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: 98GG2

Calculation Name: 5EFS-A-Xray372

Preferred Name: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5EFS

Chain ID: A

ChEMBL ID: CHEMBL2046259

UniProt ID: Q8N5Z0

Base Structure: X-ray

Registration Date: 2023-09-20

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 425
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7416032.6098
FMO2-HF: Nuclear repulsion 7249290.241637
FMO2-HF: Total energy -166742.368163
FMO2-MP2: Total energy -167226.029773


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-9.334-3.3185.951-5.343-6.625-0.03
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.018
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].
3A3TYR00.016-0.0273.138-1.7701.1820.272-1.263-1.961-0.003
4A4ALA00.0130.0145.096-0.125-0.014-0.001-0.004-0.1050.000
5A5ARG10.8380.9386.403-2.356-2.3560.0000.0000.0000.000
6A6PHE0-0.060-0.0304.769-0.520-0.378-0.001-0.015-0.1270.000
7A7ILE0-0.024-0.0088.824-0.225-0.2250.0000.0000.0000.000
8A8THR00.0360.03111.646-0.019-0.0190.0000.0000.0000.000
9A9ALA00.0480.00915.239-0.053-0.0530.0000.0000.0000.000
10A10ALA00.0180.00617.413-0.042-0.0420.0000.0000.0000.000
11A11SER0-0.011-0.00914.434-0.061-0.0610.0000.0000.0000.000
12A12ALA00.0200.00013.801-0.058-0.0580.0000.0000.0000.000
13A13ALA0-0.0190.00415.240-0.047-0.0470.0000.0000.0000.000
14A14ARG10.8960.97118.074-0.001-0.0010.0000.0000.0000.000
15A15ASN00.0340.01218.483-0.045-0.0450.0000.0000.0000.000
16A16PRO00.004-0.01719.6200.0130.0130.0000.0000.0000.000
17A17SER00.0610.02521.8650.0140.0140.0000.0000.0000.000
18A18PRO0-0.067-0.02125.247-0.011-0.0110.0000.0000.0000.000
19A19ILE00.0170.00827.4200.0080.0080.0000.0000.0000.000
20A20ARG10.9450.95121.6790.2080.2080.0000.0000.0000.000
21A21THR00.0140.01625.9460.0000.0000.0000.0000.0000.000
22A22MET00.0640.02528.339-0.006-0.0060.0000.0000.0000.000
23A23THR0-0.092-0.03831.5330.0050.0050.0000.0000.0000.000
24A24ASP-1-0.901-0.93327.320-0.208-0.2080.0000.0000.0000.000
25A25ILE0-0.010-0.00230.4350.0000.0000.0000.0000.0000.000
26A26LEU0-0.008-0.01632.8540.0090.0090.0000.0000.0000.000
27A27SER0-0.024-0.00532.8030.0050.0050.0000.0000.0000.000
28A28ARG10.9530.96531.5480.1800.1800.0000.0000.0000.000
29A29GLY00.0300.01434.468-0.002-0.0020.0000.0000.0000.000
30A30PRO0-0.014-0.01036.5440.0040.0040.0000.0000.0000.000
31A31LYS11.0261.00339.6130.1020.1020.0000.0000.0000.000
32A32SER0-0.061-0.02840.5970.0030.0030.0000.0000.0000.000
33A33MET00.0130.02138.2570.0000.0000.0000.0000.0000.000
34A34ILE00.0180.01541.8650.0000.0000.0000.0000.0000.000
35A35SER00.0040.00138.224-0.003-0.0030.0000.0000.0000.000
36A36LEU0-0.026-0.01840.2930.0020.0020.0000.0000.0000.000
37A37ALA00.0330.01436.1750.0020.0020.0000.0000.0000.000
38A38GLY0-0.028-0.00435.342-0.003-0.0030.0000.0000.0000.000
39A39GLY00.0450.02035.1500.0050.0050.0000.0000.0000.000
40A40LEU0-0.044-0.01733.6700.0020.0020.0000.0000.0000.000
41A41PRO00.0370.03037.3440.0020.0020.0000.0000.0000.000
42A42ASN00.0700.02440.377-0.004-0.0040.0000.0000.0000.000
43A43PRO00.0780.03540.5890.0040.0040.0000.0000.0000.000
44A44ASN0-0.075-0.05242.5940.0030.0030.0000.0000.0000.000
45A45MET0-0.028-0.01845.6090.0030.0030.0000.0000.0000.000
46A46PHE0-0.0090.01439.7180.0030.0030.0000.0000.0000.000
47A47PRO00.0240.00444.966-0.001-0.0010.0000.0000.0000.000
48A48PHE00.0050.00143.1710.0010.0010.0000.0000.0000.000
49A49LYS10.9170.96245.3490.0410.0410.0000.0000.0000.000
50A50THR00.0150.00545.592-0.002-0.0020.0000.0000.0000.000
51A51ALA00.002-0.00442.8590.0030.0030.0000.0000.0000.000
52A52VAL00.0140.01244.807-0.003-0.0030.0000.0000.0000.000
53A53ILE00.000-0.00340.2700.0030.0030.0000.0000.0000.000
54A54THR0-0.009-0.00443.391-0.003-0.0030.0000.0000.0000.000
55A55VAL00.0190.01039.9120.0010.0010.0000.0000.0000.000
56A56GLU-1-0.938-0.95342.260-0.021-0.0210.0000.0000.0000.000
57A57ASN0-0.056-0.04241.3200.0000.0000.0000.0000.0000.000
58A58GLY00.0790.03340.962-0.003-0.0030.0000.0000.0000.000
59A59LYS10.9160.97741.5350.0650.0650.0000.0000.0000.000
60A60THR0-0.016-0.01742.0970.0000.0000.0000.0000.0000.000
61A61ILE0-0.0020.01437.871-0.003-0.0030.0000.0000.0000.000
62A62GLN00.000-0.01141.8800.0040.0040.0000.0000.0000.000
63A63PHE0-0.077-0.03137.202-0.005-0.0050.0000.0000.0000.000
64A64GLY00.0870.02742.5630.0040.0040.0000.0000.0000.000
65A65GLU-1-0.852-0.93443.851-0.053-0.0530.0000.0000.0000.000
66A66GLU-1-0.889-0.95242.250-0.070-0.0700.0000.0000.0000.000
67A67MET0-0.024-0.00637.184-0.005-0.0050.0000.0000.0000.000
68A68MET0-0.0070.01639.184-0.002-0.0020.0000.0000.0000.000
69A69LYS10.8670.93740.3940.0610.0610.0000.0000.0000.000
70A70ARG10.8000.89031.2140.1130.1130.0000.0000.0000.000
71A71ALA00.003-0.01335.892-0.003-0.0030.0000.0000.0000.000
72A72LEU0-0.057-0.02736.3940.0020.0020.0000.0000.0000.000
73A73GLN0-0.0050.01735.2190.0040.0040.0000.0000.0000.000
74A74TYR0-0.001-0.00731.665-0.003-0.0030.0000.0000.0000.000
75A75SER0-0.055-0.04029.589-0.007-0.0070.0000.0000.0000.000
76A76PRO0-0.026-0.02625.2450.0010.0010.0000.0000.0000.000
77A77SER00.003-0.02322.8180.0000.0000.0000.0000.0000.000
78A78ALA00.0070.00919.9980.0090.0090.0000.0000.0000.000
79A79GLY00.0410.02021.655-0.002-0.0020.0000.0000.0000.000
80A80ILE0-0.073-0.03024.741-0.012-0.0120.0000.0000.0000.000
81A81PRO00.0420.01225.304-0.006-0.0060.0000.0000.0000.000
82A82GLU-1-0.749-0.87025.939-0.145-0.1450.0000.0000.0000.000
83A83LEU00.0150.01225.7960.0020.0020.0000.0000.0000.000
84A84LEU00.000-0.00120.347-0.004-0.0040.0000.0000.0000.000
85A85SER0-0.066-0.02622.413-0.015-0.0150.0000.0000.0000.000
86A86TRP00.0740.03124.254-0.013-0.0130.0000.0000.0000.000
87A87LEU00.005-0.00222.2800.0010.0010.0000.0000.0000.000
88A88LYS10.9570.98617.0200.4550.4550.0000.0000.0000.000
89A89GLN0-0.013-0.01220.742-0.012-0.0120.0000.0000.0000.000
90A90LEU00.0420.04023.3530.0060.0060.0000.0000.0000.000
91A91GLN0-0.024-0.02518.1640.0230.0230.0000.0000.0000.000
92A92ILE0-0.042-0.02418.749-0.009-0.0090.0000.0000.0000.000
93A93LYS10.9250.98120.4190.1190.1190.0000.0000.0000.000
94A94LEU0-0.092-0.04722.1020.0180.0180.0000.0000.0000.000
95A95HIS0-0.007-0.02117.5130.0020.0020.0000.0000.0000.000
96A96ASN0-0.036-0.00217.710-0.035-0.0350.0000.0000.0000.000
97A97PRO0-0.004-0.00313.546-0.009-0.0090.0000.0000.0000.000
98A98PRO00.0390.01610.995-0.045-0.0450.0000.0000.0000.000
99A99THR00.0240.0168.4280.0010.0010.0000.0000.0000.000
100A100ILE0-0.035-0.00711.017-0.089-0.0890.0000.0000.0000.000
101A101HIS0-0.003-0.01614.044-0.021-0.0210.0000.0000.0000.000
102A102TYR0-0.055-0.0227.2710.1120.1120.0000.0000.0000.000
103A103PRO00.0430.0088.5730.1710.1710.0000.0000.0000.000
104A104PRO00.017-0.0078.704-0.294-0.2940.0000.0000.0000.000
105A105SER0-0.005-0.0117.142-0.171-0.1710.0000.0000.0000.000
106A106GLN0-0.047-0.0392.258-4.373-3.1085.675-3.776-3.164-0.026
107A107GLY00.0700.0454.882-0.393-0.269-0.001-0.004-0.1190.000
108A108GLN0-0.114-0.0386.1490.5020.5020.0000.0000.0000.000
109A109MET0-0.0020.0099.9300.0860.0860.0000.0000.0000.000
110A110ASP-1-0.910-0.95911.990-0.450-0.4500.0000.0000.0000.000
111A111LEU0-0.028-0.02013.8860.0410.0410.0000.0000.0000.000
112A112CYS0-0.043-0.01116.8430.0020.0020.0000.0000.0000.000
113A113VAL0-0.0030.00618.8020.0240.0240.0000.0000.0000.000
114A114THR0-0.028-0.03320.135-0.001-0.0010.0000.0000.0000.000
115A115SER00.0200.00823.1190.0020.0020.0000.0000.0000.000
116A116GLY0-0.027-0.02526.1710.0140.0140.0000.0000.0000.000
117A117SER00.0380.01922.158-0.004-0.0040.0000.0000.0000.000
118A118GLN00.0460.02621.720-0.002-0.0020.0000.0000.0000.000
119A119GLN00.0190.01022.6890.0030.0030.0000.0000.0000.000
120A120GLY00.0390.01119.3930.0020.0020.0000.0000.0000.000
121A121LEU00.0220.01517.7300.0070.0070.0000.0000.0000.000
122A122CYS0-0.0100.00518.5860.0290.0290.0000.0000.0000.000
123A123LYS10.8950.95818.6980.0210.0210.0000.0000.0000.000
124A124VAL00.0030.00313.3430.0030.0030.0000.0000.0000.000
125A125PHE00.011-0.00415.0540.0550.0550.0000.0000.0000.000
126A126GLU-1-0.866-0.95217.2660.1070.1070.0000.0000.0000.000
127A127MET0-0.117-0.02911.159-0.035-0.0350.0000.0000.0000.000
128A128ILE0-0.032-0.01111.3790.0340.0340.0000.0000.0000.000
129A129ILE0-0.062-0.02313.8950.0670.0670.0000.0000.0000.000
130A130ASN0-0.017-0.00816.303-0.102-0.1020.0000.0000.0000.000
131A131PRO00.0200.00219.0900.0240.0240.0000.0000.0000.000
132A132GLY00.0020.00721.8600.0080.0080.0000.0000.0000.000
133A133ASP-1-0.813-0.87916.4580.5750.5750.0000.0000.0000.000
134A134ASN0-0.038-0.02717.433-0.099-0.0990.0000.0000.0000.000
135A135VAL0-0.013-0.00616.4720.0920.0920.0000.0000.0000.000
136A136LEU00.0000.00715.439-0.036-0.0360.0000.0000.0000.000
137A137LEU00.0110.00118.3180.0000.0000.0000.0000.0000.000
138A138ASP-1-0.847-0.90320.8530.2350.2350.0000.0000.0000.000
139A139GLU-1-0.864-0.91223.9080.1870.1870.0000.0000.0000.000
140A140PRO0-0.022-0.01927.357-0.001-0.0010.0000.0000.0000.000
141A141ALA00.0250.00925.2110.0020.0020.0000.0000.0000.000
142A142TYR0-0.027-0.02125.723-0.016-0.0160.0000.0000.0000.000
143A143SER00.0750.03227.3260.0070.0070.0000.0000.0000.000
144A144GLY0-0.025-0.01328.2140.0030.0030.0000.0000.0000.000
145A145THR0-0.014-0.02522.214-0.007-0.0070.0000.0000.0000.000
146A146LEU00.0220.02124.4570.0150.0150.0000.0000.0000.000
147A147GLN0-0.007-0.01026.5660.0070.0070.0000.0000.0000.000
148A148SER0-0.093-0.03323.437-0.002-0.0020.0000.0000.0000.000
149A149LEU00.025-0.01019.8440.0060.0060.0000.0000.0000.000
150A150HIS00.0260.03323.5130.0190.0190.0000.0000.0000.000
151A151PRO0-0.031-0.02026.0260.0050.0050.0000.0000.0000.000
152A152LEU0-0.040-0.01820.138-0.003-0.0030.0000.0000.0000.000
153A153GLY00.0110.01622.8530.0170.0170.0000.0000.0000.000
154A154CYS0-0.055-0.00920.2260.0080.0080.0000.0000.0000.000
155A155ASN0-0.020-0.01021.709-0.060-0.0600.0000.0000.0000.000
156A156ILE00.024-0.00121.4020.0440.0440.0000.0000.0000.000
157A157ILE0-0.046-0.02419.733-0.017-0.0170.0000.0000.0000.000
158A158ASN00.0610.02522.0550.0210.0210.0000.0000.0000.000
159A159VAL0-0.050-0.03319.9390.0190.0190.0000.0000.0000.000
160A160ALA00.0130.00523.399-0.025-0.0250.0000.0000.0000.000
161A161SER00.008-0.01624.9150.0140.0140.0000.0000.0000.000
162A162ASP-1-0.739-0.84426.9140.1660.1660.0000.0000.0000.000
163A163GLU-1-0.892-0.95129.0220.1290.1290.0000.0000.0000.000
164A164SER0-0.058-0.02526.890-0.013-0.0130.0000.0000.0000.000
165A165GLY0-0.012-0.01224.7010.0100.0100.0000.0000.0000.000
166A166ILE00.017-0.00119.6590.0060.0060.0000.0000.0000.000
167A167VAL00.0280.01923.191-0.004-0.0040.0000.0000.0000.000
168A168PRO0-0.012-0.01419.7700.0290.0290.0000.0000.0000.000
169A169ASP-1-0.831-0.91420.8150.3310.3310.0000.0000.0000.000
170A170SER0-0.0140.01123.1270.0130.0130.0000.0000.0000.000
171A171LEU00.0220.00915.9800.0220.0220.0000.0000.0000.000
172A172ARG10.8480.91118.026-0.365-0.3650.0000.0000.0000.000
173A173ASP-1-0.925-0.95919.4060.3720.3720.0000.0000.0000.000
174A174ILE00.0300.03619.6410.0150.0150.0000.0000.0000.000
175A175LEU0-0.040-0.03614.7290.0390.0390.0000.0000.0000.000
176A176SER0-0.091-0.04117.7070.0480.0480.0000.0000.0000.000
177A177ARG10.9590.99519.786-0.471-0.4710.0000.0000.0000.000
178A178TRP0-0.096-0.05115.744-0.003-0.0030.0000.0000.0000.000
179A179LYS10.9620.97315.980-0.526-0.5260.0000.0000.0000.000
180A180PRO00.0120.00210.8270.0420.0420.0000.0000.0000.000
181A181GLU-1-0.891-0.94910.8051.0791.0790.0000.0000.0000.000
182A182ASP-1-0.855-0.94111.9620.7020.7020.0000.0000.0000.000
183A183ALA0-0.0190.0028.558-0.076-0.0760.0000.0000.0000.000
184A184LYS10.8830.9345.044-2.712-2.7120.0000.0000.0000.000
185A185ASN00.0050.0029.833-0.247-0.2470.0000.0000.0000.000
186A186PRO00.0190.00113.5640.0310.0310.0000.0000.0000.000
187A187GLN0-0.003-0.00715.028-0.009-0.0090.0000.0000.0000.000
188A188LYS10.8790.96015.198-0.552-0.5520.0000.0000.0000.000
189A189ASN0-0.021-0.01415.8780.0160.0160.0000.0000.0000.000
190A190THR00.0090.01511.321-0.057-0.0570.0000.0000.0000.000
191A191PRO00.0180.00213.9310.0180.0180.0000.0000.0000.000
192A192LYS10.8890.94811.708-0.566-0.5660.0000.0000.0000.000
193A193PHE00.000-0.02510.8670.1790.1790.0000.0000.0000.000
194A194LEU0-0.0020.01712.857-0.049-0.0490.0000.0000.0000.000
195A195TYR0-0.062-0.04814.755-0.028-0.0280.0000.0000.0000.000
196A196THR00.011-0.01217.423-0.005-0.0050.0000.0000.0000.000
197A197VAL0-0.045-0.00619.469-0.022-0.0220.0000.0000.0000.000
198A198PRO0-0.044-0.01419.3810.0040.0040.0000.0000.0000.000
199A199ASN0-0.020-0.02922.0200.0000.0000.0000.0000.0000.000
200A200GLY00.0130.00725.274-0.006-0.0060.0000.0000.0000.000
201A201ASN00.0480.02525.318-0.013-0.0130.0000.0000.0000.000
202A202ASN0-0.0260.01827.430-0.008-0.0080.0000.0000.0000.000
203A203PRO00.008-0.00628.7870.0060.0060.0000.0000.0000.000
204A204THR00.012-0.01729.208-0.009-0.0090.0000.0000.0000.000
205A205GLY00.0320.01430.790-0.005-0.0050.0000.0000.0000.000
206A206ASN00.0060.00128.737-0.016-0.0160.0000.0000.0000.000
207A207SER0-0.004-0.01025.931-0.003-0.0030.0000.0000.0000.000
208A208LEU0-0.024-0.00119.8190.0040.0040.0000.0000.0000.000
209A209THR00.0370.02323.916-0.014-0.0140.0000.0000.0000.000
210A210SER00.004-0.01321.4420.0180.0180.0000.0000.0000.000
211A211GLU-1-0.897-0.96620.3020.1420.1420.0000.0000.0000.000
212A212ARG10.8420.91020.211-0.160-0.1600.0000.0000.0000.000
213A213LYS10.8840.96017.394-0.048-0.0480.0000.0000.0000.000
214A214LYS10.9710.98115.730-0.078-0.0780.0000.0000.0000.000
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