FMO DATABASE

FMODB ID: 6Y6MZ

Calculation Name: 2BK8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BK8

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WZ42

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-701802.128198
FMO2-HF: Nuclear repulsion	662630.327843
FMO2-HF: Total energy	-39171.800354
FMO2-MP2: Total energy	-39284.728972

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
3.874	-10.592	20.997	-0.669	-5.859	-0.055

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.008

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	2	MET	0	-0.032	-0.032	1.874	2.580	-9.832	11.453	4.626	-3.667	-0.044
4	A	3	VAL	0	-0.005	0.009	3.995	-1.051	-1.063	0.000	0.001	0.012	0.000
5	A	4	SER	0	-0.011	-0.006	6.723	0.453	0.453	0.000	0.000	0.000	0.000
6	A	5	GLY	0	0.025	0.015	9.970	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.050	-0.037	12.321	-0.010	-0.010	0.000	0.000	0.000	0.000
8	A	7	ILE	0	0.002	0.013	15.994	0.047	0.047	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.031	-0.018	18.663	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	9	HIS	0	0.042	0.024	22.294	0.013	0.013	0.000	0.000	0.000	0.000
11	A	10	ALA	0	0.001	0.005	25.436	0.011	0.011	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.023	-0.009	28.226	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	12	GLY	0	0.025	0.016	32.016	0.008	0.008	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.985	-0.996	33.290	0.032	0.032	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.878	-0.951	36.717	0.023	0.023	0.000	0.000	0.000	0.000
16	A	15	GLY	0	-0.026	-0.009	38.148	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.008	0.009	35.992	0.005	0.005	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.018	-0.018	30.814	0.003	0.003	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.021	0.003	27.274	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.935	0.976	24.023	-0.120	-0.120	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.044	-0.031	20.863	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.001	-0.009	17.532	0.019	0.019	0.000	0.000	0.000	0.000
23	A	22	CYS	0	-0.053	-0.021	13.638	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.963	0.985	11.910	-0.484	-0.484	0.000	0.000	0.000	0.000
25	A	24	ILE	0	0.009	-0.006	7.065	-0.134	-0.134	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.942	-0.959	5.837	1.090	1.090	0.000	0.000	0.000	0.000
27	A	26	ASN	0	-0.016	-0.035	2.077	-1.795	-4.586	9.539	-5.059	-1.688	-0.011
28	A	27	TYR	0	-0.002	0.020	3.810	1.827	2.307	0.005	-0.188	-0.297	0.000
29	A	28	ASP	-1	-0.848	-0.939	6.135	3.553	3.553	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.062	-0.047	8.024	-0.519	-0.519	0.000	0.000	0.000	0.000
31	A	30	SER	0	0.020	0.024	8.032	-0.373	-0.373	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.029	-0.014	7.962	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.002	0.007	9.848	-0.085	-0.085	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.015	-0.010	12.671	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.031	-0.009	14.745	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	35	TRP	0	0.057	0.011	17.610	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	36	TYR	0	-0.021	-0.019	18.419	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	37	PHE	0	0.008	0.030	22.726	0.001	0.001	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.026	0.009	25.919	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.055	-0.041	25.130	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.921	0.966	26.356	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	41	GLN	0	0.034	0.021	22.162	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.068	-0.030	23.409	0.001	0.001	0.000	0.000	0.000	0.000
44	A	43	GLU	-1	-0.932	-0.963	23.595	0.096	0.096	0.000	0.000	0.000	0.000
45	A	44	ASN	0	-0.026	-0.030	24.096	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.017	-0.002	27.235	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.934	-0.973	30.962	0.072	0.072	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.808	0.917	30.897	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	48	TYR	0	-0.028	-0.026	26.331	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	49	GLU	-1	-0.897	-0.943	26.232	0.169	0.169	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.056	-0.036	20.731	0.003	0.003	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.031	0.012	20.805	0.011	0.011	0.000	0.000	0.000	0.000
53	A	52	TYR	0	-0.004	-0.019	11.070	0.019	0.019	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.919	-0.959	16.110	0.424	0.424	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.926	-0.951	13.230	0.952	0.952	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.060	0.032	10.778	0.019	0.019	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.060	-0.028	11.476	-0.118	-0.118	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.006	0.011	14.667	-0.020	-0.020	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.015	-0.019	16.208	-0.045	-0.045	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.012	0.012	19.913	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	60	TYR	0	-0.100	-0.032	22.514	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	61	VAL	0	0.060	0.001	26.151	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	62	LYN	0	0.096	0.036	28.613	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.894	-0.944	32.404	0.056	0.056	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.049	-0.006	31.145	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	65	THR	0	0.008	-0.004	35.168	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	66	LYS	1	0.887	0.909	35.753	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.044	-0.020	35.443	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.774	-0.865	31.457	0.032	0.032	0.000	0.000	0.000	0.000
70	A	69	ASP	-1	-0.787	-0.871	30.751	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.010	-0.003	29.629	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	71	THR	0	-0.043	-0.043	23.512	0.002	0.002	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.026	-0.026	22.755	0.004	0.004	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.888	0.943	16.198	0.159	0.159	0.000	0.000	0.000	0.000
75	A	74	CYS	0	-0.019	0.006	15.187	0.037	0.037	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.890	0.941	14.157	0.134	0.134	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.022	0.001	9.472	0.087	0.087	0.000	0.000	0.000	0.000
78	A	77	VAL	0	0.023	0.005	9.694	-0.188	-0.188	0.000	0.000	0.000	0.000
79	A	78	ASN	0	0.022	-0.006	3.830	-0.822	-0.764	-0.001	-0.013	-0.043	0.000
80	A	79	ASP	-1	-0.890	-0.945	7.937	0.115	0.115	0.000	0.000	0.000	0.000
81	A	80	TYR	0	-0.109	-0.047	4.033	-0.831	-0.620	0.001	-0.036	-0.176	0.000
82	A	81	GLY	0	-0.012	-0.004	6.243	-0.354	-0.354	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.951	-0.977	7.693	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.777	-0.876	8.746	-0.831	-0.831	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.092	-0.057	10.600	0.194	0.194	0.000	0.000	0.000	0.000
86	A	85	SER	0	-0.004	0.018	13.566	-0.073	-0.073	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.014	-0.026	15.646	0.038	0.038	0.000	0.000	0.000	0.000
88	A	87	ALA	0	-0.017	0.001	19.492	0.002	0.002	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.769	-0.862	22.473	-0.045	-0.045	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.013	0.021	26.276	0.012	0.012	0.000	0.000	0.000	0.000
91	A	90	PHE	0	-0.032	-0.029	28.852	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.040	0.021	32.339	0.007	0.007	0.000	0.000	0.000	0.000
93	A	92	LYS	1	0.959	0.965	35.580	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	93	GLY	0	-0.027	-0.031	39.005	0.002	0.002	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.033	0.009	35.854	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.780	0.876	29.420	0.022	0.022	0.000	0.000	0.000	0.000
97	A	96	GLU	-1	-0.983	-0.982	37.557	-0.026	-0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)