FMO DATABASE

FMODB ID: 52LKZ

Calculation Name: 1KU9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KU9

Chain ID: A

ChEMBL ID:

UniProt ID: Q58958

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	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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1322416.169354
FMO2-HF: Nuclear repulsion	1261169.945983
FMO2-HF: Total energy	-61246.223371
FMO2-MP2: Total energy	-61424.599775

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:1:MET)

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

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.
-5.381	-0.625	2.997	-1.844	-5.908	-0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : -0.002

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	3	ILE	0	0.026	0.015	2.378	-4.228	-1.242	1.599	-1.225	-3.360	0.001
4	A	4	MET	0	0.034	0.027	2.361	-1.643	-0.054	1.399	-0.604	-2.384	-0.003
5	A	5	GLU	-1	-0.809	-0.908	4.948	-0.388	-0.207	-0.001	-0.015	-0.164	0.000
6	A	6	GLU	-1	-0.846	-0.915	6.902	0.518	0.518	0.000	0.000	0.000	0.000
7	A	7	ALA	0	-0.019	-0.026	7.055	0.078	0.078	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.761	0.890	8.611	0.816	0.816	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.853	0.890	10.601	-0.052	-0.052	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.024	0.009	10.543	0.071	0.071	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.055	0.018	11.337	0.049	0.049	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.006	-0.008	14.522	0.040	0.040	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.925	-0.947	16.204	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.067	-0.028	17.088	0.028	0.028	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.013	-0.031	17.245	0.029	0.029	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.051	-0.020	20.289	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.761	-0.886	22.157	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.011	0.013	21.903	0.012	0.012	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.018	0.000	25.263	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.833	0.910	26.700	0.050	0.050	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.004	0.011	26.889	0.011	0.011	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.102	-0.049	28.208	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.002	-0.005	31.328	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.035	-0.016	28.897	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.017	-0.021	29.162	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LYS	1	1.074	1.032	24.887	0.043	0.043	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.005	-0.018	24.259	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.025	-0.011	24.247	-0.021	-0.021	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.038	0.032	23.469	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.029	0.005	20.173	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.052	-0.052	19.773	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.023	0.011	20.902	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.048	0.030	16.549	-0.031	-0.031	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.027	-0.001	15.998	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.059	-0.044	16.682	-0.052	-0.052	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.047	-0.005	14.727	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.014	-0.017	11.209	-0.040	-0.040	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.070	-0.016	13.283	-0.143	-0.143	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.794	-0.873	14.432	-0.765	-0.765	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.791	0.877	15.204	0.784	0.784	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.026	0.020	19.139	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.000	0.018	17.593	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.020	-0.044	21.883	0.044	0.044	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.000	-0.023	23.718	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.020	-0.037	24.367	0.005	0.005	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.751	-0.822	19.947	-0.338	-0.338	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.052	0.022	19.873	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.090	-0.032	20.585	0.012	0.012	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.927	-0.942	19.469	-0.226	-0.226	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.799	-0.893	14.260	-0.583	-0.583	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.055	-0.024	16.832	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.847	0.926	16.198	0.276	0.276	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.020	0.004	21.988	0.029	0.029	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.061	0.024	25.198	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	55	LYS	1	1.024	0.992	27.985	0.115	0.115	0.000	0.000	0.000	0.000
56	A	56	GLY	0	-0.009	-0.001	29.633	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.031	0.011	26.552	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.048	0.047	24.788	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.008	-0.007	27.325	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	MET	0	-0.087	-0.049	30.582	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.008	-0.022	26.506	0.004	0.004	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.009	0.007	25.023	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.947	0.982	28.612	0.114	0.114	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.875	0.925	30.433	0.108	0.108	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.030	0.017	24.735	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.794	-0.875	28.875	-0.177	-0.177	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.868	-0.903	31.089	-0.105	-0.105	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.092	-0.057	29.882	0.003	0.003	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.004	0.006	30.741	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	70	PHE	0	-0.013	-0.003	24.844	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.022	-0.003	24.201	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.829	0.906	26.702	0.269	0.269	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.800	0.881	27.934	0.151	0.151	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.002	0.015	25.925	0.003	0.003	0.000	0.000	0.000	0.000
75	A	75	TRP	0	-0.040	-0.026	29.095	0.006	0.006	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.042	0.027	25.861	-0.009	-0.009	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.960	0.970	29.550	0.213	0.213	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.009	-0.012	30.807	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.825	-0.898	28.283	-0.200	-0.200	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.849	0.918	31.433	0.170	0.170	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.875	0.941	27.193	0.214	0.214	0.000	0.000	0.000	0.000
82	A	82	ASN	0	0.011	0.004	30.140	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.032	-0.001	23.804	0.007	0.007	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.039	-0.025	24.795	0.027	0.027	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.734	-0.859	22.575	-0.333	-0.333	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.028	0.007	20.960	0.032	0.032	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.032	-0.021	23.041	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.850	-0.938	23.473	-0.284	-0.284	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.075	0.025	22.739	0.023	0.023	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.061	0.036	20.056	0.027	0.027	0.000	0.000	0.000	0.000
91	A	91	SER	0	0.029	0.026	25.484	0.024	0.024	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.076	-0.055	26.564	0.017	0.017	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.035	-0.025	25.248	0.014	0.014	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.889	0.950	28.990	0.191	0.191	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.839	-0.925	31.810	-0.138	-0.138	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.073	-0.030	30.601	0.013	0.013	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.036	-0.027	33.278	0.010	0.010	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.940	0.981	35.015	0.136	0.136	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.988	1.006	33.667	0.131	0.131	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.948	0.967	34.078	0.103	0.103	0.000	0.000	0.000	0.000
101	A	101	HIS	0	-0.002	0.008	39.371	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.862	-0.946	41.178	-0.081	-0.081	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.079	-0.028	41.632	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	ILE	0	-0.041	-0.025	41.290	0.005	0.005	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.004	0.009	44.932	0.004	0.004	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.865	0.924	46.876	0.057	0.057	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.012	-0.004	47.914	0.004	0.004	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.044	-0.070	49.137	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.858	-0.911	50.882	-0.049	-0.049	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.825	-0.917	53.002	-0.047	-0.047	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.053	-0.038	51.684	0.002	0.002	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.873	0.943	54.699	0.036	0.036	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.886	0.923	56.032	0.046	0.046	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.082	-0.037	57.848	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.845	-0.929	58.125	-0.029	-0.029	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.969	-0.961	60.774	-0.032	-0.032	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.911	0.957	63.217	0.034	0.034	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.031	-0.014	63.125	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	ASN	0	-0.001	-0.028	64.302	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.847	-0.910	66.661	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.931	-0.978	67.606	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.863	-0.939	64.778	-0.020	-0.020	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.823	0.960	62.304	0.021	0.021	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.834	-0.936	61.526	-0.023	-0.023	0.000	0.000	0.000	0.000
125	A	125	PHE	0	-0.013	0.005	61.020	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.025	-0.005	57.391	0.000	0.000	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.813	0.899	56.764	0.023	0.023	0.000	0.000	0.000	0.000
128	A	128	GLN	0	-0.051	-0.008	55.430	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.932	0.947	51.761	0.025	0.025	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.101	0.067	51.660	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.970	0.979	51.014	0.022	0.022	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.041	-0.012	48.160	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	ILE	0	0.020	-0.003	46.780	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.814	-0.856	47.411	-0.038	-0.038	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.905	0.952	44.393	0.027	0.027	0.000	0.000	0.000	0.000
136	A	136	MET	0	0.012	0.001	41.852	-0.003	-0.003	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.867	0.928	42.102	0.049	0.049	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.900	0.942	42.765	0.036	0.036	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.061	-0.028	37.779	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	140	SER	0	-0.034	-0.022	37.855	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.727	-0.856	38.597	-0.061	-0.061	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.988	1.002	36.782	0.049	0.049	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.031	-0.011	32.364	-0.004	-0.004	0.000	0.000	0.000	0.000
144	A	144	LEU	0	-0.010	0.009	33.343	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.912	-0.977	34.624	-0.075	-0.075	0.000	0.000	0.000	0.000
146	A	146	ALA	0	-0.003	-0.007	31.471	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	147	LEU	0	-0.044	-0.026	28.823	-0.009	-0.009	0.000	0.000	0.000	0.000
148	A	148	ASN	0	-0.166	-0.075	30.693	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.870	-0.933	31.419	-0.089	-0.089	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.103	-0.047	26.052	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	151	ASP	-1	-0.871	-0.908	26.967	-0.169	-0.169	0.000	0.000	0.000	0.000

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