FMO DATABASE

FMODB ID: Z6Y1N

Calculation Name: 3ILA-I-Xray372

Preferred Name: Ryanodine receptor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ILA

Chain ID: I

ChEMBL ID: CHEMBL3288

UniProt ID: P11716

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1016164.83365
FMO2-HF: Nuclear repulsion	967115.109312
FMO2-HF: Total energy	-49049.724338
FMO2-MP2: Total energy	-49187.303827

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(I:12:GLN)

Summations of interaction energy for fragment #1(I:12:GLN)

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.
-22.998	-22.089	13.89	-6.775	-8.024	0.043

Interaction energy analysis for fragmet #1(I:12:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.046

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	I	14	LEU	0	0.037	0.026	3.288	2.493	6.287	0.275	-1.984	-2.085	0.001
4	I	15	ARG	1	0.782	0.886	1.764	-25.785	-30.137	12.038	-4.125	-3.562	0.048
5	I	16	THR	0	0.030	-0.019	7.897	-0.427	-0.427	0.000	0.000	0.000	0.000
6	I	17	ASP	-1	-0.927	-0.946	10.072	1.099	1.099	0.000	0.000	0.000	0.000
7	I	18	ASP	-1	-0.875	-0.927	6.149	2.745	2.745	0.000	0.000	0.000	0.000
8	I	19	GLU	-1	-0.851	-0.910	9.520	-0.331	-0.331	0.000	0.000	0.000	0.000
9	I	20	VAL	0	-0.047	-0.036	8.143	-0.332	-0.332	0.000	0.000	0.000	0.000
10	I	21	VAL	0	0.009	0.004	10.795	0.121	0.121	0.000	0.000	0.000	0.000
11	I	22	LEU	0	0.035	0.017	11.962	-0.125	-0.125	0.000	0.000	0.000	0.000
12	I	23	GLN	0	0.000	-0.003	11.816	0.120	0.120	0.000	0.000	0.000	0.000
13	I	24	CYS	0	0.042	0.031	15.407	0.003	0.003	0.000	0.000	0.000	0.000
14	I	25	SER	0	0.016	0.010	17.964	-0.025	-0.025	0.000	0.000	0.000	0.000
15	I	34	LYS	1	0.917	0.953	14.882	0.865	0.865	0.000	0.000	0.000	0.000
16	I	35	LEU	0	-0.050	-0.028	19.709	0.016	0.016	0.000	0.000	0.000	0.000
17	I	36	CYS	0	-0.028	-0.026	16.883	-0.069	-0.069	0.000	0.000	0.000	0.000
18	I	37	LEU	0	0.033	0.035	17.957	0.037	0.037	0.000	0.000	0.000	0.000
19	I	62	LEU	0	0.024	-0.014	14.868	0.018	0.018	0.000	0.000	0.000	0.000
20	I	63	ALA	0	0.032	0.014	17.760	0.009	0.009	0.000	0.000	0.000	0.000
21	I	64	ILE	0	0.013	0.032	19.305	0.029	0.029	0.000	0.000	0.000	0.000
22	I	65	CYS	0	-0.069	-0.039	17.624	0.019	0.019	0.000	0.000	0.000	0.000
23	I	66	CYS	0	-0.071	-0.009	14.512	-0.074	-0.074	0.000	0.000	0.000	0.000
24	I	67	PHE	0	0.009	0.005	14.613	0.074	0.074	0.000	0.000	0.000	0.000
25	I	68	THR	0	0.029	0.006	13.700	0.000	0.000	0.000	0.000	0.000	0.000
26	I	69	LEU	0	-0.016	-0.018	9.897	-0.004	-0.004	0.000	0.000	0.000	0.000
27	I	70	GLU	-1	-0.775	-0.867	13.854	0.283	0.283	0.000	0.000	0.000	0.000
28	I	71	GLN	0	0.037	0.019	16.692	0.093	0.093	0.000	0.000	0.000	0.000
29	I	72	SER	0	-0.008	-0.014	13.348	-0.059	-0.059	0.000	0.000	0.000	0.000
30	I	73	LEU	0	-0.004	0.018	16.255	0.085	0.085	0.000	0.000	0.000	0.000
31	I	74	SER	0	0.040	0.021	18.983	-0.037	-0.037	0.000	0.000	0.000	0.000
32	I	75	VAL	0	0.053	0.012	20.631	-0.016	-0.016	0.000	0.000	0.000	0.000
33	I	76	ARG	1	0.856	0.907	23.771	-0.231	-0.231	0.000	0.000	0.000	0.000
34	I	77	ALA	0	-0.024	-0.001	21.994	-0.008	-0.008	0.000	0.000	0.000	0.000
35	I	78	LEU	0	-0.015	0.005	22.776	0.001	0.001	0.000	0.000	0.000	0.000
36	I	79	GLN	0	0.028	0.006	24.594	-0.007	-0.007	0.000	0.000	0.000	0.000
37	I	80	GLU	-1	-0.844	-0.922	27.502	0.201	0.201	0.000	0.000	0.000	0.000
38	I	81	MET	0	-0.102	-0.020	25.733	-0.006	-0.006	0.000	0.000	0.000	0.000
39	I	82	LEU	0	-0.031	-0.005	28.397	-0.016	-0.016	0.000	0.000	0.000	0.000
40	I	99	ARG	1	0.804	0.882	11.355	-0.809	-0.809	0.000	0.000	0.000	0.000
41	I	100	THR	0	0.001	-0.005	7.330	-0.145	-0.145	0.000	0.000	0.000	0.000
42	I	101	LEU	0	0.048	0.035	8.947	-0.534	-0.534	0.000	0.000	0.000	0.000
43	I	102	LEU	0	-0.036	-0.021	10.487	0.101	0.101	0.000	0.000	0.000	0.000
44	I	103	TYR	0	0.011	-0.014	10.479	-0.065	-0.065	0.000	0.000	0.000	0.000
45	I	104	GLY	0	-0.026	-0.010	15.051	0.070	0.070	0.000	0.000	0.000	0.000
46	I	105	HIS	0	-0.021	-0.003	15.792	0.053	0.053	0.000	0.000	0.000	0.000
47	I	106	ALA	0	0.006	0.006	17.412	-0.064	-0.064	0.000	0.000	0.000	0.000
48	I	107	ILE	0	-0.037	-0.019	13.394	0.073	0.073	0.000	0.000	0.000	0.000
49	I	108	LEU	0	-0.001	0.011	16.860	-0.066	-0.066	0.000	0.000	0.000	0.000
50	I	109	LEU	0	-0.045	-0.031	14.087	0.026	0.026	0.000	0.000	0.000	0.000
51	I	110	ARG	1	0.804	0.880	17.713	-0.070	-0.070	0.000	0.000	0.000	0.000
52	I	111	HIS	0	0.049	0.018	18.163	-0.026	-0.026	0.000	0.000	0.000	0.000
53	I	112	ALA	0	-0.039	-0.037	17.197	0.026	0.026	0.000	0.000	0.000	0.000
54	I	133	PHE	0	-0.024	-0.019	30.064	0.005	0.005	0.000	0.000	0.000	0.000
55	I	134	ASP	-1	-0.914	-0.967	29.804	-0.111	-0.111	0.000	0.000	0.000	0.000
56	I	135	VAL	0	-0.056	-0.029	23.743	0.009	0.009	0.000	0.000	0.000	0.000
57	I	136	GLY	0	0.053	0.038	26.666	-0.018	-0.018	0.000	0.000	0.000	0.000
58	I	137	LEU	0	-0.053	-0.021	22.906	0.003	0.003	0.000	0.000	0.000	0.000
59	I	138	GLN	0	-0.028	-0.032	26.119	0.017	0.017	0.000	0.000	0.000	0.000
60	I	139	GLU	-1	-0.920	-0.954	26.559	-0.007	-0.007	0.000	0.000	0.000	0.000
61	I	140	ASP	-1	-0.853	-0.898	27.189	0.056	0.056	0.000	0.000	0.000	0.000
62	I	141	ALA	0	-0.002	-0.011	25.260	0.016	0.016	0.000	0.000	0.000	0.000
63	I	142	THR	0	-0.064	-0.069	27.356	0.011	0.011	0.000	0.000	0.000	0.000
64	I	143	GLY	0	0.050	0.020	29.747	0.006	0.006	0.000	0.000	0.000	0.000
65	I	144	GLU	-1	-0.921	-0.954	26.217	0.084	0.084	0.000	0.000	0.000	0.000
66	I	145	ALA	0	-0.026	-0.015	25.434	-0.001	-0.001	0.000	0.000	0.000	0.000
67	I	146	CYS	0	-0.034	-0.008	23.238	-0.019	-0.019	0.000	0.000	0.000	0.000
68	I	147	TRP	0	0.026	0.017	20.160	-0.008	-0.008	0.000	0.000	0.000	0.000
69	I	148	TRP	0	0.019	-0.001	18.528	-0.038	-0.038	0.000	0.000	0.000	0.000
70	I	149	THR	0	-0.045	-0.018	18.226	0.019	0.019	0.000	0.000	0.000	0.000
71	I	150	MET	0	0.009	0.017	13.311	-0.070	-0.070	0.000	0.000	0.000	0.000
72	I	151	HIS	0	0.038	0.012	16.822	0.043	0.043	0.000	0.000	0.000	0.000
73	I	152	PRO	0	0.002	0.020	14.429	-0.055	-0.055	0.000	0.000	0.000	0.000
74	I	153	ALA	0	0.041	0.020	15.622	0.056	0.056	0.000	0.000	0.000	0.000
75	I	154	SER	0	0.009	-0.023	11.905	0.097	0.097	0.000	0.000	0.000	0.000
76	I	155	LYS	1	0.810	0.924	14.740	0.206	0.206	0.000	0.000	0.000	0.000
77	I	156	GLN	0	-0.033	-0.020	14.218	0.069	0.069	0.000	0.000	0.000	0.000
78	I	157	ARG	1	0.853	0.890	17.686	-0.037	-0.037	0.000	0.000	0.000	0.000
79	I	158	SER	0	0.011	0.007	18.114	0.027	0.027	0.000	0.000	0.000	0.000
80	I	159	GLU	-1	-0.803	-0.883	17.732	0.321	0.321	0.000	0.000	0.000	0.000
81	I	160	GLY	0	0.012	0.003	15.715	-0.054	-0.054	0.000	0.000	0.000	0.000
82	I	161	GLU	-1	-0.810	-0.893	8.793	0.377	0.377	0.000	0.000	0.000	0.000
83	I	162	LYS	1	0.852	0.913	7.523	-0.789	-0.789	0.000	0.000	0.000	0.000
84	I	163	VAL	0	0.009	0.009	8.224	-0.386	-0.386	0.000	0.000	0.000	0.000
85	I	164	ARG	1	0.848	0.922	4.655	1.285	1.428	-0.001	-0.032	-0.109	0.000
86	I	165	VAL	0	0.005	-0.004	2.453	-0.704	0.464	1.579	-0.621	-2.126	-0.006
87	I	166	GLY	0	-0.009	0.000	5.010	-0.306	-0.268	-0.001	-0.004	-0.033	0.000
88	I	167	ASP	-1	-0.845	-0.890	7.978	-0.983	-0.983	0.000	0.000	0.000	0.000
89	I	168	ASP	-1	-0.858	-0.923	9.797	-0.612	-0.612	0.000	0.000	0.000	0.000
90	I	169	LEU	0	-0.037	-0.028	10.763	0.134	0.134	0.000	0.000	0.000	0.000
91	I	170	ILE	0	-0.013	0.005	14.780	0.003	0.003	0.000	0.000	0.000	0.000
92	I	171	LEU	0	0.018	0.005	14.937	0.036	0.036	0.000	0.000	0.000	0.000
93	I	172	VAL	0	-0.017	-0.013	18.999	-0.016	-0.016	0.000	0.000	0.000	0.000
94	I	173	SER	0	-0.006	0.018	22.333	0.031	0.031	0.000	0.000	0.000	0.000
95	I	174	VAL	0	0.025	-0.010	23.051	-0.001	-0.001	0.000	0.000	0.000	0.000
96	I	175	SER	0	0.008	0.017	25.656	-0.002	-0.002	0.000	0.000	0.000	0.000
97	I	176	SER	0	-0.008	-0.006	28.074	-0.007	-0.007	0.000	0.000	0.000	0.000
98	I	177	GLU	-1	-0.962	-0.975	27.468	0.005	0.005	0.000	0.000	0.000	0.000
99	I	178	ARG	1	0.834	0.928	27.058	0.038	0.038	0.000	0.000	0.000	0.000
100	I	179	TYR	0	-0.019	-0.017	22.880	0.006	0.006	0.000	0.000	0.000	0.000
101	I	180	LEU	0	0.021	0.026	18.883	0.003	0.003	0.000	0.000	0.000	0.000
102	I	181	HIS	0	-0.078	-0.042	22.177	-0.049	-0.049	0.000	0.000	0.000	0.000
103	I	189	LEU	0	0.000	0.004	26.224	0.001	0.001	0.000	0.000	0.000	0.000
104	I	190	GLN	0	-0.084	-0.062	27.535	-0.005	-0.005	0.000	0.000	0.000	0.000
105	I	191	VAL	0	-0.013	-0.007	22.276	-0.013	-0.013	0.000	0.000	0.000	0.000
106	I	192	ASP	-1	-0.782	-0.875	25.498	-0.146	-0.146	0.000	0.000	0.000	0.000
107	I	193	ALA	0	0.036	0.018	25.692	-0.013	-0.013	0.000	0.000	0.000	0.000
108	I	194	SER	0	0.022	0.020	26.981	0.019	0.019	0.000	0.000	0.000	0.000
109	I	195	PHE	0	0.041	-0.004	27.816	0.004	0.004	0.000	0.000	0.000	0.000
110	I	196	MET	0	-0.046	0.008	26.583	0.006	0.006	0.000	0.000	0.000	0.000
111	I	197	GLN	0	-0.021	-0.030	23.025	-0.014	-0.014	0.000	0.000	0.000	0.000
112	I	198	THR	0	0.002	-0.007	20.287	0.002	0.002	0.000	0.000	0.000	0.000
113	I	199	LEU	0	-0.026	0.000	17.383	0.015	0.015	0.000	0.000	0.000	0.000
114	I	200	TRP	0	-0.016	-0.029	15.468	-0.046	-0.046	0.000	0.000	0.000	0.000
115	I	201	ASN	0	-0.029	-0.033	11.811	-0.190	-0.190	0.000	0.000	0.000	0.000
116	I	202	MET	0	0.007	0.024	9.466	-0.024	-0.024	0.000	0.000	0.000	0.000
117	I	203	ASN	0	-0.050	-0.041	7.146	-0.663	-0.663	0.000	0.000	0.000	0.000
118	I	204	PRO	0	0.039	0.038	4.304	0.050	0.168	0.000	-0.009	-0.109	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:12:GLN)