FMO DATABASE

FMODB ID: 6YR6Z

Calculation Name: 1KJN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KJN

Chain ID: A

ChEMBL ID:

UniProt ID: O26871

Base Structure: X-ray

Registration Date: 2023-09-23

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1453408.469737
FMO2-HF: Nuclear repulsion	1394546.728688
FMO2-HF: Total energy	-58861.741048
FMO2-MP2: Total energy	-59032.428377

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:6:THR)

Summations of interaction energy for fragment #1(A:6:THR)

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.
-12.298	-11.315	6.645	-3.995	-3.633	-0.034

Interaction energy analysis for fragmet #1(A:6:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.052

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	8	LYS	1	0.764	0.890	3.858	-0.483	1.027	-0.011	-0.819	-0.680	0.001
4	A	9	ALA	0	-0.022	-0.017	6.906	0.555	0.555	0.000	0.000	0.000	0.000
5	A	10	LEU	0	0.000	0.016	9.065	-0.061	-0.061	0.000	0.000	0.000	0.000
6	A	11	MET	0	-0.062	-0.023	12.837	0.115	0.115	0.000	0.000	0.000	0.000
7	A	12	VAL	0	0.066	0.041	15.387	0.003	0.003	0.000	0.000	0.000	0.000
8	A	13	LEU	0	-0.084	-0.045	19.038	0.027	0.027	0.000	0.000	0.000	0.000
9	A	14	GLY	0	0.107	0.054	21.883	0.005	0.005	0.000	0.000	0.000	0.000
10	A	15	CYS	0	-0.103	-0.059	25.655	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	16	PRO	0	-0.046	-0.025	27.191	0.001	0.001	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.856	-0.901	28.544	-0.131	-0.131	0.000	0.000	0.000	0.000
13	A	18	SER	0	0.006	-0.007	28.583	0.007	0.007	0.000	0.000	0.000	0.000
14	A	19	PRO	0	-0.012	-0.009	28.141	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	20	VAL	0	-0.044	-0.019	25.826	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	21	GLN	0	0.031	0.018	23.305	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	22	ILE	0	0.039	0.029	22.005	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	23	PRO	0	-0.007	-0.011	21.035	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.024	-0.009	20.300	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.051	0.054	17.819	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	26	ILE	0	0.042	0.016	16.174	-0.053	-0.053	0.000	0.000	0.000	0.000
22	A	27	TYR	0	-0.101	-0.082	15.691	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	28	THR	0	0.013	-0.030	13.872	0.005	0.005	0.000	0.000	0.000	0.000
24	A	29	SER	0	0.004	-0.014	11.927	-0.068	-0.068	0.000	0.000	0.000	0.000
25	A	30	HIS	0	0.014	0.005	10.807	-0.166	-0.166	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.806	0.893	11.118	0.116	0.116	0.000	0.000	0.000	0.000
27	A	32	LEU	0	0.027	0.022	8.277	0.070	0.070	0.000	0.000	0.000	0.000
28	A	33	LYS	1	0.861	0.923	6.624	0.936	0.936	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.835	0.920	6.887	0.154	0.154	0.000	0.000	0.000	0.000
30	A	35	LYS	1	0.849	0.932	6.606	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	36	GLY	0	-0.030	-0.002	3.277	0.685	1.154	0.027	-0.190	-0.306	0.000
32	A	37	PHE	0	-0.020	-0.004	1.960	-8.403	-9.518	6.630	-2.975	-2.540	-0.035
33	A	38	ARG	1	0.823	0.890	4.088	2.367	2.486	-0.001	-0.011	-0.107	0.000
34	A	39	VAL	0	-0.026	-0.023	6.506	0.173	0.173	0.000	0.000	0.000	0.000
35	A	40	THR	0	0.003	-0.013	9.713	0.042	0.042	0.000	0.000	0.000	0.000
36	A	41	VAL	0	-0.034	-0.024	12.817	0.072	0.072	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.007	-0.015	16.021	0.016	0.016	0.000	0.000	0.000	0.000
38	A	43	ALA	0	0.048	0.009	19.068	0.028	0.028	0.000	0.000	0.000	0.000
39	A	44	ASN	0	0.090	0.056	22.559	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	45	PRO	0	0.061	0.006	25.592	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	46	ALA	0	-0.028	-0.004	27.156	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	47	ALA	0	0.036	0.012	24.203	0.000	0.000	0.000	0.000	0.000	0.000
43	A	48	LEU	0	0.014	0.012	19.919	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	49	ARG	1	0.963	0.972	22.919	0.208	0.208	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.036	-0.021	25.636	0.006	0.006	0.000	0.000	0.000	0.000
46	A	51	VAL	0	0.032	0.014	18.575	0.008	0.008	0.000	0.000	0.000	0.000
47	A	52	GLN	0	-0.003	-0.008	21.683	0.014	0.014	0.000	0.000	0.000	0.000
48	A	53	VAL	0	-0.059	-0.025	22.760	0.009	0.009	0.000	0.000	0.000	0.000
49	A	54	ALA	0	-0.048	-0.012	22.790	0.017	0.017	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.819	-0.912	16.996	-0.470	-0.470	0.000	0.000	0.000	0.000
51	A	56	PRO	0	-0.030	-0.004	20.285	-0.025	-0.025	0.000	0.000	0.000	0.000
52	A	57	GLU	-1	-0.963	-0.987	20.244	-0.251	-0.251	0.000	0.000	0.000	0.000
53	A	58	GLY	0	-0.028	0.000	17.159	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	59	ILE	0	-0.048	-0.020	15.132	-0.066	-0.066	0.000	0.000	0.000	0.000
55	A	60	TYR	0	-0.064	-0.044	13.860	-0.050	-0.050	0.000	0.000	0.000	0.000
56	A	61	THR	0	-0.015	0.005	12.819	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	62	ASP	-1	-0.814	-0.886	9.454	-1.578	-1.578	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.829	-0.865	12.273	-1.000	-1.000	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.039	-0.019	14.666	0.035	0.035	0.000	0.000	0.000	0.000
60	A	65	VAL	0	0.006	0.014	17.223	0.030	0.030	0.000	0.000	0.000	0.000
61	A	66	ASP	-1	-0.814	-0.895	19.890	-0.277	-0.277	0.000	0.000	0.000	0.000
62	A	67	LEU	0	-0.007	0.018	22.098	-0.023	-0.023	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.807	-0.893	23.293	-0.243	-0.243	0.000	0.000	0.000	0.000
64	A	69	SER	0	-0.071	-0.070	23.198	0.002	0.002	0.000	0.000	0.000	0.000
65	A	70	CYS	0	-0.094	-0.028	18.382	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	71	ILE	0	0.012	-0.005	20.432	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	72	ASN	0	-0.149	-0.078	22.742	0.032	0.032	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.897	-0.940	18.905	-0.324	-0.324	0.000	0.000	0.000	0.000
69	A	74	LEU	0	-0.070	-0.004	15.205	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	75	ALA	0	-0.001	-0.012	16.169	0.066	0.066	0.000	0.000	0.000	0.000
71	A	76	GLU	-1	-0.847	-0.916	15.084	-0.273	-0.273	0.000	0.000	0.000	0.000
72	A	77	GLY	0	-0.052	-0.022	11.363	0.003	0.003	0.000	0.000	0.000	0.000
73	A	78	ASP	-1	-0.877	-0.937	10.082	-1.239	-1.239	0.000	0.000	0.000	0.000
74	A	79	TYR	0	0.010	-0.011	9.087	-0.385	-0.385	0.000	0.000	0.000	0.000
75	A	80	GLU	-1	-0.834	-0.900	5.074	-2.194	-2.194	0.000	0.000	0.000	0.000
76	A	81	PHE	0	-0.025	-0.022	8.319	0.251	0.251	0.000	0.000	0.000	0.000
77	A	82	LEU	0	0.028	0.028	10.805	-0.186	-0.186	0.000	0.000	0.000	0.000
78	A	83	ALA	0	-0.001	0.004	14.010	0.086	0.086	0.000	0.000	0.000	0.000
79	A	84	GLY	0	0.047	0.013	15.729	-0.038	-0.038	0.000	0.000	0.000	0.000
80	A	85	PHE	0	-0.111	-0.054	17.573	0.039	0.039	0.000	0.000	0.000	0.000
81	A	86	VAL	0	0.009	-0.007	21.926	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	87	PRO	0	-0.015	-0.009	25.350	0.013	0.013	0.000	0.000	0.000	0.000
83	A	88	ASN	0	0.019	-0.015	28.535	0.004	0.004	0.000	0.000	0.000	0.000
84	A	89	ASP	-1	-0.775	-0.903	29.083	-0.123	-0.123	0.000	0.000	0.000	0.000
85	A	90	ALA	0	-0.037	0.001	29.952	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	91	ALA	0	-0.019	-0.009	25.283	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	92	ALA	0	0.020	0.019	24.965	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	93	ALA	0	0.057	0.028	25.803	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	94	TYR	0	-0.072	-0.052	23.651	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.016	-0.001	19.225	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	96	VAL	0	0.038	0.016	21.762	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	97	THR	0	-0.044	-0.029	23.309	0.003	0.003	0.000	0.000	0.000	0.000
93	A	98	PHE	0	-0.028	-0.041	18.797	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	99	ALA	0	0.023	0.002	18.330	-0.030	-0.030	0.000	0.000	0.000	0.000
95	A	100	GLY	0	-0.016	-0.002	19.001	0.005	0.005	0.000	0.000	0.000	0.000
96	A	101	ILE	0	-0.065	-0.025	18.257	0.012	0.012	0.000	0.000	0.000	0.000
97	A	102	LEU	0	-0.031	-0.024	12.902	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	103	ASN	0	-0.092	-0.046	14.799	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	104	THR	0	-0.007	-0.005	11.020	0.064	0.064	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.870	-0.934	12.043	0.110	0.110	0.000	0.000	0.000	0.000
101	A	106	THR	0	0.014	-0.013	13.938	-0.091	-0.091	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.064	-0.027	15.915	0.043	0.043	0.000	0.000	0.000	0.000
103	A	108	ALA	0	0.058	0.036	17.812	-0.037	-0.037	0.000	0.000	0.000	0.000
104	A	109	ILE	0	-0.058	-0.039	17.629	0.022	0.022	0.000	0.000	0.000	0.000
105	A	110	ILE	0	0.035	0.024	21.999	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	111	PHE	0	-0.089	-0.073	24.013	0.009	0.009	0.000	0.000	0.000	0.000
107	A	112	ASP	-1	-0.652	-0.797	28.266	-0.102	-0.102	0.000	0.000	0.000	0.000
108	A	113	ARG	1	0.706	0.801	31.983	0.082	0.082	0.000	0.000	0.000	0.000
109	A	114	ASP	-1	-0.843	-0.921	34.883	-0.062	-0.062	0.000	0.000	0.000	0.000
110	A	115	ALA	0	-0.103	-0.071	34.871	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.876	-0.922	35.562	-0.056	-0.056	0.000	0.000	0.000	0.000
112	A	117	VAL	0	0.053	0.028	33.539	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	118	LEU	0	-0.083	-0.043	29.717	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	119	GLU	-1	-0.925	-0.946	31.491	-0.054	-0.054	0.000	0.000	0.000	0.000
115	A	120	GLU	-1	-0.912	-0.954	32.992	-0.075	-0.075	0.000	0.000	0.000	0.000
116	A	121	LEU	0	-0.017	-0.008	29.196	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	122	VAL	0	-0.060	-0.038	28.027	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	123	ASN	0	-0.042	-0.029	29.028	0.001	0.001	0.000	0.000	0.000	0.000
119	A	124	GLU	-1	-0.874	-0.934	29.218	-0.108	-0.108	0.000	0.000	0.000	0.000
120	A	125	ILE	0	-0.038	-0.010	24.014	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	126	MET	0	-0.052	-0.035	26.700	0.003	0.003	0.000	0.000	0.000	0.000
122	A	127	GLU	-1	-0.984	-0.981	28.292	-0.053	-0.053	0.000	0.000	0.000	0.000
123	A	128	THR	0	-0.095	-0.065	27.577	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	129	LEU	0	-0.072	-0.042	21.940	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	130	ASP	-1	-0.957	-0.954	20.721	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	131	ALA	0	0.003	-0.010	19.618	-0.017	-0.017	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.876	-0.912	18.583	0.014	0.014	0.000	0.000	0.000	0.000
128	A	133	ILE	0	0.030	0.001	20.441	-0.027	-0.027	0.000	0.000	0.000	0.000
129	A	134	ILE	0	-0.067	-0.020	19.071	0.016	0.016	0.000	0.000	0.000	0.000
130	A	135	ALA	0	0.102	0.056	23.022	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	136	ALA	0	-0.089	-0.058	26.468	0.012	0.012	0.000	0.000	0.000	0.000
132	A	137	ARG	1	0.982	1.018	28.777	0.056	0.056	0.000	0.000	0.000	0.000
133	A	138	ALA	0	-0.064	-0.023	28.464	0.006	0.006	0.000	0.000	0.000	0.000
134	A	139	HIS	0	0.071	0.020	30.587	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	140	HIS	0	0.064	0.019	30.336	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	141	ASN	0	0.001	0.009	29.785	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	142	PRO	0	0.097	0.037	24.602	0.003	0.003	0.000	0.000	0.000	0.000
138	A	143	ALA	0	-0.006	0.000	25.325	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	144	PRO	0	-0.021	-0.020	25.764	0.003	0.003	0.000	0.000	0.000	0.000
140	A	145	LEU	0	0.065	0.044	23.243	0.008	0.008	0.000	0.000	0.000	0.000
141	A	146	ARG	1	0.900	0.934	20.755	0.129	0.129	0.000	0.000	0.000	0.000
142	A	147	VAL	0	-0.027	-0.017	20.835	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	148	ARG	1	0.877	0.939	21.856	0.085	0.085	0.000	0.000	0.000	0.000
144	A	149	ILE	0	0.079	0.044	16.564	0.013	0.013	0.000	0.000	0.000	0.000
145	A	150	ASP	-1	-0.794	-0.858	17.030	-0.138	-0.138	0.000	0.000	0.000	0.000
146	A	151	ARG	1	0.797	0.871	17.497	0.030	0.030	0.000	0.000	0.000	0.000
147	A	152	PHE	0	0.097	0.064	13.732	0.018	0.018	0.000	0.000	0.000	0.000
148	A	153	MET	0	-0.017	-0.014	12.277	0.039	0.039	0.000	0.000	0.000	0.000
149	A	154	GLU	-1	-0.933	-0.957	13.177	0.035	0.035	0.000	0.000	0.000	0.000
150	A	155	GLU	-1	-0.905	-0.945	15.486	0.101	0.101	0.000	0.000	0.000	0.000
151	A	156	LYS	1	0.823	0.902	13.845	-0.020	-0.020	0.000	0.000	0.000	0.000
152	A	157	PRO	0	-0.060	0.003	8.467	0.192	0.192	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:6:THR)