FMO DATABASE

FMODB ID: M3YNZ

Calculation Name: 1Y9B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y9B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K2J6

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-358617.76165
FMO2-HF: Nuclear repulsion	328638.885819
FMO2-HF: Total energy	-29978.875831
FMO2-MP2: Total energy	-30066.426923

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(A:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-2.733	-0.351	0.044	-0.858	-1.568	0.001

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.023

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	A	5	LEU	0	0.009	0.014	3.729	-2.573	-1.117	-0.003	-0.584	-0.869	0.002
4	A	6	PRO	0	0.014	0.008	3.572	-1.625	-1.195	0.018	-0.163	-0.285	-0.001
5	A	7	ARG	1	0.964	0.979	3.391	1.538	2.034	0.029	-0.111	-0.414	0.000
6	A	8	ILE	0	0.057	0.027	5.884	-0.024	-0.024	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.059	-0.039	8.804	-0.105	-0.105	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.003	0.007	11.034	0.022	0.022	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.950	0.984	14.784	0.238	0.238	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.009	0.002	17.227	0.026	0.026	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.851	-0.917	19.848	-0.093	-0.093	0.000	0.000	0.000	0.000
12	A	14	VAL	0	0.025	-0.010	22.966	0.003	0.003	0.000	0.000	0.000	0.000
13	A	15	ASP	-1	-0.837	-0.913	24.767	-0.049	-0.049	0.000	0.000	0.000	0.000
14	A	16	THR	0	-0.056	-0.030	21.176	0.016	0.016	0.000	0.000	0.000	0.000
15	A	17	GLN	0	-0.048	-0.029	19.742	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.841	-0.927	21.818	-0.050	-0.050	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.057	-0.011	24.687	0.013	0.013	0.000	0.000	0.000	0.000
18	A	20	LEU	0	-0.026	-0.032	18.578	0.015	0.015	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.005	0.014	21.970	0.016	0.016	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.967	0.981	22.800	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.043	-0.026	23.795	0.008	0.008	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.007	0.003	20.670	0.014	0.014	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.009	0.009	22.547	0.011	0.011	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.044	-0.023	25.352	0.006	0.006	0.000	0.000	0.000	0.000
25	A	27	ALA	0	-0.036	-0.005	23.504	0.006	0.006	0.000	0.000	0.000	0.000
26	A	28	GLY	0	0.001	0.007	24.450	0.015	0.015	0.000	0.000	0.000	0.000
27	A	29	MET	0	-0.074	-0.030	19.286	0.016	0.016	0.000	0.000	0.000	0.000
28	A	30	SER	0	-0.012	-0.005	17.760	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	31	SER	0	0.020	-0.002	14.964	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	32	ILE	0	0.103	0.048	16.583	0.031	0.031	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.003	-0.010	11.517	0.025	0.025	0.000	0.000	0.000	0.000
32	A	34	SER	0	0.004	-0.004	13.369	0.071	0.071	0.000	0.000	0.000	0.000
33	A	35	PHE	0	0.050	0.029	14.968	0.043	0.043	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.006	0.001	14.334	0.021	0.021	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.014	0.002	10.361	0.025	0.025	0.000	0.000	0.000	0.000
36	A	38	ASN	0	-0.013	-0.018	14.202	0.020	0.020	0.000	0.000	0.000	0.000
37	A	39	ALA	0	0.075	0.041	16.980	0.004	0.004	0.000	0.000	0.000	0.000
38	A	40	ALA	0	-0.041	-0.030	15.263	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	41	ILE	0	-0.010	-0.016	12.988	0.013	0.013	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.928	-0.961	17.221	0.192	0.192	0.000	0.000	0.000	0.000
41	A	43	LYS	1	0.917	0.975	20.459	-0.150	-0.150	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.010	-0.002	18.177	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	45	LYS	1	0.950	0.977	18.196	-0.441	-0.441	0.000	0.000	0.000	0.000
44	A	46	GLN	0	0.088	0.039	22.325	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	47	VAL	0	-0.091	-0.052	22.919	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	48	ILE	0	0.013	0.006	20.258	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.908	-0.948	24.669	0.185	0.185	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.905	0.955	27.143	-0.142	-0.142	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.913	-0.956	27.488	0.117	0.117	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.024	-0.023	27.364	0.003	0.003	0.000	0.000	0.000	0.000
51	A	53	ALA	0	-0.010	-0.005	30.549	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.005	0.001	32.400	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.923	0.966	30.832	-0.137	-0.137	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.001	0.011	34.811	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.022	0.014	36.931	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	58	GLN	0	0.004	0.002	37.933	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	59	ALA	0	-0.030	-0.029	38.563	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.876	-0.942	40.388	0.088	0.088	0.000	0.000	0.000	0.000
59	A	61	ALA	0	-0.040	-0.013	42.790	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.032	-0.014	42.352	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	63	LEU	0	0.016	0.011	43.751	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.015	-0.002	46.795	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	65	MET	0	-0.020	-0.009	48.148	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	66	GLU	-1	-0.926	-0.959	49.209	0.060	0.060	0.000	0.000	0.000	0.000
65	A	67	ALA	0	-0.031	-0.035	50.982	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.054	-0.047	52.004	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.866	-0.916	53.192	0.042	0.042	0.000	0.000	0.000	0.000
68	A	70	ASN	0	-0.142	-0.064	54.225	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	71	PRO	0	0.094	0.047	57.228	0.001	0.001	0.000	0.000	0.000	0.000
70	A	72	ALA	0	-0.020	-0.018	58.836	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	VAL	0	0.042	0.015	56.853	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.057	0.001	54.545	0.002	0.002	0.000	0.000	0.000	0.000
73	A	75	ASN	0	0.043	-0.006	57.139	0.002	0.002	0.000	0.000	0.000	0.000
74	A	76	ALA	0	-0.037	-0.009	60.307	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.963	0.968	52.942	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.008	0.002	55.102	0.002	0.002	0.000	0.000	0.000	0.000
77	A	79	LYS	1	0.934	0.982	58.319	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	80	LEU	0	-0.017	-0.005	59.332	0.000	0.000	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.018	-0.004	56.463	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	SER	0	-0.051	-0.019	58.440	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-1.007	-0.997	61.033	0.043	0.043	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)