FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 14K6Z

Calculation Name: 1Z5S-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z5S

Chain ID: D

ChEMBL ID:

UniProt ID: P46060

Base Structure: X-ray

Registration Date: 2023-06-20

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 65
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -294787.309491
FMO2-HF: Nuclear repulsion 268958.276747
FMO2-HF: Total energy -25829.032744
FMO2-MP2: Total energy -25904.935355


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(D:2629:SER)


Summations of interaction energy for fragment #1(D:2629:SER)
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.
-9.073-5.3670.086-1.91-1.88-0.005
Interaction energy analysis for fragmet #1(D:2629:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : 0.006
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].
3D2631ASP-1-0.930-0.9533.073-9.750-6.1130.087-1.903-1.821-0.005
4D2632VAL0-0.007-0.0054.8430.6460.715-0.001-0.007-0.0590.000
5D2633LEU0-0.014-0.0058.2420.1550.1550.0000.0000.0000.000
6D2634ILE00.0090.00010.6060.0220.0220.0000.0000.0000.000
7D2635VAL0-0.009-0.00314.2720.0070.0070.0000.0000.0000.000
8D2636TYR0-0.008-0.01116.3010.0300.0300.0000.0000.0000.000
9D2637GLU-1-0.933-0.95819.254-0.043-0.0430.0000.0000.0000.000
10D2638LEU00.0100.00321.5400.0010.0010.0000.0000.0000.000
11D2639THR0-0.023-0.01824.6130.0180.0180.0000.0000.0000.000
12D2640PRO0-0.0080.00226.849-0.004-0.0040.0000.0000.0000.000
13D2641THR00.0220.01130.6200.0000.0000.0000.0000.0000.000
14D2642ALA0-0.011-0.01733.3360.0060.0060.0000.0000.0000.000
15D2643GLU-1-0.900-0.95334.228-0.009-0.0090.0000.0000.0000.000
16D2644GLN00.0400.01134.2660.0030.0030.0000.0000.0000.000
17D2645LYS10.9941.00427.599-0.002-0.0020.0000.0000.0000.000
18D2646ALA00.0060.01633.4100.0070.0070.0000.0000.0000.000
19D2647LEU0-0.006-0.00336.3370.0050.0050.0000.0000.0000.000
20D2648ALA00.0210.00833.9730.0030.0030.0000.0000.0000.000
21D2649THR0-0.016-0.03033.4270.0070.0070.0000.0000.0000.000
22D2650LYS10.9030.95535.073-0.005-0.0050.0000.0000.0000.000
23D2651LEU0-0.025-0.01638.5220.0020.0020.0000.0000.0000.000
24D2652LYS10.8790.94435.574-0.043-0.0430.0000.0000.0000.000
25D2653LEU00.0240.03834.7090.0040.0040.0000.0000.0000.000
26D2654PRO00.0260.01029.8350.0030.0030.0000.0000.0000.000
27D2655PRO00.008-0.02428.476-0.007-0.0070.0000.0000.0000.000
28D2656THR00.0270.01126.620-0.001-0.0010.0000.0000.0000.000
29D2657PHE0-0.0150.00530.033-0.006-0.0060.0000.0000.0000.000
30D2658PHE00.041-0.00833.337-0.004-0.0040.0000.0000.0000.000
31D2659CYS0-0.0230.00529.914-0.002-0.0020.0000.0000.0000.000
32D2660TYR00.0140.01733.292-0.006-0.0060.0000.0000.0000.000
33D2661LYS10.8310.90735.5480.0190.0190.0000.0000.0000.000
34D2662ASN0-0.012-0.00333.4470.0060.0060.0000.0000.0000.000
35D2663ARG10.8010.90533.6120.0510.0510.0000.0000.0000.000
36D2664PRO0-0.001-0.00134.3170.0030.0030.0000.0000.0000.000
37D2665ASP-1-0.865-0.92036.453-0.071-0.0710.0000.0000.0000.000
38D2666TYR00.021-0.00839.0990.0000.0000.0000.0000.0000.000
39D2667VAL0-0.030-0.00740.1560.0020.0020.0000.0000.0000.000
40D2668SER0-0.039-0.02042.537-0.001-0.0010.0000.0000.0000.000
41D2669GLU-1-0.866-0.92843.900-0.022-0.0220.0000.0000.0000.000
42D2670GLU-1-0.935-0.96746.794-0.016-0.0160.0000.0000.0000.000
43D2671GLU-1-0.928-0.97048.780-0.024-0.0240.0000.0000.0000.000
44D2672GLU-1-1.017-0.99050.920-0.009-0.0090.0000.0000.0000.000
45D2673ASP-1-1.008-0.99249.661-0.010-0.0100.0000.0000.0000.000
46D2674ASP-1-0.932-0.97951.997-0.008-0.0080.0000.0000.0000.000
47D2675GLU-1-0.863-0.90250.877-0.016-0.0160.0000.0000.0000.000
48D2676ASP-1-0.836-0.92853.249-0.004-0.0040.0000.0000.0000.000
49D2677PHE0-0.014-0.01148.684-0.001-0.0010.0000.0000.0000.000
50D2678GLU-1-0.918-0.96152.566-0.009-0.0090.0000.0000.0000.000
51D2679THR0-0.023-0.01154.837-0.002-0.0020.0000.0000.0000.000
52D2680ALA00.0450.02449.735-0.002-0.0020.0000.0000.0000.000
53D2681VAL0-0.042-0.02449.678-0.002-0.0020.0000.0000.0000.000
54D2682LYS10.9250.96151.1560.0110.0110.0000.0000.0000.000
55D2683LYS10.8160.87750.5320.0170.0170.0000.0000.0000.000
56D2684LEU0-0.0120.01845.443-0.002-0.0020.0000.0000.0000.000
57D2685ASN0-0.093-0.04049.286-0.003-0.0030.0000.0000.0000.000
58D2686GLY0-0.0010.00749.4190.0010.0010.0000.0000.0000.000
59D2687LYS10.9160.94045.5210.0340.0340.0000.0000.0000.000
60D2688LEU00.0260.01843.778-0.001-0.0010.0000.0000.0000.000
61D2689TYR0-0.030-0.01840.1150.0010.0010.0000.0000.0000.000
62D2690LEU00.0460.03636.5370.0000.0000.0000.0000.0000.000
63D2691ASP-1-0.892-0.94937.324-0.053-0.0530.0000.0000.0000.000
64D2692GLY0-0.023-0.01539.8840.0030.0030.0000.0000.0000.000
65D2693SER0-0.103-0.04340.334-0.002-0.0020.0000.0000.0000.000