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

tag_button

FMODB ID: JQ6Y9

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 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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1823934.250472
FMO2-HF: Nuclear repulsion 1753478.735293
FMO2-HF: Total energy -70455.51518
FMO2-MP2: Total energy -70663.846796


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.
-19.155-23.62740.658-15.267-20.918-0.028
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 : -0.017 / q_NPA : 0.007
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].
3A3ARG10.9090.9773.169-1.8530.527-0.015-1.118-1.2470.000
4A4TRP0-0.017-0.0082.098-4.141-4.84012.462-5.375-6.387-0.020
5A5ASP-1-0.766-0.8674.896-0.388-0.3880.0000.0000.0000.000
6A6PRO00.0100.0135.975-0.440-0.4400.0000.0000.0000.000
7A7GLY00.0200.0178.1340.1320.1320.0000.0000.0000.000
8A8ALA00.0050.0074.4970.0690.145-0.001-0.008-0.0670.000
9A9GLU-1-0.896-0.9566.4740.2830.2830.0000.0000.0000.000
10A10GLN00.0480.0297.9990.0770.0770.0000.0000.0000.000
11A11ARG10.7530.8387.2830.2910.2910.0000.0000.0000.000
12A12LEU0-0.0130.0066.0720.0500.0500.0000.0000.0000.000
13A13LYS10.8970.94510.2730.0520.0520.0000.0000.0000.000
14A14ARG10.8780.93913.1790.0420.0420.0000.0000.0000.000
15A15ALA00.0310.01312.7970.0110.0110.0000.0000.0000.000
16A16ALA0-0.015-0.01414.1570.0080.0080.0000.0000.0000.000
17A17LEU0-0.023-0.00815.7810.0050.0050.0000.0000.0000.000
18A18GLU-1-0.921-0.95218.122-0.003-0.0030.0000.0000.0000.000
19A19LEU0-0.010-0.00316.1220.0030.0030.0000.0000.0000.000
20A20TYR0-0.095-0.08516.674-0.002-0.0020.0000.0000.0000.000
21A21SER0-0.044-0.02421.3720.0010.0010.0000.0000.0000.000
22A22GLU-1-0.886-0.94721.8620.0060.0060.0000.0000.0000.000
23A23HIS0-0.032-0.00522.538-0.001-0.0010.0000.0000.0000.000
24A24GLY00.0920.04524.5500.0000.0000.0000.0000.0000.000
25A25TYR00.0290.00719.238-0.002-0.0020.0000.0000.0000.000
26A26ASP-1-0.905-0.95721.478-0.025-0.0250.0000.0000.0000.000
27A27ASN0-0.094-0.03823.392-0.003-0.0030.0000.0000.0000.000
28A28VAL00.0200.03917.1580.0020.0020.0000.0000.0000.000
29A29THR0-0.068-0.05116.010-0.010-0.0100.0000.0000.0000.000
30A30VAL00.030-0.00811.1030.0110.0110.0000.0000.0000.000
31A31THR0-0.023-0.01111.6010.0120.0120.0000.0000.0000.000
32A32ASP-1-0.749-0.84712.6660.0490.0490.0000.0000.0000.000
33A33ILE0-0.023-0.01011.3700.0140.0140.0000.0000.0000.000
34A34ALA0-0.043-0.0368.688-0.004-0.0040.0000.0000.0000.000
35A35GLU-1-0.902-0.9499.8980.1850.1850.0000.0000.0000.000
36A36ARG10.8380.95312.293-0.021-0.0210.0000.0000.0000.000
37A37ALA00.0000.0039.387-0.027-0.0270.0000.0000.0000.000
38A38GLY0-0.023-0.0109.545-0.052-0.0520.0000.0000.0000.000
39A39LEU0-0.075-0.0404.1300.1130.301-0.001-0.020-0.1670.000
40A40THR00.0610.0224.926-0.547-0.5470.0000.0000.0000.000
41A41ARG11.0070.9796.6500.2170.2170.0000.0000.0000.000
42A42ARG10.9330.9613.6500.6210.8650.003-0.030-0.2160.000
43A43SER00.007-0.0442.134-5.495-13.64619.776-6.741-4.8830.014
44A44TYR00.0640.0233.324-2.158-2.0100.0230.611-0.783-0.006
45A45PHE0-0.025-0.0126.011-0.112-0.1120.0000.0000.0000.000
46A46ARG10.8580.9572.130-3.684-3.1534.560-1.236-3.8560.002
47A47TYR0-0.081-0.0662.422-2.466-1.6553.851-1.350-3.312-0.018
48A48PHE00.0910.0396.2490.1460.1460.0000.0000.0000.000
49A49PRO00.0020.0109.114-0.085-0.0850.0000.0000.0000.000
50A50ASP-1-0.768-0.88211.451-0.083-0.0830.0000.0000.0000.000
51A51LYS10.8330.91613.2240.0320.0320.0000.0000.0000.000
52A52ARG10.9821.01215.1860.0460.0460.0000.0000.0000.000
53A53GLU-1-0.775-0.91713.556-0.004-0.0040.0000.0000.0000.000
54A54VAL0-0.0300.01311.9570.0140.0140.0000.0000.0000.000
55A55LEU00.007-0.00513.5840.0060.0060.0000.0000.0000.000
56A56PHE0-0.065-0.03316.0600.0080.0080.0000.0000.0000.000
57A57GLY0-0.0070.00213.0870.0080.0080.0000.0000.0000.000
58A58GLY00.0330.02913.8270.0260.0260.0000.0000.0000.000
59A59SER0-0.100-0.05114.704-0.007-0.0070.0000.0000.0000.000
60A60GLU-1-0.857-0.93116.9880.0360.0360.0000.0000.0000.000
61A61LEU00.0080.02019.6440.0090.0090.0000.0000.0000.000
62A62LEU00.0320.00916.408-0.002-0.0020.0000.0000.0000.000
63A63PRO00.1080.04020.6840.0010.0010.0000.0000.0000.000
64A64PRO0-0.013-0.01121.287-0.001-0.0010.0000.0000.0000.000
65A65ALA0-0.037-0.02021.0740.0010.0010.0000.0000.0000.000
66A66VAL00.0740.04123.171-0.003-0.0030.0000.0000.0000.000
67A67ALA00.0100.00326.121-0.004-0.0040.0000.0000.0000.000
68A68ARG10.9260.94621.279-0.102-0.1020.0000.0000.0000.000
69A69ALA00.0230.02327.076-0.002-0.0020.0000.0000.0000.000
70A70VAL00.0040.00628.707-0.004-0.0040.0000.0000.0000.000
71A71LEU0-0.084-0.04229.794-0.002-0.0020.0000.0000.0000.000
72A72ALA0-0.034-0.00630.660-0.002-0.0020.0000.0000.0000.000
73A73ALA0-0.0020.02232.608-0.001-0.0010.0000.0000.0000.000
74A74ASP-1-0.840-0.91934.9530.0240.0240.0000.0000.0000.000
75A75PRO0-0.055-0.04338.613-0.001-0.0010.0000.0000.0000.000
76A76GLY0-0.0120.00940.518-0.001-0.0010.0000.0000.0000.000
77A77ALA0-0.040-0.01139.177-0.001-0.0010.0000.0000.0000.000
78A78ALA00.0180.01141.2990.0000.0000.0000.0000.0000.000
79A79PRO00.0630.01638.8400.0010.0010.0000.0000.0000.000
80A80LEU00.013-0.00136.8770.0010.0010.0000.0000.0000.000
81A81THR00.0250.01336.5870.0000.0000.0000.0000.0000.000
82A82ALA00.0370.03035.7080.0020.0020.0000.0000.0000.000
83A83VAL0-0.021-0.01532.1790.0030.0030.0000.0000.0000.000
84A84LEU00.012-0.00431.6900.0020.0020.0000.0000.0000.000
85A85ASP-1-0.865-0.92231.5920.0270.0270.0000.0000.0000.000
86A86ALA0-0.049-0.01829.3220.0030.0030.0000.0000.0000.000
87A87MET0-0.065-0.04227.2960.0040.0040.0000.0000.0000.000
88A88SER00.0220.00626.6820.0010.0010.0000.0000.0000.000
89A89GLN0-0.047-0.02026.2620.0060.0060.0000.0000.0000.000
90A90VAL0-0.062-0.03622.1960.0060.0060.0000.0000.0000.000
91A91GLY00.012-0.00322.1720.0060.0060.0000.0000.0000.000
92A92ALA0-0.0080.00723.683-0.005-0.0050.0000.0000.0000.000
93A93GLN0-0.035-0.02818.824-0.008-0.0080.0000.0000.0000.000
94A94LEU00.0150.01120.841-0.006-0.0060.0000.0000.0000.000
95A95VAL0-0.042-0.00922.240-0.005-0.0050.0000.0000.0000.000
96A96ALA0-0.0300.00423.5150.0000.0000.0000.0000.0000.000
97A97GLN0-0.017-0.02222.401-0.005-0.0050.0000.0000.0000.000
98A98VAL00.0260.01423.718-0.001-0.0010.0000.0000.0000.000
99A99GLU-1-0.876-0.93220.511-0.012-0.0120.0000.0000.0000.000
100A100GLY00.0410.03121.110-0.001-0.0010.0000.0000.0000.000
101A101ALA0-0.033-0.01722.192-0.001-0.0010.0000.0000.0000.000
102A102ALA00.0670.01424.1220.0000.0000.0000.0000.0000.000
103A103GLN00.0070.00422.205-0.001-0.0010.0000.0000.0000.000
104A104ARG10.9170.94519.421-0.004-0.0040.0000.0000.0000.000
105A105ARG10.8210.89322.682-0.003-0.0030.0000.0000.0000.000
106A106ALA00.0510.02726.1140.0000.0000.0000.0000.0000.000
107A107VAL0-0.011-0.00721.818-0.001-0.0010.0000.0000.0000.000
108A108ILE0-0.046-0.03322.157-0.001-0.0010.0000.0000.0000.000
109A109ASP-1-0.843-0.93725.387-0.001-0.0010.0000.0000.0000.000
110A110ALA0-0.037-0.00627.8190.0000.0000.0000.0000.0000.000
111A111SER0-0.0060.00024.861-0.001-0.0010.0000.0000.0000.000
112A112PRO00.0460.01727.4150.0010.0010.0000.0000.0000.000
113A113GLU-1-0.859-0.93122.286-0.033-0.0330.0000.0000.0000.000
114A114LEU0-0.022-0.01420.9080.0000.0000.0000.0000.0000.000
115A115GLN0-0.023-0.01024.2590.0040.0040.0000.0000.0000.000
116A116GLU-1-0.976-0.99127.054-0.010-0.0100.0000.0000.0000.000
117A117ARG0-0.0310.02419.0060.0060.0060.0000.0000.0000.000
118A118GLU-1-0.836-0.89323.6890.0090.0090.0000.0000.0000.000
119A119ARG10.9280.96824.9230.0060.0060.0000.0000.0000.000
120A120THR0-0.0080.00224.4700.0020.0020.0000.0000.0000.000
121A121LYS10.7920.86517.671-0.008-0.0080.0000.0000.0000.000
122A122SER0-0.023-0.01524.2510.0050.0050.0000.0000.0000.000
123A123ALA00.0040.00927.3730.0020.0020.0000.0000.0000.000
124A124ALA00.0160.00424.7910.0020.0020.0000.0000.0000.000
125A125ILE0-0.040-0.01523.8170.0050.0050.0000.0000.0000.000
126A126SER00.015-0.00426.9730.0020.0020.0000.0000.0000.000
127A127ARG10.9130.93329.753-0.019-0.0190.0000.0000.0000.000
128A128ALA0-0.0080.00027.0150.0010.0010.0000.0000.0000.000
129A129VAL0-0.015-0.01129.0820.0020.0020.0000.0000.0000.000
130A130GLN00.0170.01531.410-0.001-0.0010.0000.0000.0000.000
131A131ASP-1-0.807-0.89431.5320.0260.0260.0000.0000.0000.000
132A132ALA0-0.092-0.02931.2050.0010.0010.0000.0000.0000.000
133A133LEU00.0330.00833.2370.0000.0000.0000.0000.0000.000
134A134VAL00.0470.03736.453-0.001-0.0010.0000.0000.0000.000
135A135ARG10.8080.88430.060-0.039-0.0390.0000.0000.0000.000
136A136ARG10.7980.87434.902-0.033-0.0330.0000.0000.0000.000
137A137GLN0-0.033-0.00838.925-0.002-0.0020.0000.0000.0000.000
138A138VAL0-0.0010.02839.900-0.001-0.0010.0000.0000.0000.000
139A139ASP-1-0.820-0.89341.2620.0140.0140.0000.0000.0000.000
140A140ALA00.026-0.01040.3520.0000.0000.0000.0000.0000.000
141A141ASP-1-0.852-0.91740.6250.0110.0110.0000.0000.0000.000
142A142THR0-0.057-0.05442.1360.0000.0000.0000.0000.0000.000
143A143ALA0-0.062-0.04437.6440.0010.0010.0000.0000.0000.000
144A144GLU-1-0.953-0.97837.4070.0120.0120.0000.0000.0000.000
145A145LEU00.0250.01137.7710.0000.0000.0000.0000.0000.000
146A146VAL0-0.032-0.01036.8340.0000.0000.0000.0000.0000.000
147A147ALA00.0090.01033.4290.0010.0010.0000.0000.0000.000
148A148GLN00.0400.03333.9750.0020.0020.0000.0000.0000.000
149A149LEU0-0.0040.00535.652-0.001-0.0010.0000.0000.0000.000
150A150ALA00.0170.00433.4880.0000.0000.0000.0000.0000.000
151A151THR0-0.030-0.01430.6390.0010.0010.0000.0000.0000.000
152A152VAL0-0.011-0.00432.191-0.001-0.0010.0000.0000.0000.000
153A153ALA0-0.010-0.00334.771-0.001-0.0010.0000.0000.0000.000
154A154PHE00.0430.00926.843-0.001-0.0010.0000.0000.0000.000
155A155GLY00.0160.01129.9300.0000.0000.0000.0000.0000.000
156A156SER0-0.048-0.04230.981-0.002-0.0020.0000.0000.0000.000
157A157ALA0-0.0110.00432.790-0.001-0.0010.0000.0000.0000.000
158A158PHE00.0200.01324.301-0.001-0.0010.0000.0000.0000.000
159A159ARG10.9140.96030.113-0.004-0.0040.0000.0000.0000.000
160A160ARG10.9680.97531.468-0.009-0.0090.0000.0000.0000.000
161A161TRP00.002-0.00725.553-0.001-0.0010.0000.0000.0000.000
162A162ILE0-0.066-0.03327.074-0.001-0.0010.0000.0000.0000.000
163A163ASP-1-0.924-0.96330.2270.0030.0030.0000.0000.0000.000
164A164ALA0-0.069-0.01833.6400.0000.0000.0000.0000.0000.000
165A165GLU-1-0.946-0.98231.1220.0030.0030.0000.0000.0000.000
166A166GLY0-0.015-0.00431.1840.0000.0000.0000.0000.0000.000
167A167HIS0-0.065-0.02931.7700.0010.0010.0000.0000.0000.000
168A168ALA0-0.022-0.01034.3390.0000.0000.0000.0000.0000.000
169A169ASP-1-0.810-0.85532.9330.0140.0140.0000.0000.0000.000
170A170PHE00.026-0.01630.1070.0000.0000.0000.0000.0000.000
171A171GLY00.0250.01332.2310.0000.0000.0000.0000.0000.000
172A172SER00.062-0.00734.8940.0000.0000.0000.0000.0000.000
173A173CYS0-0.123-0.03634.160-0.001-0.0010.0000.0000.0000.000
174A174LEU00.018-0.00633.486-0.001-0.0010.0000.0000.0000.000
175A175ASP-1-0.856-0.91336.0550.0150.0150.0000.0000.0000.000
176A176THR0-0.066-0.03739.422-0.001-0.0010.0000.0000.0000.000
177A177VAL0-0.050-0.02536.357-0.001-0.0010.0000.0000.0000.000
178A178THR0-0.021-0.02238.082-0.001-0.0010.0000.0000.0000.000
179A179ASP-1-0.789-0.87140.6520.0110.0110.0000.0000.0000.000
180A180ARG10.8750.94342.501-0.007-0.0070.0000.0000.0000.000
181A181LEU0-0.010-0.01638.869-0.001-0.0010.0000.0000.0000.000
182A182ARG10.8800.92643.465-0.012-0.0120.0000.0000.0000.000
183A183ALA00.0040.00046.1490.0000.0000.0000.0000.0000.000
184A184VAL0-0.037-0.00845.567-0.001-0.0010.0000.0000.0000.000
185A185LEU0-0.017-0.01045.0700.0000.0000.0000.0000.0000.000
186A186THR0-0.112-0.04548.7130.0000.0000.0000.0000.0000.000
187A187GLY0-0.041-0.01451.2210.0000.0000.0000.0000.0000.000