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: J3879

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2129617.491511
FMO2-HF: Nuclear repulsion 2056129.667792
FMO2-HF: Total energy -73487.823719
FMO2-MP2: Total energy -73706.654247


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.
-19.03-7.50814.408-8.694-17.2370.032
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 : 0.106 / q_NPA : 0.030
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].
3A6TRP00.0650.0032.236-7.173-0.9501.925-3.478-4.6710.008
4A7ARG10.9591.0003.944-0.0800.2460.000-0.036-0.2900.000
5A8LYS10.9200.9744.399-0.363-0.277-0.001-0.027-0.0580.000
6A9GLY00.0800.0434.5160.6220.718-0.001-0.005-0.0900.000
7A10SER0-0.116-0.0564.5730.6790.832-0.001-0.018-0.1330.000
8A11LEU00.0450.0082.261-1.193-0.5844.660-1.537-3.7330.002
9A12SER00.0640.0402.867-1.0170.2470.457-0.593-1.1280.000
10A13LYS10.8670.9264.252-1.585-1.5710.001-0.012-0.0020.000
11A14VAL00.0260.0376.011-0.091-0.0910.0000.0000.0000.000
12A15ASN0-0.071-0.0665.848-0.787-0.7870.0000.0000.0000.000
13A16THR0-0.028-0.0148.1320.0130.0130.0000.0000.0000.000
14A17CYS0-0.022-0.0029.7760.0110.0110.0000.0000.0000.000
15A18TYR0-0.016-0.02211.6410.0300.0300.0000.0000.0000.000
16A19VAL00.013-0.00314.8670.0010.0010.0000.0000.0000.000
17A20LEU0-0.031-0.01716.8030.0160.0160.0000.0000.0000.000
18A21ALA00.0370.00620.0200.0020.0020.0000.0000.0000.000
19A22GLY0-0.041-0.00422.9970.0060.0060.0000.0000.0000.000
20A23GLY00.0550.01825.7380.0010.0010.0000.0000.0000.000
21A24LYS10.8640.92629.3700.0410.0410.0000.0000.0000.000
22A25SER0-0.025-0.03831.084-0.003-0.0030.0000.0000.0000.000
23A26LYS11.0051.00627.2220.0700.0700.0000.0000.0000.000
24A27ARG10.8710.96031.6520.0510.0510.0000.0000.0000.000
25A28PHE00.043-0.00133.6270.0010.0010.0000.0000.0000.000
26A29GLY00.0250.00437.330-0.001-0.0010.0000.0000.0000.000
27A30GLU-1-0.888-0.94339.539-0.031-0.0310.0000.0000.0000.000
28A31ASP-1-0.900-0.93936.481-0.038-0.0380.0000.0000.0000.000
29A32LYS10.7870.88035.1210.0380.0380.0000.0000.0000.000
30A33LEU00.0700.03234.146-0.002-0.0020.0000.0000.0000.000
31A34LEU00.0470.02233.682-0.002-0.0020.0000.0000.0000.000
32A35TYR0-0.023-0.02729.488-0.002-0.0020.0000.0000.0000.000
33A36GLU-1-0.805-0.87029.378-0.047-0.0470.0000.0000.0000.000
34A37ILE0-0.020-0.01329.664-0.002-0.0020.0000.0000.0000.000
35A38LYN00.0350.03724.924-0.001-0.0010.0000.0000.0000.000
36A39GLY00.0340.00125.680-0.003-0.0030.0000.0000.0000.000
37A40LYS10.9410.98024.6640.0410.0410.0000.0000.0000.000
38A41LYS10.8500.89724.1040.0400.0400.0000.0000.0000.000
39A42VAL0-0.062-0.01320.7160.0000.0000.0000.0000.0000.000
40A43ILE00.0340.02519.906-0.005-0.0050.0000.0000.0000.000
41A44GLU-1-0.812-0.88019.259-0.058-0.0580.0000.0000.0000.000
42A45ARG10.9180.94117.8350.0550.0550.0000.0000.0000.000
43A46VAL0-0.0400.00115.1270.0000.0000.0000.0000.0000.000
44A47TYR00.0170.00014.343-0.038-0.0380.0000.0000.0000.000
45A48GLU-1-0.910-0.95114.448-0.073-0.0730.0000.0000.0000.000
46A49THR0-0.049-0.03310.5700.0180.0180.0000.0000.0000.000
47A50ALA00.0480.03210.169-0.008-0.0080.0000.0000.0000.000
48A51LYS10.8690.9549.6290.1760.1760.0000.0000.0000.000
49A52SER0-0.038-0.0359.3670.0110.0110.0000.0000.0000.000
50A53VAL0-0.060-0.0284.2840.0560.210-0.001-0.027-0.1260.000
51A54PHE00.0220.0135.619-0.932-0.9320.0000.0000.0000.000
52A55LYS10.9120.9527.9040.6240.6240.0000.0000.0000.000
53A56GLU-1-0.894-0.91910.321-0.125-0.1250.0000.0000.0000.000
54A57VAL0-0.032-0.01911.603-0.058-0.0580.0000.0000.0000.000
55A58TYR0-0.040-0.03413.9440.0490.0490.0000.0000.0000.000
56A59ILE00.0210.02217.047-0.008-0.0080.0000.0000.0000.000
57A60VAL0-0.0020.00419.1750.0080.0080.0000.0000.0000.000
58A61ALA0-0.003-0.00921.6650.0020.0020.0000.0000.0000.000
59A62LYS10.7980.88125.2000.0580.0580.0000.0000.0000.000
60A63ASP-1-0.886-0.94028.455-0.046-0.0460.0000.0000.0000.000
61A64ARG10.9180.93825.7750.0640.0640.0000.0000.0000.000
62A65GLU-1-0.792-0.87828.139-0.051-0.0510.0000.0000.0000.000
63A66LYS10.8130.94528.2900.0610.0610.0000.0000.0000.000
64A67PHE0-0.021-0.04824.501-0.001-0.0010.0000.0000.0000.000
65A68SER00.0560.01225.305-0.007-0.0070.0000.0000.0000.000
66A69PHE0-0.068-0.03124.909-0.001-0.0010.0000.0000.0000.000
67A70LEU0-0.0180.00021.0530.0010.0010.0000.0000.0000.000
68A71ASN0-0.040-0.01221.847-0.004-0.0040.0000.0000.0000.000
69A72ALA0-0.0010.00619.410-0.008-0.0080.0000.0000.0000.000
70A73PRO00.0010.01318.7020.0110.0110.0000.0000.0000.000
71A74VAL00.0210.00120.475-0.010-0.0100.0000.0000.0000.000
72A75VAL0-0.047-0.02019.9510.0070.0070.0000.0000.0000.000
73A76LEU0-0.022-0.02622.894-0.001-0.0010.0000.0000.0000.000
74A77ASP-1-0.816-0.89725.490-0.063-0.0630.0000.0000.0000.000
75A78GLU-1-0.897-0.98027.067-0.049-0.0490.0000.0000.0000.000
76A79PHE0-0.0010.02528.3560.0040.0040.0000.0000.0000.000
77A80GLU-1-0.811-0.90331.834-0.042-0.0420.0000.0000.0000.000
78A81GLU-1-0.871-0.90632.918-0.040-0.0400.0000.0000.0000.000
79A82SER0-0.010-0.01929.448-0.004-0.0040.0000.0000.0000.000
80A83ALA00.0170.00928.5540.0010.0010.0000.0000.0000.000
81A84SER00.014-0.01023.3210.0000.0000.0000.0000.0000.000
82A85ILE00.0140.02223.488-0.006-0.0060.0000.0000.0000.000
83A86ILE00.0520.03624.709-0.001-0.0010.0000.0000.0000.000
84A87GLY00.0160.02623.025-0.001-0.0010.0000.0000.0000.000
85A88LEU0-0.017-0.01318.423-0.008-0.0080.0000.0000.0000.000
86A89TYR0-0.045-0.04520.743-0.006-0.0060.0000.0000.0000.000
87A90THR0-0.019-0.02222.8740.0010.0010.0000.0000.0000.000
88A91ALA0-0.024-0.00617.533-0.003-0.0030.0000.0000.0000.000
89A92LEU00.0170.00416.777-0.007-0.0070.0000.0000.0000.000
90A93LYS10.9450.99719.5170.0590.0590.0000.0000.0000.000
91A94HIS0-0.0160.00819.122-0.002-0.0020.0000.0000.0000.000
92A95ALA00.0300.03216.334-0.004-0.0040.0000.0000.0000.000
93A96LYS10.9090.95116.2590.1230.1230.0000.0000.0000.000
94A97GLU-1-0.787-0.87910.941-0.346-0.3460.0000.0000.0000.000
95A98GLU-1-0.794-0.88114.5920.0030.0030.0000.0000.0000.000
96A99ASN0-0.0010.00711.265-0.001-0.0010.0000.0000.0000.000
97A100VAL00.0140.01311.003-0.049-0.0490.0000.0000.0000.000
98A101PHE00.0320.0027.9320.0270.0270.0000.0000.0000.000
99A102VAL0-0.029-0.00910.7740.0120.0120.0000.0000.0000.000
100A103LEU00.023-0.00311.817-0.006-0.0060.0000.0000.0000.000
101A104SER0-0.012-0.03314.7160.0120.0120.0000.0000.0000.000
102A105GLY00.0220.00617.762-0.007-0.0070.0000.0000.0000.000
103A106ASP-1-0.903-0.93719.746-0.091-0.0910.0000.0000.0000.000
104A107LEU00.011-0.00116.4260.0030.0030.0000.0000.0000.000
105A108PRO0-0.024-0.01918.1010.0010.0010.0000.0000.0000.000
106A109LEU00.0230.00517.6970.0110.0110.0000.0000.0000.000
107A110MET0-0.0180.02812.453-0.016-0.0160.0000.0000.0000.000
108A111LYS10.9390.95710.5490.0990.0990.0000.0000.0000.000
109A112LYS10.9010.9466.629-1.223-1.2230.0000.0000.0000.000
110A113GLU-1-0.815-0.9085.5250.1790.1790.0000.0000.0000.000
111A114THR00.0280.0006.131-0.418-0.4180.0000.0000.0000.000
112A115VAL0-0.022-0.0086.437-0.064-0.0640.0000.0000.0000.000
113A116LEU0-0.061-0.0392.063-1.963-0.9527.317-2.566-5.7620.024
114A117TYR00.0490.0404.243-0.643-0.291-0.001-0.051-0.3010.000
115A118VAL00.003-0.0035.9100.2610.2610.0000.0000.0000.000
116A119LEU0-0.082-0.0442.941-0.587-0.0210.049-0.156-0.459-0.001
117A120GLU-1-1.000-0.9893.765-3.015-2.3470.004-0.188-0.484-0.001
118A121ASN0-0.058-0.0345.6670.1730.1730.0000.0000.0000.000
119A122PHE0-0.046-0.0188.597-0.080-0.0800.0000.0000.0000.000
120A123LYS10.9350.96610.265-0.056-0.0560.0000.0000.0000.000
121A124GLU-1-0.828-0.88613.6600.0430.0430.0000.0000.0000.000
122A125PRO00.0020.00215.881-0.003-0.0030.0000.0000.0000.000
123A126VAL00.045-0.00815.366-0.012-0.0120.0000.0000.0000.000
124A127SER0-0.0080.02412.1540.0230.0230.0000.0000.0000.000
125A128VAL0-0.040-0.01813.297-0.020-0.0200.0000.0000.0000.000
126A129ALA00.0450.02413.619-0.003-0.0030.0000.0000.0000.000
127A130LYS10.7960.89315.0740.1330.1330.0000.0000.0000.000
128A131THR00.0530.03516.415-0.017-0.0170.0000.0000.0000.000
129A132GLU-1-0.795-0.87118.631-0.115-0.1150.0000.0000.0000.000
130A133LYS10.8910.95621.4340.1220.1220.0000.0000.0000.000
131A134LEU0-0.0040.00819.579-0.012-0.0120.0000.0000.0000.000
132A135HIS0-0.030-0.04817.2930.0160.0160.0000.0000.0000.000
133A136THR00.0130.00317.531-0.009-0.0090.0000.0000.0000.000
134A137LEU0-0.0280.00017.7190.0040.0040.0000.0000.0000.000
135A138VAL00.0360.01312.836-0.010-0.0100.0000.0000.0000.000
136A139GLY00.0430.01711.8480.0020.0020.0000.0000.0000.000
137A140VAL0-0.0610.0048.537-0.037-0.0370.0000.0000.0000.000
138A141TYR0-0.001-0.03411.6860.0380.0380.0000.0000.0000.000
139A142SER00.0630.02214.343-0.014-0.0140.0000.0000.0000.000
140A143LYS10.8240.88416.2830.0640.0640.0000.0000.0000.000
141A144LYS10.8010.88717.569-0.043-0.0430.0000.0000.0000.000
142A145LEU0-0.029-0.00818.6620.0010.0010.0000.0000.0000.000
143A146LEU0-0.030-0.01521.936-0.003-0.0030.0000.0000.0000.000
144A147GLU-1-0.895-0.94123.581-0.014-0.0140.0000.0000.0000.000
145A148LYS10.8640.91725.2850.0200.0200.0000.0000.0000.000
146A149ILE0-0.024-0.02421.458-0.002-0.0020.0000.0000.0000.000
147A150GLU-1-0.854-0.90926.056-0.036-0.0360.0000.0000.0000.000
148A151GLU-1-0.852-0.90428.616-0.019-0.0190.0000.0000.0000.000
149A152ARG10.8170.86828.1940.0330.0330.0000.0000.0000.000
150A153ILE00.0050.00626.7220.0000.0000.0000.0000.0000.000
151A154LYS10.9530.99031.0300.0250.0250.0000.0000.0000.000
152A155LYS10.7880.87233.7390.0230.0230.0000.0000.0000.000
153A156GLY00.0390.03434.3650.0010.0010.0000.0000.0000.000
154A157ASP-1-0.805-0.84731.945-0.039-0.0390.0000.0000.0000.000
155A158TYR0-0.047-0.06929.689-0.002-0.0020.0000.0000.0000.000
156A159ARG10.8180.87628.3720.0330.0330.0000.0000.0000.000
157A160ILE00.0650.01721.9160.0020.0020.0000.0000.0000.000
158A161TRP0-0.001-0.00124.6110.0040.0040.0000.0000.0000.000
159A162ALA0-0.009-0.00326.2630.0020.0020.0000.0000.0000.000
160A163LEU00.0170.01322.7070.0030.0030.0000.0000.0000.000
161A164LEU00.0160.00019.9550.0040.0040.0000.0000.0000.000
162A165LYS10.9270.96823.6170.0480.0480.0000.0000.0000.000
163A166ASP-1-0.873-0.89526.507-0.019-0.0190.0000.0000.0000.000
164A167VAL0-0.005-0.01021.7780.0030.0030.0000.0000.0000.000
165A168GLY00.0250.03623.0440.0070.0070.0000.0000.0000.000
166A169TYR0-0.103-0.07319.0160.0010.0010.0000.0000.0000.000
167A170ASN0-0.028-0.01215.8760.0030.0030.0000.0000.0000.000
168A171GLU-1-0.777-0.88916.609-0.106-0.1060.0000.0000.0000.000
169A172VAL00.0030.00210.6580.0010.0010.0000.0000.0000.000
170A173GLU-1-0.933-0.96914.005-0.210-0.2100.0000.0000.0000.000
171A174ILE0-0.065-0.04311.477-0.062-0.0620.0000.0000.0000.000
172A175PRO00.0600.0329.2490.0480.0480.0000.0000.0000.000
173A176GLU-1-0.796-0.92412.590-0.174-0.1740.0000.0000.0000.000
174A177GLU-1-0.926-0.96512.861-0.281-0.2810.0000.0000.0000.000
175A178LEU0-0.032-0.0278.1140.0110.0110.0000.0000.0000.000
176A179ARG10.8030.92412.7870.2050.2050.0000.0000.0000.000
177A180TYR00.0230.00514.2180.0350.0350.0000.0000.0000.000
178A181THR0-0.048-0.02612.4990.0160.0160.0000.0000.0000.000
179A182LEU0-0.019-0.01514.1750.0100.0100.0000.0000.0000.000
180A183LEU0-0.0340.00917.4050.0120.0120.0000.0000.0000.000
181A184ASN00.000-0.00920.821-0.001-0.0010.0000.0000.0000.000
182A185MET00.0220.00823.4900.0030.0030.0000.0000.0000.000
183A186ASN0-0.069-0.08626.1190.0050.0050.0000.0000.0000.000
184A187THR0-0.049-0.04828.9360.0040.0040.0000.0000.0000.000
185A188LYS11.0831.12231.8690.0480.0480.0000.0000.0000.000