FMO DATABASE

FMODB ID: MN85Z

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1642225.439644
FMO2-HF: Nuclear repulsion	1579263.414031
FMO2-HF: Total energy	-62962.025613
FMO2-MP2: Total energy	-63145.055115

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.
-108.442	-103.726	16.541	-10.498	-10.759	-0.107

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 : 0.893 / q_NPA : 0.935

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	-0.031	-0.004	2.847	-9.671	-6.268	0.635	-1.753	-2.285	-0.004
4	A	20	THR	0	-0.019	-0.003	3.785	3.664	3.952	0.000	-0.026	-0.262	0.000
5	A	21	LEU	0	0.013	0.015	5.722	0.456	0.456	0.000	0.000	0.000	0.000
6	A	22	LEU	0	-0.056	-0.024	9.143	0.397	0.397	0.000	0.000	0.000	0.000
7	A	23	GLU	-1	-0.887	-0.965	11.261	-18.502	-18.502	0.000	0.000	0.000	0.000
8	A	24	LYS	1	0.827	0.889	14.689	17.321	17.321	0.000	0.000	0.000	0.000
9	A	25	GLY	0	0.073	0.032	15.009	-1.403	-1.403	0.000	0.000	0.000	0.000
10	A	26	LYS	1	0.826	0.892	16.372	13.948	13.948	0.000	0.000	0.000	0.000
11	A	27	PRO	0	-0.039	-0.026	12.368	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	28	VAL	0	0.059	0.020	12.023	-1.108	-1.108	0.000	0.000	0.000	0.000
13	A	29	ALA	0	0.058	0.044	13.422	-0.065	-0.065	0.000	0.000	0.000	0.000
14	A	30	ASN	0	-0.061	-0.038	14.846	1.007	1.007	0.000	0.000	0.000	0.000
15	A	31	MET	0	-0.065	-0.024	8.982	-1.370	-1.370	0.000	0.000	0.000	0.000
16	A	32	ILE	0	0.040	0.017	12.831	0.039	0.039	0.000	0.000	0.000	0.000
17	A	33	LYS	1	0.867	0.929	15.409	15.743	15.743	0.000	0.000	0.000	0.000
18	A	34	LYS	1	0.874	0.925	14.310	18.815	18.815	0.000	0.000	0.000	0.000
19	A	35	ALA	0	-0.028	0.020	13.594	-0.116	-0.116	0.000	0.000	0.000	0.000
20	A	36	LYS	1	0.909	0.945	15.109	16.891	16.891	0.000	0.000	0.000	0.000
21	A	37	ARG	1	0.756	0.825	16.527	15.797	15.797	0.000	0.000	0.000	0.000
22	A	38	PRO	0	0.028	0.021	15.288	-0.908	-0.908	0.000	0.000	0.000	0.000
23	A	39	LEU	0	0.003	0.005	15.255	1.258	1.258	0.000	0.000	0.000	0.000
24	A	40	LEU	0	-0.032	-0.012	15.359	-1.596	-1.596	0.000	0.000	0.000	0.000
25	A	41	ILE	0	0.004	-0.012	14.914	1.131	1.131	0.000	0.000	0.000	0.000
26	A	42	VAL	0	0.009	-0.009	17.911	-0.615	-0.615	0.000	0.000	0.000	0.000
27	A	43	GLY	0	-0.005	0.001	20.247	0.577	0.577	0.000	0.000	0.000	0.000
28	A	44	PRO	0	-0.005	-0.031	21.776	0.268	0.268	0.000	0.000	0.000	0.000
29	A	45	ASP	-1	-0.808	-0.845	21.539	-13.730	-13.730	0.000	0.000	0.000	0.000
30	A	46	MET	0	-0.019	-0.013	22.326	-0.654	-0.654	0.000	0.000	0.000	0.000
31	A	47	THR	0	0.004	-0.052	24.491	0.491	0.491	0.000	0.000	0.000	0.000
32	A	48	ASP	-1	-0.807	-0.902	26.908	-10.395	-10.395	0.000	0.000	0.000	0.000
33	A	49	GLU	-1	-0.857	-0.915	27.604	-10.759	-10.759	0.000	0.000	0.000	0.000
34	A	50	MET	0	-0.045	0.016	20.575	-0.098	-0.098	0.000	0.000	0.000	0.000
35	A	51	PHE	0	0.037	0.005	24.878	-0.253	-0.253	0.000	0.000	0.000	0.000
36	A	52	GLU	-1	-0.808	-0.883	26.907	-10.134	-10.134	0.000	0.000	0.000	0.000
37	A	53	ARG	1	0.722	0.819	23.335	12.126	12.126	0.000	0.000	0.000	0.000
38	A	54	VAL	0	-0.001	0.006	22.321	-0.197	-0.197	0.000	0.000	0.000	0.000
39	A	55	LYS	1	0.848	0.913	24.499	10.083	10.083	0.000	0.000	0.000	0.000
40	A	56	LYS	1	0.914	0.954	26.056	11.195	11.195	0.000	0.000	0.000	0.000
41	A	57	PHE	0	-0.002	-0.020	19.087	-0.108	-0.108	0.000	0.000	0.000	0.000
42	A	58	VAL	0	-0.004	0.021	23.646	-0.188	-0.188	0.000	0.000	0.000	0.000
43	A	59	GLU	-1	-0.851	-0.908	26.009	-10.406	-10.406	0.000	0.000	0.000	0.000
44	A	60	LYS	1	0.807	0.913	22.925	12.461	12.461	0.000	0.000	0.000	0.000
45	A	61	ASP	-1	-0.916	-0.953	23.071	-13.178	-13.178	0.000	0.000	0.000	0.000
46	A	62	ILE	0	-0.041	-0.027	17.152	-0.955	-0.955	0.000	0.000	0.000	0.000
47	A	63	THR	0	0.011	0.028	20.144	0.795	0.795	0.000	0.000	0.000	0.000
48	A	64	VAL	0	0.019	0.012	20.105	-0.917	-0.917	0.000	0.000	0.000	0.000
49	A	65	VAL	0	0.013	0.011	19.588	0.593	0.593	0.000	0.000	0.000	0.000
50	A	66	ALA	0	-0.009	0.011	21.466	-0.589	-0.589	0.000	0.000	0.000	0.000
51	A	67	THR	0	-0.005	-0.021	20.650	0.086	0.086	0.000	0.000	0.000	0.000
52	A	68	GLY	0	0.005	-0.006	23.682	0.102	0.102	0.000	0.000	0.000	0.000
53	A	69	SER	0	0.040	-0.005	26.631	0.260	0.260	0.000	0.000	0.000	0.000
54	A	70	ALA	0	-0.020	0.005	24.988	0.348	0.348	0.000	0.000	0.000	0.000
55	A	71	ILE	0	0.016	0.003	27.003	0.117	0.117	0.000	0.000	0.000	0.000
56	A	72	THR	0	0.008	0.002	28.858	0.153	0.153	0.000	0.000	0.000	0.000
57	A	73	ARG	1	0.899	0.953	28.193	11.105	11.105	0.000	0.000	0.000	0.000
58	A	74	PHE	0	0.010	-0.004	24.516	0.099	0.099	0.000	0.000	0.000	0.000
59	A	75	ILE	0	0.003	0.004	30.654	0.229	0.229	0.000	0.000	0.000	0.000
60	A	76	ASP	-1	-0.908	-0.942	33.902	-8.842	-8.842	0.000	0.000	0.000	0.000
61	A	77	ALA	0	-0.106	-0.053	32.456	0.197	0.197	0.000	0.000	0.000	0.000
62	A	78	GLY	0	0.008	0.001	34.592	0.058	0.058	0.000	0.000	0.000	0.000
63	A	79	LEU	0	-0.035	-0.029	29.642	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	80	GLY	0	-0.004	-0.006	30.747	-0.328	-0.328	0.000	0.000	0.000	0.000
65	A	81	GLU	-1	-0.942	-0.977	31.302	-8.927	-8.927	0.000	0.000	0.000	0.000
66	A	82	LYS	1	0.773	0.882	28.681	10.934	10.934	0.000	0.000	0.000	0.000
67	A	83	VAL	0	-0.061	-0.023	25.901	-0.529	-0.529	0.000	0.000	0.000	0.000
68	A	84	ASN	0	-0.015	0.000	23.958	0.625	0.625	0.000	0.000	0.000	0.000
69	A	85	TYR	0	0.027	0.005	25.643	-0.202	-0.202	0.000	0.000	0.000	0.000
70	A	86	ALA	0	-0.007	-0.008	22.401	-0.043	-0.043	0.000	0.000	0.000	0.000
71	A	87	VAL	0	0.050	0.035	24.411	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	88	LEU	0	0.012	-0.003	17.506	-0.281	-0.281	0.000	0.000	0.000	0.000
73	A	89	HIS	0	0.045	0.022	19.343	-1.126	-1.126	0.000	0.000	0.000	0.000
74	A	90	GLU	-1	-0.910	-0.953	20.242	-12.505	-12.505	0.000	0.000	0.000	0.000
75	A	91	LEU	0	0.017	0.005	17.854	-0.168	-0.168	0.000	0.000	0.000	0.000
76	A	92	THR	0	-0.046	-0.045	14.726	-1.055	-1.055	0.000	0.000	0.000	0.000
77	A	93	GLN	0	-0.022	-0.010	16.644	-0.639	-0.639	0.000	0.000	0.000	0.000
78	A	94	PHE	0	-0.010	-0.011	18.841	-0.069	-0.069	0.000	0.000	0.000	0.000
79	A	95	LEU	0	-0.006	-0.001	14.296	-0.195	-0.195	0.000	0.000	0.000	0.000
80	A	96	LEU	0	0.003	-0.006	13.181	-0.878	-0.878	0.000	0.000	0.000	0.000
81	A	97	ASP	-1	-0.883	-0.926	15.369	-15.346	-15.346	0.000	0.000	0.000	0.000
82	A	98	PRO	0	-0.041	-0.029	15.964	-0.258	-0.258	0.000	0.000	0.000	0.000
83	A	99	ASP	-1	-0.922	-0.962	17.190	-14.474	-14.474	0.000	0.000	0.000	0.000
84	A	100	TRP	0	-0.051	0.003	18.526	0.773	0.773	0.000	0.000	0.000	0.000
85	A	101	LYS	1	0.938	0.958	20.612	11.347	11.347	0.000	0.000	0.000	0.000
86	A	102	GLY	0	0.056	0.042	21.227	0.134	0.134	0.000	0.000	0.000	0.000
87	A	103	PHE	0	-0.023	-0.047	20.683	0.509	0.509	0.000	0.000	0.000	0.000
88	A	104	ASP	-1	-0.786	-0.846	24.271	-12.818	-12.818	0.000	0.000	0.000	0.000
89	A	105	GLY	0	-0.052	-0.020	25.624	0.412	0.412	0.000	0.000	0.000	0.000
90	A	106	GLN	0	-0.055	-0.031	24.837	0.296	0.296	0.000	0.000	0.000	0.000
91	A	107	GLY	0	-0.002	-0.010	21.253	-0.225	-0.225	0.000	0.000	0.000	0.000
92	A	108	ASN	0	0.020	0.030	16.161	-0.298	-0.298	0.000	0.000	0.000	0.000
93	A	109	TYR	0	0.002	-0.012	15.446	0.727	0.727	0.000	0.000	0.000	0.000
94	A	110	ASP	-1	-0.751	-0.855	12.771	-22.373	-22.373	0.000	0.000	0.000	0.000
95	A	111	LEU	0	-0.061	-0.020	9.386	-3.342	-3.342	0.000	0.000	0.000	0.000
96	A	112	VAL	0	0.046	0.026	10.561	2.335	2.335	0.000	0.000	0.000	0.000
97	A	113	LEU	0	-0.037	-0.026	10.779	-2.896	-2.896	0.000	0.000	0.000	0.000
98	A	114	MET	0	-0.028	-0.002	12.755	0.938	0.938	0.000	0.000	0.000	0.000
99	A	115	LEU	0	0.005	0.002	14.550	-0.663	-0.663	0.000	0.000	0.000	0.000
100	A	116	GLY	0	0.087	0.042	17.301	0.691	0.691	0.000	0.000	0.000	0.000
101	A	117	SER	0	-0.044	-0.017	16.327	0.455	0.455	0.000	0.000	0.000	0.000
102	A	118	ILE	0	0.018	0.008	18.668	0.005	0.005	0.000	0.000	0.000	0.000
103	A	119	TYR	0	-0.018	-0.023	12.848	-0.279	-0.279	0.000	0.000	0.000	0.000
104	A	120	TYR	0	0.023	0.004	16.094	-1.100	-1.100	0.000	0.000	0.000	0.000
105	A	121	HIS	0	0.057	0.013	16.653	-1.211	-1.211	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.033	0.016	15.393	-0.560	-0.560	0.000	0.000	0.000	0.000
107	A	123	SER	0	0.022	0.009	12.239	-2.457	-2.457	0.000	0.000	0.000	0.000
108	A	124	GLN	0	-0.014	-0.010	12.054	-2.739	-2.739	0.000	0.000	0.000	0.000
109	A	125	MET	0	0.012	0.023	13.132	-0.242	-0.242	0.000	0.000	0.000	0.000
110	A	126	LEU	0	-0.011	-0.018	8.694	-1.528	-1.528	0.000	0.000	0.000	0.000
111	A	127	ALA	0	-0.015	-0.001	8.734	-3.394	-3.394	0.000	0.000	0.000	0.000
112	A	128	ALA	0	-0.003	0.002	9.702	-0.991	-0.991	0.000	0.000	0.000	0.000
113	A	129	ILE	0	0.039	0.003	8.035	0.226	0.226	0.000	0.000	0.000	0.000
114	A	130	LYS	1	0.782	0.887	2.228	74.725	76.275	0.944	-0.733	-1.761	-0.003
115	A	131	ASN	0	-0.074	-0.046	7.111	-2.552	-2.552	0.000	0.000	0.000	0.000
116	A	132	PHE	0	-0.046	-0.030	9.422	1.218	1.218	0.000	0.000	0.000	0.000
117	A	133	ALA	0	-0.002	0.009	10.217	1.997	1.997	0.000	0.000	0.000	0.000
118	A	134	PRO	0	0.022	0.018	7.888	-2.340	-2.340	0.000	0.000	0.000	0.000
119	A	135	HIS	0	-0.061	-0.020	8.754	-2.676	-2.676	0.000	0.000	0.000	0.000
120	A	136	ILE	0	-0.012	0.004	9.436	1.199	1.199	0.000	0.000	0.000	0.000
121	A	137	ARG	1	0.868	0.940	5.279	36.117	36.117	0.000	0.000	0.000	0.000
122	A	138	ALA	0	0.057	0.025	5.933	4.638	4.638	0.000	0.000	0.000	0.000
123	A	139	LEU	0	-0.045	-0.043	6.569	-6.603	-6.603	0.000	0.000	0.000	0.000
124	A	140	ALA	0	0.020	0.021	8.999	3.022	3.022	0.000	0.000	0.000	0.000
125	A	141	ILE	0	-0.021	-0.027	10.972	-0.590	-0.590	0.000	0.000	0.000	0.000
126	A	142	ASP	-1	-0.750	-0.869	13.923	-16.579	-16.579	0.000	0.000	0.000	0.000
127	A	143	ARG	1	0.805	0.884	15.595	13.860	13.860	0.000	0.000	0.000	0.000
128	A	144	TYR	0	-0.065	-0.075	15.590	0.781	0.781	0.000	0.000	0.000	0.000
129	A	145	TYR	0	-0.073	-0.040	6.699	0.076	0.076	0.000	0.000	0.000	0.000
130	A	146	HIS	0	0.054	0.029	9.938	0.446	0.446	0.000	0.000	0.000	0.000
131	A	147	PRO	0	-0.005	-0.001	6.813	-3.666	-3.666	0.000	0.000	0.000	0.000
132	A	148	ASN	0	0.046	0.011	5.095	-8.021	-8.030	-0.001	-0.005	0.015	0.000
133	A	149	ALA	0	0.045	0.039	6.224	-2.021	-2.021	0.000	0.000	0.000	0.000
134	A	150	ASP	-1	-0.805	-0.870	1.732	-126.858	-128.749	14.846	-7.438	-5.517	-0.092
135	A	151	MET	0	-0.057	-0.025	3.105	-4.502	-3.127	0.117	-0.543	-0.949	-0.008
136	A	152	SER	0	0.054	0.019	5.821	3.216	3.216	0.000	0.000	0.000	0.000
137	A	153	PHE	0	0.017	0.039	8.844	0.234	0.234	0.000	0.000	0.000	0.000
138	A	154	GLY	0	0.097	0.043	11.779	-1.269	-1.269	0.000	0.000	0.000	0.000
139	A	155	ASN	0	-0.042	-0.020	13.722	0.396	0.396	0.000	0.000	0.000	0.000
140	A	156	LEU	0	0.032	0.008	16.711	0.678	0.678	0.000	0.000	0.000	0.000
141	A	157	TRP	0	0.028	0.012	18.925	1.114	1.114	0.000	0.000	0.000	0.000
142	A	158	LYS	1	0.870	0.943	21.592	13.635	13.635	0.000	0.000	0.000	0.000
143	A	159	LYS	1	0.852	0.931	23.413	12.144	12.144	0.000	0.000	0.000	0.000
144	A	160	GLU	-1	-0.759	-0.861	23.317	-13.105	-13.105	0.000	0.000	0.000	0.000
145	A	161	GLU	-1	-0.756	-0.872	23.610	-11.890	-11.890	0.000	0.000	0.000	0.000
146	A	162	ASP	-1	-0.881	-0.950	21.656	-13.109	-13.109	0.000	0.000	0.000	0.000
147	A	163	TYR	0	-0.017	-0.035	17.188	-0.113	-0.113	0.000	0.000	0.000	0.000
148	A	164	LEU	0	-0.010	-0.011	20.469	-0.552	-0.552	0.000	0.000	0.000	0.000
149	A	165	LYS	1	0.905	0.957	22.938	12.784	12.784	0.000	0.000	0.000	0.000
150	A	166	LEU	0	-0.012	0.011	16.151	-0.108	-0.108	0.000	0.000	0.000	0.000
151	A	167	LEU	0	-0.008	-0.015	18.280	-0.423	-0.423	0.000	0.000	0.000	0.000
152	A	168	ASP	-1	-0.798	-0.881	20.451	-12.397	-12.397	0.000	0.000	0.000	0.000
153	A	169	GLU	-1	-0.838	-0.894	19.610	-15.564	-15.564	0.000	0.000	0.000	0.000
154	A	170	ILE	0	-0.065	-0.023	16.214	-0.103	-0.103	0.000	0.000	0.000	0.000
155	A	171	LEU	0	0.007	0.002	19.294	0.334	0.334	0.000	0.000	0.000	0.000
156	A	172	ALA	0	-0.050	-0.021	22.653	0.393	0.393	0.000	0.000	0.000	0.000
157	A	173	GLU	-1	-0.830	-0.903	20.280	-13.962	-13.962	0.000	0.000	0.000	0.000
158	A	174	LEU	0	-0.025	0.024	18.623	0.323	0.323	0.000	0.000	0.000	0.000

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