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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: QY5JY

Calculation Name: 3AXL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AXL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1807713.011836
FMO2-HF: Nuclear repulsion 1732957.418057
FMO2-HF: Total energy -74755.593779
FMO2-MP2: Total energy -74969.924442


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:3:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-12.63-6.0788.013-5.469-9.095-0.002
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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].
3A5GLU-1-0.924-0.9503.826-3.484-1.749-0.018-0.747-0.9700.000
4A6GLN0-0.020-0.0345.9590.6150.6150.0000.0000.0000.000
5A7SER0-0.0390.0109.547-0.112-0.1120.0000.0000.0000.000
6A8PRO00.0720.03212.6710.0750.0750.0000.0000.0000.000
7A9ALA00.0740.01813.4730.0220.0220.0000.0000.0000.000
8A10SER00.004-0.00814.3870.0540.0540.0000.0000.0000.000
9A11LEU0-0.061-0.02317.954-0.028-0.0280.0000.0000.0000.000
10A12VAL00.0410.00921.1050.0190.0190.0000.0000.0000.000
11A13LEU0-0.036-0.00423.972-0.008-0.0080.0000.0000.0000.000
12A14GLN00.0500.03327.0770.0080.0080.0000.0000.0000.000
13A15GLU-1-0.817-0.91429.8980.0380.0380.0000.0000.0000.000
14A16GLY0-0.017-0.02030.763-0.005-0.0050.0000.0000.0000.000
15A17GLU-1-0.897-0.94327.9200.0130.0130.0000.0000.0000.000
16A18ASN0-0.046-0.01826.4990.0250.0250.0000.0000.0000.000
17A19ALA00.0160.00022.180-0.016-0.0160.0000.0000.0000.000
18A20GLU-1-0.876-0.94919.6510.1360.1360.0000.0000.0000.000
19A21LEU0-0.0260.00415.624-0.039-0.0390.0000.0000.0000.000
20A22GLN0-0.014-0.01712.7970.0940.0940.0000.0000.0000.000
21A23CYS0-0.025-0.0098.9470.0570.0570.0000.0000.0000.000
22A24THR0-0.0080.0017.2860.3050.3050.0000.0000.0000.000
23A25TYR0-0.013-0.0202.155-1.256-0.7423.279-1.182-2.611-0.003
24A26SER0-0.021-0.0042.413-4.920-2.3744.511-2.969-4.088-0.004
25A27THR00.0350.0222.993-1.536-0.2470.152-0.468-0.9740.005
26A28THR00.0690.0295.470-0.963-0.996-0.0010.0000.0350.000
27A29LEU0-0.065-0.0207.2930.6150.6150.0000.0000.0000.000
28A30ASN0-0.041-0.0178.994-0.301-0.3010.0000.0000.0000.000
29A31SER00.0050.01111.661-0.254-0.2540.0000.0000.0000.000
30A32MET00.015-0.0099.8290.2490.2490.0000.0000.0000.000
31A40GLN0-0.0130.02311.793-0.235-0.2350.0000.0000.0000.000
32A41TRP00.0680.04212.5930.0500.0500.0000.0000.0000.000
33A42PHE0-0.020-0.01813.258-0.029-0.0290.0000.0000.0000.000
34A43TYR0-0.019-0.01016.592-0.015-0.0150.0000.0000.0000.000
35A44GLN0-0.038-0.03418.6620.0320.0320.0000.0000.0000.000
36A45ARG11.0111.01220.788-0.130-0.1300.0000.0000.0000.000
37A46PRO00.0770.03422.7800.0150.0150.0000.0000.0000.000
38A47GLY00.0160.01023.855-0.006-0.0060.0000.0000.0000.000
39A48GLY0-0.053-0.01824.9280.0050.0050.0000.0000.0000.000
40A49ARG10.9680.98722.368-0.236-0.2360.0000.0000.0000.000
41A50LEU00.0210.00116.172-0.009-0.0090.0000.0000.0000.000
42A51VAL0-0.031-0.00919.8020.0190.0190.0000.0000.0000.000
43A52SER0-0.042-0.03718.2030.0030.0030.0000.0000.0000.000
44A53LEU0-0.007-0.00318.604-0.030-0.0300.0000.0000.0000.000
45A54LEU0-0.032-0.01917.366-0.022-0.0220.0000.0000.0000.000
46A55TYR0-0.044-0.03315.5770.0500.0500.0000.0000.0000.000
47A56SER00.002-0.00314.959-0.084-0.0840.0000.0000.0000.000
48A57PRO00.0060.00516.0920.1020.1020.0000.0000.0000.000
49A58SER0-0.001-0.02518.596-0.009-0.0090.0000.0000.0000.000
50A59TRP0-0.055-0.01614.245-0.076-0.0760.0000.0000.0000.000
51A60ALA00.0060.00117.701-0.045-0.0450.0000.0000.0000.000
52A61GLU-1-0.717-0.82819.1250.4300.4300.0000.0000.0000.000
53A62GLN0-0.054-0.03121.213-0.055-0.0550.0000.0000.0000.000
54A63ARG10.9140.93521.016-0.348-0.3480.0000.0000.0000.000
55A64GLY0-0.0350.00324.686-0.018-0.0180.0000.0000.0000.000
56A70GLY0-0.022-0.02426.890-0.014-0.0140.0000.0000.0000.000
57A71ARG10.8150.89527.752-0.120-0.1200.0000.0000.0000.000
58A72LEU00.0180.00921.340-0.010-0.0100.0000.0000.0000.000
59A80THR0-0.023-0.01722.4080.0150.0150.0000.0000.0000.000
60A81SER00.0160.00617.091-0.014-0.0140.0000.0000.0000.000
61A82SER0-0.0130.00017.329-0.023-0.0230.0000.0000.0000.000
62A83ALA00.0530.05014.2040.0350.0350.0000.0000.0000.000
63A84ALA00.003-0.01314.470-0.084-0.0840.0000.0000.0000.000
64A84SER00.0090.00714.7870.0890.0890.0000.0000.0000.000
65A84ASN0-0.047-0.02712.917-0.087-0.0870.0000.0000.0000.000
66A84GLU-1-0.849-0.9149.2551.6821.6820.0000.0000.0000.000
67A85SER00.011-0.0198.251-0.293-0.2930.0000.0000.0000.000
68A86ARG10.8330.9279.321-0.210-0.2100.0000.0000.0000.000
69A87SER0-0.0130.00011.0010.0160.0160.0000.0000.0000.000
70A88SER00.017-0.00112.843-0.077-0.0770.0000.0000.0000.000
71A89LEU0-0.033-0.00715.5720.0460.0460.0000.0000.0000.000
72A90HIS10.8990.96718.132-0.224-0.2240.0000.0000.0000.000
73A91ILE0-0.027-0.02220.6520.0260.0260.0000.0000.0000.000
74A92SER00.0230.01724.117-0.021-0.0210.0000.0000.0000.000
75A93SER0-0.026-0.01527.7660.0030.0030.0000.0000.0000.000
76A94SER0-0.032-0.00926.2890.0020.0020.0000.0000.0000.000
77A95GLN00.0440.02228.202-0.007-0.0070.0000.0000.0000.000
78A96ILE00.1490.05828.6720.0070.0070.0000.0000.0000.000
79A97THR0-0.0350.00028.540-0.003-0.0030.0000.0000.0000.000
80A98ASP-1-0.799-0.86424.9200.1220.1220.0000.0000.0000.000
81A99SER00.0180.01423.7880.0040.0040.0000.0000.0000.000
82A100GLY0-0.063-0.02822.2030.0150.0150.0000.0000.0000.000
83A101THR0-0.0200.00815.921-0.033-0.0330.0000.0000.0000.000
84A102TYR0-0.025-0.03216.5370.0560.0560.0000.0000.0000.000
85A103LEU00.0080.01411.823-0.028-0.0280.0000.0000.0000.000
86A105ALA00.0050.0128.4130.1520.1520.0000.0000.0000.000
87A106ILE00.0190.0095.041-0.233-0.2330.0000.0000.0000.000
88A107ALA00.0470.0167.3920.2850.2850.0000.0000.0000.000
89A108SER00.0220.0046.725-0.534-0.5340.0000.0000.0000.000
90A109SER00.0170.0048.871-0.229-0.2290.0000.0000.0000.000
91A110SER0-0.0060.00712.319-0.005-0.0050.0000.0000.0000.000
92A113PHE00.003-0.00814.717-0.063-0.0630.0000.0000.0000.000
93A114SER0-0.030-0.0019.362-0.186-0.1860.0000.0000.0000.000
94A115LYS10.9510.9726.842-1.280-1.2800.0000.0000.0000.000
95A116LEU00.0230.0118.6670.3030.3030.0000.0000.0000.000
96A117VAL0-0.060-0.0292.871-0.752-0.2510.090-0.103-0.4870.000
97A118PHE0-0.016-0.0226.0880.0730.0730.0000.0000.0000.000
98A119GLY00.0310.0076.4290.3060.3060.0000.0000.0000.000
99A120GLN0-0.011-0.0196.2150.1150.1150.0000.0000.0000.000
100A121GLY0-0.034-0.0189.284-0.051-0.0510.0000.0000.0000.000
101A122THR0-0.027-0.00312.450-0.076-0.0760.0000.0000.0000.000
102A123SER0-0.069-0.03914.9210.0470.0470.0000.0000.0000.000
103A124LEU00.0220.00518.278-0.026-0.0260.0000.0000.0000.000
104A125SER0-0.002-0.00521.0040.0110.0110.0000.0000.0000.000
105A126VAL0-0.0010.00124.488-0.010-0.0100.0000.0000.0000.000
106A127VAL00.001-0.00227.3570.0030.0030.0000.0000.0000.000
107A128PRO00.0440.02630.5470.0010.0010.0000.0000.0000.000
108A129ASN0-0.023-0.00234.120-0.011-0.0110.0000.0000.0000.000
109A130ILE0-0.022-0.00236.4750.0040.0040.0000.0000.0000.000
110A131GLN0-0.033-0.01239.388-0.003-0.0030.0000.0000.0000.000
111A132ASN0-0.039-0.02542.448-0.001-0.0010.0000.0000.0000.000
112A133PRO0-0.027-0.00941.6610.0020.0020.0000.0000.0000.000
113A134ASP-1-0.935-0.97543.573-0.007-0.0070.0000.0000.0000.000
114A135PRO00.0140.01742.7920.0000.0000.0000.0000.0000.000
115A136ALA00.0340.03444.6230.0000.0000.0000.0000.0000.000
116A137VAL0-0.025-0.01644.439-0.001-0.0010.0000.0000.0000.000
117A138TYR00.0180.01446.8160.0000.0000.0000.0000.0000.000
118A139GLN00.0450.00747.9740.0000.0000.0000.0000.0000.000
119A140LEU0-0.020-0.00946.1410.0020.0020.0000.0000.0000.000
120A141ARG10.8690.92049.8440.0050.0050.0000.0000.0000.000
121A142ASP-1-0.942-0.95350.8220.0060.0060.0000.0000.0000.000
122A150VAL0-0.030-0.02644.153-0.001-0.0010.0000.0000.0000.000
123A151CYS0-0.056-0.01945.012-0.001-0.0010.0000.0000.0000.000
124A152LEU00.0150.01142.1230.0000.0000.0000.0000.0000.000
125A153PHE00.0220.02538.5930.0000.0000.0000.0000.0000.000
126A154THR00.006-0.05541.0860.0030.0030.0000.0000.0000.000
127A155ASP-1-0.787-0.85741.4620.0000.0000.0000.0000.0000.000
128A156PHE00.0370.04035.854-0.001-0.0010.0000.0000.0000.000
129A157ASP-1-0.768-0.88937.735-0.026-0.0260.0000.0000.0000.000
130A158SER0-0.001-0.04233.247-0.004-0.0040.0000.0000.0000.000
131A159GLN0-0.109-0.04833.484-0.009-0.0090.0000.0000.0000.000
132A160THR0-0.0060.01033.635-0.009-0.0090.0000.0000.0000.000
133A161ASN0-0.062-0.04430.8620.0050.0050.0000.0000.0000.000
134A162VAL00.0410.02833.112-0.002-0.0020.0000.0000.0000.000
135A163SER0-0.047-0.01433.076-0.006-0.0060.0000.0000.0000.000
136A164GLN00.0320.00531.3270.0070.0070.0000.0000.0000.000
137A165SER00.0380.02735.233-0.006-0.0060.0000.0000.0000.000
138A166LYS10.9130.94736.2230.0890.0890.0000.0000.0000.000
139A167ASP-1-0.869-0.92638.621-0.049-0.0490.0000.0000.0000.000
140A168SER0-0.023-0.02839.3410.0010.0010.0000.0000.0000.000
141A169ASP-1-0.866-0.90540.333-0.038-0.0380.0000.0000.0000.000
142A170VAL0-0.020-0.01341.3000.0040.0040.0000.0000.0000.000
143A171TYR0-0.062-0.03038.356-0.003-0.0030.0000.0000.0000.000
144A172ILE00.0110.00736.9300.0040.0040.0000.0000.0000.000
145A173THR0-0.054-0.01134.718-0.002-0.0020.0000.0000.0000.000
146A174ASP-1-0.880-0.93329.405-0.040-0.0400.0000.0000.0000.000
147A175LYS10.8500.90631.0780.0440.0440.0000.0000.0000.000
148A176CYS0-0.089-0.04232.1740.0040.0040.0000.0000.0000.000
149A177VAL00.0480.01632.213-0.002-0.0020.0000.0000.0000.000
150A178LEU0-0.058-0.01834.9940.0080.0080.0000.0000.0000.000
151A179ASP-1-0.866-0.95936.5760.0470.0470.0000.0000.0000.000
152A180MET0-0.028-0.01138.5390.0040.0040.0000.0000.0000.000
153A181ARG10.9940.97837.771-0.064-0.0640.0000.0000.0000.000
154A182SER0-0.082-0.03441.8370.0010.0010.0000.0000.0000.000
155A183MET0-0.040-0.01145.6300.0010.0010.0000.0000.0000.000
156A184ASP-1-0.955-0.97141.2110.0370.0370.0000.0000.0000.000
157A185PHE00.0150.01842.514-0.003-0.0030.0000.0000.0000.000
158A186LYS10.8450.90535.702-0.037-0.0370.0000.0000.0000.000
159A187SER0-0.035-0.01939.033-0.004-0.0040.0000.0000.0000.000
160A188ASN0-0.033-0.01835.3190.0060.0060.0000.0000.0000.000
161A189SER0-0.0030.00036.916-0.001-0.0010.0000.0000.0000.000
162A190ALA00.0220.01836.6230.0000.0000.0000.0000.0000.000
163A191VAL0-0.006-0.00538.1960.0010.0010.0000.0000.0000.000
164A192ALA00.0210.01539.348-0.003-0.0030.0000.0000.0000.000
165A193TRP0-0.020-0.03338.5130.0030.0030.0000.0000.0000.000
166A194SER00.0820.04942.961-0.002-0.0020.0000.0000.0000.000
167A195ASN0-0.092-0.03845.4380.0030.0030.0000.0000.0000.000
168A196LYS10.7950.87346.0550.0390.0390.0000.0000.0000.000
169A197SER0-0.0160.00150.2770.0010.0010.0000.0000.0000.000
170A198ASP-1-0.891-0.96150.483-0.033-0.0330.0000.0000.0000.000
171A199PHE0-0.0080.01044.2680.0000.0000.0000.0000.0000.000
172A200ALA00.0530.01448.9540.0030.0030.0000.0000.0000.000
173A202ALA00.0080.01547.8780.0000.0000.0000.0000.0000.000
174A203ASN0-0.021-0.02147.046-0.003-0.0030.0000.0000.0000.000
175A204ALA0-0.0260.00243.884-0.003-0.0030.0000.0000.0000.000
176A205PHE00.0540.00739.610-0.001-0.0010.0000.0000.0000.000
177A206ASN00.0290.01841.312-0.002-0.0020.0000.0000.0000.000
178A207ASN0-0.077-0.03637.275-0.003-0.0030.0000.0000.0000.000
179A208SER00.0060.01237.195-0.006-0.0060.0000.0000.0000.000
180A209ILE0-0.0040.00336.3280.0010.0010.0000.0000.0000.000
181A210ILE0-0.026-0.02038.3620.0010.0010.0000.0000.0000.000
182A211PRO00.0310.02140.149-0.002-0.0020.0000.0000.0000.000
183A212GLU-1-0.933-0.96342.809-0.036-0.0360.0000.0000.0000.000
184A213ASP-1-0.938-0.95945.906-0.026-0.0260.0000.0000.0000.000
185A214THR0-0.065-0.04244.5640.0030.0030.0000.0000.0000.000
186A215PHE0-0.016-0.02146.838-0.001-0.0010.0000.0000.0000.000
187A216PHE00.012-0.01246.1880.0010.0010.0000.0000.0000.000
188A217PRO0-0.0380.00050.8410.0000.0000.0000.0000.0000.000
189A218SER0-0.041-0.01954.017-0.001-0.0010.0000.0000.0000.000