FMO DATABASE

FMODB ID: 6N68Z

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1008324.613575
FMO2-HF: Nuclear repulsion	959275.44475
FMO2-HF: Total energy	-49049.168825
FMO2-MP2: Total energy	-49186.701665

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.
-30.51	-31.591	15.894	-6.771	-8.043	0.058

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 : 0.069 / q_NPA : 0.043

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	0.018	0.014	3.496	2.391	5.918	0.044	-1.759	-1.812	0.003
4	I	15	ARG	1	0.835	0.910	1.827	-33.406	-39.109	14.948	-4.576	-4.670	0.059
5	I	16	THR	0	-0.009	-0.018	7.503	-0.446	-0.446	0.000	0.000	0.000	0.000
6	I	17	ASP	-1	-0.931	-0.958	10.007	1.285	1.285	0.000	0.000	0.000	0.000
7	I	18	ASP	-1	-0.898	-0.940	6.408	3.026	3.026	0.000	0.000	0.000	0.000
8	I	19	GLU	-1	-0.881	-0.947	9.836	-0.251	-0.251	0.000	0.000	0.000	0.000
9	I	20	VAL	0	-0.036	-0.021	7.877	-0.364	-0.364	0.000	0.000	0.000	0.000
10	I	21	VAL	0	-0.007	-0.005	10.563	0.118	0.118	0.000	0.000	0.000	0.000
11	I	22	LEU	0	0.027	0.010	12.022	-0.129	-0.129	0.000	0.000	0.000	0.000
12	I	23	GLN	0	-0.018	-0.016	12.653	0.105	0.105	0.000	0.000	0.000	0.000
13	I	24	CYS	0	0.059	0.036	15.851	-0.006	-0.006	0.000	0.000	0.000	0.000
14	I	25	SER	0	0.023	0.015	18.589	-0.024	-0.024	0.000	0.000	0.000	0.000
15	I	34	LYS	1	0.901	0.945	14.845	0.908	0.908	0.000	0.000	0.000	0.000
16	I	35	LEU	0	-0.040	-0.027	19.661	-0.001	-0.001	0.000	0.000	0.000	0.000
17	I	36	CYS	0	-0.017	-0.011	16.962	-0.042	-0.042	0.000	0.000	0.000	0.000
18	I	37	LEU	0	0.042	0.032	18.507	0.035	0.035	0.000	0.000	0.000	0.000
19	I	62	LEU	0	-0.036	-0.037	15.316	0.020	0.020	0.000	0.000	0.000	0.000
20	I	63	ALA	0	0.056	0.025	16.926	-0.008	-0.008	0.000	0.000	0.000	0.000
21	I	64	ILE	0	0.032	0.018	19.126	0.027	0.027	0.000	0.000	0.000	0.000
22	I	65	CYS	0	-0.049	-0.020	17.481	0.019	0.019	0.000	0.000	0.000	0.000
23	I	66	CYS	0	-0.074	-0.014	14.759	-0.074	-0.074	0.000	0.000	0.000	0.000
24	I	67	PHE	0	0.029	0.016	14.466	0.070	0.070	0.000	0.000	0.000	0.000
25	I	68	THR	0	0.034	0.027	13.442	0.031	0.031	0.000	0.000	0.000	0.000
26	I	69	LEU	0	-0.032	-0.023	9.630	-0.024	-0.024	0.000	0.000	0.000	0.000
27	I	70	GLU	-1	-0.788	-0.880	13.590	0.406	0.406	0.000	0.000	0.000	0.000
28	I	71	GLN	0	0.027	0.015	16.435	0.114	0.114	0.000	0.000	0.000	0.000
29	I	72	SER	0	-0.013	-0.012	13.888	-0.066	-0.066	0.000	0.000	0.000	0.000
30	I	73	LEU	0	-0.005	0.004	16.574	0.061	0.061	0.000	0.000	0.000	0.000
31	I	74	SER	0	0.044	0.020	19.256	-0.044	-0.044	0.000	0.000	0.000	0.000
32	I	75	VAL	0	0.064	0.014	20.932	-0.014	-0.014	0.000	0.000	0.000	0.000
33	I	76	ARG	1	0.939	0.962	24.055	-0.244	-0.244	0.000	0.000	0.000	0.000
34	I	77	ALA	0	-0.005	0.005	22.497	-0.005	-0.005	0.000	0.000	0.000	0.000
35	I	78	LEU	0	-0.025	-0.002	22.936	0.000	0.000	0.000	0.000	0.000	0.000
36	I	79	GLN	0	0.018	-0.006	24.995	-0.008	-0.008	0.000	0.000	0.000	0.000
37	I	80	GLU	-1	-0.950	-0.973	27.742	0.217	0.217	0.000	0.000	0.000	0.000
38	I	81	MET	0	-0.114	-0.024	26.033	-0.009	-0.009	0.000	0.000	0.000	0.000
39	I	82	LEU	0	0.005	0.014	28.674	-0.014	-0.014	0.000	0.000	0.000	0.000
40	I	99	ARG	1	0.829	0.904	11.229	-0.844	-0.844	0.000	0.000	0.000	0.000
41	I	100	THR	0	0.011	-0.004	8.078	0.068	0.068	0.000	0.000	0.000	0.000
42	I	101	LEU	0	0.061	0.047	9.377	-0.486	-0.486	0.000	0.000	0.000	0.000
43	I	102	LEU	0	-0.041	-0.019	10.634	-0.022	-0.022	0.000	0.000	0.000	0.000
44	I	103	TYR	0	0.054	0.012	11.439	-0.048	-0.048	0.000	0.000	0.000	0.000
45	I	104	GLY	0	0.002	0.009	15.600	0.052	0.052	0.000	0.000	0.000	0.000
46	I	105	HIS	0	-0.040	-0.021	15.971	0.072	0.072	0.000	0.000	0.000	0.000
47	I	106	ALA	0	0.001	0.001	17.498	-0.061	-0.061	0.000	0.000	0.000	0.000
48	I	107	ILE	0	-0.038	-0.023	13.675	0.071	0.071	0.000	0.000	0.000	0.000
49	I	108	LEU	0	0.005	0.002	17.104	-0.074	-0.074	0.000	0.000	0.000	0.000
50	I	109	LEU	0	-0.037	-0.020	14.277	0.035	0.035	0.000	0.000	0.000	0.000
51	I	110	ARG	1	0.870	0.929	17.622	-0.137	-0.137	0.000	0.000	0.000	0.000
52	I	111	HIS	0	0.027	0.013	18.139	-0.016	-0.016	0.000	0.000	0.000	0.000
53	I	112	ALA	0	-0.033	-0.027	17.273	0.027	0.027	0.000	0.000	0.000	0.000
54	I	133	PHE	0	-0.017	-0.015	30.299	0.005	0.005	0.000	0.000	0.000	0.000
55	I	134	ASP	-1	-0.928	-0.972	30.032	-0.104	-0.104	0.000	0.000	0.000	0.000
56	I	135	VAL	0	-0.031	-0.014	23.958	0.013	0.013	0.000	0.000	0.000	0.000
57	I	136	GLY	0	0.046	0.021	26.856	-0.015	-0.015	0.000	0.000	0.000	0.000
58	I	137	LEU	0	-0.051	-0.018	23.152	0.002	0.002	0.000	0.000	0.000	0.000
59	I	138	GLN	0	-0.036	-0.033	26.322	0.015	0.015	0.000	0.000	0.000	0.000
60	I	139	GLU	-1	-0.923	-0.958	27.388	0.030	0.030	0.000	0.000	0.000	0.000
61	I	140	ASP	-1	-0.850	-0.891	27.768	0.093	0.093	0.000	0.000	0.000	0.000
62	I	141	ALA	0	-0.015	-0.027	25.391	0.013	0.013	0.000	0.000	0.000	0.000
63	I	142	THR	0	-0.075	-0.085	27.521	0.011	0.011	0.000	0.000	0.000	0.000
64	I	143	GLY	0	0.109	0.045	29.461	0.009	0.009	0.000	0.000	0.000	0.000
65	I	144	GLU	-1	-0.969	-0.957	26.190	0.096	0.096	0.000	0.000	0.000	0.000
66	I	145	ALA	0	-0.051	-0.052	25.887	-0.006	-0.006	0.000	0.000	0.000	0.000
67	I	146	CYS	0	-0.045	0.002	23.450	-0.021	-0.021	0.000	0.000	0.000	0.000
68	I	147	TRP	0	0.015	0.016	20.322	-0.010	-0.010	0.000	0.000	0.000	0.000
69	I	148	TRP	0	0.017	0.001	18.894	-0.047	-0.047	0.000	0.000	0.000	0.000
70	I	149	THR	0	-0.048	-0.018	18.558	0.026	0.026	0.000	0.000	0.000	0.000
71	I	150	MET	0	0.003	0.009	13.231	-0.078	-0.078	0.000	0.000	0.000	0.000
72	I	151	HIS	0	0.052	0.025	17.072	0.030	0.030	0.000	0.000	0.000	0.000
73	I	152	PRO	0	-0.014	0.009	15.306	-0.062	-0.062	0.000	0.000	0.000	0.000
74	I	153	ALA	0	0.038	0.031	15.684	0.046	0.046	0.000	0.000	0.000	0.000
75	I	154	SER	0	0.072	0.008	12.614	0.092	0.092	0.000	0.000	0.000	0.000
76	I	155	LYS	1	0.834	0.953	15.701	0.236	0.236	0.000	0.000	0.000	0.000
77	I	156	GLN	0	-0.039	-0.029	15.033	0.075	0.075	0.000	0.000	0.000	0.000
78	I	157	ARG	1	0.848	0.885	18.191	-0.001	-0.001	0.000	0.000	0.000	0.000
79	I	158	SER	0	0.009	0.013	18.741	0.028	0.028	0.000	0.000	0.000	0.000
80	I	159	GLU	-1	-0.806	-0.905	18.215	0.322	0.322	0.000	0.000	0.000	0.000
81	I	160	GLY	0	0.013	0.019	16.130	-0.071	-0.071	0.000	0.000	0.000	0.000
82	I	161	GLU	-1	-0.822	-0.905	9.431	0.233	0.233	0.000	0.000	0.000	0.000
83	I	162	LYS	1	0.860	0.921	7.736	-0.645	-0.645	0.000	0.000	0.000	0.000
84	I	163	VAL	0	0.014	0.010	8.773	-0.355	-0.355	0.000	0.000	0.000	0.000
85	I	164	ARG	1	0.865	0.932	4.989	1.388	1.388	0.000	0.000	0.000	0.000
86	I	165	VAL	0	-0.010	-0.005	2.537	-0.464	0.455	0.900	-0.413	-1.406	-0.004
87	I	166	GLY	0	-0.003	0.004	5.441	-0.582	-0.582	0.000	0.000	0.000	0.000
88	I	167	ASP	-1	-0.937	-0.954	8.030	-1.568	-1.568	0.000	0.000	0.000	0.000
89	I	168	ASP	-1	-0.875	-0.933	10.228	-0.655	-0.655	0.000	0.000	0.000	0.000
90	I	169	LEU	0	-0.080	-0.049	10.758	0.099	0.099	0.000	0.000	0.000	0.000
91	I	170	ILE	0	-0.023	-0.012	14.918	0.015	0.015	0.000	0.000	0.000	0.000
92	I	171	LEU	0	0.016	0.004	15.238	0.043	0.043	0.000	0.000	0.000	0.000
93	I	172	VAL	0	-0.023	-0.009	19.249	-0.017	-0.017	0.000	0.000	0.000	0.000
94	I	173	SER	0	-0.001	0.011	22.387	0.032	0.032	0.000	0.000	0.000	0.000
95	I	174	VAL	0	0.030	0.001	23.500	-0.001	-0.001	0.000	0.000	0.000	0.000
96	I	175	SER	0	0.019	0.018	26.066	-0.005	-0.005	0.000	0.000	0.000	0.000
97	I	176	SER	0	0.007	0.002	28.737	-0.006	-0.006	0.000	0.000	0.000	0.000
98	I	177	GLU	-1	-0.958	-0.962	27.581	0.007	0.007	0.000	0.000	0.000	0.000
99	I	178	ARG	1	0.839	0.917	27.139	0.038	0.038	0.000	0.000	0.000	0.000
100	I	179	TYR	0	-0.023	-0.013	23.126	0.004	0.004	0.000	0.000	0.000	0.000
101	I	180	LEU	0	0.018	0.022	19.309	0.005	0.005	0.000	0.000	0.000	0.000
102	I	181	HIS	0	-0.049	-0.009	22.501	-0.052	-0.052	0.000	0.000	0.000	0.000
103	I	189	LEU	0	-0.005	0.002	26.554	0.001	0.001	0.000	0.000	0.000	0.000
104	I	190	GLN	0	-0.082	-0.060	27.795	-0.009	-0.009	0.000	0.000	0.000	0.000
105	I	191	VAL	0	-0.027	-0.022	22.852	-0.011	-0.011	0.000	0.000	0.000	0.000
106	I	192	ASP	-1	-0.792	-0.890	26.063	-0.146	-0.146	0.000	0.000	0.000	0.000
107	I	193	ALA	0	0.007	0.012	26.252	-0.012	-0.012	0.000	0.000	0.000	0.000
108	I	194	SER	0	0.033	0.013	27.353	0.016	0.016	0.000	0.000	0.000	0.000
109	I	195	PHE	0	0.035	-0.011	27.904	0.000	0.000	0.000	0.000	0.000	0.000
110	I	196	MET	0	-0.039	0.006	26.726	0.005	0.005	0.000	0.000	0.000	0.000
111	I	197	GLN	0	-0.003	-0.008	23.231	-0.019	-0.019	0.000	0.000	0.000	0.000
112	I	198	THR	0	-0.007	-0.015	20.557	-0.008	-0.008	0.000	0.000	0.000	0.000
113	I	199	LEU	0	-0.035	-0.005	17.586	0.020	0.020	0.000	0.000	0.000	0.000
114	I	200	TRP	0	-0.008	-0.014	15.807	-0.059	-0.059	0.000	0.000	0.000	0.000
115	I	201	ASN	0	-0.057	-0.040	11.892	-0.172	-0.172	0.000	0.000	0.000	0.000
116	I	202	MET	0	0.021	0.024	9.243	0.063	0.063	0.000	0.000	0.000	0.000
117	I	203	ASN	0	-0.027	-0.027	7.076	-0.684	-0.684	0.000	0.000	0.000	0.000
118	I	204	PRO	0	0.063	0.044	3.929	-0.027	0.149	0.002	-0.023	-0.155	0.000

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