Manual

About

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: 3JLGL

Calculation Name: 1BGF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BGF

Chain ID: A

ChEMBL ID:

UniProt ID: P42228

Base Structure: X-ray

Registration Date: 2023-09-23

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 124
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1101123.457814
FMO2-HF: Nuclear repulsion 1050239.048268
FMO2-HF: Total energy -50884.409546
FMO2-MP2: Total energy -51032.438754


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
0.7582.09-0.028-0.653-0.6520
Interaction energy analysis for fragmet #1(A:0:GLY)
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 : -0.019
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].
3A2SER00.0030.0033.773-0.0861.246-0.028-0.653-0.6520.000
4A3GLN0-0.025-0.0406.9390.3950.3950.0000.0000.0000.000
5A4TRP0-0.013-0.0269.6390.1090.1090.0000.0000.0000.000
6A5ASN0-0.042-0.0206.1250.3540.3540.0000.0000.0000.000
7A6GLN00.0210.0076.3850.2220.2220.0000.0000.0000.000
8A7VAL00.0250.0089.7810.0030.0030.0000.0000.0000.000
9A8GLN0-0.055-0.03111.062-0.049-0.0490.0000.0000.0000.000
10A9GLN0-0.077-0.0309.352-0.020-0.0200.0000.0000.0000.000
11A10LEU0-0.0370.00612.5080.0080.0080.0000.0000.0000.000
12A11GLU-1-0.830-0.90515.7580.1290.1290.0000.0000.0000.000
13A12ILE00.0540.01119.101-0.005-0.0050.0000.0000.0000.000
14A13LYS10.8130.87820.649-0.161-0.1610.0000.0000.0000.000
15A14PHE00.0280.02417.683-0.006-0.0060.0000.0000.0000.000
16A15LEU0-0.0070.00020.128-0.010-0.0100.0000.0000.0000.000
17A16GLU-1-0.959-0.98022.1010.0500.0500.0000.0000.0000.000
18A17GLN0-0.004-0.00523.344-0.002-0.0020.0000.0000.0000.000
19A18VAL00.004-0.00219.967-0.001-0.0010.0000.0000.0000.000
20A19ASP-1-0.938-0.95223.402-0.009-0.0090.0000.0000.0000.000
21A20GLN0-0.005-0.01326.215-0.010-0.0100.0000.0000.0000.000
22A21PHE0-0.084-0.04323.359-0.001-0.0010.0000.0000.0000.000
23A22TYR0-0.040-0.01918.978-0.012-0.0120.0000.0000.0000.000
24A23ASP-1-0.702-0.84425.606-0.022-0.0220.0000.0000.0000.000
25A24ASP-1-0.933-0.96527.942-0.043-0.0430.0000.0000.0000.000
26A25ASN0-0.163-0.10628.197-0.010-0.0100.0000.0000.0000.000
27A26PHE00.011-0.02118.875-0.012-0.0120.0000.0000.0000.000
28A27PRO00.0740.05924.4550.0060.0060.0000.0000.0000.000
29A28MET00.0720.02019.946-0.016-0.0160.0000.0000.0000.000
30A29GLU-1-0.862-0.93619.925-0.107-0.1070.0000.0000.0000.000
31A30ILE0-0.024-0.01319.954-0.028-0.0280.0000.0000.0000.000
32A31ARG10.7180.83612.6830.0970.0970.0000.0000.0000.000
33A32HIS00.0160.00514.895-0.032-0.0320.0000.0000.0000.000
34A33LEU0-0.053-0.03314.934-0.058-0.0580.0000.0000.0000.000
35A34LEU0-0.038-0.01015.780-0.046-0.0460.0000.0000.0000.000
36A35ALA00.0110.02811.9610.0060.0060.0000.0000.0000.000
37A36GLN00.013-0.0117.671-0.244-0.2440.0000.0000.0000.000
38A37TRP00.0460.04111.5730.0550.0550.0000.0000.0000.000
39A38ILE00.0300.00515.0770.0430.0430.0000.0000.0000.000
40A39GLU-1-0.723-0.8489.860-0.293-0.2930.0000.0000.0000.000
41A40THR0-0.063-0.03012.8300.0090.0090.0000.0000.0000.000
42A41GLN0-0.066-0.03414.3280.0450.0450.0000.0000.0000.000
43A42ASP-1-0.866-0.92517.760-0.013-0.0130.0000.0000.0000.000
44A43TRP0-0.014-0.04117.8340.0080.0080.0000.0000.0000.000
45A44GLU-1-0.761-0.88219.2390.0090.0090.0000.0000.0000.000
46A45VAL0-0.0040.01222.9680.0040.0040.0000.0000.0000.000
47A46ALA0-0.044-0.02224.2430.0000.0000.0000.0000.0000.000
48A47SER0-0.074-0.04625.7440.0020.0020.0000.0000.0000.000
49A48ASN0-0.064-0.03227.5830.0050.0050.0000.0000.0000.000
50A49ASN00.0330.01228.845-0.002-0.0020.0000.0000.0000.000
51A50GLU-1-0.835-0.92129.934-0.032-0.0320.0000.0000.0000.000
52A51THR00.0040.01131.328-0.004-0.0040.0000.0000.0000.000
53A52MET0-0.021-0.01424.670-0.004-0.0040.0000.0000.0000.000
54A53ALA00.0190.02026.852-0.009-0.0090.0000.0000.0000.000
55A54THR0-0.048-0.03327.770-0.006-0.0060.0000.0000.0000.000
56A55ILE00.0030.00225.671-0.007-0.0070.0000.0000.0000.000
57A56LEU00.0070.00721.780-0.011-0.0110.0000.0000.0000.000
58A57LEU00.0110.01724.195-0.013-0.0130.0000.0000.0000.000
59A58GLN0-0.001-0.01326.601-0.001-0.0010.0000.0000.0000.000
60A59ASN00.001-0.00822.778-0.004-0.0040.0000.0000.0000.000
61A60LEU00.0180.02721.274-0.016-0.0160.0000.0000.0000.000
62A61LEU0-0.049-0.03923.367-0.010-0.0100.0000.0000.0000.000
63A62ILE0-0.0090.01023.992-0.002-0.0020.0000.0000.0000.000
64A63GLN0-0.009-0.01418.164-0.035-0.0350.0000.0000.0000.000
65A64LEU0-0.0020.00221.950-0.012-0.0120.0000.0000.0000.000
66A65ASP-1-0.818-0.90423.811-0.114-0.1140.0000.0000.0000.000
67A66GLU-1-0.886-0.93420.723-0.225-0.2250.0000.0000.0000.000
68A67GLN0-0.017-0.01017.969-0.014-0.0140.0000.0000.0000.000
69A68LEU0-0.028-0.01622.1190.0060.0060.0000.0000.0000.000
70A69GLY00.0110.02525.4990.0080.0080.0000.0000.0000.000
71A70ARG10.8670.92116.1550.3360.3360.0000.0000.0000.000
72A71VAL00.0370.01022.5230.0060.0060.0000.0000.0000.000
73A72SER0-0.060-0.05024.5650.0180.0180.0000.0000.0000.000
74A73LYS10.9100.96424.8860.1670.1670.0000.0000.0000.000
75A74GLU-1-0.872-0.92820.424-0.239-0.2390.0000.0000.0000.000
76A75LYS10.9030.95825.4110.1060.1060.0000.0000.0000.000
77A76ASN00.0560.03722.8950.0210.0210.0000.0000.0000.000
78A77LEU00.016-0.01526.6120.0010.0010.0000.0000.0000.000
79A78LEU00.0420.03026.1920.0020.0020.0000.0000.0000.000
80A79LEU00.0620.02721.5860.0030.0030.0000.0000.0000.000
81A80ILE0-0.0040.00926.0430.0020.0020.0000.0000.0000.000
82A81HIS0-0.029-0.01028.5450.0090.0090.0000.0000.0000.000
83A82ASN0-0.021-0.02727.2780.0080.0080.0000.0000.0000.000
84A83LEU00.0620.02723.1520.0040.0040.0000.0000.0000.000
85A84LYS10.9190.96927.3490.0950.0950.0000.0000.0000.000
86A85ARG10.8490.92430.7830.0590.0590.0000.0000.0000.000
87A86ILE00.0700.04225.5210.0040.0040.0000.0000.0000.000
88A87ARG10.8540.91229.0420.1000.1000.0000.0000.0000.000
89A88LYS10.9260.96529.8780.0600.0600.0000.0000.0000.000
90A89VAL00.0190.01331.0130.0030.0030.0000.0000.0000.000
91A90LEU00.0500.01425.8190.0030.0030.0000.0000.0000.000
92A91GLN0-0.017-0.01030.3030.0010.0010.0000.0000.0000.000
93A92GLY00.0180.02233.0150.0030.0030.0000.0000.0000.000
94A93LYS10.8470.92730.3040.0420.0420.0000.0000.0000.000
95A94PHE0-0.051-0.03231.3440.0020.0020.0000.0000.0000.000
96A95HIS0-0.069-0.03932.7710.0020.0020.0000.0000.0000.000
97A96GLY0-0.0030.01335.3480.0030.0030.0000.0000.0000.000
98A97ASN00.003-0.00633.4200.0010.0010.0000.0000.0000.000
99A98PRO00.0600.02229.8970.0000.0000.0000.0000.0000.000
100A99MET00.0300.01328.855-0.003-0.0030.0000.0000.0000.000
101A100HIS0-0.0160.00128.8110.0030.0030.0000.0000.0000.000
102A101VAL00.0040.00125.3900.0020.0020.0000.0000.0000.000
103A102ALA0-0.0040.01524.441-0.002-0.0020.0000.0000.0000.000
104A103VAL00.0310.02924.2290.0040.0040.0000.0000.0000.000
105A104VAL0-0.033-0.01124.7970.0070.0070.0000.0000.0000.000
106A105ILE0-0.0090.00019.7260.0050.0050.0000.0000.0000.000
107A106SER00.010-0.00820.4320.0060.0060.0000.0000.0000.000
108A107ASN0-0.081-0.05220.8860.0200.0200.0000.0000.0000.000
109A108CYS0-0.0100.02220.1190.0110.0110.0000.0000.0000.000
110A109LEU00.0440.01714.8630.0150.0150.0000.0000.0000.000
111A110ARG10.9470.96616.919-0.043-0.0430.0000.0000.0000.000
112A111GLU-1-0.751-0.84019.2430.1130.1130.0000.0000.0000.000
113A112GLU-1-0.759-0.83814.9420.0170.0170.0000.0000.0000.000
114A113ARG10.8400.92714.300-0.033-0.0330.0000.0000.0000.000
115A114ARG10.7610.85116.153-0.076-0.0760.0000.0000.0000.000
116A115ILE0-0.012-0.01417.9220.0180.0180.0000.0000.0000.000
117A116LEU0-0.038-0.02911.8940.0190.0190.0000.0000.0000.000
118A117ALA0-0.045-0.01015.5940.0400.0400.0000.0000.0000.000
119A118ALA0-0.050-0.02617.334-0.002-0.0020.0000.0000.0000.000
120A119ALA0-0.0160.01016.813-0.017-0.0170.0000.0000.0000.000
121A120ASN0-0.019-0.01218.5770.0240.0240.0000.0000.0000.000
122A121MET00.005-0.00412.0130.0210.0210.0000.0000.0000.000
123A122PRO0-0.0310.00116.940-0.023-0.0230.0000.0000.0000.000
124A123ILE00.0070.00317.0480.0540.0540.0000.0000.0000.000