FMO DATABASE

FMODB ID: 76N9K

Calculation Name: 1YTL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YTL

Chain ID: A

ChEMBL ID:

UniProt ID: O30273

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1645403.892162
FMO2-HF: Nuclear repulsion	1582441.480821
FMO2-HF: Total energy	-62962.411342
FMO2-MP2: Total energy	-63145.376733

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:17:LYS)

Summations of interaction energy for fragment #1(A:17:LYS)

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.
-114.529	-109.256	19.722	-12.029	-12.964	-0.132

Interaction energy analysis for fragmet #1(A:17:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.867 / q_NPA : 0.926

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	19	ALA	0	-0.037	0.005	2.621	-13.085	-9.665	1.645	-2.104	-2.961	-0.010
4	A	20	THR	0	-0.021	-0.010	3.371	2.968	3.606	0.016	-0.163	-0.491	-0.001
5	A	21	LEU	0	0.010	0.012	5.225	1.216	1.231	-0.001	0.000	-0.013	0.000
6	A	22	LEU	0	-0.042	-0.016	8.605	-0.207	-0.207	0.000	0.000	0.000	0.000
7	A	23	GLU	-1	-0.886	-0.961	11.078	-19.031	-19.031	0.000	0.000	0.000	0.000
8	A	24	LYS	1	0.834	0.893	14.239	17.716	17.716	0.000	0.000	0.000	0.000
9	A	25	GLY	0	0.074	0.032	14.394	-1.537	-1.537	0.000	0.000	0.000	0.000
10	A	26	LYS	1	0.837	0.899	15.633	14.273	14.273	0.000	0.000	0.000	0.000
11	A	27	PRO	0	-0.028	-0.022	11.539	0.002	0.002	0.000	0.000	0.000	0.000
12	A	28	VAL	0	0.058	0.031	11.252	-1.177	-1.177	0.000	0.000	0.000	0.000
13	A	29	ALA	0	0.041	0.032	12.744	-0.052	-0.052	0.000	0.000	0.000	0.000
14	A	30	ASN	0	-0.032	-0.030	14.484	1.104	1.104	0.000	0.000	0.000	0.000
15	A	31	MET	0	-0.050	-0.011	8.331	-1.830	-1.830	0.000	0.000	0.000	0.000
16	A	32	ILE	0	0.075	0.033	12.325	0.183	0.183	0.000	0.000	0.000	0.000
17	A	33	LYS	1	0.809	0.909	15.011	16.363	16.363	0.000	0.000	0.000	0.000
18	A	34	LYS	1	0.851	0.921	13.996	19.202	19.202	0.000	0.000	0.000	0.000
19	A	35	ALA	0	-0.017	0.014	13.234	-0.084	-0.084	0.000	0.000	0.000	0.000
20	A	36	LYS	1	0.904	0.938	14.711	17.346	17.346	0.000	0.000	0.000	0.000
21	A	37	ARG	1	0.766	0.850	16.488	15.975	15.975	0.000	0.000	0.000	0.000
22	A	38	PRO	0	0.022	0.018	15.057	-0.947	-0.947	0.000	0.000	0.000	0.000
23	A	39	LEU	0	0.002	-0.003	15.105	1.365	1.365	0.000	0.000	0.000	0.000
24	A	40	LEU	0	-0.034	-0.012	15.219	-1.568	-1.568	0.000	0.000	0.000	0.000
25	A	41	ILE	0	0.024	-0.001	14.850	1.160	1.160	0.000	0.000	0.000	0.000
26	A	42	VAL	0	0.004	-0.005	17.750	-0.573	-0.573	0.000	0.000	0.000	0.000
27	A	43	GLY	0	0.015	0.018	20.323	0.519	0.519	0.000	0.000	0.000	0.000
28	A	44	PRO	0	-0.017	-0.034	21.732	0.256	0.256	0.000	0.000	0.000	0.000
29	A	45	ASP	-1	-0.810	-0.845	21.576	-13.797	-13.797	0.000	0.000	0.000	0.000
30	A	46	MET	0	-0.025	-0.018	22.552	-0.597	-0.597	0.000	0.000	0.000	0.000
31	A	47	THR	0	0.014	-0.035	24.584	0.542	0.542	0.000	0.000	0.000	0.000
32	A	48	ASP	-1	-0.799	-0.888	26.803	-10.568	-10.568	0.000	0.000	0.000	0.000
33	A	49	GLU	-1	-0.823	-0.896	27.358	-11.006	-11.006	0.000	0.000	0.000	0.000
34	A	50	MET	0	-0.032	0.016	20.508	-0.198	-0.198	0.000	0.000	0.000	0.000
35	A	51	PHE	0	0.030	0.008	24.551	-0.259	-0.259	0.000	0.000	0.000	0.000
36	A	52	GLU	-1	-0.787	-0.881	26.620	-10.309	-10.309	0.000	0.000	0.000	0.000
37	A	53	ARG	1	0.695	0.806	22.837	12.335	12.335	0.000	0.000	0.000	0.000
38	A	54	VAL	0	-0.003	-0.005	21.818	-0.198	-0.198	0.000	0.000	0.000	0.000
39	A	55	LYS	1	0.842	0.904	23.991	10.150	10.150	0.000	0.000	0.000	0.000
40	A	56	LYS	1	0.892	0.940	25.660	11.299	11.299	0.000	0.000	0.000	0.000
41	A	57	PHE	0	0.005	-0.016	18.411	-0.208	-0.208	0.000	0.000	0.000	0.000
42	A	58	VAL	0	-0.021	0.008	23.163	-0.215	-0.215	0.000	0.000	0.000	0.000
43	A	59	GLU	-1	-0.842	-0.899	25.499	-10.567	-10.567	0.000	0.000	0.000	0.000
44	A	60	LYS	1	0.789	0.905	22.449	12.812	12.812	0.000	0.000	0.000	0.000
45	A	61	ASP	-1	-0.925	-0.954	22.599	-13.387	-13.387	0.000	0.000	0.000	0.000
46	A	62	ILE	0	-0.046	-0.033	16.663	-1.051	-1.051	0.000	0.000	0.000	0.000
47	A	63	THR	0	0.010	0.029	19.691	0.907	0.907	0.000	0.000	0.000	0.000
48	A	64	VAL	0	0.013	0.006	19.807	-0.901	-0.901	0.000	0.000	0.000	0.000
49	A	65	VAL	0	-0.003	0.008	19.501	0.637	0.637	0.000	0.000	0.000	0.000
50	A	66	ALA	0	0.011	0.021	21.363	-0.577	-0.577	0.000	0.000	0.000	0.000
51	A	67	THR	0	-0.013	-0.025	20.575	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	68	GLY	0	0.043	0.012	23.695	0.020	0.020	0.000	0.000	0.000	0.000
53	A	69	SER	0	0.007	-0.026	26.526	0.258	0.258	0.000	0.000	0.000	0.000
54	A	70	ALA	0	-0.017	0.008	24.637	0.262	0.262	0.000	0.000	0.000	0.000
55	A	71	ILE	0	0.019	0.006	26.713	0.116	0.116	0.000	0.000	0.000	0.000
56	A	72	THR	0	-0.005	0.002	28.869	0.156	0.156	0.000	0.000	0.000	0.000
57	A	73	ARG	1	0.887	0.934	28.193	11.005	11.005	0.000	0.000	0.000	0.000
58	A	74	PHE	0	0.023	-0.002	24.229	0.057	0.057	0.000	0.000	0.000	0.000
59	A	75	ILE	0	-0.009	-0.004	30.401	0.217	0.217	0.000	0.000	0.000	0.000
60	A	76	ASP	-1	-0.897	-0.946	33.816	-9.017	-9.017	0.000	0.000	0.000	0.000
61	A	77	ALA	0	-0.095	-0.047	31.932	0.187	0.187	0.000	0.000	0.000	0.000
62	A	78	GLY	0	0.000	0.001	34.046	0.031	0.031	0.000	0.000	0.000	0.000
63	A	79	LEU	0	-0.025	-0.017	28.851	-0.036	-0.036	0.000	0.000	0.000	0.000
64	A	80	GLY	0	-0.001	-0.003	30.727	-0.300	-0.300	0.000	0.000	0.000	0.000
65	A	81	GLU	-1	-0.959	-0.973	31.588	-8.877	-8.877	0.000	0.000	0.000	0.000
66	A	82	LYS	1	0.770	0.876	28.152	11.117	11.117	0.000	0.000	0.000	0.000
67	A	83	VAL	0	-0.044	-0.015	25.665	-0.486	-0.486	0.000	0.000	0.000	0.000
68	A	84	ASN	0	-0.016	-0.005	23.875	0.639	0.639	0.000	0.000	0.000	0.000
69	A	85	TYR	0	-0.006	-0.019	25.443	-0.211	-0.211	0.000	0.000	0.000	0.000
70	A	86	ALA	0	0.022	0.012	22.597	0.040	0.040	0.000	0.000	0.000	0.000
71	A	87	VAL	0	0.008	0.015	24.397	-0.094	-0.094	0.000	0.000	0.000	0.000
72	A	88	LEU	0	0.028	0.008	17.758	-0.293	-0.293	0.000	0.000	0.000	0.000
73	A	89	HIS	0	0.010	0.015	19.279	-1.326	-1.326	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.873	-0.939	20.455	-12.571	-12.571	0.000	0.000	0.000	0.000
75	A	91	LEU	0	0.020	0.008	17.899	-0.226	-0.226	0.000	0.000	0.000	0.000
76	A	92	THR	0	-0.026	-0.036	15.066	-1.103	-1.103	0.000	0.000	0.000	0.000
77	A	93	GLN	0	-0.014	-0.010	16.802	-0.590	-0.590	0.000	0.000	0.000	0.000
78	A	94	PHE	0	-0.030	-0.028	19.176	0.072	0.072	0.000	0.000	0.000	0.000
79	A	95	LEU	0	0.019	0.013	14.354	-0.132	-0.132	0.000	0.000	0.000	0.000
80	A	96	LEU	0	-0.027	-0.019	13.764	-1.051	-1.051	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.869	-0.924	15.848	-14.847	-14.847	0.000	0.000	0.000	0.000
82	A	98	PRO	0	-0.041	-0.015	16.327	-0.284	-0.284	0.000	0.000	0.000	0.000
83	A	99	ASP	-1	-0.906	-0.956	17.593	-14.342	-14.342	0.000	0.000	0.000	0.000
84	A	100	TRP	0	-0.028	0.000	18.795	0.703	0.703	0.000	0.000	0.000	0.000
85	A	101	LYS	1	0.922	0.949	20.830	11.273	11.273	0.000	0.000	0.000	0.000
86	A	102	GLY	0	0.035	0.026	21.521	0.204	0.204	0.000	0.000	0.000	0.000
87	A	103	PHE	0	-0.039	-0.044	20.837	0.466	0.466	0.000	0.000	0.000	0.000
88	A	104	ASP	-1	-0.792	-0.856	24.040	-12.921	-12.921	0.000	0.000	0.000	0.000
89	A	105	GLY	0	-0.045	-0.014	25.775	0.458	0.458	0.000	0.000	0.000	0.000
90	A	106	GLN	0	-0.063	-0.038	24.663	0.129	0.129	0.000	0.000	0.000	0.000
91	A	107	GLY	0	-0.003	0.000	21.102	-0.301	-0.301	0.000	0.000	0.000	0.000
92	A	108	ASN	0	0.019	0.025	16.116	-0.499	-0.499	0.000	0.000	0.000	0.000
93	A	109	TYR	0	0.008	-0.015	15.569	0.671	0.671	0.000	0.000	0.000	0.000
94	A	110	ASP	-1	-0.756	-0.861	12.466	-22.760	-22.760	0.000	0.000	0.000	0.000
95	A	111	LEU	0	-0.071	-0.031	9.073	-3.412	-3.412	0.000	0.000	0.000	0.000
96	A	112	VAL	0	0.056	0.040	10.416	2.265	2.265	0.000	0.000	0.000	0.000
97	A	113	LEU	0	-0.031	-0.023	10.491	-3.013	-3.013	0.000	0.000	0.000	0.000
98	A	114	MET	0	-0.003	0.008	12.728	0.868	0.868	0.000	0.000	0.000	0.000
99	A	115	LEU	0	0.006	0.011	14.350	-0.764	-0.764	0.000	0.000	0.000	0.000
100	A	116	GLY	0	0.086	0.048	17.150	0.565	0.565	0.000	0.000	0.000	0.000
101	A	117	SER	0	-0.052	-0.023	16.285	0.317	0.317	0.000	0.000	0.000	0.000
102	A	118	ILE	0	0.024	-0.005	18.192	-0.311	-0.311	0.000	0.000	0.000	0.000
103	A	119	TYR	0	-0.021	-0.021	12.739	-0.108	-0.108	0.000	0.000	0.000	0.000
104	A	120	TYR	0	0.028	0.011	15.927	-1.270	-1.270	0.000	0.000	0.000	0.000
105	A	121	HIS	0	0.061	0.019	16.315	-1.280	-1.280	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.029	0.022	15.370	-0.511	-0.511	0.000	0.000	0.000	0.000
107	A	123	SER	0	0.036	0.015	11.968	-2.339	-2.339	0.000	0.000	0.000	0.000
108	A	124	GLN	0	-0.015	-0.001	11.784	-2.931	-2.931	0.000	0.000	0.000	0.000
109	A	125	MET	0	0.004	0.016	13.517	-0.318	-0.318	0.000	0.000	0.000	0.000
110	A	126	LEU	0	-0.009	-0.016	8.764	-1.464	-1.464	0.000	0.000	0.000	0.000
111	A	127	ALA	0	-0.010	-0.002	8.904	-3.046	-3.046	0.000	0.000	0.000	0.000
112	A	128	ALA	0	-0.017	-0.005	9.985	-0.474	-0.474	0.000	0.000	0.000	0.000
113	A	129	ILE	0	0.033	0.001	8.276	0.120	0.120	0.000	0.000	0.000	0.000
114	A	130	LYS	1	0.775	0.875	2.312	72.156	73.475	0.622	-0.542	-1.399	-0.002
115	A	131	ASN	0	-0.049	-0.026	7.396	-2.559	-2.559	0.000	0.000	0.000	0.000
116	A	132	PHE	0	-0.046	-0.029	9.554	1.476	1.476	0.000	0.000	0.000	0.000
117	A	133	ALA	0	0.010	0.020	10.704	1.841	1.841	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.019	0.009	8.244	-2.065	-2.065	0.000	0.000	0.000	0.000
119	A	135	HIS	0	-0.069	-0.020	9.299	-1.882	-1.882	0.000	0.000	0.000	0.000
120	A	136	ILE	0	-0.010	-0.004	9.433	1.312	1.312	0.000	0.000	0.000	0.000
121	A	137	ARG	1	0.855	0.938	5.066	38.965	38.965	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.057	0.018	5.571	4.714	4.714	0.000	0.000	0.000	0.000
123	A	139	LEU	0	-0.033	-0.037	6.238	-7.232	-7.232	0.000	0.000	0.000	0.000
124	A	140	ALA	0	0.024	0.019	8.617	3.577	3.577	0.000	0.000	0.000	0.000
125	A	141	ILE	0	-0.011	-0.014	10.630	-0.383	-0.383	0.000	0.000	0.000	0.000
126	A	142	ASP	-1	-0.756	-0.867	13.632	-15.922	-15.922	0.000	0.000	0.000	0.000
127	A	143	ARG	1	0.761	0.852	15.273	14.116	14.116	0.000	0.000	0.000	0.000
128	A	144	TYR	0	-0.078	-0.080	15.312	0.679	0.679	0.000	0.000	0.000	0.000
129	A	145	TYR	0	-0.063	-0.034	6.608	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	146	HIS	0	0.049	0.024	9.995	0.707	0.707	0.000	0.000	0.000	0.000
131	A	147	PRO	0	-0.006	-0.006	6.893	-3.644	-3.644	0.000	0.000	0.000	0.000
132	A	148	ASN	0	0.027	-0.003	5.160	-7.500	-7.520	-0.001	-0.005	0.026	0.000
133	A	149	ALA	0	0.056	0.044	5.973	-1.591	-1.591	0.000	0.000	0.000	0.000
134	A	150	ASP	-1	-0.817	-0.880	1.735	-125.884	-127.977	16.593	-8.337	-6.163	-0.097
135	A	151	MET	0	-0.034	-0.013	2.707	-11.308	-9.314	0.848	-0.878	-1.963	-0.022
136	A	152	SER	0	0.033	0.013	5.480	3.818	3.818	0.000	0.000	0.000	0.000
137	A	153	PHE	0	0.003	0.027	8.620	0.183	0.183	0.000	0.000	0.000	0.000
138	A	154	GLY	0	0.085	0.035	11.779	-0.942	-0.942	0.000	0.000	0.000	0.000
139	A	155	ASN	0	-0.024	-0.007	13.745	0.380	0.380	0.000	0.000	0.000	0.000
140	A	156	LEU	0	0.022	0.007	16.567	0.923	0.923	0.000	0.000	0.000	0.000
141	A	157	TRP	0	0.039	0.015	18.586	1.209	1.209	0.000	0.000	0.000	0.000
142	A	158	LYS	1	0.877	0.950	21.302	13.979	13.979	0.000	0.000	0.000	0.000
143	A	159	LYS	1	0.838	0.912	23.006	12.461	12.461	0.000	0.000	0.000	0.000
144	A	160	GLU	-1	-0.735	-0.839	22.700	-13.462	-13.462	0.000	0.000	0.000	0.000
145	A	161	GLU	-1	-0.763	-0.868	23.404	-12.139	-12.139	0.000	0.000	0.000	0.000
146	A	162	ASP	-1	-0.864	-0.927	21.466	-13.179	-13.179	0.000	0.000	0.000	0.000
147	A	163	TYR	0	-0.036	-0.041	16.761	-0.104	-0.104	0.000	0.000	0.000	0.000
148	A	164	LEU	0	-0.006	-0.006	20.170	-0.476	-0.476	0.000	0.000	0.000	0.000
149	A	165	LYS	1	0.872	0.923	22.644	12.818	12.818	0.000	0.000	0.000	0.000
150	A	166	LEU	0	-0.034	-0.008	16.042	-0.134	-0.134	0.000	0.000	0.000	0.000
151	A	167	LEU	0	0.016	-0.004	17.610	-0.558	-0.558	0.000	0.000	0.000	0.000
152	A	168	ASP	-1	-0.798	-0.874	19.733	-12.629	-12.629	0.000	0.000	0.000	0.000
153	A	169	GLU	-1	-0.832	-0.898	19.051	-15.899	-15.899	0.000	0.000	0.000	0.000
154	A	170	ILE	0	-0.081	-0.025	15.654	-0.154	-0.154	0.000	0.000	0.000	0.000
155	A	171	LEU	0	0.006	0.007	18.845	0.322	0.322	0.000	0.000	0.000	0.000
156	A	172	ALA	0	-0.011	-0.001	22.284	0.491	0.491	0.000	0.000	0.000	0.000
157	A	173	GLU	-1	-0.821	-0.903	19.581	-14.458	-14.458	0.000	0.000	0.000	0.000
158	A	174	LEU	0	-0.029	-0.003	18.121	0.415	0.415	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:LYS)