Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 9G392

Calculation Name: 2DOK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DOK

Chain ID: A

ChEMBL ID:

UniProt ID: Q86US8

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1865378.443663
FMO2-HF: Nuclear repulsion 1794915.032785
FMO2-HF: Total energy -70463.410878
FMO2-MP2: Total energy -70669.058738


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:GLY)


Summations of interaction energy for fragment #1(A:1: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.
-0.7180.4890.034-0.601-0.6390.001
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.004
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].
3A3PRO0-0.032-0.0323.489-1.465-0.2530.035-0.599-0.6480.001
4A4GLU-1-0.913-0.9445.334-0.010-0.0100.0000.0000.0000.000
5A5PHE0-0.064-0.0276.8520.0330.0330.0000.0000.0000.000
6A6MET0-0.0150.00310.0300.0500.0500.0000.0000.0000.000
7A7GLU-1-0.833-0.90312.0860.3890.3890.0000.0000.0000.000
8A8LEU0-0.019-0.01614.806-0.018-0.0180.0000.0000.0000.000
9A9GLU-1-0.841-0.90918.4200.1790.1790.0000.0000.0000.000
10A10ILE0-0.044-0.02720.244-0.019-0.0190.0000.0000.0000.000
11A11ARG10.8350.89723.125-0.101-0.1010.0000.0000.0000.000
12A12PRO0-0.056-0.02726.390-0.007-0.0070.0000.0000.0000.000
13A13LEU00.0340.03429.5700.0010.0010.0000.0000.0000.000
14A14PHE00.017-0.00130.810-0.004-0.0040.0000.0000.0000.000
15A15LEU0-0.018-0.01032.1020.0020.0020.0000.0000.0000.000
16A16VAL00.0370.01733.268-0.003-0.0030.0000.0000.0000.000
17A17PRO0-0.0040.00935.1690.0000.0000.0000.0000.0000.000
18A18ASP-1-0.765-0.86137.6310.0120.0120.0000.0000.0000.000
19A19THR00.019-0.04139.4180.0020.0020.0000.0000.0000.000
20A20ASN0-0.035-0.02641.474-0.001-0.0010.0000.0000.0000.000
21A21GLY00.001-0.00440.7070.0010.0010.0000.0000.0000.000
22A22PHE00.005-0.00741.4940.0020.0020.0000.0000.0000.000
23A23ILE0-0.030-0.01044.8410.0000.0000.0000.0000.0000.000
24A24ASP-1-0.860-0.93144.4190.0130.0130.0000.0000.0000.000
25A25HIS0-0.032-0.01340.6670.0020.0020.0000.0000.0000.000
26A26LEU00.0380.03544.1950.0020.0020.0000.0000.0000.000
27A27ALA00.012-0.00246.0810.0010.0010.0000.0000.0000.000
28A28SER0-0.006-0.00641.9240.0010.0010.0000.0000.0000.000
29A29LEU00.0030.00539.8200.0020.0020.0000.0000.0000.000
30A30ALA0-0.0100.01042.6690.0010.0010.0000.0000.0000.000
31A31ARG10.9400.95544.276-0.031-0.0310.0000.0000.0000.000
32A32LEU0-0.028-0.00937.7130.0020.0020.0000.0000.0000.000
33A33LEU0-0.0010.02940.9380.0020.0020.0000.0000.0000.000
34A34GLU-1-0.884-0.95042.9090.0280.0280.0000.0000.0000.000
35A35SER0-0.099-0.06240.2720.0020.0020.0000.0000.0000.000
36A36ARG10.7760.85241.710-0.028-0.0280.0000.0000.0000.000
37A37LYS10.8630.93436.494-0.054-0.0540.0000.0000.0000.000
38A38TYR0-0.006-0.00333.1850.0040.0040.0000.0000.0000.000
39A39ILE0-0.008-0.00435.414-0.003-0.0030.0000.0000.0000.000
40A40LEU0-0.0140.00336.5140.0000.0000.0000.0000.0000.000
41A41VAL0-0.006-0.01636.159-0.002-0.0020.0000.0000.0000.000
42A42VAL00.0280.00637.8520.0000.0000.0000.0000.0000.000
43A43PRO00.0350.00637.161-0.001-0.0010.0000.0000.0000.000
44A44LEU0-0.014-0.00739.7490.0000.0000.0000.0000.0000.000
45A45ILE00.0350.01739.9470.0000.0000.0000.0000.0000.000
46A46VAL0-0.0040.00540.1360.0000.0000.0000.0000.0000.000
47A47ILE0-0.016-0.00843.2080.0010.0010.0000.0000.0000.000
48A48ASN00.0290.00946.0890.0000.0000.0000.0000.0000.000
49A49GLU-1-0.817-0.86543.1890.0020.0020.0000.0000.0000.000
50A50LEU0-0.038-0.01645.8170.0000.0000.0000.0000.0000.000
51A51ASP-1-0.732-0.83448.9530.0050.0050.0000.0000.0000.000
52A52GLY00.0150.01550.8990.0000.0000.0000.0000.0000.000
53A53LEU0-0.045-0.03148.0710.0000.0000.0000.0000.0000.000
54A54ALA0-0.0070.00552.3720.0000.0000.0000.0000.0000.000
55A55LYS10.8150.90654.743-0.004-0.0040.0000.0000.0000.000
56A63ALA00.0300.00059.6590.0000.0000.0000.0000.0000.000
57A64GLY00.0230.01561.5930.0000.0000.0000.0000.0000.000
58A65GLY00.0220.00259.8240.0000.0000.0000.0000.0000.000
59A66TYR00.0630.02049.3560.0000.0000.0000.0000.0000.000
60A67ALA00.0440.02855.2540.0000.0000.0000.0000.0000.000
61A68ARG10.9480.97256.336-0.008-0.0080.0000.0000.0000.000
62A69VAL0-0.016-0.00553.4800.0010.0010.0000.0000.0000.000
63A70VAL00.0400.02150.0740.0010.0010.0000.0000.0000.000
64A71GLN00.0490.04252.4260.0000.0000.0000.0000.0000.000
65A72GLU-1-0.910-0.95054.9670.0120.0120.0000.0000.0000.000
66A73LYS10.8480.90749.023-0.013-0.0130.0000.0000.0000.000
67A74ALA00.0060.01350.3600.0010.0010.0000.0000.0000.000
68A75ARG10.8470.92351.427-0.006-0.0060.0000.0000.0000.000
69A76LYS10.8980.94752.873-0.012-0.0120.0000.0000.0000.000
70A77SER0-0.022-0.01947.9370.0010.0010.0000.0000.0000.000
71A78ILE0-0.0110.00249.3310.0010.0010.0000.0000.0000.000
72A79GLU-1-0.902-0.96351.2190.0110.0110.0000.0000.0000.000
73A80PHE0-0.014-0.00945.7340.0010.0010.0000.0000.0000.000
74A81LEU00.0080.00144.9890.0010.0010.0000.0000.0000.000
75A82GLU-1-0.811-0.89848.8960.0090.0090.0000.0000.0000.000
76A83GLN00.0450.02551.8430.0010.0010.0000.0000.0000.000
77A84ARG10.7720.89147.550-0.019-0.0190.0000.0000.0000.000
78A85PHE00.020-0.00444.4270.0010.0010.0000.0000.0000.000
79A86GLU-1-0.961-0.97349.5400.0110.0110.0000.0000.0000.000
80A87SER0-0.087-0.05151.1700.0000.0000.0000.0000.0000.000
81A88ARG10.8100.90248.424-0.012-0.0120.0000.0000.0000.000
82A89ASP-1-0.729-0.84045.4490.0260.0260.0000.0000.0000.000
83A90SER00.0250.00743.8060.0000.0000.0000.0000.0000.000
84A91CYS0-0.063-0.00140.3400.0010.0010.0000.0000.0000.000
85A92LEU0-0.030-0.01140.9380.0010.0010.0000.0000.0000.000
86A93ARG10.8780.91736.922-0.024-0.0240.0000.0000.0000.000
87A94ALA00.0190.02141.5050.0000.0000.0000.0000.0000.000
88A95LEU0-0.050-0.01434.9010.0000.0000.0000.0000.0000.000
89A96THR0-0.028-0.02439.501-0.001-0.0010.0000.0000.0000.000
90A97SER0-0.020-0.04937.6380.0000.0000.0000.0000.0000.000
91A98ARG10.8610.92136.3860.0010.0010.0000.0000.0000.000
92A99GLY00.0370.02635.859-0.001-0.0010.0000.0000.0000.000
93A100ASN0-0.067-0.02136.5710.0000.0000.0000.0000.0000.000
94A101GLU-1-0.718-0.81936.4450.0180.0180.0000.0000.0000.000
95A102LEU0-0.040-0.02040.544-0.001-0.0010.0000.0000.0000.000
96A103GLU-1-0.819-0.90544.1230.0150.0150.0000.0000.0000.000
97A104SER0-0.040-0.03146.1780.0010.0010.0000.0000.0000.000
98A105ILE00.0490.02446.768-0.001-0.0010.0000.0000.0000.000
99A106ALA00.0350.03549.561-0.001-0.0010.0000.0000.0000.000
100A107PHE0-0.056-0.04252.6110.0000.0000.0000.0000.0000.000
101A108ARG10.6820.80249.060-0.007-0.0070.0000.0000.0000.000
102A109SER0-0.011-0.01448.560-0.001-0.0010.0000.0000.0000.000
103A110GLU-1-0.868-0.93247.902-0.001-0.0010.0000.0000.0000.000
104A111ASP-1-0.797-0.86541.217-0.002-0.0020.0000.0000.0000.000
105A112ILE00.0060.00842.157-0.001-0.0010.0000.0000.0000.000
106A113THR00.0720.02840.7550.0000.0000.0000.0000.0000.000
107A114GLY0-0.059-0.01640.646-0.002-0.0020.0000.0000.0000.000
108A115GLN0-0.036-0.02935.205-0.001-0.0010.0000.0000.0000.000
109A116LEU00.0050.00830.478-0.001-0.0010.0000.0000.0000.000
110A117GLY0-0.008-0.00235.077-0.002-0.0020.0000.0000.0000.000
111A118ASN0-0.067-0.03335.9760.0030.0030.0000.0000.0000.000
112A119ASN00.048-0.00137.833-0.001-0.0010.0000.0000.0000.000
113A120ASP-1-0.804-0.88634.923-0.004-0.0040.0000.0000.0000.000
114A121ASP-1-0.844-0.92732.751-0.017-0.0170.0000.0000.0000.000
115A122LEU00.0250.02533.9200.0010.0010.0000.0000.0000.000
116A123ILE00.0240.01734.5420.0020.0020.0000.0000.0000.000
117A124LEU0-0.014-0.01128.8930.0030.0030.0000.0000.0000.000
118A125SER0-0.010-0.01930.7530.0010.0010.0000.0000.0000.000
119A126CYS0-0.063-0.02332.2850.0020.0020.0000.0000.0000.000
120A127CYS0-0.030-0.01029.4450.0040.0040.0000.0000.0000.000
121A128LEU00.029-0.01625.8960.0040.0040.0000.0000.0000.000
122A129HIS0-0.0230.00728.402-0.003-0.0030.0000.0000.0000.000
123A130TYR0-0.039-0.06329.3850.0000.0000.0000.0000.0000.000
124A131CYS0-0.068-0.01524.0200.0050.0050.0000.0000.0000.000
125A132LYS10.8850.96124.307-0.010-0.0100.0000.0000.0000.000
126A133ASP-1-0.751-0.82919.9930.0280.0280.0000.0000.0000.000
127A134LYS10.7450.84421.126-0.034-0.0340.0000.0000.0000.000
128A135ALA00.0350.00518.6780.0040.0040.0000.0000.0000.000
129A136LYS10.9510.96417.114-0.022-0.0220.0000.0000.0000.000
130A137ASP-1-0.771-0.86616.8820.0420.0420.0000.0000.0000.000
131A138PHE0-0.018-0.01113.4520.0210.0210.0000.0000.0000.000
132A139MET0-0.047-0.02011.524-0.022-0.0220.0000.0000.0000.000
133A140PRO00.0010.0278.7690.0000.0000.0000.0000.0000.000
134A141ALA0-0.048-0.04711.878-0.039-0.0390.0000.0000.0000.000
135A142SER0-0.102-0.06412.534-0.003-0.0030.0000.0000.0000.000
136A143LYS10.8280.8738.888-0.507-0.5070.0000.0000.0000.000
137A144GLU-1-0.877-0.9224.7760.6160.611-0.001-0.0020.0090.000
138A145GLU-1-0.774-0.8367.1210.6370.6370.0000.0000.0000.000
139A146PRO0-0.003-0.0018.464-0.042-0.0420.0000.0000.0000.000
140A147ILE00.0290.0238.073-0.067-0.0670.0000.0000.0000.000
141A148ARG10.8190.89411.291-0.337-0.3370.0000.0000.0000.000
142A149LEU00.0180.02214.782-0.013-0.0130.0000.0000.0000.000
143A150LEU0-0.047-0.01717.8850.0090.0090.0000.0000.0000.000
144A151ARG10.7450.82320.694-0.049-0.0490.0000.0000.0000.000
145A152GLU-1-0.810-0.90323.8490.0740.0740.0000.0000.0000.000
146A153VAL0-0.023-0.00426.995-0.004-0.0040.0000.0000.0000.000
147A154VAL0-0.028-0.01827.6530.0040.0040.0000.0000.0000.000
148A155LEU00.0090.01029.828-0.003-0.0030.0000.0000.0000.000
149A156LEU0-0.036-0.03031.8240.0030.0030.0000.0000.0000.000
150A157THR00.004-0.03433.019-0.004-0.0040.0000.0000.0000.000
151A158ASP-1-0.821-0.91634.7380.0270.0270.0000.0000.0000.000
152A159ASP-1-0.786-0.86836.3580.0030.0030.0000.0000.0000.000
153A160ARG10.8260.89533.264-0.018-0.0180.0000.0000.0000.000
154A161ASN0-0.029-0.04432.128-0.004-0.0040.0000.0000.0000.000
155A162LEU00.0260.01231.874-0.002-0.0020.0000.0000.0000.000
156A163ARG10.9740.99527.362-0.029-0.0290.0000.0000.0000.000
157A164VAL0-0.007-0.00327.3820.0020.0020.0000.0000.0000.000
158A165LYS10.8680.93626.9570.0070.0070.0000.0000.0000.000
159A166ALA00.0230.01127.247-0.004-0.0040.0000.0000.0000.000
160A167LEU0-0.007-0.00823.5940.0010.0010.0000.0000.0000.000
161A168THR0-0.047-0.04322.386-0.002-0.0020.0000.0000.0000.000
162A169ARG10.8590.94422.5340.0090.0090.0000.0000.0000.000
163A170ASN00.0010.00518.7020.0130.0130.0000.0000.0000.000
164A171VAL00.0270.01821.9010.0080.0080.0000.0000.0000.000
165A172PRO00.0070.00523.8110.0000.0000.0000.0000.0000.000
166A173VAL0-0.016-0.00725.835-0.006-0.0060.0000.0000.0000.000
167A174ARG10.7850.88428.763-0.047-0.0470.0000.0000.0000.000
168A175ASP-1-0.725-0.83231.5250.0380.0380.0000.0000.0000.000
169A176ILE00.0500.02035.1560.0040.0040.0000.0000.0000.000
170A177PRO00.0240.01137.6930.0020.0020.0000.0000.0000.000
171A178ALA00.0100.01633.9030.0030.0030.0000.0000.0000.000
172A179PHE00.0070.00531.2000.0050.0050.0000.0000.0000.000
173A180LEU00.0090.00034.6780.0030.0030.0000.0000.0000.000
174A181THR0-0.042-0.03136.6890.0010.0010.0000.0000.0000.000
175A182TRP0-0.028-0.01228.9510.0000.0000.0000.0000.0000.000
176A183ALA00.0030.01334.1700.0030.0030.0000.0000.0000.000
177A184GLN0-0.095-0.03135.528-0.003-0.0030.0000.0000.0000.000