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: R5L78

Calculation Name: 3SFT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SFT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYN9

Base Structure: X-ray

Registration Date: 2023-03-14

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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2068064.997767
FMO2-HF: Nuclear repulsion 1996721.242945
FMO2-HF: Total energy -71343.754822
FMO2-MP2: Total energy -71552.928148


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:156:VAL)


Summations of interaction energy for fragment #1(A:156:VAL)
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.
-11.336-1.4915.531-5.181-10.199-0.015
Interaction energy analysis for fragmet #1(A:156:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.021
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].
3A158GLY00.0330.0103.132-2.5401.0320.110-1.915-1.7680.004
4A159LYS10.8680.9184.2280.1830.272-0.001-0.027-0.0620.000
5A160ILE00.0040.0135.9610.0600.0600.0000.0000.0000.000
6A161VAL00.0110.0137.8290.0190.0190.0000.0000.0000.000
7A162VAL0-0.014-0.00310.1950.0540.0540.0000.0000.0000.000
8A163ILE00.013-0.00312.827-0.004-0.0040.0000.0000.0000.000
9A164GLY00.0150.01416.5950.0240.0240.0000.0000.0000.000
10A165SER0-0.007-0.02319.206-0.009-0.0090.0000.0000.0000.000
11A166SER00.0130.00422.7590.0130.0130.0000.0000.0000.000
12A167THR00.0570.03126.0640.0000.0000.0000.0000.0000.000
13A168GLY00.0250.00429.073-0.005-0.0050.0000.0000.0000.000
14A169GLY00.0160.01425.583-0.006-0.0060.0000.0000.0000.000
15A170PRO00.014-0.01625.596-0.008-0.0080.0000.0000.0000.000
16A171ARG10.9070.96426.8410.0650.0650.0000.0000.0000.000
17A172SER0-0.018-0.03725.8220.0000.0000.0000.0000.0000.000
18A173LEU00.0140.00220.635-0.010-0.0100.0000.0000.0000.000
19A174ASP-1-0.753-0.83423.932-0.072-0.0720.0000.0000.0000.000
20A175MET0-0.058-0.02226.503-0.001-0.0010.0000.0000.0000.000
21A176ILE0-0.017-0.02620.150-0.010-0.0100.0000.0000.0000.000
22A177ILE00.008-0.00518.293-0.012-0.0120.0000.0000.0000.000
23A178PRO0-0.0060.00321.320-0.007-0.0070.0000.0000.0000.000
24A179ASN0-0.086-0.03523.3860.0080.0080.0000.0000.0000.000
25A180LEU0-0.0190.00517.053-0.020-0.0200.0000.0000.0000.000
26A181PRO00.0030.00318.1200.0170.0170.0000.0000.0000.000
27A182LYS10.8690.90918.2600.0760.0760.0000.0000.0000.000
28A183ASN0-0.039-0.03116.3950.0070.0070.0000.0000.0000.000
29A184PHE00.0340.02112.816-0.054-0.0540.0000.0000.0000.000
30A185PRO00.012-0.00110.7800.0120.0120.0000.0000.0000.000
31A186ALA0-0.057-0.0158.561-0.135-0.1350.0000.0000.0000.000
32A187PRO0-0.0060.0086.5050.0990.0990.0000.0000.0000.000
33A188ILE00.0110.0049.741-0.065-0.0650.0000.0000.0000.000
34A189VAL0-0.017-0.00810.1380.0620.0620.0000.0000.0000.000
35A190VAL00.0140.00413.094-0.025-0.0250.0000.0000.0000.000
36A191VAL0-0.009-0.00415.7330.0290.0290.0000.0000.0000.000
37A192GLN00.0120.00718.405-0.020-0.0200.0000.0000.0000.000
38A193HIS0-0.048-0.04022.1050.0150.0150.0000.0000.0000.000
39A194MET0-0.005-0.01224.773-0.008-0.0080.0000.0000.0000.000
40A195PRO0-0.0030.01726.8680.0060.0060.0000.0000.0000.000
41A196PRO00.0360.00427.383-0.001-0.0010.0000.0000.0000.000
42A197GLY00.0280.01027.357-0.001-0.0010.0000.0000.0000.000
43A198PHE0-0.0060.00028.124-0.002-0.0020.0000.0000.0000.000
44A199THR0-0.016-0.01822.643-0.006-0.0060.0000.0000.0000.000
45A200LYS11.0081.01323.911-0.045-0.0450.0000.0000.0000.000
46A201SER0-0.063-0.04925.323-0.006-0.0060.0000.0000.0000.000
47A202LEU00.0070.00522.790-0.004-0.0040.0000.0000.0000.000
48A203ALA00.0230.01321.905-0.008-0.0080.0000.0000.0000.000
49A204MET00.0200.00923.135-0.003-0.0030.0000.0000.0000.000
50A205ARG10.7660.85626.1110.0460.0460.0000.0000.0000.000
51A206LEU00.018-0.00521.696-0.004-0.0040.0000.0000.0000.000
52A207ASP-1-0.856-0.90622.080-0.044-0.0440.0000.0000.0000.000
53A208SER0-0.053-0.03023.7720.0000.0000.0000.0000.0000.000
54A209THR0-0.035-0.02026.1460.0020.0020.0000.0000.0000.000
55A210SER0-0.047-0.03421.821-0.014-0.0140.0000.0000.0000.000
56A211GLU-1-0.798-0.88221.754-0.089-0.0890.0000.0000.0000.000
57A212LEU0-0.056-0.01415.6770.0020.0020.0000.0000.0000.000
58A213THR00.0160.01917.4350.0130.0130.0000.0000.0000.000
59A214VAL0-0.049-0.02517.302-0.006-0.0060.0000.0000.0000.000
60A215LYS10.7680.84316.110-0.082-0.0820.0000.0000.0000.000
61A216GLU-1-0.822-0.90618.2120.0280.0280.0000.0000.0000.000
62A217ALA0-0.029-0.00714.5610.0120.0120.0000.0000.0000.000
63A218GLU-1-0.861-0.91115.6680.1280.1280.0000.0000.0000.000
64A219ASP-1-0.864-0.94615.0370.3350.3350.0000.0000.0000.000
65A220GLY0-0.029-0.01312.9910.0020.0020.0000.0000.0000.000
66A221GLU-1-0.830-0.89912.5600.1990.1990.0000.0000.0000.000
67A222GLU-1-0.840-0.9057.5720.7430.7430.0000.0000.0000.000
68A223VAL0-0.036-0.0326.453-0.123-0.1230.0000.0000.0000.000
69A224LYS10.9250.9616.646-0.162-0.1620.0000.0000.0000.000
70A225PRO00.0140.0017.609-0.015-0.0150.0000.0000.0000.000
71A226GLY00.0600.02710.1830.0580.0580.0000.0000.0000.000
72A227PHE0-0.049-0.02012.5350.0530.0530.0000.0000.0000.000
73A228VAL00.002-0.00113.320-0.044-0.0440.0000.0000.0000.000
74A229TYR0-0.009-0.00610.7540.0170.0170.0000.0000.0000.000
75A230ILE0-0.017-0.00215.463-0.019-0.0190.0000.0000.0000.000
76A231ALA00.003-0.00416.9280.0240.0240.0000.0000.0000.000
77A232PRO00.0340.02918.102-0.010-0.0100.0000.0000.0000.000
78A233GLY00.009-0.00721.149-0.001-0.0010.0000.0000.0000.000
79A234ASP-1-0.815-0.91423.6180.0840.0840.0000.0000.0000.000
80A235PHE00.0100.00919.7620.0090.0090.0000.0000.0000.000
81A236HIS00.031-0.01217.834-0.028-0.0280.0000.0000.0000.000
82A237LEU0-0.0080.00913.2620.0240.0240.0000.0000.0000.000
83A238GLY00.0330.01812.636-0.042-0.0420.0000.0000.0000.000
84A239LEU0-0.006-0.0096.775-0.012-0.0120.0000.0000.0000.000
85A240LYS10.9250.9697.158-0.656-0.6560.0000.0000.0000.000
86A241ALA00.0440.0232.951-0.4640.0030.242-0.177-0.5330.001
87A242GLN0-0.015-0.0264.326-0.495-0.465-0.001-0.010-0.0190.000
88A243ASN00.002-0.0055.8080.0480.0480.0000.0000.0000.000
89A244GLY00.0190.0113.120-1.868-1.0250.223-0.448-0.6170.004
90A245LYS10.8160.9072.859-4.161-1.7950.715-1.246-1.835-0.014
91A246VAL00.0290.0072.5190.1240.2052.780-0.517-2.344-0.002
92A247PHE0-0.0120.0054.659-0.344-0.290-0.001-0.015-0.0380.000
93A248PHE00.0460.0208.399-0.023-0.0230.0000.0000.0000.000
94A249PHE0-0.062-0.04010.7180.0600.0600.0000.0000.0000.000
95A250LEU00.0020.01113.762-0.044-0.0440.0000.0000.0000.000
96A251ASP-1-0.809-0.87716.5050.1790.1790.0000.0000.0000.000
97A252LYS10.7960.88218.357-0.120-0.1200.0000.0000.0000.000
98A253SER0-0.043-0.02720.025-0.014-0.0140.0000.0000.0000.000
99A254ASP-1-0.860-0.93722.6170.0630.0630.0000.0000.0000.000
100A255LYS10.8630.94323.777-0.032-0.0320.0000.0000.0000.000
101A256ILE00.0220.02920.330-0.002-0.0020.0000.0000.0000.000
102A257ASN0-0.017-0.01324.447-0.011-0.0110.0000.0000.0000.000
103A258ASN00.018-0.00227.5100.0110.0110.0000.0000.0000.000
104A259VAL0-0.013-0.02223.5430.0010.0010.0000.0000.0000.000
105A260ARG10.8110.92122.046-0.071-0.0710.0000.0000.0000.000
106A261PRO00.0040.00919.1640.0020.0020.0000.0000.0000.000
107A262ALA0-0.052-0.00919.889-0.011-0.0110.0000.0000.0000.000
108A263VAL00.032-0.00416.2480.0060.0060.0000.0000.0000.000
109A264ASP-1-0.832-0.92916.111-0.079-0.0790.0000.0000.0000.000
110A265PHE0-0.020-0.01014.461-0.006-0.0060.0000.0000.0000.000
111A266THR00.001-0.01611.9310.0130.0130.0000.0000.0000.000
112A267LEU0-0.0030.00311.382-0.027-0.0270.0000.0000.0000.000
113A268ASP-1-0.869-0.89911.776-0.006-0.0060.0000.0000.0000.000
114A269LYS10.8540.9299.738-0.139-0.1390.0000.0000.0000.000
115A270ALA00.0080.0017.2000.0080.0080.0000.0000.0000.000
116A271ALA00.0170.0106.964-0.196-0.1960.0000.0000.0000.000
117A272GLU-1-0.850-0.8848.909-0.021-0.0210.0000.0000.0000.000
118A273ILE0-0.074-0.0222.816-0.6760.0490.298-0.171-0.853-0.001
119A274TYR0-0.007-0.0182.985-2.246-0.6601.167-0.654-2.099-0.007
120A275LYS10.8710.9375.1800.0530.085-0.001-0.001-0.0310.000
121A276SER00.0670.0478.711-0.061-0.0610.0000.0000.0000.000
122A277LYS10.8610.9345.9341.9801.9800.0000.0000.0000.000
123A278THR00.006-0.0187.849-0.045-0.0450.0000.0000.0000.000
124A279ILE0-0.0020.0019.3030.0710.0710.0000.0000.0000.000
125A280ALA00.0010.00512.2970.0240.0240.0000.0000.0000.000
126A281VAL00.0060.00014.7470.0040.0040.0000.0000.0000.000
127A282ILE0-0.031-0.00417.8260.0220.0220.0000.0000.0000.000
128A283LEU00.0180.00020.6730.0020.0020.0000.0000.0000.000
129A284THR00.028-0.00523.4290.0100.0100.0000.0000.0000.000
130A285GLY0-0.012-0.02226.0840.0020.0020.0000.0000.0000.000
131A286MET0-0.010-0.00427.957-0.002-0.0020.0000.0000.0000.000
132A287GLY00.0160.00728.0260.0010.0010.0000.0000.0000.000
133A288LYS10.8970.92926.2220.0580.0580.0000.0000.0000.000
134A289ASP-1-0.766-0.86021.185-0.049-0.0490.0000.0000.0000.000
135A290GLY00.0810.02119.283-0.007-0.0070.0000.0000.0000.000
136A291THR0-0.0360.01219.729-0.019-0.0190.0000.0000.0000.000
137A292LYS10.9980.99720.7620.0080.0080.0000.0000.0000.000
138A293GLY0-0.008-0.01016.690-0.005-0.0050.0000.0000.0000.000
139A294ALA00.0140.00715.937-0.032-0.0320.0000.0000.0000.000
140A295PHE00.0110.01217.647-0.025-0.0250.0000.0000.0000.000
141A296LYS10.8740.91814.1880.0370.0370.0000.0000.0000.000
142A297VAL00.0010.00512.188-0.034-0.0340.0000.0000.0000.000
143A298LYS10.8090.88614.0650.2620.2620.0000.0000.0000.000
144A299PHE0-0.045-0.00415.340-0.015-0.0150.0000.0000.0000.000
145A300TYR0-0.072-0.06411.318-0.022-0.0220.0000.0000.0000.000
146A301GLY0-0.013-0.01012.289-0.103-0.1030.0000.0000.0000.000
147A302GLY0-0.0060.00612.249-0.064-0.0640.0000.0000.0000.000
148A303THR0-0.085-0.04412.9880.0610.0610.0000.0000.0000.000
149A304VAL0-0.013-0.01314.957-0.010-0.0100.0000.0000.0000.000
150A305ILE0-0.013-0.00217.5330.0120.0120.0000.0000.0000.000
151A306ALA0-0.0020.00419.9500.0100.0100.0000.0000.0000.000
152A307GLU-1-0.714-0.82522.964-0.108-0.1080.0000.0000.0000.000
153A308ASP-1-0.827-0.93325.266-0.099-0.0990.0000.0000.0000.000
154A309LYS10.9430.96128.7340.0720.0720.0000.0000.0000.000
155A310GLU-1-0.884-0.90931.719-0.092-0.0920.0000.0000.0000.000
156A311THR0-0.002-0.02528.3710.0030.0030.0000.0000.0000.000
157A312CYS0-0.078-0.00228.7490.0020.0020.0000.0000.0000.000
158A313VAL0-0.044-0.01330.5750.0050.0050.0000.0000.0000.000
159A314VAL0-0.011-0.02331.0100.0050.0050.0000.0000.0000.000
160A315PHE00.0060.00628.798-0.001-0.0010.0000.0000.0000.000
161A316GLY0-0.004-0.00429.6950.0020.0020.0000.0000.0000.000
162A317MET0-0.044-0.00322.7620.0020.0020.0000.0000.0000.000
163A318PRO00.0250.01224.626-0.006-0.0060.0000.0000.0000.000
164A319LYS10.7990.89025.6890.0610.0610.0000.0000.0000.000
165A320SER00.011-0.01525.8920.0020.0020.0000.0000.0000.000
166A321VAL0-0.011-0.00221.490-0.002-0.0020.0000.0000.0000.000
167A322ILE0-0.017-0.02324.348-0.007-0.0070.0000.0000.0000.000
168A323GLU-1-0.846-0.90726.619-0.072-0.0720.0000.0000.0000.000
169A324GLU-1-0.860-0.91325.192-0.075-0.0750.0000.0000.0000.000
170A325GLY0-0.0130.00526.092-0.002-0.0020.0000.0000.0000.000
171A326TYR0-0.082-0.06420.623-0.015-0.0150.0000.0000.0000.000
172A327ALA0-0.029-0.01220.738-0.022-0.0220.0000.0000.0000.000
173A328ASP-1-0.779-0.85118.564-0.296-0.2960.0000.0000.0000.000
174A329TYR0-0.004-0.01718.8850.0100.0100.0000.0000.0000.000
175A330VAL00.0220.01423.0750.0010.0010.0000.0000.0000.000
176A331LEU0-0.011-0.00922.4410.0010.0010.0000.0000.0000.000
177A332PRO00.0460.05025.9560.0010.0010.0000.0000.0000.000
178A333ALA00.025-0.02225.085-0.011-0.0110.0000.0000.0000.000
179A334TYR0-0.016-0.05724.765-0.014-0.0140.0000.0000.0000.000
180A335LYS10.8670.91825.6760.1450.1450.0000.0000.0000.000
181A336ILE0-0.045-0.00520.019-0.018-0.0180.0000.0000.0000.000
182A337PRO0-0.0040.02020.107-0.028-0.0280.0000.0000.0000.000
183A338GLU-1-0.827-0.89920.011-0.186-0.1860.0000.0000.0000.000
184A339LYS10.8450.92419.0760.2470.2470.0000.0000.0000.000
185A340LEU0-0.021-0.02314.887-0.037-0.0370.0000.0000.0000.000
186A341ILE0-0.009-0.01215.816-0.053-0.0530.0000.0000.0000.000
187A342GLU-1-0.881-0.90817.339-0.287-0.2870.0000.0000.0000.000
188A343LEU0-0.043-0.00414.604-0.028-0.0280.0000.0000.0000.000
189A344VAL0-0.053-0.00311.398-0.109-0.1090.0000.0000.0000.000