FMO DATABASE

FMODB ID: Q83VY

Calculation Name: 3O8V-A-Xray308

Preferred Name: Fragile X mental retardation syndrome-related protein 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3O8V

Chain ID: A

ChEMBL ID: CHEMBL3879858

UniProt ID: P51114

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1009705.283213
FMO2-HF: Nuclear repulsion	960930.727215
FMO2-HF: Total energy	-48774.555998
FMO2-MP2: Total energy	-48917.010955

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:2:ACE )

Summations of interaction energy for fragment #1(A:2:ACE )

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.
0.261	2.176	0.061	-0.955	-1.023	-0.004

Interaction energy analysis for fragmet #1(A:2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.003

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	4	THR	0	-0.018	-0.002	3.863	0.730	1.695	-0.005	-0.484	-0.476	-0.001
4	A	5	VAL	0	-0.016	-0.013	6.943	0.000	0.000	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.763	-0.880	9.898	-0.151	-0.151	0.000	0.000	0.000	0.000
6	A	7	VAL	0	0.008	-0.011	12.451	-0.012	-0.012	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.877	0.954	15.041	0.127	0.127	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.014	-0.004	18.760	0.013	0.013	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.015	-0.025	20.463	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	11	ASN	0	-0.019	-0.011	23.065	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.013	0.005	23.882	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.062	0.046	22.079	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	14	PHE	0	-0.036	-0.032	16.531	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.019	0.019	15.886	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.920	0.974	10.736	0.168	0.168	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.049	0.016	9.574	0.088	0.088	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.053	-0.029	3.806	-0.311	-0.094	0.009	-0.087	-0.140	0.000
18	A	19	ILE	0	0.002	0.008	4.845	0.390	0.390	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.845	0.925	3.234	-1.592	-0.902	0.057	-0.381	-0.367	-0.003
20	A	21	ASP	-1	-0.854	-0.943	5.153	0.354	0.397	0.000	-0.003	-0.040	0.000
21	A	22	VAL	0	-0.050	-0.012	7.624	-0.144	-0.144	0.000	0.000	0.000	0.000
22	A	23	HIS	0	-0.009	-0.003	10.033	0.025	0.025	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.916	-0.951	13.782	-0.079	-0.079	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.899	-0.987	17.069	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.048	-0.016	14.657	0.003	0.003	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.009	-0.016	9.365	-0.034	-0.034	0.000	0.000	0.000	0.000
27	A	28	THR	0	0.011	0.017	9.198	0.020	0.020	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.010	0.004	7.866	0.031	0.031	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.027	0.010	7.352	0.058	0.058	0.000	0.000	0.000	0.000
30	A	31	PHE	0	-0.001	-0.005	9.044	-0.086	-0.086	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.940	-0.960	9.144	0.029	0.029	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.024	-0.060	11.554	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.017	0.007	14.979	0.036	0.036	0.000	0.000	0.000	0.000
34	A	35	TRP	0	-0.032	-0.001	17.034	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	36	GLN	0	0.006	0.015	16.042	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.016	0.014	15.125	0.023	0.023	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.873	-0.961	10.787	0.423	0.423	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.903	0.960	12.459	-0.047	-0.047	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.009	0.008	12.648	0.021	0.021	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.075	-0.037	12.793	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.081	0.060	14.950	-0.015	-0.015	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.076	0.046	13.116	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.023	-0.009	15.794	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.949	-1.002	17.139	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.001	0.025	11.196	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.818	0.887	13.838	0.204	0.204	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.023	0.023	10.174	-0.043	-0.043	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.035	0.050	10.831	0.094	0.094	0.000	0.000	0.000	0.000
49	A	50	PRO	0	0.014	-0.008	13.848	-0.030	-0.030	0.000	0.000	0.000	0.000
50	A	51	PRO	0	-0.015	0.001	15.651	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.022	-0.030	16.249	0.028	0.028	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.815	-0.897	19.093	-0.124	-0.124	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.059	-0.047	22.447	0.005	0.005	0.000	0.000	0.000	0.000
54	A	55	LYS	1	0.776	0.870	24.186	0.092	0.092	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.940	1.011	22.902	0.112	0.112	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.898	-0.943	26.461	-0.062	-0.062	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.029	-0.016	26.372	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.047	0.030	30.531	0.007	0.007	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.793	-0.910	33.919	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.058	-0.005	36.299	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.860	-0.937	31.085	-0.076	-0.076	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.983	-1.017	28.997	-0.082	-0.082	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.031	-0.010	26.992	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.741	-0.846	21.308	-0.154	-0.154	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.013	-0.036	24.585	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.010	0.017	17.206	0.007	0.007	0.000	0.000	0.000	0.000
67	A	68	SER	0	0.006	-0.003	22.911	0.010	0.010	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.835	0.923	23.238	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	70	ALA	0	0.018	0.014	25.324	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.025	-0.002	28.136	0.002	0.002	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.925	-0.946	29.642	0.010	0.010	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.018	-0.023	25.077	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.748	-0.888	24.927	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	PRO	0	-0.057	-0.033	20.029	0.002	0.002	0.000	0.000	0.000	0.000
75	A	76	CYS	0	-0.033	-0.028	20.162	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.005	0.011	18.694	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.060	-0.034	16.931	0.005	0.005	0.000	0.000	0.000	0.000
78	A	79	TRP	0	0.003	-0.006	21.031	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.009	0.007	24.562	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.013	-0.001	26.840	0.009	0.009	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.848	0.936	29.767	0.061	0.061	0.000	0.000	0.000	0.000
82	A	83	VAL	0	0.017	0.007	31.561	0.004	0.004	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.849	0.906	33.904	0.042	0.042	0.000	0.000	0.000	0.000
84	A	85	MET	0	0.006	-0.002	36.955	0.003	0.003	0.000	0.000	0.000	0.000
85	A	86	MET	0	-0.052	-0.011	34.811	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.926	0.969	37.494	0.031	0.031	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.009	-0.004	38.323	0.001	0.001	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.897	-0.952	33.873	-0.037	-0.037	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.081	-0.036	33.337	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	TYR	0	0.016	0.001	31.597	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.047	-0.018	33.971	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	ILE	0	-0.032	-0.011	29.527	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.840	-0.923	33.286	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	95	TYR	0	-0.004	-0.002	28.257	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.009	-0.003	31.774	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.017	0.010	34.303	0.003	0.003	0.000	0.000	0.000	0.000
97	A	98	CYS	0	-0.092	-0.029	29.952	0.002	0.002	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.746	-0.868	26.680	-0.069	-0.069	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.021	-0.019	29.519	0.004	0.004	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.068	-0.042	31.425	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	TYR	0	0.004	0.006	32.580	0.004	0.004	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.006	-0.013	34.633	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.827	-0.902	30.326	-0.030	-0.030	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.035	-0.011	33.963	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	106	VAL	0	0.008	0.013	28.920	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	THR	0	0.059	0.011	29.006	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.050	0.020	27.269	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.897	-0.951	24.363	-0.062	-0.062	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.737	0.854	23.192	0.035	0.035	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.003	0.009	24.764	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.734	0.847	17.043	0.175	0.175	0.000	0.000	0.000	0.000
112	A	113	PRO	0	0.073	0.038	23.496	0.006	0.006	0.000	0.000	0.000	0.000
113	A	114	VAL	0	0.012	0.016	23.178	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	115	ASN	0	-0.071	-0.042	16.297	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	116	GLN	0	0.056	0.025	20.729	0.006	0.006	0.000	0.000	0.000	0.000
116	A	117	ASN	0	-0.111	-0.043	15.682	0.025	0.025	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.889	0.943	18.831	0.197	0.197	0.000	0.000	0.000	0.000
118	A	119	THR	0	-0.022	-0.017	16.744	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	120	VAL	0	0.037	0.026	12.508	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.780	0.892	15.953	0.230	0.230	0.000	0.000	0.000	0.000
121	A	122	NME	0	0.085	0.054	16.819	-0.021	-0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ACE )