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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: 39G6L

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 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 108
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -781753.28933
FMO2-HF: Nuclear repulsion 740038.921458
FMO2-HF: Total energy -41714.367872
FMO2-MP2: Total energy -41836.083958


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.
-13.494-12.10620.355-8.805-12.936-0.042
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 : 0.025 / q_NPA : 0.018
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].
3A3THR0-0.021-0.0013.847-1.4801.735-0.023-1.825-1.3670.003
4A4ASN00.0350.0266.171-0.164-0.1640.0000.0000.0000.000
5A5TYR0-0.045-0.0337.8750.2370.2370.0000.0000.0000.000
6A6LEU00.0350.0276.388-0.494-0.4940.0000.0000.0000.000
7A7LEU0-0.008-0.0158.8800.2870.2870.0000.0000.0000.000
8A8SER0-0.007-0.00411.959-0.010-0.0100.0000.0000.0000.000
9A9GLY0-0.011-0.00114.1200.0010.0010.0000.0000.0000.000
10A10GLN0-0.0140.0038.544-0.148-0.1480.0000.0000.0000.000
11A11THR0-0.014-0.0277.8260.2260.2260.0000.0000.0000.000
12A12LEU0-0.049-0.0062.077-0.985-1.3622.500-0.845-1.278-0.002
13A13ASP-1-0.793-0.8964.5230.7820.885-0.001-0.004-0.0980.000
14A14THR00.004-0.0295.8690.8100.8100.0000.0000.0000.000
15A15GLU-1-0.882-0.9335.2781.5591.5590.0000.0000.0000.000
16A16GLY0-0.0250.0102.3490.8591.6123.075-1.879-1.9480.000
17A17HIS0-0.078-0.0732.062-7.995-12.22711.582-1.682-5.668-0.008
18A18LEU0-0.018-0.0102.307-7.813-5.9673.223-2.567-2.501-0.035
19A19LYS10.8440.9155.0690.4140.494-0.001-0.003-0.0760.000
20A20ASN0-0.055-0.0557.671-0.180-0.1800.0000.0000.0000.000
21A21GLY00.0270.02711.2710.0680.0680.0000.0000.0000.000
22A22ASP-1-0.907-0.95912.2430.0710.0710.0000.0000.0000.000
23A23PHE0-0.0380.01512.6000.0680.0680.0000.0000.0000.000
24A24ASP-1-0.773-0.8787.4060.4080.4080.0000.0000.0000.000
25A25LEU0-0.045-0.0147.4650.0550.0550.0000.0000.0000.000
26A26VAL00.0420.0095.9730.1420.1420.0000.0000.0000.000
27A27MET0-0.048-0.0076.332-0.670-0.6700.0000.0000.0000.000
28A28GLN00.0180.0138.0450.2570.2570.0000.0000.0000.000
29A29ASP-1-0.879-0.9599.8520.4670.4670.0000.0000.0000.000
30A30ASP-1-0.874-0.94911.4810.3510.3510.0000.0000.0000.000
31A31CYS0-0.115-0.01412.626-0.172-0.1720.0000.0000.0000.000
32A32ASN0-0.0030.01014.124-0.102-0.1020.0000.0000.0000.000
33A33LEU00.0190.0168.7480.1110.1110.0000.0000.0000.000
34A34VAL0-0.010-0.01110.901-0.132-0.1320.0000.0000.0000.000
35A35LEU0-0.016-0.00210.7940.0700.0700.0000.0000.0000.000
36A36TYR0-0.001-0.0259.686-0.022-0.0220.0000.0000.0000.000
37A37ASN0-0.032-0.04813.654-0.044-0.0440.0000.0000.0000.000
38A38GLY00.0410.02215.603-0.033-0.0330.0000.0000.0000.000
39A39ASN0-0.105-0.04916.878-0.003-0.0030.0000.0000.0000.000
40A40TRP00.0350.02912.880-0.021-0.0210.0000.0000.0000.000
41A41GLN00.0320.00915.0010.0700.0700.0000.0000.0000.000
42A42SER00.006-0.00114.895-0.023-0.0230.0000.0000.0000.000
43A43ASN0-0.060-0.02916.554-0.019-0.0190.0000.0000.0000.000
44A44THR0-0.015-0.01215.307-0.027-0.0270.0000.0000.0000.000
45A45ALA00.0320.02017.2820.0240.0240.0000.0000.0000.000
46A46ASN0-0.029-0.01417.746-0.018-0.0180.0000.0000.0000.000
47A47ASN0-0.065-0.02518.670-0.041-0.0410.0000.0000.0000.000
48A48GLY00.0310.00618.371-0.029-0.0290.0000.0000.0000.000
49A49ARG10.8480.92615.136-0.341-0.3410.0000.0000.0000.000
50A50ASP-1-0.822-0.91512.4660.3100.3100.0000.0000.0000.000
51A52LYS10.8580.9409.133-0.229-0.2290.0000.0000.0000.000
52A53LEU00.0300.0127.909-0.069-0.0690.0000.0000.0000.000
53A54THR0-0.062-0.0309.154-0.158-0.1580.0000.0000.0000.000
54A55LEU00.0120.01211.5400.0640.0640.0000.0000.0000.000
55A56THR0-0.016-0.01613.570-0.013-0.0130.0000.0000.0000.000
56A57ASP-1-0.859-0.92717.231-0.262-0.2620.0000.0000.0000.000
57A58TYR00.014-0.00719.8210.0140.0140.0000.0000.0000.000
58A59GLY00.0480.02017.9740.0200.0200.0000.0000.0000.000
59A60GLU-1-0.841-0.90617.647-0.101-0.1010.0000.0000.0000.000
60A61LEU00.0360.01211.563-0.036-0.0360.0000.0000.0000.000
61A62VAL0-0.041-0.03413.9400.0550.0550.0000.0000.0000.000
62A63ILE00.0420.03012.164-0.046-0.0460.0000.0000.0000.000
63A64LYS10.8870.94313.5000.0850.0850.0000.0000.0000.000
64A65ASN00.0520.00913.8930.0360.0360.0000.0000.0000.000
65A66GLY00.0270.02615.201-0.028-0.0280.0000.0000.0000.000
66A67ASP-1-0.890-0.92316.1570.0900.0900.0000.0000.0000.000
67A68GLY0-0.031-0.01016.741-0.029-0.0290.0000.0000.0000.000
68A69SER0-0.070-0.04717.790-0.025-0.0250.0000.0000.0000.000
69A70THR0-0.047-0.04918.2810.0030.0030.0000.0000.0000.000
70A71VAL00.0240.01916.872-0.006-0.0060.0000.0000.0000.000
71A72TRP00.0380.01214.885-0.005-0.0050.0000.0000.0000.000
72A73LYS10.9050.95117.3410.0260.0260.0000.0000.0000.000
73A74SER00.0280.02016.8790.0040.0040.0000.0000.0000.000
74A75GLY0-0.0130.01118.7420.0040.0040.0000.0000.0000.000
75A76ALA0-0.031-0.01821.1350.0040.0040.0000.0000.0000.000
76A77GLN0-0.073-0.04521.125-0.014-0.0140.0000.0000.0000.000
77A78SER00.0000.00723.2820.0150.0150.0000.0000.0000.000
78A79VAL00.0270.00724.804-0.001-0.0010.0000.0000.0000.000
79A80LYS10.8810.94522.6090.1830.1830.0000.0000.0000.000
80A81GLY0-0.026-0.01322.6240.0100.0100.0000.0000.0000.000
81A82ASN0-0.042-0.01918.443-0.019-0.0190.0000.0000.0000.000
82A83TYR0-0.010-0.02216.9910.0280.0280.0000.0000.0000.000
83A84ALA00.002-0.00213.684-0.070-0.0700.0000.0000.0000.000
84A85ALA00.0080.01911.1750.0940.0940.0000.0000.0000.000
85A86VAL0-0.016-0.02611.181-0.168-0.1680.0000.0000.0000.000
86A87VAL00.0450.0308.9810.1160.1160.0000.0000.0000.000
87A88HIS0-0.0030.00211.889-0.022-0.0220.0000.0000.0000.000
88A89PRO00.018-0.00915.5270.0300.0300.0000.0000.0000.000
89A90ASP-1-0.833-0.89916.687-0.098-0.0980.0000.0000.0000.000
90A91GLY00.0120.00916.0890.0270.0270.0000.0000.0000.000
91A92ARG10.7950.88016.4590.1600.1600.0000.0000.0000.000
92A93LEU00.0220.01911.239-0.054-0.0540.0000.0000.0000.000
93A94VAL0-0.055-0.02514.3200.0450.0450.0000.0000.0000.000
94A95VAL00.011-0.00214.659-0.073-0.0730.0000.0000.0000.000
95A96PHE0-0.026-0.00616.4060.0520.0520.0000.0000.0000.000
96A97GLY00.0160.00618.199-0.044-0.0440.0000.0000.0000.000
97A98PRO00.0210.01820.9520.0210.0210.0000.0000.0000.000
98A99SER0-0.035-0.03820.567-0.001-0.0010.0000.0000.0000.000
99A100VAL00.0050.01922.2840.0130.0130.0000.0000.0000.000
100A101PHE0-0.001-0.00824.3530.0150.0150.0000.0000.0000.000
101A102LYS10.8760.92721.2290.2610.2610.0000.0000.0000.000
102A103ILE00.0190.02323.5460.0200.0200.0000.0000.0000.000
103A104ASP-1-0.833-0.92722.912-0.302-0.3020.0000.0000.0000.000
104A105PRO0-0.0130.00421.4340.0230.0230.0000.0000.0000.000
105A106TRP0-0.0070.00018.0840.0230.0230.0000.0000.0000.000
106A107VAL00.0110.01024.4320.0150.0150.0000.0000.0000.000
107A108ARG10.9210.96427.9450.1300.1300.0000.0000.0000.000
108A109GLY00.0080.00730.5140.0120.0120.0000.0000.0000.000