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

tag_button

FMODB ID: N964Q

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 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 108
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -781093.0105
FMO2-HF: Nuclear repulsion 739379.384424
FMO2-HF: Total energy -41713.626075
FMO2-MP2: Total energy -41835.378926


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.
-6.652-2.9279.059-3.9-8.886-0.02
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 : 0.026 / q_NPA : 0.015
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].
3A3THR0-0.033-0.0033.802-1.6231.551-0.028-1.791-1.3560.002
4A4ASN00.0330.0276.5400.0050.0050.0000.0000.0000.000
5A5TYR0-0.020-0.0288.6470.1840.1840.0000.0000.0000.000
6A6LEU00.0160.0236.410-0.358-0.3580.0000.0000.0000.000
7A7LEU0-0.009-0.0159.2080.2600.2600.0000.0000.0000.000
8A8SER00.0350.02111.592-0.043-0.0430.0000.0000.0000.000
9A9GLY0-0.020-0.00713.6040.0100.0100.0000.0000.0000.000
10A10GLN0-0.0130.0038.257-0.095-0.0950.0000.0000.0000.000
11A11THR0-0.023-0.0237.4160.2410.2410.0000.0000.0000.000
12A12LEU0-0.039-0.0072.564-1.613-1.1140.279-0.228-0.550-0.001
13A13ASP-1-0.846-0.9354.4040.7090.822-0.001-0.006-0.1070.000
14A14THR0-0.005-0.0345.2941.0841.0840.0000.0000.0000.000
15A15GLU-1-0.858-0.9255.6851.7941.7940.0000.0000.0000.000
16A16GLY0-0.0230.0092.5222.5162.3893.930-2.134-1.6690.002
17A17HIS0-0.046-0.0432.184-6.939-8.2694.5241.239-4.433-0.014
18A18LEU0-0.047-0.0172.988-4.286-2.8900.355-0.980-0.771-0.009
19A19LYS10.8880.9385.7230.2460.2460.0000.0000.0000.000
20A20ASN0-0.067-0.0537.988-0.151-0.1510.0000.0000.0000.000
21A21GLY00.0350.02811.5960.0520.0520.0000.0000.0000.000
22A22ASP-1-0.880-0.93712.4460.1280.1280.0000.0000.0000.000
23A23PHE0-0.064-0.00712.7830.0590.0590.0000.0000.0000.000
24A24ASP-1-0.831-0.9377.2530.7150.7150.0000.0000.0000.000
25A25LEU0-0.055-0.0338.2160.0160.0160.0000.0000.0000.000
26A26VAL00.0780.0346.4490.1980.1980.0000.0000.0000.000
27A27MET0-0.053-0.0106.664-0.655-0.6550.0000.0000.0000.000
28A28GLN00.0240.0208.1870.3720.3720.0000.0000.0000.000
29A29ASP-1-0.831-0.92810.2700.7220.7220.0000.0000.0000.000
30A30ASP-1-0.970-0.98411.7910.3660.3660.0000.0000.0000.000
31A31CYS0-0.131-0.05912.341-0.212-0.2120.0000.0000.0000.000
32A32ASN00.0230.04514.389-0.104-0.1040.0000.0000.0000.000
33A33LEU00.0090.0139.3350.1090.1090.0000.0000.0000.000
34A34VAL00.010-0.00511.455-0.131-0.1310.0000.0000.0000.000
35A35LEU0-0.0110.00511.4670.0820.0820.0000.0000.0000.000
36A36TYR0-0.004-0.01310.058-0.042-0.0420.0000.0000.0000.000
37A37ASN0-0.030-0.04013.700-0.053-0.0530.0000.0000.0000.000
38A38GLY00.0480.02416.015-0.035-0.0350.0000.0000.0000.000
39A39ASN0-0.111-0.04617.292-0.011-0.0110.0000.0000.0000.000
40A40TRP00.0110.00613.595-0.026-0.0260.0000.0000.0000.000
41A41GLN00.0220.00215.7200.0560.0560.0000.0000.0000.000
42A42SER00.0070.00615.400-0.020-0.0200.0000.0000.0000.000
43A43ASN0-0.055-0.01517.057-0.015-0.0150.0000.0000.0000.000
44A44THR0-0.027-0.04515.884-0.030-0.0300.0000.0000.0000.000
45A45ALA00.0480.02517.5680.0210.0210.0000.0000.0000.000
46A46ASN0-0.088-0.05318.141-0.015-0.0150.0000.0000.0000.000
47A47ASN0-0.045-0.01718.886-0.046-0.0460.0000.0000.0000.000
48A48GLY00.0160.00017.911-0.031-0.0310.0000.0000.0000.000
49A49ARG10.8840.95115.904-0.294-0.2940.0000.0000.0000.000
50A50ASP-1-0.824-0.92312.4420.2820.2820.0000.0000.0000.000
51A52LYS10.9360.9939.068-0.061-0.0610.0000.0000.0000.000
52A53LEU00.0310.0138.156-0.046-0.0460.0000.0000.0000.000
53A54THR0-0.057-0.0178.918-0.190-0.1900.0000.0000.0000.000
54A55LEU00.0230.00511.5100.0630.0630.0000.0000.0000.000
55A56THR0-0.003-0.00913.786-0.030-0.0300.0000.0000.0000.000
56A57ASP-1-0.880-0.94717.298-0.258-0.2580.0000.0000.0000.000
57A58TYR0-0.043-0.03119.8340.0110.0110.0000.0000.0000.000
58A59GLY00.0410.01817.8960.0170.0170.0000.0000.0000.000
59A60GLU-1-0.834-0.89518.277-0.062-0.0620.0000.0000.0000.000
60A61LEU00.0220.00411.986-0.034-0.0340.0000.0000.0000.000
61A62VAL0-0.033-0.02614.0030.0460.0460.0000.0000.0000.000
62A63ILE00.0590.03012.468-0.039-0.0390.0000.0000.0000.000
63A64LYS10.9020.95413.4470.0660.0660.0000.0000.0000.000
64A65ASN00.0940.05713.8640.0280.0280.0000.0000.0000.000
65A66GLY00.0230.01815.074-0.031-0.0310.0000.0000.0000.000
66A67ASP-1-0.920-0.94816.0810.0620.0620.0000.0000.0000.000
67A68GLY0-0.030-0.00417.089-0.028-0.0280.0000.0000.0000.000
68A69SER0-0.085-0.06118.131-0.020-0.0200.0000.0000.0000.000
69A70THR0-0.081-0.06618.2720.0060.0060.0000.0000.0000.000
70A71VAL00.0330.01616.808-0.002-0.0020.0000.0000.0000.000
71A72TRP00.0280.00515.0320.0020.0020.0000.0000.0000.000
72A73LYS10.9010.96117.3140.0110.0110.0000.0000.0000.000
73A74SER00.0360.01717.3180.0040.0040.0000.0000.0000.000
74A75GLY0-0.0200.00019.2040.0040.0040.0000.0000.0000.000
75A76ALA0-0.035-0.01521.5730.0040.0040.0000.0000.0000.000
76A77GLN0-0.084-0.05521.462-0.010-0.0100.0000.0000.0000.000
77A78SER00.0040.01423.3250.0140.0140.0000.0000.0000.000
78A79VAL00.0270.00424.940-0.001-0.0010.0000.0000.0000.000
79A80LYS10.9641.00123.7220.1580.1580.0000.0000.0000.000
80A81GLY0-0.044-0.02222.4460.0090.0090.0000.0000.0000.000
81A82ASN0-0.035-0.00618.377-0.017-0.0170.0000.0000.0000.000
82A83TYR00.008-0.01817.0820.0280.0280.0000.0000.0000.000
83A84ALA0-0.009-0.00513.932-0.065-0.0650.0000.0000.0000.000
84A85ALA0-0.0140.00711.4050.0880.0880.0000.0000.0000.000
85A86VAL00.009-0.00111.534-0.137-0.1370.0000.0000.0000.000
86A87VAL00.0370.0269.7050.0820.0820.0000.0000.0000.000
87A88HIS0-0.012-0.01212.788-0.024-0.0240.0000.0000.0000.000
88A89PRO00.003-0.00416.0040.0240.0240.0000.0000.0000.000
89A90ASP-1-0.911-0.95717.014-0.036-0.0360.0000.0000.0000.000
90A91GLY0-0.020-0.01116.1600.0180.0180.0000.0000.0000.000
91A92ARG10.9230.96617.2110.1050.1050.0000.0000.0000.000
92A93LEU00.0200.01211.604-0.034-0.0340.0000.0000.0000.000
93A94VAL0-0.055-0.02915.0770.0290.0290.0000.0000.0000.000
94A95VAL00.0140.00915.142-0.057-0.0570.0000.0000.0000.000
95A96PHE0-0.026-0.01317.0680.0420.0420.0000.0000.0000.000
96A97GLY0-0.002-0.00218.600-0.037-0.0370.0000.0000.0000.000
97A98PRO00.0160.01421.2560.0190.0190.0000.0000.0000.000
98A99SER0-0.045-0.04420.7720.0000.0000.0000.0000.0000.000
99A100VAL00.0120.00722.4800.0140.0140.0000.0000.0000.000
100A101PHE0-0.003-0.01324.4960.0130.0130.0000.0000.0000.000
101A102LYS10.9600.98020.4790.2690.2690.0000.0000.0000.000
102A103ILE00.0110.01523.4530.0190.0190.0000.0000.0000.000
103A104ASP-1-0.872-0.94822.901-0.254-0.2540.0000.0000.0000.000
104A105PRO0-0.041-0.01621.3710.0190.0190.0000.0000.0000.000
105A106TRP0-0.019-0.01118.0990.0150.0150.0000.0000.0000.000
106A107VAL00.0000.01624.2040.0120.0120.0000.0000.0000.000
107A108ARG10.9210.96227.6990.1180.1180.0000.0000.0000.000
108A109GLY00.0240.01431.1910.0030.0030.0000.0000.0000.000