FMO DATABASE

FMODB ID: YY8N2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-295269.023196
FMO2-HF: Nuclear repulsion	269441.063067
FMO2-HF: Total energy	-25827.960129
FMO2-MP2: Total energy	-25904.033475

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.
-1.756	0.223	-0.016	-0.806	-1.157	0.002

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 : 0.000 / q_NPA : -0.011

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	2631	ASP	-1	-0.904	-0.945	3.810	-2.118	-0.139	-0.016	-0.806	-1.157	0.002
4	D	2632	VAL	0	-0.027	-0.019	5.591	0.094	0.094	0.000	0.000	0.000	0.000
5	D	2633	LEU	0	-0.011	0.006	8.759	0.202	0.202	0.000	0.000	0.000	0.000
6	D	2634	ILE	0	0.002	-0.006	11.079	-0.051	-0.051	0.000	0.000	0.000	0.000
7	D	2635	VAL	0	-0.004	-0.003	14.311	-0.044	-0.044	0.000	0.000	0.000	0.000
8	D	2636	TYR	0	-0.013	-0.020	16.927	-0.024	-0.024	0.000	0.000	0.000	0.000
9	D	2637	GLU	-1	-0.944	-0.960	19.846	0.257	0.257	0.000	0.000	0.000	0.000
10	D	2638	LEU	0	-0.027	-0.010	21.716	-0.017	-0.017	0.000	0.000	0.000	0.000
11	D	2639	THR	0	0.021	0.008	24.990	0.019	0.019	0.000	0.000	0.000	0.000
12	D	2640	PRO	0	-0.072	-0.028	27.320	-0.012	-0.012	0.000	0.000	0.000	0.000
13	D	2641	THR	0	0.008	-0.004	31.031	-0.003	-0.003	0.000	0.000	0.000	0.000
14	D	2642	ALA	0	0.003	-0.011	33.563	0.008	0.008	0.000	0.000	0.000	0.000
15	D	2643	GLU	-1	-0.879	-0.962	34.600	0.066	0.066	0.000	0.000	0.000	0.000
16	D	2644	GLN	0	0.057	0.044	34.324	0.006	0.006	0.000	0.000	0.000	0.000
17	D	2645	LYS	1	1.025	1.015	27.752	-0.147	-0.147	0.000	0.000	0.000	0.000
18	D	2646	ALA	0	0.002	0.018	33.136	0.008	0.008	0.000	0.000	0.000	0.000
19	D	2647	LEU	0	0.015	0.021	35.840	0.001	0.001	0.000	0.000	0.000	0.000
20	D	2648	ALA	0	0.021	0.004	33.715	0.001	0.001	0.000	0.000	0.000	0.000
21	D	2649	THR	0	-0.032	-0.037	33.364	0.009	0.009	0.000	0.000	0.000	0.000
22	D	2650	LYS	1	0.909	0.967	34.848	-0.078	-0.078	0.000	0.000	0.000	0.000
23	D	2651	LEU	0	-0.043	-0.033	37.878	-0.001	-0.001	0.000	0.000	0.000	0.000
24	D	2652	LYS	1	0.897	0.961	34.766	-0.130	-0.130	0.000	0.000	0.000	0.000
25	D	2653	LEU	0	0.014	0.020	34.110	0.006	0.006	0.000	0.000	0.000	0.000
26	D	2654	PRO	0	0.010	0.003	29.414	0.005	0.005	0.000	0.000	0.000	0.000
27	D	2655	PRO	0	0.026	-0.019	28.009	-0.011	-0.011	0.000	0.000	0.000	0.000
28	D	2656	THR	0	0.013	0.006	26.538	-0.006	-0.006	0.000	0.000	0.000	0.000
29	D	2657	PHE	0	0.011	0.020	29.764	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	2658	PHE	0	0.000	-0.023	33.175	-0.005	-0.005	0.000	0.000	0.000	0.000
31	D	2659	CYS	0	0.023	0.012	31.073	-0.003	-0.003	0.000	0.000	0.000	0.000
32	D	2660	TYR	0	0.053	0.022	33.421	-0.005	-0.005	0.000	0.000	0.000	0.000
33	D	2661	LYS	1	0.987	0.994	35.508	-0.071	-0.071	0.000	0.000	0.000	0.000
34	D	2662	ASN	0	-0.037	-0.008	32.778	-0.005	-0.005	0.000	0.000	0.000	0.000
35	D	2663	ARG	1	0.812	0.925	33.533	-0.056	-0.056	0.000	0.000	0.000	0.000
36	D	2664	PRO	0	0.005	0.002	34.792	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	2665	ASP	-1	-0.900	-0.944	37.481	0.028	0.028	0.000	0.000	0.000	0.000
38	D	2666	TYR	0	0.010	-0.015	38.410	0.000	0.000	0.000	0.000	0.000	0.000
39	D	2667	VAL	0	-0.020	0.000	40.099	0.006	0.006	0.000	0.000	0.000	0.000
40	D	2668	SER	0	-0.034	-0.025	42.682	-0.003	-0.003	0.000	0.000	0.000	0.000
41	D	2669	GLU	-1	-1.013	-1.010	44.695	0.052	0.052	0.000	0.000	0.000	0.000
42	D	2670	GLU	-1	-0.951	-0.976	47.176	0.035	0.035	0.000	0.000	0.000	0.000
43	D	2671	GLU	-1	-0.963	-0.979	48.746	0.036	0.036	0.000	0.000	0.000	0.000
44	D	2672	GLU	-1	-1.005	-0.982	50.912	0.039	0.039	0.000	0.000	0.000	0.000
45	D	2673	ASP	-1	-1.023	-1.003	49.076	0.055	0.055	0.000	0.000	0.000	0.000
46	D	2674	ASP	-1	-0.894	-0.972	51.806	0.040	0.040	0.000	0.000	0.000	0.000
47	D	2675	GLU	-1	-0.931	-0.930	49.187	0.050	0.050	0.000	0.000	0.000	0.000
48	D	2676	ASP	-1	-0.867	-0.921	53.147	0.046	0.046	0.000	0.000	0.000	0.000
49	D	2677	PHE	0	0.005	-0.025	48.640	0.000	0.000	0.000	0.000	0.000	0.000
50	D	2678	GLU	-1	-0.952	-0.984	52.027	0.046	0.046	0.000	0.000	0.000	0.000
51	D	2679	THR	0	0.018	0.010	54.109	-0.002	-0.002	0.000	0.000	0.000	0.000
52	D	2680	ALA	0	0.040	0.015	49.213	-0.001	-0.001	0.000	0.000	0.000	0.000
53	D	2681	VAL	0	-0.018	-0.004	49.466	0.000	0.000	0.000	0.000	0.000	0.000
54	D	2682	LYS	1	0.975	0.985	50.549	-0.035	-0.035	0.000	0.000	0.000	0.000
55	D	2683	LYS	1	0.814	0.904	50.123	-0.046	-0.046	0.000	0.000	0.000	0.000
56	D	2684	LEU	0	-0.001	0.016	45.172	-0.001	-0.001	0.000	0.000	0.000	0.000
57	D	2685	ASN	0	-0.098	-0.055	48.826	-0.004	-0.004	0.000	0.000	0.000	0.000
58	D	2686	GLY	0	-0.068	-0.029	49.100	0.000	0.000	0.000	0.000	0.000	0.000
59	D	2687	LYS	1	0.948	0.958	45.378	-0.039	-0.039	0.000	0.000	0.000	0.000
60	D	2688	LEU	0	0.072	0.036	43.317	0.000	0.000	0.000	0.000	0.000	0.000
61	D	2689	TYR	0	-0.042	-0.020	39.207	0.002	0.002	0.000	0.000	0.000	0.000
62	D	2690	LEU	0	0.018	0.016	36.531	-0.004	-0.004	0.000	0.000	0.000	0.000
63	D	2691	ASP	-1	-0.923	-0.964	36.586	0.057	0.057	0.000	0.000	0.000	0.000
64	D	2692	GLY	0	-0.021	-0.005	39.335	-0.002	-0.002	0.000	0.000	0.000	0.000
65	D	2693	SER	0	-0.057	-0.017	39.790	-0.003	-0.003	0.000	0.000	0.000	0.000

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