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: G5LR1

Calculation Name: 2DG8-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2DG8

Chain ID: A

ChEMBL ID:
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UniProt ID: Q93J02

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:


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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1785392.296576
FMO2-HF: Nuclear repulsion 1716639.349424
FMO2-HF: Total energy -68752.947152
FMO2-MP2: Total energy -68957.587317


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:7:ASP)


Summations of interaction energy for fragment #1(A:7:ASP)
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.
-117.262-115.12312.373-7.314-7.1990.082
Interaction energy analysis for fragmet #1(A:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.850 / q_NPA : -0.934
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].
3A9GLN00.0970.0522.699-6.567-3.5690.131-1.235-1.8950.003
4A10ARG10.9330.9703.227-64.522-62.5420.054-0.885-1.1490.007
5A11ARG10.7990.8734.596-29.047-28.8700.000-0.038-0.1390.000
6A12GLU-1-0.859-0.9407.44627.43927.4390.0000.0000.0000.000
7A13ARG10.9010.9331.761-93.138-96.15412.188-5.156-4.0160.072
8A14ILE0-0.036-0.0058.259-2.991-2.9910.0000.0000.0000.000
9A15LEU0-0.0030.01510.292-2.255-2.2550.0000.0000.0000.000
10A16ALA00.0000.00311.523-1.745-1.7450.0000.0000.0000.000
11A17ALA00.0490.03111.848-1.524-1.5240.0000.0000.0000.000
12A18THR0-0.054-0.05513.582-1.637-1.6370.0000.0000.0000.000
13A19LEU00.0010.00216.083-1.054-1.0540.0000.0000.0000.000
14A20ASP-1-0.828-0.89815.23718.45718.4570.0000.0000.0000.000
15A21LEU0-0.093-0.03717.563-0.799-0.7990.0000.0000.0000.000
16A22ILE0-0.033-0.01719.377-0.825-0.8250.0000.0000.0000.000
17A23ALA00.0060.00221.340-0.700-0.7000.0000.0000.0000.000
18A24GLU-1-0.869-0.93319.72915.02415.0240.0000.0000.0000.000
19A25GLU-1-0.863-0.91021.87313.56013.5600.0000.0000.0000.000
20A26GLY00.0680.05124.525-0.511-0.5110.0000.0000.0000.000
21A27ILE00.014-0.00823.6260.4830.4830.0000.0000.0000.000
22A28ALA0-0.026-0.01624.7500.2810.2810.0000.0000.0000.000
23A29ARG10.7940.88123.584-12.594-12.5940.0000.0000.0000.000
24A30VAL00.0450.03219.6520.7790.7790.0000.0000.0000.000
25A31SER0-0.048-0.04119.703-0.202-0.2020.0000.0000.0000.000
26A32HIS00.1130.03916.7311.2561.2560.0000.0000.0000.000
27A33ARG10.9500.96415.704-13.307-13.3070.0000.0000.0000.000
28A34ARG10.8890.95916.250-12.970-12.9700.0000.0000.0000.000
29A35ILE00.0630.04012.9230.4690.4690.0000.0000.0000.000
30A36ALA00.0080.00311.5891.5381.5380.0000.0000.0000.000
31A37GLN0-0.010-0.00311.2772.0272.0270.0000.0000.0000.000
32A38ARG10.7980.89912.749-15.998-15.9980.0000.0000.0000.000
33A39ALA00.0010.0128.5990.7690.7690.0000.0000.0000.000
34A40GLY00.0090.0177.7804.9734.9730.0000.0000.0000.000
35A41VAL0-0.069-0.0425.7676.9446.9440.0000.0000.0000.000
36A42PRO00.0160.0107.589-4.126-4.1260.0000.0000.0000.000
37A43LEU00.0840.01810.8330.3210.3210.0000.0000.0000.000
38A44GLY00.0110.00413.583-0.494-0.4940.0000.0000.0000.000
39A45SER0-0.019-0.0218.7411.2981.2980.0000.0000.0000.000
40A46MET0-0.032-0.00210.690-0.036-0.0360.0000.0000.0000.000
41A47THR00.0380.00413.214-0.415-0.4150.0000.0000.0000.000
42A48TYR0-0.078-0.01210.257-0.659-0.6590.0000.0000.0000.000
43A49HIS0-0.021-0.0167.755-1.779-1.7790.0000.0000.0000.000
44A50PHE00.0190.01211.695-0.519-0.5190.0000.0000.0000.000
45A51THR0-0.0020.00015.942-0.182-0.1820.0000.0000.0000.000
46A52GLY00.0350.00719.233-0.697-0.6970.0000.0000.0000.000
47A53ILE00.000-0.01119.3500.6050.6050.0000.0000.0000.000
48A54GLU-1-0.892-0.93020.94612.18512.1850.0000.0000.0000.000
49A55GLN00.0740.03717.7820.6100.6100.0000.0000.0000.000
50A56LEU0-0.0140.00414.6290.2390.2390.0000.0000.0000.000
51A57LEU00.012-0.00917.8750.2950.2950.0000.0000.0000.000
52A58ARG10.8860.95320.589-12.313-12.3130.0000.0000.0000.000
53A59GLU-1-0.790-0.87815.77619.16419.1640.0000.0000.0000.000
54A60ALA0-0.049-0.02016.9740.4210.4210.0000.0000.0000.000
55A61PHE00.035-0.00617.9020.0070.0070.0000.0000.0000.000
56A62GLY00.0350.03120.524-0.522-0.5220.0000.0000.0000.000
57A63ARG10.9420.98610.791-22.755-22.7550.0000.0000.0000.000
58A64PHE0-0.055-0.02718.0720.0820.0820.0000.0000.0000.000
59A65THR00.0160.00620.391-0.464-0.4640.0000.0000.0000.000
60A66ASP-1-0.912-0.96219.20314.31514.3150.0000.0000.0000.000
61A67HIS0-0.069-0.03119.3470.1380.1380.0000.0000.0000.000
62A68ILE00.0680.04221.105-0.347-0.3470.0000.0000.0000.000
63A69VAL0-0.049-0.02224.451-0.483-0.4830.0000.0000.0000.000
64A70ALA00.001-0.00622.251-0.394-0.3940.0000.0000.0000.000
65A71VAL00.0640.04724.311-0.232-0.2320.0000.0000.0000.000
66A72PHE0-0.023-0.02026.339-0.469-0.4690.0000.0000.0000.000
67A73ASP-1-0.990-0.99926.27810.70910.7090.0000.0000.0000.000
68A74GLU-1-0.959-0.97025.62111.21211.2120.0000.0000.0000.000
69A75HIS00.0020.00627.986-0.587-0.5870.0000.0000.0000.000
70A76LEU0-0.086-0.05531.504-0.358-0.3580.0000.0000.0000.000
71A77GLY0-0.030-0.01830.830-0.292-0.2920.0000.0000.0000.000
72A78ALA0-0.048-0.02031.868-0.121-0.1210.0000.0000.0000.000
73A79ALA0-0.0240.00733.473-0.219-0.2190.0000.0000.0000.000
74A80ALA00.001-0.00336.8930.0480.0480.0000.0000.0000.000
75A81ASP-1-0.877-0.95539.5797.0507.0500.0000.0000.0000.000
76A82ARG10.9340.95141.233-6.451-6.4510.0000.0000.0000.000
77A83ASP-1-0.923-0.95542.5356.7356.7350.0000.0000.0000.000
78A84GLU-1-0.822-0.89339.4047.8277.8270.0000.0000.0000.000
79A85ALA0-0.008-0.00338.1200.1890.1890.0000.0000.0000.000
80A86ARG10.8510.90538.631-6.710-6.7100.0000.0000.0000.000
81A87GLU-1-0.839-0.90740.1537.3237.3230.0000.0000.0000.000
82A88ALA00.0390.02235.1980.1030.1030.0000.0000.0000.000
83A89VAL0-0.019-0.01635.4510.2090.2090.0000.0000.0000.000
84A90ALA0-0.047-0.02636.6170.0840.0840.0000.0000.0000.000
85A91ASP-1-0.834-0.89234.4548.4138.4130.0000.0000.0000.000
86A92LEU00.0070.01330.4300.1630.1630.0000.0000.0000.000
87A93VAL0-0.047-0.02732.7880.1400.1400.0000.0000.0000.000
88A94HIS0-0.068-0.05234.8090.0540.0540.0000.0000.0000.000
89A95GLU-1-0.810-0.89127.84410.76710.7670.0000.0000.0000.000
90A96LEU0-0.045-0.03428.5480.2920.2920.0000.0000.0000.000
91A97SER0-0.141-0.05530.849-0.020-0.0200.0000.0000.0000.000
92A98GLU-1-0.935-0.98532.5878.5738.5730.0000.0000.0000.000
93A99ASP-1-0.823-0.88028.23710.22510.2250.0000.0000.0000.000
94A100SER0-0.009-0.00124.0900.3800.3800.0000.0000.0000.000
95A101GLN00.0250.00527.0110.0250.0250.0000.0000.0000.000
96A102ARG10.8470.90917.406-16.298-16.2980.0000.0000.0000.000
97A103ASP-1-0.789-0.91722.88913.46813.4680.0000.0000.0000.000
98A104LEU00.0450.04625.165-0.126-0.1260.0000.0000.0000.000
99A105VAL0-0.005-0.01026.193-0.221-0.2210.0000.0000.0000.000
100A106LEU0-0.043-0.01820.9090.0220.0220.0000.0000.0000.000
101A107THR0-0.008-0.00825.250-0.024-0.0240.0000.0000.0000.000
102A108GLN00.015-0.00327.808-0.355-0.3550.0000.0000.0000.000
103A109GLU-1-0.916-0.96625.80211.24211.2420.0000.0000.0000.000
104A110LEU0-0.034-0.00725.586-0.180-0.1800.0000.0000.0000.000
105A111TYR0-0.017-0.04027.676-0.081-0.0810.0000.0000.0000.000
106A112THR0-0.026-0.00230.962-0.453-0.4530.0000.0000.0000.000
107A113LEU0-0.058-0.02625.794-0.257-0.2570.0000.0000.0000.000
108A114ALA00.0270.00929.988-0.193-0.1930.0000.0000.0000.000
109A115ALA0-0.0160.01231.606-0.326-0.3260.0000.0000.0000.000
110A116ARG10.9060.94932.477-9.424-9.4240.0000.0000.0000.000
111A117GLN00.0020.00229.107-0.045-0.0450.0000.0000.0000.000
112A118PRO00.0360.00731.7760.2720.2720.0000.0000.0000.000
113A119ALA00.0880.05829.9520.0400.0400.0000.0000.0000.000
114A120TYR00.015-0.01724.1680.1840.1840.0000.0000.0000.000
115A121ARG10.8400.90829.268-8.669-8.6690.0000.0000.0000.000
116A122GLU-1-0.943-0.96529.05310.59510.5950.0000.0000.0000.000
117A123LEU0-0.004-0.00523.4490.0800.0800.0000.0000.0000.000
118A124THR00.0650.03427.5220.0290.0290.0000.0000.0000.000
119A125HIS0-0.055-0.02030.062-0.217-0.2170.0000.0000.0000.000
120A126GLU-1-0.842-0.93226.38610.73010.7300.0000.0000.0000.000
121A127TRP0-0.010-0.00827.4990.1240.1240.0000.0000.0000.000
122A128MET00.0610.01728.502-0.223-0.2230.0000.0000.0000.000
123A129ARG10.8080.91228.181-10.720-10.7200.0000.0000.0000.000
124A130ARG10.8740.92522.423-12.758-12.7580.0000.0000.0000.000
125A131SER00.0570.04129.6880.1170.1170.0000.0000.0000.000
126A132ARG10.9650.97031.213-8.921-8.9210.0000.0000.0000.000
127A133VAL0-0.0290.01131.053-0.170-0.1700.0000.0000.0000.000
128A134HIS00.0450.00227.360-0.423-0.4230.0000.0000.0000.000
129A135LEU00.0140.01432.663-0.186-0.1860.0000.0000.0000.000
130A136GLU-1-0.943-0.99135.8957.9677.9670.0000.0000.0000.000
131A137LYS10.8430.95230.149-9.944-9.9440.0000.0000.0000.000
132A138HIS10.7950.90135.359-8.487-8.4870.0000.0000.0000.000
133A139PHE0-0.0170.00439.435-0.250-0.2500.0000.0000.0000.000
134A140ASP-1-0.812-0.89740.9597.0517.0510.0000.0000.0000.000
135A141PRO00.0630.00640.7080.0450.0450.0000.0000.0000.000
136A142GLY0-0.033-0.00541.4960.0960.0960.0000.0000.0000.000
137A143THR00.003-0.01243.4370.1160.1160.0000.0000.0000.000
138A144ALA00.0530.03938.3050.0900.0900.0000.0000.0000.000
139A145ARG10.9160.95338.642-7.718-7.7180.0000.0000.0000.000
140A146GLN0-0.045-0.02940.1420.0320.0320.0000.0000.0000.000
141A147LEU00.0090.00438.747-0.006-0.0060.0000.0000.0000.000
142A148ASP-1-0.883-0.95134.5559.1629.1620.0000.0000.0000.000
143A149ALA0-0.022-0.00436.9630.1160.1160.0000.0000.0000.000
144A150LEU0-0.032-0.00639.299-0.024-0.0240.0000.0000.0000.000
145A151ILE00.0380.01734.426-0.020-0.0200.0000.0000.0000.000
146A152GLU-1-0.875-0.89633.6769.5149.5140.0000.0000.0000.000
147A153GLY00.003-0.00936.2990.0510.0510.0000.0000.0000.000
148A154LEU0-0.052-0.03739.140-0.085-0.0850.0000.0000.0000.000
149A155THR00.0280.00032.829-0.008-0.0080.0000.0000.0000.000
150A156LEU0-0.034-0.01035.1590.0900.0900.0000.0000.0000.000
151A157HIS0-0.012-0.02936.8340.0760.0760.0000.0000.0000.000
152A158ARG10.7640.88637.081-8.326-8.3260.0000.0000.0000.000
153A159ALA00.0660.03134.089-0.025-0.0250.0000.0000.0000.000
154A160LEU0-0.121-0.04835.0440.0690.0690.0000.0000.0000.000
155A161ALA0-0.0010.02538.064-0.222-0.2220.0000.0000.0000.000
156A162ARG10.8660.93540.342-7.207-7.2070.0000.0000.0000.000
157A163GLU-1-0.950-0.99942.8746.6746.6740.0000.0000.0000.000
158A164PRO00.0000.02239.859-0.139-0.1390.0000.0000.0000.000
159A165HIS00.0020.00641.562-0.206-0.2060.0000.0000.0000.000
160A166GLY00.0510.01842.3580.1710.1710.0000.0000.0000.000
161A167ARG10.8430.86138.448-7.867-7.8670.0000.0000.0000.000
162A168ALA00.0110.01442.872-0.014-0.0140.0000.0000.0000.000
163A169LEU00.0130.01144.956-0.062-0.0620.0000.0000.0000.000
164A170THR00.0250.01539.7920.0560.0560.0000.0000.0000.000
165A171LEU00.0510.02042.5130.0200.0200.0000.0000.0000.000
166A172GLU-1-0.953-0.97044.2746.1186.1180.0000.0000.0000.000
167A173ALA0-0.014-0.00444.421-0.076-0.0760.0000.0000.0000.000
168A174ILE00.0290.02140.049-0.041-0.0410.0000.0000.0000.000
169A175ALA00.0180.02043.910-0.028-0.0280.0000.0000.0000.000
170A176ARG10.9010.95446.882-6.242-6.2420.0000.0000.0000.000
171A177ILE0-0.012-0.00143.140-0.076-0.0760.0000.0000.0000.000
172A178THR0-0.061-0.03242.778-0.017-0.0170.0000.0000.0000.000
173A179THR0-0.048-0.02545.937-0.075-0.0750.0000.0000.0000.000
174A180THR0-0.050-0.03248.5840.0410.0410.0000.0000.0000.000
175A181ASP-1-0.982-0.97951.3495.5455.5450.0000.0000.0000.000