FMO DATABASE

FMODB ID: LNJ39

Calculation Name: 1Y2I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y2I

Chain ID: A

ChEMBL ID:

UniProt ID: Q83LS2

Base Structure: X-ray

Registration Date: 2023-09-21

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-714541.016614
FMO2-HF: Nuclear repulsion	673374.160062
FMO2-HF: Total energy	-41166.856553
FMO2-MP2: Total energy	-41285.809291

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-15.008	-7.659	19.273	-6.219	-20.402	-0.081

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : 0.015

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	A	3	PHE	0	0.042	0.014	2.820	-4.024	0.543	2.816	-2.336	-5.046	-0.012
4	A	4	SER	0	-0.018	-0.024	4.708	0.155	0.189	-0.001	-0.006	-0.026	0.000
5	A	5	THR	0	0.054	0.031	8.328	0.178	0.178	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.027	0.003	11.408	0.057	0.057	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.047	0.019	11.534	0.030	0.030	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.020	0.004	12.625	0.071	0.071	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.007	0.005	7.890	-0.070	-0.070	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.888	-0.942	12.451	-0.150	-0.150	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.071	-0.034	14.119	-0.056	-0.056	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.048	-0.029	8.993	0.022	0.022	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.031	-0.030	13.184	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.026	0.017	10.225	0.016	0.016	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.080	-0.048	11.620	-0.042	-0.042	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.811	-0.892	10.256	0.196	0.196	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.009	0.003	9.886	0.065	0.065	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.041	-0.029	7.530	-0.060	-0.060	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.030	0.025	9.679	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.030	-0.023	9.666	0.119	0.119	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.029	-0.007	6.279	0.020	0.020	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.017	-0.042	9.745	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.005	0.009	9.785	0.037	0.037	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.890	-0.959	10.676	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.003	0.002	13.771	0.006	0.006	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.012	-0.005	16.187	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.039	-0.003	19.912	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.040	0.004	22.100	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.070	0.010	25.493	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.062	-0.028	27.222	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.079	0.051	23.844	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.061	0.027	26.330	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.919	0.942	28.332	0.037	0.037	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.936	-0.957	29.474	-0.054	-0.054	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.055	-0.036	26.751	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.013	-0.016	23.204	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.003	-0.004	29.470	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.009	0.015	32.973	0.003	0.003	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.080	-0.033	28.948	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.931	0.974	33.559	0.069	0.069	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.908	-0.957	35.064	-0.074	-0.074	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.005	0.003	30.836	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.011	0.021	28.668	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.037	0.034	26.685	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.072	0.012	22.862	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.933	0.954	23.148	0.196	0.196	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.004	0.001	24.763	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.009	0.014	26.999	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.025	-0.028	25.369	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.071	0.010	23.705	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.790	-0.852	18.835	-0.289	-0.289	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.844	0.931	20.108	0.129	0.129	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.795	-0.885	19.623	-0.136	-0.136	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.017	0.018	18.902	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.910	0.958	15.746	0.250	0.250	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.822	0.907	14.610	0.099	0.099	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.022	0.012	14.867	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.855	0.887	12.514	0.368	0.368	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.949	-0.964	9.435	-0.726	-0.726	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.009	0.001	9.786	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.017	0.027	10.389	0.029	0.029	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.005	-0.027	5.663	0.118	0.118	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.965	-0.972	5.371	-0.116	-0.116	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.909	-0.948	6.540	0.174	0.174	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.001	0.031	5.495	0.083	0.083	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.013	-0.017	2.484	-0.414	0.139	1.178	-0.783	-0.948	0.001
67	A	67	SER	0	-0.114	-0.053	2.754	-1.933	-0.962	0.416	-0.030	-1.357	-0.016
68	A	68	GLN	0	0.058	0.026	5.412	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.021	0.002	2.502	-0.514	-0.288	1.551	-0.453	-1.324	-0.001
70	A	70	ARG	1	0.937	0.961	2.519	-4.523	-2.710	0.639	-0.534	-1.917	0.000
71	A	71	ALA	0	-0.049	-0.012	3.820	0.195	0.267	0.012	0.020	-0.104	0.000
72	A	72	LEU	0	-0.028	-0.003	6.137	0.060	0.060	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.043	-0.010	5.900	0.086	0.086	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.053	-0.025	3.206	-0.007	0.352	0.018	-0.085	-0.292	0.000
75	A	75	ASP	-1	-0.849	-0.909	2.597	-2.873	-1.200	1.453	-1.208	-1.918	-0.015
76	A	76	ALA	0	-0.003	-0.022	2.423	-1.617	-0.760	6.991	-3.361	-4.487	-0.031
77	A	77	VAL	0	0.021	0.003	2.752	1.900	-1.862	4.199	2.578	-3.016	-0.007
78	A	78	VAL	0	-0.037	-0.013	4.889	-1.221	-1.235	0.001	-0.021	0.033	0.000
79	A	79	GLY	0	-0.027	-0.019	8.463	0.091	0.091	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.064	-0.035	5.726	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.880	-0.939	10.355	-0.163	-0.163	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.090	-0.058	11.425	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.886	-0.929	14.125	-0.092	-0.092	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.035	-0.034	17.509	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.805	-0.895	19.596	-0.061	-0.061	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.062	-0.023	22.863	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.021	0.011	24.339	0.008	0.008	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.005	-0.010	26.945	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.024	-0.034	29.958	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.014	-0.005	32.595	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.039	0.044	30.190	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.028	-0.037	29.505	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.067	-0.030	25.206	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.017	0.003	21.411	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.020	0.000	18.561	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.025	-0.026	14.546	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	97	SER	0	0.052	0.025	14.586	0.009	0.009	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.047	-0.013	9.085	-0.035	-0.035	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.013	0.011	10.863	0.077	0.077	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.085	0.036	8.986	-0.098	-0.098	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.064	-0.021	8.988	0.005	0.005	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.034	0.029	5.151	0.298	0.298	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.028	-0.023	5.412	-0.550	-0.550	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.872	0.942	5.468	-0.021	-0.021	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.076	-0.064	7.163	-0.213	-0.213	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.959	0.980	9.698	-0.088	-0.088	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.940	0.971	11.826	0.132	0.132	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.012	0.008	13.169	0.043	0.043	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.001	0.016	15.996	-0.006	-0.006	0.000	0.000	0.000	0.000

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