FMO DATABASE

FMODB ID: R98R8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1697689.669243
FMO2-HF: Nuclear repulsion	1631767.610168
FMO2-HF: Total energy	-65922.059076
FMO2-MP2: Total energy	-66117.071479

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.
-10.582	-3.149	3.586	-2.338	-8.681	-0.008

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 : 0.014 / 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	7	TRP	0	0.068	0.017	2.816	-7.056	-0.184	3.577	-2.336	-8.114	-0.008
4	A	8	ASP	-1	-0.820	-0.892	3.735	-0.623	-0.457	0.011	0.025	-0.202	0.000
5	A	9	SER	0	-0.012	-0.023	5.338	0.444	0.444	0.000	0.000	0.000	0.000
6	A	10	TYR	0	-0.025	-0.028	4.078	-0.491	-0.128	-0.001	-0.025	-0.337	0.000
7	A	11	LEU	0	0.021	0.011	6.226	0.239	0.239	0.000	0.000	0.000	0.000
8	A	12	ASN	0	0.017	0.004	8.439	0.225	0.225	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.906	-0.960	8.827	-0.754	-0.754	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.706	0.827	8.207	1.057	1.057	0.000	0.000	0.000	0.000
11	A	15	LEU	0	-0.009	0.013	11.099	0.083	0.083	0.000	0.000	0.000	0.000
12	A	16	LEU	0	0.015	0.020	12.673	0.083	0.083	0.000	0.000	0.000	0.000
13	A	17	ALA	0	0.017	0.009	14.105	0.076	0.076	0.000	0.000	0.000	0.000
14	A	18	THR	0	-0.061	-0.039	15.771	0.069	0.069	0.000	0.000	0.000	0.000
15	A	19	ASN	0	-0.060	-0.030	18.088	0.059	0.059	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.019	-0.003	19.717	0.043	0.043	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.033	-0.025	15.903	0.009	0.009	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.010	0.008	19.090	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.027	0.007	15.812	0.004	0.004	0.000	0.000	0.000	0.000
20	A	24	ALA	0	-0.047	-0.007	12.140	0.030	0.030	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.048	0.014	10.272	-0.058	-0.058	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.040	-0.003	5.599	0.081	0.081	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.026	0.016	9.656	-0.056	-0.056	0.000	0.000	0.000	0.000
24	A	28	SER	0	0.000	-0.015	11.642	0.000	0.000	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.845	-0.923	12.577	-0.208	-0.208	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.926	-0.942	13.604	-0.286	-0.286	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.880	-0.948	15.769	-0.367	-0.367	0.000	0.000	0.000	0.000
28	A	32	GLY	0	0.011	0.007	16.294	0.027	0.027	0.000	0.000	0.000	0.000
29	A	33	VAL	0	-0.050	-0.034	15.017	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	34	VAL	0	-0.037	-0.022	11.916	-0.082	-0.082	0.000	0.000	0.000	0.000
31	A	35	TYR	0	-0.040	-0.033	5.500	-0.158	-0.158	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.041	-0.027	6.675	-0.178	-0.178	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.028	-0.006	8.661	0.138	0.138	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.007	0.018	9.793	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	39	ALA	0	0.055	0.007	12.577	0.031	0.031	0.000	0.000	0.000	0.000
36	A	40	GLN	0	0.008	0.005	16.291	0.011	0.011	0.000	0.000	0.000	0.000
37	A	41	GLY	0	-0.036	-0.001	18.596	0.032	0.032	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.913	-0.964	18.691	-0.288	-0.288	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.969	-0.980	20.653	-0.157	-0.157	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.043	-0.029	23.769	0.009	0.009	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.844	-0.934	24.770	-0.177	-0.177	0.000	0.000	0.000	0.000
42	A	46	PRO	0	-0.027	-0.001	22.624	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.117	-0.073	22.331	0.011	0.011	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.007	0.013	19.606	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.820	-0.915	18.632	-0.354	-0.354	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.803	0.900	10.984	0.843	0.843	0.000	0.000	0.000	0.000
47	A	51	TRP	0	0.012	-0.007	10.871	-0.057	-0.057	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.040	-0.022	17.205	0.004	0.004	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.025	-0.007	18.451	0.021	0.021	0.000	0.000	0.000	0.000
50	A	54	PHE	0	-0.046	-0.052	15.123	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	55	TYR	0	0.001	-0.006	16.679	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	56	LYS	1	0.836	0.953	18.639	0.201	0.201	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.953	-0.963	22.104	-0.160	-0.160	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.859	-0.923	23.228	-0.171	-0.171	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.038	-0.050	24.769	0.022	0.022	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.857	-0.905	28.976	-0.105	-0.105	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.060	-0.024	31.133	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.845	-0.921	33.938	-0.078	-0.078	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.030	-0.020	35.274	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.838	-0.905	38.273	-0.071	-0.071	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.780	-0.872	40.806	-0.076	-0.076	0.000	0.000	0.000	0.000
62	A	66	GLU	-1	-0.917	-0.966	43.039	-0.081	-0.081	0.000	0.000	0.000	0.000
63	A	67	ASN	0	-0.168	-0.091	45.873	0.005	0.005	0.000	0.000	0.000	0.000
64	A	68	GLY	0	-0.007	0.009	46.651	0.003	0.003	0.000	0.000	0.000	0.000
65	A	69	THR	0	-0.086	-0.065	44.525	0.003	0.003	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.734	0.864	42.690	0.076	0.076	0.000	0.000	0.000	0.000
67	A	71	THR	0	-0.081	-0.041	39.716	0.003	0.003	0.000	0.000	0.000	0.000
68	A	72	THR	0	-0.014	-0.023	35.907	0.000	0.000	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.847	0.921	32.882	0.115	0.115	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.020	-0.011	29.154	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.044	-0.015	25.746	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.019	-0.009	22.188	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.700	-0.845	20.921	-0.279	-0.279	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.053	0.057	19.066	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	79	GLN	0	0.018	-0.002	19.757	0.017	0.017	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.088	-0.048	22.768	0.011	0.011	0.000	0.000	0.000	0.000
77	A	81	ILE	0	0.024	0.010	17.537	0.006	0.006	0.000	0.000	0.000	0.000
78	A	82	LEU	0	-0.007	0.002	17.701	0.006	0.006	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.046	-0.012	21.313	0.015	0.015	0.000	0.000	0.000	0.000
80	A	84	VAL	0	0.026	0.013	23.305	0.012	0.012	0.000	0.000	0.000	0.000
81	A	85	PHE	0	0.007	0.001	18.414	0.011	0.011	0.000	0.000	0.000	0.000
82	A	86	ASN	0	-0.042	-0.016	21.576	0.007	0.007	0.000	0.000	0.000	0.000
83	A	87	GLU	-1	-0.886	-0.914	24.314	-0.106	-0.106	0.000	0.000	0.000	0.000
84	A	88	GLY	0	-0.034	-0.009	26.782	0.009	0.009	0.000	0.000	0.000	0.000
85	A	89	TYR	0	-0.123	-0.087	27.973	0.002	0.002	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.054	0.013	27.601	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	91	PRO	0	-0.028	-0.010	29.183	0.004	0.004	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.795	-0.876	29.665	-0.123	-0.123	0.000	0.000	0.000	0.000
89	A	93	GLY	0	-0.070	-0.035	29.451	0.000	0.000	0.000	0.000	0.000	0.000
90	A	94	VAL	0	0.024	-0.001	22.769	0.001	0.001	0.000	0.000	0.000	0.000
91	A	95	TRP	0	-0.020	-0.037	24.138	0.015	0.015	0.000	0.000	0.000	0.000
92	A	96	LEU	0	0.000	0.008	17.556	-0.016	-0.016	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.059	0.042	21.089	0.007	0.007	0.000	0.000	0.000	0.000
94	A	98	GLY	0	-0.086	-0.062	21.906	0.021	0.021	0.000	0.000	0.000	0.000
95	A	99	THR	0	-0.082	-0.026	24.586	0.024	0.024	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.861	0.947	25.462	0.141	0.141	0.000	0.000	0.000	0.000
97	A	101	TYR	0	-0.003	-0.016	22.563	0.001	0.001	0.000	0.000	0.000	0.000
98	A	102	GLN	0	-0.053	-0.017	27.268	0.008	0.008	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.062	0.005	26.143	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	104	ILE	0	-0.107	-0.048	27.837	0.013	0.013	0.000	0.000	0.000	0.000
101	A	105	ASN	0	-0.041	-0.041	27.717	0.021	0.021	0.000	0.000	0.000	0.000
102	A	106	ILE	0	0.013	0.003	23.145	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.871	-0.896	24.644	-0.208	-0.208	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.834	0.880	23.300	0.156	0.156	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.910	-0.951	21.480	-0.158	-0.158	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.024	0.001	21.440	0.008	0.008	0.000	0.000	0.000	0.000
107	A	111	GLU	-1	-0.903	-0.944	20.840	-0.180	-0.180	0.000	0.000	0.000	0.000
108	A	112	PHE	0	-0.026	-0.027	16.742	0.003	0.003	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.951	-0.988	18.306	-0.360	-0.360	0.000	0.000	0.000	0.000
110	A	114	GLY	0	-0.036	-0.026	18.216	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	115	TYR	0	-0.054	-0.019	13.615	0.014	0.014	0.000	0.000	0.000	0.000
112	A	116	ASN	0	-0.021	-0.013	17.446	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	117	PHE	0	-0.008	-0.011	13.290	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.796	-0.888	18.524	-0.186	-0.186	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.014	-0.008	18.770	-0.034	-0.034	0.000	0.000	0.000	0.000
116	A	120	ALA	0	0.000	0.007	20.879	0.028	0.028	0.000	0.000	0.000	0.000
117	A	121	THR	0	-0.025	-0.023	21.935	-0.022	-0.022	0.000	0.000	0.000	0.000
118	A	122	CYS	0	-0.022	-0.001	23.741	0.026	0.026	0.000	0.000	0.000	0.000
119	A	123	ALA	0	-0.007	-0.005	25.561	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.965	0.998	25.386	0.239	0.239	0.000	0.000	0.000	0.000
121	A	125	LEU	0	-0.008	-0.013	28.966	0.005	0.005	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.856	0.899	30.014	0.153	0.153	0.000	0.000	0.000	0.000
123	A	127	GLY	0	0.041	0.024	26.503	-0.009	-0.009	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.019	-0.021	24.811	0.019	0.019	0.000	0.000	0.000	0.000
125	A	129	LEU	0	-0.037	0.005	20.113	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	130	HIS	0	0.003	0.001	19.179	0.039	0.039	0.000	0.000	0.000	0.000
127	A	131	LEU	0	0.013	0.017	17.388	-0.040	-0.040	0.000	0.000	0.000	0.000
128	A	132	VAL	0	0.001	-0.007	15.357	0.041	0.041	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.863	0.939	14.574	0.193	0.193	0.000	0.000	0.000	0.000
130	A	134	VAL	0	-0.009	-0.010	9.837	0.002	0.002	0.000	0.000	0.000	0.000
131	A	135	PRO	0	0.014	0.003	8.002	0.005	0.005	0.000	0.000	0.000	0.000
132	A	136	GLY	0	-0.023	-0.013	7.259	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.018	0.029	8.306	-0.085	-0.085	0.000	0.000	0.000	0.000
134	A	138	ASN	0	-0.007	0.005	7.102	-0.283	-0.283	0.000	0.000	0.000	0.000
135	A	139	ILE	0	0.010	0.007	10.945	0.089	0.089	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.008	0.007	11.177	-0.100	-0.100	0.000	0.000	0.000	0.000
137	A	141	VAL	0	0.006	0.004	12.716	0.096	0.096	0.000	0.000	0.000	0.000
138	A	142	VAL	0	-0.016	-0.018	14.150	-0.070	-0.070	0.000	0.000	0.000	0.000
139	A	143	LEU	0	0.017	0.016	16.557	0.055	0.055	0.000	0.000	0.000	0.000
140	A	144	TYR	0	-0.015	-0.024	19.358	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	145	ASP	-1	-0.807	-0.907	22.131	-0.217	-0.217	0.000	0.000	0.000	0.000
142	A	146	GLU	-1	-0.817	-0.892	25.156	-0.199	-0.199	0.000	0.000	0.000	0.000
143	A	147	GLU	-1	-0.925	-0.942	28.318	-0.162	-0.162	0.000	0.000	0.000	0.000
144	A	148	LYS	1	0.764	0.877	24.951	0.234	0.234	0.000	0.000	0.000	0.000
145	A	149	GLU	-1	-0.932	-0.960	25.644	-0.203	-0.203	0.000	0.000	0.000	0.000
146	A	150	GLN	0	0.028	0.023	22.393	-0.028	-0.028	0.000	0.000	0.000	0.000
147	A	151	ASP	-1	-0.823	-0.921	25.377	-0.224	-0.224	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.910	0.957	24.917	0.187	0.187	0.000	0.000	0.000	0.000
149	A	153	GLY	0	-0.014	-0.003	25.053	-0.009	-0.009	0.000	0.000	0.000	0.000
150	A	154	ASN	0	-0.025	-0.026	23.532	-0.034	-0.034	0.000	0.000	0.000	0.000
151	A	155	SER	0	0.040	-0.003	20.720	-0.025	-0.025	0.000	0.000	0.000	0.000
152	A	156	LYS	1	0.826	0.920	19.613	0.217	0.217	0.000	0.000	0.000	0.000
153	A	157	ILE	0	0.028	0.012	19.957	-0.018	-0.018	0.000	0.000	0.000	0.000
154	A	158	ALA	0	0.013	0.024	17.517	-0.030	-0.030	0.000	0.000	0.000	0.000
155	A	159	ALA	0	0.015	0.000	15.664	-0.063	-0.063	0.000	0.000	0.000	0.000
156	A	160	LEU	0	-0.002	-0.003	15.131	-0.043	-0.043	0.000	0.000	0.000	0.000
157	A	161	THR	0	-0.006	-0.016	14.451	-0.005	-0.005	0.000	0.000	0.000	0.000
158	A	162	PHE	0	-0.012	-0.012	7.354	-0.061	-0.061	0.000	0.000	0.000	0.000
159	A	163	ALA	0	0.016	0.001	10.502	-0.086	-0.086	0.000	0.000	0.000	0.000
160	A	164	LYS	1	0.817	0.916	11.350	0.447	0.447	0.000	0.000	0.000	0.000
161	A	165	GLU	-1	-0.741	-0.819	8.345	-1.218	-1.218	0.000	0.000	0.000	0.000
162	A	166	LEU	0	-0.005	0.019	5.872	-0.224	-0.224	0.000	0.000	0.000	0.000
163	A	167	ALA	0	-0.003	-0.003	7.402	0.175	0.175	0.000	0.000	0.000	0.000
164	A	168	GLU	-1	-0.860	-0.919	9.930	-0.472	-0.472	0.000	0.000	0.000	0.000
165	A	169	SER	0	-0.060	-0.059	4.602	-0.080	-0.048	-0.001	-0.002	-0.028	0.000
166	A	170	SER	0	0.004	0.007	6.331	0.335	0.335	0.000	0.000	0.000	0.000
167	A	171	GLN	0	-0.009	0.003	7.117	0.189	0.189	0.000	0.000	0.000	0.000
168	A	172	LEU	0	-0.083	-0.032	7.398	0.095	0.095	0.000	0.000	0.000	0.000
169	A	173	GLN	0	-0.033	-0.002	8.386	0.114	0.114	0.000	0.000	0.000	0.000
170	A	174	HIS	1	0.896	0.938	9.346	-0.109	-0.109	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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