FMO DATABASE

FMODB ID: 6YYLZ

Calculation Name: 3N53-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N53

Chain ID: B

ChEMBL ID:

UniProt ID: Q3A6W4

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742815.871344
FMO2-HF: Nuclear repulsion	704386.662155
FMO2-HF: Total energy	-38429.209189
FMO2-MP2: Total energy	-38542.816571

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(B:1:LEU)

Summations of interaction energy for fragment #1(B:1: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.
-11.056	-4.233	1.849	-3.049	-5.622	-0.019

Interaction energy analysis for fragmet #1(B:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / 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

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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	B	3	LYS	1	0.960	0.980	3.459	-1.988	-0.074	0.012	-0.860	-1.066	0.001
4	B	4	ILE	0	0.017	0.023	5.625	0.526	0.526	0.000	0.000	0.000	0.000
5	B	5	LEU	0	-0.025	-0.004	8.435	-0.055	-0.055	0.000	0.000	0.000	0.000
6	B	6	ILE	0	0.013	0.004	11.549	0.076	0.076	0.000	0.000	0.000	0.000
7	B	7	ILE	0	-0.024	-0.014	14.043	0.025	0.025	0.000	0.000	0.000	0.000
8	B	8	ASP	-1	-0.757	-0.901	17.656	-0.284	-0.284	0.000	0.000	0.000	0.000
9	B	9	GLN	0	0.012	0.004	20.054	-0.004	-0.004	0.000	0.000	0.000	0.000
10	B	10	GLN	0	-0.048	-0.038	22.716	0.009	0.009	0.000	0.000	0.000	0.000
11	B	11	ASP	-1	-0.789	-0.893	20.439	-0.292	-0.292	0.000	0.000	0.000	0.000
12	B	12	PHE	0	-0.020	-0.005	19.536	-0.031	-0.031	0.000	0.000	0.000	0.000
13	B	13	SER	0	0.007	0.004	19.695	-0.014	-0.014	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.821	0.904	15.970	0.342	0.342	0.000	0.000	0.000	0.000
15	B	15	ILE	0	-0.058	-0.037	15.236	-0.066	-0.066	0.000	0.000	0.000	0.000
16	B	16	GLU	-1	-0.947	-0.960	14.669	-0.416	-0.416	0.000	0.000	0.000	0.000
17	B	17	LEU	0	-0.042	-0.023	13.400	-0.029	-0.029	0.000	0.000	0.000	0.000
18	B	18	LYS	1	0.908	0.964	10.218	0.579	0.579	0.000	0.000	0.000	0.000
19	B	19	ASN	0	0.012	-0.016	10.121	-0.177	-0.177	0.000	0.000	0.000	0.000
20	B	20	PHE	0	-0.064	-0.024	11.164	-0.029	-0.029	0.000	0.000	0.000	0.000
21	B	21	LEU	0	-0.005	-0.013	8.216	-0.004	-0.004	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.851	-0.938	6.307	-1.705	-1.705	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.142	-0.055	5.242	-0.356	-0.356	0.000	0.000	0.000	0.000
24	B	24	GLU	-1	-0.966	-0.982	3.819	-0.983	-0.725	0.003	-0.059	-0.202	0.000
25	B	25	TYR	0	-0.030	-0.019	2.554	-3.929	-1.435	1.370	-1.526	-2.337	-0.018
26	B	26	LEU	0	-0.021	-0.002	2.630	-1.657	0.397	0.461	-0.577	-1.938	-0.002
27	B	27	VAL	0	0.018	0.007	4.129	0.336	0.439	0.003	-0.027	-0.079	0.000
28	B	28	ILE	0	-0.033	-0.007	7.717	0.188	0.188	0.000	0.000	0.000	0.000
29	B	29	GLU	-1	-0.825	-0.917	10.587	-0.515	-0.515	0.000	0.000	0.000	0.000
30	B	30	SER	0	0.007	0.009	14.206	0.050	0.050	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.879	0.950	17.410	0.239	0.239	0.000	0.000	0.000	0.000
32	B	32	ASN	0	0.001	-0.017	20.791	0.023	0.023	0.000	0.000	0.000	0.000
33	B	33	GLU	-1	-0.823	-0.926	21.281	-0.156	-0.156	0.000	0.000	0.000	0.000
34	B	34	LYS	1	0.893	0.953	22.134	0.152	0.152	0.000	0.000	0.000	0.000
35	B	35	GLU	-1	-0.828	-0.923	19.600	-0.300	-0.300	0.000	0.000	0.000	0.000
36	B	36	ALA	0	0.010	0.010	17.554	-0.022	-0.022	0.000	0.000	0.000	0.000
37	B	37	LEU	0	-0.038	-0.035	17.568	-0.014	-0.014	0.000	0.000	0.000	0.000
38	B	38	GLU	-1	-0.893	-0.939	19.288	-0.196	-0.196	0.000	0.000	0.000	0.000
39	B	39	GLN	0	0.026	-0.001	13.894	0.029	0.029	0.000	0.000	0.000	0.000
40	B	40	ILE	0	-0.050	-0.036	14.281	-0.041	-0.041	0.000	0.000	0.000	0.000
41	B	41	ASP	-1	-0.910	-0.946	15.166	-0.143	-0.143	0.000	0.000	0.000	0.000
42	B	42	HIS	0	-0.042	-0.013	15.372	0.034	0.034	0.000	0.000	0.000	0.000
43	B	43	HIS	0	-0.143	-0.087	10.283	-0.053	-0.053	0.000	0.000	0.000	0.000
44	B	44	HIS	0	-0.050	-0.006	10.411	-0.065	-0.065	0.000	0.000	0.000	0.000
45	B	45	PRO	0	-0.048	-0.012	9.158	-0.042	-0.042	0.000	0.000	0.000	0.000
46	B	46	ASP	-1	-0.853	-0.933	6.436	-0.452	-0.452	0.000	0.000	0.000	0.000
47	B	47	LEU	0	-0.010	-0.011	9.719	0.147	0.147	0.000	0.000	0.000	0.000
48	B	48	VAL	0	0.001	0.009	11.140	-0.145	-0.145	0.000	0.000	0.000	0.000
49	B	49	ILE	0	0.009	0.018	12.343	0.061	0.061	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.012	-0.018	15.377	-0.019	-0.019	0.000	0.000	0.000	0.000
51	B	51	ASP	-1	-0.826	-0.891	18.810	-0.222	-0.222	0.000	0.000	0.000	0.000
52	B	52	MET	0	-0.053	-0.037	21.338	0.012	0.012	0.000	0.000	0.000	0.000
53	B	53	ASP	-1	-0.865	-0.908	24.793	-0.159	-0.159	0.000	0.000	0.000	0.000
54	B	61	ASN	0	0.008	-0.013	28.376	0.003	0.003	0.000	0.000	0.000	0.000
55	B	62	LEU	0	0.050	0.027	23.020	0.004	0.004	0.000	0.000	0.000	0.000
56	B	63	CYS	0	0.029	0.010	22.849	-0.010	-0.010	0.000	0.000	0.000	0.000
57	B	64	LEU	0	0.001	-0.003	23.193	0.001	0.001	0.000	0.000	0.000	0.000
58	B	65	LYS	1	0.851	0.945	24.427	0.112	0.112	0.000	0.000	0.000	0.000
59	B	66	LEU	0	-0.018	0.017	19.323	0.006	0.006	0.000	0.000	0.000	0.000
60	B	75	VAL	0	-0.048	-0.031	13.396	0.024	0.024	0.000	0.000	0.000	0.000
61	B	76	PRO	0	0.006	0.024	13.065	-0.011	-0.011	0.000	0.000	0.000	0.000
62	B	77	LEU	0	-0.006	-0.017	15.080	-0.068	-0.068	0.000	0.000	0.000	0.000
63	B	78	ILE	0	-0.003	-0.009	14.520	0.030	0.030	0.000	0.000	0.000	0.000
64	B	79	LEU	0	-0.007	-0.019	17.992	-0.028	-0.028	0.000	0.000	0.000	0.000
65	B	80	LEU	0	0.008	0.007	17.968	0.008	0.008	0.000	0.000	0.000	0.000
66	B	81	PHE	0	0.007	0.002	21.748	0.005	0.005	0.000	0.000	0.000	0.000
67	B	82	SER	0	-0.013	-0.001	25.419	0.003	0.003	0.000	0.000	0.000	0.000
68	B	97	ALA	0	-0.022	-0.018	21.604	-0.004	-0.004	0.000	0.000	0.000	0.000
69	B	98	ASP	-1	-0.886	-0.943	18.545	-0.050	-0.050	0.000	0.000	0.000	0.000
70	B	99	ASP	-1	-0.805	-0.900	19.151	-0.098	-0.098	0.000	0.000	0.000	0.000
71	B	100	TYR	0	-0.056	-0.029	21.020	-0.014	-0.014	0.000	0.000	0.000	0.000
72	B	101	LEU	0	-0.010	-0.001	18.235	0.004	0.004	0.000	0.000	0.000	0.000
73	B	102	THR	0	-0.026	-0.008	22.318	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	103	LYS	1	0.730	0.846	22.403	0.210	0.210	0.000	0.000	0.000	0.000
75	B	104	PRO	0	-0.017	-0.035	24.161	0.011	0.011	0.000	0.000	0.000	0.000
76	B	105	PHE	0	0.068	0.040	16.934	0.010	0.010	0.000	0.000	0.000	0.000
77	B	106	ASN	0	0.008	-0.006	20.263	-0.039	-0.039	0.000	0.000	0.000	0.000
78	B	107	ARG	1	0.954	0.986	15.837	0.347	0.347	0.000	0.000	0.000	0.000
79	B	108	ASN	0	0.017	-0.001	15.351	-0.039	-0.039	0.000	0.000	0.000	0.000
80	B	109	ASP	-1	-0.885	-0.927	15.675	-0.138	-0.138	0.000	0.000	0.000	0.000
81	B	110	LEU	0	0.034	0.021	13.608	0.018	0.018	0.000	0.000	0.000	0.000
82	B	111	LEU	0	0.032	0.014	9.536	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	112	SER	0	0.017	0.030	11.714	0.042	0.042	0.000	0.000	0.000	0.000
84	B	113	ARG	1	0.861	0.911	14.154	0.165	0.165	0.000	0.000	0.000	0.000
85	B	114	ILE	0	0.019	0.022	9.009	0.042	0.042	0.000	0.000	0.000	0.000
86	B	115	GLU	-1	-0.926	-0.970	9.485	-0.056	-0.056	0.000	0.000	0.000	0.000
87	B	116	ILE	0	-0.084	-0.053	10.988	0.147	0.147	0.000	0.000	0.000	0.000
88	B	117	HIS	0	-0.033	-0.037	13.614	0.074	0.074	0.000	0.000	0.000	0.000
89	B	118	LEU	0	-0.017	-0.005	6.937	0.069	0.069	0.000	0.000	0.000	0.000
90	B	119	ARG	1	0.909	0.948	10.815	-0.185	-0.185	0.000	0.000	0.000	0.000
91	B	120	THR	0	-0.035	0.000	12.101	0.056	0.056	0.000	0.000	0.000	0.000
92	B	121	GLN	0	-0.014	0.005	12.972	-0.016	-0.016	0.000	0.000	0.000	0.000
93	B	122	ASN	0	-0.110	-0.042	9.302	0.056	0.056	0.000	0.000	0.000	0.000

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