FMO DATABASE

FMODB ID: 98732

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1642574.179278
FMO2-HF: Nuclear repulsion	1579613.242177
FMO2-HF: Total energy	-62960.937101
FMO2-MP2: Total energy	-63144.0649

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.
-99.123	-93.805	15.145	-9.022	-11.441	-0.102

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 : 0.871 / q_NPA : 0.919

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	-0.006	2.922	-8.663	-6.056	0.524	-1.246	-1.886	-0.007
4	A	20	THR	0	-0.011	0.008	3.936	3.789	4.031	-0.001	-0.012	-0.229	0.000
5	A	21	LEU	0	0.008	0.015	5.896	0.348	0.348	0.000	0.000	0.000	0.000
6	A	22	LEU	0	-0.062	-0.030	9.241	0.333	0.333	0.000	0.000	0.000	0.000
7	A	23	GLU	-1	-0.884	-0.964	11.372	-17.648	-17.648	0.000	0.000	0.000	0.000
8	A	24	LYS	1	0.949	0.968	14.817	17.385	17.385	0.000	0.000	0.000	0.000
9	A	25	GLY	0	0.074	0.042	15.255	-1.412	-1.412	0.000	0.000	0.000	0.000
10	A	26	LYS	1	0.931	0.959	16.524	14.090	14.090	0.000	0.000	0.000	0.000
11	A	27	PRO	0	-0.056	-0.033	12.713	0.015	0.015	0.000	0.000	0.000	0.000
12	A	28	VAL	0	0.079	0.025	11.930	-1.137	-1.137	0.000	0.000	0.000	0.000
13	A	29	ALA	0	0.055	0.049	13.517	-0.141	-0.141	0.000	0.000	0.000	0.000
14	A	30	ASN	0	-0.074	-0.051	14.960	0.955	0.955	0.000	0.000	0.000	0.000
15	A	31	MET	0	-0.062	-0.020	9.254	-1.225	-1.225	0.000	0.000	0.000	0.000
16	A	32	ILE	0	0.045	0.021	12.846	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	33	LYS	1	0.876	0.931	15.319	15.486	15.486	0.000	0.000	0.000	0.000
18	A	34	LYS	1	0.858	0.923	14.197	18.726	18.726	0.000	0.000	0.000	0.000
19	A	35	ALA	0	-0.025	0.018	13.399	-0.159	-0.159	0.000	0.000	0.000	0.000
20	A	36	LYS	1	0.911	0.943	14.926	16.875	16.875	0.000	0.000	0.000	0.000
21	A	37	ARG	1	0.750	0.841	16.228	16.086	16.086	0.000	0.000	0.000	0.000
22	A	38	PRO	0	0.042	0.027	14.955	-0.990	-0.990	0.000	0.000	0.000	0.000
23	A	39	LEU	0	0.007	0.005	15.046	1.310	1.310	0.000	0.000	0.000	0.000
24	A	40	LEU	0	-0.030	-0.012	15.214	-1.603	-1.603	0.000	0.000	0.000	0.000
25	A	41	ILE	0	0.002	-0.017	14.311	1.100	1.100	0.000	0.000	0.000	0.000
26	A	42	VAL	0	0.015	-0.003	17.756	-0.586	-0.586	0.000	0.000	0.000	0.000
27	A	43	GLY	0	-0.021	-0.007	20.097	0.565	0.565	0.000	0.000	0.000	0.000
28	A	44	PRO	0	0.007	-0.021	21.579	0.269	0.269	0.000	0.000	0.000	0.000
29	A	45	ASP	-1	-0.855	-0.908	21.386	-13.602	-13.602	0.000	0.000	0.000	0.000
30	A	46	MET	0	-0.023	-0.012	22.295	-0.602	-0.602	0.000	0.000	0.000	0.000
31	A	47	THR	0	-0.018	-0.088	24.458	0.464	0.464	0.000	0.000	0.000	0.000
32	A	48	ASP	-1	-0.832	-0.932	26.898	-10.298	-10.298	0.000	0.000	0.000	0.000
33	A	49	GLU	-1	-0.849	-0.928	27.736	-10.608	-10.608	0.000	0.000	0.000	0.000
34	A	50	MET	0	-0.061	0.014	20.692	-0.162	-0.162	0.000	0.000	0.000	0.000
35	A	51	PHE	0	0.031	0.002	24.853	-0.280	-0.280	0.000	0.000	0.000	0.000
36	A	52	GLU	-1	-0.870	-0.926	26.871	-10.095	-10.095	0.000	0.000	0.000	0.000
37	A	53	ARG	1	0.728	0.841	23.233	12.018	12.018	0.000	0.000	0.000	0.000
38	A	54	VAL	0	-0.007	0.004	22.028	-0.204	-0.204	0.000	0.000	0.000	0.000
39	A	55	LYS	1	0.891	0.951	24.336	10.056	10.056	0.000	0.000	0.000	0.000
40	A	56	LYS	1	0.957	0.975	25.906	11.057	11.057	0.000	0.000	0.000	0.000
41	A	57	PHE	0	0.002	-0.019	19.142	-0.108	-0.108	0.000	0.000	0.000	0.000
42	A	58	VAL	0	-0.002	0.019	23.494	-0.201	-0.201	0.000	0.000	0.000	0.000
43	A	59	GLU	-1	-0.950	-0.982	25.789	-10.268	-10.268	0.000	0.000	0.000	0.000
44	A	60	LYS	1	0.800	0.914	22.706	12.617	12.617	0.000	0.000	0.000	0.000
45	A	61	ASP	-1	-0.927	-0.958	22.813	-13.516	-13.516	0.000	0.000	0.000	0.000
46	A	62	ILE	0	-0.032	-0.016	16.945	-0.940	-0.940	0.000	0.000	0.000	0.000
47	A	63	THR	0	-0.002	0.014	19.891	0.819	0.819	0.000	0.000	0.000	0.000
48	A	64	VAL	0	0.016	0.015	19.936	-0.942	-0.942	0.000	0.000	0.000	0.000
49	A	65	VAL	0	0.005	0.005	19.367	0.548	0.548	0.000	0.000	0.000	0.000
50	A	66	ALA	0	-0.007	0.010	21.259	-0.587	-0.587	0.000	0.000	0.000	0.000
51	A	67	THR	0	-0.015	-0.025	20.233	0.119	0.119	0.000	0.000	0.000	0.000
52	A	68	GLY	0	0.015	-0.004	23.417	0.121	0.121	0.000	0.000	0.000	0.000
53	A	69	SER	0	0.038	-0.008	26.355	0.243	0.243	0.000	0.000	0.000	0.000
54	A	70	ALA	0	-0.020	0.005	24.817	0.358	0.358	0.000	0.000	0.000	0.000
55	A	71	ILE	0	0.011	0.004	26.812	0.114	0.114	0.000	0.000	0.000	0.000
56	A	72	THR	0	0.025	0.006	28.644	0.160	0.160	0.000	0.000	0.000	0.000
57	A	73	ARG	1	0.890	0.957	27.687	11.314	11.314	0.000	0.000	0.000	0.000
58	A	74	PHE	0	0.011	-0.005	24.422	0.088	0.088	0.000	0.000	0.000	0.000
59	A	75	ILE	0	-0.004	0.004	30.510	0.224	0.224	0.000	0.000	0.000	0.000
60	A	76	ASP	-1	-0.899	-0.939	33.731	-8.810	-8.810	0.000	0.000	0.000	0.000
61	A	77	ALA	0	-0.112	-0.054	32.287	0.200	0.200	0.000	0.000	0.000	0.000
62	A	78	GLY	0	0.010	-0.001	34.456	0.059	0.059	0.000	0.000	0.000	0.000
63	A	79	LEU	0	-0.040	-0.031	29.338	-0.053	-0.053	0.000	0.000	0.000	0.000
64	A	80	GLY	0	0.002	-0.004	30.599	-0.334	-0.334	0.000	0.000	0.000	0.000
65	A	81	GLU	-1	-0.941	-0.979	31.108	-8.957	-8.957	0.000	0.000	0.000	0.000
66	A	82	LYS	1	0.861	0.957	28.580	10.888	10.888	0.000	0.000	0.000	0.000
67	A	83	VAL	0	-0.065	-0.029	25.647	-0.529	-0.529	0.000	0.000	0.000	0.000
68	A	84	ASN	0	0.009	0.017	23.206	0.755	0.755	0.000	0.000	0.000	0.000
69	A	85	TYR	0	0.024	-0.001	25.412	-0.186	-0.186	0.000	0.000	0.000	0.000
70	A	86	ALA	0	-0.002	-0.001	22.064	-0.052	-0.052	0.000	0.000	0.000	0.000
71	A	87	VAL	0	0.055	0.035	23.977	0.020	0.020	0.000	0.000	0.000	0.000
72	A	88	LEU	0	0.017	-0.005	16.768	-0.271	-0.271	0.000	0.000	0.000	0.000
73	A	89	HIS	0	0.042	0.015	18.968	-1.140	-1.140	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.918	-0.952	19.821	-12.680	-12.680	0.000	0.000	0.000	0.000
75	A	91	LEU	0	0.011	0.004	17.600	-0.196	-0.196	0.000	0.000	0.000	0.000
76	A	92	THR	0	-0.039	-0.045	14.248	-1.104	-1.104	0.000	0.000	0.000	0.000
77	A	93	GLN	0	-0.013	-0.004	16.212	-0.705	-0.705	0.000	0.000	0.000	0.000
78	A	94	PHE	0	-0.014	-0.012	18.400	-0.099	-0.099	0.000	0.000	0.000	0.000
79	A	95	LEU	0	-0.007	-0.005	13.712	-0.193	-0.193	0.000	0.000	0.000	0.000
80	A	96	LEU	0	-0.021	-0.017	12.859	-0.962	-0.962	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.865	-0.912	14.927	-15.784	-15.784	0.000	0.000	0.000	0.000
82	A	98	PRO	0	-0.027	-0.027	15.644	-0.190	-0.190	0.000	0.000	0.000	0.000
83	A	99	ASP	-1	-0.914	-0.954	16.815	-14.767	-14.767	0.000	0.000	0.000	0.000
84	A	100	TRP	0	-0.073	-0.017	18.117	0.834	0.834	0.000	0.000	0.000	0.000
85	A	101	LYS	1	0.939	0.965	20.284	11.590	11.590	0.000	0.000	0.000	0.000
86	A	102	GLY	0	0.046	0.037	20.922	0.150	0.150	0.000	0.000	0.000	0.000
87	A	103	PHE	0	-0.022	-0.053	20.589	0.543	0.543	0.000	0.000	0.000	0.000
88	A	104	ASP	-1	-0.787	-0.868	24.086	-12.804	-12.804	0.000	0.000	0.000	0.000
89	A	105	GLY	0	-0.052	-0.020	25.344	0.411	0.411	0.000	0.000	0.000	0.000
90	A	106	GLN	0	-0.057	-0.029	24.591	0.343	0.343	0.000	0.000	0.000	0.000
91	A	107	GLY	0	-0.006	-0.014	21.012	-0.237	-0.237	0.000	0.000	0.000	0.000
92	A	108	ASN	0	0.025	0.037	16.013	-0.329	-0.329	0.000	0.000	0.000	0.000
93	A	109	TYR	0	0.009	-0.005	15.109	0.862	0.862	0.000	0.000	0.000	0.000
94	A	110	ASP	-1	-0.750	-0.852	12.564	-22.682	-22.682	0.000	0.000	0.000	0.000
95	A	111	LEU	0	-0.061	-0.015	9.328	-3.426	-3.426	0.000	0.000	0.000	0.000
96	A	112	VAL	0	0.045	0.023	10.403	2.434	2.434	0.000	0.000	0.000	0.000
97	A	113	LEU	0	-0.039	-0.026	10.649	-2.918	-2.918	0.000	0.000	0.000	0.000
98	A	114	MET	0	-0.029	0.003	12.616	0.992	0.992	0.000	0.000	0.000	0.000
99	A	115	LEU	0	0.014	0.004	14.417	-0.613	-0.613	0.000	0.000	0.000	0.000
100	A	116	GLY	0	0.060	0.020	17.243	0.679	0.679	0.000	0.000	0.000	0.000
101	A	117	SER	0	-0.049	-0.018	16.165	0.263	0.263	0.000	0.000	0.000	0.000
102	A	118	ILE	0	0.019	0.011	18.596	0.060	0.060	0.000	0.000	0.000	0.000
103	A	119	TYR	0	-0.008	-0.034	12.646	-0.425	-0.425	0.000	0.000	0.000	0.000
104	A	120	TYR	0	0.032	0.005	16.024	-1.116	-1.116	0.000	0.000	0.000	0.000
105	A	121	HIS	0	0.053	0.012	16.573	-1.189	-1.189	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.035	0.015	15.273	-0.593	-0.593	0.000	0.000	0.000	0.000
107	A	123	SER	0	0.001	0.004	12.156	-2.556	-2.556	0.000	0.000	0.000	0.000
108	A	124	GLN	0	-0.015	-0.016	11.961	-2.600	-2.600	0.000	0.000	0.000	0.000
109	A	125	MET	0	0.016	0.023	12.745	-0.623	-0.623	0.000	0.000	0.000	0.000
110	A	126	LEU	0	0.006	-0.009	8.389	-1.602	-1.602	0.000	0.000	0.000	0.000
111	A	127	ALA	0	-0.020	-0.005	8.330	-3.640	-3.640	0.000	0.000	0.000	0.000
112	A	128	ALA	0	-0.015	-0.005	9.585	-1.166	-1.166	0.000	0.000	0.000	0.000
113	A	129	ILE	0	0.039	0.007	7.561	0.236	0.236	0.000	0.000	0.000	0.000
114	A	130	LYS	1	0.857	0.944	1.960	74.895	74.799	3.947	-0.953	-2.897	-0.001
115	A	131	ASN	0	-0.066	-0.041	6.635	-2.532	-2.532	0.000	0.000	0.000	0.000
116	A	132	PHE	0	-0.050	-0.029	9.263	1.183	1.183	0.000	0.000	0.000	0.000
117	A	133	ALA	0	0.003	0.011	9.743	2.123	2.123	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.010	0.011	7.514	-2.554	-2.554	0.000	0.000	0.000	0.000
119	A	135	HIS	0	-0.074	-0.030	8.468	-2.710	-2.710	0.000	0.000	0.000	0.000
120	A	136	ILE	0	-0.008	0.006	8.901	1.396	1.396	0.000	0.000	0.000	0.000
121	A	137	ARG	1	0.908	0.966	4.864	38.090	38.090	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.054	0.018	5.725	5.368	5.368	0.000	0.000	0.000	0.000
123	A	139	LEU	0	-0.049	-0.049	6.495	-6.436	-6.436	0.000	0.000	0.000	0.000
124	A	140	ALA	0	0.014	0.019	8.831	2.951	2.951	0.000	0.000	0.000	0.000
125	A	141	ILE	0	-0.024	-0.025	10.931	-0.543	-0.543	0.000	0.000	0.000	0.000
126	A	142	ASP	-1	-0.715	-0.837	13.913	-16.563	-16.563	0.000	0.000	0.000	0.000
127	A	143	ARG	1	0.851	0.916	15.631	13.851	13.851	0.000	0.000	0.000	0.000
128	A	144	TYR	0	-0.037	-0.038	15.613	0.905	0.905	0.000	0.000	0.000	0.000
129	A	145	TYR	0	-0.074	-0.039	6.584	-0.122	-0.122	0.000	0.000	0.000	0.000
130	A	146	HIS	0	0.044	0.038	9.798	0.275	0.275	0.000	0.000	0.000	0.000
131	A	147	PRO	0	-0.010	0.002	6.810	-3.821	-3.821	0.000	0.000	0.000	0.000
132	A	148	ASN	0	0.058	0.013	5.052	-8.617	-8.649	-0.001	-0.006	0.039	0.000
133	A	149	ALA	0	0.018	0.035	6.139	-2.590	-2.590	0.000	0.000	0.000	0.000
134	A	150	ASP	-1	-0.857	-0.927	1.887	-121.932	-120.373	10.582	-6.558	-5.583	-0.087
135	A	151	MET	0	-0.076	-0.045	3.147	-1.681	-0.643	0.094	-0.247	-0.885	-0.007
136	A	152	SER	0	0.046	0.005	5.847	2.895	2.895	0.000	0.000	0.000	0.000
137	A	153	PHE	0	0.021	0.040	8.893	0.296	0.296	0.000	0.000	0.000	0.000
138	A	154	GLY	0	0.101	0.047	11.860	-1.243	-1.243	0.000	0.000	0.000	0.000
139	A	155	ASN	0	-0.035	-0.019	13.833	0.374	0.374	0.000	0.000	0.000	0.000
140	A	156	LEU	0	0.041	0.014	16.725	0.651	0.651	0.000	0.000	0.000	0.000
141	A	157	TRP	0	0.011	0.005	19.014	1.020	1.020	0.000	0.000	0.000	0.000
142	A	158	LYS	1	0.875	0.945	21.662	13.231	13.231	0.000	0.000	0.000	0.000
143	A	159	LYS	1	0.947	0.996	23.504	12.008	12.008	0.000	0.000	0.000	0.000
144	A	160	GLU	-1	-0.744	-0.819	23.390	-12.541	-12.541	0.000	0.000	0.000	0.000
145	A	161	GLU	-1	-0.861	-0.937	23.672	-11.686	-11.686	0.000	0.000	0.000	0.000
146	A	162	ASP	-1	-0.924	-0.977	21.559	-13.093	-13.093	0.000	0.000	0.000	0.000
147	A	163	TYR	0	-0.031	-0.052	17.186	-0.154	-0.154	0.000	0.000	0.000	0.000
148	A	164	LEU	0	-0.010	-0.009	20.517	-0.552	-0.552	0.000	0.000	0.000	0.000
149	A	165	LYS	1	0.953	0.990	22.990	12.479	12.479	0.000	0.000	0.000	0.000
150	A	166	LEU	0	0.001	0.019	16.323	-0.162	-0.162	0.000	0.000	0.000	0.000
151	A	167	LEU	0	-0.018	-0.019	18.341	-0.436	-0.436	0.000	0.000	0.000	0.000
152	A	168	ASP	-1	-0.804	-0.892	20.501	-12.288	-12.288	0.000	0.000	0.000	0.000
153	A	169	GLU	-1	-0.925	-0.966	20.087	-15.184	-15.184	0.000	0.000	0.000	0.000
154	A	170	ILE	0	-0.074	-0.026	16.166	-0.158	-0.158	0.000	0.000	0.000	0.000
155	A	171	LEU	0	-0.002	-0.008	19.373	0.325	0.325	0.000	0.000	0.000	0.000
156	A	172	ALA	0	-0.050	-0.012	22.680	0.372	0.372	0.000	0.000	0.000	0.000
157	A	173	GLU	-1	-0.930	-0.968	20.264	-13.695	-13.695	0.000	0.000	0.000	0.000
158	A	174	LEU	0	-0.025	0.019	18.514	0.059	0.059	0.000	0.000	0.000	0.000

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