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

tag_button

FMODB ID: 7GY1K

Calculation Name: 1F6F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F6F

Chain ID: A

ChEMBL ID:

UniProt ID: P16038

Base Structure: X-ray

Registration Date: 2023-03-13

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010047.715661
FMO2-HF: Nuclear repulsion 1934540.219453
FMO2-HF: Total energy -75507.496208
FMO2-MP2: Total energy -75726.933586


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-0.7620.829-0.004-0.885-0.7020.001
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.002
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].
3A3HIS00.0200.0103.516-1.872-0.281-0.004-0.885-0.7020.001
4A4PRO00.005-0.0056.2540.4200.4200.0000.0000.0000.000
5A5PRO00.0310.0049.835-0.121-0.1210.0000.0000.0000.000
6A6TYR00.0920.01612.668-0.026-0.0260.0000.0000.0000.000
7A7CYS0-0.0040.0169.836-0.009-0.0090.0000.0000.0000.000
8A8ARG10.9590.9979.7540.3250.3250.0000.0000.0000.000
9A9ASN0-0.062-0.05912.5910.1070.1070.0000.0000.0000.000
10A10GLN00.0420.01314.357-0.024-0.0240.0000.0000.0000.000
11A11PRO0-0.0060.01114.991-0.023-0.0230.0000.0000.0000.000
12A12GLY00.0590.03113.041-0.043-0.0430.0000.0000.0000.000
13A13LYS10.9100.96411.6840.2330.2330.0000.0000.0000.000
14A15GLN0-0.0170.00211.9160.0290.0290.0000.0000.0000.000
15A16ILE0-0.0030.00914.567-0.003-0.0030.0000.0000.0000.000
16A17PRO00.0490.01816.0540.0090.0090.0000.0000.0000.000
17A18LEU00.0630.02519.0410.0160.0160.0000.0000.0000.000
18A19GLN00.0640.03322.4860.0080.0080.0000.0000.0000.000
19A20SER0-0.005-0.00619.1790.0050.0050.0000.0000.0000.000
20A21LEU0-0.031-0.01519.2090.0160.0160.0000.0000.0000.000
21A22PHE00.1070.04022.1930.0140.0140.0000.0000.0000.000
22A23ASP-1-0.853-0.90923.441-0.045-0.0450.0000.0000.0000.000
23A24ARG10.9620.97216.2290.0660.0660.0000.0000.0000.000
24A25ALA00.0420.03924.2270.0090.0090.0000.0000.0000.000
25A26THR0-0.002-0.02327.0230.0060.0060.0000.0000.0000.000
26A27THR0-0.033-0.01825.9480.0040.0040.0000.0000.0000.000
27A28VAL00.0300.02526.0470.0060.0060.0000.0000.0000.000
28A29ALA00.0310.01028.9260.0030.0030.0000.0000.0000.000
29A30ASN0-0.021-0.01731.8270.0010.0010.0000.0000.0000.000
30A31TYR0-0.056-0.04131.1180.0020.0020.0000.0000.0000.000
31A32ASN00.0460.01331.7490.0050.0050.0000.0000.0000.000
32A33SER00.0100.00634.8070.0000.0000.0000.0000.0000.000
33A34LYS10.8760.94835.638-0.007-0.0070.0000.0000.0000.000
34A35LEU00.0520.02834.3050.0000.0000.0000.0000.0000.000
35A36ALA00.0230.00738.2150.0010.0010.0000.0000.0000.000
36A37GLY00.0340.02040.6710.0000.0000.0000.0000.0000.000
37A38GLU-1-0.860-0.92239.0040.0260.0260.0000.0000.0000.000
38A39MET0-0.078-0.03439.5200.0010.0010.0000.0000.0000.000
39A40VAL00.002-0.00244.1340.0000.0000.0000.0000.0000.000
40A41ASN0-0.027-0.01745.8630.0000.0000.0000.0000.0000.000
41A42ARG10.9320.96945.084-0.022-0.0220.0000.0000.0000.000
42A43PHE0-0.025-0.01448.3220.0000.0000.0000.0000.0000.000
43A44ASP-1-0.801-0.91450.0580.0070.0070.0000.0000.0000.000
44A45GLU-1-0.991-0.97551.7910.0110.0110.0000.0000.0000.000
45A46GLN0-0.059-0.04850.9610.0030.0030.0000.0000.0000.000
46A47TYR0-0.0540.00351.4190.0000.0000.0000.0000.0000.000
47A57VAL0-0.015-0.01856.3800.0000.0000.0000.0000.0000.000
48A58ILE0-0.0100.00150.3280.0000.0000.0000.0000.0000.000
49A59ASN00.006-0.00952.552-0.001-0.0010.0000.0000.0000.000
50A60CYS0-0.113-0.04746.159-0.001-0.0010.0000.0000.0000.000
51A61HIS00.0720.04943.414-0.001-0.0010.0000.0000.0000.000
52A62THR0-0.052-0.04542.802-0.001-0.0010.0000.0000.0000.000
53A63SER0-0.082-0.04445.897-0.002-0.0020.0000.0000.0000.000
54A64SER00.0070.00847.971-0.001-0.0010.0000.0000.0000.000
55A65ILE00.0020.01241.862-0.001-0.0010.0000.0000.0000.000
56A66THR0-0.006-0.00945.7750.0010.0010.0000.0000.0000.000
57A67THR0-0.033-0.01943.027-0.001-0.0010.0000.0000.0000.000
58A68PRO0-0.0010.03342.8930.0010.0010.0000.0000.0000.000
59A69ASN00.005-0.00544.9570.0000.0000.0000.0000.0000.000
60A70SER00.0070.01847.4890.0010.0010.0000.0000.0000.000
61A71LYS11.0010.97544.3010.0210.0210.0000.0000.0000.000
62A72ALA00.0070.00245.248-0.002-0.0020.0000.0000.0000.000
63A73GLU-1-0.792-0.90346.352-0.023-0.0230.0000.0000.0000.000
64A74ALA00.0040.01042.131-0.002-0.0020.0000.0000.0000.000
65A75ILE0-0.053-0.03741.209-0.002-0.0020.0000.0000.0000.000
66A76ASN00.0190.00441.672-0.004-0.0040.0000.0000.0000.000
67A77THR0-0.0400.00340.547-0.001-0.0010.0000.0000.0000.000
68A78GLU-1-0.825-0.91338.552-0.050-0.0500.0000.0000.0000.000
69A79ASP-1-0.827-0.93933.295-0.063-0.0630.0000.0000.0000.000
70A80LYS10.8680.92934.6610.0630.0630.0000.0000.0000.000
71A81ILE00.0250.00936.3480.0020.0020.0000.0000.0000.000
72A82LEU0-0.030-0.00536.2890.0030.0030.0000.0000.0000.000
73A83PHE00.0240.00029.6310.0020.0020.0000.0000.0000.000
74A84LYS10.8450.92834.3230.0490.0490.0000.0000.0000.000
75A85LEU00.0220.01936.7190.0030.0030.0000.0000.0000.000
76A86VAL0-0.035-0.01833.1000.0030.0030.0000.0000.0000.000
77A87ILE0-0.005-0.00431.2010.0030.0030.0000.0000.0000.000
78A88SER00.0270.01334.4870.0030.0030.0000.0000.0000.000
79A89LEU0-0.0320.00437.9320.0030.0030.0000.0000.0000.000
80A90LEU0-0.026-0.02032.0270.0030.0030.0000.0000.0000.000
81A91HIS00.0030.00431.8820.0060.0060.0000.0000.0000.000
82A92SER0-0.026-0.03336.5380.0020.0020.0000.0000.0000.000
83A93TRP0-0.046-0.04038.4110.0030.0030.0000.0000.0000.000
84A94ASP-1-0.820-0.89235.3220.0080.0080.0000.0000.0000.000
85A95GLU-1-0.815-0.91337.9670.0020.0020.0000.0000.0000.000
86A96PRO00.0260.01241.2630.0020.0020.0000.0000.0000.000
87A97LEU0-0.020-0.01237.7690.0020.0020.0000.0000.0000.000
88A98HIS00.0220.01239.5680.0030.0030.0000.0000.0000.000
89A99HIS0-0.036-0.01240.8930.0030.0030.0000.0000.0000.000
90A100ALA0-0.0190.00043.3430.0010.0010.0000.0000.0000.000
91A101VAL0-0.017-0.02239.2550.0020.0020.0000.0000.0000.000
92A102THR0-0.034-0.01742.5770.0020.0020.0000.0000.0000.000
93A103GLU-1-0.801-0.88044.6390.0140.0140.0000.0000.0000.000
94A104LEU0-0.077-0.05044.3480.0010.0010.0000.0000.0000.000
95A105ALA00.0260.01843.4590.0020.0020.0000.0000.0000.000
96A106ASN0-0.080-0.01745.3940.0010.0010.0000.0000.0000.000
97A107SER00.0550.01747.7620.0000.0000.0000.0000.0000.000
98A108LYS10.8960.95449.622-0.019-0.0190.0000.0000.0000.000
99A109GLY00.0520.03249.5260.0010.0010.0000.0000.0000.000
100A110THR0-0.069-0.05547.622-0.001-0.0010.0000.0000.0000.000
101A111SER00.0570.04544.6260.0000.0000.0000.0000.0000.000
102A112PRO00.002-0.00146.0590.0020.0020.0000.0000.0000.000
103A113ALA0-0.002-0.01042.8910.0020.0020.0000.0000.0000.000
104A114LEU00.002-0.00442.0710.0010.0010.0000.0000.0000.000
105A115LEU00.0480.02841.1340.0000.0000.0000.0000.0000.000
106A116THR0-0.0010.01137.2560.0010.0010.0000.0000.0000.000
107A117LYS10.8380.90437.422-0.027-0.0270.0000.0000.0000.000
108A118ALA00.0330.01337.640-0.001-0.0010.0000.0000.0000.000
109A119GLN00.0150.00135.9040.0000.0000.0000.0000.0000.000
110A120GLU-1-0.754-0.84131.2710.0430.0430.0000.0000.0000.000
111A121ILE0-0.028-0.01332.976-0.001-0.0010.0000.0000.0000.000
112A122LYS10.8110.91434.221-0.014-0.0140.0000.0000.0000.000
113A123GLU-1-0.805-0.88930.0500.0230.0230.0000.0000.0000.000
114A124LYS10.8250.88828.305-0.045-0.0450.0000.0000.0000.000
115A125ALA0-0.0150.00329.932-0.005-0.0050.0000.0000.0000.000
116A126LYS10.8560.90529.559-0.023-0.0230.0000.0000.0000.000
117A127VAL0-0.029-0.00324.475-0.004-0.0040.0000.0000.0000.000
118A128LEU0-0.041-0.02726.230-0.007-0.0070.0000.0000.0000.000
119A129VAL00.009-0.00228.137-0.008-0.0080.0000.0000.0000.000
120A130ASP-1-0.910-0.93123.081-0.042-0.0420.0000.0000.0000.000
121A131GLY0-0.001-0.00223.885-0.011-0.0110.0000.0000.0000.000
122A132VAL0-0.046-0.04424.893-0.011-0.0110.0000.0000.0000.000
123A133GLU-1-0.793-0.88927.259-0.049-0.0490.0000.0000.0000.000
124A134VAL0-0.029-0.00920.822-0.012-0.0120.0000.0000.0000.000
125A135ILE0-0.065-0.03924.100-0.014-0.0140.0000.0000.0000.000
126A136GLN00.0240.00225.445-0.007-0.0070.0000.0000.0000.000
127A137LYS10.8620.92125.5140.0600.0600.0000.0000.0000.000
128A138ARG10.8020.92218.5620.1800.1800.0000.0000.0000.000
129A139ILE0-0.033-0.02124.752-0.008-0.0080.0000.0000.0000.000
130A140HIS0-0.029-0.01427.8620.0000.0000.0000.0000.0000.000
131A141PRO0-0.0010.00026.7990.0050.0050.0000.0000.0000.000
132A142GLY0-0.020-0.00629.0070.0040.0040.0000.0000.0000.000
133A143GLU-1-0.773-0.85131.340-0.051-0.0510.0000.0000.0000.000
134A144LYS10.9260.95432.5770.0510.0510.0000.0000.0000.000
135A145ASN0-0.006-0.01732.1090.0010.0010.0000.0000.0000.000
136A146GLU-1-0.878-0.93336.103-0.032-0.0320.0000.0000.0000.000
137A147PRO0-0.037-0.01539.3290.0010.0010.0000.0000.0000.000
138A148TYR0-0.0060.00337.746-0.002-0.0020.0000.0000.0000.000
139A149PRO0-0.015-0.00542.0060.0010.0010.0000.0000.0000.000
140A150VAL00.0580.02143.8150.0010.0010.0000.0000.0000.000
141A151TRP0-0.040-0.02746.1380.0000.0000.0000.0000.0000.000
142A152SER00.0330.00348.2470.0010.0010.0000.0000.0000.000
143A153GLU-1-0.786-0.85650.886-0.001-0.0010.0000.0000.0000.000
144A154GLN00.0050.00545.6880.0020.0020.0000.0000.0000.000
145A155SER00.0310.02049.8840.0010.0010.0000.0000.0000.000
146A156SER0-0.038-0.03451.9810.0010.0010.0000.0000.0000.000
147A157LEU0-0.020-0.01447.1970.0010.0010.0000.0000.0000.000
148A158THR0-0.039-0.02650.2720.0010.0010.0000.0000.0000.000
149A159SER0-0.033-0.00152.8000.0000.0000.0000.0000.0000.000
150A160GLN00.0240.00156.4600.0010.0010.0000.0000.0000.000
151A161ASP-1-0.902-0.93558.9440.0070.0070.0000.0000.0000.000
152A162GLU-1-0.789-0.89558.5460.0110.0110.0000.0000.0000.000
153A163ASN00.0140.00358.1940.0010.0010.0000.0000.0000.000
154A164VAL0-0.005-0.01357.6110.0000.0000.0000.0000.0000.000
155A165ARG10.8700.93551.870-0.013-0.0130.0000.0000.0000.000
156A166ARG10.8130.88353.729-0.010-0.0100.0000.0000.0000.000
157A167VAL00.008-0.00554.0730.0000.0000.0000.0000.0000.000
158A168ALA0-0.0040.01651.966-0.001-0.0010.0000.0000.0000.000
159A169PHE00.022-0.00446.7310.0000.0000.0000.0000.0000.000
160A170TYR0-0.0100.01649.2720.0000.0000.0000.0000.0000.000
161A171ARG10.8130.86250.1970.0000.0000.0000.0000.0000.000
162A172LEU00.0100.01244.622-0.001-0.0010.0000.0000.0000.000
163A173PHE00.025-0.00343.8390.0000.0000.0000.0000.0000.000
164A174HIS00.002-0.00145.353-0.002-0.0020.0000.0000.0000.000
165A176LEU00.0570.04539.496-0.001-0.0010.0000.0000.0000.000
166A177HIS0-0.0030.00941.404-0.001-0.0010.0000.0000.0000.000
167A178ARG10.9520.96842.4290.0040.0040.0000.0000.0000.000
168A179ASP-1-0.755-0.87640.675-0.011-0.0110.0000.0000.0000.000
169A180SER0-0.033-0.02137.948-0.002-0.0020.0000.0000.0000.000
170A181SER00.0010.00237.802-0.002-0.0020.0000.0000.0000.000
171A182LYS10.8940.94639.6680.0120.0120.0000.0000.0000.000
172A183ILE00.0210.01834.326-0.003-0.0030.0000.0000.0000.000
173A184TYR00.0310.01233.342-0.004-0.0040.0000.0000.0000.000
174A185THR0-0.023-0.03035.414-0.003-0.0030.0000.0000.0000.000
175A186TYR0-0.003-0.01536.896-0.003-0.0030.0000.0000.0000.000
176A187LEU00.0120.01330.230-0.004-0.0040.0000.0000.0000.000
177A188ARG10.8630.94232.3750.0130.0130.0000.0000.0000.000
178A189ILE0-0.017-0.00234.162-0.003-0.0030.0000.0000.0000.000
179A190LEU00.0150.01331.954-0.003-0.0030.0000.0000.0000.000
180A191LYS10.8390.93927.5640.0360.0360.0000.0000.0000.000
181A197CYS0-0.102-0.06229.764-0.001-0.0010.0000.0000.0000.000
182A193ARG10.8230.91733.5340.0450.0450.0000.0000.0000.000
183A194LEU0-0.010-0.00929.782-0.003-0.0030.0000.0000.0000.000
184A195THR0-0.107-0.05125.966-0.009-0.0090.0000.0000.0000.000
185A196SER00.0360.02327.4880.0020.0020.0000.0000.0000.000