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: Z6R2N

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2296853.607921
FMO2-HF: Nuclear repulsion 2214011.413293
FMO2-HF: Total energy -82842.194627
FMO2-MP2: Total energy -83088.945737


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.
-13.595-8.4291.277-2.388-4.0550.008
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 : -0.016 / q_NPA : -0.025
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].
3A35LEU0-0.036-0.0082.268-2.3771.1261.187-1.695-2.9950.002
4A36THR00.0740.0284.7940.0230.066-0.001-0.010-0.0320.000
5A37GLU-1-0.840-0.9577.0033.4173.4170.0000.0000.0000.000
6A38GLU-1-0.927-0.9548.7931.3641.3640.0000.0000.0000.000
7A39GLN00.0370.0136.6910.2320.2320.0000.0000.0000.000
8A40LYS10.8340.9343.186-8.553-7.1720.087-0.647-0.8210.006
9A41GLU-1-0.904-0.9556.0061.4601.4600.0000.0000.0000.000
10A42THR0-0.027-0.0089.134-0.416-0.4160.0000.0000.0000.000
11A43LEU0-0.009-0.0053.736-0.545-0.3060.004-0.036-0.2070.000
12A44LYS10.9260.9595.405-5.172-5.1720.0000.0000.0000.000
13A45LYS10.9830.9989.143-1.340-1.3400.0000.0000.0000.000
14A46LEU00.0340.02110.165-0.203-0.2030.0000.0000.0000.000
15A47LYS10.9000.9628.590-0.989-0.9890.0000.0000.0000.000
16A48LEU00.0100.01811.535-0.162-0.1620.0000.0000.0000.000
17A49TYR00.0600.00514.445-0.057-0.0570.0000.0000.0000.000
18A50GLN0-0.0210.00113.903-0.042-0.0420.0000.0000.0000.000
19A51LYS10.8570.92915.491-0.391-0.3910.0000.0000.0000.000
20A52GLU-1-0.868-0.94517.0040.3450.3450.0000.0000.0000.000
21A53TYR0-0.064-0.01918.923-0.038-0.0380.0000.0000.0000.000
22A54TYR00.008-0.01115.641-0.017-0.0170.0000.0000.0000.000
23A55ASP-1-0.910-0.93220.8830.2620.2620.0000.0000.0000.000
24A56TYR0-0.042-0.03123.258-0.040-0.0400.0000.0000.0000.000
25A57GLU-1-0.893-0.95522.8550.0940.0940.0000.0000.0000.000
26A58SER0-0.003-0.00624.051-0.024-0.0240.0000.0000.0000.000
27A59LYS10.9060.94826.419-0.204-0.2040.0000.0000.0000.000
28A60PHE00.0290.02628.555-0.012-0.0120.0000.0000.0000.000
29A61GLU-1-0.917-0.96928.1800.0450.0450.0000.0000.0000.000
30A62TYR0-0.024-0.00930.432-0.012-0.0120.0000.0000.0000.000
31A63GLU-1-0.928-0.97732.6250.0950.0950.0000.0000.0000.000
32A64LEU0-0.042-0.00632.712-0.009-0.0090.0000.0000.0000.000
33A65PHE0-0.031-0.02431.197-0.008-0.0080.0000.0000.0000.000
34A66LEU0-0.0020.00236.208-0.006-0.0060.0000.0000.0000.000
35A67LEU0-0.021-0.00138.362-0.005-0.0050.0000.0000.0000.000
36A68ARG10.9720.96235.463-0.030-0.0300.0000.0000.0000.000
37A69GLN00.0220.02839.639-0.006-0.0060.0000.0000.0000.000
38A70LYS10.9880.99842.244-0.050-0.0500.0000.0000.0000.000
39A71TYR0-0.028-0.03643.6960.0000.0000.0000.0000.0000.000
40A72HIS0-0.0050.02544.103-0.002-0.0020.0000.0000.0000.000
41A73ASP-1-0.898-0.96046.0170.0230.0230.0000.0000.0000.000
42A74LEU0-0.114-0.05148.1520.0000.0000.0000.0000.0000.000
43A75TYR0-0.016-0.02045.764-0.001-0.0010.0000.0000.0000.000
44A76GLY00.0440.03850.496-0.002-0.0020.0000.0000.0000.000
45A77PRO00.0480.01452.148-0.002-0.0020.0000.0000.0000.000
46A78ILE0-0.069-0.04153.280-0.001-0.0010.0000.0000.0000.000
47A79TYR00.0010.00148.787-0.002-0.0020.0000.0000.0000.000
48A80ASP-1-0.883-0.94655.3470.0070.0070.0000.0000.0000.000
49A81LYS10.9090.95957.803-0.016-0.0160.0000.0000.0000.000
50A82ARG10.9020.95753.742-0.003-0.0030.0000.0000.0000.000
51A83ARG10.9781.00058.028-0.004-0.0040.0000.0000.0000.000
52A84GLU-1-0.963-0.97760.4880.0040.0040.0000.0000.0000.000
53A85ALA00.0100.00663.3720.0000.0000.0000.0000.0000.000
54A86LEU0-0.035-0.01360.452-0.001-0.0010.0000.0000.0000.000
55A87VAL0-0.043-0.04262.525-0.001-0.0010.0000.0000.0000.000
56A88GLY00.0020.02565.4800.0000.0000.0000.0000.0000.000
57A89ASN0-0.056-0.05166.8390.0000.0000.0000.0000.0000.000
58A90GLY00.0320.00969.5550.0000.0000.0000.0000.0000.000
59A91GLU-1-0.937-0.95268.074-0.003-0.0030.0000.0000.0000.000
60A92ALA0-0.018-0.00369.2870.0000.0000.0000.0000.0000.000
61A93LYS10.8910.93468.9400.0090.0090.0000.0000.0000.000
62A94ILE00.009-0.00567.795-0.001-0.0010.0000.0000.0000.000
63A95GLY00.0670.04464.3070.0010.0010.0000.0000.0000.000
64A96THR0-0.061-0.04362.0180.0000.0000.0000.0000.0000.000
65A97PRO0-0.0310.00365.0790.0000.0000.0000.0000.0000.000
66A98ASN0-0.062-0.03167.6870.0000.0000.0000.0000.0000.000
67A99LEU0-0.073-0.03963.8920.0010.0010.0000.0000.0000.000
68A100PRO00.0350.00865.563-0.001-0.0010.0000.0000.0000.000
69A101GLU-1-0.843-0.92464.169-0.011-0.0110.0000.0000.0000.000
70A102PHE0-0.0100.01258.0860.0000.0000.0000.0000.0000.000
71A103TRP00.022-0.01754.6930.0000.0000.0000.0000.0000.000
72A104LEU00.0270.03857.857-0.001-0.0010.0000.0000.0000.000
73A105ARG10.9300.94958.8790.0080.0080.0000.0000.0000.000
74A106ALA0-0.026-0.00356.0540.0000.0000.0000.0000.0000.000
75A107LEU0-0.030-0.03353.1390.0000.0000.0000.0000.0000.000
76A108ARG10.8770.93654.5970.0200.0200.0000.0000.0000.000
77A109ASN0-0.086-0.04456.327-0.002-0.0020.0000.0000.0000.000
78A110ASN0-0.023-0.00448.761-0.001-0.0010.0000.0000.0000.000
79A111ASN0-0.003-0.01649.831-0.001-0.0010.0000.0000.0000.000
80A112THR00.0450.02645.5960.0000.0000.0000.0000.0000.000
81A113VAL0-0.005-0.01748.686-0.002-0.0020.0000.0000.0000.000
82A114SER0-0.025-0.00950.840-0.001-0.0010.0000.0000.0000.000
83A115HIS0-0.014-0.01049.0720.0000.0000.0000.0000.0000.000
84A116VAL0-0.0160.00849.147-0.002-0.0020.0000.0000.0000.000
85A117ILE0-0.068-0.02652.4590.0010.0010.0000.0000.0000.000
86A118GLU-1-0.887-0.95355.899-0.032-0.0320.0000.0000.0000.000
87A119ASP-1-0.886-0.94958.813-0.023-0.0230.0000.0000.0000.000
88A120HIS0-0.090-0.06358.8520.0020.0020.0000.0000.0000.000
89A121ASP-1-0.706-0.81357.366-0.028-0.0280.0000.0000.0000.000
90A122GLU-1-0.847-0.92760.420-0.017-0.0170.0000.0000.0000.000
91A123GLU-1-0.956-0.97462.516-0.018-0.0180.0000.0000.0000.000
92A124ILE0-0.009-0.01760.5090.0010.0010.0000.0000.0000.000
93A125LEU00.010-0.01256.9120.0010.0010.0000.0000.0000.000
94A126VAL0-0.0070.02060.8630.0010.0010.0000.0000.0000.000
95A127TYR0-0.054-0.03363.3830.0020.0020.0000.0000.0000.000
96A128LEU0-0.050-0.01256.3340.0010.0010.0000.0000.0000.000
97A129ASN00.0600.00860.3320.0010.0010.0000.0000.0000.000
98A130ASP-1-0.891-0.97856.5660.0000.0000.0000.0000.0000.000
99A131ILE0-0.0020.03351.492-0.002-0.0020.0000.0000.0000.000
100A132ARG10.8420.93651.4150.0010.0010.0000.0000.0000.000
101A133CYS00.0260.00645.119-0.003-0.0030.0000.0000.0000.000
102A134ASP-1-0.902-0.92746.4210.0040.0040.0000.0000.0000.000
103A135TYR00.0270.01439.755-0.004-0.0040.0000.0000.0000.000
104A136ILE0-0.0060.00439.5980.0010.0010.0000.0000.0000.000
105A137LYS10.9010.95141.6890.0010.0010.0000.0000.0000.000
106A145GLY00.004-0.00136.901-0.001-0.0010.0000.0000.0000.000
107A146PHE0-0.023-0.02238.3040.0060.0060.0000.0000.0000.000
108A147ILE0-0.0120.00041.816-0.004-0.0040.0000.0000.0000.000
109A148LEU0-0.0140.00145.1970.0030.0030.0000.0000.0000.000
110A149SER0-0.003-0.01647.905-0.002-0.0020.0000.0000.0000.000
111A150PHE00.0090.00449.8920.0020.0020.0000.0000.0000.000
112A151TYR00.001-0.01153.899-0.001-0.0010.0000.0000.0000.000
113A152PHE00.0260.01256.4430.0000.0000.0000.0000.0000.000
114A153ALA00.0060.02360.9130.0010.0010.0000.0000.0000.000
115A154THR00.015-0.01764.542-0.001-0.0010.0000.0000.0000.000
116A155ASN00.0170.02762.796-0.001-0.0010.0000.0000.0000.000
117A156PRO0-0.037-0.02266.8400.0000.0000.0000.0000.0000.000
118A157PHE0-0.007-0.00963.243-0.001-0.0010.0000.0000.0000.000
119A158PHE00.0250.00859.316-0.002-0.0020.0000.0000.0000.000
120A159SER0-0.0100.00462.7850.0010.0010.0000.0000.0000.000
121A160ASN00.0170.03457.1570.0010.0010.0000.0000.0000.000
122A161SER00.0430.02260.0780.0000.0000.0000.0000.0000.000
123A162VAL0-0.009-0.02254.1410.0010.0010.0000.0000.0000.000
124A163LEU0-0.0080.00253.703-0.001-0.0010.0000.0000.0000.000
125A164THR0-0.013-0.02249.2920.0000.0000.0000.0000.0000.000
126A165LYS10.8860.93844.2440.0370.0370.0000.0000.0000.000
127A166THR0-0.025-0.02241.9610.0040.0040.0000.0000.0000.000
128A167TYR0-0.003-0.04039.524-0.003-0.0030.0000.0000.0000.000
129A168HIS0-0.038-0.02936.9490.0060.0060.0000.0000.0000.000
130A169MET0-0.015-0.02433.943-0.005-0.0050.0000.0000.0000.000
131A170LYS10.9630.99826.9160.0730.0730.0000.0000.0000.000
132A179VAL0-0.004-0.01028.765-0.001-0.0010.0000.0000.0000.000
133A180LEU00.023-0.00431.2770.0070.0070.0000.0000.0000.000
134A181LEU0-0.108-0.03031.105-0.009-0.0090.0000.0000.0000.000
135A182HIS0-0.009-0.00434.274-0.009-0.0090.0000.0000.0000.000
136A183THR00.0270.00637.9060.0050.0050.0000.0000.0000.000
137A184GLU-1-0.891-0.93141.526-0.036-0.0360.0000.0000.0000.000
138A185ALA00.0080.02344.7620.0030.0030.0000.0000.0000.000
139A186THR0-0.0810.01048.198-0.001-0.0010.0000.0000.0000.000
140A187VAL00.0340.01551.583-0.002-0.0020.0000.0000.0000.000
141A188ILE0-0.017-0.01553.8030.0020.0020.0000.0000.0000.000
142A189ASP-1-0.924-0.96856.781-0.025-0.0250.0000.0000.0000.000
143A190TRP0-0.032-0.03357.2460.0020.0020.0000.0000.0000.000
144A191TYR0-0.021-0.01062.0550.0000.0000.0000.0000.0000.000
145A192ASP-1-0.854-0.94765.605-0.024-0.0240.0000.0000.0000.000
146A193ASN0-0.087-0.04767.0730.0000.0000.0000.0000.0000.000
147A194LYS10.8820.94864.7250.0210.0210.0000.0000.0000.000
148A195ASN00.0320.02458.4660.0000.0000.0000.0000.0000.000
149A196ILE00.0430.03558.780-0.001-0.0010.0000.0000.0000.000
150A197LEU0-0.0340.00054.672-0.001-0.0010.0000.0000.0000.000
151A198LYS10.8760.93055.7840.0370.0370.0000.0000.0000.000
152A199LYS10.9650.99660.6800.0310.0310.0000.0000.0000.000
153A222ARG10.9210.97156.9860.0300.0300.0000.0000.0000.000
154A223ASP-1-0.890-0.93953.262-0.043-0.0430.0000.0000.0000.000
155A224SER0-0.057-0.07654.1950.0020.0020.0000.0000.0000.000
156A225PHE00.1090.05251.355-0.002-0.0020.0000.0000.0000.000
157A226PHE0-0.025-0.04052.4470.0000.0000.0000.0000.0000.000
158A227HIS0-0.071-0.03150.437-0.001-0.0010.0000.0000.0000.000
159A228PHE00.0300.02546.217-0.002-0.0020.0000.0000.0000.000
160A229PHE0-0.057-0.02148.000-0.001-0.0010.0000.0000.0000.000
161A230THR0-0.012-0.01046.4360.0000.0000.0000.0000.0000.000
162A231SER0-0.037-0.02244.6260.0000.0000.0000.0000.0000.000
163A232HIS00.0240.01940.852-0.003-0.0030.0000.0000.0000.000
164A233LYS10.9290.95037.7780.0700.0700.0000.0000.0000.000
165A234VAL00.0800.05233.322-0.002-0.0020.0000.0000.0000.000
166A247GLU-1-0.976-0.99639.223-0.109-0.1090.0000.0000.0000.000
167A248VAL00.024-0.00533.7090.0040.0040.0000.0000.0000.000
168A249ALA00.0630.03537.1370.0030.0030.0000.0000.0000.000
169A250GLN0-0.0120.00238.2310.0020.0020.0000.0000.0000.000
170A251LEU00.009-0.01138.3380.0050.0050.0000.0000.0000.000
171A252GLU-1-0.956-0.95233.995-0.109-0.1090.0000.0000.0000.000
172A253MET00.0370.01837.5730.0060.0060.0000.0000.0000.000
173A254ILE0-0.010-0.01340.5160.0050.0050.0000.0000.0000.000
174A255ILE0-0.051-0.02937.2570.0050.0050.0000.0000.0000.000
175A256GLU-1-0.921-0.97336.306-0.077-0.0770.0000.0000.0000.000
176A257GLY00.0500.03039.3280.0050.0050.0000.0000.0000.000
177A258ASP-1-0.866-0.90442.679-0.037-0.0370.0000.0000.0000.000
178A259TYR00.031-0.01437.0230.0060.0060.0000.0000.0000.000
179A260GLU-1-0.923-0.95141.191-0.038-0.0380.0000.0000.0000.000
180A261VAL00.0150.01242.2160.0060.0060.0000.0000.0000.000
181A262ALA0-0.023-0.01443.0160.0040.0040.0000.0000.0000.000
182A263LEU0-0.011-0.00638.8940.0050.0050.0000.0000.0000.000
183A264THR0-0.0040.00642.8280.0050.0050.0000.0000.0000.000
184A265ILE00.007-0.00645.7040.0040.0040.0000.0000.0000.000
185A266LYS10.9250.95840.5490.0090.0090.0000.0000.0000.000
186A267GLU-1-0.969-0.99540.334-0.004-0.0040.0000.0000.0000.000
187A268ARG10.9070.95945.0200.0070.0070.0000.0000.0000.000
188A269ILE0-0.0080.00347.9460.0020.0020.0000.0000.0000.000
189A270ILE00.0060.00948.5580.0020.0020.0000.0000.0000.000
190A271PRO0-0.0330.00246.9730.0020.0020.0000.0000.0000.000
191A272TYR0-0.006-0.00947.0600.0010.0010.0000.0000.0000.000
192A273ALA0-0.0030.02552.655-0.001-0.0010.0000.0000.0000.000
193A274VAL00.041-0.00255.160-0.001-0.0010.0000.0000.0000.000
194A275ASP-1-0.844-0.91754.9800.0040.0040.0000.0000.0000.000
195A276TYR0-0.022-0.00549.860-0.001-0.0010.0000.0000.0000.000
196A277TYR0-0.0350.00856.124-0.001-0.0010.0000.0000.0000.000
197A278LEU0-0.053-0.04759.588-0.001-0.0010.0000.0000.0000.000
198A279GLY00.0170.02057.8740.0000.0000.0000.0000.0000.000
199A280ILE0-0.097-0.03856.9340.0000.0000.0000.0000.0000.000
200A281ILE0-0.048-0.01751.2780.0010.0010.0000.0000.0000.000