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: Z6VJN

Calculation Name: 2F6I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F6I

Chain ID: A

ChEMBL ID:

UniProt ID: O97252

Base Structure: X-ray

Registration Date: 2023-06-22

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2041742.53945
FMO2-HF: Nuclear repulsion 1968279.118682
FMO2-HF: Total energy -73463.420768
FMO2-MP2: Total energy -73678.783375


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:177:HIS)


Summations of interaction energy for fragment #1(A:177:HIS)
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.
-7.318-3.3521.726-2.056-3.6360.001
Interaction energy analysis for fragmet #1(A:177:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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].
3A179ASP-1-0.871-0.9152.663-10.887-7.1881.722-1.990-3.4310.001
4A180ILE0-0.024-0.0134.413-1.197-0.9300.004-0.066-0.2050.000
5A181LYS10.8210.9116.0182.3182.3180.0000.0000.0000.000
6A182ASP-1-0.762-0.87410.756-0.128-0.1280.0000.0000.0000.000
7A183MET00.010-0.00212.9190.0520.0520.0000.0000.0000.000
8A184LYS10.9190.96214.8620.0450.0450.0000.0000.0000.000
9A185LYS10.9440.96314.1190.7120.7120.0000.0000.0000.000
10A186ASP-1-0.804-0.93610.791-1.100-1.1000.0000.0000.0000.000
11A187VAL00.0150.02511.545-0.176-0.1760.0000.0000.0000.000
12A188LYS10.9370.96312.8790.1670.1670.0000.0000.0000.000
13A189LEU00.0190.02311.214-0.062-0.0620.0000.0000.0000.000
14A190PHE0-0.011-0.0135.977-0.126-0.1260.0000.0000.0000.000
15A191PHE0-0.027-0.02910.128-0.094-0.0940.0000.0000.0000.000
16A192PHE00.0390.04012.860-0.017-0.0170.0000.0000.0000.000
17A193LYS10.9500.9688.8712.3572.3570.0000.0000.0000.000
18A194LYS10.8830.9547.8331.2341.2340.0000.0000.0000.000
19A195ARG10.8310.93012.5690.7220.7220.0000.0000.0000.000
20A196ILE0-0.051-0.01513.9950.1090.1090.0000.0000.0000.000
21A197ILE00.0390.01216.813-0.045-0.0450.0000.0000.0000.000
22A198TYR0-0.057-0.04215.4540.0710.0710.0000.0000.0000.000
23A199LEU00.0320.03621.614-0.007-0.0070.0000.0000.0000.000
24A200THR0-0.081-0.06823.2400.0170.0170.0000.0000.0000.000
25A201ASP-1-0.860-0.93425.972-0.109-0.1090.0000.0000.0000.000
26A202GLU-1-0.910-0.92928.820-0.097-0.0970.0000.0000.0000.000
27A203ILE0-0.027-0.01431.297-0.015-0.0150.0000.0000.0000.000
28A204ASN00.0540.02532.185-0.005-0.0050.0000.0000.0000.000
29A205LYS10.9540.96732.8910.1540.1540.0000.0000.0000.000
30A206LYS10.9360.97326.5600.2160.2160.0000.0000.0000.000
31A207THR00.004-0.00628.053-0.023-0.0230.0000.0000.0000.000
32A208ALA00.0210.01627.975-0.022-0.0220.0000.0000.0000.000
33A209ASP-1-0.915-0.95229.161-0.300-0.3000.0000.0000.0000.000
34A210GLU-1-0.908-0.94324.595-0.319-0.3190.0000.0000.0000.000
35A211LEU0-0.023-0.01524.038-0.039-0.0390.0000.0000.0000.000
36A212ILE00.0340.01225.197-0.025-0.0250.0000.0000.0000.000
37A213SER0-0.017-0.02024.825-0.020-0.0200.0000.0000.0000.000
38A214GLN0-0.066-0.04520.425-0.043-0.0430.0000.0000.0000.000
39A215LEU00.0040.00821.752-0.045-0.0450.0000.0000.0000.000
40A216LEU00.0310.01623.697-0.020-0.0200.0000.0000.0000.000
41A217TYR0-0.019-0.00716.066-0.028-0.0280.0000.0000.0000.000
42A218LEU0-0.013-0.02217.141-0.052-0.0520.0000.0000.0000.000
43A219ASP-1-0.775-0.86420.288-0.409-0.4090.0000.0000.0000.000
44A220ASN0-0.041-0.01022.559-0.013-0.0130.0000.0000.0000.000
45A221ILE0-0.060-0.00616.552-0.028-0.0280.0000.0000.0000.000
46A222ASN0-0.010-0.01917.1550.0590.0590.0000.0000.0000.000
47A223HIS00.0130.00221.0450.0340.0340.0000.0000.0000.000
48A224ASN0-0.0150.00117.7960.0770.0770.0000.0000.0000.000
49A225ASP-1-0.775-0.87921.069-0.297-0.2970.0000.0000.0000.000
50A226ILE00.0020.01819.630-0.060-0.0600.0000.0000.0000.000
51A227LYS10.9020.96316.9430.3110.3110.0000.0000.0000.000
52A228ILE00.0260.00620.256-0.033-0.0330.0000.0000.0000.000
53A229TYR0-0.039-0.01917.3020.0260.0260.0000.0000.0000.000
54A230ILE0-0.009-0.01622.776-0.013-0.0130.0000.0000.0000.000
55A231ASN00.013-0.00125.7950.0260.0260.0000.0000.0000.000
56A232SER00.010-0.00727.610-0.002-0.0020.0000.0000.0000.000
57A233PRO00.0450.02730.6320.0040.0040.0000.0000.0000.000
58A234GLY00.0430.01833.4490.0030.0030.0000.0000.0000.000
59A235GLY00.0710.03534.717-0.004-0.0040.0000.0000.0000.000
60A236SER0-0.014-0.01636.6690.0080.0080.0000.0000.0000.000
61A237ILE00.0230.00037.337-0.009-0.0090.0000.0000.0000.000
62A238ASN00.0200.01838.741-0.007-0.0070.0000.0000.0000.000
63A239GLU-1-0.852-0.94234.370-0.175-0.1750.0000.0000.0000.000
64A240GLY00.002-0.00734.156-0.012-0.0120.0000.0000.0000.000
65A241LEU00.002-0.01834.636-0.007-0.0070.0000.0000.0000.000
66A242ALA00.0400.04134.526-0.006-0.0060.0000.0000.0000.000
67A243ILE0-0.030-0.01629.393-0.014-0.0140.0000.0000.0000.000
68A244LEU0-0.021-0.01131.391-0.012-0.0120.0000.0000.0000.000
69A245ASP-1-0.878-0.93533.570-0.173-0.1730.0000.0000.0000.000
70A246ILE0-0.043-0.03828.499-0.011-0.0110.0000.0000.0000.000
71A247PHE0-0.032-0.04027.378-0.021-0.0210.0000.0000.0000.000
72A248ASN0-0.056-0.03129.788-0.007-0.0070.0000.0000.0000.000
73A249TYR0-0.0780.00431.3560.0050.0050.0000.0000.0000.000
74A250ILE0-0.069-0.03125.261-0.011-0.0110.0000.0000.0000.000
75A251LYS10.9300.95327.4540.2920.2920.0000.0000.0000.000
76A252SER0-0.073-0.05623.397-0.005-0.0050.0000.0000.0000.000
77A253ASP-1-0.828-0.90425.359-0.214-0.2140.0000.0000.0000.000
78A254ILE00.0160.00024.424-0.028-0.0280.0000.0000.0000.000
79A255GLN0-0.111-0.05421.8220.0430.0430.0000.0000.0000.000
80A256THR0-0.008-0.00524.246-0.017-0.0170.0000.0000.0000.000
81A257ILE0-0.019-0.01221.1230.0200.0200.0000.0000.0000.000
82A258SER00.0500.03724.823-0.011-0.0110.0000.0000.0000.000
83A259PHE0-0.065-0.05221.5880.0190.0190.0000.0000.0000.000
84A260GLY00.0100.01326.575-0.010-0.0100.0000.0000.0000.000
85A261LEU00.0160.00428.6320.0070.0070.0000.0000.0000.000
86A262VAL00.004-0.00529.986-0.012-0.0120.0000.0000.0000.000
87A263ALA00.0150.00832.6080.0080.0080.0000.0000.0000.000
88A264SER00.0570.03835.632-0.013-0.0130.0000.0000.0000.000
89A265MET00.017-0.00235.2130.0010.0010.0000.0000.0000.000
90A266ALA0-0.0120.02231.658-0.010-0.0100.0000.0000.0000.000
91A267SER0-0.002-0.02432.414-0.005-0.0050.0000.0000.0000.000
92A268VAL00.0170.01434.458-0.002-0.0020.0000.0000.0000.000
93A269ILE00.0040.00629.493-0.005-0.0050.0000.0000.0000.000
94A270LEU0-0.028-0.00328.929-0.011-0.0110.0000.0000.0000.000
95A271ALA00.0200.00331.190-0.004-0.0040.0000.0000.0000.000
96A272SER0-0.068-0.03831.854-0.002-0.0020.0000.0000.0000.000
97A273GLY00.0080.01529.469-0.011-0.0110.0000.0000.0000.000
98A274LYS10.8700.94028.4610.2040.2040.0000.0000.0000.000
99A275LYS10.9270.96230.2400.1240.1240.0000.0000.0000.000
100A276GLY0-0.009-0.00931.209-0.005-0.0050.0000.0000.0000.000
101A277LYS10.7520.85025.3760.2250.2250.0000.0000.0000.000
102A278ARG10.7750.92426.8910.0860.0860.0000.0000.0000.000
103A279LYS10.9680.97622.8670.1110.1110.0000.0000.0000.000
104A280SER00.0570.02227.252-0.011-0.0110.0000.0000.0000.000
105A281LEU0-0.049-0.01022.5050.0130.0130.0000.0000.0000.000
106A282PRO00.0520.01126.409-0.008-0.0080.0000.0000.0000.000
107A283ASN0-0.021-0.02428.382-0.010-0.0100.0000.0000.0000.000
108A284CYS0-0.0690.01228.935-0.004-0.0040.0000.0000.0000.000
109A285ARG10.9010.96530.614-0.010-0.0100.0000.0000.0000.000
110A286ILE00.022-0.00431.954-0.008-0.0080.0000.0000.0000.000
111A287MET00.0220.03835.3650.0070.0070.0000.0000.0000.000
112A288ILE00.0350.01537.943-0.009-0.0090.0000.0000.0000.000
113A289HIS00.0890.06040.550-0.009-0.0090.0000.0000.0000.000
114A290GLN0-0.018-0.03540.166-0.001-0.0010.0000.0000.0000.000
115A291PRO0-0.0010.00637.2680.0030.0030.0000.0000.0000.000
116A292LEU0-0.008-0.00235.8620.0050.0050.0000.0000.0000.000
117A293GLY00.0420.03940.2360.0000.0000.0000.0000.0000.000
118A294ASN0-0.083-0.05142.758-0.003-0.0030.0000.0000.0000.000
119A295ALA0-0.031-0.00944.578-0.004-0.0040.0000.0000.0000.000
120A296PHE00.0360.02640.252-0.002-0.0020.0000.0000.0000.000
121A305GLN00.0300.00649.8260.0030.0030.0000.0000.0000.000
122A306THR00.0860.02850.763-0.003-0.0030.0000.0000.0000.000
123A307LYS10.9810.97951.8430.0590.0590.0000.0000.0000.000
124A308GLU-1-0.868-0.92846.945-0.094-0.0940.0000.0000.0000.000
125A309ILE0-0.028-0.00846.960-0.003-0.0030.0000.0000.0000.000
126A310LEU0-0.026-0.02247.522-0.001-0.0010.0000.0000.0000.000
127A311TYR0-0.0030.00546.1270.0020.0020.0000.0000.0000.000
128A312LEU00.0370.01243.058-0.002-0.0020.0000.0000.0000.000
129A313LYS10.9400.98244.2000.0560.0560.0000.0000.0000.000
130A314LYS11.0171.01445.4780.0670.0670.0000.0000.0000.000
131A315LEU0-0.0190.00043.0390.0010.0010.0000.0000.0000.000
132A316LEU00.0010.00139.799-0.004-0.0040.0000.0000.0000.000
133A317TYR00.015-0.01142.008-0.002-0.0020.0000.0000.0000.000
134A318HIS0-0.010-0.00844.2160.0030.0030.0000.0000.0000.000
135A319TYR00.0270.01839.3300.0000.0000.0000.0000.0000.000
136A320LEU00.0270.01738.277-0.003-0.0030.0000.0000.0000.000
137A321SER0-0.038-0.01640.6330.0020.0020.0000.0000.0000.000
138A322SER0-0.040-0.02441.0760.0000.0000.0000.0000.0000.000
139A323PHE0-0.038-0.02836.591-0.005-0.0050.0000.0000.0000.000
140A324THR0-0.058-0.04638.3460.0020.0020.0000.0000.0000.000
141A325ASN0-0.052-0.02240.3270.0030.0030.0000.0000.0000.000
142A326GLN00.0140.02943.0320.0070.0070.0000.0000.0000.000
143A327THR00.0470.04145.392-0.004-0.0040.0000.0000.0000.000
144A328VAL00.0620.01247.2810.0000.0000.0000.0000.0000.000
145A329GLU-1-0.888-0.94648.689-0.049-0.0490.0000.0000.0000.000
146A330THR0-0.046-0.03346.7190.0050.0050.0000.0000.0000.000
147A331ILE0-0.0200.00143.0190.0020.0020.0000.0000.0000.000
148A332GLU-1-0.912-0.95246.061-0.050-0.0500.0000.0000.0000.000
149A333LYS10.8650.95148.2240.0340.0340.0000.0000.0000.000
150A334ASP-1-0.825-0.92144.737-0.027-0.0270.0000.0000.0000.000
151A335SER0-0.052-0.02944.6710.0010.0010.0000.0000.0000.000
152A336ASP-1-0.913-0.95945.653-0.039-0.0390.0000.0000.0000.000
153A337ARG10.7970.91546.4920.0220.0220.0000.0000.0000.000
154A338ASP-1-0.928-0.95844.436-0.022-0.0220.0000.0000.0000.000
155A339TYR0-0.029-0.02442.8980.0040.0040.0000.0000.0000.000
156A340TYR0-0.041-0.03438.106-0.004-0.0040.0000.0000.0000.000
157A341MET0-0.0250.00837.8210.0030.0030.0000.0000.0000.000
158A342ASN0-0.022-0.00535.443-0.002-0.0020.0000.0000.0000.000
159A343ALA00.0800.02031.495-0.006-0.0060.0000.0000.0000.000
160A344LEU00.0190.00533.441-0.008-0.0080.0000.0000.0000.000
161A345GLU-1-0.841-0.93235.837-0.002-0.0020.0000.0000.0000.000
162A346ALA00.0420.01934.542-0.006-0.0060.0000.0000.0000.000
163A347LYS10.8870.94833.3680.0100.0100.0000.0000.0000.000
164A348GLN0-0.069-0.03835.977-0.005-0.0050.0000.0000.0000.000
165A349TYR0-0.028-0.03339.082-0.005-0.0050.0000.0000.0000.000
166A350GLY00.0490.02438.087-0.004-0.0040.0000.0000.0000.000
167A351ILE0-0.046-0.02633.833-0.010-0.0100.0000.0000.0000.000
168A352ILE0-0.045-0.02130.836-0.011-0.0110.0000.0000.0000.000
169A353ASP-1-0.770-0.87530.898-0.091-0.0910.0000.0000.0000.000
170A354GLU-1-0.992-1.01427.088-0.023-0.0230.0000.0000.0000.000
171A355VAL0-0.0070.00129.355-0.007-0.0070.0000.0000.0000.000
172A356ILE0-0.026-0.01422.8010.0040.0040.0000.0000.0000.000
173A357GLU-1-0.834-0.90526.2970.0900.0900.0000.0000.0000.000
174A358THR0-0.072-0.05423.2860.0150.0150.0000.0000.0000.000
175A359LYS10.9280.94719.293-0.336-0.3360.0000.0000.0000.000
176A360LEU0-0.022-0.00524.9710.0100.0100.0000.0000.0000.000
177A361PRO00.0490.04327.703-0.012-0.0120.0000.0000.0000.000
178A362HIS00.0300.01730.9130.0060.0060.0000.0000.0000.000
179A363PRO0-0.003-0.01633.036-0.004-0.0040.0000.0000.0000.000
180A364TYR0-0.020-0.01836.436-0.002-0.0020.0000.0000.0000.000
181A365PHE0-0.034-0.00332.486-0.009-0.0090.0000.0000.0000.000
182A366ASN00.0070.00734.5310.0000.0000.0000.0000.0000.000