FMO DATABASE

FMODB ID: 989V2

Calculation Name: 3ZIT-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZIT

Chain ID: B

ChEMBL ID:

UniProt ID: Q819J1

Base Structure: X-ray

Registration Date: 2023-09-23

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-524419.281463
FMO2-HF: Nuclear repulsion	492891.624262
FMO2-HF: Total energy	-31527.657201
FMO2-MP2: Total energy	-31619.256789

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-10.813	-7.389	12.99	-5.462	-10.95	-0.044

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : 0.002

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	B	3	LYS	1	0.934	0.970	3.074	-1.167	1.452	0.151	-1.253	-1.517	0.000
4	B	4	ILE	0	0.075	0.031	5.542	0.515	0.515	0.000	0.000	0.000	0.000
5	B	5	GLU	-1	-0.804	-0.838	2.276	-5.215	-4.015	4.184	-2.714	-2.670	-0.026
6	B	6	VAL	0	-0.002	-0.007	6.382	0.276	0.276	0.000	0.000	0.000	0.000
7	B	7	TYR	0	-0.022	-0.029	4.960	0.256	0.256	0.000	0.000	0.000	0.000
8	B	8	ALA	0	0.028	-0.020	11.207	0.007	0.007	0.000	0.000	0.000	0.000
9	B	9	GLN	0	0.027	0.019	14.922	0.040	0.040	0.000	0.000	0.000	0.000
10	B	10	PRO	0	-0.022	-0.019	17.819	-0.013	-0.013	0.000	0.000	0.000	0.000
11	B	11	ASP	-1	-0.917	-0.953	21.305	0.058	0.058	0.000	0.000	0.000	0.000
12	B	12	CYS	0	0.000	0.027	17.243	0.002	0.002	0.000	0.000	0.000	0.000
13	B	13	PRO	0	0.050	0.014	21.210	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	14	PRO	0	0.045	0.014	20.120	-0.009	-0.009	0.000	0.000	0.000	0.000
15	B	16	VAL	0	-0.012	0.007	17.859	-0.016	-0.016	0.000	0.000	0.000	0.000
16	B	17	ILE	0	0.019	0.005	20.380	-0.012	-0.012	0.000	0.000	0.000	0.000
17	B	18	VAL	0	0.023	0.015	14.569	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.908	0.955	15.053	-0.018	-0.018	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.864	-0.932	17.016	-0.062	-0.062	0.000	0.000	0.000	0.000
20	B	21	PHE	0	-0.007	-0.001	17.367	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	LEU	0	0.010	0.013	12.814	-0.013	-0.013	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.848	0.904	16.816	0.037	0.037	0.000	0.000	0.000	0.000
23	B	24	HIS	0	-0.017	0.005	18.974	-0.004	-0.004	0.000	0.000	0.000	0.000
24	B	25	ASN	0	-0.054	-0.032	18.546	0.001	0.001	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.069	-0.021	18.896	-0.014	-0.014	0.000	0.000	0.000	0.000
26	B	27	VAL	0	0.024	0.015	12.610	-0.031	-0.031	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.041	-0.015	12.709	0.027	0.027	0.000	0.000	0.000	0.000
28	B	29	TYR	0	-0.035	-0.019	9.729	-0.113	-0.113	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.874	-0.938	7.329	0.004	0.004	0.000	0.000	0.000	0.000
30	B	31	GLU	-1	-0.873	-0.955	8.916	-0.081	-0.081	0.000	0.000	0.000	0.000
31	B	32	PHE	0	-0.005	-0.010	5.902	0.126	0.126	0.000	0.000	0.000	0.000
32	B	33	ASP	-1	-0.789	-0.893	10.935	0.100	0.100	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.056	0.011	11.928	0.027	0.027	0.000	0.000	0.000	0.000
34	B	35	LYS	1	0.813	0.896	14.413	-0.122	-0.122	0.000	0.000	0.000	0.000
35	B	36	LYS	1	0.842	0.918	16.748	-0.108	-0.108	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.826	-0.902	11.018	0.458	0.458	0.000	0.000	0.000	0.000
37	B	38	ALA	0	0.019	-0.002	13.342	0.002	0.002	0.000	0.000	0.000	0.000
38	B	39	ALA	0	0.013	0.010	10.158	0.001	0.001	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.001	0.000	8.788	0.016	0.016	0.000	0.000	0.000	0.000
40	B	41	ARG	1	0.898	0.941	9.666	-0.227	-0.227	0.000	0.000	0.000	0.000
41	B	42	ASN	0	-0.013	-0.018	11.369	-0.027	-0.027	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.971	0.996	4.402	-0.454	-0.303	-0.001	-0.006	-0.143	0.000
43	B	44	LEU	0	-0.061	-0.020	7.767	0.089	0.089	0.000	0.000	0.000	0.000
44	B	45	LEU	0	-0.071	-0.035	9.528	0.039	0.039	0.000	0.000	0.000	0.000
45	B	46	TYR	0	-0.079	-0.038	10.820	-0.031	-0.031	0.000	0.000	0.000	0.000
46	B	47	ASP	-1	-0.875	-0.923	5.749	0.437	0.437	0.000	0.000	0.000	0.000
47	B	48	TYR	0	-0.084	-0.069	2.379	-3.659	-3.205	5.180	-1.732	-3.902	-0.018
48	B	49	ASP	-1	-0.918	-0.931	7.893	0.356	0.356	0.000	0.000	0.000	0.000
49	B	50	SER	0	-0.032	-0.030	11.418	-0.090	-0.090	0.000	0.000	0.000	0.000
50	B	51	TYR	0	0.007	-0.012	12.831	-0.022	-0.022	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.103	-0.054	15.196	-0.034	-0.034	0.000	0.000	0.000	0.000
52	B	53	THR	0	-0.008	0.034	13.813	0.019	0.019	0.000	0.000	0.000	0.000
53	B	54	PRO	0	0.002	-0.042	14.696	-0.010	-0.010	0.000	0.000	0.000	0.000
54	B	55	THR	0	0.018	0.023	9.345	0.023	0.023	0.000	0.000	0.000	0.000
55	B	56	VAL	0	-0.041	-0.018	9.200	-0.055	-0.055	0.000	0.000	0.000	0.000
56	B	57	VAL	0	0.014	0.020	3.299	-0.610	-0.090	0.610	-0.250	-0.880	0.000
57	B	58	ILE	0	-0.004	-0.014	5.969	-0.522	-0.522	0.000	0.000	0.000	0.000
58	B	59	ASP	-1	-0.938	-0.991	4.466	-1.625	-1.529	-0.001	-0.014	-0.080	0.000
59	B	60	GLY	0	-0.016	-0.006	2.318	-1.364	-1.221	2.818	-1.575	-1.386	0.002
60	B	61	GLU	-1	-0.946	-0.961	2.942	2.509	0.750	0.049	2.082	-0.372	-0.002
61	B	62	VAL	0	-0.011	0.000	6.279	0.069	0.069	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.004	0.002	8.215	-0.165	-0.165	0.000	0.000	0.000	0.000
63	B	64	ALA	0	0.042	0.018	11.575	-0.011	-0.011	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.015	0.013	13.422	-0.036	-0.036	0.000	0.000	0.000	0.000
65	B	66	PHE	0	-0.056	-0.040	16.191	-0.012	-0.012	0.000	0.000	0.000	0.000
66	B	67	GLN	0	0.001	-0.012	15.573	-0.023	-0.023	0.000	0.000	0.000	0.000
67	B	68	ILE	0	0.031	0.007	17.351	-0.009	-0.009	0.000	0.000	0.000	0.000
68	B	69	GLU	-1	-0.897	-0.949	18.823	-0.060	-0.060	0.000	0.000	0.000	0.000
69	B	70	LYS	1	0.962	0.999	13.440	0.003	0.003	0.000	0.000	0.000	0.000
70	B	71	LEU	0	-0.001	-0.021	12.908	-0.020	-0.020	0.000	0.000	0.000	0.000
71	B	72	GLN	0	0.034	0.019	15.238	-0.039	-0.039	0.000	0.000	0.000	0.000
72	B	73	GLN	0	-0.056	-0.031	16.855	-0.018	-0.018	0.000	0.000	0.000	0.000
73	B	74	LEU	0	-0.002	-0.001	10.656	-0.017	-0.017	0.000	0.000	0.000	0.000
74	B	75	LEU	0	-0.018	-0.004	11.264	-0.068	-0.068	0.000	0.000	0.000	0.000
75	B	76	ASN	0	-0.095	-0.035	14.119	0.005	0.005	0.000	0.000	0.000	0.000
76	B	77	ILE	0	-0.005	-0.007	16.513	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	78	GLU	-1	-0.997	-0.979	19.086	-0.082	-0.082	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)