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

tag_button

FMODB ID: QY78Y

Calculation Name: 3FS3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FS3

Chain ID: A

ChEMBL ID:

UniProt ID: Q8I608

Base Structure: X-ray

Registration Date: 2023-06-21

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2300679.512332
FMO2-HF: Nuclear repulsion 2217835.883727
FMO2-HF: Total energy -82843.628605
FMO2-MP2: Total energy -83090.303902


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:33:THR)


Summations of interaction energy for fragment #1(A:33:THR)
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.
-7.34-2.4450.854-2.071-3.6780.01
Interaction energy analysis for fragmet #1(A:33:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.045
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].
3A35LEU0-0.0110.0072.488-1.4661.7340.332-1.394-2.1380.003
4A36THR00.018-0.0084.894-0.066-0.040-0.001-0.009-0.0160.000
5A37GLU-1-0.798-0.9126.9802.7272.7270.0000.0000.0000.000
6A38GLU-1-0.817-0.8748.6841.2791.2790.0000.0000.0000.000
7A39GLN0-0.019-0.0176.9390.1350.1350.0000.0000.0000.000
8A40LYS10.7950.8942.939-4.033-2.6040.522-0.635-1.3160.007
9A41GLU-1-0.819-0.9055.9911.5511.597-0.0010.000-0.0450.000
10A42THR0-0.083-0.0449.638-0.405-0.4050.0000.0000.0000.000
11A43LEU00.0120.0083.819-0.579-0.3850.002-0.033-0.1630.000
12A44LYS10.8450.9046.639-3.257-3.2570.0000.0000.0000.000
13A45LYS10.9570.9879.525-1.421-1.4210.0000.0000.0000.000
14A46LEU00.0430.02110.503-0.180-0.1800.0000.0000.0000.000
15A47LYS10.9080.9548.455-1.456-1.4560.0000.0000.0000.000
16A48LEU00.0090.01711.463-0.161-0.1610.0000.0000.0000.000
17A49TYR00.0460.00614.566-0.069-0.0690.0000.0000.0000.000
18A50GLN0-0.0210.00813.731-0.055-0.0550.0000.0000.0000.000
19A51LYS10.8450.90715.386-0.544-0.5440.0000.0000.0000.000
20A52GLU-1-0.865-0.92616.9350.4130.4130.0000.0000.0000.000
21A53TYR0-0.071-0.05518.921-0.039-0.0390.0000.0000.0000.000
22A54TYR00.0290.00315.484-0.007-0.0070.0000.0000.0000.000
23A55ASP-1-0.865-0.89920.9300.3260.3260.0000.0000.0000.000
24A56TYR0-0.065-0.03523.137-0.053-0.0530.0000.0000.0000.000
25A57GLU-1-0.851-0.90222.2420.2940.2940.0000.0000.0000.000
26A58SER00.006-0.01923.808-0.028-0.0280.0000.0000.0000.000
27A59LYS10.8040.89426.017-0.309-0.3090.0000.0000.0000.000
28A60PHE00.0540.02628.682-0.019-0.0190.0000.0000.0000.000
29A61GLU-1-0.938-0.96627.9730.1660.1660.0000.0000.0000.000
30A62TYR0-0.004-0.00130.334-0.018-0.0180.0000.0000.0000.000
31A63GLU-1-0.925-0.97332.5610.1660.1660.0000.0000.0000.000
32A64LEU0-0.034-0.00732.329-0.014-0.0140.0000.0000.0000.000
33A65PHE0-0.018-0.01830.871-0.012-0.0120.0000.0000.0000.000
34A66LEU0-0.0050.00236.060-0.010-0.0100.0000.0000.0000.000
35A67LEU0-0.035-0.01638.163-0.009-0.0090.0000.0000.0000.000
36A68ARG10.9490.96635.294-0.120-0.1200.0000.0000.0000.000
37A69GLN00.0250.01839.569-0.005-0.0050.0000.0000.0000.000
38A70LYS10.9610.99442.172-0.102-0.1020.0000.0000.0000.000
39A71TYR0-0.013-0.01943.299-0.003-0.0030.0000.0000.0000.000
40A72HIS0-0.0190.00943.955-0.003-0.0030.0000.0000.0000.000
41A73ASP-1-0.875-0.95145.8460.0700.0700.0000.0000.0000.000
42A74LEU0-0.091-0.04547.848-0.003-0.0030.0000.0000.0000.000
43A75TYR0-0.013-0.01545.602-0.002-0.0020.0000.0000.0000.000
44A76GLY00.0430.03950.210-0.003-0.0030.0000.0000.0000.000
45A77PRO00.0400.00951.844-0.003-0.0030.0000.0000.0000.000
46A78ILE0-0.076-0.03852.675-0.002-0.0020.0000.0000.0000.000
47A79TYR00.0100.00348.426-0.003-0.0030.0000.0000.0000.000
48A80ASP-1-0.830-0.89955.0880.0420.0420.0000.0000.0000.000
49A81LYS10.9130.95857.545-0.052-0.0520.0000.0000.0000.000
50A82ARG10.8280.92953.322-0.047-0.0470.0000.0000.0000.000
51A83ARG10.8360.91157.675-0.040-0.0400.0000.0000.0000.000
52A84GLU-1-0.860-0.93860.4270.0330.0330.0000.0000.0000.000
53A85ALA0-0.026-0.01463.036-0.001-0.0010.0000.0000.0000.000
54A86LEU0-0.034-0.00760.090-0.001-0.0010.0000.0000.0000.000
55A87VAL0-0.032-0.02662.475-0.002-0.0020.0000.0000.0000.000
56A88GLY0-0.0060.02065.501-0.001-0.0010.0000.0000.0000.000
57A89ASN0-0.054-0.04966.3730.0010.0010.0000.0000.0000.000
58A90GLY00.0330.01469.139-0.001-0.0010.0000.0000.0000.000
59A91GLU-1-0.948-0.95967.8300.0240.0240.0000.0000.0000.000
60A92ALA0-0.0050.00169.144-0.001-0.0010.0000.0000.0000.000
61A93LYS10.8960.94168.718-0.014-0.0140.0000.0000.0000.000
62A94ILE0-0.004-0.00767.528-0.001-0.0010.0000.0000.0000.000
63A95GLY00.0340.02964.1460.0010.0010.0000.0000.0000.000
64A96THR0-0.062-0.04861.8550.0000.0000.0000.0000.0000.000
65A97PRO0-0.0090.00864.9260.0000.0000.0000.0000.0000.000
66A98ASN0-0.055-0.02967.455-0.002-0.0020.0000.0000.0000.000
67A99LEU0-0.083-0.03863.8910.0000.0000.0000.0000.0000.000
68A100PRO00.0500.02565.6110.0000.0000.0000.0000.0000.000
69A101GLU-1-0.825-0.90064.3520.0210.0210.0000.0000.0000.000
70A102PHE0-0.0070.00458.1470.0010.0010.0000.0000.0000.000
71A103TRP00.008-0.02454.5170.0020.0020.0000.0000.0000.000
72A104LEU00.0280.03157.9650.0010.0010.0000.0000.0000.000
73A105ARG10.8780.92059.198-0.023-0.0230.0000.0000.0000.000
74A106ALA0-0.021-0.01156.2250.0000.0000.0000.0000.0000.000
75A107LEU0-0.027-0.02353.2060.0010.0010.0000.0000.0000.000
76A108ARG10.7990.87254.980-0.018-0.0180.0000.0000.0000.000
77A109ASN0-0.059-0.01657.036-0.002-0.0020.0000.0000.0000.000
78A110ASN0-0.029-0.01849.6340.0010.0010.0000.0000.0000.000
79A111ASN0-0.004-0.00850.248-0.002-0.0020.0000.0000.0000.000
80A112THR00.013-0.00645.926-0.002-0.0020.0000.0000.0000.000
81A113VAL0-0.005-0.01249.065-0.002-0.0020.0000.0000.0000.000
82A114SER0-0.014-0.00851.177-0.003-0.0030.0000.0000.0000.000
83A115HIS0-0.039-0.02549.536-0.003-0.0030.0000.0000.0000.000
84A116VAL0-0.0270.00349.450-0.002-0.0020.0000.0000.0000.000
85A117ILE0-0.038-0.01452.8210.0000.0000.0000.0000.0000.000
86A118GLU-1-0.873-0.93256.3590.0100.0100.0000.0000.0000.000
87A119ASP-1-0.873-0.94259.3100.0120.0120.0000.0000.0000.000
88A120HIS0-0.037-0.04059.0000.0000.0000.0000.0000.0000.000
89A121ASP-1-0.714-0.83257.6490.0130.0130.0000.0000.0000.000
90A122GLU-1-0.833-0.90360.5550.0180.0180.0000.0000.0000.000
91A123GLU-1-0.948-0.98262.5950.0110.0110.0000.0000.0000.000
92A124ILE0-0.014-0.01060.8950.0000.0000.0000.0000.0000.000
93A125LEU00.005-0.00856.9620.0010.0010.0000.0000.0000.000
94A126VAL0-0.0160.00561.0300.0020.0020.0000.0000.0000.000
95A127TYR0-0.026-0.01763.5300.0000.0000.0000.0000.0000.000
96A128LEU0-0.050-0.00556.3120.0010.0010.0000.0000.0000.000
97A129ASN00.0640.00860.3990.0010.0010.0000.0000.0000.000
98A130ASP-1-0.868-0.95256.4390.0390.0390.0000.0000.0000.000
99A131ILE0-0.0100.00951.616-0.002-0.0020.0000.0000.0000.000
100A132ARG10.8410.92250.568-0.043-0.0430.0000.0000.0000.000
101A133CYS00.0300.01044.835-0.001-0.0010.0000.0000.0000.000
102A134ASP-1-0.823-0.87246.2120.0530.0530.0000.0000.0000.000
103A135TYR00.0260.01438.974-0.001-0.0010.0000.0000.0000.000
104A136ILE0-0.0090.00839.461-0.003-0.0030.0000.0000.0000.000
105A137LYS10.8120.89141.727-0.051-0.0510.0000.0000.0000.000
106A145GLY00.0070.00136.611-0.001-0.0010.0000.0000.0000.000
107A146PHE0-0.024-0.02837.9980.0030.0030.0000.0000.0000.000
108A147ILE00.0130.01041.562-0.004-0.0040.0000.0000.0000.000
109A148LEU00.0030.00945.0130.0020.0020.0000.0000.0000.000
110A149SER0-0.013-0.02047.754-0.003-0.0030.0000.0000.0000.000
111A150PHE00.0210.01149.8440.0020.0020.0000.0000.0000.000
112A151TYR00.0230.01353.658-0.001-0.0010.0000.0000.0000.000
113A152PHE00.026-0.00256.5390.0000.0000.0000.0000.0000.000
114A153ALA00.0170.02160.9400.0000.0000.0000.0000.0000.000
115A154THR0-0.018-0.02564.588-0.001-0.0010.0000.0000.0000.000
116A155ASN00.0170.02163.172-0.001-0.0010.0000.0000.0000.000
117A156PRO0-0.018-0.01167.010-0.001-0.0010.0000.0000.0000.000
118A157PHE0-0.022-0.01363.314-0.001-0.0010.0000.0000.0000.000
119A158PHE00.013-0.00359.386-0.001-0.0010.0000.0000.0000.000
120A159SER0-0.036-0.00962.8130.0010.0010.0000.0000.0000.000
121A160ASN0-0.023-0.01657.5860.0000.0000.0000.0000.0000.000
122A161SER00.0450.02260.1340.0000.0000.0000.0000.0000.000
123A162VAL0-0.032-0.02254.3760.0020.0020.0000.0000.0000.000
124A163LEU0-0.0120.02453.966-0.001-0.0010.0000.0000.0000.000
125A164THR0-0.006-0.02449.5470.0020.0020.0000.0000.0000.000
126A165LYS10.8160.88944.439-0.026-0.0260.0000.0000.0000.000
127A166THR0-0.035-0.01041.8120.0040.0040.0000.0000.0000.000
128A167TYR00.002-0.02939.434-0.003-0.0030.0000.0000.0000.000
129A168HIS0-0.014-0.00836.9010.0100.0100.0000.0000.0000.000
130A169MET0-0.008-0.01333.943-0.002-0.0020.0000.0000.0000.000
131A170LYS10.9420.98327.232-0.068-0.0680.0000.0000.0000.000
132A179VAL0-0.001-0.01228.284-0.002-0.0020.0000.0000.0000.000
133A180LEU00.0280.01131.3450.0030.0030.0000.0000.0000.000
134A181LEU0-0.082-0.03130.642-0.002-0.0020.0000.0000.0000.000
135A182HIS0-0.078-0.05334.311-0.007-0.0070.0000.0000.0000.000
136A183THR00.0240.01638.0090.0040.0040.0000.0000.0000.000
137A184GLU-1-0.846-0.91541.5970.0230.0230.0000.0000.0000.000
138A185ALA00.0320.02544.8920.0030.0030.0000.0000.0000.000
139A186THR0-0.069-0.01848.511-0.002-0.0020.0000.0000.0000.000
140A187VAL00.0000.00251.875-0.001-0.0010.0000.0000.0000.000
141A188ILE00.0220.01654.0310.0020.0020.0000.0000.0000.000
142A189ASP-1-0.880-0.92356.9990.0090.0090.0000.0000.0000.000
143A190TRP0-0.020-0.03257.4510.0010.0010.0000.0000.0000.000
144A191TYR0-0.021-0.00362.215-0.001-0.0010.0000.0000.0000.000
145A192ASP-1-0.813-0.91565.6280.0020.0020.0000.0000.0000.000
146A193ASN0-0.112-0.07267.3780.0000.0000.0000.0000.0000.000
147A194LYS10.8780.94265.296-0.006-0.0060.0000.0000.0000.000
148A195ASN00.0390.03058.9340.0010.0010.0000.0000.0000.000
149A196ILE00.0180.01659.386-0.002-0.0020.0000.0000.0000.000
150A197LEU00.0240.03854.895-0.001-0.0010.0000.0000.0000.000
151A198LYS10.8540.93056.091-0.002-0.0020.0000.0000.0000.000
152A199LYS11.0051.01060.8650.0000.0000.0000.0000.0000.000
153A222ARG10.8110.90657.446-0.005-0.0050.0000.0000.0000.000
154A223ASP-1-0.863-0.92353.5930.0030.0030.0000.0000.0000.000
155A224SER0-0.039-0.05654.6210.0000.0000.0000.0000.0000.000
156A225PHE00.0700.03652.0020.0000.0000.0000.0000.0000.000
157A226PHE0-0.025-0.03152.8130.0010.0010.0000.0000.0000.000
158A227HIS0-0.044-0.03050.8630.0000.0000.0000.0000.0000.000
159A228PHE00.0140.03246.0600.0000.0000.0000.0000.0000.000
160A229PHE0-0.029-0.01248.5090.0020.0020.0000.0000.0000.000
161A230THR0-0.034-0.02946.886-0.003-0.0030.0000.0000.0000.000
162A231SER0-0.017-0.00944.7680.0030.0030.0000.0000.0000.000
163A232HIS00.0210.01541.237-0.002-0.0020.0000.0000.0000.000
164A233LYS10.9360.95137.6230.0030.0030.0000.0000.0000.000
165A234VAL00.0660.04833.2600.0020.0020.0000.0000.0000.000
166A247GLU-1-0.946-0.98039.695-0.040-0.0400.0000.0000.0000.000
167A248VAL0-0.005-0.01534.0250.0040.0040.0000.0000.0000.000
168A249ALA00.0780.03537.5040.0040.0040.0000.0000.0000.000
169A250GLN0-0.021-0.00538.4700.0010.0010.0000.0000.0000.000
170A251LEU0-0.012-0.00738.8140.0040.0040.0000.0000.0000.000
171A252GLU-1-0.928-0.96033.777-0.002-0.0020.0000.0000.0000.000
172A253MET00.0380.02637.8710.0040.0040.0000.0000.0000.000
173A254ILE00.000-0.00740.7720.0030.0030.0000.0000.0000.000
174A255ILE0-0.047-0.02737.4250.0040.0040.0000.0000.0000.000
175A256GLU-1-0.946-0.96937.0690.0260.0260.0000.0000.0000.000
176A257GLY00.0280.02039.7720.0040.0040.0000.0000.0000.000
177A258ASP-1-0.821-0.88542.7770.0260.0260.0000.0000.0000.000
178A259TYR00.041-0.00537.5180.0040.0040.0000.0000.0000.000
179A260GLU-1-0.876-0.91041.3570.0370.0370.0000.0000.0000.000
180A261VAL00.0370.02542.6180.0030.0030.0000.0000.0000.000
181A262ALA0-0.019-0.00442.7840.0020.0020.0000.0000.0000.000
182A263LEU0-0.024-0.01139.0530.0030.0030.0000.0000.0000.000
183A264THR00.002-0.01042.7550.0040.0040.0000.0000.0000.000
184A265ILE00.009-0.00845.8720.0010.0010.0000.0000.0000.000
185A266LYS10.8090.89340.175-0.069-0.0690.0000.0000.0000.000
186A267GLU-1-0.889-0.93840.4250.0780.0780.0000.0000.0000.000
187A268ARG10.8840.94945.067-0.055-0.0550.0000.0000.0000.000
188A269ILE00.0100.00948.1920.0000.0000.0000.0000.0000.000
189A270ILE00.0110.01348.2780.0000.0000.0000.0000.0000.000
190A271PRO00.0060.00547.103-0.001-0.0010.0000.0000.0000.000
191A272TYR0-0.005-0.00447.5960.0010.0010.0000.0000.0000.000
192A273ALA00.0100.02552.817-0.002-0.0020.0000.0000.0000.000
193A274VAL00.0270.00155.335-0.002-0.0020.0000.0000.0000.000
194A275ASP-1-0.863-0.93755.0250.0460.0460.0000.0000.0000.000
195A276TYR0-0.001-0.00650.3360.0000.0000.0000.0000.0000.000
196A277TYR0-0.029-0.00156.422-0.002-0.0020.0000.0000.0000.000
197A278LEU0-0.055-0.03759.949-0.002-0.0020.0000.0000.0000.000
198A279GLY00.0360.02958.422-0.001-0.0010.0000.0000.0000.000
199A280ILE0-0.105-0.03457.3430.0000.0000.0000.0000.0000.000
200A281ILE0-0.049-0.01751.5620.0030.0030.0000.0000.0000.000