FMO DATABASE

FMODB ID: 6NY9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1694815.851306
FMO2-HF: Nuclear repulsion	1628895.589411
FMO2-HF: Total energy	-65920.261896
FMO2-MP2: Total energy	-66115.234984

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.
-8.962	-0.378	2.35	-2.345	-8.59	-0.01

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 : 0.009 / q_NPA : -0.017

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	0.081	0.006	2.729	-7.603	0.416	2.318	-2.405	-7.933	-0.010
4	A	8	ASP	-1	-0.845	-0.915	3.433	-0.480	-0.394	0.031	0.107	-0.224	0.000
5	A	9	SER	0	-0.006	-0.014	5.074	0.277	0.277	0.000	0.000	0.000	0.000
6	A	10	TYR	0	0.009	0.013	3.775	-0.632	-0.153	0.001	-0.047	-0.433	0.000
7	A	11	LEU	0	0.017	0.007	5.914	0.161	0.161	0.000	0.000	0.000	0.000
8	A	12	ASN	0	0.002	-0.009	8.661	0.144	0.144	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.915	-0.958	9.019	-0.537	-0.537	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.789	0.901	7.517	0.807	0.807	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.011	0.016	10.609	0.072	0.072	0.000	0.000	0.000	0.000
12	A	16	LEU	0	0.004	0.024	12.757	0.053	0.053	0.000	0.000	0.000	0.000
13	A	17	ALA	0	0.000	0.011	13.994	0.043	0.043	0.000	0.000	0.000	0.000
14	A	18	THR	0	-0.069	-0.064	15.413	0.042	0.042	0.000	0.000	0.000	0.000
15	A	19	ASN	0	-0.042	-0.020	17.853	0.018	0.018	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.001	-0.001	19.286	0.028	0.028	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.032	-0.010	15.840	0.017	0.017	0.000	0.000	0.000	0.000
18	A	22	SER	0	0.006	0.002	18.953	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	23	GLY	0	0.002	-0.002	15.761	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	24	ALA	0	-0.011	-0.002	12.206	0.020	0.020	0.000	0.000	0.000	0.000
21	A	25	GLY	0	0.026	0.009	10.616	-0.066	-0.066	0.000	0.000	0.000	0.000
22	A	26	LEU	0	-0.021	0.002	6.143	0.028	0.028	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.024	0.017	10.113	-0.051	-0.051	0.000	0.000	0.000	0.000
24	A	28	SER	0	0.016	0.025	11.676	0.074	0.074	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.854	-0.914	12.472	0.240	0.240	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.951	-0.985	13.795	0.324	0.324	0.000	0.000	0.000	0.000
27	A	31	ASP	-1	-0.916	-0.967	15.632	0.086	0.086	0.000	0.000	0.000	0.000
28	A	32	GLY	0	-0.015	0.003	16.173	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	33	VAL	0	-0.043	-0.028	15.184	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	34	VAL	0	-0.053	-0.025	12.093	0.026	0.026	0.000	0.000	0.000	0.000
31	A	35	TYR	0	-0.051	-0.044	6.121	0.005	0.005	0.000	0.000	0.000	0.000
32	A	36	ALA	0	-0.044	-0.027	6.863	-0.147	-0.147	0.000	0.000	0.000	0.000
33	A	37	CYS	0	-0.004	0.003	8.763	0.112	0.112	0.000	0.000	0.000	0.000
34	A	38	VAL	0	-0.016	0.017	9.612	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	39	ALA	0	0.051	0.003	12.341	0.045	0.045	0.000	0.000	0.000	0.000
36	A	40	GLN	0	0.030	0.008	16.087	0.004	0.004	0.000	0.000	0.000	0.000
37	A	41	GLY	0	-0.030	0.004	18.262	0.010	0.010	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.886	-0.961	18.672	-0.265	-0.265	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-1.006	-1.012	20.691	-0.123	-0.123	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.113	-0.065	22.957	0.008	0.008	0.000	0.000	0.000	0.000
41	A	45	ASP	-1	-0.902	-0.931	23.701	-0.122	-0.122	0.000	0.000	0.000	0.000
42	A	46	PRO	0	-0.002	0.003	22.517	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.061	-0.041	22.055	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	48	PHE	0	0.022	0.029	19.462	0.003	0.003	0.000	0.000	0.000	0.000
45	A	49	ASP	-1	-0.862	-0.933	18.928	-0.202	-0.202	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.859	0.943	11.024	0.525	0.525	0.000	0.000	0.000	0.000
47	A	51	TRP	0	0.030	0.004	11.459	0.008	0.008	0.000	0.000	0.000	0.000
48	A	52	SER	0	-0.067	-0.049	17.173	0.023	0.023	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.018	-0.013	18.285	0.016	0.016	0.000	0.000	0.000	0.000
50	A	54	PHE	0	-0.031	-0.038	15.408	0.008	0.008	0.000	0.000	0.000	0.000
51	A	55	TYR	0	-0.018	-0.012	16.879	0.020	0.020	0.000	0.000	0.000	0.000
52	A	56	LYS	1	0.927	0.973	18.777	0.048	0.048	0.000	0.000	0.000	0.000
53	A	57	GLU	-1	-0.982	-0.966	22.324	-0.036	-0.036	0.000	0.000	0.000	0.000
54	A	58	ASP	-1	-0.850	-0.939	23.790	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	59	TYR	0	-0.117	-0.121	25.246	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.828	-0.875	29.548	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	61	ILE	0	-0.073	-0.036	31.362	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	62	GLU	-1	-0.932	-0.983	34.220	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.059	-0.033	36.065	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.893	-0.952	38.779	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.857	-0.926	42.056	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	66	GLU	-1	-0.901	-0.966	43.308	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	67	ASN	0	-0.146	-0.077	45.993	0.000	0.000	0.000	0.000	0.000	0.000
64	A	68	GLY	0	-0.016	0.010	46.909	0.000	0.000	0.000	0.000	0.000	0.000
65	A	69	THR	0	-0.109	-0.052	44.614	0.000	0.000	0.000	0.000	0.000	0.000
66	A	70	LYS	1	0.946	0.983	43.089	0.013	0.013	0.000	0.000	0.000	0.000
67	A	71	THR	0	-0.056	-0.031	40.021	0.002	0.002	0.000	0.000	0.000	0.000
68	A	72	THR	0	0.020	0.010	35.979	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	73	LYS	1	0.849	0.940	33.400	0.005	0.005	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.016	-0.020	29.618	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.067	-0.032	26.296	0.005	0.005	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.064	0.029	22.792	0.000	0.000	0.000	0.000	0.000	0.000
73	A	77	GLU	-1	-0.698	-0.809	21.724	-0.047	-0.047	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.067	0.077	19.711	0.001	0.001	0.000	0.000	0.000	0.000
75	A	79	GLN	0	0.047	0.005	20.358	0.013	0.013	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.103	-0.064	23.174	0.001	0.001	0.000	0.000	0.000	0.000
77	A	81	ILE	0	0.019	0.003	18.221	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	82	LEU	0	0.000	-0.001	18.016	0.005	0.005	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.028	0.003	21.618	0.004	0.004	0.000	0.000	0.000	0.000
80	A	84	VAL	0	0.030	0.021	23.784	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	85	PHE	0	-0.026	-0.021	19.098	0.003	0.003	0.000	0.000	0.000	0.000
82	A	86	ASN	0	-0.026	-0.011	22.267	0.012	0.012	0.000	0.000	0.000	0.000
83	A	87	GLU	-1	-0.932	-0.964	24.624	0.055	0.055	0.000	0.000	0.000	0.000
84	A	88	GLY	0	-0.069	-0.030	27.157	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	89	TYR	0	-0.056	-0.028	28.456	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.046	0.010	28.314	0.004	0.004	0.000	0.000	0.000	0.000
87	A	91	PRO	0	-0.019	-0.001	29.765	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.862	-0.932	29.962	0.003	0.003	0.000	0.000	0.000	0.000
89	A	93	GLY	0	-0.084	-0.038	29.805	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	94	VAL	0	0.049	0.010	23.122	0.005	0.005	0.000	0.000	0.000	0.000
91	A	95	TRP	0	-0.043	-0.024	24.850	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	96	LEU	0	-0.003	-0.005	18.001	0.006	0.006	0.000	0.000	0.000	0.000
93	A	97	GLY	0	0.049	0.033	21.410	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	98	GLY	0	-0.070	-0.041	21.977	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	99	THR	0	-0.087	-0.035	24.839	0.004	0.004	0.000	0.000	0.000	0.000
96	A	100	LYS	1	0.940	0.979	25.835	0.026	0.026	0.000	0.000	0.000	0.000
97	A	101	TYR	0	-0.017	-0.020	22.490	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	102	GLN	0	-0.035	-0.023	27.574	0.005	0.005	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.031	0.004	26.545	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	104	ILE	0	-0.099	-0.041	28.284	0.000	0.000	0.000	0.000	0.000	0.000
101	A	105	ASN	0	-0.010	-0.023	27.845	0.007	0.007	0.000	0.000	0.000	0.000
102	A	106	ILE	0	0.012	0.012	22.947	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.911	-0.945	24.331	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.866	0.917	22.848	-0.052	-0.052	0.000	0.000	0.000	0.000
105	A	109	ASP	-1	-0.888	-0.946	21.286	0.049	0.049	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.041	-0.003	20.731	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	111	GLU	-1	-0.939	-0.972	20.689	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	112	PHE	0	-0.025	-0.021	16.919	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	113	GLU	-1	-0.963	-0.989	18.350	-0.173	-0.173	0.000	0.000	0.000	0.000
110	A	114	GLY	0	-0.032	-0.025	18.323	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	115	TYR	0	-0.044	-0.020	13.739	0.007	0.007	0.000	0.000	0.000	0.000
112	A	116	ASN	0	0.002	0.008	17.437	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	117	PHE	0	-0.018	-0.016	13.124	0.007	0.007	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.839	-0.898	18.039	0.067	0.067	0.000	0.000	0.000	0.000
115	A	119	VAL	0	-0.023	-0.028	18.632	0.003	0.003	0.000	0.000	0.000	0.000
116	A	120	ALA	0	0.001	0.004	20.658	0.000	0.000	0.000	0.000	0.000	0.000
117	A	121	THR	0	-0.031	-0.038	22.327	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	122	CYS	0	-0.029	-0.010	24.071	0.011	0.011	0.000	0.000	0.000	0.000
119	A	123	ALA	0	-0.033	-0.013	25.564	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.983	1.003	25.544	0.085	0.085	0.000	0.000	0.000	0.000
121	A	125	LEU	0	-0.030	-0.020	28.926	0.000	0.000	0.000	0.000	0.000	0.000
122	A	126	LYS	1	0.884	0.931	29.657	0.066	0.066	0.000	0.000	0.000	0.000
123	A	127	GLY	0	0.094	0.049	26.486	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.039	-0.028	24.692	0.011	0.011	0.000	0.000	0.000	0.000
125	A	129	LEU	0	-0.015	0.010	20.074	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	130	HIS	0	-0.004	0.011	19.327	0.022	0.022	0.000	0.000	0.000	0.000
127	A	131	LEU	0	0.005	0.009	17.757	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	132	VAL	0	0.015	0.005	15.101	0.001	0.001	0.000	0.000	0.000	0.000
129	A	133	LYS	1	0.918	0.982	14.706	-0.146	-0.146	0.000	0.000	0.000	0.000
130	A	134	VAL	0	-0.007	-0.003	9.427	-0.055	-0.055	0.000	0.000	0.000	0.000
131	A	135	PRO	0	0.026	0.012	7.198	0.064	0.064	0.000	0.000	0.000	0.000
132	A	136	GLY	0	-0.050	-0.043	7.439	0.223	0.223	0.000	0.000	0.000	0.000
133	A	137	GLY	0	0.031	0.020	8.421	-0.021	-0.021	0.000	0.000	0.000	0.000
134	A	138	ASN	0	0.034	0.019	6.932	-0.203	-0.203	0.000	0.000	0.000	0.000
135	A	139	ILE	0	0.003	0.002	11.006	-0.063	-0.063	0.000	0.000	0.000	0.000
136	A	140	LEU	0	-0.022	-0.001	11.008	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	141	VAL	0	-0.004	-0.010	13.207	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	142	VAL	0	0.001	-0.003	14.473	-0.042	-0.042	0.000	0.000	0.000	0.000
139	A	143	LEU	0	0.011	0.012	16.709	0.025	0.025	0.000	0.000	0.000	0.000
140	A	144	TYR	0	0.021	0.019	19.470	-0.012	-0.012	0.000	0.000	0.000	0.000
141	A	145	ASP	-1	-0.844	-0.942	22.392	-0.100	-0.100	0.000	0.000	0.000	0.000
142	A	146	GLU	-1	-0.913	-0.974	25.227	-0.077	-0.077	0.000	0.000	0.000	0.000
143	A	147	GLU	-1	-0.992	-0.995	28.484	-0.078	-0.078	0.000	0.000	0.000	0.000
144	A	148	LYS	1	0.858	0.931	23.894	0.130	0.130	0.000	0.000	0.000	0.000
145	A	149	GLU	-1	-0.960	-0.971	26.283	-0.117	-0.117	0.000	0.000	0.000	0.000
146	A	150	GLN	0	0.006	0.023	21.965	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	151	ASP	-1	-0.840	-0.936	25.435	-0.092	-0.092	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.940	0.963	25.025	0.051	0.051	0.000	0.000	0.000	0.000
149	A	153	GLY	0	-0.018	-0.014	24.610	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	154	ASN	0	0.048	0.013	23.041	-0.013	-0.013	0.000	0.000	0.000	0.000
151	A	155	SER	0	0.032	0.022	20.583	-0.012	-0.012	0.000	0.000	0.000	0.000
152	A	156	LYS	1	0.876	0.952	19.470	0.044	0.044	0.000	0.000	0.000	0.000
153	A	157	ILE	0	0.011	0.011	19.400	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	158	ALA	0	0.027	0.019	17.235	-0.018	-0.018	0.000	0.000	0.000	0.000
155	A	159	ALA	0	0.000	-0.011	15.350	-0.037	-0.037	0.000	0.000	0.000	0.000
156	A	160	LEU	0	-0.021	-0.012	14.592	-0.008	-0.008	0.000	0.000	0.000	0.000
157	A	161	THR	0	-0.020	-0.010	14.316	-0.005	-0.005	0.000	0.000	0.000	0.000
158	A	162	PHE	0	0.028	0.009	7.057	-0.067	-0.067	0.000	0.000	0.000	0.000
159	A	163	ALA	0	-0.002	-0.007	10.223	-0.077	-0.077	0.000	0.000	0.000	0.000
160	A	164	LYS	1	0.854	0.927	10.864	0.233	0.233	0.000	0.000	0.000	0.000
161	A	165	GLU	-1	-0.858	-0.926	8.708	-0.808	-0.808	0.000	0.000	0.000	0.000
162	A	166	LEU	0	-0.047	-0.029	5.602	-0.293	-0.293	0.000	0.000	0.000	0.000
163	A	167	ALA	0	0.005	-0.011	7.080	0.068	0.068	0.000	0.000	0.000	0.000
164	A	168	GLU	-1	-0.856	-0.906	9.807	-0.314	-0.314	0.000	0.000	0.000	0.000
165	A	169	SER	0	-0.092	-0.047	5.213	-0.311	-0.311	0.000	0.000	0.000	0.000
166	A	170	SER	0	0.028	0.010	6.157	0.160	0.160	0.000	0.000	0.000	0.000
167	A	171	GLN	0	-0.031	-0.022	6.964	0.291	0.291	0.000	0.000	0.000	0.000
168	A	172	LEU	0	-0.092	-0.017	8.289	0.065	0.065	0.000	0.000	0.000	0.000
169	A	173	GLN	0	0.020	0.019	7.771	0.017	0.017	0.000	0.000	0.000	0.000
170	A	174	HIS	1	0.908	0.955	9.638	-0.159	-0.159	0.000	0.000	0.000	0.000

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