FMO DATABASE

FMODB ID: 494JN

Calculation Name: 2YHF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NY25

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	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	115
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1056908.981051
FMO2-HF: Nuclear repulsion	1007472.678718
FMO2-HF: Total energy	-49436.302333
FMO2-MP2: Total energy	-49577.398714

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:70:MET)

Summations of interaction energy for fragment #1(A:70: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.
-4.54	-0.355	1.806	-2.698	-3.291	-0.011

Interaction energy analysis for fragmet #1(A:70:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.016

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	72	PRO	0	0.001	-0.010	2.362	-5.403	-1.812	1.804	-2.609	-2.785	-0.011
4	A	73	LYS	1	1.005	0.987	4.902	-0.359	-0.218	-0.001	-0.010	-0.129	0.000
5	A	74	ASP	-1	-0.876	-0.935	6.573	-0.187	-0.187	0.000	0.000	0.000	0.000
6	A	75	TRP	0	-0.095	-0.044	6.800	-0.157	-0.157	0.000	0.000	0.000	0.000
7	A	76	GLU	-1	-0.899	-0.955	6.580	0.085	0.085	0.000	0.000	0.000	0.000
8	A	77	PHE	0	0.009	-0.021	3.900	-0.342	-0.035	0.003	-0.061	-0.248	0.000
9	A	78	TYR	0	0.035	0.013	6.170	0.298	0.298	0.000	0.000	0.000	0.000
10	A	79	GLN	0	-0.019	-0.009	9.033	-0.166	-0.166	0.000	0.000	0.000	0.000
11	A	80	ALA	0	0.000	0.005	7.212	-0.067	-0.067	0.000	0.000	0.000	0.000
12	A	81	ARG	1	0.875	0.938	8.232	0.315	0.315	0.000	0.000	0.000	0.000
13	A	83	PHE	0	0.029	0.000	8.047	0.095	0.095	0.000	0.000	0.000	0.000
14	A	84	PHE	0	-0.005	0.004	10.519	0.003	0.003	0.000	0.000	0.000	0.000
15	A	85	LEU	0	0.076	0.041	12.903	0.006	0.006	0.000	0.000	0.000	0.000
16	A	86	SER	0	-0.064	-0.014	15.802	0.023	0.023	0.000	0.000	0.000	0.000
17	A	87	THR	0	0.044	0.010	18.115	0.014	0.014	0.000	0.000	0.000	0.000
18	A	88	SER	0	0.012	0.002	20.522	0.001	0.001	0.000	0.000	0.000	0.000
19	A	89	GLU	-1	-0.899	-0.958	22.566	-0.076	-0.076	0.000	0.000	0.000	0.000
20	A	90	SER	0	-0.042	-0.026	25.072	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	91	SER	0	0.052	0.049	26.858	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	92	TRP	0	0.033	0.016	24.818	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	93	ASN	0	0.001	-0.020	25.848	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	94	GLU	-1	-0.805	-0.894	26.128	-0.140	-0.140	0.000	0.000	0.000	0.000
25	A	95	SER	0	-0.028	-0.019	22.511	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	96	ARG	1	0.852	0.920	21.412	0.163	0.163	0.000	0.000	0.000	0.000
27	A	97	ASP	-1	-0.877	-0.937	21.808	-0.249	-0.249	0.000	0.000	0.000	0.000
28	A	98	PHE	0	-0.020	-0.017	19.636	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	99	CYS	0	-0.120	-0.038	14.607	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	100	LYS	1	1.012	1.040	16.870	0.202	0.202	0.000	0.000	0.000	0.000
31	A	101	GLY	0	-0.007	0.010	18.333	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	102	LYS	1	0.902	0.958	13.247	0.366	0.366	0.000	0.000	0.000	0.000
33	A	103	GLY	0	-0.011	-0.006	13.391	-0.164	-0.164	0.000	0.000	0.000	0.000
34	A	104	SER	0	-0.108	-0.071	13.718	-0.097	-0.097	0.000	0.000	0.000	0.000
35	A	105	THR	0	0.012	0.000	15.623	0.070	0.070	0.000	0.000	0.000	0.000
36	A	106	LEU	0	-0.003	-0.005	16.965	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	107	ALA	0	0.020	0.008	16.409	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	108	ILE	0	-0.021	-0.002	17.245	0.053	0.053	0.000	0.000	0.000	0.000
39	A	109	VAL	0	-0.017	0.003	17.666	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	110	ASN	0	0.050	0.011	19.597	0.017	0.017	0.000	0.000	0.000	0.000
41	A	111	THR	0	0.019	0.016	18.408	0.002	0.002	0.000	0.000	0.000	0.000
42	A	112	PRO	0	0.058	0.022	20.616	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	113	GLU	-1	-0.878	-0.943	17.030	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	114	LYS	1	0.890	0.953	14.980	0.249	0.249	0.000	0.000	0.000	0.000
45	A	115	LEU	0	-0.008	-0.009	17.034	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	116	LYS	1	0.917	0.968	19.252	-0.081	-0.081	0.000	0.000	0.000	0.000
47	A	117	PHE	0	-0.009	-0.004	10.535	0.008	0.008	0.000	0.000	0.000	0.000
48	A	118	LEU	0	0.022	0.002	14.344	0.005	0.005	0.000	0.000	0.000	0.000
49	A	119	GLN	0	-0.038	-0.035	16.961	0.018	0.018	0.000	0.000	0.000	0.000
50	A	120	ASP	-1	-0.886	-0.945	17.664	0.085	0.085	0.000	0.000	0.000	0.000
51	A	121	ILE	0	-0.037	-0.006	13.111	0.015	0.015	0.000	0.000	0.000	0.000
52	A	122	THR	0	-0.124	-0.051	17.150	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	123	ASP	-1	-0.889	-0.939	19.555	0.058	0.058	0.000	0.000	0.000	0.000
54	A	124	ALA	0	-0.027	-0.023	22.378	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	125	GLU	-1	-0.927	-0.963	23.327	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	126	LYS	1	0.898	0.954	24.141	0.036	0.036	0.000	0.000	0.000	0.000
57	A	127	TYR	0	-0.008	-0.011	19.226	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	128	PHE	0	-0.016	-0.005	23.150	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	129	ILE	0	0.009	0.003	20.042	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	130	GLY	0	-0.014	-0.015	20.991	0.009	0.009	0.000	0.000	0.000	0.000
61	A	131	LEU	0	-0.066	-0.030	22.434	0.000	0.000	0.000	0.000	0.000	0.000
62	A	132	ILE	0	0.020	0.008	25.614	0.007	0.007	0.000	0.000	0.000	0.000
63	A	133	TYR	0	-0.020	-0.012	29.024	0.004	0.004	0.000	0.000	0.000	0.000
64	A	134	HIS	0	-0.019	-0.011	30.534	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	135	ARG	1	0.972	0.969	34.445	0.088	0.088	0.000	0.000	0.000	0.000
66	A	136	GLU	-1	-0.864	-0.941	35.307	-0.101	-0.101	0.000	0.000	0.000	0.000
67	A	137	GLU	-1	-0.836	-0.884	34.323	-0.106	-0.106	0.000	0.000	0.000	0.000
68	A	138	LYS	1	0.884	0.948	37.784	0.061	0.061	0.000	0.000	0.000	0.000
69	A	139	ARG	1	0.898	0.955	32.489	0.094	0.094	0.000	0.000	0.000	0.000
70	A	140	TRP	0	0.026	0.018	29.780	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	141	ARG	1	0.833	0.895	28.476	0.130	0.130	0.000	0.000	0.000	0.000
72	A	142	TRP	0	0.030	0.012	22.481	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	143	ILE	0	-0.010	-0.011	20.821	0.003	0.003	0.000	0.000	0.000	0.000
74	A	144	ASN	0	-0.009	0.007	20.832	0.004	0.004	0.000	0.000	0.000	0.000
75	A	145	ASN	0	-0.020	-0.003	22.887	0.014	0.014	0.000	0.000	0.000	0.000
76	A	146	SER	0	-0.034	-0.020	24.220	0.010	0.010	0.000	0.000	0.000	0.000
77	A	147	VAL	0	-0.002	-0.011	26.859	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	148	PHE	0	-0.004	0.002	25.989	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	149	ASN	0	-0.025	-0.018	24.237	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	150	GLY	0	0.030	0.024	28.028	0.009	0.009	0.000	0.000	0.000	0.000
81	A	151	ASN	0	-0.023	-0.018	28.851	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	152	VAL	0	0.004	0.014	29.596	0.000	0.000	0.000	0.000	0.000	0.000
83	A	153	THR	0	-0.023	-0.035	31.623	0.004	0.004	0.000	0.000	0.000	0.000
84	A	154	ASN	0	-0.016	-0.031	33.955	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	155	GLN	0	0.022	0.021	34.910	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	156	ASN	0	0.047	0.016	37.150	0.002	0.002	0.000	0.000	0.000	0.000
87	A	157	GLN	0	-0.002	-0.006	38.901	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	158	ASN	0	-0.019	-0.005	39.655	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	159	PHE	0	-0.058	-0.019	34.313	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	160	ASN	0	0.021	-0.003	33.630	0.001	0.001	0.000	0.000	0.000	0.000
91	A	161	CYS	0	-0.014	-0.009	28.815	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	162	ALA	0	0.053	0.018	27.365	0.011	0.011	0.000	0.000	0.000	0.000
93	A	163	THR	0	-0.046	-0.010	25.269	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	164	ILE	0	0.010	0.002	19.746	0.005	0.005	0.000	0.000	0.000	0.000
95	A	165	GLY	0	0.096	0.046	23.446	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	166	LEU	0	0.008	0.023	24.052	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	167	THR	0	-0.094	-0.074	26.813	0.010	0.010	0.000	0.000	0.000	0.000
98	A	168	LYS	1	0.946	0.961	26.662	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	169	THR	0	-0.065	-0.060	27.270	0.002	0.002	0.000	0.000	0.000	0.000
100	A	170	PHE	0	0.030	0.024	23.156	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	171	ASP	-1	-0.745	-0.804	27.746	-0.041	-0.041	0.000	0.000	0.000	0.000
102	A	172	ALA	0	-0.001	-0.003	29.776	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	173	ALA	0	-0.007	-0.003	30.032	0.006	0.006	0.000	0.000	0.000	0.000
104	A	174	SER	0	-0.002	-0.007	32.121	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	176	ASP	-1	-0.876	-0.939	31.119	-0.099	-0.099	0.000	0.000	0.000	0.000
106	A	177	ILE	0	-0.045	-0.011	31.636	0.004	0.004	0.000	0.000	0.000	0.000
107	A	178	SER	0	-0.033	-0.028	28.887	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	179	TYR	0	0.048	0.020	25.886	0.011	0.011	0.000	0.000	0.000	0.000
109	A	180	ARG	1	0.965	1.013	21.093	0.028	0.028	0.000	0.000	0.000	0.000
110	A	181	ARG	1	0.915	0.954	18.612	0.220	0.220	0.000	0.000	0.000	0.000
111	A	182	ILE	0	0.066	0.031	15.440	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	184	GLU	-1	-0.782	-0.895	12.508	-0.511	-0.511	0.000	0.000	0.000	0.000
113	A	185	LYS	1	0.868	0.933	9.099	1.432	1.432	0.000	0.000	0.000	0.000
114	A	186	ASN	0	-0.020	-0.007	9.216	0.111	0.111	0.000	0.000	0.000	0.000
115	A	187	ALA	0	0.008	0.014	3.996	-0.213	-0.067	0.000	-0.018	-0.129	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:70:MET)