FMO DATABASE

FMODB ID: LZJN9

Calculation Name: 2YX8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YX8

Chain ID: A

ChEMBL ID:

UniProt ID: O60894

Base Structure: X-ray

Registration Date: 2023-06-21

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-558700.027246
FMO2-HF: Nuclear repulsion	523876.143292
FMO2-HF: Total energy	-34823.883954
FMO2-MP2: Total energy	-34920.31901

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:27:CYS)

Summations of interaction energy for fragment #1(A:27:CYS)

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.
-43.33	-31.914	21.592	-9.888	-23.121	-0.049

Interaction energy analysis for fragmet #1(A:27:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : 0.011

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	29	GLU	-1	-0.906	-1.002	2.369	-1.804	4.244	4.111	-3.964	-6.195	0.007
4	A	30	ALA	0	-0.011	0.004	3.787	0.393	-0.945	0.024	1.844	-0.530	-0.001
5	A	31	ASN	0	0.017	-0.019	5.830	0.370	0.370	0.000	0.000	0.000	0.000
6	A	32	TYR	0	0.023	0.010	3.331	-2.353	-0.424	2.935	-1.020	-3.844	-0.007
7	A	33	GLY	0	0.067	0.028	5.307	-1.041	-0.988	-0.002	-0.022	-0.030	0.000
8	A	34	ALA	0	-0.072	-0.027	8.189	-0.409	-0.409	0.000	0.000	0.000	0.000
9	A	35	LEU	0	0.048	0.026	6.838	-0.276	-0.276	0.000	0.000	0.000	0.000
10	A	36	LEU	0	0.015	0.012	6.904	-0.408	-0.408	0.000	0.000	0.000	0.000
11	A	37	ARG	1	0.884	0.937	9.798	-0.338	-0.338	0.000	0.000	0.000	0.000
12	A	38	GLU	-1	-0.912	-0.973	12.832	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	39	LEU	0	-0.029	-0.006	11.707	-0.065	-0.065	0.000	0.000	0.000	0.000
14	A	40	CYS	0	-0.051	-0.003	10.475	-0.501	-0.501	0.000	0.000	0.000	0.000
15	A	41	LEU	0	-0.052	-0.017	13.529	0.022	0.022	0.000	0.000	0.000	0.000
16	A	42	THR	0	0.003	-0.003	15.642	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	43	GLN	0	-0.023	-0.015	17.482	0.016	0.016	0.000	0.000	0.000	0.000
18	A	44	PHE	0	0.021	0.002	17.350	0.024	0.024	0.000	0.000	0.000	0.000
19	A	45	GLN	0	-0.070	-0.044	19.257	0.030	0.030	0.000	0.000	0.000	0.000
20	A	46	VAL	0	0.032	0.039	21.740	0.023	0.023	0.000	0.000	0.000	0.000
21	A	47	ASP	-1	-0.874	-0.930	21.404	-0.389	-0.389	0.000	0.000	0.000	0.000
22	A	48	MET	0	-0.028	-0.020	21.936	0.014	0.014	0.000	0.000	0.000	0.000
23	A	49	GLU	-1	-0.991	-0.975	24.722	-0.106	-0.106	0.000	0.000	0.000	0.000
24	A	50	ALA	0	-0.044	-0.025	27.276	0.013	0.013	0.000	0.000	0.000	0.000
25	A	51	VAL	0	-0.081	-0.018	26.644	0.007	0.007	0.000	0.000	0.000	0.000
26	A	52	GLY	0	0.051	0.022	29.129	0.012	0.012	0.000	0.000	0.000	0.000
27	A	53	GLU	-1	-0.887	-0.956	28.809	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	54	THR	0	-0.063	-0.043	29.724	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	55	LEU	0	-0.047	-0.033	31.019	0.002	0.002	0.000	0.000	0.000	0.000
30	A	56	TRP	0	0.024	0.001	25.783	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	57	CYS	0	-0.053	-0.012	26.184	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	58	ASP	-1	-0.874	-0.925	28.138	-0.168	-0.168	0.000	0.000	0.000	0.000
33	A	59	TRP	0	0.065	0.028	22.184	-0.023	-0.023	0.000	0.000	0.000	0.000
34	A	60	GLY	0	-0.025	0.000	26.392	-0.027	-0.027	0.000	0.000	0.000	0.000
35	A	61	ARG	1	0.870	0.934	28.333	0.150	0.150	0.000	0.000	0.000	0.000
36	A	62	THR	0	0.006	0.007	23.663	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	63	ILE	0	-0.003	0.001	21.449	-0.032	-0.032	0.000	0.000	0.000	0.000
38	A	64	ARG	1	0.936	0.980	21.050	0.398	0.398	0.000	0.000	0.000	0.000
39	A	65	SER	0	0.036	0.007	20.131	-0.052	-0.052	0.000	0.000	0.000	0.000
40	A	66	TYR	0	-0.029	-0.036	16.988	-0.056	-0.056	0.000	0.000	0.000	0.000
41	A	67	ARG	1	0.903	0.950	16.443	0.676	0.676	0.000	0.000	0.000	0.000
42	A	68	GLU	-1	-0.890	-0.949	15.570	-0.874	-0.874	0.000	0.000	0.000	0.000
43	A	69	LEU	0	-0.020	0.000	13.581	-0.120	-0.120	0.000	0.000	0.000	0.000
44	A	70	ALA	0	-0.009	-0.009	11.834	-0.104	-0.104	0.000	0.000	0.000	0.000
45	A	71	ASP	-1	-0.821	-0.904	10.592	-1.381	-1.381	0.000	0.000	0.000	0.000
46	A	73	THR	0	-0.031	-0.036	7.923	-0.314	-0.314	0.000	0.000	0.000	0.000
47	A	74	TRP	0	0.000	0.007	6.063	-0.863	-0.863	0.000	0.000	0.000	0.000
48	A	75	HIS	0	0.005	-0.006	6.292	-1.140	-1.140	0.000	0.000	0.000	0.000
49	A	76	MET	0	-0.037	-0.026	6.433	-1.223	-1.223	0.000	0.000	0.000	0.000
50	A	77	ALA	0	-0.011	-0.001	2.366	-1.550	0.141	1.164	-0.936	-1.919	-0.003
51	A	78	GLU	-1	-0.887	-0.937	1.839	-20.286	-24.326	9.924	-2.301	-3.583	-0.043
52	A	79	LYS	1	0.896	0.948	3.316	-0.838	-1.307	0.157	0.898	-0.586	-0.006
53	A	80	LEU	0	-0.079	-0.045	2.449	-2.553	0.259	3.036	-1.992	-3.856	-0.003
56	A	84	TRP	0	-0.002	0.032	3.293	-6.883	-2.944	0.099	-2.141	-1.897	0.009
57	A	85	PRO	0	0.025	-0.002	5.884	0.434	0.434	0.000	0.000	0.000	0.000
58	A	86	ASN	0	0.020	-0.022	3.084	0.744	1.535	0.144	-0.254	-0.681	-0.002
59	A	87	ALA	0	0.097	0.032	5.800	-0.157	-0.157	0.000	0.000	0.000	0.000
60	A	88	GLU	-1	-0.898	-0.924	5.864	1.011	1.011	0.000	0.000	0.000	0.000
61	A	89	VAL	0	0.032	-0.003	6.275	-0.229	-0.229	0.000	0.000	0.000	0.000
62	A	90	ASP	-1	-0.894	-0.940	7.921	0.059	0.059	0.000	0.000	0.000	0.000
63	A	91	ARG	1	0.844	0.913	10.485	-0.864	-0.864	0.000	0.000	0.000	0.000
64	A	92	PHE	0	-0.032	-0.017	10.550	-0.060	-0.060	0.000	0.000	0.000	0.000
65	A	93	PHE	0	0.068	0.011	10.439	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	94	LEU	0	-0.007	0.011	14.043	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	95	ALA	0	-0.033	-0.014	15.588	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	96	VAL	0	-0.018	-0.001	15.388	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	97	HIS	0	0.045	0.037	17.893	-0.058	-0.058	0.000	0.000	0.000	0.000
70	A	98	GLY	0	0.001	0.010	19.864	0.000	0.000	0.000	0.000	0.000	0.000
71	A	99	ARG	1	0.875	0.936	21.062	0.035	0.035	0.000	0.000	0.000	0.000
72	A	100	TYR	0	0.004	-0.009	20.038	0.004	0.004	0.000	0.000	0.000	0.000
73	A	101	PHE	0	-0.008	-0.005	19.486	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	102	ARG	1	0.953	0.990	23.973	0.028	0.028	0.000	0.000	0.000	0.000
75	A	103	SER	0	-0.021	-0.028	26.397	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	105	PRO	0	0.026	0.007	28.750	0.005	0.005	0.000	0.000	0.000	0.000
77	A	106	ILE	0	0.016	0.022	28.988	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	107	SER	0	-0.021	-0.010	31.268	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:27:CYS)