FMO DATABASE

FMODB ID: 6Y62Z

Calculation Name: 1YNB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YNB

Chain ID: A

ChEMBL ID:

UniProt ID: O28840

Base Structure: X-ray

Registration Date: 2023-09-21

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1693702.359157
FMO2-HF: Nuclear repulsion	1626531.23411
FMO2-HF: Total energy	-67171.125048
FMO2-MP2: Total energy	-67367.084198

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:7:MET)

Summations of interaction energy for fragment #1(A:7: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.
0.957	6.061	1.403	-1.946	-4.563	-0.001

Interaction energy analysis for fragmet #1(A:7:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.072 / q_NPA : 0.028

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	9	ASP	-1	-0.891	-0.937	3.092	-3.091	-0.847	0.006	-0.925	-1.325	0.000
4	A	10	VAL	0	0.030	0.013	2.700	-0.628	1.088	1.285	-0.652	-2.350	-0.001
5	A	11	VAL	0	-0.030	-0.015	2.742	0.001	1.031	0.113	-0.362	-0.782	0.000
6	A	12	LYS	1	0.872	0.918	5.169	2.577	2.691	-0.001	-0.007	-0.106	0.000
7	A	13	PHE	0	0.088	0.058	7.596	0.307	0.307	0.000	0.000	0.000	0.000
8	A	14	ILE	0	-0.008	-0.005	5.831	0.173	0.173	0.000	0.000	0.000	0.000
9	A	15	HIS	0	-0.043	-0.027	9.030	0.194	0.194	0.000	0.000	0.000	0.000
10	A	16	GLU	-1	-0.791	-0.856	11.425	-0.165	-0.165	0.000	0.000	0.000	0.000
11	A	17	VAL	0	0.035	0.035	12.554	0.048	0.048	0.000	0.000	0.000	0.000
12	A	18	GLY	0	-0.029	-0.007	13.755	0.033	0.033	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.029	-0.033	15.570	0.016	0.016	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.073	0.044	17.756	0.009	0.009	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.889	0.935	16.749	0.023	0.023	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.080	-0.042	19.749	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	23	THR	0	0.026	0.027	21.784	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	24	PRO	0	-0.047	-0.025	24.209	0.013	0.013	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.928	0.979	27.443	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.029	-0.057	29.297	0.001	0.001	0.000	0.000	0.000	0.000
21	A	27	GLY	0	-0.039	-0.032	31.766	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	28	TRP	0	0.014	-0.016	32.213	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	29	LEU	0	0.038	0.030	31.746	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	30	LYS	1	0.838	0.926	35.983	0.007	0.007	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.070	-0.028	38.833	0.001	0.001	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.000	0.002	39.575	0.001	0.001	0.000	0.000	0.000	0.000
27	A	33	ILE	0	-0.030	-0.005	35.302	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	34	ARG	1	0.929	0.949	35.872	0.036	0.036	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.010	0.008	30.961	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	36	PRO	0	-0.049	-0.026	30.888	0.004	0.004	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.721	-0.824	28.606	0.018	0.018	0.000	0.000	0.000	0.000
32	A	38	SER	0	-0.027	-0.055	24.037	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.028	-0.006	22.552	0.011	0.011	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.027	0.018	20.326	0.016	0.016	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.887	-0.913	21.904	0.025	0.025	0.000	0.000	0.000	0.000
36	A	42	HIS	1	0.812	0.918	24.991	-0.041	-0.041	0.000	0.000	0.000	0.000
37	A	43	ASN	0	-0.029	-0.045	21.761	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.019	-0.001	22.162	0.017	0.017	0.000	0.000	0.000	0.000
39	A	45	ARG	1	0.774	0.846	23.596	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	46	ALA	0	0.028	0.013	25.940	0.003	0.003	0.000	0.000	0.000	0.000
41	A	47	ALA	0	0.027	0.017	22.577	0.004	0.004	0.000	0.000	0.000	0.000
42	A	48	ILE	0	-0.022	-0.011	24.525	0.005	0.005	0.000	0.000	0.000	0.000
43	A	49	ILE	0	-0.026	-0.024	26.720	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	50	ALA	0	0.048	0.021	26.073	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	51	PHE	0	-0.039	-0.014	25.352	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	52	ILE	0	-0.011	-0.018	27.625	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	53	LEU	0	-0.030	-0.007	31.118	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	54	ALA	0	0.034	0.048	29.166	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	55	LEU	0	-0.001	0.001	29.695	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.821	0.897	32.428	-0.068	-0.068	0.000	0.000	0.000	0.000
51	A	57	SER	0	-0.075	-0.052	34.052	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.051	-0.023	35.504	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.814	-0.855	30.234	0.123	0.123	0.000	0.000	0.000	0.000
54	A	60	SER	0	-0.026	-0.040	27.858	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.074	0.031	25.616	0.004	0.004	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.831	-0.891	23.548	0.170	0.170	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.869	0.921	23.710	-0.122	-0.122	0.000	0.000	0.000	0.000
58	A	64	ALA	0	0.015	-0.002	25.661	0.002	0.002	0.000	0.000	0.000	0.000
59	A	65	CYS	0	-0.068	-0.049	21.380	0.000	0.000	0.000	0.000	0.000	0.000
60	A	66	LYS	1	0.827	0.911	20.872	-0.197	-0.197	0.000	0.000	0.000	0.000
61	A	67	ALA	0	0.036	0.017	22.119	0.003	0.003	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.025	-0.009	22.382	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	69	THR	0	-0.025	-0.034	16.910	0.008	0.008	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.021	0.016	19.182	0.006	0.006	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.014	0.005	21.129	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.088	-0.046	17.663	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.029	-0.022	12.850	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	74	HIS	0	-0.023	0.016	18.713	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.799	-0.892	22.066	0.050	0.050	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.018	0.009	14.408	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	77	HIS	0	0.115	0.066	18.343	-0.026	-0.026	0.000	0.000	0.000	0.000
72	A	78	GLU	-1	-0.886	-0.963	19.545	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	79	ALA	0	-0.071	-0.030	17.549	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.780	0.866	13.203	0.201	0.201	0.000	0.000	0.000	0.000
75	A	81	THR	0	-0.024	-0.023	20.366	0.000	0.000	0.000	0.000	0.000	0.000
76	A	82	MET	0	-0.094	-0.039	23.438	0.002	0.002	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.747	-0.856	25.405	0.005	0.005	0.000	0.000	0.000	0.000
78	A	84	LEU	0	-0.025	0.007	27.541	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	85	HIS	0	0.049	0.022	30.243	0.012	0.012	0.000	0.000	0.000	0.000
80	A	86	LYN	0	0.043	-0.011	33.362	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	87	ILE	0	-0.037	-0.021	36.357	0.000	0.000	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.038	0.022	33.705	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	89	ARG	1	0.965	0.977	31.542	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	90	ARG	1	0.895	0.966	34.939	0.007	0.007	0.000	0.000	0.000	0.000
85	A	91	TYR	0	-0.059	-0.041	37.271	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.027	-0.002	31.032	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.017	0.001	31.669	0.005	0.005	0.000	0.000	0.000	0.000
88	A	94	CYS	0	-0.029	-0.027	25.904	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	95	ASP	-1	-0.845	-0.915	24.446	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	96	GLU	-1	-0.842	-0.918	23.149	0.046	0.046	0.000	0.000	0.000	0.000
91	A	97	GLU	-1	-0.798	-0.875	21.139	0.094	0.094	0.000	0.000	0.000	0.000
92	A	98	GLY	0	0.017	0.021	20.502	0.006	0.006	0.000	0.000	0.000	0.000
93	A	99	ALA	0	-0.043	-0.030	19.061	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	100	ARG	1	0.788	0.849	17.363	-0.106	-0.106	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.871	-0.921	16.005	0.151	0.151	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.937	-0.980	14.474	-0.137	-0.137	0.000	0.000	0.000	0.000
97	A	103	GLN	0	-0.128	-0.073	12.835	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.032	-0.037	11.614	0.001	0.001	0.000	0.000	0.000	0.000
99	A	105	SER	0	-0.031	-0.011	10.653	0.071	0.071	0.000	0.000	0.000	0.000
100	A	106	TRP	0	-0.053	-0.023	5.997	0.209	0.209	0.000	0.000	0.000	0.000
101	A	107	MET	0	-0.090	-0.034	7.541	0.376	0.376	0.000	0.000	0.000	0.000
102	A	108	GLU	-1	-0.896	-0.925	8.901	0.688	0.688	0.000	0.000	0.000	0.000
103	A	109	SER	0	-0.083	-0.062	11.372	-0.155	-0.155	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.894	0.943	13.307	-0.142	-0.142	0.000	0.000	0.000	0.000
105	A	111	PRO	0	-0.022	-0.014	14.427	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.810	-0.876	17.393	0.154	0.154	0.000	0.000	0.000	0.000
107	A	113	PHE	0	0.029	-0.007	17.273	0.008	0.008	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.032	-0.012	22.897	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	115	ASP	-1	-0.942	-0.951	24.955	0.168	0.168	0.000	0.000	0.000	0.000
110	A	116	VAL	0	-0.029	-0.014	24.042	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	117	GLU	-1	-0.830	-0.917	24.612	0.124	0.124	0.000	0.000	0.000	0.000
112	A	118	VAL	0	-0.104	-0.051	27.894	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	119	TYR	0	-0.034	-0.049	28.489	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	120	VAL	0	0.071	0.048	24.632	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	121	SER	0	-0.018	-0.002	27.611	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	122	ASP	-1	-0.703	-0.846	30.466	0.056	0.056	0.000	0.000	0.000	0.000
117	A	123	ALA	0	0.008	0.008	28.530	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	124	ASP	-1	-0.884	-0.931	28.411	0.047	0.047	0.000	0.000	0.000	0.000
119	A	125	LYS	1	0.808	0.885	29.880	-0.062	-0.062	0.000	0.000	0.000	0.000
120	A	126	LEU	0	-0.008	-0.012	33.397	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	127	GLU	-1	-0.782	-0.858	28.901	0.038	0.038	0.000	0.000	0.000	0.000
122	A	128	LEU	0	-0.001	0.012	32.137	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	129	ALA	0	0.012	-0.001	33.958	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	130	PHE	0	-0.023	-0.025	34.603	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	131	GLN	0	0.021	0.023	32.562	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	132	GLY	0	0.026	0.013	35.268	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	133	VAL	0	-0.015	-0.016	38.419	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	134	GLU	-1	-0.867	-0.894	34.973	0.030	0.030	0.000	0.000	0.000	0.000
129	A	135	TYR	0	0.060	0.013	32.496	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	136	SER	0	-0.125	-0.056	39.156	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	137	GLN	0	-0.044	-0.031	42.058	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	138	GLN	0	-0.071	-0.024	38.024	0.000	0.000	0.000	0.000	0.000	0.000
133	A	139	VAL	0	0.012	0.001	41.881	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	140	SER	0	0.048	0.021	43.398	0.001	0.001	0.000	0.000	0.000	0.000
135	A	141	TYR	0	-0.003	-0.012	43.057	0.002	0.002	0.000	0.000	0.000	0.000
136	A	142	ALA	0	0.033	0.016	39.733	0.001	0.001	0.000	0.000	0.000	0.000
137	A	143	ILE	0	-0.002	0.001	40.816	0.002	0.002	0.000	0.000	0.000	0.000
138	A	144	ARG	1	0.850	0.911	43.003	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	145	PHE	0	-0.080	-0.038	36.630	0.000	0.000	0.000	0.000	0.000	0.000
140	A	146	ALA	0	0.027	0.020	38.718	0.003	0.003	0.000	0.000	0.000	0.000
141	A	147	GLU	-1	-0.864	-0.902	40.559	0.016	0.016	0.000	0.000	0.000	0.000
142	A	148	ASN	0	-0.043	-0.025	42.618	0.000	0.000	0.000	0.000	0.000	0.000
143	A	149	VAL	0	0.004	0.015	37.793	0.000	0.000	0.000	0.000	0.000	0.000
144	A	150	GLU	-1	-0.889	-0.929	39.633	0.033	0.033	0.000	0.000	0.000	0.000
145	A	151	LEU	0	-0.059	-0.019	36.063	0.003	0.003	0.000	0.000	0.000	0.000
146	A	152	LYS	1	0.930	0.938	33.067	-0.071	-0.071	0.000	0.000	0.000	0.000
147	A	153	THR	0	-0.028	-0.037	34.455	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	154	ASP	-1	-0.821	-0.912	37.707	0.052	0.052	0.000	0.000	0.000	0.000
149	A	155	ALA	0	0.018	0.020	36.201	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	156	ALA	0	0.037	0.007	35.421	-0.002	-0.002	0.000	0.000	0.000	0.000
151	A	157	LYS	1	0.839	0.906	37.187	-0.056	-0.056	0.000	0.000	0.000	0.000
152	A	158	GLU	-1	-0.891	-0.918	40.820	0.052	0.052	0.000	0.000	0.000	0.000
153	A	159	ILE	0	0.002	-0.009	35.697	-0.003	-0.003	0.000	0.000	0.000	0.000
154	A	160	TYR	0	-0.017	-0.035	39.262	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	161	ARG	1	0.839	0.911	40.510	-0.036	-0.036	0.000	0.000	0.000	0.000
156	A	162	VAL	0	0.025	0.010	42.421	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	163	LEU	0	-0.055	-0.009	38.803	-0.003	-0.003	0.000	0.000	0.000	0.000
158	A	164	MET	0	0.011	0.001	41.897	-0.004	-0.004	0.000	0.000	0.000	0.000
159	A	165	GLU	-1	-0.850	-0.892	44.698	0.029	0.029	0.000	0.000	0.000	0.000
160	A	166	ARG	1	0.850	0.921	42.234	-0.034	-0.034	0.000	0.000	0.000	0.000
161	A	167	LYS	1	0.851	0.915	43.944	-0.023	-0.023	0.000	0.000	0.000	0.000
162	A	168	ASN	0	0.033	0.017	43.748	-0.003	-0.003	0.000	0.000	0.000	0.000
163	A	169	PRO	0	0.022	0.012	39.627	0.003	0.003	0.000	0.000	0.000	0.000
164	A	170	VAL	0	-0.033	0.004	39.852	0.001	0.001	0.000	0.000	0.000	0.000
165	A	171	TRP	0	-0.001	-0.008	35.444	0.002	0.002	0.000	0.000	0.000	0.000
166	A	172	TRP	0	0.032	0.017	38.928	0.002	0.002	0.000	0.000	0.000	0.000
167	A	173	ARG	1	0.950	0.985	41.467	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:MET)