FMO DATABASE

FMODB ID: 3QRKL

Calculation Name: 1ZS4-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZS4

Chain ID: D

ChEMBL ID:

UniProt ID: P03042

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-392678.413102
FMO2-HF: Nuclear repulsion	363842.169087
FMO2-HF: Total energy	-28836.244015
FMO2-MP2: Total energy	-28919.831781

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(D:7:ARG)

Summations of interaction energy for fragment #1(D:7:ARG)

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.
0.31100000000001	3.222	-0.01	-0.978	-1.925	0.004

Interaction energy analysis for fragmet #1(D:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.028 / q_NPA : 1.011

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 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	D	9	GLU	-1	-0.756	-0.858	3.659	-43.165	-40.953	-0.008	-0.919	-1.286	0.004
4	D	10	ALA	0	0.045	0.024	5.155	1.135	1.283	-0.001	-0.007	-0.140	0.000
5	D	11	LEU	0	0.010	-0.002	4.793	1.252	1.409	-0.001	-0.004	-0.152	0.000
6	D	12	ARG	1	0.830	0.910	3.904	35.599	35.993	0.000	-0.048	-0.347	0.000
7	D	13	ILE	0	0.028	0.014	5.871	2.815	2.815	0.000	0.000	0.000	0.000
8	D	14	GLU	-1	-0.863	-0.941	9.237	-22.909	-22.909	0.000	0.000	0.000	0.000
9	D	15	SER	0	-0.039	-0.015	7.199	1.519	1.519	0.000	0.000	0.000	0.000
10	D	16	ALA	0	0.016	0.004	9.141	2.224	2.224	0.000	0.000	0.000	0.000
11	D	17	LEU	0	-0.003	0.005	10.793	2.424	2.424	0.000	0.000	0.000	0.000
12	D	18	LEU	0	0.007	-0.008	12.323	1.922	1.922	0.000	0.000	0.000	0.000
13	D	19	ASN	0	-0.016	-0.007	10.014	2.867	2.867	0.000	0.000	0.000	0.000
14	D	20	LYS	1	0.954	0.975	13.885	18.637	18.637	0.000	0.000	0.000	0.000
15	D	21	ILE	0	-0.002	-0.010	16.333	1.297	1.297	0.000	0.000	0.000	0.000
16	D	22	ALA	0	-0.042	-0.020	16.605	1.030	1.030	0.000	0.000	0.000	0.000
17	D	23	MET	0	-0.064	-0.032	17.040	0.418	0.418	0.000	0.000	0.000	0.000
18	D	24	LEU	0	-0.039	0.004	19.763	0.745	0.745	0.000	0.000	0.000	0.000
19	D	25	GLY	0	0.062	0.039	21.757	0.752	0.752	0.000	0.000	0.000	0.000
20	D	26	THR	0	-0.060	-0.046	23.559	-0.137	-0.137	0.000	0.000	0.000	0.000
21	D	27	GLU	-1	-0.809	-0.885	25.334	-9.950	-9.950	0.000	0.000	0.000	0.000
22	D	28	LYS	1	0.916	0.923	26.315	10.638	10.638	0.000	0.000	0.000	0.000
23	D	29	THR	0	-0.021	-0.023	22.159	-0.370	-0.370	0.000	0.000	0.000	0.000
24	D	30	ALA	0	-0.020	-0.011	24.960	-0.074	-0.074	0.000	0.000	0.000	0.000
25	D	31	GLU	-1	-0.826	-0.892	28.036	-10.271	-10.271	0.000	0.000	0.000	0.000
26	D	32	ALA	0	-0.022	-0.005	25.839	0.203	0.203	0.000	0.000	0.000	0.000
27	D	33	VAL	0	-0.048	-0.027	24.287	-0.114	-0.114	0.000	0.000	0.000	0.000
28	D	34	GLY	0	0.019	0.028	27.730	0.168	0.168	0.000	0.000	0.000	0.000
29	D	35	VAL	0	-0.055	-0.016	27.432	0.261	0.261	0.000	0.000	0.000	0.000
30	D	36	ASP	-1	-0.757	-0.869	30.261	-9.754	-9.754	0.000	0.000	0.000	0.000
31	D	37	LYS	1	0.850	0.904	29.662	9.618	9.618	0.000	0.000	0.000	0.000
32	D	38	SER	0	-0.058	-0.042	29.295	-0.324	-0.324	0.000	0.000	0.000	0.000
33	D	39	GLN	0	-0.005	-0.014	28.874	-0.416	-0.416	0.000	0.000	0.000	0.000
34	D	40	ILE	0	0.020	0.018	24.436	-0.530	-0.530	0.000	0.000	0.000	0.000
35	D	41	SER	0	-0.023	-0.026	23.296	-0.905	-0.905	0.000	0.000	0.000	0.000
36	D	42	ARG	1	0.925	0.965	22.491	10.700	10.700	0.000	0.000	0.000	0.000
37	D	43	TRP	0	0.043	0.022	21.893	-0.671	-0.671	0.000	0.000	0.000	0.000
38	D	44	LYS	1	0.970	0.985	19.343	14.210	14.210	0.000	0.000	0.000	0.000
39	D	45	ARG	1	0.871	0.916	18.524	12.891	12.891	0.000	0.000	0.000	0.000
40	D	46	ASP	-1	-0.825	-0.895	19.044	-13.817	-13.817	0.000	0.000	0.000	0.000
41	D	47	TRP	0	-0.009	-0.015	19.818	0.190	0.190	0.000	0.000	0.000	0.000
42	D	48	ILE	0	0.012	0.027	14.559	-0.135	-0.135	0.000	0.000	0.000	0.000
43	D	49	PRO	0	0.070	0.058	13.498	-0.798	-0.798	0.000	0.000	0.000	0.000
44	D	50	LYS	1	0.818	0.919	13.845	13.562	13.562	0.000	0.000	0.000	0.000
45	D	51	PHE	0	0.024	0.000	15.919	-0.050	-0.050	0.000	0.000	0.000	0.000
46	D	52	SER	0	0.018	-0.001	11.007	-0.260	-0.260	0.000	0.000	0.000	0.000
47	D	53	MET	0	-0.020	-0.010	10.251	-1.802	-1.802	0.000	0.000	0.000	0.000
48	D	54	LEU	0	-0.006	-0.003	12.460	-0.049	-0.049	0.000	0.000	0.000	0.000
49	D	55	LEU	0	0.007	-0.007	13.352	0.263	0.263	0.000	0.000	0.000	0.000
50	D	56	ALA	0	-0.021	-0.010	9.083	-0.249	-0.249	0.000	0.000	0.000	0.000
51	D	57	VAL	0	-0.047	-0.022	10.863	0.124	0.124	0.000	0.000	0.000	0.000
52	D	58	LEU	0	-0.047	-0.017	13.088	0.989	0.989	0.000	0.000	0.000	0.000
53	D	59	GLU	-1	-0.920	-0.955	10.793	-18.993	-18.993	0.000	0.000	0.000	0.000
54	D	60	TRP	0	0.009	-0.004	12.149	0.573	0.573	0.000	0.000	0.000	0.000
55	D	61	GLY	0	-0.032	-0.013	11.526	-1.916	-1.916	0.000	0.000	0.000	0.000
56	D	62	VAL	0	-0.035	-0.015	8.901	-0.697	-0.697	0.000	0.000	0.000	0.000
57	D	63	VAL	0	0.070	0.029	11.492	0.563	0.563	0.000	0.000	0.000	0.000
58	D	64	ASP	-1	-0.877	-0.933	14.825	-16.769	-16.769	0.000	0.000	0.000	0.000
59	D	65	ASP	-1	-0.812	-0.889	11.252	-21.875	-21.875	0.000	0.000	0.000	0.000
60	D	66	ASP	-1	-0.798	-0.897	13.856	-17.236	-17.236	0.000	0.000	0.000	0.000
61	D	67	MET	0	-0.069	-0.027	15.313	1.192	1.192	0.000	0.000	0.000	0.000
62	D	68	ALA	0	0.030	0.014	16.115	0.681	0.681	0.000	0.000	0.000	0.000
63	D	69	ARG	1	0.689	0.842	11.443	20.364	20.364	0.000	0.000	0.000	0.000
64	D	70	LEU	0	0.075	0.030	17.267	0.642	0.642	0.000	0.000	0.000	0.000
65	D	71	ALA	0	-0.010	0.002	20.500	0.610	0.610	0.000	0.000	0.000	0.000
66	D	72	ARG	1	0.807	0.880	14.366	18.783	18.783	0.000	0.000	0.000	0.000
67	D	73	GLN	0	-0.002	-0.005	19.540	0.133	0.133	0.000	0.000	0.000	0.000
68	D	74	VAL	0	0.016	0.000	22.760	0.501	0.501	0.000	0.000	0.000	0.000
69	D	75	ALA	0	0.012	0.009	25.012	0.457	0.457	0.000	0.000	0.000	0.000
70	D	76	ALA	0	-0.010	0.011	24.947	0.371	0.371	0.000	0.000	0.000	0.000
71	D	77	ILE	0	-0.032	-0.011	26.872	0.374	0.374	0.000	0.000	0.000	0.000
72	D	78	LEU	0	-0.034	-0.023	29.250	0.351	0.351	0.000	0.000	0.000	0.000
73	D	79	THR	0	-0.114	-0.047	29.302	0.499	0.499	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(D:7:ARG)