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: ZYLNN

Calculation Name: 2AJ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AJ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KUP8

Base Structure: X-ray

Registration Date: 2023-03-13

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972144.557868
FMO2-HF: Nuclear repulsion 1898155.858743
FMO2-HF: Total energy -73988.699125
FMO2-MP2: Total energy -74201.66687


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:6:SER)


Summations of interaction energy for fragment #1(A:6:SER)
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.
-3.3860.323-0.021-1.831-1.856-0.008
Interaction energy analysis for fragmet #1(A:6:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.063
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].
3A8ILE0-0.0030.0193.183-0.7642.945-0.021-1.831-1.856-0.008
4A9GLU-1-0.905-0.9576.193-2.139-2.1390.0000.0000.0000.000
5A10VAL0-0.057-0.0228.7990.3420.3420.0000.0000.0000.000
6A11GLY00.0190.00311.314-0.067-0.0670.0000.0000.0000.000
7A12HIS0-0.047-0.04414.0720.0360.0360.0000.0000.0000.000
8A13SER0-0.023-0.00217.7920.0140.0140.0000.0000.0000.000
9A14MET00.0360.03119.9120.0190.0190.0000.0000.0000.000
10A15ASN0-0.0230.00323.0580.0240.0240.0000.0000.0000.000
11A16LEU00.022-0.00125.4250.0120.0120.0000.0000.0000.000
12A17THR00.010-0.00928.7140.0180.0180.0000.0000.0000.000
13A18ASN00.0380.02430.8380.0050.0050.0000.0000.0000.000
14A19HIS0-0.027-0.01328.6590.0040.0040.0000.0000.0000.000
15A20PHE0-0.041-0.01432.8580.0040.0040.0000.0000.0000.000
16A21LEU00.0060.00832.605-0.006-0.0060.0000.0000.0000.000
17A22VAL0-0.037-0.02435.2270.0090.0090.0000.0000.0000.000
18A23ALA00.0070.01836.352-0.005-0.0050.0000.0000.0000.000
19A24MET00.0170.01035.1950.0070.0070.0000.0000.0000.000
20A25PRO0-0.023-0.02738.3210.0030.0030.0000.0000.0000.000
21A26SER0-0.039-0.01137.4210.0040.0040.0000.0000.0000.000
22A27MET0-0.0140.02437.458-0.005-0.0050.0000.0000.0000.000
23A28LYS10.9370.96935.3620.1340.1340.0000.0000.0000.000
24A29ASP-1-0.777-0.91740.703-0.090-0.0900.0000.0000.0000.000
25A30PRO0-0.059-0.03942.4450.0010.0010.0000.0000.0000.000
26A31TYR00.0140.01843.4440.0050.0050.0000.0000.0000.000
27A32PHE00.0520.02140.4910.0010.0010.0000.0000.0000.000
28A33LYS10.8250.91642.1290.0820.0820.0000.0000.0000.000
29A34ARG10.8980.95243.1060.0680.0680.0000.0000.0000.000
30A35SER00.0180.01641.2260.0020.0020.0000.0000.0000.000
31A36VAL00.001-0.01139.301-0.003-0.0030.0000.0000.0000.000
32A37ILE00.0070.01337.4220.0050.0050.0000.0000.0000.000
33A38TYR00.0030.00636.410-0.004-0.0040.0000.0000.0000.000
34A39ILE0-0.0120.00031.4490.0030.0030.0000.0000.0000.000
35A40CYS0-0.046-0.03434.4130.0040.0040.0000.0000.0000.000
36A41GLU-1-0.893-0.96331.339-0.132-0.1320.0000.0000.0000.000
37A42HIS0-0.044-0.01825.8940.0040.0040.0000.0000.0000.000
38A43ASN00.0380.00825.632-0.014-0.0140.0000.0000.0000.000
39A44GLN00.0270.00019.9540.0260.0260.0000.0000.0000.000
40A45ASP-1-0.900-0.93624.794-0.186-0.1860.0000.0000.0000.000
41A46GLY0-0.057-0.02928.1590.0090.0090.0000.0000.0000.000
42A47ALA0-0.027-0.00729.378-0.005-0.0050.0000.0000.0000.000
43A48MET00.0190.03531.6940.0080.0080.0000.0000.0000.000
44A49GLY00.0330.00135.097-0.003-0.0030.0000.0000.0000.000
45A50LEU00.0030.02137.3960.0050.0050.0000.0000.0000.000
46A51MET0-0.045-0.01040.878-0.001-0.0010.0000.0000.0000.000
47A52ILE00.0050.00841.3260.0050.0050.0000.0000.0000.000
48A53ASN0-0.037-0.05144.2320.0020.0020.0000.0000.0000.000
49A54ALA00.0330.02246.8040.0020.0020.0000.0000.0000.000
50A55PRO0-0.058-0.01148.6120.0000.0000.0000.0000.0000.000
51A56ILE00.015-0.00351.9660.0000.0000.0000.0000.0000.000
52A57ASP-1-0.956-0.97754.031-0.044-0.0440.0000.0000.0000.000
53A58ILE0-0.030-0.00955.1650.0020.0020.0000.0000.0000.000
54A59THR00.0250.01456.825-0.001-0.0010.0000.0000.0000.000
55A60VAL00.0050.01655.1610.0000.0000.0000.0000.0000.000
56A61GLY00.0540.01056.7160.0000.0000.0000.0000.0000.000
57A62GLY0-0.059-0.02560.1870.0010.0010.0000.0000.0000.000
58A63MET00.0100.01553.4560.0010.0010.0000.0000.0000.000
59A64LEU00.0470.02556.3010.0000.0000.0000.0000.0000.000
60A65LYS10.9740.97358.9200.0340.0340.0000.0000.0000.000
61A66GLN0-0.084-0.02659.3030.0010.0010.0000.0000.0000.000
62A67VAL0-0.074-0.04356.0430.0000.0000.0000.0000.0000.000
63A68ASP-1-0.966-0.98359.135-0.034-0.0340.0000.0000.0000.000
64A69ILE0-0.075-0.03156.6280.0000.0000.0000.0000.0000.000
65A70GLU-1-0.950-0.97060.150-0.030-0.0300.0000.0000.0000.000
66A71PRO0-0.064-0.02260.545-0.001-0.0010.0000.0000.0000.000
67A72ALA00.0270.01259.7100.0010.0010.0000.0000.0000.000
68A73TYR0-0.033-0.02858.7490.0020.0020.0000.0000.0000.000
69A74PRO00.004-0.00363.355-0.001-0.0010.0000.0000.0000.000
70A75GLN00.0280.01262.223-0.002-0.0020.0000.0000.0000.000
71A76SER00.0360.01263.4390.0010.0010.0000.0000.0000.000
72A77HIS10.8150.92657.7530.0360.0360.0000.0000.0000.000
73A78GLN0-0.065-0.06461.091-0.002-0.0020.0000.0000.0000.000
74A79GLU-1-0.858-0.93261.645-0.034-0.0340.0000.0000.0000.000
75A80ASN0-0.052-0.05155.8280.0000.0000.0000.0000.0000.000
76A81LEU00.0800.02657.541-0.002-0.0020.0000.0000.0000.000
77A82LYS10.9280.95859.8350.0330.0330.0000.0000.0000.000
78A83LYS10.9060.99453.9780.0450.0450.0000.0000.0000.000
79A84PRO00.0380.01753.7390.0010.0010.0000.0000.0000.000
80A85VAL00.0220.01751.940-0.001-0.0010.0000.0000.0000.000
81A86PHE0-0.021-0.04248.2510.0010.0010.0000.0000.0000.000
82A87ASN0-0.0090.00047.127-0.002-0.0020.0000.0000.0000.000
83A88GLY00.0230.00144.656-0.002-0.0020.0000.0000.0000.000
84A89GLY00.040-0.01142.646-0.006-0.0060.0000.0000.0000.000
85A90PRO0-0.0110.01241.8560.0030.0030.0000.0000.0000.000
86A91VAL0-0.0150.00639.6300.0020.0020.0000.0000.0000.000
87A92SER0-0.001-0.01743.0550.0000.0000.0000.0000.0000.000
88A93GLU-1-0.884-0.95445.435-0.070-0.0700.0000.0000.0000.000
89A94ASP-1-0.948-0.95148.112-0.063-0.0630.0000.0000.0000.000
90A95ARG10.9120.95543.8700.0730.0730.0000.0000.0000.000
91A96GLY0-0.023-0.00547.622-0.001-0.0010.0000.0000.0000.000
92A97PHE0-0.009-0.01942.168-0.003-0.0030.0000.0000.0000.000
93A98ILE0-0.0150.00645.6410.0010.0010.0000.0000.0000.000
94A99LEU00.0270.03141.019-0.002-0.0020.0000.0000.0000.000
95A100HIS00.031-0.00144.2600.0030.0030.0000.0000.0000.000
96A101ARG10.9240.98143.9550.0500.0500.0000.0000.0000.000
97A102PRO0-0.134-0.04342.2050.0020.0020.0000.0000.0000.000
98A103ARG10.8830.96245.2930.0400.0400.0000.0000.0000.000
99A104ASP-1-0.901-0.94348.815-0.037-0.0370.0000.0000.0000.000
100A105HIS0-0.082-0.04245.165-0.001-0.0010.0000.0000.0000.000
101A106TYR00.0370.00246.4940.0010.0010.0000.0000.0000.000
102A107GLU-1-0.980-1.00246.045-0.048-0.0480.0000.0000.0000.000
103A108SER0-0.036-0.02443.500-0.003-0.0030.0000.0000.0000.000
104A109SER0-0.015-0.00742.624-0.001-0.0010.0000.0000.0000.000
105A110MET00.0290.02235.120-0.001-0.0010.0000.0000.0000.000
106A111LYS10.9280.95138.2170.0630.0630.0000.0000.0000.000
107A112MET0-0.029-0.00133.714-0.005-0.0050.0000.0000.0000.000
108A113THR00.0190.00635.217-0.002-0.0020.0000.0000.0000.000
109A114ASP-1-0.937-0.96937.498-0.058-0.0580.0000.0000.0000.000
110A115ASP-1-0.917-0.97640.381-0.054-0.0540.0000.0000.0000.000
111A116ILE0-0.017-0.01738.6400.0020.0020.0000.0000.0000.000
112A117ALA0-0.0200.00039.674-0.003-0.0030.0000.0000.0000.000
113A118VAL00.0340.01339.7090.0020.0020.0000.0000.0000.000
114A119THR0-0.005-0.00242.051-0.001-0.0010.0000.0000.0000.000
115A120THR0-0.074-0.03742.7580.0000.0000.0000.0000.0000.000
116A121SER0-0.024-0.04945.5760.0000.0000.0000.0000.0000.000
117A122LYS11.0290.99748.2750.0430.0430.0000.0000.0000.000
118A123ASP-1-0.771-0.81449.982-0.049-0.0490.0000.0000.0000.000
119A124ILE00.0430.02048.4690.0020.0020.0000.0000.0000.000
120A125LEU0-0.021-0.02451.8760.0010.0010.0000.0000.0000.000
121A126THR0-0.059-0.03554.4630.0020.0020.0000.0000.0000.000
122A127VAL00.0440.03253.4390.0020.0020.0000.0000.0000.000
123A128LEU00.0420.06552.5920.0010.0010.0000.0000.0000.000
124A129GLY0-0.0120.00256.4430.0010.0010.0000.0000.0000.000
125A130THR0-0.083-0.07658.1120.0020.0020.0000.0000.0000.000
126A131GLU-1-0.861-0.95758.201-0.032-0.0320.0000.0000.0000.000
127A132ALA0-0.015-0.01156.5210.0000.0000.0000.0000.0000.000
128A133GLU-1-0.800-0.87154.190-0.042-0.0420.0000.0000.0000.000
129A134PRO0-0.025-0.01249.4730.0010.0010.0000.0000.0000.000
130A135GLU-1-0.900-0.96250.936-0.038-0.0380.0000.0000.0000.000
131A136GLY0-0.047-0.04549.2680.0000.0000.0000.0000.0000.000
132A137TYR0-0.072-0.04848.085-0.003-0.0030.0000.0000.0000.000
133A138ILE0-0.0270.00545.1020.0020.0020.0000.0000.0000.000
134A139VAL00.0070.02247.769-0.002-0.0020.0000.0000.0000.000
135A140ALA00.0090.00545.6340.0010.0010.0000.0000.0000.000
136A141LEU0-0.012-0.00847.7100.0010.0010.0000.0000.0000.000
137A142GLY00.0850.04645.241-0.001-0.0010.0000.0000.0000.000
138A143TYR0-0.039-0.03837.721-0.001-0.0010.0000.0000.0000.000
139A144SER0-0.049-0.03338.5500.0010.0010.0000.0000.0000.000
140A145GLY00.0030.01236.215-0.003-0.0030.0000.0000.0000.000
141A146TRP0-0.054-0.02531.8610.0030.0030.0000.0000.0000.000
142A147SER00.004-0.01631.4490.0030.0030.0000.0000.0000.000
143A148ALA00.0880.03926.646-0.005-0.0050.0000.0000.0000.000
144A149GLY0-0.0160.01425.573-0.003-0.0030.0000.0000.0000.000
145A150GLN00.000-0.04626.254-0.010-0.0100.0000.0000.0000.000
146A151LEU0-0.0010.01129.3330.0060.0060.0000.0000.0000.000
147A152GLU-1-0.845-0.93323.794-0.245-0.2450.0000.0000.0000.000
148A153VAL0-0.026-0.00426.206-0.009-0.0090.0000.0000.0000.000
149A154GLU-1-0.811-0.90227.673-0.136-0.1360.0000.0000.0000.000
150A155LEU0-0.058-0.01926.6600.0100.0100.0000.0000.0000.000
151A156THR0-0.133-0.04724.5570.0020.0020.0000.0000.0000.000
152A157GLU-1-0.909-0.93627.315-0.157-0.1570.0000.0000.0000.000
153A158ASN0-0.029-0.03230.972-0.002-0.0020.0000.0000.0000.000
154A159SER0-0.046-0.03533.2910.0130.0130.0000.0000.0000.000
155A160TRP00.0310.00232.6130.0130.0130.0000.0000.0000.000
156A161LEU0-0.0010.00131.367-0.006-0.0060.0000.0000.0000.000
157A162THR0-0.017-0.01429.5050.0020.0020.0000.0000.0000.000
158A163ILE0-0.025-0.00431.102-0.001-0.0010.0000.0000.0000.000
159A164GLU-1-0.919-0.94331.262-0.110-0.1100.0000.0000.0000.000
160A165ALA0-0.014-0.02232.7560.0060.0060.0000.0000.0000.000
161A166ASP-1-0.830-0.93936.243-0.068-0.0680.0000.0000.0000.000
162A167PRO00.0350.00939.251-0.001-0.0010.0000.0000.0000.000
163A168GLU-1-0.814-0.91742.311-0.057-0.0570.0000.0000.0000.000
164A169LEU0-0.095-0.04940.9470.0030.0030.0000.0000.0000.000
165A170ILE00.001-0.01340.230-0.001-0.0010.0000.0000.0000.000
166A171PHE0-0.040-0.02043.7790.0020.0020.0000.0000.0000.000
167A172ASN0-0.055-0.01747.3350.0020.0020.0000.0000.0000.000
168A173THR0-0.0400.02045.5530.0020.0020.0000.0000.0000.000
169A174PRO00.0230.00648.834-0.002-0.0020.0000.0000.0000.000
170A175VAL00.0690.01849.071-0.002-0.0020.0000.0000.0000.000
171A176HIS0-0.031-0.02348.661-0.004-0.0040.0000.0000.0000.000
172A177GLU-1-0.918-0.95948.529-0.050-0.0500.0000.0000.0000.000
173A178LYS10.7880.93744.6370.0620.0620.0000.0000.0000.000
174A179TRP00.0360.00840.9580.0020.0020.0000.0000.0000.000
175A180GLN0-0.023-0.01042.727-0.003-0.0030.0000.0000.0000.000
176A181LYS11.0150.99542.9340.0590.0590.0000.0000.0000.000
177A182ALA0-0.0020.00339.303-0.001-0.0010.0000.0000.0000.000
178A183ILE00.0590.01738.512-0.002-0.0020.0000.0000.0000.000
179A184GLN00.0010.01138.8900.0000.0000.0000.0000.0000.000
180A185LYS10.8900.95737.0400.0770.0770.0000.0000.0000.000
181A186LEU0-0.059-0.03133.370-0.002-0.0020.0000.0000.0000.000
182A187GLY0-0.0090.00635.793-0.003-0.0030.0000.0000.0000.000
183A188ILE0-0.030-0.00936.5730.0010.0010.0000.0000.0000.000
184A189SER0-0.027-0.04039.4580.0040.0040.0000.0000.0000.000
185A190PRO0-0.043-0.02142.721-0.002-0.0020.0000.0000.0000.000
186A191ALA00.0150.00544.1190.0020.0020.0000.0000.0000.000
187A192GLN00.0090.03244.9770.0040.0040.0000.0000.0000.000