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: Z23MN

Calculation Name: 3SFT-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2073130.113684
FMO2-HF: Nuclear repulsion 2001636.31461
FMO2-HF: Total energy -71493.799074
FMO2-MP2: Total energy -71703.351135


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:155:ACE )


Summations of interaction energy for fragment #1(A:155:ACE )
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.
1.5331.8610.38-0.006-0.699-0.001
Interaction energy analysis for fragmet #1(A:155:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.009
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].
3A157SER 0-0.051-0.0093.9021.1401.710-0.004-0.236-0.3290.000
4A158GLY 00.0340.0156.831-0.026-0.0260.0000.0000.0000.000
5A159LYS 10.8650.9149.6870.0940.0940.0000.0000.0000.000
6A160ILE 00.0030.01312.380-0.044-0.0440.0000.0000.0000.000
7A161VAL 00.0230.02014.1760.0430.0430.0000.0000.0000.000
8A162VAL 0-0.020-0.00616.593-0.011-0.0110.0000.0000.0000.000
9A163ILE 00.022-0.00119.2980.0210.0210.0000.0000.0000.000
10A164GLY 00.0030.00623.096-0.005-0.0050.0000.0000.0000.000
11A165SER 0-0.006-0.02525.5590.0060.0060.0000.0000.0000.000
12A166SER 00.0280.01929.2190.0010.0010.0000.0000.0000.000
13A167THR 00.0450.02632.4950.0000.0000.0000.0000.0000.000
14A168GLY 00.0260.00935.5530.0000.0000.0000.0000.0000.000
15A169GLY 00.0160.01132.2420.0000.0000.0000.0000.0000.000
16A170PRO 00.012-0.01532.286-0.002-0.0020.0000.0000.0000.000
17A171ARG 10.9170.97533.5190.0620.0620.0000.0000.0000.000
18A172SER 0-0.004-0.04032.1830.0030.0030.0000.0000.0000.000
19A173LEU 00.0070.00027.280-0.002-0.0020.0000.0000.0000.000
20A174ASP -1-0.762-0.85930.471-0.086-0.0860.0000.0000.0000.000
21A175MET 0-0.075-0.02833.0260.0040.0040.0000.0000.0000.000
22A176ILE 0-0.025-0.03526.5360.0000.0000.0000.0000.0000.000
23A177ILE 0-0.005-0.01124.897-0.004-0.0040.0000.0000.0000.000
24A178PRO 0-0.0030.00627.729-0.004-0.0040.0000.0000.0000.000
25A179ASN 0-0.068-0.02329.7750.0070.0070.0000.0000.0000.000
26A180LEU 0-0.0180.00223.334-0.001-0.0010.0000.0000.0000.000
27A181PRO 00.0000.00723.7480.0020.0020.0000.0000.0000.000
28A182LYS 11.0561.00624.1010.0960.0960.0000.0000.0000.000
29A183ASN 0-0.070-0.04121.501-0.016-0.0160.0000.0000.0000.000
30A184PHE 00.0480.02719.222-0.004-0.0040.0000.0000.0000.000
31A185PRO 00.0190.00415.911-0.023-0.0230.0000.0000.0000.000
32A186ALA 0-0.041-0.00614.697-0.057-0.0570.0000.0000.0000.000
33A187PRO 0-0.0180.00012.9600.0460.0460.0000.0000.0000.000
34A188ILE 00.0240.01316.174-0.001-0.0010.0000.0000.0000.000
35A189VAL 0-0.018-0.00816.7220.0010.0010.0000.0000.0000.000
36A190VAL 00.0110.00319.7140.0140.0140.0000.0000.0000.000
37A191VAL 0-0.014-0.00622.1660.0010.0010.0000.0000.0000.000
38A192GLN 00.0100.00324.8480.0060.0060.0000.0000.0000.000
39A193HIS 0-0.063-0.05628.4750.0080.0080.0000.0000.0000.000
40A194MET 0-0.016-0.01631.0730.0060.0060.0000.0000.0000.000
41A195PRO 0-0.0180.00732.903-0.003-0.0030.0000.0000.0000.000
42A196PRO 00.0540.02133.081-0.004-0.0040.0000.0000.0000.000
43A197GLY 00.0340.01333.0620.0050.0050.0000.0000.0000.000
44A198PHE 00.0000.00034.1160.0020.0020.0000.0000.0000.000
45A199THR 0-0.008-0.00228.7230.0030.0030.0000.0000.0000.000
46A200LYS 11.0291.01830.0780.0960.0960.0000.0000.0000.000
47A201SER 0-0.077-0.06131.2560.0020.0020.0000.0000.0000.000
48A202LEU 00.0060.00529.1700.0030.0030.0000.0000.0000.000
49A203ALA 00.0280.01428.089-0.001-0.0010.0000.0000.0000.000
50A204MET 00.0130.00429.3610.0020.0020.0000.0000.0000.000
51A205ARG 10.7910.88632.3300.0840.0840.0000.0000.0000.000
52A206LEU 00.009-0.01528.1400.0030.0030.0000.0000.0000.000
53A207ASP -1-0.864-0.91528.332-0.119-0.1190.0000.0000.0000.000
54A208SER 0-0.040-0.01730.0950.0050.0050.0000.0000.0000.000
55A209THR 0-0.074-0.03432.7380.0040.0040.0000.0000.0000.000
56A210SER 0-0.015-0.01528.1720.0010.0010.0000.0000.0000.000
57A211GLU -1-0.907-0.94427.885-0.090-0.0900.0000.0000.0000.000
58A212LEU 0-0.101-0.04121.856-0.007-0.0070.0000.0000.0000.000
59A213THR 00.0040.01323.3610.0070.0070.0000.0000.0000.000
60A214VAL 0-0.035-0.01223.529-0.021-0.0210.0000.0000.0000.000
61A215LYS 10.7790.86821.7590.2130.2130.0000.0000.0000.000
62A216GLU -1-0.859-0.93024.272-0.136-0.1360.0000.0000.0000.000
63A217ALA 0-0.032-0.01120.045-0.008-0.0080.0000.0000.0000.000
64A218GLU -1-0.881-0.93820.795-0.148-0.1480.0000.0000.0000.000
65A219ASP -1-0.881-0.96319.561-0.233-0.2330.0000.0000.0000.000
66A220GLY 0-0.028-0.01216.6380.0120.0120.0000.0000.0000.000
67A221GLU -1-0.817-0.89616.390-0.266-0.2660.0000.0000.0000.000
68A222GLU -1-0.959-0.99011.718-0.577-0.5770.0000.0000.0000.000
69A223VAL 0-0.051-0.03112.2550.0580.0580.0000.0000.0000.000
70A224LYS 10.9310.96012.4480.1950.1950.0000.0000.0000.000
71A225PRO 00.0110.00313.2610.0300.0300.0000.0000.0000.000
72A226GLY 00.0520.02416.1550.0190.0190.0000.0000.0000.000
73A227PHE 0-0.047-0.02118.4810.0280.0280.0000.0000.0000.000
74A228VAL 00.0030.00419.734-0.019-0.0190.0000.0000.0000.000
75A229TYR 00.010-0.00316.986-0.001-0.0010.0000.0000.0000.000
76A230ILE 0-0.022-0.00221.657-0.001-0.0010.0000.0000.0000.000
77A231ALA 00.004-0.01023.077-0.002-0.0020.0000.0000.0000.000
78A232PRO 00.0260.02723.6370.0150.0150.0000.0000.0000.000
79A233GLY 00.0210.00426.8180.0000.0000.0000.0000.0000.000
80A234ASP -1-0.937-0.97928.754-0.093-0.0930.0000.0000.0000.000
81A235PHE 0-0.018-0.01024.4680.0070.0070.0000.0000.0000.000
82A236HIS 00.026-0.00722.665-0.009-0.0090.0000.0000.0000.000
83A237LEU 00.0040.01318.917-0.001-0.0010.0000.0000.0000.000
84A238GLY 00.0210.01817.472-0.006-0.0060.0000.0000.0000.000
85A239LEU 00.008-0.00212.428-0.018-0.0180.0000.0000.0000.000
86A240LYS 10.9290.96911.0200.3670.3670.0000.0000.0000.000
87A241ALA 00.0520.0305.416-0.055-0.0550.0000.0000.0000.000
88A242GLN 0-0.017-0.0297.1430.2740.2740.0000.0000.0000.000
89A243ASN 0-0.008-0.0105.7260.0170.0170.0000.0000.0000.000
90A244GLY 00.008-0.0022.9340.4750.2970.3780.130-0.329-0.001
91A245LYS 10.9380.9803.8740.4980.4340.0060.100-0.0410.000
92A246VAL 00.0280.0127.169-0.116-0.1160.0000.0000.0000.000
93A247PHE 0-0.0140.0079.3530.1450.1450.0000.0000.0000.000
94A248PHE 00.0360.02012.728-0.019-0.0190.0000.0000.0000.000
95A249PHE 0-0.048-0.03214.7640.0170.0170.0000.0000.0000.000
96A250LEU 0-0.0040.01418.0460.0010.0010.0000.0000.0000.000
97A251ASP -1-0.824-0.90020.730-0.135-0.1350.0000.0000.0000.000
98A252LYS 10.8420.90122.5900.1060.1060.0000.0000.0000.000
99A253SER 0-0.040-0.00924.2000.0140.0140.0000.0000.0000.000
100A254ASP -1-0.863-0.94626.637-0.074-0.0740.0000.0000.0000.000
101A255LYS 10.8910.95328.1930.0680.0680.0000.0000.0000.000
102A256ILE 00.0290.03524.8820.0040.0040.0000.0000.0000.000
103A257ASN 0-0.003-0.00529.2540.0010.0010.0000.0000.0000.000
104A258ASN 0-0.022-0.02232.5580.0020.0020.0000.0000.0000.000
105A259VAL 0-0.018-0.02329.1590.0020.0020.0000.0000.0000.000
106A260ARG 10.8870.96627.1010.0970.0970.0000.0000.0000.000
107A261PRO 0-0.0050.00624.9760.0070.0070.0000.0000.0000.000
108A262ALA 0-0.032-0.00125.4170.0080.0080.0000.0000.0000.000
109A263VAL 00.029-0.00522.225-0.014-0.0140.0000.0000.0000.000
110A264ASP -1-0.838-0.93221.755-0.135-0.1350.0000.0000.0000.000
111A265PHE 0-0.036-0.01719.104-0.012-0.0120.0000.0000.0000.000
112A266THR 00.004-0.02017.945-0.011-0.0110.0000.0000.0000.000
113A267LEU 0-0.005-0.00616.916-0.041-0.0410.0000.0000.0000.000
114A268ASP -1-0.919-0.95316.577-0.197-0.1970.0000.0000.0000.000
115A269LYS 10.8960.96614.3940.2140.2140.0000.0000.0000.000
116A270ALA 00.0060.00112.695-0.066-0.0660.0000.0000.0000.000
117A271ALA 00.0160.00811.806-0.076-0.0760.0000.0000.0000.000
118A272GLU -1-0.939-0.95111.776-0.214-0.2140.0000.0000.0000.000
119A273ILE 0-0.085-0.0356.930-0.028-0.0280.0000.0000.0000.000
120A274TYR 0-0.004-0.0197.233-0.237-0.2370.0000.0000.0000.000
121A275LYS 10.8900.9537.8800.3320.3320.0000.0000.0000.000
122A276SER 00.0500.02911.314-0.015-0.0150.0000.0000.0000.000
123A277LYS 10.8770.9449.8430.2160.2160.0000.0000.0000.000
124A278THR 00.017-0.00312.297-0.066-0.0660.0000.0000.0000.000
125A279ILE 00.0110.01214.2360.0520.0520.0000.0000.0000.000
126A280ALA 0-0.013-0.00517.764-0.018-0.0180.0000.0000.0000.000
127A281VAL 00.0190.01120.4250.0180.0180.0000.0000.0000.000
128A282ILE 0-0.041-0.01223.819-0.004-0.0040.0000.0000.0000.000
129A283LEU 00.0340.00426.6500.0100.0100.0000.0000.0000.000
130A284THR 00.038-0.01029.6750.0050.0050.0000.0000.0000.000
131A285GLY 0-0.006-0.02232.443-0.006-0.0060.0000.0000.0000.000
132A286MET 00.001-0.00634.1840.0030.0030.0000.0000.0000.000
133A287GLY 00.0140.00933.934-0.004-0.0040.0000.0000.0000.000
134A288LYS 10.9830.97231.2730.0650.0650.0000.0000.0000.000
135A289ASP -1-0.757-0.84726.676-0.126-0.1260.0000.0000.0000.000
136A290GLY 00.0850.02724.7770.0010.0010.0000.0000.0000.000
137A291THR 0-0.0020.02524.875-0.001-0.0010.0000.0000.0000.000
138A292LYS 10.9710.97824.7650.0840.0840.0000.0000.0000.000
139A293GLY 00.003-0.00321.270-0.004-0.0040.0000.0000.0000.000
140A294ALA 00.0310.01520.487-0.013-0.0130.0000.0000.0000.000
141A295PHE 00.0040.00721.700-0.002-0.0020.0000.0000.0000.000
142A296LYS 10.8840.94317.8740.1440.1440.0000.0000.0000.000
143A297VAL 00.0160.01716.917-0.006-0.0060.0000.0000.0000.000
144A298LYS 10.8120.89217.3930.0910.0910.0000.0000.0000.000
145A299PHE 0-0.048-0.00517.1990.0150.0150.0000.0000.0000.000
146A300TYR 0-0.016-0.01113.5250.0190.0190.0000.0000.0000.000
147A301GLY 0-0.012-0.01114.362-0.007-0.0070.0000.0000.0000.000
148A302GLY 0-0.0020.00815.953-0.005-0.0050.0000.0000.0000.000
149A303THR 0-0.070-0.03316.6370.0330.0330.0000.0000.0000.000
150A304VAL 0-0.014-0.01119.698-0.022-0.0220.0000.0000.0000.000
151A305ILE 0-0.0030.00422.5350.0140.0140.0000.0000.0000.000
152A306ALA 0-0.006-0.00125.321-0.007-0.0070.0000.0000.0000.000
153A307GLU -1-0.726-0.83028.476-0.079-0.0790.0000.0000.0000.000
154A308ASP -1-0.833-0.93431.126-0.050-0.0500.0000.0000.0000.000
155A309LYS 10.9270.94834.4020.0460.0460.0000.0000.0000.000
156A310GLU -1-0.884-0.91437.528-0.050-0.0500.0000.0000.0000.000
157A311THR 0-0.003-0.01734.5670.0010.0010.0000.0000.0000.000
158A312CYS 0-0.087-0.01034.803-0.004-0.0040.0000.0000.0000.000
159A313VAL 0-0.043-0.00636.8290.0040.0040.0000.0000.0000.000
160A314VAL 0-0.014-0.02437.2220.0040.0040.0000.0000.0000.000
161A315PHE 0-0.005-0.00234.289-0.003-0.0030.0000.0000.0000.000
162A316GLY 0-0.018-0.01235.6220.0030.0030.0000.0000.0000.000
163A317MET 0-0.056-0.00529.1400.0010.0010.0000.0000.0000.000
164A318PRO 00.0250.01330.218-0.001-0.0010.0000.0000.0000.000
165A319LYS 10.9470.98331.3040.0490.0490.0000.0000.0000.000
166A320SER 00.014-0.01830.9030.0040.0040.0000.0000.0000.000
167A321VAL 0-0.0190.00126.7090.0000.0000.0000.0000.0000.000
168A322ILE 0-0.025-0.03129.2480.0020.0020.0000.0000.0000.000
169A323GLU -1-0.981-0.99431.307-0.044-0.0440.0000.0000.0000.000
170A324GLU -1-0.976-0.97229.119-0.050-0.0500.0000.0000.0000.000
171A325GLY 0-0.031-0.00429.8240.0030.0030.0000.0000.0000.000
172A326TYR 0-0.042-0.03824.817-0.002-0.0020.0000.0000.0000.000
173A327ALA 0-0.032-0.01524.939-0.009-0.0090.0000.0000.0000.000
174A328ASP -1-0.781-0.85922.753-0.082-0.0820.0000.0000.0000.000
175A329TYR 0-0.014-0.02023.5450.0090.0090.0000.0000.0000.000
176A330VAL 00.0220.01428.064-0.006-0.0060.0000.0000.0000.000
177A331LEU 0-0.016-0.01828.0140.0050.0050.0000.0000.0000.000
178A332PRO 00.0400.04631.730-0.005-0.0050.0000.0000.0000.000
179A333ALA 00.037-0.01931.287-0.003-0.0030.0000.0000.0000.000
180A334TYR 0-0.015-0.04731.050-0.006-0.0060.0000.0000.0000.000
181A335LYS 10.9510.98131.6770.0550.0550.0000.0000.0000.000
182A336ILE 0-0.055-0.00726.183-0.003-0.0030.0000.0000.0000.000
183A337PRO 0-0.0100.01526.403-0.008-0.0080.0000.0000.0000.000
184A338GLU -1-0.893-0.95026.117-0.071-0.0710.0000.0000.0000.000
185A339LYS 10.8460.92824.6460.0730.0730.0000.0000.0000.000
186A340LEU 0-0.025-0.02721.157-0.005-0.0050.0000.0000.0000.000
187A341ILE 0-0.012-0.00921.612-0.011-0.0110.0000.0000.0000.000
188A342GLU -1-0.895-0.92422.747-0.067-0.0670.0000.0000.0000.000
189A343LEU 0-0.080-0.02619.8510.0040.0040.0000.0000.0000.000
190A344VAL -1-0.953-0.95517.010-0.160-0.1600.0000.0000.0000.000