FMO DATABASE

FMODB ID: LJV39

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1000627.527674
FMO2-HF: Nuclear repulsion	952023.929763
FMO2-HF: Total energy	-48603.597912
FMO2-MP2: Total energy	-48745.541077

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.
-9.373	-1.753	3.703	-3.817	-7.508	-0.018

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 : 0.015 / q_NPA : 0.002

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	-0.021	-0.012	2.833	-4.004	-0.838	0.385	-1.484	-2.068	-0.005
4	A	6	GLU	-1	-0.761	-0.879	5.017	0.160	0.260	-0.001	-0.008	-0.091	0.000
5	A	7	VAL	0	0.016	-0.008	8.883	-0.104	-0.104	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.873	0.952	11.336	0.443	0.443	0.000	0.000	0.000	0.000
7	A	9	GLY	0	0.014	-0.003	14.859	-0.008	-0.008	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.014	-0.025	17.457	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.010	-0.009	19.951	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	12	GLY	0	0.012	0.005	19.716	0.013	0.013	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.041	0.032	18.205	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	14	PHE	0	-0.035	-0.030	11.842	-0.043	-0.043	0.000	0.000	0.000	0.000
13	A	15	TYR	0	-0.015	0.022	13.126	0.053	0.053	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.918	0.972	8.734	-0.840	-0.840	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.045	0.014	7.842	0.138	0.138	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.028	-0.018	2.689	-0.711	0.333	0.220	-0.366	-0.898	0.002
17	A	19	ILE	0	-0.011	0.001	2.139	-0.547	0.266	2.701	-0.866	-2.648	-0.006
18	A	20	LYS	1	0.851	0.929	3.041	-3.045	-1.394	0.078	-0.899	-0.830	-0.009
19	A	21	ASP	-1	-0.851	-0.942	5.661	-0.604	-0.604	0.000	0.000	0.000	0.000
20	A	22	VAL	0	-0.064	-0.021	6.353	-0.194	-0.194	0.000	0.000	0.000	0.000
21	A	23	HIS	0	0.017	0.014	8.998	0.105	0.105	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.911	-0.956	11.973	-0.453	-0.453	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.915	-0.991	14.019	-0.409	-0.409	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.040	-0.011	12.661	0.036	0.036	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.010	-0.016	5.718	-0.113	-0.113	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.009	0.018	9.047	0.188	0.188	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.009	0.003	7.266	-0.386	-0.386	0.000	0.000	0.000	0.000
28	A	30	VAL	0	0.024	0.010	7.166	0.247	0.247	0.000	0.000	0.000	0.000
29	A	31	PHE	0	-0.002	-0.006	8.049	-0.069	-0.069	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.940	-0.961	9.073	0.998	0.998	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.019	-0.057	11.237	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	34	ASN	0	0.015	0.006	14.776	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	35	TRP	0	-0.035	-0.001	17.146	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	36	GLN	0	0.003	0.013	15.084	0.005	0.005	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.013	0.013	14.636	0.024	0.024	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.872	-0.961	10.847	-0.270	-0.270	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.903	0.959	11.924	0.380	0.380	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.011	0.010	12.006	-0.078	-0.078	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.078	-0.038	10.941	0.084	0.084	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.080	0.061	12.020	-0.071	-0.071	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.073	0.044	8.841	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	44	ASN	0	-0.029	-0.012	10.821	-0.049	-0.049	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.946	-1.001	12.419	-0.324	-0.324	0.000	0.000	0.000	0.000
44	A	46	VAL	0	0.004	0.028	6.503	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.807	0.884	7.939	0.440	0.440	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.024	0.023	2.701	-1.098	-0.252	0.320	-0.194	-0.973	0.000
47	A	49	PRO	0	0.032	0.049	4.941	0.233	0.233	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.027	-0.003	7.656	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	51	PRO	0	-0.022	-0.001	9.478	0.075	0.075	0.000	0.000	0.000	0.000
50	A	52	PRO	0	0.006	-0.011	10.337	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.813	-0.881	13.356	0.051	0.051	0.000	0.000	0.000	0.000
52	A	54	ILE	0	-0.020	-0.009	16.673	0.007	0.007	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.880	0.916	17.675	-0.098	-0.098	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.855	0.915	22.306	-0.046	-0.046	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.881	-0.903	25.111	0.006	0.006	0.000	0.000	0.000	0.000
56	A	58	ILE	0	-0.047	-0.032	22.902	0.005	0.005	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.018	-0.015	25.768	0.007	0.007	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.793	-0.902	28.345	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.054	-0.001	30.890	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.863	-0.937	25.252	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.979	-1.017	23.029	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.025	-0.006	21.473	0.001	0.001	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.753	-0.855	16.066	-0.186	-0.186	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.007	-0.030	19.964	0.021	0.021	0.000	0.000	0.000	0.000
65	A	67	TYR	0	-0.006	0.016	15.594	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	68	SER	0	0.001	-0.007	19.923	0.021	0.021	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.825	0.932	20.945	-0.048	-0.048	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.049	0.050	23.415	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.045	-0.045	26.514	0.015	0.015	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.854	-0.933	28.269	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	73	GLN	0	0.003	0.004	23.278	-0.024	-0.024	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.832	-0.927	24.131	0.043	0.043	0.000	0.000	0.000	0.000
73	A	75	PRO	0	-0.039	-0.012	19.112	0.018	0.018	0.000	0.000	0.000	0.000
74	A	76	CYS	0	-0.031	-0.026	19.026	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.000	0.008	16.029	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	78	TRP	0	-0.048	-0.026	13.641	0.023	0.023	0.000	0.000	0.000	0.000
77	A	79	TRP	0	0.020	-0.005	17.128	-0.041	-0.041	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.025	0.023	20.026	0.008	0.008	0.000	0.000	0.000	0.000
79	A	81	ALA	0	0.011	-0.004	21.872	0.007	0.007	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.878	0.948	24.970	0.050	0.050	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.018	0.009	26.621	0.005	0.005	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.849	0.906	29.128	0.026	0.026	0.000	0.000	0.000	0.000
83	A	85	MET	0	0.005	-0.003	32.558	0.001	0.001	0.000	0.000	0.000	0.000
84	A	86	MET	0	-0.058	-0.012	30.192	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.920	0.968	33.206	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	88	GLY	0	-0.005	-0.002	34.911	0.001	0.001	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.893	-0.948	31.022	0.051	0.051	0.000	0.000	0.000	0.000
88	A	90	PHE	0	-0.074	-0.034	30.182	0.002	0.002	0.000	0.000	0.000	0.000
89	A	91	TYR	0	0.005	-0.004	27.446	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.045	-0.017	30.470	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.027	-0.010	25.638	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.838	-0.923	28.840	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	95	TYR	0	0.008	-0.003	24.883	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.005	-0.008	27.230	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	97	ALA	0	-0.041	-0.003	24.988	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	98	CYS	0	-0.032	-0.018	22.745	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.883	-0.921	25.061	-0.101	-0.101	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.048	-0.029	26.970	0.008	0.008	0.000	0.000	0.000	0.000
99	A	101	THR	0	-0.046	-0.033	28.868	0.005	0.005	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.005	0.004	28.729	0.005	0.005	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.008	-0.015	30.689	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.822	-0.900	27.481	0.017	0.017	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.032	-0.011	30.524	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.007	0.013	25.907	0.005	0.005	0.000	0.000	0.000	0.000
105	A	107	THR	0	0.053	0.009	26.656	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	108	PHE	0	0.047	0.017	22.704	0.001	0.001	0.000	0.000	0.000	0.000
107	A	109	GLU	-1	-0.876	-0.939	21.497	0.099	0.099	0.000	0.000	0.000	0.000
108	A	110	ARG	1	0.732	0.850	20.469	-0.025	-0.025	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.012	-0.005	21.319	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.752	0.873	12.604	0.127	0.127	0.000	0.000	0.000	0.000
111	A	113	PRO	0	0.047	0.025	17.786	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	114	VAL	0	0.010	0.015	17.400	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.066	-0.040	10.201	0.024	0.024	0.000	0.000	0.000	0.000
114	A	116	GLN	0	0.050	0.022	14.392	-0.030	-0.030	0.000	0.000	0.000	0.000
115	A	117	ASN	0	-0.109	-0.043	8.559	0.039	0.039	0.000	0.000	0.000	0.000
116	A	118	LYS	1	0.887	0.943	11.199	0.280	0.280	0.000	0.000	0.000	0.000
117	A	119	THR	0	-0.023	-0.015	9.951	-0.059	-0.059	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.048	0.030	6.528	0.061	0.061	0.000	0.000	0.000	0.000
119	A	121	LYS	1	0.856	0.942	9.463	0.535	0.535	0.000	0.000	0.000	0.000

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