FMO DATABASE

FMODB ID: R9758

Calculation Name: 2BK0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BK0

Chain ID: A

ChEMBL ID:

UniProt ID: P49372

Base Structure: X-ray

Registration Date: 2023-09-20

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1310453.835257
FMO2-HF: Nuclear repulsion	1254416.678527
FMO2-HF: Total energy	-56037.156729
FMO2-MP2: Total energy	-56203.212713

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:2:GLY)

Summations of interaction energy for fragment #1(A:2: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.
-3.088	-13.689	28.142	-10.536	-7.009	-0.061

Interaction energy analysis for fragmet #1(A:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.006

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	4	GLN	0	0.001	-0.003	3.803	0.373	1.833	-0.015	-0.744	-0.701	0.002
4	A	5	THR	0	-0.016	-0.012	6.723	0.052	0.052	0.000	0.000	0.000	0.000
5	A	6	HIS	0	-0.002	0.006	10.414	-0.011	-0.011	0.000	0.000	0.000	0.000
6	A	7	VAL	0	-0.008	-0.001	13.603	0.008	0.008	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.018	-0.001	17.127	0.014	0.014	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.929	-0.972	20.423	-0.239	-0.239	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.030	-0.007	23.839	0.010	0.010	0.000	0.000	0.000	0.000
10	A	11	THR	0	-0.008	-0.003	27.055	0.009	0.009	0.000	0.000	0.000	0.000
11	A	12	SER	0	-0.042	-0.059	30.562	0.001	0.001	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.018	-0.007	33.376	0.007	0.007	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.007	0.001	35.132	0.009	0.009	0.000	0.000	0.000	0.000
14	A	15	SER	0	0.064	0.028	35.140	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.068	0.016	32.023	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.926	-0.960	32.903	-0.100	-0.100	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.846	0.931	34.915	0.108	0.108	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.017	-0.003	29.997	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	20	PHE	0	0.019	0.013	27.550	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.024	0.009	30.863	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.011	-0.004	32.943	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.012	-0.025	25.638	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.070	-0.019	26.616	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.064	-0.024	28.655	0.002	0.002	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.864	-0.931	31.812	-0.116	-0.116	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.019	0.010	27.811	0.003	0.003	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.785	-0.881	29.326	-0.184	-0.184	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.050	-0.026	31.768	0.009	0.009	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.052	-0.037	33.310	0.006	0.006	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.044	0.018	27.517	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	PRO	0	-0.047	-0.014	32.137	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.873	0.950	34.631	0.116	0.116	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.030	-0.002	34.153	0.005	0.005	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.017	-0.018	31.788	0.000	0.000	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.002	0.004	32.485	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	37	GLY	0	-0.006	-0.005	33.220	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.021	0.000	28.414	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.034	-0.023	27.772	-0.018	-0.018	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.865	0.946	28.976	0.180	0.180	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.035	0.022	29.392	0.014	0.014	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.005	-0.031	27.715	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.967	-0.948	28.184	-0.128	-0.128	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.006	-0.021	27.578	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	45	LYS	1	0.910	0.963	26.173	0.154	0.154	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.035	0.006	27.321	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.916	-0.956	29.480	-0.112	-0.112	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.028	0.009	29.212	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.023	0.004	27.675	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	50	PRO	0	-0.006	0.016	24.239	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.009	0.008	23.085	0.017	0.017	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.081	-0.071	24.031	0.002	0.002	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.025	-0.019	21.413	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.856	0.888	22.953	0.235	0.235	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.007	0.013	22.982	-0.030	-0.030	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.009	0.004	22.430	0.022	0.022	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.015	-0.011	24.026	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.008	-0.010	21.983	0.011	0.011	0.000	0.000	0.000	0.000
58	A	59	PRO	0	-0.023	-0.018	26.386	0.014	0.014	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.860	-0.925	28.057	-0.172	-0.172	0.000	0.000	0.000	0.000
60	A	61	GLY	0	-0.045	-0.010	28.673	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	62	GLY	0	-0.006	-0.002	26.155	0.003	0.003	0.000	0.000	0.000	0.000
62	A	63	PRO	0	-0.057	-0.035	21.308	0.005	0.005	0.000	0.000	0.000	0.000
63	A	64	ILE	0	-0.001	0.022	18.039	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.021	-0.001	21.298	0.035	0.035	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.013	-0.013	21.015	0.032	0.032	0.000	0.000	0.000	0.000
66	A	67	MET	0	-0.064	0.009	18.172	-0.043	-0.043	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.003	-0.007	18.436	0.047	0.047	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.023	-0.004	17.996	-0.054	-0.054	0.000	0.000	0.000	0.000
69	A	70	ARG	1	0.939	0.978	14.760	0.376	0.376	0.000	0.000	0.000	0.000
70	A	71	ILE	0	0.021	0.015	19.532	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.851	-0.927	17.388	-0.340	-0.340	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.001	-0.009	20.688	0.034	0.034	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.000	-0.001	23.512	-0.019	-0.019	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.014	-0.005	26.559	0.021	0.021	0.000	0.000	0.000	0.000
75	A	76	LYS	1	1.000	0.980	28.647	0.100	0.100	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.917	-0.954	31.824	-0.087	-0.087	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.048	-0.017	28.138	0.003	0.003	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.035	-0.002	29.015	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	80	THR	0	0.002	-0.001	23.319	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.033	-0.024	23.264	0.013	0.013	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.826	-0.892	19.014	-0.302	-0.302	0.000	0.000	0.000	0.000
82	A	83	TYR	0	0.012	0.006	18.467	0.036	0.036	0.000	0.000	0.000	0.000
83	A	84	SER	0	0.010	-0.003	14.068	-0.086	-0.086	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.058	-0.027	13.816	0.086	0.086	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.027	-0.032	13.177	-0.104	-0.104	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.886	-0.945	14.770	-0.311	-0.311	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.024	0.016	16.374	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.795	-0.919	16.049	-0.424	-0.424	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.071	-0.005	15.173	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.055	-0.014	11.053	-0.087	-0.087	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.032	-0.018	11.433	-0.127	-0.127	0.000	0.000	0.000	0.000
92	A	93	GLY	0	-0.008	0.002	12.343	0.079	0.079	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.030	-0.033	6.622	0.155	0.155	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.016	-0.007	6.598	-0.563	-0.563	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.978	-0.987	6.542	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	97	SER	0	-0.011	-0.003	7.840	0.357	0.357	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.015	-0.002	8.657	-0.402	-0.402	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.788	-0.850	10.771	-0.436	-0.436	0.000	0.000	0.000	0.000
99	A	100	ASN	0	-0.021	-0.019	12.636	-0.084	-0.084	0.000	0.000	0.000	0.000
100	A	101	HIS	1	0.780	0.849	14.571	0.497	0.497	0.000	0.000	0.000	0.000
101	A	102	VAL	0	-0.010	-0.004	18.554	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.004	-0.003	21.848	0.024	0.024	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.016	-0.012	24.450	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.002	0.004	27.496	0.011	0.011	0.000	0.000	0.000	0.000
105	A	106	PRO	0	0.011	-0.002	30.120	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	107	THR	0	0.006	0.000	32.957	0.001	0.001	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.013	-0.019	35.391	0.004	0.004	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.932	-0.962	37.548	-0.103	-0.103	0.000	0.000	0.000	0.000
109	A	110	GLY	0	-0.024	-0.002	38.883	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	GLY	0	-0.012	0.015	36.274	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	112	SER	0	-0.061	-0.051	31.622	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	ILE	0	0.015	-0.005	27.172	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	114	CYS	0	-0.033	-0.012	25.577	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.967	0.993	19.831	0.243	0.243	0.000	0.000	0.000	0.000
115	A	116	THR	0	0.003	-0.003	19.277	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.026	-0.028	14.535	0.000	0.000	0.000	0.000	0.000	0.000
117	A	118	ALA	0	0.047	0.033	13.449	0.018	0.018	0.000	0.000	0.000	0.000
118	A	119	ILE	0	-0.016	-0.025	8.471	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	120	PHE	0	-0.012	-0.003	7.540	0.159	0.159	0.000	0.000	0.000	0.000
120	A	121	HIS	0	0.018	0.011	4.586	-1.374	-1.404	-0.001	-0.020	0.050	0.000
121	A	122	THR	0	-0.052	-0.042	2.872	-0.842	0.359	0.411	-0.712	-0.901	-0.005
122	A	123	LYS	1	0.976	0.992	2.244	-2.219	-1.539	2.590	-1.725	-1.545	-0.019
123	A	124	GLY	0	-0.006	-0.008	3.673	-1.678	-0.928	0.040	-0.394	-0.396	0.000
124	A	125	ASP	-1	-0.868	-0.949	1.685	6.040	-8.907	25.115	-6.828	-3.340	-0.039
125	A	126	ALA	0	-0.072	-0.015	3.549	-0.334	-0.108	0.003	-0.077	-0.153	0.000
126	A	127	VAL	0	0.034	0.032	4.148	-1.459	-1.400	-0.001	-0.036	-0.023	0.000
127	A	128	VAL	0	-0.025	-0.007	6.869	0.317	0.317	0.000	0.000	0.000	0.000
128	A	129	PRO	0	-0.003	-0.003	9.675	0.136	0.136	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.878	-0.949	12.932	-0.448	-0.448	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.909	-0.964	15.388	-0.380	-0.380	0.000	0.000	0.000	0.000
131	A	132	ASN	0	-0.063	-0.039	14.003	-0.051	-0.051	0.000	0.000	0.000	0.000
132	A	133	ILE	0	0.048	0.034	11.176	0.029	0.029	0.000	0.000	0.000	0.000
133	A	134	LYS	1	0.911	0.959	15.603	0.356	0.356	0.000	0.000	0.000	0.000
134	A	135	TYR	0	0.010	0.002	18.942	0.050	0.050	0.000	0.000	0.000	0.000
135	A	136	ALA	0	0.048	0.020	17.256	0.040	0.040	0.000	0.000	0.000	0.000
136	A	137	ASN	0	0.041	0.027	18.864	0.003	0.003	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.923	-0.955	21.064	-0.249	-0.249	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.033	-0.014	22.191	0.037	0.037	0.000	0.000	0.000	0.000
139	A	140	ASN	0	-0.026	-0.028	19.530	0.041	0.041	0.000	0.000	0.000	0.000
140	A	141	THR	0	-0.032	-0.019	23.304	0.028	0.028	0.000	0.000	0.000	0.000
141	A	142	ALA	0	-0.021	-0.010	26.007	0.023	0.023	0.000	0.000	0.000	0.000
142	A	143	LEU	0	0.019	0.015	25.197	0.020	0.020	0.000	0.000	0.000	0.000
143	A	144	PHE	0	0.021	0.010	26.837	0.016	0.016	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.976	0.973	28.648	0.195	0.195	0.000	0.000	0.000	0.000
145	A	146	ALA	0	-0.009	0.011	31.177	0.015	0.015	0.000	0.000	0.000	0.000
146	A	147	LEU	0	0.014	0.003	28.985	0.013	0.013	0.000	0.000	0.000	0.000
147	A	148	GLU	-1	-0.822	-0.863	32.433	-0.145	-0.145	0.000	0.000	0.000	0.000
148	A	149	ALA	0	-0.015	-0.002	34.221	0.011	0.011	0.000	0.000	0.000	0.000
149	A	150	TYR	0	0.039	0.016	36.291	0.009	0.009	0.000	0.000	0.000	0.000
150	A	151	LEU	0	0.013	0.002	33.794	0.009	0.009	0.000	0.000	0.000	0.000
151	A	152	ILE	0	-0.050	-0.014	37.820	0.008	0.008	0.000	0.000	0.000	0.000
152	A	153	ALA	0	-0.037	-0.005	40.225	0.006	0.006	0.000	0.000	0.000	0.000
153	A	154	ASN	0	-0.079	-0.036	41.058	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLY)