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: Q165Y

Calculation Name: 2QH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QH9

Chain ID: A

ChEMBL ID:

UniProt ID: O28839

Base Structure: X-ray

Registration Date: 2023-06-20

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1948064.07061
FMO2-HF: Nuclear repulsion 1876418.678269
FMO2-HF: Total energy -71645.392341
FMO2-MP2: Total energy -71849.705091


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:-2:GLY)


Summations of interaction energy for fragment #1(A:-2:GLY)
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.
-5.922-3.144.813-3.373-4.2210.005
Interaction energy analysis for fragmet #1(A:-2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.030
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].
3A0ALA0-0.0050.0083.312-2.640-0.4270.068-1.194-1.0860.007
4A1MET00.0380.0292.075-5.009-4.8884.727-2.129-2.720-0.001
5A2LYS10.9530.9743.4001.9672.3720.019-0.038-0.386-0.001
6A3LYS10.9100.9546.0270.0260.0260.0000.0000.0000.000
7A4TRP00.0040.0046.3160.0040.0040.0000.0000.0000.000
8A5ARG10.8320.8978.729-0.019-0.0190.0000.0000.0000.000
9A6PHE0-0.004-0.0076.7830.0110.0110.0000.0000.0000.000
10A7LEU00.0100.01112.9450.0290.0290.0000.0000.0000.000
11A8GLY00.014-0.00616.525-0.014-0.0140.0000.0000.0000.000
12A9ILE0-0.032-0.01617.8110.0220.0220.0000.0000.0000.000
13A10ASP-1-0.814-0.93421.340-0.175-0.1750.0000.0000.0000.000
14A11ASP-1-0.834-0.94223.977-0.092-0.0920.0000.0000.0000.000
15A12SER00.0000.01527.849-0.004-0.0040.0000.0000.0000.000
16A13PHE00.0100.00531.0600.0030.0030.0000.0000.0000.000
17A14ASP-1-0.779-0.88734.657-0.061-0.0610.0000.0000.0000.000
18A15ASP-1-0.862-0.92238.212-0.049-0.0490.0000.0000.0000.000
19A16ARG10.7890.88240.3960.0470.0470.0000.0000.0000.000
20A17LYS10.8220.89535.9640.0570.0570.0000.0000.0000.000
21A18CYS00.0050.03632.053-0.004-0.0040.0000.0000.0000.000
22A19CYS0-0.102-0.02031.6780.0020.0020.0000.0000.0000.000
23A20VAL00.0540.00626.157-0.006-0.0060.0000.0000.0000.000
24A21VAL0-0.016-0.00424.3850.0070.0070.0000.0000.0000.000
25A22GLY00.0180.00322.066-0.012-0.0120.0000.0000.0000.000
26A23CYS0-0.040-0.00819.8290.0090.0090.0000.0000.0000.000
27A24VAL00.0230.00216.669-0.023-0.0230.0000.0000.0000.000
28A25THR00.006-0.00214.475-0.010-0.0100.0000.0000.0000.000
29A26CYS0-0.0280.00511.4550.0060.0060.0000.0000.0000.000
30A27GLY00.0340.01610.4100.0310.0310.0000.0000.0000.000
31A28GLY0-0.029-0.01611.3370.0080.0080.0000.0000.0000.000
32A29TYR0-0.0170.00514.1720.0370.0370.0000.0000.0000.000
33A30VAL00.0250.00216.529-0.008-0.0080.0000.0000.0000.000
34A31GLU-1-0.838-0.91116.237-0.057-0.0570.0000.0000.0000.000
35A32GLY0-0.033-0.02220.0030.0200.0200.0000.0000.0000.000
36A33PHE00.0080.00121.565-0.018-0.0180.0000.0000.0000.000
37A34LEU0-0.077-0.02921.8490.0110.0110.0000.0000.0000.000
38A35TYR00.027-0.01625.526-0.008-0.0080.0000.0000.0000.000
39A36THR0-0.010-0.01828.2980.0090.0090.0000.0000.0000.000
40A37GLU-1-0.768-0.83030.588-0.061-0.0610.0000.0000.0000.000
41A38ILE0-0.067-0.03730.0550.0020.0020.0000.0000.0000.000
42A39ASP-1-0.831-0.91433.721-0.050-0.0500.0000.0000.0000.000
43A40ILE00.0260.01535.756-0.003-0.0030.0000.0000.0000.000
44A41ASP-1-0.830-0.90035.877-0.061-0.0610.0000.0000.0000.000
45A42GLY00.0130.02036.3280.0030.0030.0000.0000.0000.000
46A43LEU0-0.036-0.03234.852-0.002-0.0020.0000.0000.0000.000
47A44ASP-1-0.737-0.84233.815-0.060-0.0600.0000.0000.0000.000
48A45ALA00.0420.02029.070-0.001-0.0010.0000.0000.0000.000
49A46THR00.006-0.00127.216-0.006-0.0060.0000.0000.0000.000
50A47ASP-1-0.813-0.88127.785-0.054-0.0540.0000.0000.0000.000
51A48LYS10.7760.88929.8250.0580.0580.0000.0000.0000.000
52A49LEU00.0320.01523.699-0.001-0.0010.0000.0000.0000.000
53A50ILE0-0.0230.00125.113-0.002-0.0020.0000.0000.0000.000
54A51SER0-0.018-0.01426.1870.0040.0040.0000.0000.0000.000
55A52MET0-0.038-0.01123.7830.0050.0050.0000.0000.0000.000
56A53VAL0-0.010-0.00920.9620.0000.0000.0000.0000.0000.000
57A54ARG10.9300.95323.5450.0400.0400.0000.0000.0000.000
58A55ARG10.8960.96125.9490.0640.0640.0000.0000.0000.000
59A56SER0-0.0130.00820.7420.0050.0050.0000.0000.0000.000
60A57LYS10.9490.96722.8160.0440.0440.0000.0000.0000.000
61A58PHE00.0240.00918.2180.0080.0080.0000.0000.0000.000
62A59ARG10.8440.91518.2350.0110.0110.0000.0000.0000.000
63A60GLU-1-0.802-0.87118.6630.0090.0090.0000.0000.0000.000
64A61GLN00.015-0.00715.6960.0050.0050.0000.0000.0000.000
65A62ILE0-0.023-0.00813.7870.0020.0020.0000.0000.0000.000
66A63LYS10.7750.87310.0210.0350.0350.0000.0000.0000.000
67A64CYS0-0.020-0.00210.707-0.038-0.0380.0000.0000.0000.000
68A65ILE00.0180.02012.6740.0010.0010.0000.0000.0000.000
69A66PHE0-0.025-0.02010.243-0.023-0.0230.0000.0000.0000.000
70A67LEU00.0430.02316.4760.0220.0220.0000.0000.0000.000
71A68PRO00.0210.02119.587-0.020-0.0200.0000.0000.0000.000
72A69GLY00.028-0.00821.7840.0040.0040.0000.0000.0000.000
73A70ILE0-0.004-0.00423.574-0.004-0.0040.0000.0000.0000.000
74A71THR0-0.052-0.03425.1450.0110.0110.0000.0000.0000.000
75A72LEU0-0.023-0.00924.919-0.011-0.0110.0000.0000.0000.000
76A73GLY00.051-0.00828.9760.0060.0060.0000.0000.0000.000
77A74GLY0-0.0060.02231.9820.0060.0060.0000.0000.0000.000
78A75PHE0-0.033-0.02731.941-0.006-0.0060.0000.0000.0000.000
79A76ASN0-0.039-0.01932.1920.0030.0030.0000.0000.0000.000
80A77LEU0-0.005-0.00129.187-0.007-0.0070.0000.0000.0000.000
81A78VAL00.000-0.01724.2720.0040.0040.0000.0000.0000.000
82A79ASP-1-0.739-0.87625.894-0.080-0.0800.0000.0000.0000.000
83A80ILE00.011-0.00820.2120.0020.0020.0000.0000.0000.000
84A81GLN0-0.009-0.01021.202-0.001-0.0010.0000.0000.0000.000
85A82ARG10.7230.83223.2560.0610.0610.0000.0000.0000.000
86A83VAL00.0240.01320.6550.0060.0060.0000.0000.0000.000
87A84TYR0-0.0070.03417.1930.0090.0090.0000.0000.0000.000
88A85ARG10.8190.90920.6110.0690.0690.0000.0000.0000.000
89A86GLU-1-0.857-0.93423.705-0.038-0.0380.0000.0000.0000.000
90A87THR0-0.073-0.05920.5960.0030.0030.0000.0000.0000.000
91A88LYS10.9080.95919.4640.0250.0250.0000.0000.0000.000
92A89ILE0-0.0180.00914.8480.0010.0010.0000.0000.0000.000
93A90PRO0-0.0160.00112.7800.0040.0040.0000.0000.0000.000
94A91VAL00.020-0.00215.239-0.020-0.0200.0000.0000.0000.000
95A92VAL0-0.028-0.01912.373-0.006-0.0060.0000.0000.0000.000
96A93VAL00.0110.02815.682-0.010-0.0100.0000.0000.0000.000
97A94VAL0-0.022-0.02714.664-0.024-0.0240.0000.0000.0000.000
98A95MET00.0440.03317.6830.0200.0200.0000.0000.0000.000
99A96ARG10.9140.93719.5470.2080.2080.0000.0000.0000.000
100A97ARG10.8970.93420.7380.1560.1560.0000.0000.0000.000
101A98LYS10.9891.01124.0610.0960.0960.0000.0000.0000.000
102A99PRO00.0300.02224.5370.0060.0060.0000.0000.0000.000
103A100ASP-1-0.848-0.92427.514-0.077-0.0770.0000.0000.0000.000
104A101MET00.000-0.02328.728-0.002-0.0020.0000.0000.0000.000
105A102GLU-1-0.920-0.94831.749-0.057-0.0570.0000.0000.0000.000
106A103GLU-1-0.953-0.97334.366-0.071-0.0710.0000.0000.0000.000
107A104PHE00.0010.01031.6880.0020.0020.0000.0000.0000.000
108A105ASP-1-0.785-0.88334.290-0.051-0.0510.0000.0000.0000.000
109A106SER0-0.094-0.06836.5970.0040.0040.0000.0000.0000.000
110A107ALA00.0270.02537.4220.0030.0030.0000.0000.0000.000
111A108MET00.0010.00734.3360.0010.0010.0000.0000.0000.000
112A109ARG10.8820.92537.7840.0500.0500.0000.0000.0000.000
113A110ASN0-0.110-0.04740.8010.0050.0050.0000.0000.0000.000
114A111LEU0-0.0200.00937.6360.0010.0010.0000.0000.0000.000
115A112GLU-1-0.922-0.96141.224-0.038-0.0380.0000.0000.0000.000
116A113ASN00.001-0.01639.116-0.003-0.0030.0000.0000.0000.000
117A114TYR00.0410.00737.914-0.002-0.0020.0000.0000.0000.000
118A115GLU-1-0.811-0.89337.461-0.044-0.0440.0000.0000.0000.000
119A116LEU0-0.076-0.02733.806-0.002-0.0020.0000.0000.0000.000
120A117ARG10.8040.88733.6820.0520.0520.0000.0000.0000.000
121A118ARG10.8310.86432.6890.0430.0430.0000.0000.0000.000
122A119LYS11.0001.00332.0690.0430.0430.0000.0000.0000.000
123A120ILE0-0.057-0.03028.174-0.003-0.0030.0000.0000.0000.000
124A121VAL00.008-0.00528.087-0.008-0.0080.0000.0000.0000.000
125A122GLU-1-0.855-0.89328.038-0.060-0.0600.0000.0000.0000.000
126A123VAL0-0.068-0.03726.711-0.002-0.0020.0000.0000.0000.000
127A124ALA0-0.027-0.00923.889-0.006-0.0060.0000.0000.0000.000
128A125GLY00.0130.01222.753-0.014-0.0140.0000.0000.0000.000
129A126GLU-1-0.878-0.92922.110-0.110-0.1100.0000.0000.0000.000
130A127ILE0-0.007-0.00821.558-0.016-0.0160.0000.0000.0000.000
131A128HIS0-0.031-0.01817.774-0.008-0.0080.0000.0000.0000.000
132A129ARG10.8540.90718.7600.1430.1430.0000.0000.0000.000
133A130ILE0-0.004-0.00613.4260.0030.0030.0000.0000.0000.000
134A131GLY0-0.0010.01815.038-0.033-0.0330.0000.0000.0000.000
135A132ASP-1-0.888-0.93816.566-0.154-0.1540.0000.0000.0000.000
136A133ILE0-0.090-0.04114.0260.0040.0040.0000.0000.0000.000
137A134TYR00.0340.00217.8410.0050.0050.0000.0000.0000.000
138A135ILE0-0.045-0.02314.028-0.020-0.0200.0000.0000.0000.000
139A136GLN00.0280.01318.0150.0160.0160.0000.0000.0000.000
140A137THR0-0.058-0.04115.298-0.020-0.0200.0000.0000.0000.000
141A138ALA00.0580.04017.1980.0250.0250.0000.0000.0000.000
142A139GLY00.012-0.00916.586-0.017-0.0170.0000.0000.0000.000
143A140LEU0-0.042-0.01610.722-0.015-0.0150.0000.0000.0000.000
144A141THR00.000-0.02513.0220.0040.0040.0000.0000.0000.000
145A142PRO00.0680.02913.305-0.057-0.0570.0000.0000.0000.000
146A143SER00.0550.00610.898-0.054-0.0540.0000.0000.0000.000
147A144GLU-1-0.873-0.8928.696-0.323-0.3230.0000.0000.0000.000
148A145ALA00.0540.0278.538-0.182-0.1820.0000.0000.0000.000
149A146GLU-1-0.819-0.8769.666-0.484-0.4840.0000.0000.0000.000
150A147LYS10.8350.9104.9300.4480.4480.0000.0000.0000.000
151A148LEU00.0380.0055.590-0.470-0.4700.0000.0000.0000.000
152A149VAL00.0370.0237.463-0.025-0.0250.0000.0000.0000.000
153A150LYS10.8330.9026.1040.5530.5530.0000.0000.0000.000
154A151ALA0-0.066-0.0334.273-0.180-0.137-0.001-0.012-0.0290.000
155A152SER00.008-0.0025.8480.2160.2160.0000.0000.0000.000
156A153LEU0-0.0390.0009.1700.1710.1710.0000.0000.0000.000
157A154ILE0-0.015-0.00410.245-0.076-0.0760.0000.0000.0000.000
158A155LYS10.9450.96012.9400.2430.2430.0000.0000.0000.000
159A156GLY00.0310.01815.1890.0390.0390.0000.0000.0000.000
160A157ASN00.0170.01114.503-0.038-0.0380.0000.0000.0000.000
161A158MET00.0230.01715.7610.0050.0050.0000.0000.0000.000
162A159PRO00.0310.02113.067-0.012-0.0120.0000.0000.0000.000
163A160GLU-1-0.767-0.85313.513-0.242-0.2420.0000.0000.0000.000
164A161PRO0-0.035-0.01714.3340.0410.0410.0000.0000.0000.000
165A162VAL00.0110.02316.9860.0260.0260.0000.0000.0000.000
166A163ARG10.7930.87618.0900.2600.2600.0000.0000.0000.000
167A164ILE0-0.021-0.01718.6300.0230.0230.0000.0000.0000.000
168A165SER00.006-0.02321.2110.0220.0220.0000.0000.0000.000
169A166HIS00.0130.02322.7130.0090.0090.0000.0000.0000.000
170A167LEU0-0.027-0.00123.4220.0120.0120.0000.0000.0000.000
171A168VAL0-0.017-0.00825.6420.0110.0110.0000.0000.0000.000
172A169ALA00.0500.01527.1430.0090.0090.0000.0000.0000.000
173A170SER0-0.017-0.03128.0850.0080.0080.0000.0000.0000.000
174A171ALA0-0.029-0.01130.2760.0060.0060.0000.0000.0000.000
175A172ILE0-0.038-0.01230.3550.0060.0060.0000.0000.0000.000
176A173ILE0-0.0380.00033.5100.0050.0050.0000.0000.0000.000
177A174HIS0-0.035-0.00732.8590.0070.0070.0000.0000.0000.000
178A175GLY0-0.093-0.05536.0890.0040.0040.0000.0000.0000.000