.058-0.0580.0000.0000.0000.000
173A184GLN00.013-0.00349.941-0.004-0.0040.0000.0000.0000.000
174A185SER0-0.0330.00251.6300.0000.0000.0000.0000.0000.000
175A186SER00.0190.00149.2660.0000.0000.0000.0000.0000.000
176A187ARG10.8100.89940.3190.0950.0950.0000.0000.0000.000
177A188SER00.0090.05247.0960.0010.0010.0000.0000.0000.000
178A189ALA0-0.033-0.03946.064-0.003-0.0030.0000.0000.0000.000
179A190HIS00.036-0.02646.544-0.002-0.0020.0000.0000.0000.000
180A191LYS10.8540.95446.8480.0630.0630.0000.0000.0000.000
181A192GLN00.0640.01841.518-0.001-0.0010.0000.0000.0000.000
182A193GLU-1-0.908-0.98343.847-0.084-0.0840.0000.0000.0000.000
183A194THR0-0.0250.00144.3370.0020.0020.0000.0000.0000.000
184A195HIS0-0.037-0.01444.3350.0010.0010.0000.0000.0000.000
185A196THR00.0250.03548.9180.0020.0020.0000.0000.0000.000
186A197MET0-0.015-0.01151.870-0.001-0.0010.0000.0000.0000.000
187A198GLU-1-0.863-0.93653.268-0.052-0.0520.0000.0000.0000.000
188A199ALA00.0460.01550.3890.0000.0000.0000.0000.0000.000
189A200VAL0-0.015-0.01947.648-0.001-0.0010.0000.0000.0000.000
190A201LYS10.9370.94749.4220.0490.0490.0000.0000.0000.000
191A202LEU00.0110.02851.7510.0010.0010.0000.0000.0000.000
192A203VAL00.0200.03744.9790.0000.0000.0000.0000.0000.000
193A204GLU-1-0.866-0.94546.492-0.063-0.0630.0000.0000.0000.000
194A205PHE00.0260.01747.5670.0010.0010.0000.0000.0000.000
195A206ASP-1-0.801-0.91347.265-0.064-0.0640.0000.0000.0000.000
196A207LEU0-0.0090.00341.3600.0000.0000.0000.0000.0000.000
197A208LYS10.8870.93444.9400.0610.0610.0000.0000.0000.000
198A209GLN0-0.0320.03846.7790.0010.0010.0000.0000.0000.000
199A210THR0-0.087-0.06843.7110.0020.0020.0000.0000.0000.000
200A211LEU00.0100.00040.3720.0010.0010.0000.0000.0000.000
201A212THR0-0.018-0.05944.4730.0020.0020.0000.0000.0000.000
202A213ARG10.8340.93647.5340.0530.0530.0000.0000.0000.000
203A214LEU00.006-0.00140.8210.0010.0010.0000.0000.0000.000
204A215MET00.000-0.00240.8000.0010.0010.0000.0000.0000.000
205A216ALA00.0520.03744.8990.0010.0010.0000.0000.0000.000
206A217HIS0-0.048-0.01545.1410.0000.0000.0000.0000.0000.000
207A218LEU0-0.060-0.02640.7020.0020.0020.0000.0000.0000.000
208A219PHE0-0.060-0.05340.9860.0020.0020.0000.0000.0000.000
209A220GLY0-0.072-0.04746.2200.0030.0030.0000.0000.0000.000
210A221ASP-1-0.934-0.97549.927-0.039-0.0390.0000.0000.0000.000
211A222GLU-1-0.964-0.95850.998-0.029-0.0290.0000.0000.0000.000
212A223LEU0-0.048-0.01246.2630.0000.0000.0000.0000.0000.000
213A224GLU-1-0.882-0.93148.247-0.037-0.0370.0000.0000.0000.000
214A225ILE0-0.004-0.01845.989-0.003-0.0030.0000.0000.0000.000
215A226ARG10.8320.92844.1850.0530.0530.0000.0000.0000.000
216A227TRP0-0.015-0.01442.964-0.004-0.0040.0000.0000.0000.000
217A228VAL0-0.0080.01941.6200.0030.0030.0000.0000.0000.000
218A229ASP-1-0.892-0.95742.562-0.067-0.0670.0000.0000.0000.000
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262A273GLY00.0420.00842.3060.0020.0020.0000.0000.0000.000
263A274TRP0-0.0280.02139.229-0.003-0.0030.0000.0000.0000.000
264A275ALA00.0710.01535.936-0.002-0.0020.0000.0000.0000.000
265A276PHE00.027-0.01336.5890.0040.0040.0000.0000.0000.000
266A277GLY00.0410.04133.173-0.003-0.0030.0000.0000.0000.000
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270A281GLU-1-0.745-0.86527.790-0.101-0.1010.0000.0000.0000.000
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272A283LEU00.0680.02934.5920.0050.0050.0000.0000.0000.000
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278A289ASP-1-0.867-0.92140.608-0.025-0.0250.0000.0000.0000.000
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289A300ASP-1-0.880-0.93930.4390.0120.0120.0000.0000.0000.000
290A301GLU-1-0.828-0.92633.642-0.008-0.0080.0000.0000.0000.000
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293A304LEU00.0320.01632.245-0.002-0.0020.0000.0000.0000.000
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