FMO DATABASE

FMODB ID: J3G49

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	OptHSide
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	-391750.024199
FMO2-HF: Nuclear repulsion	362913.98567
FMO2-HF: Total energy	-28836.038529
FMO2-MP2: Total energy	-28919.667843

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.
-0.133	2.666	-0.017	-1.032	-1.749	0.005

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 : 1.006 / q_NPA : 1.004

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

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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	-0.718	-0.850	3.681	-42.250	-39.985	-0.016	-0.989	-1.260	0.005
4	D	10	ALA	0	0.046	0.026	5.520	1.035	1.035	0.000	0.000	0.000	0.000
5	D	11	LEU	0	0.004	0.001	4.795	0.453	0.615	-0.001	-0.006	-0.155	0.000
6	D	12	ARG	1	0.840	0.916	4.047	35.735	36.107	0.000	-0.037	-0.334	0.000
7	D	13	ILE	0	0.013	0.002	5.917	2.459	2.459	0.000	0.000	0.000	0.000
8	D	14	GLU	-1	-0.875	-0.948	9.402	-23.194	-23.194	0.000	0.000	0.000	0.000
9	D	15	SER	0	-0.047	-0.014	7.083	1.259	1.259	0.000	0.000	0.000	0.000
10	D	16	ALA	0	0.012	-0.003	8.982	2.348	2.348	0.000	0.000	0.000	0.000
11	D	17	LEU	0	0.002	0.008	10.264	2.505	2.505	0.000	0.000	0.000	0.000
12	D	18	LEU	0	0.011	-0.009	12.219	2.055	2.055	0.000	0.000	0.000	0.000
13	D	19	ASN	0	0.004	0.005	9.494	2.687	2.687	0.000	0.000	0.000	0.000
14	D	20	LYS	1	0.967	0.983	13.534	18.785	18.785	0.000	0.000	0.000	0.000
15	D	21	ILE	0	-0.018	-0.015	15.895	1.349	1.349	0.000	0.000	0.000	0.000
16	D	22	ALA	0	-0.043	-0.019	16.452	1.059	1.059	0.000	0.000	0.000	0.000
17	D	23	MET	0	-0.061	-0.033	16.587	0.453	0.453	0.000	0.000	0.000	0.000
18	D	24	LEU	0	-0.041	0.004	19.242	0.798	0.798	0.000	0.000	0.000	0.000
19	D	25	GLY	0	0.059	0.038	21.531	0.762	0.762	0.000	0.000	0.000	0.000
20	D	26	THR	0	-0.060	-0.047	23.477	-0.138	-0.138	0.000	0.000	0.000	0.000
21	D	27	GLU	-1	-0.840	-0.904	25.259	-9.917	-9.917	0.000	0.000	0.000	0.000
22	D	28	LYS	1	0.978	0.977	25.849	10.772	10.772	0.000	0.000	0.000	0.000
23	D	29	THR	0	-0.017	-0.015	22.111	-0.294	-0.294	0.000	0.000	0.000	0.000
24	D	30	ALA	0	-0.053	-0.031	24.891	-0.025	-0.025	0.000	0.000	0.000	0.000
25	D	31	GLU	-1	-0.853	-0.914	27.767	-10.234	-10.234	0.000	0.000	0.000	0.000
26	D	32	ALA	0	-0.025	-0.006	25.698	0.176	0.176	0.000	0.000	0.000	0.000
27	D	33	VAL	0	-0.048	-0.036	24.376	0.024	0.024	0.000	0.000	0.000	0.000
28	D	34	GLY	0	0.025	0.039	27.724	0.175	0.175	0.000	0.000	0.000	0.000
29	D	35	VAL	0	-0.072	-0.030	27.751	0.206	0.206	0.000	0.000	0.000	0.000
30	D	36	ASP	-1	-0.761	-0.862	30.332	-9.623	-9.623	0.000	0.000	0.000	0.000
31	D	37	LYS	1	0.897	0.914	29.266	9.802	9.802	0.000	0.000	0.000	0.000
32	D	38	SER	0	-0.080	-0.059	28.893	-0.379	-0.379	0.000	0.000	0.000	0.000
33	D	39	GLN	0	-0.002	-0.011	28.967	-0.351	-0.351	0.000	0.000	0.000	0.000
34	D	40	ILE	0	0.026	0.023	24.025	-0.499	-0.499	0.000	0.000	0.000	0.000
35	D	41	SER	0	-0.008	-0.010	22.766	-0.846	-0.846	0.000	0.000	0.000	0.000
36	D	42	ARG	1	0.943	0.965	22.337	10.548	10.548	0.000	0.000	0.000	0.000
37	D	43	TRP	0	0.061	0.032	21.966	-0.629	-0.629	0.000	0.000	0.000	0.000
38	D	44	LYS	1	0.950	0.975	19.307	14.550	14.550	0.000	0.000	0.000	0.000
39	D	45	ARG	1	0.853	0.904	18.768	12.938	12.938	0.000	0.000	0.000	0.000
40	D	46	ASP	-1	-0.847	-0.905	18.896	-14.195	-14.195	0.000	0.000	0.000	0.000
41	D	47	TRP	0	-0.018	-0.030	19.647	-0.430	-0.430	0.000	0.000	0.000	0.000
42	D	48	ILE	0	0.010	0.030	14.836	-0.092	-0.092	0.000	0.000	0.000	0.000
43	D	49	PRO	0	0.077	0.059	14.010	-0.868	-0.868	0.000	0.000	0.000	0.000
44	D	50	LYS	1	0.855	0.942	14.429	13.669	13.669	0.000	0.000	0.000	0.000
45	D	51	PHE	0	0.029	-0.005	16.474	-0.023	-0.023	0.000	0.000	0.000	0.000
46	D	52	SER	0	0.013	0.004	11.388	-0.468	-0.468	0.000	0.000	0.000	0.000
47	D	53	MET	0	-0.029	-0.011	10.807	-1.644	-1.644	0.000	0.000	0.000	0.000
48	D	54	LEU	0	-0.004	0.002	13.144	-0.022	-0.022	0.000	0.000	0.000	0.000
49	D	55	LEU	0	0.002	-0.010	13.484	0.228	0.228	0.000	0.000	0.000	0.000
50	D	56	ALA	0	-0.018	-0.009	9.331	-0.236	-0.236	0.000	0.000	0.000	0.000
51	D	57	VAL	0	-0.035	-0.014	10.970	0.102	0.102	0.000	0.000	0.000	0.000
52	D	58	LEU	0	-0.061	-0.025	13.226	0.743	0.743	0.000	0.000	0.000	0.000
53	D	59	GLU	-1	-0.915	-0.954	11.018	-18.346	-18.346	0.000	0.000	0.000	0.000
54	D	60	TRP	0	-0.002	-0.011	12.384	0.725	0.725	0.000	0.000	0.000	0.000
55	D	61	GLY	0	-0.031	-0.014	11.968	-1.808	-1.808	0.000	0.000	0.000	0.000
56	D	62	VAL	0	0.001	0.003	9.263	-0.489	-0.489	0.000	0.000	0.000	0.000
57	D	63	VAL	0	0.073	0.034	11.792	0.501	0.501	0.000	0.000	0.000	0.000
58	D	64	ASP	-1	-0.907	-0.953	15.184	-16.328	-16.328	0.000	0.000	0.000	0.000
59	D	65	ASP	-1	-0.875	-0.919	10.939	-22.371	-22.371	0.000	0.000	0.000	0.000
60	D	66	ASP	-1	-0.842	-0.924	13.403	-17.181	-17.181	0.000	0.000	0.000	0.000
61	D	67	MET	0	-0.057	-0.025	15.034	1.108	1.108	0.000	0.000	0.000	0.000
62	D	68	ALA	0	-0.017	0.002	15.736	0.667	0.667	0.000	0.000	0.000	0.000
63	D	69	ARG	1	0.738	0.831	11.135	20.243	20.243	0.000	0.000	0.000	0.000
64	D	70	LEU	0	0.052	0.027	17.106	0.676	0.676	0.000	0.000	0.000	0.000
65	D	71	ALA	0	-0.014	-0.001	20.273	0.639	0.639	0.000	0.000	0.000	0.000
66	D	72	ARG	1	0.929	0.965	14.786	17.709	17.709	0.000	0.000	0.000	0.000
67	D	73	GLN	0	-0.009	-0.006	19.879	0.294	0.294	0.000	0.000	0.000	0.000
68	D	74	VAL	0	0.030	0.004	22.766	0.486	0.486	0.000	0.000	0.000	0.000
69	D	75	ALA	0	0.002	0.007	24.941	0.447	0.447	0.000	0.000	0.000	0.000
70	D	76	ALA	0	-0.015	0.006	25.071	0.377	0.377	0.000	0.000	0.000	0.000
71	D	77	ILE	0	-0.055	-0.019	26.976	0.350	0.350	0.000	0.000	0.000	0.000
72	D	78	LEU	0	-0.036	-0.024	29.328	0.340	0.340	0.000	0.000	0.000	0.000
73	D	79	THR	0	-0.090	-0.033	29.250	0.510	0.510	0.000	0.000	0.000	0.000

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