FMO DATABASE

FMODB ID: R85Z8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-705358.054012
FMO2-HF: Nuclear repulsion	666185.388049
FMO2-HF: Total energy	-39172.665963
FMO2-MP2: Total energy	-39285.567602

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.
-0.33	-5.605	9.865	-0.129	-4.463	-0.037

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 : 0.015 / q_NPA : 0.009

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	-0.017	0.007	2.007	-1.541	-7.284	7.807	1.246	-3.310	-0.034
4	A	3	VAL	0	-0.030	-0.012	4.059	-0.948	-0.968	0.000	-0.003	0.022	0.000
5	A	4	SER	0	-0.028	-0.019	7.077	0.439	0.439	0.000	0.000	0.000	0.000
6	A	5	GLY	0	0.014	0.005	10.466	-0.094	-0.094	0.000	0.000	0.000	0.000
7	A	6	GLN	0	-0.023	-0.030	12.842	0.007	0.007	0.000	0.000	0.000	0.000
8	A	7	ILE	0	-0.011	0.004	16.343	0.043	0.043	0.000	0.000	0.000	0.000
9	A	8	MET	0	-0.034	-0.013	19.182	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	9	HIS	0	0.043	0.018	22.812	0.015	0.015	0.000	0.000	0.000	0.000
11	A	10	ALA	0	0.000	0.009	25.754	0.009	0.009	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.030	-0.018	28.544	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	12	GLY	0	0.042	0.015	32.335	0.007	0.007	0.000	0.000	0.000	0.000
14	A	13	GLU	-1	-0.984	-0.991	33.977	0.017	0.017	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.812	-0.910	37.227	0.011	0.011	0.000	0.000	0.000	0.000
16	A	15	GLY	0	-0.030	-0.007	38.886	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.013	0.007	36.627	0.004	0.004	0.000	0.000	0.000	0.000
18	A	17	HIS	0	-0.018	-0.011	31.645	0.001	0.001	0.000	0.000	0.000	0.000
19	A	18	VAL	0	-0.013	-0.001	28.173	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.925	0.970	24.682	-0.091	-0.091	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.051	-0.034	21.417	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	21	VAL	0	-0.007	-0.017	17.932	0.019	0.019	0.000	0.000	0.000	0.000
23	A	22	CYS	0	-0.036	-0.011	14.114	-0.035	-0.035	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.858	0.925	10.756	-0.507	-0.507	0.000	0.000	0.000	0.000
25	A	24	ILE	0	0.014	0.002	7.477	-0.132	-0.132	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.849	-0.898	5.928	0.763	0.763	0.000	0.000	0.000	0.000
27	A	26	ASN	0	-0.059	-0.062	2.311	-2.027	-2.046	2.060	-1.276	-0.766	-0.003
28	A	27	TYR	0	-0.010	0.014	4.095	1.840	2.111	0.000	-0.064	-0.207	0.000
29	A	28	ASP	-1	-0.792	-0.858	6.011	3.331	3.331	0.000	0.000	0.000	0.000
30	A	29	GLN	0	-0.026	-0.035	8.518	-0.252	-0.252	0.000	0.000	0.000	0.000
31	A	30	SER	0	-0.053	-0.023	8.483	-0.311	-0.311	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.033	-0.031	8.241	-0.087	-0.087	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.016	0.006	10.209	-0.099	-0.099	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.015	-0.018	12.506	-0.037	-0.037	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.028	-0.006	14.892	0.010	0.010	0.000	0.000	0.000	0.000
36	A	35	TRP	0	0.068	0.022	17.706	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	36	TYR	0	-0.038	-0.041	18.460	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	37	PHE	0	0.016	0.021	22.924	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	38	GLY	0	0.005	-0.001	26.224	0.000	0.000	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.042	-0.026	25.084	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.907	0.967	26.404	0.010	0.010	0.000	0.000	0.000	0.000
42	A	41	GLN	0	0.058	0.031	21.784	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.058	-0.018	23.558	0.000	0.000	0.000	0.000	0.000	0.000
44	A	43	GLU	-1	-0.933	-0.972	23.680	0.093	0.093	0.000	0.000	0.000	0.000
45	A	44	ASN	0	-0.019	-0.017	24.254	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	45	SER	0	-0.027	-0.018	27.458	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.937	-0.978	31.108	0.062	0.062	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.767	0.888	31.809	-0.036	-0.036	0.000	0.000	0.000	0.000
49	A	48	TYR	0	-0.024	-0.018	27.004	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	49	GLU	-1	-0.859	-0.910	26.629	0.133	0.133	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.045	-0.026	21.070	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	51	THR	0	0.009	0.010	20.942	0.006	0.006	0.000	0.000	0.000	0.000
53	A	52	TYR	0	0.007	-0.022	11.397	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.941	-0.957	16.618	0.381	0.381	0.000	0.000	0.000	0.000
55	A	54	ASP	-1	-0.886	-0.927	13.559	0.907	0.907	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.067	0.034	10.997	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	56	VAL	0	-0.058	-0.045	11.799	-0.110	-0.110	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.005	0.016	14.870	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.044	-0.035	16.576	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	59	LEU	0	0.014	0.016	20.257	0.002	0.002	0.000	0.000	0.000	0.000
61	A	60	TYR	0	0.025	0.000	22.965	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	61	VAL	0	-0.023	-0.013	26.611	0.000	0.000	0.000	0.000	0.000	0.000
63	A	62	LYN	0	0.025	-0.003	29.188	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	63	ASP	-1	-0.873	-0.943	32.660	0.044	0.044	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.052	-0.006	31.595	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	65	THR	0	0.000	-0.012	35.617	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	66	LYS	1	0.815	0.870	36.230	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.040	-0.014	36.402	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.771	-0.865	32.021	0.020	0.020	0.000	0.000	0.000	0.000
70	A	69	ASP	-1	-0.766	-0.861	31.167	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.011	-0.007	30.038	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	71	THR	0	-0.046	-0.044	23.818	0.003	0.003	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.030	-0.030	23.288	0.007	0.007	0.000	0.000	0.000	0.000
74	A	73	ARG	1	0.857	0.919	15.670	0.172	0.172	0.000	0.000	0.000	0.000
75	A	74	CYS	0	-0.018	0.008	14.846	0.036	0.036	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.783	0.868	14.336	0.105	0.105	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.051	0.013	9.326	0.081	0.081	0.000	0.000	0.000	0.000
78	A	77	VAL	0	-0.004	-0.017	9.752	-0.197	-0.197	0.000	0.000	0.000	0.000
79	A	78	ASN	0	0.040	-0.005	3.717	-0.900	-0.828	-0.001	-0.018	-0.054	0.000
80	A	79	ASP	-1	-0.893	-0.955	8.228	0.284	0.284	0.000	0.000	0.000	0.000
81	A	80	TYR	0	-0.105	-0.051	4.157	-0.358	-0.194	-0.001	-0.014	-0.148	0.000
82	A	81	GLY	0	-0.023	-0.003	6.212	-0.560	-0.560	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.845	-0.903	7.748	0.069	0.069	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.768	-0.845	8.814	-0.810	-0.810	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.083	-0.056	10.609	0.198	0.198	0.000	0.000	0.000	0.000
86	A	85	SER	0	0.028	0.038	13.485	-0.053	-0.053	0.000	0.000	0.000	0.000
87	A	86	TYR	0	-0.037	-0.036	15.842	0.049	0.049	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.003	0.009	19.650	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.760	-0.851	22.745	-0.063	-0.063	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.017	0.030	26.560	0.012	0.012	0.000	0.000	0.000	0.000
91	A	90	PHE	0	-0.014	-0.008	29.223	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.038	0.016	32.777	0.007	0.007	0.000	0.000	0.000	0.000
93	A	92	LYS	1	0.949	0.960	36.090	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	93	GLY	0	-0.012	-0.018	39.506	0.003	0.003	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.029	0.010	36.212	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.731	0.842	30.157	0.038	0.038	0.000	0.000	0.000	0.000
97	A	96	GLU	-1	-0.977	-0.977	38.178	-0.038	-0.038	0.000	0.000	0.000	0.000

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