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: N22NQ

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 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 404
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6979174.758635
FMO2-HF: Nuclear repulsion 6814195.778203
FMO2-HF: Total energy -164978.980432
FMO2-MP2: Total energy -165464.323075


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.
-2.0750.7770.032-1.429-1.4560.003
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 : 0.061 / q_NPA : 0.028
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].
3A14VAL0-0.038-0.0123.154-0.2801.9250.023-1.222-1.0060.004
4A15VAL00.0090.0113.794-0.2700.0280.006-0.126-0.178-0.001
5A16GLU-1-0.947-0.9706.381-0.092-0.0920.0000.0000.0000.000
6A17LEU0-0.037-0.0239.7890.1330.1330.0000.0000.0000.000
7A18LEU0-0.005-0.00712.9080.0660.0660.0000.0000.0000.000
8A19GLY00.0250.02215.738-0.019-0.0190.0000.0000.0000.000
9A20LYS10.9580.97914.3570.2630.2630.0000.0000.0000.000
10A21SER00.0480.0189.7240.0000.0000.0000.0000.0000.000
11A22TYR0-0.044-0.0199.3210.1100.1100.0000.0000.0000.000
12A23PRO00.0440.0097.929-0.422-0.4220.0000.0000.0000.000
13A24GLN0-0.0100.0273.422-0.2940.0550.003-0.081-0.2720.000
14A25ASP-1-0.738-0.8676.836-0.988-0.9880.0000.0000.0000.000
15A26ASP-1-0.874-0.9218.615-0.873-0.8730.0000.0000.0000.000
16A27HIS0-0.022-0.03610.9400.2770.2770.0000.0000.0000.000
17A28SER0-0.038-0.0316.0520.4290.4290.0000.0000.0000.000
18A29ASN0-0.038-0.0479.0570.0320.0320.0000.0000.0000.000
19A30LEU00.0190.0268.7690.2240.2240.0000.0000.0000.000
20A31THR00.0510.0338.1850.1700.1700.0000.0000.0000.000
21A32ARG11.0411.0169.579-0.785-0.7850.0000.0000.0000.000
22A33LYS10.8460.92010.799-0.393-0.3930.0000.0000.0000.000
23A34VAL00.0580.04813.452-0.037-0.0370.0000.0000.0000.000
24A35LEU00.0760.0298.905-0.019-0.0190.0000.0000.0000.000
25A36THR0-0.053-0.04712.804-0.039-0.0390.0000.0000.0000.000
26A37ARG10.8710.93615.409-0.170-0.1700.0000.0000.0000.000
27A38VAL00.0240.02214.311-0.027-0.0270.0000.0000.0000.000
28A39GLY00.0200.01617.1900.0210.0210.0000.0000.0000.000
29A40ARG10.7260.84619.956-0.109-0.1090.0000.0000.0000.000
30A41ASN0-0.028-0.02022.1620.0020.0020.0000.0000.0000.000
31A42LEU00.0520.02324.450-0.003-0.0030.0000.0000.0000.000
32A43HIS00.0100.02225.1410.0120.0120.0000.0000.0000.000
33A44ASN0-0.003-0.03328.604-0.005-0.0050.0000.0000.0000.000
34A45GLN0-0.0020.02828.1310.0060.0060.0000.0000.0000.000
35A46GLN00.008-0.01930.7500.0040.0040.0000.0000.0000.000
36A47HIS00.0170.03534.537-0.002-0.0020.0000.0000.0000.000
37A48HIS00.0440.00829.468-0.002-0.0020.0000.0000.0000.000
38A49PRO00.0340.01533.288-0.007-0.0070.0000.0000.0000.000
39A50LEU0-0.017-0.00128.932-0.006-0.0060.0000.0000.0000.000
40A51TRP0-0.020-0.00632.155-0.006-0.0060.0000.0000.0000.000
41A52LEU0-0.0040.00433.722-0.005-0.0050.0000.0000.0000.000
42A53ILE00.0050.00434.969-0.004-0.0040.0000.0000.0000.000
43A54LYS10.7960.90231.6190.0030.0030.0000.0000.0000.000
44A55GLU-1-0.773-0.89235.415-0.013-0.0130.0000.0000.0000.000
45A56ARG10.7780.88638.402-0.009-0.0090.0000.0000.0000.000
46A57VAL00.0290.01437.790-0.002-0.0020.0000.0000.0000.000
47A58LYS10.7730.87434.9980.0150.0150.0000.0000.0000.000
48A59GLU-1-0.811-0.88339.759-0.004-0.0040.0000.0000.0000.000
49A60HIS0-0.014-0.00342.933-0.003-0.0030.0000.0000.0000.000
50A61PHE00.021-0.00539.835-0.001-0.0010.0000.0000.0000.000
51A62TYR0-0.054-0.01743.3830.0000.0000.0000.0000.0000.000
52A63LYS10.8500.89544.9220.0060.0060.0000.0000.0000.000
53A64GLN0-0.0240.00947.0360.0000.0000.0000.0000.0000.000
54A65TYR0-0.026-0.03545.3900.0000.0000.0000.0000.0000.000
55A66VAL0-0.0040.00746.196-0.001-0.0010.0000.0000.0000.000
56A67GLY00.0420.02647.9780.0000.0000.0000.0000.0000.000
57A68ARG10.9360.97448.8680.0380.0380.0000.0000.0000.000
58A69PHE00.003-0.01850.1850.0010.0010.0000.0000.0000.000
59A70GLY00.0250.02850.5100.0000.0000.0000.0000.0000.000
60A71THR0-0.054-0.04044.7020.0000.0000.0000.0000.0000.000
61A72PRO00.0320.00743.113-0.001-0.0010.0000.0000.0000.000
62A73LEU00.0050.01243.394-0.002-0.0020.0000.0000.0000.000
63A74PHE00.0180.01839.604-0.003-0.0030.0000.0000.0000.000
64A75SER0-0.0170.00337.5750.0020.0020.0000.0000.0000.000
65A76VAL00.016-0.00535.513-0.003-0.0030.0000.0000.0000.000
66A77TYR00.0150.01630.469-0.001-0.0010.0000.0000.0000.000
67A78ASP-1-0.783-0.87629.791-0.023-0.0230.0000.0000.0000.000
68A79ASN0-0.024-0.02225.7610.0060.0060.0000.0000.0000.000
69A80LEU00.0830.03725.453-0.007-0.0070.0000.0000.0000.000
70A81SER0-0.057-0.03319.7650.0100.0100.0000.0000.0000.000
71A82PRO00.0330.01318.198-0.013-0.0130.0000.0000.0000.000
72A83VAL0-0.0440.00014.755-0.015-0.0150.0000.0000.0000.000
73A84VAL00.0020.02117.3020.0200.0200.0000.0000.0000.000
74A85THR00.004-0.02817.758-0.054-0.0540.0000.0000.0000.000
75A86THR00.006-0.01518.2160.0440.0440.0000.0000.0000.000
76A87TRP00.0250.01819.9370.0240.0240.0000.0000.0000.000
77A88GLN00.0110.01322.457-0.009-0.0090.0000.0000.0000.000
78A89ASN0-0.002-0.01021.3200.0410.0410.0000.0000.0000.000
79A90PHE0-0.009-0.01619.6510.0170.0170.0000.0000.0000.000
80A91ASP-1-0.769-0.87424.267-0.254-0.2540.0000.0000.0000.000
81A92SER0-0.047-0.01226.8000.0200.0200.0000.0000.0000.000
82A93LEU00.000-0.00928.2260.0150.0150.0000.0000.0000.000
83A94LEU00.0180.00230.0730.0070.0070.0000.0000.0000.000
84A95ILE0-0.0270.00926.3560.0050.0050.0000.0000.0000.000
85A96PRO00.0310.02127.934-0.016-0.0160.0000.0000.0000.000
86A97ALA00.0410.01625.989-0.012-0.0120.0000.0000.0000.000
87A98ASP-1-0.934-0.96924.021-0.234-0.2340.0000.0000.0000.000
88A99HIS00.0540.06325.4820.0070.0070.0000.0000.0000.000
89A100PRO00.0450.00524.955-0.015-0.0150.0000.0000.0000.000
90A101SER0-0.023-0.02024.099-0.006-0.0060.0000.0000.0000.000
91A102ARG10.8050.87921.1760.2380.2380.0000.0000.0000.000
92A103LYS10.8350.92119.4690.0940.0940.0000.0000.0000.000
93A104LYS10.8890.95110.4570.5840.5840.0000.0000.0000.000
94A105GLY0-0.030-0.01415.8710.0140.0140.0000.0000.0000.000
95A106ASP-1-0.779-0.86118.197-0.088-0.0880.0000.0000.0000.000
96A107ASN0-0.029-0.02517.1800.0280.0280.0000.0000.0000.000
97A108TYR00.0310.00312.6200.0340.0340.0000.0000.0000.000
98A109TYR0-0.012-0.00612.2050.0060.0060.0000.0000.0000.000
99A110LEU0-0.040-0.0309.104-0.027-0.0270.0000.0000.0000.000
100A111ASN00.008-0.0058.666-0.263-0.2630.0000.0000.0000.000
101A112ARG10.9170.94411.1100.6850.6850.0000.0000.0000.000
102A113THR0-0.053-0.03314.4580.1160.1160.0000.0000.0000.000
103A114HIS00.0420.03213.4660.0020.0020.0000.0000.0000.000
104A115MET0-0.0260.00413.529-0.094-0.0940.0000.0000.0000.000
105A116LEU0-0.019-0.00113.8250.0360.0360.0000.0000.0000.000
106A117ARG10.7770.86016.5850.1100.1100.0000.0000.0000.000
107A118ALA00.0690.04120.3370.0270.0270.0000.0000.0000.000
108A119HIS10.8170.91021.8200.1590.1590.0000.0000.0000.000
109A120THR00.017-0.01224.954-0.014-0.0140.0000.0000.0000.000
110A121SER0-0.027-0.03926.950-0.007-0.0070.0000.0000.0000.000
111A122ALA0-0.065-0.02323.766-0.006-0.0060.0000.0000.0000.000
112A123HIS0-0.0010.00723.489-0.002-0.0020.0000.0000.0000.000
113A124GLN0-0.033-0.02127.8580.0050.0050.0000.0000.0000.000
114A125TRP00.0160.00529.6720.0020.0020.0000.0000.0000.000
115A126ASP-1-0.823-0.91026.965-0.168-0.1680.0000.0000.0000.000
116A127LEU0-0.034-0.01830.5330.0050.0050.0000.0000.0000.000
117A128LEU00.0250.01733.3420.0070.0070.0000.0000.0000.000
118A129HIS0-0.060-0.01333.0830.0030.0030.0000.0000.0000.000
119A130ALA0-0.033-0.01933.7160.0030.0030.0000.0000.0000.000
120A131GLY00.0070.01535.6520.0050.0050.0000.0000.0000.000
121A132LEU0-0.094-0.04035.4590.0070.0070.0000.0000.0000.000
122A133ASP-1-0.795-0.90338.847-0.065-0.0650.0000.0000.0000.000
123A134ALA0-0.015-0.00940.0600.0020.0020.0000.0000.0000.000
124A135PHE0-0.039-0.01433.466-0.001-0.0010.0000.0000.0000.000
125A136LEU00.0060.00235.4330.0020.0020.0000.0000.0000.000
126A137VAL0-0.034-0.01628.781-0.003-0.0030.0000.0000.0000.000
127A138VAL00.003-0.01130.1440.0040.0040.0000.0000.0000.000
128A139GLY00.002-0.00125.991-0.003-0.0030.0000.0000.0000.000
129A140ASP-1-0.811-0.88120.862-0.041-0.0410.0000.0000.0000.000
130A141VAL0-0.040-0.00421.835-0.022-0.0220.0000.0000.0000.000
131A142TYR0-0.043-0.05817.2660.0300.0300.0000.0000.0000.000
132A143ARG10.9510.97319.7120.0550.0550.0000.0000.0000.000
133A144ARG10.7710.88915.1300.0770.0770.0000.0000.0000.000
134A145ASP-1-0.856-0.92818.071-0.011-0.0110.0000.0000.0000.000
135A146GLN0-0.010-0.02220.7930.0360.0360.0000.0000.0000.000
136A147ILE0-0.060-0.03619.8830.0020.0020.0000.0000.0000.000
137A148ASP-1-0.835-0.89724.2930.0500.0500.0000.0000.0000.000
138A149SER00.007-0.01928.1350.0020.0020.0000.0000.0000.000
139A150GLN00.006-0.00130.102-0.007-0.0070.0000.0000.0000.000
140A151HIS10.8320.92025.559-0.025-0.0250.0000.0000.0000.000
141A152TYR00.0610.01722.4420.0310.0310.0000.0000.0000.000
142A153PRO0-0.043-0.01818.083-0.013-0.0130.0000.0000.0000.000
143A154ILE0-0.042-0.00919.288-0.019-0.0190.0000.0000.0000.000
144A155PHE00.0020.01321.2230.0140.0140.0000.0000.0000.000
145A156HIS10.8000.87524.301-0.020-0.0200.0000.0000.0000.000
146A157GLN00.0530.01926.945-0.007-0.0070.0000.0000.0000.000
147A158LEU00.0180.00329.166-0.001-0.0010.0000.0000.0000.000
148A159GLU-1-0.776-0.83530.463-0.088-0.0880.0000.0000.0000.000
149A160ALA0-0.0070.00633.2780.0010.0010.0000.0000.0000.000
150A161VAL00.0210.00135.108-0.003-0.0030.0000.0000.0000.000
151A162ARG10.8490.93138.0380.0450.0450.0000.0000.0000.000
152A163LEU00.0100.00739.056-0.001-0.0010.0000.0000.0000.000
153A164PHE0-0.036-0.01943.0560.0040.0040.0000.0000.0000.000
154A165SER00.0420.00346.848-0.003-0.0030.0000.0000.0000.000
155A166LYS10.8940.94549.2710.0460.0460.0000.0000.0000.000
156A167HIS0-0.002-0.01451.6730.0000.0000.0000.0000.0000.000
157A168GLU-1-0.854-0.90849.081-0.043-0.0430.0000.0000.0000.000
158A169LEU0-0.034-0.00249.0770.0020.0020.0000.0000.0000.000
159A170PHE00.001-0.01452.0490.0010.0010.0000.0000.0000.000
160A171ALA0-0.007-0.00455.5220.0010.0010.0000.0000.0000.000
161A172GLY0-0.0100.01857.3060.0010.0010.0000.0000.0000.000
162A173ILE0-0.035-0.02458.2260.0010.0010.0000.0000.0000.000
163A174LYS10.9070.94561.1510.0230.0230.0000.0000.0000.000
164A175ASP-1-0.887-0.93262.787-0.029-0.0290.0000.0000.0000.000
165A176GLY00.0440.00963.1680.0010.0010.0000.0000.0000.000
166A177GLU-1-0.910-0.93059.213-0.035-0.0350.0000.0000.0000.000
167A178SER0-0.060-0.03760.025-0.002-0.0020.0000.0000.0000.000
168A179LEU0-0.043-0.03056.6420.0000.0000.0000.0000.0000.000
169A180GLN00.0340.01654.022-0.001-0.0010.0000.0000.0000.000
170A181LEU00.0000.00647.9440.0010.0010.0000.0000.0000.000
171A182PHE00.006-0.00246.1450.0000.0000.0000.0000.0000.000
172A183GLU-1-0.840-0.93050.413-0.051-0.0510.0000.0000.0000.000
173A184GLN0-0.005-0.00248.782-0.003-0.0030.0000.0000.0000.000
174A185SER0-0.0370.00751.103-0.001-0.0010.0000.0000.0000.000
175A186SER0-0.033-0.02248.7580.0010.0010.0000.0000.0000.000
176A187ARG10.7580.85840.0250.0810.0810.0000.0000.0000.000
177A188SER0-0.004-0.00146.7290.0010.0010.0000.0000.0000.000
178A189ALA0-0.005-0.01945.602-0.002-0.0020.0000.0000.0000.000
179A190HIS00.0230.01945.660-0.001-0.0010.0000.0000.0000.000
180A191LYS10.8500.92046.5910.0550.0550.0000.0000.0000.000
181A192GLN00.0760.03041.120-0.003-0.0030.0000.0000.0000.000
182A193GLU-1-0.863-0.92743.324-0.073-0.0730.0000.0000.0000.000
183A194THR0-0.0060.00343.6650.0020.0020.0000.0000.0000.000
184A195HIS0-0.006-0.03043.3470.0010.0010.0000.0000.0000.000
185A196THR0-0.0010.01048.1970.0020.0020.0000.0000.0000.000
186A197MET0-0.005-0.01550.7040.0000.0000.0000.0000.0000.000
187A198GLU-1-0.812-0.90152.182-0.037-0.0370.0000.0000.0000.000
188A199ALA00.0300.01949.4360.0010.0010.0000.0000.0000.000
189A200VAL00.0120.01046.6960.0000.0000.0000.0000.0000.000
190A201LYS10.8500.90748.5760.0360.0360.0000.0000.0000.000
191A202LEU0-0.0010.01050.9410.0020.0020.0000.0000.0000.000
192A203VAL00.0040.00944.6610.0010.0010.0000.0000.0000.000
193A204GLU-1-0.830-0.91545.326-0.041-0.0410.0000.0000.0000.000
194A205PHE00.0050.01046.7760.0020.0020.0000.0000.0000.000
195A206ASP-1-0.808-0.88846.298-0.036-0.0360.0000.0000.0000.000
196A207LEU00.0130.01340.7530.0020.0020.0000.0000.0000.000
197A208LYS10.8360.90844.2990.0380.0380.0000.0000.0000.000
198A209GLN0-0.0030.02746.2080.0030.0030.0000.0000.0000.000
199A210THR0-0.015-0.00343.2480.0030.0030.0000.0000.0000.000
200A211LEU0-0.0040.00039.6310.0020.0020.0000.0000.0000.000
201A212THR0-0.024-0.03043.7120.0030.0030.0000.0000.0000.000
202A213ARG10.8560.91546.8050.0250.0250.0000.0000.0000.000
203A214LEU0-0.017-0.00339.8780.0020.0020.0000.0000.0000.000
204A215MET00.010-0.01139.4790.0040.0040.0000.0000.0000.000
205A216ALA00.0700.04144.2050.0030.0030.0000.0000.0000.000
206A217HIS0-0.072-0.02344.6020.0000.0000.0000.0000.0000.000
207A218LEU0-0.072-0.03240.1320.0030.0030.0000.0000.0000.000
208A219PHE00.0550.00839.9510.0030.0030.0000.0000.0000.000
209A220GLY0-0.075-0.02845.5230.0030.0030.0000.0000.0000.000
210A221ASP-1-0.871-0.94549.252-0.008-0.0080.0000.0000.0000.000
211A222GLU-1-0.958-0.97050.0330.0040.0040.0000.0000.0000.000
212A223LEU0-0.077-0.02645.5010.0010.0010.0000.0000.0000.000
213A224GLU-1-0.826-0.90848.417-0.006-0.0060.0000.0000.0000.000
214A225ILE0-0.030-0.01745.2570.0000.0000.0000.0000.0000.000
215A226ARG10.7850.86543.3880.0130.0130.0000.0000.0000.000
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217A228VAL00.0070.01240.4200.0010.0010.0000.0000.0000.000
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