FMO DATABASE

FMODB ID: 859VY

Calculation Name: 1ZBE-4-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZBE

Chain ID: 4

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2023-06-22

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	49
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-157448.689374
FMO2-HF: Nuclear repulsion	138332.423381
FMO2-HF: Total energy	-19116.265993
FMO2-MP2: Total energy	-19170.769568

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)

Summations of interaction energy for fragment #1(4:15: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.
-2.71	1.894	0.371	-2.48	-2.496	0.004

Interaction energy analysis for fragmet #1(4:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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 ES EX CT+mix DI(MP2)

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].
3	4	17	ASN	0	-0.046	-0.018	3.630	1.059	3.696	0.029	-1.524	-1.142	0.005
4	4	18	THR	0	0.010	0.002	2.753	-2.995	-1.054	0.343	-0.950	-1.335	-0.001
5	4	19	GLY	0	0.024	0.006	4.715	-0.648	-0.622	-0.001	-0.006	-0.019	0.000
6	4	20	SER	0	-0.049	-0.018	6.773	0.213	0.213	0.000	0.000	0.000	0.000
7	4	21	ILE	0	0.026	0.018	8.227	-0.078	-0.078	0.000	0.000	0.000	0.000
8	4	22	ILE	0	-0.029	-0.003	10.485	0.092	0.092	0.000	0.000	0.000	0.000
9	4	23	ASN	0	0.022	-0.002	10.182	-0.093	-0.093	0.000	0.000	0.000	0.000
10	4	24	ASN	0	-0.020	-0.021	8.174	0.047	0.047	0.000	0.000	0.000	0.000
11	4	25	TYR	0	0.019	0.019	10.854	0.055	0.055	0.000	0.000	0.000	0.000
12	4	26	TYR	0	-0.005	0.001	12.710	0.041	0.041	0.000	0.000	0.000	0.000
13	4	27	MET	0	0.017	0.003	12.403	0.011	0.011	0.000	0.000	0.000	0.000
14	4	28	GLN	0	0.060	0.013	9.156	0.014	0.014	0.000	0.000	0.000	0.000
15	4	29	GLN	0	-0.001	-0.021	11.778	0.029	0.029	0.000	0.000	0.000	0.000
16	4	30	TYR	0	-0.020	0.003	14.017	-0.026	-0.026	0.000	0.000	0.000	0.000
17	4	31	GLN	0	-0.034	0.005	8.504	-0.155	-0.155	0.000	0.000	0.000	0.000
18	4	32	ASN	0	-0.029	-0.023	6.938	0.012	0.012	0.000	0.000	0.000	0.000
19	4	33	SER	0	0.030	0.024	10.893	-0.095	-0.095	0.000	0.000	0.000	0.000
20	4	34	MET	0	-0.015	-0.004	12.437	0.145	0.145	0.000	0.000	0.000	0.000
21	4	35	SER	0	0.003	0.010	11.581	-0.027	-0.027	0.000	0.000	0.000	0.000
22	4	36	THR	0	-0.025	-0.016	13.826	-0.063	-0.063	0.000	0.000	0.000	0.000
23	4	37	GLN	0	0.003	-0.004	14.645	0.064	0.064	0.000	0.000	0.000	0.000
24	4	38	LEU	0	0.016	0.013	18.478	-0.030	-0.030	0.000	0.000	0.000	0.000
25	4	39	GLY	0	-0.002	0.007	21.283	0.002	0.002	0.000	0.000	0.000	0.000
26	4	62	THR	0	0.048	0.031	7.646	0.008	0.008	0.000	0.000	0.000	0.000
27	4	63	GLN	0	0.004	-0.017	11.015	-0.011	-0.011	0.000	0.000	0.000	0.000
28	4	64	ASN	0	0.040	0.023	12.060	-0.014	-0.014	0.000	0.000	0.000	0.000
29	4	65	ASN	0	-0.004	-0.011	13.283	-0.066	-0.066	0.000	0.000	0.000	0.000
30	4	66	ASP	-1	-0.815	-0.899	12.385	-0.101	-0.101	0.000	0.000	0.000	0.000
31	4	67	TRP	0	0.007	-0.003	14.402	-0.023	-0.023	0.000	0.000	0.000	0.000
32	4	68	PHE	0	0.053	0.019	16.289	-0.011	-0.011	0.000	0.000	0.000	0.000
33	4	69	SER	0	0.003	0.016	14.125	-0.008	-0.008	0.000	0.000	0.000	0.000
34	4	70	LYS	1	0.842	0.924	16.274	-0.049	-0.049	0.000	0.000	0.000	0.000
35	4	71	LEU	0	0.006	0.009	19.243	-0.004	-0.004	0.000	0.000	0.000	0.000
36	4	72	ALA	0	0.008	0.010	18.801	-0.001	-0.001	0.000	0.000	0.000	0.000
37	4	73	SER	0	-0.043	-0.042	18.563	-0.011	-0.011	0.000	0.000	0.000	0.000
38	4	74	SER	0	-0.105	-0.053	21.179	0.009	0.009	0.000	0.000	0.000	0.000
39	4	75	ALA	0	0.010	0.014	24.094	0.010	0.010	0.000	0.000	0.000	0.000
40	4	76	PHE	0	-0.021	-0.011	26.017	-0.006	-0.006	0.000	0.000	0.000	0.000
41	4	77	THR	0	-0.008	-0.010	26.864	-0.005	-0.005	0.000	0.000	0.000	0.000
42	4	78	GLY	0	-0.019	0.006	29.317	-0.004	-0.004	0.000	0.000	0.000	0.000
43	4	79	LEU	0	0.002	-0.004	32.899	0.000	0.000	0.000	0.000	0.000	0.000
44	4	80	PHE	0	-0.013	-0.009	36.443	0.002	0.002	0.000	0.000	0.000	0.000
45	4	81	GLY	0	0.021	0.002	38.745	0.002	0.002	0.000	0.000	0.000	0.000
46	4	82	ALA	0	-0.019	0.001	41.796	-0.001	-0.001	0.000	0.000	0.000	0.000
47	4	83	LEU	0	-0.005	-0.007	40.242	-0.001	-0.001	0.000	0.000	0.000	0.000
48	4	84	LEU	0	-0.010	-0.005	43.404	0.001	0.001	0.000	0.000	0.000	0.000
49	4	85	ALA	0	0.019	0.018	42.481	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(4:15:SER)