FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: ZYZ4N

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 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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2067017.218744
FMO2-HF: Nuclear repulsion 1995674.472204
FMO2-HF: Total energy -71342.74654
FMO2-MP2: Total energy -71551.870688


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.
-9.523-0.7074.413-4.126-9.103-0.021
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 : 0.006 / q_NPA : -0.007
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].
3A158GLY00.0250.0092.959-2.2480.2790.228-1.276-1.479-0.003
4A159LYS10.8620.9124.2150.0360.113-0.001-0.027-0.0490.000
5A160ILE00.0110.0185.9060.0050.0050.0000.0000.0000.000
6A161VAL00.0120.0157.8330.0640.0640.0000.0000.0000.000
7A162VAL0-0.014-0.00310.2720.0340.0340.0000.0000.0000.000
8A163ILE00.020-0.00112.8340.0200.0200.0000.0000.0000.000
9A164GLY00.0090.00916.5950.0110.0110.0000.0000.0000.000
10A165SER0-0.005-0.02619.2350.0020.0020.0000.0000.0000.000
11A166SER00.0240.01922.7730.0110.0110.0000.0000.0000.000
12A167THR00.0510.03026.0820.0030.0030.0000.0000.0000.000
13A168GLY00.0250.00829.078-0.004-0.0040.0000.0000.0000.000
14A169GLY00.0160.01025.572-0.003-0.0030.0000.0000.0000.000
15A170PRO00.011-0.01525.555-0.006-0.0060.0000.0000.0000.000
16A171ARG10.9210.97626.7850.1240.1240.0000.0000.0000.000
17A172SER0-0.009-0.04125.6790.0070.0070.0000.0000.0000.000
18A173LEU00.0100.00120.541-0.008-0.0080.0000.0000.0000.000
19A174ASP-1-0.763-0.86023.841-0.136-0.1360.0000.0000.0000.000
20A175MET0-0.073-0.02726.4160.0060.0060.0000.0000.0000.000
21A176ILE0-0.021-0.03420.084-0.007-0.0070.0000.0000.0000.000
22A177ILE0-0.009-0.01318.335-0.011-0.0110.0000.0000.0000.000
23A178PRO00.0000.00721.252-0.004-0.0040.0000.0000.0000.000
24A179ASN0-0.066-0.02223.2990.0210.0210.0000.0000.0000.000
25A180LEU0-0.025-0.00216.848-0.018-0.0180.0000.0000.0000.000
26A181PRO00.0000.00717.8850.0180.0180.0000.0000.0000.000
27A182LYS11.0641.01018.1890.0400.0400.0000.0000.0000.000
28A183ASN0-0.063-0.03616.356-0.019-0.0190.0000.0000.0000.000
29A184PHE00.0500.02612.739-0.028-0.0280.0000.0000.0000.000
30A185PRO00.004-0.00510.696-0.003-0.0030.0000.0000.0000.000
31A186ALA0-0.052-0.0128.445-0.136-0.1360.0000.0000.0000.000
32A187PRO0-0.0110.0066.5780.1360.1360.0000.0000.0000.000
33A188ILE00.0220.0119.811-0.097-0.0970.0000.0000.0000.000
34A189VAL0-0.015-0.00610.2020.0580.0580.0000.0000.0000.000
35A190VAL00.0110.00313.039-0.013-0.0130.0000.0000.0000.000
36A191VAL0-0.011-0.00515.7850.0260.0260.0000.0000.0000.000
37A192GLN00.0080.00318.409-0.010-0.0100.0000.0000.0000.000
38A193HIS0-0.065-0.05622.1010.0260.0260.0000.0000.0000.000
39A194MET0-0.013-0.01524.7930.0050.0050.0000.0000.0000.000
40A195PRO0-0.0150.01026.874-0.001-0.0010.0000.0000.0000.000
41A196PRO00.0530.02027.372-0.004-0.0040.0000.0000.0000.000
42A197GLY00.0340.01227.3440.0060.0060.0000.0000.0000.000
43A198PHE00.0030.00228.1240.0040.0040.0000.0000.0000.000
44A199THR0-0.011-0.00322.5390.0010.0010.0000.0000.0000.000
45A200LYS11.0311.01823.8380.0540.0540.0000.0000.0000.000
46A201SER0-0.077-0.06025.2390.0010.0010.0000.0000.0000.000
47A202LEU00.0050.00422.6110.0020.0020.0000.0000.0000.000
48A203ALA00.0270.01421.927-0.005-0.0050.0000.0000.0000.000
49A204MET00.0160.00523.0860.0040.0040.0000.0000.0000.000
50A205ARG10.7940.88726.1730.1210.1210.0000.0000.0000.000
51A206LEU00.008-0.01521.5270.0010.0010.0000.0000.0000.000
52A207ASP-1-0.865-0.91622.189-0.101-0.1010.0000.0000.0000.000
53A208SER0-0.040-0.01823.8170.0090.0090.0000.0000.0000.000
54A209THR0-0.071-0.03226.3950.0020.0020.0000.0000.0000.000
55A210SER0-0.017-0.01521.865-0.012-0.0120.0000.0000.0000.000
56A211GLU-1-0.908-0.94321.997-0.084-0.0840.0000.0000.0000.000
57A212LEU0-0.104-0.04415.6750.0040.0040.0000.0000.0000.000
58A213THR00.0060.01417.3840.0170.0170.0000.0000.0000.000
59A214VAL0-0.039-0.01517.331-0.029-0.0290.0000.0000.0000.000
60A215LYS10.7830.87116.1880.1110.1110.0000.0000.0000.000
61A216GLU-1-0.859-0.93018.215-0.124-0.1240.0000.0000.0000.000
62A217ALA0-0.033-0.01314.4210.0110.0110.0000.0000.0000.000
63A218GLU-1-0.877-0.93515.728-0.010-0.0100.0000.0000.0000.000
64A219ASP-1-0.880-0.96315.151-0.028-0.0280.0000.0000.0000.000
65A220GLY0-0.027-0.01213.1250.0260.0260.0000.0000.0000.000
66A221GLU-1-0.814-0.89512.597-0.034-0.0340.0000.0000.0000.000
67A222GLU-1-0.963-0.9907.8450.4260.4260.0000.0000.0000.000
68A223VAL0-0.046-0.0316.510-0.035-0.0350.0000.0000.0000.000
69A224LYS10.9310.9616.634-0.111-0.1110.0000.0000.0000.000
70A225PRO00.003-0.0027.499-0.037-0.0370.0000.0000.0000.000
71A226GLY00.0500.02210.1650.0870.0870.0000.0000.0000.000
72A227PHE0-0.043-0.01812.6010.0690.0690.0000.0000.0000.000
73A228VAL00.0050.00413.377-0.069-0.0690.0000.0000.0000.000
74A229TYR00.010-0.00310.7990.0210.0210.0000.0000.0000.000
75A230ILE0-0.020-0.00115.360-0.032-0.0320.0000.0000.0000.000
76A231ALA00.003-0.01016.9270.0180.0180.0000.0000.0000.000
77A232PRO00.0270.02718.0040.0100.0100.0000.0000.0000.000
78A233GLY00.0170.00221.120-0.008-0.0080.0000.0000.0000.000
79A234ASP-1-0.931-0.97523.620-0.068-0.0680.0000.0000.0000.000
80A235PHE0-0.020-0.01119.7950.0130.0130.0000.0000.0000.000
81A236HIS00.029-0.00617.836-0.028-0.0280.0000.0000.0000.000
82A237LEU00.0020.01213.2600.0190.0190.0000.0000.0000.000
83A238GLY00.0190.01812.634-0.054-0.0540.0000.0000.0000.000
84A239LEU00.010-0.0036.717-0.015-0.0150.0000.0000.0000.000
85A240LYS10.9320.9717.197-0.075-0.0750.0000.0000.0000.000
86A241ALA00.0440.0253.065-0.495-0.0310.199-0.153-0.5110.000
87A242GLN0-0.011-0.0254.429-0.083-0.042-0.001-0.008-0.0320.000
88A243ASN0-0.002-0.0065.8200.2240.2240.0000.0000.0000.000
89A244GLY00.0210.0122.871-0.6310.1350.201-0.382-0.5850.002
90A245LYS10.9370.9862.867-3.043-0.7010.626-1.167-1.801-0.013
91A246VAL00.0210.0072.556-0.921-0.4622.076-0.471-2.063-0.001
92A247PHE0-0.0100.0094.8320.0150.065-0.001-0.010-0.0400.000
93A248PHE00.0380.0218.554-0.122-0.1220.0000.0000.0000.000
94A249PHE0-0.052-0.03310.7640.0720.0720.0000.0000.0000.000
95A250LEU0-0.0040.01313.814-0.046-0.0460.0000.0000.0000.000
96A251ASP-1-0.821-0.89816.567-0.104-0.1040.0000.0000.0000.000
97A252LYS10.8440.90118.3910.0620.0620.0000.0000.0000.000
98A253SER0-0.039-0.00720.0710.0070.0070.0000.0000.0000.000
99A254ASP-1-0.862-0.94522.637-0.089-0.0890.0000.0000.0000.000
100A255LYS10.8910.95323.7730.0790.0790.0000.0000.0000.000
101A256ILE00.0280.03520.4050.0020.0020.0000.0000.0000.000
102A257ASN0-0.005-0.00624.571-0.006-0.0060.0000.0000.0000.000
103A258ASN0-0.018-0.02127.6250.0090.0090.0000.0000.0000.000
104A259VAL0-0.013-0.02223.5240.0080.0080.0000.0000.0000.000
105A260ARG10.8820.96522.2170.0970.0970.0000.0000.0000.000
106A261PRO00.0010.00919.1650.0140.0140.0000.0000.0000.000
107A262ALA0-0.035-0.00219.9510.0050.0050.0000.0000.0000.000
108A263VAL00.028-0.00516.281-0.019-0.0190.0000.0000.0000.000
109A264ASP-1-0.842-0.93416.208-0.314-0.3140.0000.0000.0000.000
110A265PHE0-0.031-0.01414.515-0.036-0.0360.0000.0000.0000.000
111A266THR00.003-0.02111.965-0.014-0.0140.0000.0000.0000.000
112A267LEU0-0.010-0.00911.492-0.095-0.0950.0000.0000.0000.000
113A268ASP-1-0.914-0.95111.931-0.448-0.4480.0000.0000.0000.000
114A269LYS10.8960.9679.7090.2780.2780.0000.0000.0000.000
115A270ALA00.0040.0007.333-0.121-0.1210.0000.0000.0000.000
116A271ALA00.0140.0077.135-0.304-0.3040.0000.0000.0000.000
117A272GLU-1-0.934-0.9499.028-0.566-0.5660.0000.0000.0000.000
118A273ILE0-0.084-0.0352.836-0.819-0.1040.302-0.166-0.850-0.001
119A274TYR0-0.012-0.0233.048-2.297-0.9580.785-0.466-1.658-0.005
120A275LYS10.8980.9585.3541.1101.146-0.0010.000-0.0350.000
121A276SER00.0550.0328.629-0.038-0.0380.0000.0000.0000.000
122A277LYS10.8680.9386.0711.7111.7110.0000.0000.0000.000
123A278THR00.017-0.0037.924-0.125-0.1250.0000.0000.0000.000
124A279ILE00.0000.0069.4200.1390.1390.0000.0000.0000.000
125A280ALA0-0.007-0.00112.373-0.006-0.0060.0000.0000.0000.000
126A281VAL00.0120.00814.8010.0320.0320.0000.0000.0000.000
127A282ILE0-0.032-0.00917.8480.0110.0110.0000.0000.0000.000
128A283LEU00.0280.00320.7160.0160.0160.0000.0000.0000.000
129A284THR00.039-0.00923.4450.0090.0090.0000.0000.0000.000
130A285GLY0-0.002-0.02126.103-0.005-0.0050.0000.0000.0000.000
131A286MET00.000-0.00527.9930.0010.0010.0000.0000.0000.000
132A287GLY00.0160.01028.094-0.005-0.0050.0000.0000.0000.000
133A288LYS10.9850.97326.4090.1660.1660.0000.0000.0000.000
134A289ASP-1-0.754-0.84621.251-0.249-0.2490.0000.0000.0000.000
135A290GLY00.0780.02519.3840.0010.0010.0000.0000.0000.000
136A291THR0-0.0040.02419.844-0.020-0.0200.0000.0000.0000.000
137A292LYS10.9760.98120.9070.1880.1880.0000.0000.0000.000
138A293GLY00.002-0.00316.839-0.018-0.0180.0000.0000.0000.000
139A294ALA00.0250.01216.086-0.053-0.0530.0000.0000.0000.000
140A295PHE00.0110.00917.796-0.030-0.0300.0000.0000.0000.000
141A296LYS10.8870.94514.4010.3380.3380.0000.0000.0000.000
142A297VAL00.0090.01312.660-0.051-0.0510.0000.0000.0000.000
143A298LYS10.8120.89114.2230.3870.3870.0000.0000.0000.000
144A299PHE0-0.037-0.00115.3930.0050.0050.0000.0000.0000.000
145A300TYR0-0.016-0.01011.242-0.005-0.0050.0000.0000.0000.000
146A301GLY0-0.011-0.01112.202-0.104-0.1040.0000.0000.0000.000
147A302GLY0-0.0050.00512.387-0.045-0.0450.0000.0000.0000.000
148A303THR0-0.077-0.03813.1310.1080.1080.0000.0000.0000.000
149A304VAL0-0.012-0.00915.058-0.040-0.0400.0000.0000.0000.000
150A305ILE0-0.0070.00117.6630.0320.0320.0000.0000.0000.000
151A306ALA0-0.0030.00220.021-0.004-0.0040.0000.0000.0000.000
152A307GLU-1-0.726-0.83123.008-0.182-0.1820.0000.0000.0000.000
153A308ASP-1-0.834-0.93425.283-0.149-0.1490.0000.0000.0000.000
154A309LYS10.9330.95128.7520.1260.1260.0000.0000.0000.000
155A310GLU-1-0.883-0.91431.742-0.127-0.1270.0000.0000.0000.000
156A311THR0-0.007-0.01828.3600.0050.0050.0000.0000.0000.000
157A312CYS0-0.088-0.01028.735-0.004-0.0040.0000.0000.0000.000
158A313VAL0-0.038-0.00430.5770.0090.0090.0000.0000.0000.000
159A314VAL0-0.010-0.02231.0200.0080.0080.0000.0000.0000.000
160A315PHE0-0.007-0.00428.721-0.005-0.0050.0000.0000.0000.000
161A316GLY0-0.017-0.01129.7420.0050.0050.0000.0000.0000.000
162A317MET0-0.053-0.00523.1210.0010.0010.0000.0000.0000.000
163A318PRO00.0180.01124.688-0.009-0.0090.0000.0000.0000.000
164A319LYS10.9510.98425.7530.1250.1250.0000.0000.0000.000
165A320SER00.017-0.01726.1240.0050.0050.0000.0000.0000.000
166A321VAL0-0.0170.00121.726-0.005-0.0050.0000.0000.0000.000
167A322ILE0-0.033-0.03424.455-0.005-0.0050.0000.0000.0000.000
168A323GLU-1-0.978-0.99326.718-0.143-0.1430.0000.0000.0000.000
169A324GLU-1-0.973-0.97025.121-0.178-0.1780.0000.0000.0000.000
170A325GLY0-0.032-0.00426.222-0.002-0.0020.0000.0000.0000.000
171A326TYR0-0.038-0.03620.754-0.019-0.0190.0000.0000.0000.000
172A327ALA0-0.035-0.01620.849-0.031-0.0310.0000.0000.0000.000
173A328ASP-1-0.779-0.85918.704-0.388-0.3880.0000.0000.0000.000
174A329TYR0-0.018-0.02418.8710.0280.0280.0000.0000.0000.000
175A330VAL00.0230.01523.146-0.009-0.0090.0000.0000.0000.000
176A331LEU0-0.016-0.01822.3670.0090.0090.0000.0000.0000.000
177A332PRO00.0450.04925.989-0.007-0.0070.0000.0000.0000.000
178A333ALA00.032-0.02125.089-0.010-0.0100.0000.0000.0000.000
179A334TYR0-0.004-0.04224.751-0.015-0.0150.0000.0000.0000.000
180A335LYS10.9480.98025.6600.1630.1630.0000.0000.0000.000
181A336ILE0-0.051-0.00620.021-0.017-0.0170.0000.0000.0000.000
182A337PRO0-0.0100.01620.070-0.032-0.0320.0000.0000.0000.000
183A338GLU-1-0.891-0.94919.958-0.198-0.1980.0000.0000.0000.000
184A339LYS10.8560.93319.1190.2690.2690.0000.0000.0000.000
185A340LEU0-0.021-0.02315.022-0.037-0.0370.0000.0000.0000.000
186A341ILE0-0.006-0.00715.772-0.049-0.0490.0000.0000.0000.000
187A342GLU-1-0.892-0.92317.268-0.265-0.2650.0000.0000.0000.000
188A343LEU0-0.050-0.00714.699-0.020-0.0200.0000.0000.0000.000
189A344VAL0-0.055-0.00611.180-0.100-0.1000.0000.0000.0000.000