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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: JLK19

Calculation Name: 3R0E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R0E

Chain ID: A

ChEMBL ID:

UniProt ID: B5LYJ9

Base Structure: X-ray

Registration Date: 2023-06-26

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 108
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -781662.29167
FMO2-HF: Nuclear repulsion 739948.069903
FMO2-HF: Total energy -41714.221768
FMO2-MP2: Total energy -41835.940606


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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-6.856-3.04810.071-4.506-9.376-0.02
Interaction energy analysis for fragmet #1(A:1:LEU)
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 : 0.011
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].
3A3THR0-0.019-0.0033.802-1.8491.566-0.030-1.895-1.4910.003
4A4ASN00.0460.0386.529-0.043-0.0430.0000.0000.0000.000
5A5TYR0-0.041-0.0328.6700.1930.1930.0000.0000.0000.000
6A6LEU00.0170.0266.524-0.361-0.3610.0000.0000.0000.000
7A7LEU0-0.003-0.0109.2740.2660.2660.0000.0000.0000.000
8A8SER00.0170.01011.709-0.044-0.0440.0000.0000.0000.000
9A9GLY0-0.014-0.00613.7180.0200.0200.0000.0000.0000.000
10A10GLN0-0.0190.0018.446-0.124-0.1240.0000.0000.0000.000
11A11THR0-0.018-0.0247.6570.2300.2300.0000.0000.0000.000
12A12LEU0-0.037-0.0032.447-1.595-1.0860.506-0.315-0.700-0.002
13A13ASP-1-0.817-0.9074.4670.7400.851-0.001-0.006-0.1040.000
14A14THR0-0.008-0.0415.2120.8900.8900.0000.0000.0000.000
15A15GLU-1-0.845-0.9215.6581.7571.7570.0000.0000.0000.000
16A16GLY0-0.0230.0112.5052.4402.3823.940-2.158-1.7250.001
17A17HIS0-0.088-0.0752.155-5.933-7.6975.2621.025-4.523-0.011
18A18LEU0-0.031-0.0082.956-4.525-2.9300.394-1.157-0.833-0.011
19A19LYS10.8320.9085.6980.3210.3210.0000.0000.0000.000
20A20ASN0-0.067-0.0627.980-0.120-0.1200.0000.0000.0000.000
21A21GLY00.0220.02011.5910.0480.0480.0000.0000.0000.000
22A22ASP-1-0.890-0.95312.4500.0940.0940.0000.0000.0000.000
23A23PHE0-0.0520.00712.7700.0520.0520.0000.0000.0000.000
24A24ASP-1-0.740-0.8647.3810.3450.3450.0000.0000.0000.000
25A25LEU0-0.068-0.0368.0440.0540.0540.0000.0000.0000.000
26A26VAL00.0620.0226.2230.0220.0220.0000.0000.0000.000
27A27MET0-0.055-0.0046.495-0.501-0.5010.0000.0000.0000.000
28A28GLN00.0220.0168.0900.3580.3580.0000.0000.0000.000
29A29ASP-1-0.850-0.94310.1900.6100.6100.0000.0000.0000.000
30A30ASP-1-0.952-0.96911.7670.2860.2860.0000.0000.0000.000
31A31CYS0-0.120-0.03312.343-0.170-0.1700.0000.0000.0000.000
32A32ASN00.0240.02214.242-0.108-0.1080.0000.0000.0000.000
33A33LEU00.0260.0179.1730.0870.0870.0000.0000.0000.000
34A34VAL0-0.008-0.00911.246-0.099-0.0990.0000.0000.0000.000
35A35LEU0-0.0030.01011.2550.0460.0460.0000.0000.0000.000
36A36TYR00.000-0.0199.589-0.012-0.0120.0000.0000.0000.000
37A37ASN0-0.037-0.04913.680-0.040-0.0400.0000.0000.0000.000
38A38GLY00.0470.01816.005-0.028-0.0280.0000.0000.0000.000
39A39ASN0-0.113-0.04617.269-0.006-0.0060.0000.0000.0000.000
40A40TRP00.0110.00813.549-0.024-0.0240.0000.0000.0000.000
41A41GLN00.0310.01815.5330.0520.0520.0000.0000.0000.000
42A42SER00.0070.00015.233-0.015-0.0150.0000.0000.0000.000
43A43ASN0-0.068-0.02616.902-0.011-0.0110.0000.0000.0000.000
44A44THR0-0.009-0.01915.770-0.027-0.0270.0000.0000.0000.000
45A45ALA00.0390.02817.4290.0190.0190.0000.0000.0000.000
46A46ASN0-0.080-0.04218.082-0.009-0.0090.0000.0000.0000.000
47A47ASN0-0.038-0.01218.675-0.038-0.0380.0000.0000.0000.000
48A48GLY00.0300.00517.821-0.028-0.0280.0000.0000.0000.000
49A49ARG10.8690.93515.835-0.264-0.2640.0000.0000.0000.000
50A50ASP-1-0.813-0.91912.5300.2730.2730.0000.0000.0000.000
51A52LYS10.8700.9419.024-0.147-0.1470.0000.0000.0000.000
52A53LEU00.0250.0078.077-0.024-0.0240.0000.0000.0000.000
53A54THR0-0.061-0.0208.949-0.188-0.1880.0000.0000.0000.000
54A55LEU00.0280.01011.5520.0600.0600.0000.0000.0000.000
55A56THR00.003-0.00513.834-0.021-0.0210.0000.0000.0000.000
56A57ASP-1-0.838-0.91517.365-0.270-0.2700.0000.0000.0000.000
57A58TYR0-0.015-0.02119.9260.0140.0140.0000.0000.0000.000
58A59GLY00.0440.02017.9410.0180.0180.0000.0000.0000.000
59A60GLU-1-0.850-0.91418.279-0.116-0.1160.0000.0000.0000.000
60A61LEU00.0200.00611.906-0.037-0.0370.0000.0000.0000.000
61A62VAL0-0.044-0.03413.9850.0560.0560.0000.0000.0000.000
62A63ILE00.0540.02912.351-0.051-0.0510.0000.0000.0000.000
63A64LYS10.9100.96013.4140.1410.1410.0000.0000.0000.000
64A65ASN00.0550.01013.8290.0170.0170.0000.0000.0000.000
65A66GLY00.0250.02315.100-0.030-0.0300.0000.0000.0000.000
66A67ASP-1-0.887-0.92316.1070.0520.0520.0000.0000.0000.000
67A68GLY0-0.0200.00217.117-0.025-0.0250.0000.0000.0000.000
68A69SER0-0.088-0.05618.157-0.022-0.0220.0000.0000.0000.000
69A70THR0-0.066-0.05918.2410.0020.0020.0000.0000.0000.000
70A71VAL00.0290.01516.7360.0040.0040.0000.0000.0000.000
71A72TRP00.0240.00415.373-0.002-0.0020.0000.0000.0000.000
72A73LYS10.9030.96317.2580.0500.0500.0000.0000.0000.000
73A74SER00.0410.02217.2750.0040.0040.0000.0000.0000.000
74A75GLY0-0.0190.00419.1370.0080.0080.0000.0000.0000.000
75A76ALA0-0.035-0.01421.5260.0080.0080.0000.0000.0000.000
76A77GLN0-0.080-0.04921.447-0.012-0.0120.0000.0000.0000.000
77A78SER00.0010.00523.3500.0170.0170.0000.0000.0000.000
78A79VAL00.0210.00224.987-0.001-0.0010.0000.0000.0000.000
79A80LYS10.9000.95822.7690.1870.1870.0000.0000.0000.000
80A81GLY0-0.031-0.01522.5460.0110.0110.0000.0000.0000.000
81A82ASN0-0.054-0.01918.533-0.022-0.0220.0000.0000.0000.000
82A83TYR00.011-0.01017.1270.0270.0270.0000.0000.0000.000
83A84ALA0-0.010-0.00713.997-0.067-0.0670.0000.0000.0000.000
84A85ALA0-0.0160.00611.4400.0920.0920.0000.0000.0000.000
85A86VAL00.003-0.00611.539-0.147-0.1470.0000.0000.0000.000
86A87VAL00.0450.0339.6760.0860.0860.0000.0000.0000.000
87A88HIS0-0.006-0.00212.763-0.012-0.0120.0000.0000.0000.000
88A89PRO00.0170.00015.9860.0210.0210.0000.0000.0000.000
89A90ASP-1-0.852-0.91117.003-0.082-0.0820.0000.0000.0000.000
90A91GLY0-0.001-0.00616.1410.0200.0200.0000.0000.0000.000
91A92ARG10.8190.90517.1910.1410.1410.0000.0000.0000.000
92A93LEU00.0230.01411.682-0.039-0.0390.0000.0000.0000.000
93A94VAL0-0.042-0.02514.9710.0370.0370.0000.0000.0000.000
94A95VAL00.0150.01015.164-0.064-0.0640.0000.0000.0000.000
95A96PHE0-0.026-0.01317.0970.0490.0490.0000.0000.0000.000
96A97GLY00.0060.00318.643-0.039-0.0390.0000.0000.0000.000
97A98PRO00.0040.00721.3060.0190.0190.0000.0000.0000.000
98A99SER0-0.025-0.02620.9300.0010.0010.0000.0000.0000.000
99A100VAL00.0100.00422.5780.0160.0160.0000.0000.0000.000
100A101PHE0-0.010-0.01724.5990.0150.0150.0000.0000.0000.000
101A102LYS10.8800.93621.3310.2450.2450.0000.0000.0000.000
102A103ILE00.0130.01823.6070.0200.0200.0000.0000.0000.000
103A104ASP-1-0.814-0.92523.035-0.268-0.2680.0000.0000.0000.000
104A105PRO0-0.032-0.00421.4650.0200.0200.0000.0000.0000.000
105A106TRP0-0.0080.00018.0250.0180.0180.0000.0000.0000.000
106A107VAL0-0.0080.00624.3340.0110.0110.0000.0000.0000.000
107A108ARG10.9300.96827.8290.1130.1130.0000.0000.0000.000
108A109GLY00.0290.01731.3220.0010.0010.0000.0000.0000.000