FMO DATABASE

FMODB ID: Z6V3N

Calculation Name: 2JKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2JKF

Chain ID: A

ChEMBL ID:

UniProt ID: P86294

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSide
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	170
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1695055.936029
FMO2-HF: Nuclear repulsion	1629134.474889
FMO2-HF: Total energy	-65921.46114
FMO2-MP2: Total energy	-66116.431848

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:5:TYR)

Summations of interaction energy for fragment #1(A:5:TYR)

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.
-7.051	0.367	4.346	-2.4	-9.365	-0.017

Interaction energy analysis for fragmet #1(A:5:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.019

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	7	TRP	0	0.088	0.010	2.799	-6.765	0.085	4.325	-2.446	-8.730	-0.017
4	A	8	ASP	-1	-0.846	-0.915	3.538	-0.147	-0.039	0.023	0.069	-0.200	0.000
5	A	9	SER	0	-0.007	-0.014	4.653	0.121	0.197	-0.001	-0.002	-0.072	0.000
6	A	10	TYR	0	-0.005	-0.007	4.284	-0.411	-0.027	-0.001	-0.021	-0.363	0.000
7	A	11	LEU	0	0.010	0.004	6.266	0.066	0.066	0.000	0.000	0.000	0.000
8	A	12	ASN	0	0.014	-0.002	8.764	0.064	0.064	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.921	-0.960	9.358	-0.403	-0.403	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.722	0.830	8.289	0.422	0.422	0.000	0.000	0.000	0.000
11	A	15	LEU	0	-0.002	0.006	11.294	0.035	0.035	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.015	0.012	13.084	0.017	0.017	0.000	0.000	0.000	0.000
13	A	17	ALA	0	0.009	0.010	14.381	0.017	0.017	0.000	0.000	0.000	0.000
14	A	18	THR	0	-0.060	-0.045	16.203	0.017	0.017	0.000	0.000	0.000	0.000
15	A	19	ASN	0	-0.064	-0.032	18.560	0.014	0.014	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.010	-0.001	19.824	0.017	0.017	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.034	-0.017	15.876	0.013	0.013	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.019	0.010	19.044	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.012	0.004	15.832	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	24	ALA	0	-0.021	-0.005	12.268	0.018	0.018	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.028	0.010	10.610	-0.050	-0.050	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.024	0.003	5.943	0.043	0.043	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.019	0.012	10.024	-0.044	-0.044	0.000	0.000	0.000	0.000
24	A	28	SER	0	0.002	-0.001	11.401	0.048	0.048	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.816	-0.903	12.288	0.209	0.209	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.942	-0.960	13.290	0.310	0.310	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.904	-0.964	15.539	0.124	0.124	0.000	0.000	0.000	0.000
28	A	32	GLY	0	-0.017	0.001	15.993	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	33	VAL	0	-0.045	-0.028	15.474	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	34	VAL	0	-0.046	-0.026	12.143	0.026	0.026	0.000	0.000	0.000	0.000
31	A	35	TYR	0	-0.041	-0.037	5.893	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.045	-0.027	6.841	-0.106	-0.106	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.027	-0.010	8.747	0.085	0.085	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.009	0.024	9.724	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	39	ALA	0	0.040	-0.001	12.439	0.037	0.037	0.000	0.000	0.000	0.000
36	A	40	GLN	0	0.030	0.012	16.187	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	41	GLY	0	-0.026	0.009	18.389	0.002	0.002	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.903	-0.970	18.658	-0.174	-0.174	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.995	-1.013	20.751	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.119	-0.057	23.127	0.004	0.004	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.855	-0.922	24.395	-0.072	-0.072	0.000	0.000	0.000	0.000
42	A	46	PRO	0	-0.005	0.003	22.648	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.077	-0.045	22.206	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	48	PHE	0	0.010	0.030	19.505	0.004	0.004	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.837	-0.929	18.714	-0.113	-0.113	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.843	0.923	11.023	0.339	0.339	0.000	0.000	0.000	0.000
47	A	51	TRP	0	0.020	-0.002	11.364	0.006	0.006	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.055	-0.024	17.210	0.019	0.019	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.029	-0.015	18.265	0.010	0.010	0.000	0.000	0.000	0.000
50	A	54	PHE	0	-0.036	-0.044	15.395	0.010	0.010	0.000	0.000	0.000	0.000
51	A	55	TYR	0	-0.016	-0.011	16.826	0.017	0.017	0.000	0.000	0.000	0.000
52	A	56	LYS	1	0.874	0.965	18.747	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.975	-0.965	22.287	0.005	0.005	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.849	-0.922	23.730	0.035	0.035	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.048	-0.055	25.351	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.839	-0.894	29.483	0.020	0.020	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.064	-0.032	31.337	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.875	-0.942	34.157	0.007	0.007	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.048	-0.034	35.902	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.850	-0.931	38.706	0.004	0.004	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.795	-0.885	41.984	0.012	0.012	0.000	0.000	0.000	0.000
62	A	66	GLU	-1	-0.911	-0.963	43.151	0.007	0.007	0.000	0.000	0.000	0.000
63	A	67	ASN	0	-0.189	-0.104	45.864	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	68	GLY	0	0.003	0.014	46.802	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	69	THR	0	-0.098	-0.052	45.039	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.782	0.901	43.013	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	71	THR	0	-0.059	-0.034	39.772	0.001	0.001	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.015	0.006	36.041	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.837	0.923	33.159	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.022	-0.008	29.656	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.069	-0.031	26.280	0.005	0.005	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.036	-0.003	22.700	0.004	0.004	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.702	-0.850	21.608	0.009	0.009	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.069	0.063	19.481	0.002	0.002	0.000	0.000	0.000	0.000
75	A	79	GLN	0	0.023	-0.004	20.146	0.009	0.009	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.085	-0.041	22.965	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	81	ILE	0	0.017	0.001	17.867	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.007	0.006	17.697	0.004	0.004	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.028	0.000	21.298	0.002	0.002	0.000	0.000	0.000	0.000
80	A	84	VAL	0	0.027	0.021	23.254	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	85	PHE	0	-0.018	-0.013	18.289	0.001	0.001	0.000	0.000	0.000	0.000
82	A	86	ASN	0	-0.030	-0.014	21.634	0.008	0.008	0.000	0.000	0.000	0.000
83	A	87	GLU	-1	-0.892	-0.926	24.065	0.064	0.064	0.000	0.000	0.000	0.000
84	A	88	GLY	0	-0.049	-0.013	26.495	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	89	TYR	0	-0.117	-0.078	27.752	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.047	0.007	27.945	0.004	0.004	0.000	0.000	0.000	0.000
87	A	91	PRO	0	-0.033	-0.007	29.438	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.824	-0.903	29.787	0.027	0.027	0.000	0.000	0.000	0.000
89	A	93	GLY	0	-0.076	-0.032	29.619	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	94	VAL	0	0.037	0.007	23.008	0.004	0.004	0.000	0.000	0.000	0.000
91	A	95	TRP	0	-0.040	-0.031	24.779	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.004	-0.004	17.867	0.007	0.007	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.064	0.041	21.363	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	98	GLY	0	-0.070	-0.045	21.959	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	99	THR	0	-0.092	-0.037	24.815	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.916	0.973	25.797	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	101	TYR	0	-0.024	-0.026	22.560	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	102	GLN	0	-0.032	-0.019	27.529	0.003	0.003	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.036	0.000	25.847	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	104	ILE	0	-0.095	-0.043	28.128	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	105	ASN	0	-0.040	-0.036	27.606	0.001	0.001	0.000	0.000	0.000	0.000
102	A	106	ILE	0	0.017	0.014	22.719	0.003	0.003	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.860	-0.903	24.145	0.012	0.012	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.840	0.895	22.792	-0.077	-0.077	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.892	-0.937	21.501	0.071	0.071	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.031	0.004	21.105	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	111	GLU	-1	-0.922	-0.962	20.973	0.022	0.022	0.000	0.000	0.000	0.000
108	A	112	PHE	0	-0.028	-0.024	16.933	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.941	-0.982	18.436	-0.096	-0.096	0.000	0.000	0.000	0.000
110	A	114	GLY	0	-0.036	-0.029	18.302	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	115	TYR	0	-0.053	-0.020	13.476	0.010	0.010	0.000	0.000	0.000	0.000
112	A	116	ASN	0	-0.024	-0.016	17.594	-0.016	-0.016	0.000	0.000	0.000	0.000
113	A	117	PHE	0	-0.010	-0.011	13.379	0.019	0.019	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.794	-0.883	18.072	0.085	0.085	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.024	-0.028	18.390	0.011	0.011	0.000	0.000	0.000	0.000
116	A	120	ALA	0	0.004	0.010	20.477	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	121	THR	0	-0.031	-0.026	21.936	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	122	CYS	0	-0.019	-0.003	24.039	0.003	0.003	0.000	0.000	0.000	0.000
119	A	123	ALA	0	-0.023	-0.008	25.531	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.977	1.000	25.374	0.032	0.032	0.000	0.000	0.000	0.000
121	A	125	LEU	0	-0.014	-0.013	28.916	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.842	0.890	29.681	0.029	0.029	0.000	0.000	0.000	0.000
123	A	127	GLY	0	0.072	0.035	26.509	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.022	-0.020	24.707	0.005	0.005	0.000	0.000	0.000	0.000
125	A	129	LEU	0	-0.032	0.000	20.047	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	130	HIS	0	-0.006	-0.007	19.309	0.011	0.011	0.000	0.000	0.000	0.000
127	A	131	LEU	0	0.004	0.011	17.532	0.001	0.001	0.000	0.000	0.000	0.000
128	A	132	VAL	0	0.015	0.003	14.949	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.881	0.947	14.023	-0.154	-0.154	0.000	0.000	0.000	0.000
130	A	134	VAL	0	-0.009	-0.004	8.999	-0.027	-0.027	0.000	0.000	0.000	0.000
131	A	135	PRO	0	0.030	0.013	7.613	0.013	0.013	0.000	0.000	0.000	0.000
132	A	136	GLY	0	-0.028	-0.017	6.958	0.150	0.150	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.015	0.027	7.964	-0.036	-0.036	0.000	0.000	0.000	0.000
134	A	138	ASN	0	-0.006	-0.001	6.622	-0.094	-0.094	0.000	0.000	0.000	0.000
135	A	139	ILE	0	0.016	0.009	10.396	-0.033	-0.033	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.025	-0.001	10.982	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	141	VAL	0	-0.004	-0.009	12.946	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	142	VAL	0	0.008	0.001	14.455	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	143	LEU	0	0.012	0.014	16.701	0.009	0.009	0.000	0.000	0.000	0.000
140	A	144	TYR	0	-0.018	-0.013	19.487	-0.007	-0.007	0.000	0.000	0.000	0.000
141	A	145	ASP	-1	-0.792	-0.895	22.429	-0.045	-0.045	0.000	0.000	0.000	0.000
142	A	146	GLU	-1	-0.842	-0.924	25.282	-0.027	-0.027	0.000	0.000	0.000	0.000
143	A	147	GLU	-1	-0.956	-0.948	28.553	-0.037	-0.037	0.000	0.000	0.000	0.000
144	A	148	LYS	1	0.800	0.884	24.595	0.056	0.056	0.000	0.000	0.000	0.000
145	A	149	GLU	-1	-0.957	-0.965	26.382	-0.064	-0.064	0.000	0.000	0.000	0.000
146	A	150	GLN	0	0.012	0.017	22.563	0.001	0.001	0.000	0.000	0.000	0.000
147	A	151	ASP	-1	-0.835	-0.934	25.627	-0.036	-0.036	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.929	0.970	25.190	0.008	0.008	0.000	0.000	0.000	0.000
149	A	153	GLY	0	-0.004	-0.003	24.867	0.003	0.003	0.000	0.000	0.000	0.000
150	A	154	ASN	0	0.030	-0.001	23.982	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	155	SER	0	0.031	0.006	20.871	-0.003	-0.003	0.000	0.000	0.000	0.000
152	A	156	LYS	1	0.837	0.925	19.847	-0.008	-0.008	0.000	0.000	0.000	0.000
153	A	157	ILE	0	0.011	0.008	20.008	0.005	0.005	0.000	0.000	0.000	0.000
154	A	158	ALA	0	0.023	0.024	18.070	-0.007	-0.007	0.000	0.000	0.000	0.000
155	A	159	ALA	0	0.002	-0.010	15.973	-0.008	-0.008	0.000	0.000	0.000	0.000
156	A	160	LEU	0	-0.017	-0.008	15.169	0.017	0.017	0.000	0.000	0.000	0.000
157	A	161	THR	0	-0.009	-0.015	15.038	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	162	PHE	0	0.003	-0.007	7.785	-0.017	-0.017	0.000	0.000	0.000	0.000
159	A	163	ALA	0	0.015	0.001	10.626	0.005	0.005	0.000	0.000	0.000	0.000
160	A	164	LYS	1	0.838	0.916	11.074	0.152	0.152	0.000	0.000	0.000	0.000
161	A	165	GLU	-1	-0.754	-0.832	8.733	-0.473	-0.473	0.000	0.000	0.000	0.000
162	A	166	LEU	0	-0.027	-0.013	5.850	-0.172	-0.172	0.000	0.000	0.000	0.000
163	A	167	ALA	0	-0.009	-0.014	7.274	0.099	0.099	0.000	0.000	0.000	0.000
164	A	168	GLU	-1	-0.848	-0.903	9.806	-0.218	-0.218	0.000	0.000	0.000	0.000
165	A	169	SER	0	-0.086	-0.046	5.160	-0.151	-0.151	0.000	0.000	0.000	0.000
166	A	170	SER	0	0.008	0.010	6.188	0.087	0.087	0.000	0.000	0.000	0.000
167	A	171	GLN	0	-0.033	-0.023	7.110	0.162	0.162	0.000	0.000	0.000	0.000
168	A	172	LEU	0	-0.087	-0.019	7.821	0.023	0.023	0.000	0.000	0.000	0.000
169	A	173	GLN	0	0.023	0.009	7.639	0.005	0.005	0.000	0.000	0.000	0.000
170	A	174	HIS	1	0.908	0.960	9.595	0.050	0.050	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:TYR)