FMO DATABASE

FMODB ID: YZ2L2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1323806.182899
FMO2-HF: Nuclear repulsion	1262558.731282
FMO2-HF: Total energy	-61247.451618
FMO2-MP2: Total energy	-61425.641725

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.
-5.157	-0.446	2.194	-1.781	-5.125	-0.003

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 : 0.044 / q_NPA : 0.004

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	0.020	0.007	2.843	-3.819	-0.878	0.379	-0.992	-2.327	0.001
4	A	4	MET	0	0.015	0.010	2.360	-1.908	-0.321	1.816	-0.770	-2.634	-0.004
5	A	5	GLU	-1	-0.805	-0.893	4.727	-0.345	-0.162	-0.001	-0.019	-0.164	0.000
6	A	6	GLU	-1	-0.822	-0.894	7.312	0.456	0.456	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.002	-0.006	7.008	0.085	0.085	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.786	0.881	8.639	0.859	0.859	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.842	0.902	10.652	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.025	-0.013	10.684	0.057	0.057	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.012	0.007	11.307	0.052	0.052	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.012	-0.010	14.503	0.044	0.044	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.930	-0.943	16.455	-0.040	-0.040	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.013	-0.001	17.207	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.024	-0.001	17.217	0.032	0.032	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.073	-0.043	20.252	0.022	0.022	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.798	-0.889	22.147	-0.039	-0.039	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.002	0.007	21.608	0.012	0.012	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.016	0.001	24.715	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.823	0.889	26.541	0.063	0.063	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.023	-0.009	26.321	0.011	0.011	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.096	-0.046	28.042	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.003	0.006	31.136	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.042	-0.015	28.775	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.004	-0.014	28.727	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	LYS	1	1.057	1.024	24.780	0.049	0.049	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.016	-0.025	24.296	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.010	-0.002	24.367	-0.021	-0.021	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.042	0.026	23.190	-0.018	-0.018	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.019	0.004	19.931	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.019	-0.032	19.569	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.001	0.004	20.986	-0.032	-0.032	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.019	0.018	16.371	-0.036	-0.036	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.010	-0.004	15.692	-0.067	-0.067	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.049	-0.038	16.669	-0.055	-0.055	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.036	-0.010	14.802	0.007	0.007	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.014	-0.005	11.099	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.065	-0.030	13.097	-0.149	-0.149	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.802	-0.872	14.014	-0.782	-0.782	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.790	0.875	15.432	0.794	0.794	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.040	0.028	19.070	0.001	0.001	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.014	0.009	17.379	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.039	-0.052	21.827	0.045	0.045	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.016	-0.014	23.479	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	45	SER	0	0.002	-0.006	24.280	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.736	-0.829	19.459	-0.333	-0.333	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.039	0.023	19.458	-0.015	-0.015	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.104	-0.036	20.870	0.016	0.016	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.923	-0.948	19.437	-0.223	-0.223	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.799	-0.894	13.765	-0.589	-0.589	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.031	-0.012	16.857	0.015	0.015	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.812	0.910	15.855	0.289	0.289	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.038	-0.001	21.536	0.031	0.031	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.044	0.007	24.780	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	55	LYS	1	1.047	0.999	27.881	0.117	0.117	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.004	0.013	29.355	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	57	ASN	0	0.027	0.020	25.899	0.004	0.004	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.058	0.047	24.470	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.018	-0.029	26.996	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	MET	0	-0.073	-0.039	30.333	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.005	-0.009	26.323	0.004	0.004	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.010	0.004	24.754	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.934	0.975	28.224	0.120	0.120	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.893	0.928	30.012	0.115	0.115	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.018	0.010	24.396	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.809	-0.882	28.549	-0.188	-0.188	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.896	-0.926	30.934	-0.114	-0.114	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.048	-0.023	29.748	0.005	0.005	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.008	0.010	30.666	0.002	0.002	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.005	0.004	24.694	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.035	-0.016	24.185	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.838	0.906	26.675	0.278	0.278	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.803	0.877	27.575	0.155	0.155	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.007	0.008	25.943	0.002	0.002	0.000	0.000	0.000	0.000
75	A	75	TRP	0	-0.030	-0.022	29.005	0.007	0.007	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.046	0.028	25.823	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.973	0.975	29.430	0.216	0.216	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.006	-0.004	31.407	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.823	-0.852	28.001	-0.189	-0.189	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.841	0.873	30.915	0.172	0.172	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.857	0.931	26.337	0.223	0.223	0.000	0.000	0.000	0.000
82	A	82	ASN	0	0.009	0.008	30.222	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	TYR	0	0.019	-0.003	23.486	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.032	-0.024	24.762	0.028	0.028	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.749	-0.860	22.558	-0.345	-0.345	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.029	0.011	20.743	0.034	0.034	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.037	-0.012	22.762	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.813	-0.925	23.336	-0.300	-0.300	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.041	0.025	22.810	0.026	0.026	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.035	0.016	20.161	0.029	0.029	0.000	0.000	0.000	0.000
91	A	91	SER	0	0.000	-0.002	25.618	0.024	0.024	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.037	-0.016	26.666	0.016	0.016	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.002	-0.013	25.099	0.018	0.018	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.903	0.960	28.753	0.208	0.208	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.805	-0.898	31.695	-0.148	-0.148	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.068	-0.023	30.173	0.013	0.013	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.039	-0.022	33.263	0.011	0.011	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.893	0.943	34.899	0.148	0.148	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.948	0.967	33.409	0.142	0.142	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.902	0.960	33.772	0.116	0.116	0.000	0.000	0.000	0.000
101	A	101	HIS	0	0.005	0.001	39.272	0.007	0.007	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.856	-0.934	41.157	-0.090	-0.090	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.027	-0.014	41.719	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	ILE	0	-0.024	0.002	41.210	0.006	0.006	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.005	-0.002	45.141	0.005	0.005	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.825	0.908	47.056	0.062	0.062	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.008	-0.026	47.718	0.004	0.004	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.068	-0.070	49.148	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.818	-0.896	50.941	-0.053	-0.053	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.828	-0.901	53.125	-0.051	-0.051	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.019	-0.020	51.652	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.836	0.916	54.776	0.040	0.040	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.845	0.911	55.623	0.051	0.051	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.060	-0.023	57.909	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.798	-0.907	57.945	-0.033	-0.033	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.937	-0.969	60.718	-0.035	-0.035	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.883	0.951	62.683	0.038	0.038	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.065	-0.021	63.128	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	ASN	0	-0.005	-0.022	64.654	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.834	-0.915	66.601	-0.024	-0.024	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.901	-0.944	67.339	-0.021	-0.021	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.862	-0.939	64.602	-0.024	-0.024	0.000	0.000	0.000	0.000
123	A	123	LYS	1	0.821	0.919	62.722	0.024	0.024	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.854	-0.940	61.405	-0.027	-0.027	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.001	0.018	60.741	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.057	0.017	57.591	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.847	0.914	56.630	0.027	0.027	0.000	0.000	0.000	0.000
128	A	128	GLN	0	-0.086	-0.029	55.174	0.000	0.000	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.895	0.946	52.201	0.030	0.030	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.071	0.048	51.566	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.987	0.988	51.116	0.026	0.026	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.044	-0.015	48.140	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	133	ILE	0	0.042	0.016	46.705	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.817	-0.878	46.813	-0.044	-0.044	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.901	0.953	44.650	0.033	0.033	0.000	0.000	0.000	0.000
136	A	136	MET	0	0.027	0.018	42.071	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	137	LYS	1	0.827	0.907	42.129	0.054	0.054	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.915	0.947	42.559	0.041	0.041	0.000	0.000	0.000	0.000
139	A	139	ILE	0	-0.069	-0.027	37.867	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	140	SER	0	-0.007	-0.019	38.147	-0.005	-0.005	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.769	-0.871	38.243	-0.068	-0.068	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.992	0.999	37.255	0.056	0.056	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.050	-0.017	32.730	-0.004	-0.004	0.000	0.000	0.000	0.000
144	A	144	LEU	0	-0.015	-0.012	33.552	-0.009	-0.009	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.916	-0.961	34.803	-0.084	-0.084	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.030	0.011	31.644	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	147	LEU	0	-0.082	-0.048	28.780	-0.010	-0.010	0.000	0.000	0.000	0.000
148	A	148	ASN	0	-0.132	-0.080	30.663	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.916	-0.939	31.923	-0.102	-0.102	0.000	0.000	0.000	0.000
150	A	150	LEU	0	-0.057	-0.031	26.131	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	151	ASP	-1	-0.861	-0.894	27.157	-0.181	-0.181	0.000	0.000	0.000	0.000

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