Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3Q28L

Calculation Name: 2E8B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2E8B

Chain ID: A

ChEMBL ID:

UniProt ID: O67413

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptAll
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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2135769.95732
FMO2-HF: Nuclear repulsion 2062281.563879
FMO2-HF: Total energy -73488.393441
FMO2-MP2: Total energy -73707.238792


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:4:PHE)


Summations of interaction energy for fragment #1(A:4:PHE)
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.
-18.337-6.66110.431-7.189-14.9170.025
Interaction energy analysis for fragmet #1(A:4:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.131 / q_NPA : 0.048
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].
3A6TRP00.0620.0142.504-5.376-0.8661.288-2.116-3.6820.004
4A7ARG10.9310.9743.9470.4880.851-0.001-0.046-0.3160.000
5A8LYS10.8780.9574.401-0.558-0.341-0.001-0.033-0.1820.000
6A9GLY00.0990.0643.8190.5270.727-0.001-0.037-0.1630.000
7A10SER0-0.093-0.0483.9620.5440.8550.000-0.093-0.2180.000
8A11LEU00.035-0.0042.320-1.125-0.0233.431-1.305-3.228-0.001
9A12SER00.0340.0252.739-0.4540.6540.511-0.546-1.0720.000
10A13LYS10.8340.8984.217-2.214-2.1720.000-0.008-0.0340.000
11A14VAL00.0360.0545.889-0.166-0.1660.0000.0000.0000.000
12A15ASN0-0.058-0.0615.846-0.556-0.5560.0000.0000.0000.000
13A16THR0-0.062-0.0447.703-0.039-0.0390.0000.0000.0000.000
14A17CYS00.0010.00710.0740.0670.0670.0000.0000.0000.000
15A18TYR0-0.016-0.02311.908-0.019-0.0190.0000.0000.0000.000
16A19VAL00.0170.00115.2040.0120.0120.0000.0000.0000.000
17A20LEU0-0.021-0.01117.217-0.007-0.0070.0000.0000.0000.000
18A21ALA00.0200.00220.427-0.001-0.0010.0000.0000.0000.000
19A22GLY0-0.0240.00123.283-0.002-0.0020.0000.0000.0000.000
20A23GLY00.0570.01926.136-0.001-0.0010.0000.0000.0000.000
21A24LYS10.8120.88129.760-0.006-0.0060.0000.0000.0000.000
22A25SER0-0.042-0.05031.7960.0010.0010.0000.0000.0000.000
23A26LYS10.9370.97026.079-0.003-0.0030.0000.0000.0000.000
24A27ARG10.7650.88831.8870.0090.0090.0000.0000.0000.000
25A28PHE00.0520.01333.8460.0000.0000.0000.0000.0000.000
26A29GLY00.0550.02337.431-0.001-0.0010.0000.0000.0000.000
27A30GLU-1-0.887-0.94439.430-0.008-0.0080.0000.0000.0000.000
28A31ASP-1-0.825-0.90936.157-0.012-0.0120.0000.0000.0000.000
29A32LYS10.7830.89035.1570.0030.0030.0000.0000.0000.000
30A33LEU00.0750.03434.1030.0010.0010.0000.0000.0000.000
31A34LEU00.0320.01433.7070.0010.0010.0000.0000.0000.000
32A35TYR0-0.026-0.03129.8520.0010.0010.0000.0000.0000.000
33A36GLU-1-0.791-0.85829.433-0.002-0.0020.0000.0000.0000.000
34A37ILE0-0.028-0.01329.6420.0020.0020.0000.0000.0000.000
35A38LYN00.0300.02824.7540.0020.0020.0000.0000.0000.000
36A39GLY00.0340.01225.7340.0020.0020.0000.0000.0000.000
37A40LYS10.9330.97024.6310.0040.0040.0000.0000.0000.000
38A41LYS10.8650.90324.185-0.001-0.0010.0000.0000.0000.000
39A42VAL0-0.070-0.01020.6770.0020.0020.0000.0000.0000.000
40A43ILE00.0220.00920.0200.0070.0070.0000.0000.0000.000
41A44GLU-1-0.806-0.87419.2610.0110.0110.0000.0000.0000.000
42A45ARG10.9300.94017.900-0.001-0.0010.0000.0000.0000.000
43A46VAL0-0.046-0.00215.4560.0230.0230.0000.0000.0000.000
44A47TYR0-0.001-0.01014.4070.0170.0170.0000.0000.0000.000
45A48GLU-1-0.899-0.94514.3930.0350.0350.0000.0000.0000.000
46A49THR0-0.042-0.02911.0120.0340.0340.0000.0000.0000.000
47A50ALA00.0430.02610.1280.0990.0990.0000.0000.0000.000
48A51LYS10.8220.9249.7060.0750.0750.0000.0000.0000.000
49A52SER0-0.029-0.0399.3730.0000.0000.0000.0000.0000.000
50A53VAL0-0.030-0.0034.233-0.0310.112-0.001-0.018-0.1240.000
51A54PHE00.0330.0045.758-0.723-0.7230.0000.0000.0000.000
52A55LYS10.8590.9417.4930.3200.3200.0000.0000.0000.000
53A56GLU-1-0.855-0.9079.737-0.043-0.0430.0000.0000.0000.000
54A57VAL0-0.023-0.02411.489-0.005-0.0050.0000.0000.0000.000
55A58TYR0-0.032-0.02513.8050.0060.0060.0000.0000.0000.000
56A59ILE00.0100.01217.1070.0100.0100.0000.0000.0000.000
57A60VAL0-0.013-0.00319.326-0.002-0.0020.0000.0000.0000.000
58A61ALA00.002-0.00421.8710.0010.0010.0000.0000.0000.000
59A62LYS10.7670.87625.479-0.012-0.0120.0000.0000.0000.000
60A63ASP-1-0.880-0.94128.4540.0010.0010.0000.0000.0000.000
61A64ARG10.9000.94925.9970.0010.0010.0000.0000.0000.000
62A65GLU-1-0.769-0.87428.094-0.003-0.0030.0000.0000.0000.000
63A66LYS10.7930.91728.559-0.005-0.0050.0000.0000.0000.000
64A67PHE0-0.023-0.04424.6380.0010.0010.0000.0000.0000.000
65A68SER00.024-0.00725.2700.0000.0000.0000.0000.0000.000
66A69PHE0-0.049-0.02024.925-0.001-0.0010.0000.0000.0000.000
67A70LEU0-0.019-0.00421.2920.0010.0010.0000.0000.0000.000
68A71ASN0-0.024-0.00221.641-0.001-0.0010.0000.0000.0000.000
69A72ALA00.0300.02119.376-0.004-0.0040.0000.0000.0000.000
70A73PRO0-0.0040.00318.2650.0030.0030.0000.0000.0000.000
71A74VAL00.0120.00820.3290.0020.0020.0000.0000.0000.000
72A75VAL0-0.030-0.01420.070-0.001-0.0010.0000.0000.0000.000
73A76LEU0-0.021-0.01523.0330.0010.0010.0000.0000.0000.000
74A77ASP-1-0.812-0.89825.6930.0170.0170.0000.0000.0000.000
75A78GLU-1-0.797-0.90327.1700.0140.0140.0000.0000.0000.000
76A79PHE00.0020.02428.598-0.001-0.0010.0000.0000.0000.000
77A80GLU-1-0.753-0.86632.0020.0050.0050.0000.0000.0000.000
78A81GLU-1-0.834-0.89033.1550.0100.0100.0000.0000.0000.000
79A82SER0-0.026-0.03129.4750.0010.0010.0000.0000.0000.000
80A83ALA00.0230.02429.380-0.001-0.0010.0000.0000.0000.000
81A84SER00.013-0.01524.0500.0010.0010.0000.0000.0000.000
82A85ILE00.0140.02023.9560.0040.0040.0000.0000.0000.000
83A86ILE00.0580.04324.9290.0040.0040.0000.0000.0000.000
84A87GLY00.0190.02923.3420.0000.0000.0000.0000.0000.000
85A88LEU0-0.009-0.01218.9830.0010.0010.0000.0000.0000.000
86A89TYR0-0.031-0.03820.8130.0040.0040.0000.0000.0000.000
87A90THR0-0.013-0.01922.8760.0010.0010.0000.0000.0000.000
88A91ALA0-0.032-0.01517.509-0.002-0.0020.0000.0000.0000.000
89A92LEU00.0100.00316.882-0.001-0.0010.0000.0000.0000.000
90A93LYS10.8600.92619.545-0.018-0.0180.0000.0000.0000.000
91A94HIS0-0.0170.00718.8920.0010.0010.0000.0000.0000.000
92A95ALA00.0150.01716.239-0.007-0.0070.0000.0000.0000.000
93A96LYS10.8960.94315.259-0.001-0.0010.0000.0000.0000.000
94A97GLU-1-0.765-0.84510.209-0.048-0.0480.0000.0000.0000.000
95A98GLU-1-0.747-0.84914.2930.1380.1380.0000.0000.0000.000
96A99ASN0-0.023-0.02111.475-0.014-0.0140.0000.0000.0000.000
97A100VAL00.0170.01511.0580.0010.0010.0000.0000.0000.000
98A101PHE00.0440.0048.7100.0260.0260.0000.0000.0000.000
99A102VAL0-0.028-0.01311.283-0.041-0.0410.0000.0000.0000.000
100A103LEU00.0130.00012.3060.0080.0080.0000.0000.0000.000
101A104SER0-0.010-0.03015.581-0.008-0.0080.0000.0000.0000.000
102A105GLY00.0270.01518.3000.0030.0030.0000.0000.0000.000
103A106ASP-1-0.854-0.90820.4190.0030.0030.0000.0000.0000.000
104A107LEU00.0180.01216.898-0.007-0.0070.0000.0000.0000.000
105A108PRO0-0.026-0.02218.7000.0070.0070.0000.0000.0000.000
106A109LEU00.0120.01217.5220.0030.0030.0000.0000.0000.000
107A110MET0-0.0070.03013.030-0.007-0.0070.0000.0000.0000.000
108A111LYS10.9210.93910.1770.1130.1130.0000.0000.0000.000
109A112LYS10.8910.9455.908-1.203-1.2030.0000.0000.0000.000
110A113GLU-1-0.807-0.9025.5580.3700.3700.0000.0000.0000.000
111A114THR00.0270.0016.093-0.367-0.3670.0000.0000.0000.000
112A115VAL0-0.020-0.0076.778-0.036-0.0360.0000.0000.0000.000
113A116LEU0-0.071-0.0352.204-2.731-0.6055.189-2.520-4.7960.025
114A117TYR00.0610.0334.600-0.638-0.372-0.001-0.020-0.2450.000
115A118VAL0-0.005-0.0025.9140.2030.2030.0000.0000.0000.000
116A119LEU0-0.074-0.0413.841-0.1970.0340.000-0.030-0.2000.000
117A120GLU-1-1.001-0.9893.467-4.466-3.4090.017-0.417-0.657-0.003
118A121ASN0-0.025-0.0235.5720.1780.1780.0000.0000.0000.000
119A122PHE0-0.044-0.0098.786-0.036-0.0360.0000.0000.0000.000
120A123LYS10.8870.93910.751-0.136-0.1360.0000.0000.0000.000
121A124GLU-1-0.783-0.84614.1030.1900.1900.0000.0000.0000.000
122A125PRO00.0120.01116.243-0.016-0.0160.0000.0000.0000.000
123A126VAL00.039-0.00816.1420.0040.0040.0000.0000.0000.000
124A127SER0-0.0080.01712.7520.0000.0000.0000.0000.0000.000
125A128VAL0-0.030-0.01214.0560.0220.0220.0000.0000.0000.000
126A129ALA00.0440.03413.332-0.024-0.0240.0000.0000.0000.000
127A130LYS10.7910.89214.7490.0570.0570.0000.0000.0000.000
128A131THR00.0320.01716.407-0.024-0.0240.0000.0000.0000.000
129A132GLU-1-0.775-0.87218.863-0.075-0.0750.0000.0000.0000.000
130A133LYS10.8480.94821.0320.0300.0300.0000.0000.0000.000
131A134LEU00.0100.00819.403-0.008-0.0080.0000.0000.0000.000
132A135HIS0-0.023-0.03417.2100.0190.0190.0000.0000.0000.000
133A136THR00.009-0.00117.8630.0120.0120.0000.0000.0000.000
134A137LEU0-0.0290.00318.5120.0110.0110.0000.0000.0000.000
135A138VAL00.025-0.00113.1700.0010.0010.0000.0000.0000.000
136A139GLY00.0320.01412.895-0.018-0.0180.0000.0000.0000.000
137A140VAL0-0.0460.0039.1940.0090.0090.0000.0000.0000.000
138A141TYR0-0.012-0.03212.390-0.020-0.0200.0000.0000.0000.000
139A142SER00.028-0.00314.899-0.001-0.0010.0000.0000.0000.000
140A143LYS10.8170.88816.646-0.072-0.0720.0000.0000.0000.000
141A144LYS10.7940.87317.571-0.174-0.1740.0000.0000.0000.000
142A145LEU0-0.019-0.00419.183-0.010-0.0100.0000.0000.0000.000
143A146LEU0-0.020-0.00422.263-0.008-0.0080.0000.0000.0000.000
144A147GLU-1-0.892-0.93623.7290.0400.0400.0000.0000.0000.000
145A148LYS10.8550.90225.561-0.043-0.0430.0000.0000.0000.000
146A149ILE0-0.024-0.01921.735-0.005-0.0050.0000.0000.0000.000
147A150GLU-1-0.852-0.91026.3160.0250.0250.0000.0000.0000.000
148A151GLU-1-0.869-0.91129.0140.0280.0280.0000.0000.0000.000
149A152ARG10.8120.87228.784-0.030-0.0300.0000.0000.0000.000
150A153ILE0-0.009-0.00927.123-0.003-0.0030.0000.0000.0000.000
151A154LYS10.9470.97931.342-0.027-0.0270.0000.0000.0000.000
152A155LYS10.8240.89934.004-0.026-0.0260.0000.0000.0000.000
153A156GLY00.0400.03734.725-0.001-0.0010.0000.0000.0000.000
154A157ASP-1-0.801-0.85032.5910.0160.0160.0000.0000.0000.000
155A158TYR0-0.056-0.07030.0370.0030.0030.0000.0000.0000.000
156A159ARG10.8300.88428.827-0.012-0.0120.0000.0000.0000.000
157A160ILE00.0680.02322.5740.0010.0010.0000.0000.0000.000
158A161TRP0-0.005-0.01025.2010.0030.0030.0000.0000.0000.000
159A162ALA0-0.025-0.00327.0880.0000.0000.0000.0000.0000.000
160A163LEU00.0350.01423.0440.0010.0010.0000.0000.0000.000
161A164LEU00.003-0.01120.7350.0040.0040.0000.0000.0000.000
162A165LYS10.9160.96224.154-0.008-0.0080.0000.0000.0000.000
163A166ASP-1-0.864-0.88727.2960.0370.0370.0000.0000.0000.000
164A167VAL0-0.013-0.01122.2380.0010.0010.0000.0000.0000.000
165A168GLY00.0210.03123.4410.0080.0080.0000.0000.0000.000
166A169TYR0-0.110-0.09219.6820.0090.0090.0000.0000.0000.000
167A170ASN0-0.017-0.00715.960-0.019-0.0190.0000.0000.0000.000
168A171GLU-1-0.761-0.87516.438-0.014-0.0140.0000.0000.0000.000
169A172VAL00.0060.00010.583-0.011-0.0110.0000.0000.0000.000
170A173GLU-1-0.915-0.96013.898-0.162-0.1620.0000.0000.0000.000
171A174ILE0-0.055-0.02211.105-0.065-0.0650.0000.0000.0000.000
172A175PRO00.0730.0289.6800.0450.0450.0000.0000.0000.000
173A176GLU-1-0.786-0.89012.944-0.137-0.1370.0000.0000.0000.000
174A177GLU-1-0.930-0.96412.930-0.310-0.3100.0000.0000.0000.000
175A178LEU0-0.041-0.0318.268-0.004-0.0040.0000.0000.0000.000
176A179ARG10.7780.89012.9380.1940.1940.0000.0000.0000.000
177A180TYR00.0210.00913.7950.0470.0470.0000.0000.0000.000
178A181THR0-0.053-0.03812.6200.0300.0300.0000.0000.0000.000
179A182LEU0-0.013-0.00913.9400.0300.0300.0000.0000.0000.000
180A183LEU00.0010.01417.5410.0090.0090.0000.0000.0000.000
181A184ASN0-0.007-0.02420.8490.0050.0050.0000.0000.0000.000
182A185MET00.0100.01023.667-0.003-0.0030.0000.0000.0000.000
183A186ASN00.010-0.01426.3900.0020.0020.0000.0000.0000.000
184A187THR00.0060.01928.8180.0000.0000.0000.0000.0000.000
185A188LYS10.9661.00031.6710.0190.0190.0000.0000.0000.000