FMO DATABASE

FMODB ID: M3L1Z

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	OptAll
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	-1003752.614126
FMO2-HF: Nuclear repulsion	955147.645898
FMO2-HF: Total energy	-48604.968228
FMO2-MP2: Total energy	-48746.716496

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.
-8.768	-0.0010000000000006	1.637	-3.934	-6.471	-0.013

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 : 0.047 / q_NPA : 0.033

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	-0.036	-0.022	2.973	-2.826	0.271	0.230	-1.614	-1.713	-0.002
4	A	6	GLU	-1	-0.761	-0.865	4.997	-0.409	-0.305	-0.001	-0.008	-0.095	0.000
5	A	7	VAL	0	0.019	0.006	8.698	0.023	0.023	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.881	0.947	11.093	0.538	0.538	0.000	0.000	0.000	0.000
7	A	9	GLY	0	0.050	0.027	14.685	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.040	-0.035	17.517	0.018	0.018	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.006	-0.018	19.867	0.001	0.001	0.000	0.000	0.000	0.000
10	A	12	GLY	0	-0.004	0.002	19.767	0.021	0.021	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.021	0.025	18.280	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	14	PHE	0	-0.018	-0.024	11.937	-0.037	-0.037	0.000	0.000	0.000	0.000
13	A	15	TYR	0	-0.027	-0.005	13.187	0.046	0.046	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.838	0.900	8.735	0.683	0.683	0.000	0.000	0.000	0.000
15	A	17	GLY	0	0.043	0.020	8.221	0.297	0.297	0.000	0.000	0.000	0.000
16	A	18	PHE	0	-0.067	-0.029	2.799	-1.278	-0.224	0.163	-0.428	-0.789	0.003
17	A	19	ILE	0	0.000	0.002	2.371	-0.541	1.324	1.017	-0.646	-2.237	-0.002
18	A	20	LYS	1	0.761	0.862	2.869	-3.073	-1.159	0.162	-1.102	-0.974	-0.012
19	A	21	ASP	-1	-0.833	-0.914	5.691	0.350	0.350	0.000	0.000	0.000	0.000
20	A	22	VAL	0	-0.073	-0.041	6.239	-0.329	-0.329	0.000	0.000	0.000	0.000
21	A	23	HIS	0	-0.006	-0.008	9.276	0.081	0.081	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.918	-0.970	12.054	-0.152	-0.152	0.000	0.000	0.000	0.000
23	A	25	ASP	-1	-0.925	-0.939	14.578	-0.296	-0.296	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.048	-0.041	12.484	-0.050	-0.050	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.032	-0.013	6.050	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	28	THR	0	0.030	0.017	9.164	0.067	0.067	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.034	-0.022	6.918	-0.456	-0.456	0.000	0.000	0.000	0.000
28	A	30	VAL	0	0.041	0.017	7.331	0.431	0.431	0.000	0.000	0.000	0.000
29	A	31	PHE	0	0.014	0.004	8.364	-0.431	-0.431	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.860	-0.910	9.137	-0.820	-0.820	0.000	0.000	0.000	0.000
31	A	33	ASN	0	-0.027	-0.044	11.272	0.193	0.193	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.015	-0.014	14.969	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	35	TRP	0	0.020	0.013	17.468	0.040	0.040	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.015	0.014	15.226	-0.040	-0.040	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.012	-0.001	14.613	-0.072	-0.072	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.809	-0.886	10.760	-0.686	-0.686	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.827	0.897	12.039	0.739	0.739	0.000	0.000	0.000	0.000
38	A	40	GLN	0	0.006	0.016	11.846	-0.117	-0.117	0.000	0.000	0.000	0.000
39	A	41	VAL	0	-0.060	-0.028	11.379	0.061	0.061	0.000	0.000	0.000	0.000
40	A	42	PRO	0	0.078	0.060	11.900	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	43	PHE	0	0.074	0.017	8.385	-0.088	-0.088	0.000	0.000	0.000	0.000
42	A	44	ASN	0	-0.026	-0.012	11.388	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	45	GLU	-1	-0.845	-0.907	13.127	-0.529	-0.529	0.000	0.000	0.000	0.000
44	A	46	VAL	0	0.019	0.023	7.169	-0.072	-0.072	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.792	0.887	8.272	0.760	0.760	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.060	0.032	3.156	-1.046	-0.313	0.066	-0.136	-0.663	0.000
47	A	49	PRO	0	0.028	0.038	4.941	0.254	0.254	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.013	0.009	7.593	0.089	0.089	0.000	0.000	0.000	0.000
49	A	51	PRO	0	-0.010	-0.004	9.569	0.028	0.028	0.000	0.000	0.000	0.000
50	A	52	PRO	0	-0.015	-0.008	10.427	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.783	-0.878	13.263	-0.098	-0.098	0.000	0.000	0.000	0.000
52	A	54	ILE	0	-0.020	-0.015	16.509	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	55	LYS	1	0.861	0.908	17.764	0.127	0.127	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.829	0.908	22.158	0.015	0.015	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.862	-0.884	24.980	-0.052	-0.052	0.000	0.000	0.000	0.000
56	A	58	ILE	0	-0.037	-0.033	22.535	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.027	-0.024	25.398	0.001	0.001	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.824	-0.927	28.384	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.008	0.004	30.552	0.004	0.004	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.828	-0.910	24.822	-0.110	-0.110	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.943	-0.954	22.821	-0.173	-0.173	0.000	0.000	0.000	0.000
62	A	64	VAL	0	-0.023	-0.019	21.279	0.002	0.002	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.736	-0.840	15.782	-0.438	-0.438	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.010	-0.006	19.743	0.014	0.014	0.000	0.000	0.000	0.000
65	A	67	TYR	0	-0.004	0.004	16.124	-0.043	-0.043	0.000	0.000	0.000	0.000
66	A	68	SER	0	0.015	-0.024	19.930	0.035	0.035	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.823	0.920	21.136	0.187	0.187	0.000	0.000	0.000	0.000
68	A	70	ALA	0	0.069	0.064	23.509	0.001	0.001	0.000	0.000	0.000	0.000
69	A	71	ASN	0	-0.041	-0.043	26.636	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	72	ASP	-1	-0.852	-0.931	28.162	-0.196	-0.196	0.000	0.000	0.000	0.000
71	A	73	GLN	0	0.019	0.011	23.371	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.864	-0.935	23.793	-0.234	-0.234	0.000	0.000	0.000	0.000
73	A	75	PRO	0	-0.039	-0.023	19.197	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	76	CYS	0	-0.035	0.001	18.599	0.016	0.016	0.000	0.000	0.000	0.000
75	A	77	GLY	0	0.032	0.016	16.255	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	78	TRP	0	-0.042	-0.026	13.907	0.073	0.073	0.000	0.000	0.000	0.000
77	A	79	TRP	0	0.001	-0.008	17.212	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	80	LEU	0	0.015	0.008	19.147	0.011	0.011	0.000	0.000	0.000	0.000
79	A	81	ALA	0	-0.003	-0.007	21.632	0.010	0.010	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.804	0.892	24.801	0.135	0.135	0.000	0.000	0.000	0.000
81	A	83	VAL	0	0.003	0.009	26.379	0.002	0.002	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.790	0.861	28.922	0.118	0.118	0.000	0.000	0.000	0.000
83	A	85	MET	0	0.000	0.002	32.492	0.007	0.007	0.000	0.000	0.000	0.000
84	A	86	MET	0	-0.043	0.006	29.697	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.910	0.955	33.200	0.083	0.083	0.000	0.000	0.000	0.000
86	A	88	GLY	0	0.000	0.008	34.695	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.890	-0.952	30.361	-0.065	-0.065	0.000	0.000	0.000	0.000
88	A	90	PHE	0	-0.059	-0.025	29.697	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	91	TYR	0	-0.009	-0.017	27.150	0.005	0.005	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.042	-0.019	30.117	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	93	ILE	0	-0.020	-0.009	26.267	0.001	0.001	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.787	-0.862	28.942	-0.120	-0.120	0.000	0.000	0.000	0.000
93	A	95	TYR	0	-0.007	-0.025	23.986	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	96	ALA	0	0.021	0.004	27.087	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	97	ALA	0	-0.028	-0.002	24.899	0.002	0.002	0.000	0.000	0.000	0.000
96	A	98	CYS	0	-0.048	-0.027	22.622	-0.026	-0.026	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.878	-0.915	24.765	-0.199	-0.199	0.000	0.000	0.000	0.000
98	A	100	ALA	0	-0.047	-0.027	26.761	0.014	0.014	0.000	0.000	0.000	0.000
99	A	101	THR	0	-0.057	-0.044	28.626	0.001	0.001	0.000	0.000	0.000	0.000
100	A	102	TYR	0	0.014	0.018	28.498	0.012	0.012	0.000	0.000	0.000	0.000
101	A	103	ASN	0	-0.058	-0.052	30.669	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.779	-0.838	27.717	-0.180	-0.180	0.000	0.000	0.000	0.000
103	A	105	ILE	0	-0.032	-0.018	31.145	0.005	0.005	0.000	0.000	0.000	0.000
104	A	106	VAL	0	-0.014	-0.002	25.783	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	107	THR	0	0.010	-0.028	26.391	0.008	0.008	0.000	0.000	0.000	0.000
106	A	108	PHE	0	0.039	0.016	21.940	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	109	GLU	-1	-0.847	-0.898	21.258	-0.128	-0.128	0.000	0.000	0.000	0.000
108	A	110	ARG	1	0.758	0.861	20.287	0.174	0.174	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.021	-0.008	21.026	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.727	0.838	12.357	0.496	0.496	0.000	0.000	0.000	0.000
111	A	113	PRO	0	0.059	0.028	18.308	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	114	VAL	0	-0.027	0.000	17.285	-0.025	-0.025	0.000	0.000	0.000	0.000
113	A	115	ASN	0	-0.039	-0.039	10.135	0.094	0.094	0.000	0.000	0.000	0.000
114	A	116	GLN	0	0.039	0.014	14.264	-0.033	-0.033	0.000	0.000	0.000	0.000
115	A	117	ASN	0	-0.061	-0.007	8.269	0.125	0.125	0.000	0.000	0.000	0.000
116	A	118	LYS	1	0.852	0.912	11.506	0.215	0.215	0.000	0.000	0.000	0.000
117	A	119	THR	0	0.005	0.005	10.141	-0.033	-0.033	0.000	0.000	0.000	0.000
118	A	120	VAL	0	0.037	0.036	6.520	0.106	0.106	0.000	0.000	0.000	0.000
119	A	121	LYS	1	0.847	0.923	9.215	0.418	0.418	0.000	0.000	0.000	0.000

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