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

tag_button

FMODB ID: K9QM3

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1808147.040142
FMO2-HF: Nuclear repulsion 1733390.472962
FMO2-HF: Total energy -74756.56718
FMO2-MP2: Total energy -74970.837684


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.
-12.426-5.7516.183-4.735-8.1240.012
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 : 0.029 / q_NPA : -0.007
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-1-0.850-0.9073.879-1.4600.212-0.016-0.742-0.9140.000
4A6GLN0-0.016-0.0326.0710.5240.5240.0000.0000.0000.000
5A7SER0-0.0320.0139.872-0.133-0.1330.0000.0000.0000.000
6A8PRO00.0740.03412.9480.0520.0520.0000.0000.0000.000
7A9ALA00.0660.02713.1550.0520.0520.0000.0000.0000.000
8A10SER0-0.028-0.01914.2270.0470.0470.0000.0000.0000.000
9A11LEU0-0.047-0.02017.993-0.031-0.0310.0000.0000.0000.000
10A12VAL00.0380.00921.1260.0190.0190.0000.0000.0000.000
11A13LEU0-0.0240.00324.514-0.012-0.0120.0000.0000.0000.000
12A14GLN00.0370.02427.4010.0050.0050.0000.0000.0000.000
13A15GLU-1-0.835-0.93830.2930.0910.0910.0000.0000.0000.000
14A16GLY0-0.012-0.01031.578-0.008-0.0080.0000.0000.0000.000
15A17GLU-1-0.840-0.91528.4270.0810.0810.0000.0000.0000.000
16A18ASN0-0.071-0.02126.8180.0290.0290.0000.0000.0000.000
17A19ALA00.001-0.00221.864-0.015-0.0150.0000.0000.0000.000
18A20GLU-1-0.852-0.93219.6140.2530.2530.0000.0000.0000.000
19A21LEU0-0.018-0.00116.175-0.031-0.0310.0000.0000.0000.000
20A22GLN00.0120.00013.1760.0970.0970.0000.0000.0000.000
21A23CYS0-0.011-0.0069.3680.1090.1090.0000.0000.0000.000
22A24THR0-0.053-0.0337.2760.0060.0060.0000.0000.0000.000
23A25TYR0-0.002-0.0072.289-0.6350.5272.174-0.955-2.3810.007
24A26SER0-0.027-0.0242.422-5.908-3.1073.296-2.586-3.5110.003
25A27THR00.0040.0233.790-2.558-1.9520.007-0.181-0.4330.001
26A28THR00.0690.0375.824-0.460-0.4600.0000.0000.0000.000
27A29LEU0-0.048-0.0127.8620.6240.6240.0000.0000.0000.000
28A30ASN0-0.050-0.0029.324-0.397-0.3970.0000.0000.0000.000
29A31SER0-0.004-0.01111.431-0.253-0.2530.0000.0000.0000.000
30A32MET00.0370.02110.4500.3030.3030.0000.0000.0000.000
31A40GLN0-0.0260.00811.926-0.237-0.2370.0000.0000.0000.000
32A41TRP00.0520.01812.7200.0970.0970.0000.0000.0000.000
33A42PHE0-0.034-0.02613.328-0.060-0.0600.0000.0000.0000.000
34A43TYR00.0080.00216.974-0.001-0.0010.0000.0000.0000.000
35A44GLN0-0.031-0.03718.1560.0450.0450.0000.0000.0000.000
36A45ARG10.9530.98320.607-0.196-0.1960.0000.0000.0000.000
37A46PRO00.0420.01123.1270.0130.0130.0000.0000.0000.000
38A47GLY00.0520.03024.382-0.010-0.0100.0000.0000.0000.000
39A48GLY0-0.0020.00524.119-0.011-0.0110.0000.0000.0000.000
40A49ARG10.9260.97622.175-0.290-0.2900.0000.0000.0000.000
41A50LEU00.0570.03315.855-0.010-0.0100.0000.0000.0000.000
42A51VAL0-0.052-0.03219.597-0.010-0.0100.0000.0000.0000.000
43A52SER0-0.019-0.03218.2470.0070.0070.0000.0000.0000.000
44A53LEU0-0.0040.00618.691-0.035-0.0350.0000.0000.0000.000
45A54LEU0-0.012-0.01017.518-0.031-0.0310.0000.0000.0000.000
46A55TYR0-0.036-0.04514.9210.0320.0320.0000.0000.0000.000
47A56SER0-0.016-0.00715.214-0.075-0.0750.0000.0000.0000.000
48A57PRO00.0420.02716.0210.1000.1000.0000.0000.0000.000
49A58SER0-0.013-0.02918.589-0.008-0.0080.0000.0000.0000.000
50A59TRP0-0.053-0.01214.373-0.069-0.0690.0000.0000.0000.000
51A60ALA00.0150.00318.017-0.036-0.0360.0000.0000.0000.000
52A61GLU-1-0.748-0.82719.3140.4750.4750.0000.0000.0000.000
53A62GLN0-0.022-0.02221.387-0.049-0.0490.0000.0000.0000.000
54A63ARG10.8490.90721.247-0.406-0.4060.0000.0000.0000.000
55A64GLY0-0.0110.00925.089-0.017-0.0170.0000.0000.0000.000
56A70GLY0-0.014-0.01627.539-0.016-0.0160.0000.0000.0000.000
57A71ARG10.7870.88727.852-0.178-0.1780.0000.0000.0000.000
58A72LEU00.0350.02421.969-0.004-0.0040.0000.0000.0000.000
59A80THR0-0.022-0.01422.3910.0110.0110.0000.0000.0000.000
60A81SER0-0.0050.00217.119-0.011-0.0110.0000.0000.0000.000
61A82SER0-0.010-0.00817.732-0.051-0.0510.0000.0000.0000.000
62A83ALA00.0180.03414.5000.0430.0430.0000.0000.0000.000
63A84ALA00.0000.00215.116-0.082-0.0820.0000.0000.0000.000
64A84SER00.003-0.00615.2520.0810.0810.0000.0000.0000.000
65A84ASN0-0.027-0.00612.958-0.071-0.0710.0000.0000.0000.000
66A84GLU-1-0.843-0.9228.9891.4291.4290.0000.0000.0000.000
67A85SER00.011-0.0318.344-0.424-0.4240.0000.0000.0000.000
68A86ARG10.8180.9359.518-0.221-0.2210.0000.0000.0000.000
69A87SER0-0.031-0.04712.0380.0390.0390.0000.0000.0000.000
70A88SER0-0.013-0.00813.722-0.049-0.0490.0000.0000.0000.000
71A89LEU0-0.0180.00616.3380.0280.0280.0000.0000.0000.000
72A90HIS10.8810.95518.047-0.336-0.3360.0000.0000.0000.000
73A91ILE00.008-0.01520.7110.0210.0210.0000.0000.0000.000
74A92SER00.0030.00424.214-0.023-0.0230.0000.0000.0000.000
75A93SER0-0.027-0.02227.8320.0040.0040.0000.0000.0000.000
76A94SER0-0.049-0.02326.6610.0030.0030.0000.0000.0000.000
77A95GLN00.023-0.00428.631-0.012-0.0120.0000.0000.0000.000
78A96ILE00.0800.03229.0710.0120.0120.0000.0000.0000.000
79A97THR0-0.026-0.00429.186-0.001-0.0010.0000.0000.0000.000
80A98ASP-1-0.792-0.86025.2680.1950.1950.0000.0000.0000.000
81A99SER00.0380.03124.1650.0130.0130.0000.0000.0000.000
82A100GLY0-0.059-0.02722.5900.0090.0090.0000.0000.0000.000
83A101THR0-0.0270.00116.142-0.027-0.0270.0000.0000.0000.000
84A102TYR0-0.023-0.03116.9050.0410.0410.0000.0000.0000.000
85A103LEU00.0010.00411.899-0.004-0.0040.0000.0000.0000.000
86A105ALA00.0130.0008.5670.1450.1450.0000.0000.0000.000
87A106ILE0-0.0080.0094.841-0.247-0.2470.0000.0000.0000.000
88A107ALA00.0550.0267.9140.1320.1320.0000.0000.0000.000
89A108SER00.0440.0256.545-0.347-0.3470.0000.0000.0000.000
90A109SER00.011-0.0068.622-0.305-0.3050.0000.0000.0000.000
91A110SER00.0070.00312.2620.0400.0400.0000.0000.0000.000
92A113PHE00.0130.00514.572-0.060-0.0600.0000.0000.0000.000
93A114SER0-0.044-0.0209.442-0.161-0.1610.0000.0000.0000.000
94A115LYS10.9000.9416.483-1.523-1.5230.0000.0000.0000.000
95A116LEU00.0410.0168.8070.2340.2340.0000.0000.0000.000
96A117VAL0-0.051-0.0152.400-0.849-0.4150.722-0.271-0.8850.001
97A118PHE00.0210.0025.854-0.004-0.0040.0000.0000.0000.000
98A119GLY00.0350.0206.1720.5720.5720.0000.0000.0000.000
99A120GLN0-0.066-0.0556.4160.0000.0000.0000.0000.0000.000
100A121GLY0-0.0190.0019.138-0.102-0.1020.0000.0000.0000.000
101A122THR0-0.037-0.02412.313-0.062-0.0620.0000.0000.0000.000
102A123SER0-0.063-0.02115.0480.0230.0230.0000.0000.0000.000
103A124LEU00.0370.00418.398-0.023-0.0230.0000.0000.0000.000
104A125SER0-0.0150.00021.4730.0050.0050.0000.0000.0000.000
105A126VAL00.0180.00825.114-0.009-0.0090.0000.0000.0000.000
106A127VAL00.004-0.00127.8920.0010.0010.0000.0000.0000.000
107A128PRO00.0650.02931.0300.0010.0010.0000.0000.0000.000
108A129ASN0-0.041-0.01134.607-0.012-0.0120.0000.0000.0000.000
109A130ILE0-0.0150.00036.8730.0010.0010.0000.0000.0000.000
110A131GLN0-0.040-0.01939.819-0.005-0.0050.0000.0000.0000.000
111A132ASN0-0.055-0.03142.654-0.001-0.0010.0000.0000.0000.000
112A133PRO0-0.0130.00241.9260.0020.0020.0000.0000.0000.000
113A134ASP-1-0.923-0.96043.9110.0200.0200.0000.0000.0000.000
114A135PRO0-0.013-0.00543.2790.0010.0010.0000.0000.0000.000
115A136ALA00.0300.03044.726-0.003-0.0030.0000.0000.0000.000
116A137VAL0-0.035-0.01844.5020.0020.0020.0000.0000.0000.000
117A138TYR00.0270.01246.822-0.002-0.0020.0000.0000.0000.000
118A139GLN00.0400.00647.9280.0000.0000.0000.0000.0000.000
119A140LEU0-0.026-0.00846.4140.0010.0010.0000.0000.0000.000
120A141ARG10.8590.90650.092-0.020-0.0200.0000.0000.0000.000
121A142ASP-1-0.931-0.94650.9240.0320.0320.0000.0000.0000.000
122A150VAL0-0.028-0.02144.494-0.001-0.0010.0000.0000.0000.000
123A151CYS0-0.046-0.02645.237-0.002-0.0020.0000.0000.0000.000
124A152LEU00.012-0.00142.2420.0020.0020.0000.0000.0000.000
125A153PHE00.0150.02938.916-0.001-0.0010.0000.0000.0000.000
126A154THR00.011-0.06041.1520.0050.0050.0000.0000.0000.000
127A155ASP-1-0.793-0.86141.7190.0360.0360.0000.0000.0000.000
128A156PHE00.0160.02536.222-0.001-0.0010.0000.0000.0000.000
129A157ASP-1-0.777-0.87937.8200.0200.0200.0000.0000.0000.000
130A158SER00.010-0.03133.659-0.003-0.0030.0000.0000.0000.000
131A159GLN0-0.100-0.05633.521-0.003-0.0030.0000.0000.0000.000
132A160THR0-0.019-0.00234.081-0.007-0.0070.0000.0000.0000.000
133A161ASN0-0.056-0.03230.9890.0130.0130.0000.0000.0000.000
134A162VAL00.0510.03533.072-0.004-0.0040.0000.0000.0000.000
135A163SER0-0.057-0.03232.820-0.006-0.0060.0000.0000.0000.000
136A164GLN00.0120.00331.1120.0020.0020.0000.0000.0000.000
137A165SER00.0450.03135.535-0.007-0.0070.0000.0000.0000.000
138A166LYS10.9040.94636.3970.0430.0430.0000.0000.0000.000
139A167ASP-1-0.868-0.91239.003-0.015-0.0150.0000.0000.0000.000
140A168SER0-0.003-0.02139.7010.0020.0020.0000.0000.0000.000
141A169ASP-1-0.857-0.89940.739-0.004-0.0040.0000.0000.0000.000
142A170VAL0-0.031-0.01241.5320.0040.0040.0000.0000.0000.000
143A171TYR0-0.021-0.00138.500-0.001-0.0010.0000.0000.0000.000
144A172ILE0-0.004-0.01637.0540.0010.0010.0000.0000.0000.000
145A173THR0-0.067-0.02734.8050.0000.0000.0000.0000.0000.000
146A174ASP-1-0.821-0.91229.7930.0270.0270.0000.0000.0000.000
147A175LYS10.8230.90831.196-0.025-0.0250.0000.0000.0000.000
148A176CYS0-0.086-0.03132.2110.0070.0070.0000.0000.0000.000
149A177VAL00.0350.01132.424-0.005-0.0050.0000.0000.0000.000
150A178LEU0-0.056-0.01135.1920.0080.0080.0000.0000.0000.000
151A179ASP-1-0.820-0.95037.1390.0900.0900.0000.0000.0000.000
152A180MET0-0.0270.00139.1540.0030.0030.0000.0000.0000.000
153A181ARG10.9810.97438.106-0.103-0.1030.0000.0000.0000.000
154A182SER0-0.076-0.04242.3340.0010.0010.0000.0000.0000.000
155A183MET0-0.064-0.02945.498-0.003-0.0030.0000.0000.0000.000
156A184ASP-1-0.926-0.96140.9890.0760.0760.0000.0000.0000.000
157A185PHE00.0070.03343.214-0.001-0.0010.0000.0000.0000.000
158A186LYS10.8640.93836.368-0.080-0.0800.0000.0000.0000.000
159A187SER0-0.020-0.02039.337-0.004-0.0040.0000.0000.0000.000
160A188ASN0-0.033-0.02335.3560.0110.0110.0000.0000.0000.000
161A189SER00.002-0.00237.163-0.003-0.0030.0000.0000.0000.000
162A190ALA00.0210.01036.7960.0040.0040.0000.0000.0000.000
163A191VAL0-0.006-0.00538.335-0.002-0.0020.0000.0000.0000.000
164A192ALA00.0190.01339.437-0.001-0.0010.0000.0000.0000.000
165A193TRP0-0.033-0.04138.6440.0010.0010.0000.0000.0000.000
166A194SER00.0250.01743.230-0.001-0.0010.0000.0000.0000.000
167A195ASN0-0.059-0.02845.7280.0030.0030.0000.0000.0000.000
168A196LYS10.7970.87246.2750.0070.0070.0000.0000.0000.000
169A197SER0-0.039-0.02950.4550.0010.0010.0000.0000.0000.000
170A198ASP-1-0.870-0.93450.727-0.006-0.0060.0000.0000.0000.000
171A199PHE0-0.0090.01844.422-0.001-0.0010.0000.0000.0000.000
172A200ALA00.0360.00349.1550.0020.0020.0000.0000.0000.000
173A202ALA00.0150.00847.6620.0000.0000.0000.0000.0000.000
174A203ASN0-0.012-0.00547.348-0.003-0.0030.0000.0000.0000.000
175A204ALA0-0.047-0.00644.527-0.002-0.0020.0000.0000.0000.000
176A205PHE00.0570.01239.8510.0010.0010.0000.0000.0000.000
177A206ASN00.0250.01041.1120.0000.0000.0000.0000.0000.000
178A207ASN0-0.066-0.02636.988-0.004-0.0040.0000.0000.0000.000
179A208SER00.0120.01137.118-0.002-0.0020.0000.0000.0000.000
180A209ILE0-0.015-0.00436.054-0.001-0.0010.0000.0000.0000.000
181A210ILE0-0.019-0.00938.2080.0030.0030.0000.0000.0000.000
182A211PRO00.0370.02040.398-0.003-0.0030.0000.0000.0000.000
183A212GLU-1-0.914-0.94443.119-0.006-0.0060.0000.0000.0000.000
184A213ASP-1-0.938-0.96846.0600.0060.0060.0000.0000.0000.000
185A214THR0-0.078-0.05144.7680.0030.0030.0000.0000.0000.000
186A215PHE00.0100.00247.082-0.002-0.0020.0000.0000.0000.000
187A216PHE00.020-0.00246.5440.0020.0020.0000.0000.0000.000
188A217PRO0-0.035-0.00451.055-0.001-0.0010.0000.0000.0000.000
189A218SER0-0.049-0.01954.220-0.001-0.0010.0000.0000.0000.000