FMO DATABASE

FMODB ID: 2J28R

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	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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1007520.162929
FMO2-HF: Nuclear repulsion	958471.346904
FMO2-HF: Total energy	-49048.816024
FMO2-MP2: Total energy	-49186.339808

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.
-31.634	-33.251	15.475	-6.078	-7.779	0.05

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 : 0.035 / q_NPA : 0.009

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	0.012	0.011	3.438	2.889	5.576	0.045	-1.236	-1.496	-0.003
4	I	15	ARG	1	0.836	0.910	1.846	-34.496	-39.941	14.456	-4.385	-4.625	0.057
5	I	16	THR	0	0.021	0.010	7.498	-0.500	-0.500	0.000	0.000	0.000	0.000
6	I	17	ASP	-1	-0.941	-0.968	9.986	1.433	1.433	0.000	0.000	0.000	0.000
7	I	18	ASP	-1	-0.898	-0.940	6.583	3.288	3.288	0.000	0.000	0.000	0.000
8	I	19	GLU	-1	-0.912	-0.973	9.797	-0.295	-0.295	0.000	0.000	0.000	0.000
9	I	20	VAL	0	-0.045	-0.026	7.877	-0.399	-0.399	0.000	0.000	0.000	0.000
10	I	21	VAL	0	-0.011	-0.007	10.595	0.125	0.125	0.000	0.000	0.000	0.000
11	I	22	LEU	0	0.025	0.006	12.097	-0.132	-0.132	0.000	0.000	0.000	0.000
12	I	23	GLN	0	0.024	0.006	13.427	0.105	0.105	0.000	0.000	0.000	0.000
13	I	24	CYS	0	0.056	0.036	15.947	0.021	0.021	0.000	0.000	0.000	0.000
14	I	25	SER	0	0.023	0.013	18.693	-0.038	-0.038	0.000	0.000	0.000	0.000
15	I	34	LYS	1	0.853	0.902	15.246	1.063	1.063	0.000	0.000	0.000	0.000
16	I	35	LEU	0	-0.009	0.002	19.744	-0.011	-0.011	0.000	0.000	0.000	0.000
17	I	36	CYS	0	-0.009	-0.005	16.966	-0.044	-0.044	0.000	0.000	0.000	0.000
18	I	37	LEU	0	0.029	0.029	18.574	0.037	0.037	0.000	0.000	0.000	0.000
19	I	62	LEU	0	-0.033	-0.035	15.174	0.021	0.021	0.000	0.000	0.000	0.000
20	I	63	ALA	0	0.057	0.026	16.938	-0.003	-0.003	0.000	0.000	0.000	0.000
21	I	64	ILE	0	0.029	0.022	19.126	0.035	0.035	0.000	0.000	0.000	0.000
22	I	65	CYS	0	-0.053	-0.030	17.486	0.018	0.018	0.000	0.000	0.000	0.000
23	I	66	CYS	0	-0.049	0.010	15.117	-0.055	-0.055	0.000	0.000	0.000	0.000
24	I	67	PHE	0	0.028	0.016	14.491	0.078	0.078	0.000	0.000	0.000	0.000
25	I	68	THR	0	0.053	0.045	13.451	0.022	0.022	0.000	0.000	0.000	0.000
26	I	69	LEU	0	-0.027	-0.026	9.632	-0.018	-0.018	0.000	0.000	0.000	0.000
27	I	70	GLU	-1	-0.774	-0.868	13.571	0.517	0.517	0.000	0.000	0.000	0.000
28	I	71	GLN	0	0.021	0.012	16.434	0.139	0.139	0.000	0.000	0.000	0.000
29	I	72	SER	0	-0.008	-0.014	13.963	-0.062	-0.062	0.000	0.000	0.000	0.000
30	I	73	LEU	0	-0.012	-0.002	16.560	0.071	0.071	0.000	0.000	0.000	0.000
31	I	74	SER	0	0.054	0.027	19.246	-0.047	-0.047	0.000	0.000	0.000	0.000
32	I	75	VAL	0	0.051	0.008	20.912	-0.029	-0.029	0.000	0.000	0.000	0.000
33	I	76	ARG	1	0.958	0.970	24.046	-0.405	-0.405	0.000	0.000	0.000	0.000
34	I	77	ALA	0	0.017	0.018	22.502	-0.013	-0.013	0.000	0.000	0.000	0.000
35	I	78	LEU	0	-0.036	-0.009	22.896	-0.009	-0.009	0.000	0.000	0.000	0.000
36	I	79	GLN	0	0.021	-0.003	24.972	-0.013	-0.013	0.000	0.000	0.000	0.000
37	I	80	GLU	-1	-0.974	-0.979	27.677	0.344	0.344	0.000	0.000	0.000	0.000
38	I	81	MET	0	-0.112	-0.028	26.035	-0.017	-0.017	0.000	0.000	0.000	0.000
39	I	82	LEU	0	0.007	0.013	28.663	-0.024	-0.024	0.000	0.000	0.000	0.000
40	I	99	ARG	1	0.848	0.909	11.123	-1.225	-1.225	0.000	0.000	0.000	0.000
41	I	100	THR	0	-0.001	-0.012	8.169	0.385	0.385	0.000	0.000	0.000	0.000
42	I	101	LEU	0	0.049	0.047	9.383	-0.568	-0.568	0.000	0.000	0.000	0.000
43	I	102	LEU	0	-0.046	-0.024	10.624	0.125	0.125	0.000	0.000	0.000	0.000
44	I	103	TYR	0	0.060	0.015	11.317	-0.107	-0.107	0.000	0.000	0.000	0.000
45	I	104	GLY	0	0.001	0.007	15.505	0.059	0.059	0.000	0.000	0.000	0.000
46	I	105	HIS	0	-0.036	-0.019	15.951	0.033	0.033	0.000	0.000	0.000	0.000
47	I	106	ALA	0	0.004	0.002	17.510	-0.068	-0.068	0.000	0.000	0.000	0.000
48	I	107	ILE	0	-0.045	-0.025	13.675	0.081	0.081	0.000	0.000	0.000	0.000
49	I	108	LEU	0	0.012	0.001	17.102	-0.090	-0.090	0.000	0.000	0.000	0.000
50	I	109	LEU	0	-0.036	-0.019	14.251	0.040	0.040	0.000	0.000	0.000	0.000
51	I	110	ARG	1	0.868	0.928	17.625	-0.205	-0.205	0.000	0.000	0.000	0.000
52	I	111	HIS	0	0.020	0.010	18.144	-0.013	-0.013	0.000	0.000	0.000	0.000
53	I	112	ALA	0	-0.027	-0.034	17.304	0.024	0.024	0.000	0.000	0.000	0.000
54	I	133	PHE	0	-0.015	-0.014	30.341	0.006	0.006	0.000	0.000	0.000	0.000
55	I	134	ASP	-1	-0.926	-0.970	30.092	-0.083	-0.083	0.000	0.000	0.000	0.000
56	I	135	VAL	0	-0.032	-0.014	23.990	0.018	0.018	0.000	0.000	0.000	0.000
57	I	136	GLY	0	0.041	0.018	26.898	-0.021	-0.021	0.000	0.000	0.000	0.000
58	I	137	LEU	0	-0.048	-0.020	23.176	0.006	0.006	0.000	0.000	0.000	0.000
59	I	138	GLN	0	-0.036	-0.027	26.340	0.017	0.017	0.000	0.000	0.000	0.000
60	I	139	GLU	-1	-0.927	-0.956	27.390	0.060	0.060	0.000	0.000	0.000	0.000
61	I	140	ASP	-1	-0.855	-0.899	27.752	0.147	0.147	0.000	0.000	0.000	0.000
62	I	141	ALA	0	-0.007	-0.017	25.458	0.019	0.019	0.000	0.000	0.000	0.000
63	I	142	THR	0	-0.074	-0.081	27.597	0.016	0.016	0.000	0.000	0.000	0.000
64	I	143	GLY	0	0.103	0.042	29.472	0.011	0.011	0.000	0.000	0.000	0.000
65	I	144	GLU	-1	-0.972	-0.956	26.201	0.185	0.185	0.000	0.000	0.000	0.000
66	I	145	ALA	0	-0.050	-0.057	25.899	-0.001	-0.001	0.000	0.000	0.000	0.000
67	I	146	CYS	0	-0.044	0.003	23.433	-0.018	-0.018	0.000	0.000	0.000	0.000
68	I	147	TRP	0	0.004	0.006	20.296	-0.012	-0.012	0.000	0.000	0.000	0.000
69	I	148	TRP	0	0.028	0.008	18.848	-0.054	-0.054	0.000	0.000	0.000	0.000
70	I	149	THR	0	-0.050	-0.020	18.580	0.047	0.047	0.000	0.000	0.000	0.000
71	I	150	MET	0	0.012	0.009	13.165	-0.084	-0.084	0.000	0.000	0.000	0.000
72	I	151	HIS	0	0.051	0.031	17.111	0.061	0.061	0.000	0.000	0.000	0.000
73	I	152	PRO	0	-0.011	0.009	15.069	-0.075	-0.075	0.000	0.000	0.000	0.000
74	I	153	ALA	0	0.043	0.036	15.499	0.022	0.022	0.000	0.000	0.000	0.000
75	I	154	SER	0	0.074	0.013	12.447	0.074	0.074	0.000	0.000	0.000	0.000
76	I	155	LYS	1	0.839	0.947	15.643	0.103	0.103	0.000	0.000	0.000	0.000
77	I	156	GLN	0	-0.047	-0.030	14.701	0.043	0.043	0.000	0.000	0.000	0.000
78	I	157	ARG	1	0.851	0.883	17.876	-0.220	-0.220	0.000	0.000	0.000	0.000
79	I	158	SER	0	0.010	0.013	18.744	0.017	0.017	0.000	0.000	0.000	0.000
80	I	159	GLU	-1	-0.817	-0.908	18.326	0.612	0.612	0.000	0.000	0.000	0.000
81	I	160	GLY	0	0.008	0.014	16.314	-0.065	-0.065	0.000	0.000	0.000	0.000
82	I	161	GLU	-1	-0.823	-0.910	9.397	1.510	1.510	0.000	0.000	0.000	0.000
83	I	162	LYS	1	0.860	0.912	8.023	-1.722	-1.722	0.000	0.000	0.000	0.000
84	I	163	VAL	0	0.003	0.008	8.860	-0.323	-0.323	0.000	0.000	0.000	0.000
85	I	164	ARG	1	0.882	0.950	4.707	0.239	0.335	-0.001	-0.020	-0.075	0.000
86	I	165	VAL	0	-0.009	-0.004	2.463	-0.580	0.298	0.974	-0.415	-1.436	-0.004
87	I	166	GLY	0	-0.006	0.002	5.505	-0.698	-0.698	0.000	0.000	0.000	0.000
88	I	167	ASP	-1	-0.943	-0.959	7.916	-1.496	-1.496	0.000	0.000	0.000	0.000
89	I	168	ASP	-1	-0.875	-0.940	10.259	-0.630	-0.630	0.000	0.000	0.000	0.000
90	I	169	LEU	0	-0.091	-0.062	10.801	0.158	0.158	0.000	0.000	0.000	0.000
91	I	170	ILE	0	-0.023	-0.006	14.999	-0.013	-0.013	0.000	0.000	0.000	0.000
92	I	171	LEU	0	0.015	0.000	15.416	0.065	0.065	0.000	0.000	0.000	0.000
93	I	172	VAL	0	-0.025	-0.006	19.307	-0.032	-0.032	0.000	0.000	0.000	0.000
94	I	173	SER	0	-0.003	0.008	22.425	0.042	0.042	0.000	0.000	0.000	0.000
95	I	174	VAL	0	0.014	-0.002	23.641	0.001	0.001	0.000	0.000	0.000	0.000
96	I	175	SER	0	0.022	0.020	26.089	-0.007	-0.007	0.000	0.000	0.000	0.000
97	I	176	SER	0	0.010	0.002	28.792	-0.011	-0.011	0.000	0.000	0.000	0.000
98	I	177	GLU	-1	-0.962	-0.956	27.663	0.086	0.086	0.000	0.000	0.000	0.000
99	I	178	ARG	1	0.845	0.912	27.177	-0.018	-0.018	0.000	0.000	0.000	0.000
100	I	179	TYR	0	-0.026	-0.016	23.377	0.016	0.016	0.000	0.000	0.000	0.000
101	I	180	LEU	0	0.027	0.027	19.394	-0.003	-0.003	0.000	0.000	0.000	0.000
102	I	181	HIS	0	-0.015	0.003	22.581	-0.055	-0.055	0.000	0.000	0.000	0.000
103	I	189	LEU	0	-0.039	-0.033	26.646	0.005	0.005	0.000	0.000	0.000	0.000
104	I	190	GLN	0	-0.054	-0.024	27.846	-0.016	-0.016	0.000	0.000	0.000	0.000
105	I	191	VAL	0	-0.022	-0.016	22.973	-0.010	-0.010	0.000	0.000	0.000	0.000
106	I	192	ASP	-1	-0.836	-0.915	26.139	-0.121	-0.121	0.000	0.000	0.000	0.000
107	I	193	ALA	0	0.002	0.011	26.323	-0.009	-0.009	0.000	0.000	0.000	0.000
108	I	194	SER	0	0.045	0.017	27.424	0.015	0.015	0.000	0.000	0.000	0.000
109	I	195	PHE	0	0.028	-0.014	27.976	0.005	0.005	0.000	0.000	0.000	0.000
110	I	196	MET	0	-0.040	0.004	26.745	0.011	0.011	0.000	0.000	0.000	0.000
111	I	197	GLN	0	-0.015	-0.011	23.293	-0.013	-0.013	0.000	0.000	0.000	0.000
112	I	198	THR	0	0.029	0.004	20.919	-0.005	-0.005	0.000	0.000	0.000	0.000
113	I	199	LEU	0	-0.053	-0.014	17.576	0.033	0.033	0.000	0.000	0.000	0.000
114	I	200	TRP	0	-0.021	-0.020	15.911	-0.085	-0.085	0.000	0.000	0.000	0.000
115	I	201	ASN	0	-0.026	-0.015	11.724	-0.140	-0.140	0.000	0.000	0.000	0.000
116	I	202	MET	0	0.018	0.026	9.363	0.036	0.036	0.000	0.000	0.000	0.000
117	I	203	ASN	0	-0.033	-0.031	7.167	-0.779	-0.779	0.000	0.000	0.000	0.000
118	I	204	PRO	0	0.054	0.042	3.973	0.012	0.179	0.001	-0.022	-0.147	0.000

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