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

tag_button

FMODB ID: LJ149

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 OptHSide
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 -1859347.590154
FMO2-HF: Nuclear repulsion 1788884.473543
FMO2-HF: Total energy -70463.116611
FMO2-MP2: Total energy -70668.715744


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.
-1.4980.3220.14-0.858-1.102-0.001
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 : 0.013 / q_NPA : 0.000
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].
3A3PRO0-0.032-0.0313.244-1.7340.0860.140-0.858-1.102-0.001
4A4GLU-1-0.903-0.9394.896-0.528-0.5280.0000.0000.0000.000
5A5PHE0-0.058-0.0286.7140.0860.0860.0000.0000.0000.000
6A6MET0-0.0230.00210.1980.0580.0580.0000.0000.0000.000
7A7GLU-1-0.815-0.88811.1510.0950.0950.0000.0000.0000.000
8A8LEU0-0.023-0.02214.549-0.001-0.0010.0000.0000.0000.000
9A9GLU-1-0.868-0.92718.0890.0770.0770.0000.0000.0000.000
10A10ILE0-0.017-0.01619.751-0.010-0.0100.0000.0000.0000.000
11A11ARG10.8820.92922.355-0.025-0.0250.0000.0000.0000.000
12A12PRO0-0.038-0.02126.142-0.004-0.0040.0000.0000.0000.000
13A13LEU00.0310.03129.2240.0050.0050.0000.0000.0000.000
14A14PHE00.0180.00630.7510.0000.0000.0000.0000.0000.000
15A15LEU0-0.014-0.00531.990-0.002-0.0020.0000.0000.0000.000
16A16VAL00.0190.00233.2430.0000.0000.0000.0000.0000.000
17A17PRO0-0.0030.01135.031-0.002-0.0020.0000.0000.0000.000
18A18ASP-1-0.775-0.87037.376-0.033-0.0330.0000.0000.0000.000
19A19THR00.016-0.05439.0860.0030.0030.0000.0000.0000.000
20A20ASN0-0.024-0.02141.2000.0010.0010.0000.0000.0000.000
21A21GLY00.0200.01240.7270.0020.0020.0000.0000.0000.000
22A22PHE0-0.005-0.01441.5230.0030.0030.0000.0000.0000.000
23A23ILE0-0.035-0.00644.7890.0020.0020.0000.0000.0000.000
24A24ASP-1-0.883-0.94543.733-0.016-0.0160.0000.0000.0000.000
25A25HIS0-0.039-0.02140.5010.0040.0040.0000.0000.0000.000
26A26LEU00.0430.03543.9790.0010.0010.0000.0000.0000.000
27A27ALA00.0150.00345.9190.0010.0010.0000.0000.0000.000
28A28SER00.008-0.00641.4830.0020.0020.0000.0000.0000.000
29A29LEU00.0060.01039.7540.0010.0010.0000.0000.0000.000
30A30ALA00.0010.01342.4910.0010.0010.0000.0000.0000.000
31A31ARG10.9580.98243.564-0.003-0.0030.0000.0000.0000.000
32A32LEU0-0.033-0.01537.4680.0020.0020.0000.0000.0000.000
33A33LEU00.0010.02940.8410.0010.0010.0000.0000.0000.000
34A34GLU-1-0.901-0.96142.6400.0020.0020.0000.0000.0000.000
35A35SER0-0.100-0.06740.0160.0020.0020.0000.0000.0000.000
36A36ARG10.7670.85641.4340.0020.0020.0000.0000.0000.000
37A37LYS10.9010.96236.208-0.017-0.0170.0000.0000.0000.000
38A38TYR0-0.014-0.01732.6920.0020.0020.0000.0000.0000.000
39A39ILE0-0.0010.00835.5780.0000.0000.0000.0000.0000.000
40A40LEU0-0.024-0.00436.385-0.002-0.0020.0000.0000.0000.000
41A41VAL00.011-0.00435.7550.0000.0000.0000.0000.0000.000
42A42VAL00.012-0.00237.730-0.002-0.0020.0000.0000.0000.000
43A43PRO00.021-0.00537.0220.0000.0000.0000.0000.0000.000
44A44LEU00.0030.00339.5740.0020.0020.0000.0000.0000.000
45A45ILE00.0480.01939.4640.0010.0010.0000.0000.0000.000
46A46VAL0-0.0040.00639.9200.0010.0010.0000.0000.0000.000
47A47ILE0-0.016-0.00842.8720.0020.0020.0000.0000.0000.000
48A48ASN00.0270.01245.5370.0000.0000.0000.0000.0000.000
49A49GLU-1-0.823-0.85943.063-0.034-0.0340.0000.0000.0000.000
50A50LEU0-0.052-0.02945.7420.0010.0010.0000.0000.0000.000
51A51ASP-1-0.740-0.84448.644-0.020-0.0200.0000.0000.0000.000
52A52GLY00.0110.01450.3780.0010.0010.0000.0000.0000.000
53A53LEU0-0.061-0.03647.9280.0010.0010.0000.0000.0000.000
54A54ALA0-0.021-0.00552.1670.0010.0010.0000.0000.0000.000
55A55LYS10.8580.94054.5690.0200.0200.0000.0000.0000.000
56A63ALA00.033-0.00259.7500.0000.0000.0000.0000.0000.000
57A64GLY00.002-0.00261.6260.0000.0000.0000.0000.0000.000
58A65GLY00.0390.01859.695-0.001-0.0010.0000.0000.0000.000
59A66TYR00.0610.01749.2410.0000.0000.0000.0000.0000.000
60A67ALA00.0610.03454.9800.0000.0000.0000.0000.0000.000
61A68ARG10.9370.97456.1390.0110.0110.0000.0000.0000.000
62A69VAL0-0.027-0.01553.1540.0010.0010.0000.0000.0000.000
63A70VAL00.0480.02750.0750.0010.0010.0000.0000.0000.000
64A71GLN00.0400.03952.572-0.001-0.0010.0000.0000.0000.000
65A72GLU-1-0.894-0.94454.834-0.010-0.0100.0000.0000.0000.000
66A73LYS10.8850.93848.6300.0140.0140.0000.0000.0000.000
67A74ALA00.0270.02150.3320.0000.0000.0000.0000.0000.000
68A75ARG10.8630.92151.3800.0140.0140.0000.0000.0000.000
69A76LYS10.8780.94352.6440.0090.0090.0000.0000.0000.000
70A77SER0-0.040-0.02847.8890.0010.0010.0000.0000.0000.000
71A78ILE00.0100.00849.2590.0000.0000.0000.0000.0000.000
72A79GLU-1-0.922-0.96151.283-0.010-0.0100.0000.0000.0000.000
73A80PHE0-0.0060.00145.5690.0010.0010.0000.0000.0000.000
74A81LEU0-0.017-0.02144.9870.0010.0010.0000.0000.0000.000
75A82GLU-1-0.806-0.90248.888-0.015-0.0150.0000.0000.0000.000
76A83GLN00.0360.02551.9380.0010.0010.0000.0000.0000.000
77A84ARG10.8070.90147.6950.0060.0060.0000.0000.0000.000
78A85PHE00.0390.00344.1330.0000.0000.0000.0000.0000.000
79A86GLU-1-0.983-0.97449.394-0.010-0.0100.0000.0000.0000.000
80A87SER0-0.096-0.05251.1530.0010.0010.0000.0000.0000.000
81A88ARG10.8830.94048.9960.0130.0130.0000.0000.0000.000
82A89ASP-1-0.734-0.83745.260-0.003-0.0030.0000.0000.0000.000
83A90SER00.0420.01243.514-0.001-0.0010.0000.0000.0000.000
84A91CYS0-0.100-0.03440.8380.0000.0000.0000.0000.0000.000
85A92LEU0-0.0050.01040.922-0.001-0.0010.0000.0000.0000.000
86A93ARG10.9120.93536.7890.0160.0160.0000.0000.0000.000
87A94ALA00.0240.02141.2920.0000.0000.0000.0000.0000.000
88A95LEU0-0.0580.00134.7870.0000.0000.0000.0000.0000.000
89A96THR0-0.030-0.02039.432-0.002-0.0020.0000.0000.0000.000
90A97SER0-0.003-0.04437.354-0.002-0.0020.0000.0000.0000.000
91A98ARG10.8670.91636.2980.0330.0330.0000.0000.0000.000
92A99GLY00.0290.01835.865-0.001-0.0010.0000.0000.0000.000
93A100ASN0-0.067-0.02136.5440.0020.0020.0000.0000.0000.000
94A101GLU-1-0.751-0.84836.680-0.024-0.0240.0000.0000.0000.000
95A102LEU0-0.061-0.02640.5740.0010.0010.0000.0000.0000.000
96A103GLU-1-0.878-0.95043.821-0.013-0.0130.0000.0000.0000.000
97A104SER0-0.058-0.04146.1450.0020.0020.0000.0000.0000.000
98A105ILE00.0360.01946.709-0.002-0.0020.0000.0000.0000.000
99A106ALA00.0300.02749.4240.0000.0000.0000.0000.0000.000
100A107PHE0-0.057-0.04352.375-0.001-0.0010.0000.0000.0000.000
101A108ARG10.6870.81548.6840.0180.0180.0000.0000.0000.000
102A109SER00.013-0.00148.4190.0000.0000.0000.0000.0000.000
103A110GLU-1-0.898-0.95247.656-0.030-0.0300.0000.0000.0000.000
104A111ASP-1-0.810-0.88741.185-0.041-0.0410.0000.0000.0000.000
105A112ILE00.0060.01642.093-0.001-0.0010.0000.0000.0000.000
106A113THR00.0560.02140.925-0.001-0.0010.0000.0000.0000.000
107A114GLY0-0.063-0.02140.486-0.002-0.0020.0000.0000.0000.000
108A115GLN0-0.014-0.01234.983-0.004-0.0040.0000.0000.0000.000
109A116LEU00.0040.00630.3580.0000.0000.0000.0000.0000.000
110A117GLY0-0.0010.00234.978-0.002-0.0020.0000.0000.0000.000
111A118ASN0-0.112-0.05936.0590.0070.0070.0000.0000.0000.000
112A119ASN00.0660.00438.128-0.002-0.0020.0000.0000.0000.000
113A120ASP-1-0.820-0.89834.936-0.054-0.0540.0000.0000.0000.000
114A121ASP-1-0.878-0.94933.152-0.075-0.0750.0000.0000.0000.000
115A122LEU00.0330.02533.859-0.001-0.0010.0000.0000.0000.000
116A123ILE00.0370.02234.3140.0010.0010.0000.0000.0000.000
117A124LEU0-0.013-0.00928.6860.0000.0000.0000.0000.0000.000
118A125SER0-0.005-0.02230.642-0.004-0.0040.0000.0000.0000.000
119A126CYS0-0.043-0.01031.9920.0010.0010.0000.0000.0000.000
120A127CYS0-0.050-0.02929.5720.0040.0040.0000.0000.0000.000
121A128LEU00.036-0.00625.7240.0010.0010.0000.0000.0000.000
122A129HIS0-0.0190.01428.121-0.008-0.0080.0000.0000.0000.000
123A130TYR0-0.027-0.05129.0230.0020.0020.0000.0000.0000.000
124A131CYS0-0.053-0.00723.7790.0030.0030.0000.0000.0000.000
125A132LYS10.8650.96224.2730.0490.0490.0000.0000.0000.000
126A133ASP-1-0.763-0.83419.816-0.089-0.0890.0000.0000.0000.000
127A134LYS10.7480.84221.3020.0580.0580.0000.0000.0000.000
128A135ALA00.0450.00818.618-0.004-0.0040.0000.0000.0000.000
129A136LYS10.9580.96317.0460.0450.0450.0000.0000.0000.000
130A137ASP-1-0.772-0.86616.821-0.062-0.0620.0000.0000.0000.000
131A138PHE0-0.017-0.01013.4970.0120.0120.0000.0000.0000.000
132A139MET0-0.035-0.00511.225-0.040-0.0400.0000.0000.0000.000
133A140PRO0-0.0030.0228.8350.0270.0270.0000.0000.0000.000
134A141ALA0-0.037-0.03612.054-0.033-0.0330.0000.0000.0000.000
135A142SER0-0.116-0.07511.7920.0430.0430.0000.0000.0000.000
136A143LYS10.8190.8709.076-0.748-0.7480.0000.0000.0000.000
137A144GLU-1-0.873-0.9204.8840.9540.9540.0000.0000.0000.000
138A145GLU-1-0.782-0.8466.3630.4440.4440.0000.0000.0000.000
139A146PRO0-0.028-0.0177.837-0.066-0.0660.0000.0000.0000.000
140A147ILE00.0570.0458.1740.0000.0000.0000.0000.0000.000
141A148ARG10.8100.87811.217-0.116-0.1160.0000.0000.0000.000
142A149LEU0-0.0050.00814.5450.0000.0000.0000.0000.0000.000
143A150LEU0-0.038-0.00618.0240.0090.0090.0000.0000.0000.000
144A151ARG10.7440.82720.5990.0690.0690.0000.0000.0000.000
145A152GLU-1-0.833-0.92623.8080.0010.0010.0000.0000.0000.000
146A153VAL0-0.043-0.00727.1210.0030.0030.0000.0000.0000.000
147A154VAL0-0.026-0.01727.529-0.001-0.0010.0000.0000.0000.000
148A155LEU0-0.020-0.00329.6630.0010.0010.0000.0000.0000.000
149A156LEU0-0.034-0.03131.6270.0020.0020.0000.0000.0000.000
150A157THR00.016-0.03232.734-0.002-0.0020.0000.0000.0000.000
151A158ASP-1-0.851-0.92134.420-0.018-0.0180.0000.0000.0000.000
152A159ASP-1-0.765-0.86935.979-0.046-0.0460.0000.0000.0000.000
153A160ARG10.8240.88433.0700.0280.0280.0000.0000.0000.000
154A161ASN0-0.010-0.03232.005-0.010-0.0100.0000.0000.0000.000
155A162LEU00.0370.01831.719-0.007-0.0070.0000.0000.0000.000
156A163ARG10.9690.99627.1820.0430.0430.0000.0000.0000.000
157A164VAL0-0.012-0.00627.044-0.004-0.0040.0000.0000.0000.000
158A165LYS10.8640.94126.6700.0570.0570.0000.0000.0000.000
159A166ALA00.0380.01326.610-0.008-0.0080.0000.0000.0000.000
160A167LEU0-0.032-0.01623.478-0.004-0.0040.0000.0000.0000.000
161A168THR0-0.054-0.04122.162-0.009-0.0090.0000.0000.0000.000
162A169ARG10.8990.96421.8690.0850.0850.0000.0000.0000.000
163A170ASN00.0020.00718.5960.0080.0080.0000.0000.0000.000
164A171VAL00.0320.01521.9030.0090.0090.0000.0000.0000.000
165A172PRO00.0110.01023.5740.0000.0000.0000.0000.0000.000
166A173VAL0-0.012-0.00725.5950.0000.0000.0000.0000.0000.000
167A174ARG10.7880.89228.3940.0130.0130.0000.0000.0000.000
168A175ASP-1-0.721-0.83831.114-0.013-0.0130.0000.0000.0000.000
169A176ILE00.0310.01034.7300.0030.0030.0000.0000.0000.000
170A177PRO00.0300.01537.2870.0030.0030.0000.0000.0000.000
171A178ALA00.0140.01033.3000.0030.0030.0000.0000.0000.000
172A179PHE00.0010.00030.8520.0040.0040.0000.0000.0000.000
173A180LEU00.0040.00134.2140.0030.0030.0000.0000.0000.000
174A181THR0-0.023-0.02236.0390.0030.0030.0000.0000.0000.000
175A182TRP0-0.029-0.00528.1080.0020.0020.0000.0000.0000.000
176A183ALA0-0.0020.01333.4330.0040.0040.0000.0000.0000.000
177A184GLN0-0.115-0.04834.9110.0040.0040.0000.0000.0000.000