FMO DATABASE

FMODB ID: VRLK1

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	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	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-294686.768233
FMO2-HF: Nuclear repulsion	268858.209298
FMO2-HF: Total energy	-25828.558935
FMO2-MP2: Total energy	-25904.542685

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: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.
-4.351	-2.167	-0.018	-1.011	-1.155	0.004

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 : 0.009 / q_NPA : 0.003

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	2631	ASP	-1	-0.917	-0.948	3.810	-5.017	-2.833	-0.018	-1.011	-1.155	0.004
4	D	2632	VAL	0	-0.021	-0.021	5.517	0.594	0.594	0.000	0.000	0.000	0.000
5	D	2633	LEU	0	-0.021	0.000	8.705	0.143	0.143	0.000	0.000	0.000	0.000
6	D	2634	ILE	0	0.014	0.002	10.800	0.031	0.031	0.000	0.000	0.000	0.000
7	D	2635	VAL	0	-0.008	-0.003	14.290	-0.013	-0.013	0.000	0.000	0.000	0.000
8	D	2636	TYR	0	-0.011	-0.018	16.644	0.021	0.021	0.000	0.000	0.000	0.000
9	D	2637	GLU	-1	-0.935	-0.958	19.901	-0.013	-0.013	0.000	0.000	0.000	0.000
10	D	2638	LEU	0	-0.012	-0.005	21.853	0.002	0.002	0.000	0.000	0.000	0.000
11	D	2639	THR	0	-0.002	-0.003	25.102	0.016	0.016	0.000	0.000	0.000	0.000
12	D	2640	PRO	0	-0.038	-0.010	27.500	-0.005	-0.005	0.000	0.000	0.000	0.000
13	D	2641	THR	0	0.015	-0.007	31.257	-0.002	-0.002	0.000	0.000	0.000	0.000
14	D	2642	ALA	0	0.006	-0.006	33.830	0.005	0.005	0.000	0.000	0.000	0.000
15	D	2643	GLU	-1	-0.896	-0.965	34.815	-0.003	-0.003	0.000	0.000	0.000	0.000
16	D	2644	GLN	0	0.044	0.022	34.715	0.003	0.003	0.000	0.000	0.000	0.000
17	D	2645	LYS	1	0.996	1.008	27.847	-0.013	-0.013	0.000	0.000	0.000	0.000
18	D	2646	ALA	0	0.006	0.014	33.519	0.007	0.007	0.000	0.000	0.000	0.000
19	D	2647	LEU	0	0.016	0.020	36.180	0.005	0.005	0.000	0.000	0.000	0.000
20	D	2648	ALA	0	0.030	0.008	34.073	0.003	0.003	0.000	0.000	0.000	0.000
21	D	2649	THR	0	-0.035	-0.038	33.588	0.007	0.007	0.000	0.000	0.000	0.000
22	D	2650	LYS	1	0.906	0.961	35.158	-0.011	-0.011	0.000	0.000	0.000	0.000
23	D	2651	LEU	0	-0.039	-0.026	38.204	0.002	0.002	0.000	0.000	0.000	0.000
24	D	2652	LYS	1	0.895	0.961	35.049	-0.049	-0.049	0.000	0.000	0.000	0.000
25	D	2653	LEU	0	0.025	0.028	34.427	0.004	0.004	0.000	0.000	0.000	0.000
26	D	2654	PRO	0	0.015	-0.002	29.779	0.002	0.002	0.000	0.000	0.000	0.000
27	D	2655	PRO	0	0.008	-0.022	28.328	-0.008	-0.008	0.000	0.000	0.000	0.000
28	D	2656	THR	0	-0.007	0.002	26.985	-0.004	-0.004	0.000	0.000	0.000	0.000
29	D	2657	PHE	0	0.026	0.024	30.223	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	2658	PHE	0	0.011	-0.012	33.603	-0.003	-0.003	0.000	0.000	0.000	0.000
31	D	2659	CYS	0	0.005	0.005	30.271	-0.002	-0.002	0.000	0.000	0.000	0.000
32	D	2660	TYR	0	0.032	0.015	33.740	-0.006	-0.006	0.000	0.000	0.000	0.000
33	D	2661	LYS	1	0.853	0.920	35.859	0.009	0.009	0.000	0.000	0.000	0.000
34	D	2662	ASN	0	0.002	0.014	34.008	0.003	0.003	0.000	0.000	0.000	0.000
35	D	2663	ARG	1	0.789	0.898	33.824	0.034	0.034	0.000	0.000	0.000	0.000
36	D	2664	PRO	0	0.005	0.003	34.657	0.002	0.002	0.000	0.000	0.000	0.000
37	D	2665	ASP	-1	-0.894	-0.936	37.214	-0.051	-0.051	0.000	0.000	0.000	0.000
38	D	2666	TYR	0	0.026	-0.003	39.022	0.000	0.000	0.000	0.000	0.000	0.000
39	D	2667	VAL	0	-0.008	0.003	40.037	0.003	0.003	0.000	0.000	0.000	0.000
40	D	2668	SER	0	-0.030	-0.024	42.808	-0.001	-0.001	0.000	0.000	0.000	0.000
41	D	2669	GLU	-1	-0.903	-0.948	44.696	-0.013	-0.013	0.000	0.000	0.000	0.000
42	D	2670	GLU	-1	-0.943	-0.973	47.397	-0.009	-0.009	0.000	0.000	0.000	0.000
43	D	2671	GLU	-1	-0.943	-0.970	49.129	-0.014	-0.014	0.000	0.000	0.000	0.000
44	D	2672	GLU	-1	-1.018	-0.983	51.291	-0.002	-0.002	0.000	0.000	0.000	0.000
45	D	2673	ASP	-1	-1.024	-1.003	49.267	0.000	0.000	0.000	0.000	0.000	0.000
46	D	2674	ASP	-1	-0.915	-0.973	52.149	0.000	0.000	0.000	0.000	0.000	0.000
47	D	2675	GLU	-1	-0.865	-0.908	50.330	-0.005	-0.005	0.000	0.000	0.000	0.000
48	D	2676	ASP	-1	-0.868	-0.930	53.458	0.005	0.005	0.000	0.000	0.000	0.000
49	D	2677	PHE	0	0.018	-0.003	48.523	-0.001	-0.001	0.000	0.000	0.000	0.000
50	D	2678	GLU	-1	-0.934	-0.976	52.343	0.002	0.002	0.000	0.000	0.000	0.000
51	D	2679	THR	0	-0.010	-0.004	54.431	-0.001	-0.001	0.000	0.000	0.000	0.000
52	D	2680	ALA	0	0.048	0.025	49.572	-0.001	-0.001	0.000	0.000	0.000	0.000
53	D	2681	VAL	0	-0.025	-0.009	49.701	-0.001	-0.001	0.000	0.000	0.000	0.000
54	D	2682	LYS	1	0.967	0.982	50.874	0.003	0.003	0.000	0.000	0.000	0.000
55	D	2683	LYS	1	0.794	0.880	50.155	0.006	0.006	0.000	0.000	0.000	0.000
56	D	2684	LEU	0	-0.017	0.003	45.340	-0.002	-0.002	0.000	0.000	0.000	0.000
57	D	2685	ASN	0	-0.135	-0.081	49.175	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	2686	GLY	0	-0.024	0.011	49.456	0.001	0.001	0.000	0.000	0.000	0.000
59	D	2687	LYS	1	0.938	0.950	45.690	0.016	0.016	0.000	0.000	0.000	0.000
60	D	2688	LEU	0	0.066	0.037	43.694	0.000	0.000	0.000	0.000	0.000	0.000
61	D	2689	TYR	0	-0.052	-0.024	39.687	0.001	0.001	0.000	0.000	0.000	0.000
62	D	2690	LEU	0	0.019	0.013	36.814	-0.001	-0.001	0.000	0.000	0.000	0.000
63	D	2691	ASP	-1	-0.918	-0.962	36.820	-0.028	-0.028	0.000	0.000	0.000	0.000
64	D	2692	GLY	0	-0.018	-0.003	39.650	0.002	0.002	0.000	0.000	0.000	0.000
65	D	2693	SER	0	-0.052	-0.015	40.107	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2629:SER)