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: 3Q6RL

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1857338.617331
FMO2-HF: Nuclear repulsion 1786876.453148
FMO2-HF: Total energy -70462.164183
FMO2-MP2: Total energy -70667.693214


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.
-1.5090.4310.139-0.936-1.141-0.002
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 : 0.023 / 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].
3A3PRO00.002-0.0193.243-1.9310.0090.139-0.936-1.141-0.002
4A4GLU-1-0.891-0.9355.022-0.421-0.4210.0000.0000.0000.000
5A5PHE0-0.067-0.0286.7130.0820.0820.0000.0000.0000.000
6A6MET0-0.0180.00410.1970.0620.0620.0000.0000.0000.000
7A7GLU-1-0.871-0.94010.5550.1130.1130.0000.0000.0000.000
8A8LEU0-0.021-0.02014.550-0.002-0.0020.0000.0000.0000.000
9A9GLU-1-0.932-0.97418.0900.1030.1030.0000.0000.0000.000
10A10ILE0-0.009-0.00919.752-0.011-0.0110.0000.0000.0000.000
11A11ARG10.9480.97522.588-0.033-0.0330.0000.0000.0000.000
12A12PRO0-0.044-0.02726.143-0.004-0.0040.0000.0000.0000.000
13A13LEU00.0420.03929.2250.0050.0050.0000.0000.0000.000
14A14PHE00.0230.00230.7290.0000.0000.0000.0000.0000.000
15A15LEU0-0.017-0.00631.991-0.002-0.0020.0000.0000.0000.000
16A16VAL00.0250.00633.4110.0000.0000.0000.0000.0000.000
17A17PRO0-0.0120.00835.032-0.002-0.0020.0000.0000.0000.000
18A18ASP-1-0.773-0.87637.425-0.032-0.0320.0000.0000.0000.000
19A19THR00.010-0.05939.0870.0030.0030.0000.0000.0000.000
20A20ASN0-0.019-0.01441.1610.0000.0000.0000.0000.0000.000
21A21GLY00.0410.02940.7240.0020.0020.0000.0000.0000.000
22A22PHE0-0.020-0.01941.5240.0030.0030.0000.0000.0000.000
23A23ILE0-0.070-0.02844.7890.0020.0020.0000.0000.0000.000
24A24ASP-1-0.919-0.96643.512-0.016-0.0160.0000.0000.0000.000
25A25HIS0-0.040-0.02541.0640.0040.0040.0000.0000.0000.000
26A26LEU00.0410.03243.9800.0010.0010.0000.0000.0000.000
27A27ALA00.0110.00245.9200.0010.0010.0000.0000.0000.000
28A28SER00.003-0.01441.4600.0020.0020.0000.0000.0000.000
29A29LEU00.0150.01539.7200.0010.0010.0000.0000.0000.000
30A30ALA00.0100.01842.4920.0010.0010.0000.0000.0000.000
31A31ARG10.9880.98843.371-0.006-0.0060.0000.0000.0000.000
32A32LEU0-0.028-0.01137.3120.0020.0020.0000.0000.0000.000
33A33LEU00.0020.02840.8420.0020.0020.0000.0000.0000.000
34A34GLU-1-0.945-0.98242.6410.0030.0030.0000.0000.0000.000
35A35SER0-0.097-0.06040.0110.0020.0020.0000.0000.0000.000
36A36ARG10.7980.88541.435-0.001-0.0010.0000.0000.0000.000
37A37LYS10.9210.96835.999-0.022-0.0220.0000.0000.0000.000
38A38TYR0-0.012-0.00732.5640.0020.0020.0000.0000.0000.000
39A39ILE0-0.0010.00335.8370.0000.0000.0000.0000.0000.000
40A40LEU0-0.0180.00036.387-0.002-0.0020.0000.0000.0000.000
41A41VAL00.004-0.00635.7450.0000.0000.0000.0000.0000.000
42A42VAL00.020-0.00237.731-0.002-0.0020.0000.0000.0000.000
43A43PRO00.023-0.00737.0710.0000.0000.0000.0000.0000.000
44A44LEU0-0.0050.00139.5730.0020.0020.0000.0000.0000.000
45A45ILE00.0410.01839.5540.0010.0010.0000.0000.0000.000
46A46VAL00.0050.01239.9270.0010.0010.0000.0000.0000.000
47A47ILE0-0.009-0.00642.8700.0020.0020.0000.0000.0000.000
48A48ASN00.0400.01945.531-0.001-0.0010.0000.0000.0000.000
49A49GLU-1-0.826-0.86443.090-0.033-0.0330.0000.0000.0000.000
50A50LEU0-0.048-0.02645.6450.0010.0010.0000.0000.0000.000
51A51ASP-1-0.748-0.85548.643-0.019-0.0190.0000.0000.0000.000
52A52GLY00.0050.00950.3800.0010.0010.0000.0000.0000.000
53A53LEU0-0.064-0.03647.9430.0010.0010.0000.0000.0000.000
54A54ALA0-0.011-0.00252.1660.0010.0010.0000.0000.0000.000
55A55LYS10.8510.93354.5680.0190.0190.0000.0000.0000.000
56A63ALA00.0380.00359.7270.0000.0000.0000.0000.0000.000
57A64GLY0-0.003-0.00761.6260.0000.0000.0000.0000.0000.000
58A65GLY00.0370.01659.696-0.001-0.0010.0000.0000.0000.000
59A66TYR00.0630.01849.2540.0000.0000.0000.0000.0000.000
60A67ALA00.0700.03754.9810.0000.0000.0000.0000.0000.000
61A68ARG10.9410.97956.1400.0110.0110.0000.0000.0000.000
62A69VAL0-0.032-0.01953.1470.0010.0010.0000.0000.0000.000
63A70VAL00.0450.02550.1740.0010.0010.0000.0000.0000.000
64A71GLN00.0390.04252.573-0.001-0.0010.0000.0000.0000.000
65A72GLU-1-0.891-0.94954.835-0.009-0.0090.0000.0000.0000.000
66A73LYS10.9520.98050.0280.0130.0130.0000.0000.0000.000
67A74ALA00.0440.02850.3340.0000.0000.0000.0000.0000.000
68A75ARG10.8780.92751.3810.0140.0140.0000.0000.0000.000
69A76LYS10.8900.95352.6010.0090.0090.0000.0000.0000.000
70A77SER0-0.033-0.02147.8990.0010.0010.0000.0000.0000.000
71A78ILE00.0100.01249.3600.0000.0000.0000.0000.0000.000
72A79GLU-1-0.932-0.96551.284-0.009-0.0090.0000.0000.0000.000
73A80PHE0-0.0050.00645.6580.0010.0010.0000.0000.0000.000
74A81LEU0-0.021-0.02745.0560.0010.0010.0000.0000.0000.000
75A82GLU-1-0.847-0.93648.889-0.013-0.0130.0000.0000.0000.000
76A83GLN00.0380.02651.9390.0010.0010.0000.0000.0000.000
77A84ARG10.8220.91447.8410.0040.0040.0000.0000.0000.000
78A85PHE00.018-0.00944.1650.0000.0000.0000.0000.0000.000
79A86GLU-1-0.984-0.98349.395-0.009-0.0090.0000.0000.0000.000
80A87SER0-0.088-0.04151.3470.0010.0010.0000.0000.0000.000
81A88ARG10.8810.94749.0280.0110.0110.0000.0000.0000.000
82A89ASP-1-0.750-0.86945.351-0.001-0.0010.0000.0000.0000.000
83A90SER00.0300.00543.572-0.001-0.0010.0000.0000.0000.000
84A91CYS0-0.096-0.03140.8370.0010.0010.0000.0000.0000.000
85A92LEU0-0.0020.01240.923-0.001-0.0010.0000.0000.0000.000
86A93ARG10.9250.95836.6260.0130.0130.0000.0000.0000.000
87A94ALA00.0290.02541.3220.0000.0000.0000.0000.0000.000
88A95LEU0-0.0350.00635.0120.0000.0000.0000.0000.0000.000
89A96THR0-0.004-0.02939.431-0.001-0.0010.0000.0000.0000.000
90A97SER0-0.012-0.07137.355-0.002-0.0020.0000.0000.0000.000
91A98ARG10.8380.93536.2970.0310.0310.0000.0000.0000.000
92A99GLY00.0260.02235.857-0.001-0.0010.0000.0000.0000.000
93A100ASN0-0.065-0.03436.5430.0000.0000.0000.0000.0000.000
94A101GLU-1-0.804-0.90636.899-0.021-0.0210.0000.0000.0000.000
95A102LEU0-0.072-0.03140.5720.0010.0010.0000.0000.0000.000
96A103GLU-1-0.880-0.95143.819-0.011-0.0110.0000.0000.0000.000
97A104SER0-0.054-0.04046.1440.0020.0020.0000.0000.0000.000
98A105ILE00.0450.02446.702-0.002-0.0020.0000.0000.0000.000
99A106ALA00.0370.02849.4230.0000.0000.0000.0000.0000.000
100A107PHE0-0.062-0.04452.374-0.001-0.0010.0000.0000.0000.000
101A108ARG10.7170.85748.6510.0170.0170.0000.0000.0000.000
102A109SER00.0190.00148.3670.0010.0010.0000.0000.0000.000
103A110GLU-1-0.929-0.96947.633-0.030-0.0300.0000.0000.0000.000
104A111ASP-1-0.805-0.85641.177-0.042-0.0420.0000.0000.0000.000
105A112ILE00.0040.01742.045-0.001-0.0010.0000.0000.0000.000
106A113THR00.0740.02540.950-0.001-0.0010.0000.0000.0000.000
107A114GLY0-0.066-0.02240.447-0.002-0.0020.0000.0000.0000.000
108A115GLN0-0.024-0.01734.994-0.005-0.0050.0000.0000.0000.000
109A116LEU0-0.0110.00330.405-0.001-0.0010.0000.0000.0000.000
110A117GLY00.0120.00435.023-0.002-0.0020.0000.0000.0000.000
111A118ASN0-0.099-0.03636.1280.0080.0080.0000.0000.0000.000
112A119ASN00.0830.01338.127-0.002-0.0020.0000.0000.0000.000
113A120ASP-1-0.910-0.95635.109-0.051-0.0510.0000.0000.0000.000
114A121ASP-1-0.903-0.97233.332-0.077-0.0770.0000.0000.0000.000
115A122LEU00.0240.01633.858-0.001-0.0010.0000.0000.0000.000
116A123ILE00.0330.02034.2290.0020.0020.0000.0000.0000.000
117A124LEU0-0.019-0.01728.6860.0000.0000.0000.0000.0000.000
118A125SER0-0.007-0.02530.641-0.003-0.0030.0000.0000.0000.000
119A126CYS0-0.0320.00531.9910.0020.0020.0000.0000.0000.000
120A127CYS0-0.037-0.01629.4290.0040.0040.0000.0000.0000.000
121A128LEU00.023-0.00725.6700.0010.0010.0000.0000.0000.000
122A129HIS0-0.068-0.01528.120-0.007-0.0070.0000.0000.0000.000
123A130TYR0-0.044-0.03029.0220.0020.0020.0000.0000.0000.000
124A131CYS0-0.051-0.01523.9250.0040.0040.0000.0000.0000.000
125A132LYS10.9370.98924.2720.0530.0530.0000.0000.0000.000
126A133ASP-1-0.760-0.84119.821-0.084-0.0840.0000.0000.0000.000
127A134LYS10.8190.89421.3150.0490.0490.0000.0000.0000.000
128A135ALA00.0500.01018.616-0.003-0.0030.0000.0000.0000.000
129A136LYS10.9530.95817.0450.0420.0420.0000.0000.0000.000
130A137ASP-1-0.826-0.90516.820-0.051-0.0510.0000.0000.0000.000
131A138PHE0-0.038-0.02213.4970.0140.0140.0000.0000.0000.000
132A139MET0-0.032-0.01011.647-0.049-0.0490.0000.0000.0000.000
133A140PRO00.0010.0318.7990.0280.0280.0000.0000.0000.000
134A141ALA0-0.034-0.03612.053-0.037-0.0370.0000.0000.0000.000
135A142SER0-0.119-0.07411.8130.0490.0490.0000.0000.0000.000
136A143LYS10.8250.8749.201-0.847-0.8470.0000.0000.0000.000
137A144GLU-1-0.881-0.9254.9311.0571.0570.0000.0000.0000.000
138A145GLU-1-0.786-0.8486.3980.5260.5260.0000.0000.0000.000
139A146PRO0-0.028-0.0247.838-0.065-0.0650.0000.0000.0000.000
140A147ILE00.0540.0468.447-0.009-0.0090.0000.0000.0000.000
141A148ARG10.8780.93711.215-0.159-0.1590.0000.0000.0000.000
142A149LEU0-0.0030.00914.547-0.002-0.0020.0000.0000.0000.000
143A150LEU0-0.0240.00218.0220.0100.0100.0000.0000.0000.000
144A151ARG10.7460.83820.7210.0620.0620.0000.0000.0000.000
145A152GLU-1-0.864-0.93923.8090.0060.0060.0000.0000.0000.000
146A153VAL0-0.038-0.00527.0820.0030.0030.0000.0000.0000.000
147A154VAL0-0.017-0.01527.5300.0000.0000.0000.0000.0000.000
148A155LEU0-0.019-0.00629.6660.0010.0010.0000.0000.0000.000
149A156LEU0-0.046-0.03531.6280.0020.0020.0000.0000.0000.000
150A157THR00.018-0.03232.773-0.002-0.0020.0000.0000.0000.000
151A158ASP-1-0.851-0.91934.420-0.016-0.0160.0000.0000.0000.000
152A159ASP-1-0.807-0.90436.018-0.045-0.0450.0000.0000.0000.000
153A160ARG10.8300.88333.0730.0280.0280.0000.0000.0000.000
154A161ASN00.0250.01132.006-0.008-0.0080.0000.0000.0000.000
155A162LEU00.0920.04131.718-0.007-0.0070.0000.0000.0000.000
156A163ARG10.9620.99527.2330.0430.0430.0000.0000.0000.000
157A164VAL0-0.022-0.01226.995-0.004-0.0040.0000.0000.0000.000
158A165LYS10.9260.96626.6690.0610.0610.0000.0000.0000.000
159A166ALA00.0340.01526.609-0.009-0.0090.0000.0000.0000.000
160A167LEU0-0.045-0.02223.542-0.003-0.0030.0000.0000.0000.000
161A168THR0-0.063-0.03722.159-0.010-0.0100.0000.0000.0000.000
162A169ARG10.9160.97121.8680.0850.0850.0000.0000.0000.000
163A170ASN00.0100.01418.4630.0090.0090.0000.0000.0000.000
164A171VAL00.0220.01021.9020.0100.0100.0000.0000.0000.000
165A172PRO00.0100.00723.5870.0000.0000.0000.0000.0000.000
166A173VAL0-0.006-0.00225.5960.0000.0000.0000.0000.0000.000
167A174ARG10.8590.93428.3940.0090.0090.0000.0000.0000.000
168A175ASP-1-0.788-0.88431.114-0.011-0.0110.0000.0000.0000.000
169A176ILE00.0100.00234.7310.0040.0040.0000.0000.0000.000
170A177PRO00.0170.00937.2880.0030.0030.0000.0000.0000.000
171A178ALA00.0210.01133.3140.0040.0040.0000.0000.0000.000
172A179PHE0-0.0010.00030.7880.0040.0040.0000.0000.0000.000
173A180LEU0-0.006-0.00634.2150.0030.0030.0000.0000.0000.000
174A181THR0-0.020-0.01435.9220.0030.0030.0000.0000.0000.000
175A182TRP0-0.050-0.01427.8010.0020.0020.0000.0000.0000.000
176A183ALA0-0.0040.00633.4330.0040.0040.0000.0000.0000.000
177A184GLN0-0.126-0.05334.9120.0040.0040.0000.0000.0000.000