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: 224VR

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 OptAll
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 -2024323.94848
FMO2-HF: Nuclear repulsion 1948816.008482
FMO2-HF: Total energy -75507.939998
FMO2-MP2: Total energy -75727.437999


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.
-0.5440.9770.002-0.822-0.7010.001
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 : 0.037 / 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].
3A3HIS00.0140.0063.532-1.890-0.3690.002-0.822-0.7010.001
4A4PRO00.012-0.0056.3170.4150.4150.0000.0000.0000.000
5A5PRO00.0290.0079.755-0.101-0.1010.0000.0000.0000.000
6A6TYR00.0500.00812.590-0.007-0.0070.0000.0000.0000.000
7A7CYS0-0.021-0.0119.8300.0090.0090.0000.0000.0000.000
8A8ARG10.9541.0068.9210.4040.4040.0000.0000.0000.000
9A9ASN0-0.043-0.04412.1350.1230.1230.0000.0000.0000.000
10A10GLN00.0520.02813.715-0.039-0.0390.0000.0000.0000.000
11A11PRO00.0050.01215.482-0.012-0.0120.0000.0000.0000.000
12A12GLY00.0610.03512.276-0.022-0.0220.0000.0000.0000.000
13A13LYS10.8960.95511.6590.2680.2680.0000.0000.0000.000
14A15GLN00.0190.00511.8120.0530.0530.0000.0000.0000.000
15A16ILE00.0130.01614.367-0.003-0.0030.0000.0000.0000.000
16A17PRO00.0320.01516.1660.0100.0100.0000.0000.0000.000
17A18LEU00.0740.03119.2050.0140.0140.0000.0000.0000.000
18A19GLN00.0790.03422.4750.0080.0080.0000.0000.0000.000
19A20SER00.0220.00319.2190.0040.0040.0000.0000.0000.000
20A21LEU0-0.0200.00219.3320.0100.0100.0000.0000.0000.000
21A22PHE00.1250.04822.3320.0140.0140.0000.0000.0000.000
22A23ASP-1-0.835-0.88123.347-0.056-0.0560.0000.0000.0000.000
23A24ARG10.9240.97716.3780.0940.0940.0000.0000.0000.000
24A25ALA00.0550.03424.2530.0090.0090.0000.0000.0000.000
25A26THR0-0.013-0.04027.1710.0070.0070.0000.0000.0000.000
26A27THR0-0.044-0.03626.1350.0070.0070.0000.0000.0000.000
27A28VAL00.0310.01325.9080.0060.0060.0000.0000.0000.000
28A29ALA00.0190.01628.8420.0040.0040.0000.0000.0000.000
29A30ASN00.0050.00531.7580.0020.0020.0000.0000.0000.000
30A31TYR0-0.052-0.04530.6870.0020.0020.0000.0000.0000.000
31A32ASN00.0620.01631.4910.0050.0050.0000.0000.0000.000
32A33SER0-0.032-0.02334.5040.0000.0000.0000.0000.0000.000
33A34LYS10.8300.92535.3870.0010.0010.0000.0000.0000.000
34A35LEU00.0560.03334.0240.0010.0010.0000.0000.0000.000
35A36ALA00.0380.02238.1860.0010.0010.0000.0000.0000.000
36A37GLY00.0380.02940.7660.0000.0000.0000.0000.0000.000
37A38GLU-1-0.849-0.91438.8610.0180.0180.0000.0000.0000.000
38A39MET0-0.053-0.01639.6690.0010.0010.0000.0000.0000.000
39A40VAL00.0070.00944.0590.0000.0000.0000.0000.0000.000
40A41ASN0-0.027-0.02345.8890.0000.0000.0000.0000.0000.000
41A42ARG10.9060.95744.751-0.016-0.0160.0000.0000.0000.000
42A43PHE0-0.0100.00147.9460.0010.0010.0000.0000.0000.000
43A44ASP-1-0.767-0.90249.8210.0020.0020.0000.0000.0000.000
44A45GLU-1-0.976-0.97851.5360.0070.0070.0000.0000.0000.000
45A46GLN0-0.100-0.05050.1810.0020.0020.0000.0000.0000.000
46A47TYR0-0.061-0.01351.0250.0000.0000.0000.0000.0000.000
47A57VAL00.004-0.00756.4520.0000.0000.0000.0000.0000.000
48A58ILE0-0.027-0.00850.1840.0000.0000.0000.0000.0000.000
49A59ASN00.015-0.00252.527-0.002-0.0020.0000.0000.0000.000
50A60CYS0-0.061-0.01246.246-0.001-0.0010.0000.0000.0000.000
51A61HIS00.0520.02943.3590.0000.0000.0000.0000.0000.000
52A62THR0-0.033-0.05042.758-0.001-0.0010.0000.0000.0000.000
53A63SER0-0.097-0.04945.721-0.002-0.0020.0000.0000.0000.000
54A64SER0-0.003-0.00547.701-0.001-0.0010.0000.0000.0000.000
55A65ILE0-0.013-0.00141.741-0.001-0.0010.0000.0000.0000.000
56A66THR00.000-0.00945.6280.0010.0010.0000.0000.0000.000
57A67THR0-0.0320.00042.446-0.001-0.0010.0000.0000.0000.000
58A68PRO0-0.0020.02242.7530.0010.0010.0000.0000.0000.000
59A69ASN0-0.016-0.01644.7090.0000.0000.0000.0000.0000.000
60A70SER0-0.013-0.01347.1730.0010.0010.0000.0000.0000.000
61A71LYS10.9820.97644.2320.0230.0230.0000.0000.0000.000
62A72ALA00.0260.00644.919-0.002-0.0020.0000.0000.0000.000
63A73GLU-1-0.760-0.86046.006-0.026-0.0260.0000.0000.0000.000
64A74ALA00.0170.01641.954-0.002-0.0020.0000.0000.0000.000
65A75ILE0-0.040-0.02841.059-0.002-0.0020.0000.0000.0000.000
66A76ASN00.0210.01241.571-0.004-0.0040.0000.0000.0000.000
67A77THR0-0.039-0.00740.728-0.001-0.0010.0000.0000.0000.000
68A78GLU-1-0.823-0.92238.438-0.053-0.0530.0000.0000.0000.000
69A79ASP-1-0.801-0.91333.354-0.067-0.0670.0000.0000.0000.000
70A80LYS10.8550.92034.8630.0660.0660.0000.0000.0000.000
71A81ILE00.0310.02336.3420.0010.0010.0000.0000.0000.000
72A82LEU0-0.033-0.01236.3180.0020.0020.0000.0000.0000.000
73A83PHE00.006-0.00729.6770.0010.0010.0000.0000.0000.000
74A84LYS10.8470.92134.4520.0540.0540.0000.0000.0000.000
75A85LEU00.0020.02736.9780.0030.0030.0000.0000.0000.000
76A86VAL0-0.017-0.01233.1660.0030.0030.0000.0000.0000.000
77A87ILE0-0.009-0.00131.3710.0030.0030.0000.0000.0000.000
78A88SER00.010-0.00934.5750.0040.0040.0000.0000.0000.000
79A89LEU0-0.032-0.00138.0650.0030.0030.0000.0000.0000.000
80A90LEU0-0.032-0.02331.9910.0030.0030.0000.0000.0000.000
81A91HIS00.015-0.00431.9400.0060.0060.0000.0000.0000.000
82A92SER0-0.024-0.02436.6170.0020.0020.0000.0000.0000.000
83A93TRP0-0.045-0.03538.4090.0030.0030.0000.0000.0000.000
84A94ASP-1-0.800-0.88535.261-0.002-0.0020.0000.0000.0000.000
85A95GLU-1-0.814-0.90137.851-0.005-0.0050.0000.0000.0000.000
86A96PRO00.0290.00741.1090.0020.0020.0000.0000.0000.000
87A97LEU0-0.014-0.00337.5680.0020.0020.0000.0000.0000.000
88A98HIS00.0210.01039.3970.0030.0030.0000.0000.0000.000
89A99HIS0-0.035-0.00640.7370.0030.0030.0000.0000.0000.000
90A100ALA0-0.0050.00643.1370.0010.0010.0000.0000.0000.000
91A101VAL0-0.035-0.03138.8750.0020.0020.0000.0000.0000.000
92A102THR0-0.049-0.03042.1640.0020.0020.0000.0000.0000.000
93A103GLU-1-0.797-0.88144.2070.0100.0100.0000.0000.0000.000
94A104LEU0-0.056-0.03443.9810.0010.0010.0000.0000.0000.000
95A105ALA00.0330.01243.3180.0020.0020.0000.0000.0000.000
96A106ASN0-0.108-0.04945.4030.0020.0020.0000.0000.0000.000
97A107SER00.0380.02648.187-0.001-0.0010.0000.0000.0000.000
98A108LYS10.8980.95049.140-0.013-0.0130.0000.0000.0000.000
99A109GLY00.0420.02848.9780.0010.0010.0000.0000.0000.000
100A110THR0-0.060-0.04947.786-0.001-0.0010.0000.0000.0000.000
101A111SER00.0440.03744.2290.0000.0000.0000.0000.0000.000
102A112PRO00.0240.02345.6570.0020.0020.0000.0000.0000.000
103A113ALA0-0.008-0.03542.2770.0000.0000.0000.0000.0000.000
104A114LEU00.0150.00741.6540.0000.0000.0000.0000.0000.000
105A115LEU00.0310.03240.632-0.001-0.0010.0000.0000.0000.000
106A116THR00.0060.01136.5720.0000.0000.0000.0000.0000.000
107A117LYS10.8360.89536.904-0.019-0.0190.0000.0000.0000.000
108A118ALA00.0540.02537.592-0.002-0.0020.0000.0000.0000.000
109A119GLN00.014-0.00435.5620.0000.0000.0000.0000.0000.000
110A120GLU-1-0.793-0.86031.3250.0260.0260.0000.0000.0000.000
111A121ILE0-0.024-0.01232.754-0.002-0.0020.0000.0000.0000.000
112A122LYS10.8110.92034.168-0.005-0.0050.0000.0000.0000.000
113A123GLU-1-0.800-0.88929.9580.0050.0050.0000.0000.0000.000
114A124LYS10.8400.88827.730-0.030-0.0300.0000.0000.0000.000
115A125ALA0-0.022-0.00229.863-0.005-0.0050.0000.0000.0000.000
116A126LYS10.8410.89629.751-0.008-0.0080.0000.0000.0000.000
117A127VAL0-0.015-0.00524.449-0.005-0.0050.0000.0000.0000.000
118A128LEU0-0.057-0.01826.247-0.008-0.0080.0000.0000.0000.000
119A129VAL00.0180.00428.321-0.007-0.0070.0000.0000.0000.000
120A130ASP-1-0.915-0.93223.240-0.064-0.0640.0000.0000.0000.000
121A131GLY00.0290.01223.852-0.011-0.0110.0000.0000.0000.000
122A132VAL0-0.025-0.02824.865-0.011-0.0110.0000.0000.0000.000
123A133GLU-1-0.789-0.88527.831-0.058-0.0580.0000.0000.0000.000
124A134VAL0-0.030-0.01221.113-0.010-0.0100.0000.0000.0000.000
125A135ILE0-0.074-0.04424.472-0.012-0.0120.0000.0000.0000.000
126A136GLN00.004-0.00425.703-0.006-0.0060.0000.0000.0000.000
127A137LYS10.8740.92225.8710.0690.0690.0000.0000.0000.000
128A138ARG10.7800.90218.4140.1920.1920.0000.0000.0000.000
129A139ILE0-0.033-0.01024.772-0.008-0.0080.0000.0000.0000.000
130A140HIS0-0.022-0.01628.0760.0010.0010.0000.0000.0000.000
131A141PRO00.0210.00026.7090.0050.0050.0000.0000.0000.000
132A142GLY0-0.009-0.00129.0780.0040.0040.0000.0000.0000.000
133A143GLU-1-0.812-0.88731.718-0.054-0.0540.0000.0000.0000.000
134A144LYS10.9190.96432.4850.0550.0550.0000.0000.0000.000
135A145ASN0-0.021-0.01432.0000.0010.0010.0000.0000.0000.000
136A146GLU-1-0.874-0.92836.021-0.036-0.0360.0000.0000.0000.000
137A147PRO0-0.019-0.01239.3350.0010.0010.0000.0000.0000.000
138A148TYR0-0.021-0.00537.981-0.001-0.0010.0000.0000.0000.000
139A149PRO0-0.0230.00342.4240.0010.0010.0000.0000.0000.000
140A150VAL00.0530.01643.7670.0000.0000.0000.0000.0000.000
141A151TRP0-0.035-0.03345.9160.0000.0000.0000.0000.0000.000
142A152SER00.017-0.00148.0570.0010.0010.0000.0000.0000.000
143A153GLU-1-0.743-0.82150.781-0.005-0.0050.0000.0000.0000.000
144A154GLN0-0.0110.00545.5670.0020.0020.0000.0000.0000.000
145A155SER00.0300.01449.7640.0010.0010.0000.0000.0000.000
146A156SER0-0.046-0.04251.8820.0010.0010.0000.0000.0000.000
147A157LEU0-0.009-0.01046.9970.0010.0010.0000.0000.0000.000
148A158THR0-0.012-0.01049.7910.0010.0010.0000.0000.0000.000
149A159SER0-0.041-0.00852.4510.0000.0000.0000.0000.0000.000
150A160GLN00.018-0.00656.1600.0010.0010.0000.0000.0000.000
151A161ASP-1-0.845-0.90958.8660.0030.0030.0000.0000.0000.000
152A162GLU-1-0.806-0.89758.0100.0070.0070.0000.0000.0000.000
153A163ASN0-0.022-0.00657.7470.0000.0000.0000.0000.0000.000
154A164VAL00.009-0.00857.0580.0000.0000.0000.0000.0000.000
155A165ARG10.8870.94951.850-0.008-0.0080.0000.0000.0000.000
156A166ARG10.8050.87653.480-0.006-0.0060.0000.0000.0000.000
157A167VAL00.001-0.00553.8060.0000.0000.0000.0000.0000.000
158A168ALA0-0.0020.01151.750-0.001-0.0010.0000.0000.0000.000
159A169PHE00.0280.00146.471-0.001-0.0010.0000.0000.0000.000
160A170TYR0-0.0240.00749.037-0.001-0.0010.0000.0000.0000.000
161A171ARG10.7730.83550.0160.0040.0040.0000.0000.0000.000
162A172LEU00.0100.01244.415-0.001-0.0010.0000.0000.0000.000
163A173PHE00.021-0.00243.593-0.001-0.0010.0000.0000.0000.000
164A174HIS0-0.024-0.02545.095-0.002-0.0020.0000.0000.0000.000
165A176LEU00.0420.03439.222-0.002-0.0020.0000.0000.0000.000
166A177HIS00.0080.01241.309-0.002-0.0020.0000.0000.0000.000
167A178ARG10.9500.97442.3280.0080.0080.0000.0000.0000.000
168A179ASP-1-0.732-0.86040.779-0.017-0.0170.0000.0000.0000.000
169A180SER0-0.019-0.02137.963-0.002-0.0020.0000.0000.0000.000
170A181SER0-0.021-0.00537.873-0.002-0.0020.0000.0000.0000.000
171A182LYS10.8940.96239.6050.0170.0170.0000.0000.0000.000
172A183ILE00.0220.01334.237-0.003-0.0030.0000.0000.0000.000
173A184TYR00.0230.00033.238-0.005-0.0050.0000.0000.0000.000
174A185THR0-0.028-0.02835.310-0.002-0.0020.0000.0000.0000.000
175A186TYR00.004-0.02036.810-0.002-0.0020.0000.0000.0000.000
176A187LEU00.0110.01530.328-0.004-0.0040.0000.0000.0000.000
177A188ARG10.8420.92532.2650.0190.0190.0000.0000.0000.000
178A189ILE0-0.018-0.00334.135-0.003-0.0030.0000.0000.0000.000
179A190LEU0-0.0050.00331.862-0.003-0.0030.0000.0000.0000.000
180A191LYS10.8570.93327.6010.0450.0450.0000.0000.0000.000
181A197CYS0-0.093-0.04529.5970.0010.0010.0000.0000.0000.000
182A193ARG10.8140.91733.5520.0490.0490.0000.0000.0000.000
183A194LEU0-0.010-0.00429.922-0.003-0.0030.0000.0000.0000.000
184A195THR0-0.122-0.06226.052-0.011-0.0110.0000.0000.0000.000
185A196SER00.0210.00627.0390.0040.0040.0000.0000.0000.000