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: M3RQZ

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2007800.396212
FMO2-HF: Nuclear repulsion 1932294.409633
FMO2-HF: Total energy -75505.986579
FMO2-MP2: Total energy -75725.468099


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.
-0.8690.765-0.003-0.899-0.7320.001
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 : 0.027 / 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].
3A3HIS00.0160.0093.505-2.016-0.382-0.003-0.899-0.7320.001
4A4PRO0-0.001-0.0056.2430.4200.4200.0000.0000.0000.000
5A5PRO00.0430.0119.824-0.120-0.1200.0000.0000.0000.000
6A6TYR00.0980.01712.656-0.022-0.0220.0000.0000.0000.000
7A7CYS0-0.0110.0089.702-0.013-0.0130.0000.0000.0000.000
8A8ARG10.9591.0019.9060.3210.3210.0000.0000.0000.000
9A9ASN0-0.066-0.06412.5870.1120.1120.0000.0000.0000.000
10A10GLN00.0470.01314.360-0.025-0.0250.0000.0000.0000.000
11A11PRO0-0.0140.01314.991-0.020-0.0200.0000.0000.0000.000
12A12GLY00.0670.02913.047-0.045-0.0450.0000.0000.0000.000
13A13LYS10.9120.97111.6950.2350.2350.0000.0000.0000.000
14A15GLN0-0.0220.00311.9150.0320.0320.0000.0000.0000.000
15A16ILE0-0.027-0.00114.565-0.004-0.0040.0000.0000.0000.000
16A17PRO00.0430.02116.0060.0120.0120.0000.0000.0000.000
17A18LEU00.0750.02619.0350.0140.0140.0000.0000.0000.000
18A19GLN00.0440.02322.4670.0080.0080.0000.0000.0000.000
19A20SER00.0140.00118.3040.0130.0130.0000.0000.0000.000
20A21LEU0-0.033-0.01319.5540.0160.0160.0000.0000.0000.000
21A22PHE00.0880.03222.1860.0140.0140.0000.0000.0000.000
22A23ASP-1-0.888-0.93723.396-0.053-0.0530.0000.0000.0000.000
23A24ARG10.9560.95816.2270.0770.0770.0000.0000.0000.000
24A25ALA00.0410.03824.2180.0090.0090.0000.0000.0000.000
25A26THR0-0.021-0.02427.0150.0070.0070.0000.0000.0000.000
26A27THR0-0.057-0.02426.2240.0060.0060.0000.0000.0000.000
27A28VAL00.0540.03726.0770.0060.0060.0000.0000.0000.000
28A29ALA00.0260.00028.9170.0030.0030.0000.0000.0000.000
29A30ASN0-0.034-0.01931.8200.0020.0020.0000.0000.0000.000
30A31TYR0-0.037-0.01331.0540.0020.0020.0000.0000.0000.000
31A32ASN00.0510.01432.0490.0050.0050.0000.0000.0000.000
32A33SER00.0120.00234.7980.0010.0010.0000.0000.0000.000
33A34LYS10.8960.95935.803-0.007-0.0070.0000.0000.0000.000
34A35LEU00.0520.02634.0550.0010.0010.0000.0000.0000.000
35A36ALA00.0230.01038.2060.0010.0010.0000.0000.0000.000
36A37GLY00.0250.01340.6630.0000.0000.0000.0000.0000.000
37A38GLU-1-0.929-0.96239.1740.0230.0230.0000.0000.0000.000
38A39MET0-0.082-0.04339.1540.0010.0010.0000.0000.0000.000
39A40VAL00.0050.00144.1260.0000.0000.0000.0000.0000.000
40A41ASN00.0190.01745.807-0.001-0.0010.0000.0000.0000.000
41A42ARG10.8890.94844.781-0.020-0.0200.0000.0000.0000.000
42A43PHE0-0.035-0.01748.3130.0000.0000.0000.0000.0000.000
43A44ASP-1-0.817-0.92250.0500.0050.0050.0000.0000.0000.000
44A45GLU-1-1.006-0.98351.7810.0090.0090.0000.0000.0000.000
45A46GLN0-0.045-0.04951.0370.0020.0020.0000.0000.0000.000
46A47TYR0-0.0620.00451.5940.0000.0000.0000.0000.0000.000
47A57VAL0-0.004-0.01156.3310.0000.0000.0000.0000.0000.000
48A58ILE0-0.005-0.00250.3400.0000.0000.0000.0000.0000.000
49A59ASN0-0.029-0.02552.490-0.001-0.0010.0000.0000.0000.000
50A60CYS0-0.109-0.05346.221-0.001-0.0010.0000.0000.0000.000
51A61HIS00.0840.04443.4620.0000.0000.0000.0000.0000.000
52A62THR0-0.057-0.03842.791-0.001-0.0010.0000.0000.0000.000
53A63SER0-0.080-0.03245.893-0.002-0.0020.0000.0000.0000.000
54A64SER00.0190.01347.901-0.001-0.0010.0000.0000.0000.000
55A65ILE00.0040.01841.851-0.001-0.0010.0000.0000.0000.000
56A66THR0-0.006-0.01245.7720.0010.0010.0000.0000.0000.000
57A67THR0-0.033-0.01543.049-0.001-0.0010.0000.0000.0000.000
58A68PRO00.0140.03842.8520.0010.0010.0000.0000.0000.000
59A69ASN00.0600.01444.9510.0000.0000.0000.0000.0000.000
60A70SER00.0250.01847.4520.0010.0010.0000.0000.0000.000
61A71LYS10.9970.97844.4370.0230.0230.0000.0000.0000.000
62A72ALA0-0.0020.00045.242-0.002-0.0020.0000.0000.0000.000
63A73GLU-1-0.864-0.93546.346-0.025-0.0250.0000.0000.0000.000
64A74ALA0-0.0020.01142.060-0.002-0.0020.0000.0000.0000.000
65A75ILE0-0.057-0.04241.238-0.002-0.0020.0000.0000.0000.000
66A76ASN00.0230.00141.666-0.004-0.0040.0000.0000.0000.000
67A77THR0-0.053-0.00540.649-0.001-0.0010.0000.0000.0000.000
68A78GLU-1-0.851-0.93138.777-0.050-0.0500.0000.0000.0000.000
69A79ASP-1-0.834-0.92833.617-0.065-0.0650.0000.0000.0000.000
70A80LYS10.9510.99035.0040.0640.0640.0000.0000.0000.000
71A81ILE00.0270.00736.3460.0010.0010.0000.0000.0000.000
72A82LEU0-0.017-0.00236.3630.0030.0030.0000.0000.0000.000
73A83PHE00.024-0.00229.7350.0020.0020.0000.0000.0000.000
74A84LYS10.9150.97334.3190.0490.0490.0000.0000.0000.000
75A85LEU00.0130.01036.7170.0030.0030.0000.0000.0000.000
76A86VAL0-0.032-0.01432.9520.0030.0030.0000.0000.0000.000
77A87ILE00.0070.00131.1070.0030.0030.0000.0000.0000.000
78A88SER00.0210.01334.4840.0030.0030.0000.0000.0000.000
79A89LEU0-0.0210.00037.9290.0030.0030.0000.0000.0000.000
80A90LEU0-0.026-0.01931.9250.0030.0030.0000.0000.0000.000
81A91HIS00.0130.01232.2030.0060.0060.0000.0000.0000.000
82A92SER0-0.026-0.02236.5350.0030.0030.0000.0000.0000.000
83A93TRP0-0.070-0.05538.3800.0030.0030.0000.0000.0000.000
84A94ASP-1-0.872-0.93835.5140.0050.0050.0000.0000.0000.000
85A95GLU-1-0.852-0.94537.9640.0010.0010.0000.0000.0000.000
86A96PRO00.0060.00541.2600.0020.0020.0000.0000.0000.000
87A97LEU0-0.011-0.00637.6810.0020.0020.0000.0000.0000.000
88A98HIS00.0000.00439.6180.0040.0040.0000.0000.0000.000
89A99HIS0-0.021-0.01040.8890.0020.0020.0000.0000.0000.000
90A100ALA0-0.0170.00043.2930.0010.0010.0000.0000.0000.000
91A101VAL0-0.014-0.01939.2470.0020.0020.0000.0000.0000.000
92A102THR0-0.021-0.00142.5720.0020.0020.0000.0000.0000.000
93A103GLU-1-0.831-0.89044.6350.0130.0130.0000.0000.0000.000
94A104LEU0-0.080-0.05444.4210.0010.0010.0000.0000.0000.000
95A105ALA00.0230.02643.4630.0020.0020.0000.0000.0000.000
96A106ASN0-0.0590.00345.3880.0020.0020.0000.0000.0000.000
97A107SER00.0350.00247.7570.0000.0000.0000.0000.0000.000
98A108LYS10.9120.96349.611-0.018-0.0180.0000.0000.0000.000
99A109GLY00.0520.03149.5630.0020.0020.0000.0000.0000.000
100A110THR0-0.068-0.06246.910-0.001-0.0010.0000.0000.0000.000
101A111SER00.0860.04844.2810.0000.0000.0000.0000.0000.000
102A112PRO0-0.039-0.00746.0050.0010.0010.0000.0000.0000.000
103A113ALA00.001-0.01842.9050.0010.0010.0000.0000.0000.000
104A114LEU00.0240.00342.0620.0010.0010.0000.0000.0000.000
105A115LEU00.0360.02241.1720.0000.0000.0000.0000.0000.000
106A116THR00.0070.01137.4670.0010.0010.0000.0000.0000.000
107A117LYS10.8810.92937.414-0.025-0.0250.0000.0000.0000.000
108A118ALA00.0340.01737.633-0.001-0.0010.0000.0000.0000.000
109A119GLN00.006-0.00435.8710.0000.0000.0000.0000.0000.000
110A120GLU-1-0.813-0.90431.5310.0400.0400.0000.0000.0000.000
111A121ILE0-0.030-0.01332.969-0.002-0.0020.0000.0000.0000.000
112A122LYS10.8870.96634.215-0.014-0.0140.0000.0000.0000.000
113A123GLU-1-0.957-0.98030.1610.0240.0240.0000.0000.0000.000
114A124LYS10.8850.93726.998-0.041-0.0410.0000.0000.0000.000
115A125ALA0-0.0040.00829.926-0.005-0.0050.0000.0000.0000.000
116A126LYS10.9870.98729.550-0.017-0.0170.0000.0000.0000.000
117A127VAL0-0.0190.00624.658-0.004-0.0040.0000.0000.0000.000
118A128LEU0-0.040-0.02826.225-0.008-0.0080.0000.0000.0000.000
119A129VAL0-0.005-0.00628.132-0.008-0.0080.0000.0000.0000.000
120A130ASP-1-0.881-0.92323.153-0.044-0.0440.0000.0000.0000.000
121A131GLY0-0.013-0.00923.881-0.012-0.0120.0000.0000.0000.000
122A132VAL0-0.037-0.03924.888-0.011-0.0110.0000.0000.0000.000
123A133GLU-1-0.904-0.95026.925-0.049-0.0490.0000.0000.0000.000
124A134VAL0-0.039-0.01220.880-0.012-0.0120.0000.0000.0000.000
125A135ILE0-0.069-0.04224.098-0.014-0.0140.0000.0000.0000.000
126A136GLN00.0370.01625.442-0.007-0.0070.0000.0000.0000.000
127A137LYS10.9360.96725.4230.0680.0680.0000.0000.0000.000
128A138ARG10.8180.91718.4030.1810.1810.0000.0000.0000.000
129A139ILE0-0.021-0.02024.752-0.008-0.0080.0000.0000.0000.000
130A140HIS0-0.058-0.03927.860-0.001-0.0010.0000.0000.0000.000
131A141PRO0-0.011-0.00426.8580.0050.0050.0000.0000.0000.000
132A142GLY0-0.029-0.01229.0080.0040.0040.0000.0000.0000.000
133A143GLU-1-0.859-0.91831.346-0.054-0.0540.0000.0000.0000.000
134A144LYS10.9020.93732.5790.0510.0510.0000.0000.0000.000
135A145ASN0-0.001-0.02132.3650.0020.0020.0000.0000.0000.000
136A146GLU-1-0.903-0.94836.103-0.032-0.0320.0000.0000.0000.000
137A147PRO0-0.040-0.00639.3280.0010.0010.0000.0000.0000.000
138A148TYR00.0090.00137.7440.0000.0000.0000.0000.0000.000
139A149PRO0-0.032-0.01142.0040.0010.0010.0000.0000.0000.000
140A150VAL00.0670.02943.8120.0010.0010.0000.0000.0000.000
141A151TRP0-0.024-0.01046.1350.0000.0000.0000.0000.0000.000
142A152SER00.035-0.00148.2430.0010.0010.0000.0000.0000.000
143A153GLU-1-0.903-0.95750.883-0.002-0.0020.0000.0000.0000.000
144A154GLN00.0240.03045.8670.0020.0020.0000.0000.0000.000
145A155SER00.0410.02349.8800.0010.0010.0000.0000.0000.000
146A156SER0-0.047-0.04651.9770.0010.0010.0000.0000.0000.000
147A157LEU0-0.035-0.02247.2680.0010.0010.0000.0000.0000.000
148A158THR0-0.017-0.01250.2520.0010.0010.0000.0000.0000.000
149A159SER0-0.065-0.01552.7960.0000.0000.0000.0000.0000.000
150A160GLN00.016-0.00656.4560.0010.0010.0000.0000.0000.000
151A161ASP-1-0.910-0.93858.9390.0060.0060.0000.0000.0000.000
152A162GLU-1-0.848-0.96158.5330.0100.0100.0000.0000.0000.000
153A163ASN0-0.022-0.00658.1880.0010.0010.0000.0000.0000.000
154A164VAL0-0.005-0.00557.2140.0000.0000.0000.0000.0000.000
155A165ARG10.8960.94251.519-0.012-0.0120.0000.0000.0000.000
156A166ARG10.9240.95653.723-0.009-0.0090.0000.0000.0000.000
157A167VAL00.0210.00554.0660.0000.0000.0000.0000.0000.000
158A168ALA00.0070.01851.882-0.001-0.0010.0000.0000.0000.000
159A169PHE00.026-0.00546.796-0.001-0.0010.0000.0000.0000.000
160A170TYR00.0010.02249.2650.0000.0000.0000.0000.0000.000
161A171ARG10.8790.93350.1900.0010.0010.0000.0000.0000.000
162A172LEU00.0110.01644.584-0.001-0.0010.0000.0000.0000.000
163A173PHE00.0350.00443.8600.0000.0000.0000.0000.0000.000
164A174HIS00.0360.02145.346-0.002-0.0020.0000.0000.0000.000
165A176LEU00.0450.04039.980-0.001-0.0010.0000.0000.0000.000
166A177HIS00.0020.00441.397-0.001-0.0010.0000.0000.0000.000
167A178ARG10.9490.96642.4210.0060.0060.0000.0000.0000.000
168A179ASP-1-0.752-0.87240.608-0.012-0.0120.0000.0000.0000.000
169A180SER0-0.0130.00237.934-0.002-0.0020.0000.0000.0000.000
170A181SER0-0.015-0.00637.795-0.003-0.0030.0000.0000.0000.000
171A182LYS10.8980.94439.6600.0130.0130.0000.0000.0000.000
172A183ILE00.0280.02434.276-0.003-0.0030.0000.0000.0000.000
173A184TYR00.0260.00933.245-0.004-0.0040.0000.0000.0000.000
174A185THR0-0.046-0.04035.406-0.003-0.0030.0000.0000.0000.000
175A186TYR00.005-0.01136.801-0.003-0.0030.0000.0000.0000.000
176A187LEU00.0200.01430.108-0.004-0.0040.0000.0000.0000.000
177A188ARG10.8980.96332.3680.0160.0160.0000.0000.0000.000
178A189ILE0-0.0170.00234.154-0.003-0.0030.0000.0000.0000.000
179A190LEU00.0130.00931.940-0.003-0.0030.0000.0000.0000.000
180A191LYS10.9110.98327.9190.0390.0390.0000.0000.0000.000
181A197CYS0-0.096-0.06729.7550.0000.0000.0000.0000.0000.000
182A193ARG10.8570.94133.5260.0480.0480.0000.0000.0000.000
183A194LEU0-0.008-0.00529.711-0.003-0.0030.0000.0000.0000.000
184A195THR0-0.093-0.03226.181-0.010-0.0100.0000.0000.0000.000
185A196SER00.0180.02028.0020.0040.0040.0000.0000.0000.000