FMO DATABASE

FMODB ID: MNY1Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-524715.12405
FMO2-HF: Nuclear repulsion	493186.770389
FMO2-HF: Total energy	-31528.353661
FMO2-MP2: Total energy	-31619.951905

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.
-12.265	-4.9	6.188	-4.83	-8.722	-0.033

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 : -0.038 / q_NPA : -0.012

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	0.817	0.898	3.100	-1.026	1.617	0.126	-1.286	-1.482	0.001
4	B	4	ILE	0	0.067	0.029	5.497	0.536	0.536	0.000	0.000	0.000	0.000
5	B	5	GLU	-1	-0.804	-0.820	2.394	-5.851	-3.867	2.627	-2.264	-2.346	-0.023
6	B	6	VAL	0	0.002	-0.004	6.600	0.301	0.301	0.000	0.000	0.000	0.000
7	B	7	TYR	0	-0.018	-0.032	4.844	0.234	0.234	0.000	0.000	0.000	0.000
8	B	8	ALA	0	0.024	-0.024	11.311	0.019	0.019	0.000	0.000	0.000	0.000
9	B	9	GLN	0	0.024	0.018	14.899	0.032	0.032	0.000	0.000	0.000	0.000
10	B	10	PRO	0	-0.018	-0.021	17.799	-0.012	-0.012	0.000	0.000	0.000	0.000
11	B	11	ASP	-1	-0.919	-0.949	21.290	0.051	0.051	0.000	0.000	0.000	0.000
12	B	12	CYS	0	0.001	0.022	17.357	0.004	0.004	0.000	0.000	0.000	0.000
13	B	13	PRO	0	0.053	0.016	21.462	-0.008	-0.008	0.000	0.000	0.000	0.000
14	B	14	PRO	0	0.040	0.011	20.318	-0.009	-0.009	0.000	0.000	0.000	0.000
15	B	16	VAL	0	-0.005	0.009	18.093	-0.019	-0.019	0.000	0.000	0.000	0.000
16	B	17	ILE	0	0.021	0.009	20.600	-0.014	-0.014	0.000	0.000	0.000	0.000
17	B	18	VAL	0	0.025	0.013	14.808	-0.012	-0.012	0.000	0.000	0.000	0.000
18	B	19	LYS	1	0.859	0.919	15.008	0.018	0.018	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.819	-0.895	17.224	-0.089	-0.089	0.000	0.000	0.000	0.000
20	B	21	PHE	0	0.001	0.006	17.752	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	22	LEU	0	0.013	0.015	12.986	-0.014	-0.014	0.000	0.000	0.000	0.000
22	B	23	LYS	1	0.804	0.872	16.968	0.063	0.063	0.000	0.000	0.000	0.000
23	B	24	HIS	0	-0.029	-0.005	19.123	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	25	ASN	0	-0.067	-0.045	18.592	0.004	0.004	0.000	0.000	0.000	0.000
25	B	26	ASN	0	-0.085	-0.027	18.986	-0.016	-0.016	0.000	0.000	0.000	0.000
26	B	27	VAL	0	0.023	0.013	12.609	-0.034	-0.034	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.034	-0.009	12.836	0.025	0.025	0.000	0.000	0.000	0.000
28	B	29	TYR	0	-0.036	-0.025	9.851	-0.130	-0.130	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.797	-0.871	7.383	-0.144	-0.144	0.000	0.000	0.000	0.000
30	B	31	GLU	-1	-0.811	-0.907	8.913	-0.123	-0.123	0.000	0.000	0.000	0.000
31	B	32	PHE	0	0.014	0.003	5.778	0.112	0.112	0.000	0.000	0.000	0.000
32	B	33	ASP	-1	-0.799	-0.890	10.935	0.083	0.083	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.078	0.018	11.998	0.023	0.023	0.000	0.000	0.000	0.000
34	B	35	LYS	1	0.824	0.915	14.397	-0.094	-0.094	0.000	0.000	0.000	0.000
35	B	36	LYS	1	0.840	0.911	16.645	-0.075	-0.075	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.823	-0.904	10.809	0.352	0.352	0.000	0.000	0.000	0.000
37	B	38	ALA	0	0.011	-0.005	13.338	0.002	0.002	0.000	0.000	0.000	0.000
38	B	39	ALA	0	0.022	0.010	10.286	0.010	0.010	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.000	0.002	8.782	0.013	0.013	0.000	0.000	0.000	0.000
40	B	41	ARG	1	0.878	0.929	9.748	-0.196	-0.196	0.000	0.000	0.000	0.000
41	B	42	ASN	0	-0.009	-0.018	11.412	-0.009	-0.009	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.936	0.985	4.507	-0.160	-0.013	-0.001	-0.006	-0.140	0.000
43	B	44	LEU	0	-0.068	-0.025	7.856	0.133	0.133	0.000	0.000	0.000	0.000
44	B	45	LEU	0	-0.062	-0.028	9.633	0.056	0.056	0.000	0.000	0.000	0.000
45	B	46	TYR	0	-0.057	-0.034	10.908	-0.027	-0.027	0.000	0.000	0.000	0.000
46	B	47	ASP	-1	-0.880	-0.933	5.957	0.564	0.564	0.000	0.000	0.000	0.000
47	B	48	TYR	0	-0.092	-0.082	2.545	-3.521	-1.562	1.925	-1.153	-2.731	-0.013
48	B	49	ASP	-1	-0.926	-0.936	8.131	0.448	0.448	0.000	0.000	0.000	0.000
49	B	50	SER	0	-0.030	-0.028	11.758	-0.104	-0.104	0.000	0.000	0.000	0.000
50	B	51	TYR	0	0.007	-0.013	13.148	-0.037	-0.037	0.000	0.000	0.000	0.000
51	B	52	SER	0	-0.055	-0.026	15.406	-0.035	-0.035	0.000	0.000	0.000	0.000
52	B	53	THR	0	-0.046	0.015	13.984	0.019	0.019	0.000	0.000	0.000	0.000
53	B	54	PRO	0	-0.006	-0.050	14.865	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	55	THR	0	0.014	0.024	9.733	0.034	0.034	0.000	0.000	0.000	0.000
55	B	56	VAL	0	-0.035	-0.014	9.327	-0.068	-0.068	0.000	0.000	0.000	0.000
56	B	57	VAL	0	0.024	0.024	3.670	-0.510	0.011	0.195	-0.152	-0.565	0.001
57	B	58	ILE	0	-0.004	-0.010	6.106	-0.558	-0.558	0.000	0.000	0.000	0.000
58	B	59	ASP	-1	-0.833	-0.919	4.403	-1.739	-1.647	-0.001	-0.015	-0.076	0.000
59	B	60	GLY	0	-0.008	-0.003	2.606	-1.493	-0.852	1.279	-0.850	-1.070	0.002
60	B	61	GLU	-1	-0.818	-0.891	3.173	1.363	0.741	0.038	0.896	-0.312	-0.001
61	B	62	VAL	0	-0.011	-0.001	6.590	0.000	0.000	0.000	0.000	0.000	0.000
62	B	63	VAL	0	0.006	0.005	8.585	-0.162	-0.162	0.000	0.000	0.000	0.000
63	B	64	ALA	0	0.040	0.017	11.977	-0.021	-0.021	0.000	0.000	0.000	0.000
64	B	65	GLY	0	0.011	0.008	13.825	-0.037	-0.037	0.000	0.000	0.000	0.000
65	B	66	PHE	0	-0.058	-0.040	16.586	-0.014	-0.014	0.000	0.000	0.000	0.000
66	B	67	GLN	0	0.008	-0.009	15.943	-0.020	-0.020	0.000	0.000	0.000	0.000
67	B	68	ILE	0	0.019	0.003	17.582	-0.009	-0.009	0.000	0.000	0.000	0.000
68	B	69	GLU	-1	-0.884	-0.938	18.951	-0.049	-0.049	0.000	0.000	0.000	0.000
69	B	70	LYS	1	0.848	0.934	13.081	-0.040	-0.040	0.000	0.000	0.000	0.000
70	B	71	LEU	0	-0.007	-0.022	12.948	-0.022	-0.022	0.000	0.000	0.000	0.000
71	B	72	GLN	0	0.000	-0.014	15.322	-0.036	-0.036	0.000	0.000	0.000	0.000
72	B	73	GLN	0	-0.045	-0.029	17.060	-0.019	-0.019	0.000	0.000	0.000	0.000
73	B	74	LEU	0	-0.027	-0.012	10.773	-0.022	-0.022	0.000	0.000	0.000	0.000
74	B	75	LEU	0	-0.027	-0.010	11.350	-0.080	-0.080	0.000	0.000	0.000	0.000
75	B	76	ASN	0	-0.119	-0.054	13.840	-0.004	-0.004	0.000	0.000	0.000	0.000
76	B	77	ILE	0	0.006	0.007	16.457	-0.003	-0.003	0.000	0.000	0.000	0.000
77	B	78	GLU	-1	-0.942	-0.946	19.121	-0.081	-0.081	0.000	0.000	0.000	0.000

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