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: R9N18

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2296639.384748
FMO2-HF: Nuclear repulsion 2213796.131115
FMO2-HF: Total energy -82843.253633
FMO2-MP2: Total energy -83089.972825


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.
-8.22-3.7360.996-2.02-3.4580.006
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 : -0.018 / q_NPA : -0.024
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].
3A35LEU0-0.0190.0012.170-2.2820.9650.957-1.565-2.6400.003
4A36THR00.0490.0244.719-0.130-0.074-0.001-0.011-0.0430.000
5A37GLU-1-0.830-0.9556.9173.1463.1460.0000.0000.0000.000
6A38GLU-1-0.850-0.9138.7931.3811.3810.0000.0000.0000.000
7A39GLN0-0.012-0.0176.6420.1660.1660.0000.0000.0000.000
8A40LYS10.8120.9173.668-4.644-3.7110.035-0.403-0.5640.003
9A41GLU-1-0.831-0.9115.9411.5531.5530.0000.0000.0000.000
10A42THR0-0.054-0.0229.182-0.401-0.4010.0000.0000.0000.000
11A43LEU00.0040.0043.654-0.633-0.3850.005-0.041-0.2110.000
12A44LYS10.8740.9216.137-3.526-3.5260.0000.0000.0000.000
13A45LYS10.9540.9849.124-1.288-1.2880.0000.0000.0000.000
14A46LEU00.0420.02610.485-0.187-0.1870.0000.0000.0000.000
15A47LYS10.9080.9658.593-0.971-0.9710.0000.0000.0000.000
16A48LEU00.0110.01911.519-0.149-0.1490.0000.0000.0000.000
17A49TYR00.0500.00214.428-0.052-0.0520.0000.0000.0000.000
18A50GLN0-0.025-0.00113.810-0.053-0.0530.0000.0000.0000.000
19A51LYS10.8140.89715.467-0.389-0.3890.0000.0000.0000.000
20A52GLU-1-0.888-0.95316.9910.3360.3360.0000.0000.0000.000
21A53TYR0-0.091-0.06018.851-0.032-0.0320.0000.0000.0000.000
22A54TYR00.0320.00415.228-0.014-0.0140.0000.0000.0000.000
23A55ASP-1-0.873-0.90120.7380.2460.2460.0000.0000.0000.000
24A56TYR0-0.052-0.03323.246-0.040-0.0400.0000.0000.0000.000
25A57GLU-1-0.837-0.90421.9980.1340.1340.0000.0000.0000.000
26A58SER0-0.011-0.01823.733-0.023-0.0230.0000.0000.0000.000
27A59LYS10.8920.94225.904-0.208-0.2080.0000.0000.0000.000
28A60PHE00.0290.02628.338-0.012-0.0120.0000.0000.0000.000
29A61GLU-1-0.923-0.96827.4950.0610.0610.0000.0000.0000.000
30A62TYR0-0.020-0.01129.951-0.012-0.0120.0000.0000.0000.000
31A63GLU-1-0.920-0.97332.2300.1020.1020.0000.0000.0000.000
32A64LEU0-0.047-0.01132.156-0.009-0.0090.0000.0000.0000.000
33A65PHE0-0.024-0.02030.495-0.008-0.0080.0000.0000.0000.000
34A66LEU0-0.0050.00435.680-0.006-0.0060.0000.0000.0000.000
35A67LEU0-0.025-0.00337.935-0.006-0.0060.0000.0000.0000.000
36A68ARG10.9660.96134.870-0.045-0.0450.0000.0000.0000.000
37A69GLN00.0280.03239.161-0.005-0.0050.0000.0000.0000.000
38A70LYS10.9670.99041.734-0.055-0.0550.0000.0000.0000.000
39A71TYR0-0.009-0.02543.1240.0000.0000.0000.0000.0000.000
40A72HIS0-0.0270.02043.634-0.003-0.0030.0000.0000.0000.000
41A73ASP-1-0.879-0.95545.4980.0280.0280.0000.0000.0000.000
42A74LEU0-0.107-0.04947.459-0.001-0.0010.0000.0000.0000.000
43A75TYR0-0.014-0.02045.235-0.001-0.0010.0000.0000.0000.000
44A76GLY00.0440.03949.991-0.002-0.0020.0000.0000.0000.000
45A77PRO00.0520.01351.655-0.002-0.0020.0000.0000.0000.000
46A78ILE0-0.073-0.04552.543-0.001-0.0010.0000.0000.0000.000
47A79TYR00.0000.00148.140-0.002-0.0020.0000.0000.0000.000
48A80ASP-1-0.829-0.90554.8480.0120.0120.0000.0000.0000.000
49A81LYS10.9020.96057.334-0.021-0.0210.0000.0000.0000.000
50A82ARG10.8710.94953.211-0.011-0.0110.0000.0000.0000.000
51A83ARG10.8860.93557.799-0.010-0.0100.0000.0000.0000.000
52A84GLU-1-0.898-0.93660.0320.0080.0080.0000.0000.0000.000
53A85ALA0-0.018-0.00862.871-0.001-0.0010.0000.0000.0000.000
54A86LEU0-0.034-0.01060.021-0.001-0.0010.0000.0000.0000.000
55A87VAL0-0.033-0.03862.130-0.001-0.0010.0000.0000.0000.000
56A88GLY00.0030.02265.055-0.001-0.0010.0000.0000.0000.000
57A89ASN0-0.061-0.05466.4290.0000.0000.0000.0000.0000.000
58A90GLY00.0320.01169.1430.0000.0000.0000.0000.0000.000
59A91GLU-1-0.931-0.94867.7160.0010.0010.0000.0000.0000.000
60A92ALA0-0.017-0.00368.9320.0000.0000.0000.0000.0000.000
61A93LYS10.8920.93668.6060.0050.0050.0000.0000.0000.000
62A94ILE00.008-0.00667.197-0.001-0.0010.0000.0000.0000.000
63A95GLY00.0570.04563.9160.0010.0010.0000.0000.0000.000
64A96THR0-0.061-0.03961.5540.0000.0000.0000.0000.0000.000
65A97PRO0-0.0200.00564.6560.0000.0000.0000.0000.0000.000
66A98ASN0-0.069-0.03767.2230.0000.0000.0000.0000.0000.000
67A99LEU0-0.076-0.03863.5970.0010.0010.0000.0000.0000.000
68A100PRO00.0400.00765.2400.0000.0000.0000.0000.0000.000
69A101GLU-1-0.830-0.90463.878-0.005-0.0050.0000.0000.0000.000
70A102PHE0-0.0060.01157.8560.0000.0000.0000.0000.0000.000
71A103TRP00.019-0.01554.1960.0000.0000.0000.0000.0000.000
72A104LEU00.0230.03557.6370.0000.0000.0000.0000.0000.000
73A105ARG10.9070.93058.6980.0020.0020.0000.0000.0000.000
74A106ALA0-0.026-0.00455.9620.0000.0000.0000.0000.0000.000
75A107LEU0-0.030-0.03452.8000.0000.0000.0000.0000.0000.000
76A108ARG10.8160.89654.4870.0130.0130.0000.0000.0000.000
77A109ASN0-0.068-0.03056.310-0.002-0.0020.0000.0000.0000.000
78A110ASN0-0.029-0.01049.017-0.001-0.0010.0000.0000.0000.000
79A111ASN00.000-0.01350.001-0.001-0.0010.0000.0000.0000.000
80A112THR00.0190.01445.5450.0000.0000.0000.0000.0000.000
81A113VAL0-0.015-0.02048.638-0.002-0.0020.0000.0000.0000.000
82A114SER0-0.012-0.00350.666-0.002-0.0020.0000.0000.0000.000
83A115HIS0-0.018-0.01048.851-0.001-0.0010.0000.0000.0000.000
84A116VAL0-0.0190.00448.847-0.002-0.0020.0000.0000.0000.000
85A117ILE0-0.066-0.02152.1700.0000.0000.0000.0000.0000.000
86A118GLU-1-0.878-0.94655.670-0.023-0.0230.0000.0000.0000.000
87A119ASP-1-0.872-0.93958.531-0.015-0.0150.0000.0000.0000.000
88A120HIS0-0.050-0.04458.3900.0020.0020.0000.0000.0000.000
89A121ASP-1-0.708-0.82757.061-0.020-0.0200.0000.0000.0000.000
90A122GLU-1-0.844-0.91260.125-0.010-0.0100.0000.0000.0000.000
91A123GLU-1-0.950-0.97862.202-0.013-0.0130.0000.0000.0000.000
92A124ILE0-0.014-0.01660.3750.0010.0010.0000.0000.0000.000
93A125LEU00.012-0.00856.4810.0010.0010.0000.0000.0000.000
94A126VAL0-0.0120.01660.5290.0010.0010.0000.0000.0000.000
95A127TYR0-0.053-0.02963.0420.0010.0010.0000.0000.0000.000
96A128LEU0-0.058-0.01356.0390.0010.0010.0000.0000.0000.000
97A129ASN00.0570.00059.9660.0010.0010.0000.0000.0000.000
98A130ASP-1-0.870-0.96356.1040.0060.0060.0000.0000.0000.000
99A131ILE0-0.0120.02151.183-0.002-0.0020.0000.0000.0000.000
100A132ARG10.8450.92650.556-0.005-0.0050.0000.0000.0000.000
101A133CYS00.0290.01144.614-0.003-0.0030.0000.0000.0000.000
102A134ASP-1-0.815-0.86946.0500.0120.0120.0000.0000.0000.000
103A135TYR00.0310.01838.997-0.004-0.0040.0000.0000.0000.000
104A136ILE0-0.0020.00739.5050.0000.0000.0000.0000.0000.000
105A137LYS10.8130.89141.405-0.007-0.0070.0000.0000.0000.000
106A145GLY0-0.001-0.00136.646-0.001-0.0010.0000.0000.0000.000
107A146PHE0-0.017-0.02037.9950.0050.0050.0000.0000.0000.000
108A147ILE0-0.003-0.00241.480-0.004-0.0040.0000.0000.0000.000
109A148LEU0-0.0080.00144.8900.0030.0030.0000.0000.0000.000
110A149SER0-0.016-0.01947.568-0.002-0.0020.0000.0000.0000.000
111A150PHE00.0130.00349.5360.0020.0020.0000.0000.0000.000
112A151TYR00.0170.00053.597-0.001-0.0010.0000.0000.0000.000
113A152PHE00.0310.01256.1430.0000.0000.0000.0000.0000.000
114A153ALA00.0040.02360.6030.0000.0000.0000.0000.0000.000
115A154THR00.015-0.01464.222-0.001-0.0010.0000.0000.0000.000
116A155ASN00.0150.01262.478-0.001-0.0010.0000.0000.0000.000
117A156PRO0-0.030-0.01666.5150.0000.0000.0000.0000.0000.000
118A157PHE0-0.017-0.00562.964-0.001-0.0010.0000.0000.0000.000
119A158PHE00.0130.00358.976-0.002-0.0020.0000.0000.0000.000
120A159SER0-0.028-0.00262.3730.0010.0010.0000.0000.0000.000
121A160ASN0-0.0060.00457.3530.0010.0010.0000.0000.0000.000
122A161SER00.0410.02459.7950.0000.0000.0000.0000.0000.000
123A162VAL0-0.027-0.03254.0030.0010.0010.0000.0000.0000.000
124A163LEU0-0.0030.01753.455-0.001-0.0010.0000.0000.0000.000
125A164THR0-0.006-0.01549.0100.0010.0010.0000.0000.0000.000
126A165LYS10.8420.91143.8850.0250.0250.0000.0000.0000.000
127A166THR0-0.029-0.02341.7810.0040.0040.0000.0000.0000.000
128A167TYR00.000-0.02139.189-0.003-0.0030.0000.0000.0000.000
129A168HIS00.000-0.00336.7310.0070.0070.0000.0000.0000.000
130A169MET0-0.008-0.01533.686-0.004-0.0040.0000.0000.0000.000
131A170LYS10.9580.99326.8170.0460.0460.0000.0000.0000.000
132A179VAL0-0.015-0.01928.127-0.001-0.0010.0000.0000.0000.000
133A180LEU00.0200.00130.9360.0050.0050.0000.0000.0000.000
134A181LEU0-0.081-0.02830.535-0.007-0.0070.0000.0000.0000.000
135A182HIS0-0.058-0.03333.981-0.009-0.0090.0000.0000.0000.000
136A183THR00.0250.00337.6260.0050.0050.0000.0000.0000.000
137A184GLU-1-0.879-0.92941.234-0.028-0.0280.0000.0000.0000.000
138A185ALA00.0120.02544.4700.0030.0030.0000.0000.0000.000
139A186THR0-0.0320.00647.905-0.001-0.0010.0000.0000.0000.000
140A187VAL0-0.006-0.00251.288-0.001-0.0010.0000.0000.0000.000
141A188ILE0-0.016-0.01053.5320.0020.0020.0000.0000.0000.000
142A189ASP-1-0.900-0.94356.503-0.019-0.0190.0000.0000.0000.000
143A190TRP0-0.025-0.03256.9140.0020.0020.0000.0000.0000.000
144A191TYR0-0.010-0.00361.7900.0000.0000.0000.0000.0000.000
145A192ASP-1-0.821-0.92465.351-0.019-0.0190.0000.0000.0000.000
146A193ASN0-0.120-0.07466.7920.0000.0000.0000.0000.0000.000
147A194LYS10.9110.96264.5380.0160.0160.0000.0000.0000.000
148A195ASN00.0240.02258.2940.0000.0000.0000.0000.0000.000
149A196ILE00.0550.04158.811-0.001-0.0010.0000.0000.0000.000
150A197LEU00.0210.03354.399-0.001-0.0010.0000.0000.0000.000
151A198LYS10.8350.91255.7450.0290.0290.0000.0000.0000.000
152A199LYS10.9851.00660.4680.0250.0250.0000.0000.0000.000
153A222ARG10.8310.91856.7690.0230.0230.0000.0000.0000.000
154A223ASP-1-0.891-0.94153.055-0.033-0.0330.0000.0000.0000.000
155A224SER0-0.046-0.06053.9480.0020.0020.0000.0000.0000.000
156A225PHE00.1030.04851.214-0.001-0.0010.0000.0000.0000.000
157A226PHE0-0.026-0.03852.1550.0000.0000.0000.0000.0000.000
158A227HIS0-0.050-0.01950.137-0.001-0.0010.0000.0000.0000.000
159A228PHE00.0170.02745.702-0.002-0.0020.0000.0000.0000.000
160A229PHE0-0.049-0.01647.7090.0000.0000.0000.0000.0000.000
161A230THR0-0.026-0.03146.508-0.001-0.0010.0000.0000.0000.000
162A231SER0-0.028-0.01644.3900.0010.0010.0000.0000.0000.000
163A232HIS00.0270.01940.657-0.003-0.0030.0000.0000.0000.000
164A233LYS10.9310.95037.5480.0570.0570.0000.0000.0000.000
165A234VAL00.0800.05233.076-0.001-0.0010.0000.0000.0000.000
166A247GLU-1-0.961-0.98639.199-0.094-0.0940.0000.0000.0000.000
167A248VAL00.014-0.01033.5310.0040.0040.0000.0000.0000.000
168A249ALA00.0680.03837.0060.0030.0030.0000.0000.0000.000
169A250GLN0-0.016-0.00438.0810.0020.0020.0000.0000.0000.000
170A251LEU00.002-0.01038.3810.0050.0050.0000.0000.0000.000
171A252GLU-1-0.958-0.96333.196-0.087-0.0870.0000.0000.0000.000
172A253MET00.0420.02337.3650.0050.0050.0000.0000.0000.000
173A254ILE0-0.009-0.01240.2990.0050.0050.0000.0000.0000.000
174A255ILE0-0.046-0.02737.0390.0050.0050.0000.0000.0000.000
175A256GLU-1-0.928-0.96636.449-0.053-0.0530.0000.0000.0000.000
176A257GLY00.0370.02139.0550.0050.0050.0000.0000.0000.000
177A258ASP-1-0.839-0.89442.403-0.025-0.0250.0000.0000.0000.000
178A259TYR00.028-0.01237.0110.0050.0050.0000.0000.0000.000
179A260GLU-1-0.892-0.93240.872-0.019-0.0190.0000.0000.0000.000
180A261VAL00.0290.01541.9660.0050.0050.0000.0000.0000.000
181A262ALA0-0.020-0.00942.6330.0040.0040.0000.0000.0000.000
182A263LEU0-0.014-0.00538.7960.0040.0040.0000.0000.0000.000
183A264THR00.0000.00342.5770.0050.0050.0000.0000.0000.000
184A265ILE00.001-0.00745.5680.0030.0030.0000.0000.0000.000
185A266LYS10.8400.91440.072-0.005-0.0050.0000.0000.0000.000
186A267GLU-1-0.899-0.95339.9980.0120.0120.0000.0000.0000.000
187A268ARG10.9040.95644.751-0.006-0.0060.0000.0000.0000.000
188A269ILE00.0070.00647.8020.0020.0020.0000.0000.0000.000
189A270ILE00.0080.01148.3250.0010.0010.0000.0000.0000.000
190A271PRO0-0.012-0.00246.6430.0010.0010.0000.0000.0000.000
191A272TYR0-0.014-0.01047.1580.0020.0020.0000.0000.0000.000
192A273ALA0-0.0020.02752.453-0.001-0.0010.0000.0000.0000.000
193A274VAL00.045-0.00154.925-0.001-0.0010.0000.0000.0000.000
194A275ASP-1-0.855-0.92354.8670.0120.0120.0000.0000.0000.000
195A276TYR0-0.018-0.00749.9540.0000.0000.0000.0000.0000.000
196A277TYR0-0.0310.00056.119-0.001-0.0010.0000.0000.0000.000
197A278LEU0-0.057-0.04559.527-0.001-0.0010.0000.0000.0000.000
198A279GLY00.0200.01858.0190.0000.0000.0000.0000.0000.000
199A280ILE0-0.103-0.03957.1940.0000.0000.0000.0000.0000.000
200A281ILE0-0.045-0.01251.4370.0020.0020.0000.0000.0000.000