FMO DATABASE

FMODB ID: 9GRV2

Calculation Name: 3O8V-A-Xray372

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: 2023-03-14

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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1001705.160585
FMO2-HF: Nuclear repulsion	953100.746307
FMO2-HF: Total energy	-48604.414279
FMO2-MP2: Total energy	-48746.269213

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-8.409	0.316	1.114	-3.786	-6.052	-0.005

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.028

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	5	VAL	0	-0.031	-0.019	3.149	-2.917	0.442	0.081	-1.679	-1.761	0.002
4	A	6	GLU	-1	-0.778	-0.876	5.255	-0.388	-0.306	-0.001	-0.005	-0.076	0.000
5	A	7	VAL	0	0.014	-0.009	9.103	0.002	0.002	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.862	0.940	11.476	0.545	0.545	0.000	0.000	0.000	0.000
7	A	9	GLY	0	0.040	0.007	14.986	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.026	-0.028	17.608	0.017	0.017	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.004	-0.020	20.010	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.006	0.005	19.848	0.021	0.021	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.036	0.040	18.431	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	14	PHE	0	-0.032	-0.022	12.183	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	15	TYR	0	-0.003	0.015	13.391	0.037	0.037	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.848	0.906	8.472	0.469	0.469	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.039	0.012	8.026	0.245	0.245	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.053	-0.029	2.623	-1.556	-0.289	0.343	-0.552	-1.058	0.004
17	A	19	ILE	0	-0.008	0.001	2.440	-0.439	1.448	0.603	-0.539	-1.951	-0.002
18	A	20	LYS	1	0.761	0.866	3.029	-2.482	-0.783	0.076	-0.936	-0.839	-0.009
19	A	21	ASP	-1	-0.842	-0.930	5.676	0.142	0.142	0.000	0.000	0.000	0.000
20	A	22	VAL	0	-0.061	-0.027	6.162	-0.304	-0.304	0.000	0.000	0.000	0.000
21	A	23	HIS	0	-0.006	-0.006	8.805	0.078	0.078	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.921	-0.965	11.839	-0.232	-0.232	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.928	-0.967	13.941	-0.350	-0.350	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.051	-0.022	12.848	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.033	-0.007	6.451	-0.055	-0.055	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.026	0.014	9.015	0.101	0.101	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.009	-0.002	7.342	-0.445	-0.445	0.000	0.000	0.000	0.000
28	A	30	VAL	0	0.038	0.019	7.110	0.428	0.428	0.000	0.000	0.000	0.000
29	A	31	PHE	0	0.013	0.000	8.162	-0.418	-0.418	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.878	-0.899	8.668	-0.565	-0.565	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.016	-0.055	10.657	0.169	0.169	0.000	0.000	0.000	0.000
32	A	34	ASN	0	0.004	0.004	14.283	-0.025	-0.025	0.000	0.000	0.000	0.000
33	A	35	TRP	0	-0.018	0.006	16.755	0.029	0.029	0.000	0.000	0.000	0.000
34	A	36	GLN	0	0.003	0.015	15.074	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.010	0.002	14.701	-0.051	-0.051	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.819	-0.903	10.677	-0.668	-0.668	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.871	0.937	12.030	0.731	0.731	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.000	0.006	12.081	-0.114	-0.114	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.101	-0.048	11.407	0.068	0.068	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.087	0.058	12.409	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.115	0.042	8.454	-0.098	-0.098	0.000	0.000	0.000	0.000
42	A	44	ASN	0	-0.039	-0.018	11.323	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.861	-0.941	12.970	-0.499	-0.499	0.000	0.000	0.000	0.000
44	A	46	VAL	0	0.008	0.026	7.334	-0.060	-0.060	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.813	0.892	8.570	0.698	0.698	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.034	0.031	3.617	-0.716	-0.285	0.012	-0.075	-0.367	0.000
47	A	49	PRO	0	0.049	0.043	5.330	0.201	0.201	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.019	0.004	7.978	0.056	0.056	0.000	0.000	0.000	0.000
49	A	51	PRO	0	-0.012	0.000	9.713	0.041	0.041	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.000	-0.008	10.573	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.797	-0.883	13.569	-0.060	-0.060	0.000	0.000	0.000	0.000
52	A	54	ILE	0	-0.014	-0.007	16.966	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.865	0.909	17.996	0.068	0.068	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.845	0.912	22.549	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.876	-0.893	25.285	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	58	ILE	0	-0.050	-0.036	23.022	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.024	-0.018	25.907	0.003	0.003	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.797	-0.900	28.669	-0.067	-0.067	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.027	0.004	31.217	0.003	0.003	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.856	-0.937	25.528	-0.094	-0.094	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-1.015	-1.019	23.622	-0.182	-0.182	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.027	-0.011	21.825	0.003	0.003	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.745	-0.851	16.216	-0.390	-0.390	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.005	-0.023	20.236	0.020	0.020	0.000	0.000	0.000	0.000
65	A	67	TYR	0	-0.002	0.013	16.188	-0.041	-0.041	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.002	-0.028	20.261	0.031	0.031	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.858	0.944	21.259	0.156	0.156	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.038	0.049	23.724	0.002	0.002	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.054	-0.053	26.605	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.847	-0.929	27.926	-0.178	-0.178	0.000	0.000	0.000	0.000
71	A	73	GLN	0	0.006	0.004	23.441	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.859	-0.934	23.569	-0.197	-0.197	0.000	0.000	0.000	0.000
73	A	75	PRO	0	-0.031	-0.012	18.715	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	76	CYS	0	-0.035	-0.020	18.503	0.012	0.012	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.010	0.006	16.346	-0.066	-0.066	0.000	0.000	0.000	0.000
76	A	78	TRP	0	-0.048	-0.030	13.975	0.070	0.070	0.000	0.000	0.000	0.000
77	A	79	TRP	0	0.004	-0.007	17.418	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.033	0.022	19.806	0.005	0.005	0.000	0.000	0.000	0.000
79	A	81	ALA	0	0.012	-0.007	22.102	0.009	0.009	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.877	0.950	25.223	0.119	0.119	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.016	0.004	26.905	0.001	0.001	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.804	0.872	29.475	0.105	0.105	0.000	0.000	0.000	0.000
83	A	85	MET	0	0.006	0.005	32.832	0.006	0.006	0.000	0.000	0.000	0.000
84	A	86	MET	0	-0.056	-0.012	29.981	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.916	0.959	33.377	0.065	0.065	0.000	0.000	0.000	0.000
86	A	88	GLY	0	-0.007	0.002	34.841	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.902	-0.954	30.920	-0.043	-0.043	0.000	0.000	0.000	0.000
88	A	90	PHE	0	-0.060	-0.027	30.115	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.006	-0.007	27.357	0.003	0.003	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.043	-0.017	30.639	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.009	-0.005	25.874	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.805	-0.881	29.110	-0.106	-0.106	0.000	0.000	0.000	0.000
93	A	95	TYR	0	0.017	0.008	24.344	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.004	-0.007	27.453	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	97	ALA	0	-0.034	0.001	25.167	0.002	0.002	0.000	0.000	0.000	0.000
96	A	98	CYS	0	-0.040	-0.021	22.969	-0.025	-0.025	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.876	-0.915	25.185	-0.189	-0.189	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.047	-0.027	26.975	0.013	0.013	0.000	0.000	0.000	0.000
99	A	101	THR	0	-0.055	-0.042	28.872	0.002	0.002	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.007	0.008	28.887	0.011	0.011	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.033	-0.041	30.962	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.794	-0.851	27.584	-0.153	-0.153	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.029	-0.013	30.846	0.002	0.002	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.008	0.002	26.003	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	107	THR	0	0.010	-0.030	26.676	0.005	0.005	0.000	0.000	0.000	0.000
106	A	108	PHE	0	0.039	0.014	22.435	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	109	GLU	-1	-0.836	-0.896	21.430	-0.084	-0.084	0.000	0.000	0.000	0.000
108	A	110	ARG	1	0.738	0.843	20.389	0.145	0.145	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.014	-0.004	21.428	-0.024	-0.024	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.740	0.849	12.648	0.416	0.416	0.000	0.000	0.000	0.000
111	A	113	PRO	0	0.054	0.025	18.294	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	114	VAL	0	-0.007	0.008	17.735	-0.023	-0.023	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.068	-0.049	10.523	0.080	0.080	0.000	0.000	0.000	0.000
114	A	116	GLN	0	0.059	0.015	14.720	-0.026	-0.026	0.000	0.000	0.000	0.000
115	A	117	ASN	0	-0.075	-0.008	8.811	0.085	0.085	0.000	0.000	0.000	0.000
116	A	118	LYS	1	0.864	0.928	11.740	0.253	0.253	0.000	0.000	0.000	0.000
117	A	119	THR	0	0.005	0.000	10.501	-0.045	-0.045	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.046	0.033	6.997	0.089	0.089	0.000	0.000	0.000	0.000
119	A	121	LYS	1	0.840	0.930	9.797	0.460	0.460	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)