FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 3J3ZL

Calculation Name: 2DG7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DG7

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RK42

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1823611.483235
FMO2-HF: Nuclear repulsion 1753155.089124
FMO2-HF: Total energy -70456.394111
FMO2-MP2: Total energy -70664.624438


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-16.894-13.76723.335-8.219-18.245-0.033
Interaction energy analysis for fragmet #1(A:1:MET)
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 : -0.005
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].
3A3ARG10.9190.9763.1511.4133.572-0.006-0.913-1.2400.000
4A4TRP0-0.027-0.0192.409-5.226-2.3946.106-3.431-5.508-0.025
5A5ASP-1-0.775-0.8744.4480.3690.655-0.001-0.017-0.2680.000
6A6PRO00.0130.0145.9360.2780.2780.0000.0000.0000.000
7A7GLY00.0170.0178.2030.3120.3120.0000.0000.0000.000
8A8ALA0-0.021-0.0045.1260.2390.2390.0000.0000.0000.000
9A9GLU-1-0.889-0.9527.0441.4071.4070.0000.0000.0000.000
10A10GLN00.0510.0278.334-0.015-0.0150.0000.0000.0000.000
11A11ARG10.7670.8407.328-0.575-0.5750.0000.0000.0000.000
12A12LEU0-0.0250.0036.7370.0410.0410.0000.0000.0000.000
13A13LYS10.8910.94710.971-0.737-0.7370.0000.0000.0000.000
14A14ARG10.8440.91313.704-0.368-0.3680.0000.0000.0000.000
15A15ALA00.0270.01213.597-0.048-0.0480.0000.0000.0000.000
16A16ALA0-0.012-0.01314.809-0.051-0.0510.0000.0000.0000.000
17A17LEU0-0.0120.00416.478-0.055-0.0550.0000.0000.0000.000
18A18GLU-1-0.864-0.90918.8720.3400.3400.0000.0000.0000.000
19A19LEU0-0.001-0.00417.175-0.027-0.0270.0000.0000.0000.000
20A20TYR0-0.084-0.08117.446-0.012-0.0120.0000.0000.0000.000
21A21SER0-0.036-0.02522.086-0.035-0.0350.0000.0000.0000.000
22A22GLU-1-0.852-0.89022.4540.2960.2960.0000.0000.0000.000
23A23HIS0-0.0120.00122.552-0.009-0.0090.0000.0000.0000.000
24A24GLY00.0890.04725.120-0.009-0.0090.0000.0000.0000.000
25A25TYR0-0.004-0.03320.2370.0380.0380.0000.0000.0000.000
26A26ASP-1-0.914-0.95722.3090.2840.2840.0000.0000.0000.000
27A27ASN0-0.106-0.04623.628-0.013-0.0130.0000.0000.0000.000
28A28VAL00.0260.04117.8320.0090.0090.0000.0000.0000.000
29A29THR0-0.068-0.06915.9170.0190.0190.0000.0000.0000.000
30A30VAL00.031-0.00511.5730.0150.0150.0000.0000.0000.000
31A31THR0-0.011-0.00211.3170.1920.1920.0000.0000.0000.000
32A32ASP-1-0.772-0.83612.4000.5350.5350.0000.0000.0000.000
33A33ILE0-0.005-0.00112.2250.0310.0310.0000.0000.0000.000
34A34ALA0-0.042-0.0358.4800.0780.0780.0000.0000.0000.000
35A35GLU-1-0.909-0.95310.1650.6970.6970.0000.0000.0000.000
36A36ARG10.7470.86412.130-0.455-0.4550.0000.0000.0000.000
37A37ALA00.0050.00610.359-0.087-0.0870.0000.0000.0000.000
38A38GLY0-0.015-0.00310.046-0.009-0.0090.0000.0000.0000.000
39A39LEU0-0.093-0.0484.7420.3220.5080.000-0.026-0.1600.000
40A40THR00.0530.0214.240-0.950-0.861-0.001-0.019-0.0700.000
41A41ARG11.0090.9726.2660.0090.0090.0000.0000.0000.000
42A42ARG10.9390.9643.7250.4930.7790.003-0.037-0.2530.000
43A43SER00.037-0.0172.254-2.927-6.51812.384-4.615-4.178-0.013
44A44TYR00.0600.0213.5712.826-0.318-0.0903.737-0.503-0.004
45A45PHE0-0.024-0.0106.640-0.082-0.0820.0000.0000.0000.000
46A46ARG10.8290.9342.383-14.411-11.7843.440-1.938-4.1290.022
47A47TYR0-0.050-0.0362.515-1.3770.0201.500-0.960-1.936-0.013
48A48PHE00.0700.0327.104-0.318-0.3180.0000.0000.0000.000
49A49PRO00.0110.01210.3670.0720.0720.0000.0000.0000.000
50A50ASP-1-0.775-0.89012.4460.4640.4640.0000.0000.0000.000
51A51LYS10.8420.91814.377-0.300-0.3000.0000.0000.0000.000
52A52ARG10.8700.94116.347-0.392-0.3920.0000.0000.0000.000
53A53GLU-1-0.747-0.89214.4170.5350.5350.0000.0000.0000.000
54A54VAL0-0.0470.01812.5200.0180.0180.0000.0000.0000.000
55A55LEU00.012-0.00714.190-0.020-0.0200.0000.0000.0000.000
56A56PHE0-0.099-0.04816.771-0.063-0.0630.0000.0000.0000.000
57A57GLY00.0150.00413.697-0.015-0.0150.0000.0000.0000.000
58A58GLY00.0300.02414.621-0.009-0.0090.0000.0000.0000.000
59A59SER0-0.102-0.05515.404-0.032-0.0320.0000.0000.0000.000
60A60GLU-1-0.796-0.90318.2560.3980.3980.0000.0000.0000.000
61A61LEU00.0030.01920.417-0.001-0.0010.0000.0000.0000.000
62A62LEU00.0360.01116.798-0.006-0.0060.0000.0000.0000.000
63A63PRO00.0760.02821.369-0.025-0.0250.0000.0000.0000.000
64A64PRO0-0.009-0.00721.380-0.020-0.0200.0000.0000.0000.000
65A65ALA0-0.042-0.01821.146-0.021-0.0210.0000.0000.0000.000
66A66VAL00.0740.03823.234-0.018-0.0180.0000.0000.0000.000
67A67ALA00.0170.00826.486-0.017-0.0170.0000.0000.0000.000
68A68ARG10.9250.94620.955-0.176-0.1760.0000.0000.0000.000
69A69ALA00.0150.01626.921-0.013-0.0130.0000.0000.0000.000
70A70VAL00.0120.00828.546-0.009-0.0090.0000.0000.0000.000
71A71LEU0-0.088-0.03929.652-0.009-0.0090.0000.0000.0000.000
72A72ALA0-0.035-0.01429.960-0.009-0.0090.0000.0000.0000.000
73A73ALA0-0.0050.02032.031-0.005-0.0050.0000.0000.0000.000
74A74ASP-1-0.839-0.91934.6300.0430.0430.0000.0000.0000.000
75A75PRO0-0.052-0.04038.1970.0020.0020.0000.0000.0000.000
76A76GLY0-0.0150.00740.174-0.001-0.0010.0000.0000.0000.000
77A77ALA0-0.036-0.00939.1700.0000.0000.0000.0000.0000.000
78A78ALA00.0190.01141.3180.0010.0010.0000.0000.0000.000
79A79PRO00.0650.01539.1540.0040.0040.0000.0000.0000.000
80A80LEU00.003-0.00437.7600.0050.0050.0000.0000.0000.000
81A81THR00.0250.01237.2360.0050.0050.0000.0000.0000.000
82A82ALA00.0400.03135.9260.0040.0040.0000.0000.0000.000
83A83VAL0-0.016-0.01632.8270.0070.0070.0000.0000.0000.000
84A84LEU00.0120.00132.2870.0100.0100.0000.0000.0000.000
85A85ASP-1-0.854-0.90832.2710.0930.0930.0000.0000.0000.000
86A86ALA0-0.053-0.02129.6590.0070.0070.0000.0000.0000.000
87A87MET0-0.061-0.04127.9770.0100.0100.0000.0000.0000.000
88A88SER00.005-0.01027.3970.0160.0160.0000.0000.0000.000
89A89GLN0-0.055-0.02326.4690.0090.0090.0000.0000.0000.000
90A90VAL0-0.063-0.04022.6080.0090.0090.0000.0000.0000.000
91A91GLY00.0180.00222.7580.0270.0270.0000.0000.0000.000
92A92ALA0-0.0170.00324.2820.0020.0020.0000.0000.0000.000
93A93GLN0-0.034-0.02719.3780.0010.0010.0000.0000.0000.000
94A94LEU00.0180.01221.3680.0030.0030.0000.0000.0000.000
95A95VAL0-0.049-0.01122.785-0.001-0.0010.0000.0000.0000.000
96A96ALA0-0.0140.00823.960-0.019-0.0190.0000.0000.0000.000
97A97GLN0-0.023-0.02422.669-0.015-0.0150.0000.0000.0000.000
98A98VAL00.0210.01324.0480.0190.0190.0000.0000.0000.000
99A99GLU-1-0.848-0.90421.0150.2520.2520.0000.0000.0000.000
100A100GLY00.0240.02321.5960.0240.0240.0000.0000.0000.000
101A101ALA0-0.022-0.01222.6820.0170.0170.0000.0000.0000.000
102A102ALA00.0720.01824.5160.0050.0050.0000.0000.0000.000
103A103GLN0-0.020-0.01322.5760.0000.0000.0000.0000.0000.000
104A104ARG10.8440.90920.452-0.334-0.3340.0000.0000.0000.000
105A105ARG10.7740.86723.127-0.219-0.2190.0000.0000.0000.000
106A106ALA00.0230.01426.612-0.008-0.0080.0000.0000.0000.000
107A107VAL0-0.008-0.00722.274-0.004-0.0040.0000.0000.0000.000
108A108ILE0-0.033-0.02222.488-0.003-0.0030.0000.0000.0000.000
109A109ASP-1-0.812-0.89025.9540.1840.1840.0000.0000.0000.000
110A110ALA0-0.0020.01528.314-0.014-0.0140.0000.0000.0000.000
111A111SER00.0070.00525.691-0.009-0.0090.0000.0000.0000.000
112A112PRO00.0370.01328.1520.0040.0040.0000.0000.0000.000
113A113GLU-1-0.745-0.84723.2440.3210.3210.0000.0000.0000.000
114A114LEU0-0.001-0.00421.6800.0140.0140.0000.0000.0000.000
115A115GLN0-0.0090.00424.990-0.006-0.0060.0000.0000.0000.000
116A116GLU-1-0.961-0.98728.1210.1830.1830.0000.0000.0000.000
117A117ARG0-0.013-0.00319.1680.0240.0240.0000.0000.0000.000
118A118GLU-1-0.729-0.85024.5360.2670.2670.0000.0000.0000.000
119A119ARG10.8900.95325.727-0.182-0.1820.0000.0000.0000.000
120A120THR0-0.013-0.01125.656-0.015-0.0150.0000.0000.0000.000
121A121LYS10.7890.89418.266-0.452-0.4520.0000.0000.0000.000
122A122SER0-0.031-0.02125.155-0.009-0.0090.0000.0000.0000.000
123A123ALA00.0000.00528.256-0.012-0.0120.0000.0000.0000.000
124A124ALA00.0180.00725.748-0.012-0.0120.0000.0000.0000.000
125A125ILE0-0.021-0.01224.577-0.009-0.0090.0000.0000.0000.000
126A126SER00.012-0.00727.861-0.015-0.0150.0000.0000.0000.000
127A127ARG10.8690.91130.327-0.115-0.1150.0000.0000.0000.000
128A128ALA0-0.0050.00127.548-0.009-0.0090.0000.0000.0000.000
129A129VAL0-0.012-0.01129.581-0.010-0.0100.0000.0000.0000.000
130A130GLN00.0520.03531.928-0.013-0.0130.0000.0000.0000.000
131A131ASP-1-0.800-0.89131.7770.1000.1000.0000.0000.0000.000
132A132ALA0-0.091-0.02731.242-0.008-0.0080.0000.0000.0000.000
133A133LEU00.0520.01533.287-0.007-0.0070.0000.0000.0000.000
134A134VAL00.0410.03636.644-0.006-0.0060.0000.0000.0000.000
135A135ARG10.8050.88229.819-0.100-0.1000.0000.0000.0000.000
136A136ARG10.8030.88334.263-0.067-0.0670.0000.0000.0000.000
137A137GLN0-0.048-0.01538.696-0.004-0.0040.0000.0000.0000.000
138A138VAL00.0100.03140.182-0.002-0.0020.0000.0000.0000.000
139A139ASP-1-0.825-0.89641.4890.0610.0610.0000.0000.0000.000
140A140ALA00.035-0.00840.8070.0030.0030.0000.0000.0000.000
141A141ASP-1-0.863-0.92441.2250.0670.0670.0000.0000.0000.000
142A142THR0-0.047-0.04842.8220.0040.0040.0000.0000.0000.000
143A143ALA0-0.060-0.04338.1420.0040.0040.0000.0000.0000.000
144A144GLU-1-0.983-0.98838.1630.0960.0960.0000.0000.0000.000
145A145LEU00.0320.01438.6730.0060.0060.0000.0000.0000.000
146A146VAL0-0.022-0.00937.5450.0040.0040.0000.0000.0000.000
147A147ALA00.0060.01334.2840.0050.0050.0000.0000.0000.000
148A148GLN00.0440.04734.8550.0160.0160.0000.0000.0000.000
149A149LEU0-0.0010.00836.5060.0050.0050.0000.0000.0000.000
150A150ALA00.0180.00434.3430.0020.0020.0000.0000.0000.000
151A151THR0-0.039-0.03331.0810.0100.0100.0000.0000.0000.000
152A152VAL0-0.015-0.00532.9850.0070.0070.0000.0000.0000.000
153A153ALA0-0.009-0.00335.5190.0020.0020.0000.0000.0000.000
154A154PHE00.0520.01227.4740.0010.0010.0000.0000.0000.000
155A155GLY00.0180.01230.6440.0070.0070.0000.0000.0000.000
156A156SER0-0.041-0.03731.7020.0030.0030.0000.0000.0000.000
157A157ALA0-0.0250.00033.490-0.001-0.0010.0000.0000.0000.000
158A158PHE00.0250.01324.7400.0020.0020.0000.0000.0000.000
159A159ARG10.8610.91330.656-0.165-0.1650.0000.0000.0000.000
160A160ARG10.9390.96632.037-0.103-0.1030.0000.0000.0000.000
161A161TRP0-0.017-0.01325.8430.0030.0030.0000.0000.0000.000
162A162ILE0-0.058-0.02827.1750.0020.0020.0000.0000.0000.000
163A163ASP-1-0.919-0.96430.6600.1390.1390.0000.0000.0000.000
164A164ALA0-0.064-0.01834.045-0.006-0.0060.0000.0000.0000.000
165A165GLU-1-0.956-0.98331.5300.1190.1190.0000.0000.0000.000
166A166GLY0-0.004-0.00231.519-0.001-0.0010.0000.0000.0000.000
167A167HIS0-0.064-0.02532.088-0.010-0.0100.0000.0000.0000.000
168A168ALA0-0.022-0.01134.690-0.007-0.0070.0000.0000.0000.000
169A169ASP-1-0.806-0.86733.3300.0980.0980.0000.0000.0000.000
170A170PHE00.038-0.01130.6060.0000.0000.0000.0000.0000.000
171A171GLY00.0360.01932.7400.0000.0000.0000.0000.0000.000
172A172SER00.0600.00735.432-0.004-0.0040.0000.0000.0000.000
173A173CYS0-0.122-0.03034.694-0.002-0.0020.0000.0000.0000.000
174A174LEU00.024-0.00533.8030.0000.0000.0000.0000.0000.000
175A175ASP-1-0.856-0.91136.6790.0770.0770.0000.0000.0000.000
176A176THR0-0.068-0.05739.999-0.003-0.0030.0000.0000.0000.000
177A177VAL0-0.050-0.02237.073-0.003-0.0030.0000.0000.0000.000
178A178THR0-0.014-0.01938.751-0.004-0.0040.0000.0000.0000.000
179A179ASP-1-0.791-0.86741.3530.0640.0640.0000.0000.0000.000
180A180ARG10.8830.94643.168-0.075-0.0750.0000.0000.0000.000
181A181LEU0-0.006-0.01439.607-0.002-0.0020.0000.0000.0000.000
182A182ARG10.8750.91744.198-0.069-0.0690.0000.0000.0000.000
183A183ALA00.0080.01346.889-0.003-0.0030.0000.0000.0000.000
184A184VAL0-0.037-0.01046.424-0.002-0.0020.0000.0000.0000.000
185A185LEU0-0.020-0.00646.003-0.001-0.0010.0000.0000.0000.000
186A186THR0-0.086-0.04549.496-0.003-0.0030.0000.0000.0000.000
187A187GLY0-0.071-0.02851.952-0.003-0.0030.0000.0000.0000.000