FMO DATABASE

FMODB ID: 52KJZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1058138.37656
FMO2-HF: Nuclear repulsion	1008701.54558
FMO2-HF: Total energy	-49436.83098
FMO2-MP2: Total energy	-49577.947072

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.
-3.718	0.741	0.646	-2.381	-2.724	-0.005

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 : 0.015

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	0.000	-0.010	2.627	-4.576	-0.685	0.645	-2.295	-2.241	-0.005
4	A	73	LYS	1	1.003	0.988	5.115	-0.411	-0.285	-0.001	-0.009	-0.116	0.000
5	A	74	ASP	-1	-0.886	-0.943	6.807	-0.147	-0.147	0.000	0.000	0.000	0.000
6	A	75	TRP	0	-0.086	-0.041	7.046	-0.173	-0.173	0.000	0.000	0.000	0.000
7	A	76	GLU	-1	-0.886	-0.947	6.572	0.125	0.125	0.000	0.000	0.000	0.000
8	A	77	PHE	0	0.008	-0.026	4.021	-0.371	-0.072	0.002	-0.060	-0.242	0.000
9	A	78	TYR	0	0.022	0.008	6.183	0.307	0.307	0.000	0.000	0.000	0.000
10	A	79	GLN	0	-0.003	-0.002	9.036	-0.172	-0.172	0.000	0.000	0.000	0.000
11	A	80	ALA	0	0.000	0.001	7.188	-0.064	-0.064	0.000	0.000	0.000	0.000
12	A	81	ARG	1	0.810	0.893	8.215	0.337	0.337	0.000	0.000	0.000	0.000
13	A	83	PHE	0	0.023	-0.001	8.052	0.092	0.092	0.000	0.000	0.000	0.000
14	A	84	PHE	0	0.002	0.007	10.518	0.012	0.012	0.000	0.000	0.000	0.000
15	A	85	LEU	0	0.069	0.042	12.891	0.000	0.000	0.000	0.000	0.000	0.000
16	A	86	SER	0	-0.062	-0.021	15.796	0.024	0.024	0.000	0.000	0.000	0.000
17	A	87	THR	0	0.042	0.010	18.284	0.013	0.013	0.000	0.000	0.000	0.000
18	A	88	SER	0	-0.020	-0.008	20.660	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	89	GLU	-1	-0.841	-0.933	22.850	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	90	SER	0	-0.065	-0.037	25.008	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	91	SER	0	0.036	0.002	27.129	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	92	TRP	0	0.018	0.014	24.873	-0.021	-0.021	0.000	0.000	0.000	0.000
23	A	93	ASN	0	0.004	-0.018	26.019	-0.029	-0.029	0.000	0.000	0.000	0.000
24	A	94	GLU	-1	-0.763	-0.842	26.356	-0.133	-0.133	0.000	0.000	0.000	0.000
25	A	95	SER	0	-0.040	-0.032	22.800	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	96	ARG	1	0.850	0.901	21.652	0.156	0.156	0.000	0.000	0.000	0.000
27	A	97	ASP	-1	-0.811	-0.883	22.019	-0.245	-0.245	0.000	0.000	0.000	0.000
28	A	98	PHE	0	0.007	-0.004	19.909	-0.028	-0.028	0.000	0.000	0.000	0.000
29	A	99	CYS	0	-0.118	-0.037	14.889	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	100	LYS	1	0.928	0.985	17.070	0.181	0.181	0.000	0.000	0.000	0.000
31	A	101	GLY	0	-0.002	0.014	18.495	-0.037	-0.037	0.000	0.000	0.000	0.000
32	A	102	LYS	1	0.900	0.960	13.456	0.348	0.348	0.000	0.000	0.000	0.000
33	A	103	GLY	0	0.003	0.005	13.560	-0.163	-0.163	0.000	0.000	0.000	0.000
34	A	104	SER	0	-0.100	-0.065	13.821	-0.097	-0.097	0.000	0.000	0.000	0.000
35	A	105	THR	0	0.017	0.002	15.649	0.067	0.067	0.000	0.000	0.000	0.000
36	A	106	LEU	0	-0.006	-0.003	16.968	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	107	ALA	0	0.019	0.008	16.413	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	108	ILE	0	-0.024	-0.002	17.228	0.048	0.048	0.000	0.000	0.000	0.000
39	A	109	VAL	0	-0.015	0.004	17.666	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	110	ASN	0	0.033	0.003	19.405	0.013	0.013	0.000	0.000	0.000	0.000
41	A	111	THR	0	-0.014	-0.011	19.009	0.002	0.002	0.000	0.000	0.000	0.000
42	A	112	PRO	0	0.051	0.018	20.617	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	113	GLU	-1	-0.834	-0.903	17.094	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	114	LYS	1	0.827	0.910	14.392	0.326	0.326	0.000	0.000	0.000	0.000
45	A	115	LEU	0	-0.015	-0.013	17.038	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	116	LYS	1	0.797	0.878	19.265	-0.075	-0.075	0.000	0.000	0.000	0.000
47	A	117	PHE	0	0.006	0.002	10.730	0.006	0.006	0.000	0.000	0.000	0.000
48	A	118	LEU	0	0.032	0.007	14.308	0.008	0.008	0.000	0.000	0.000	0.000
49	A	119	GLN	0	-0.033	-0.025	16.976	0.019	0.019	0.000	0.000	0.000	0.000
50	A	120	ASP	-1	-0.815	-0.881	17.563	0.096	0.096	0.000	0.000	0.000	0.000
51	A	121	ILE	0	-0.034	-0.005	13.314	0.017	0.017	0.000	0.000	0.000	0.000
52	A	122	THR	0	-0.109	-0.050	17.178	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	123	ASP	-1	-0.914	-0.951	19.574	0.062	0.062	0.000	0.000	0.000	0.000
54	A	124	ALA	0	0.005	-0.007	22.401	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	125	GLU	-1	-0.851	-0.912	23.213	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	126	LYS	1	0.814	0.907	24.153	0.038	0.038	0.000	0.000	0.000	0.000
57	A	127	TYR	0	-0.017	-0.016	19.332	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	128	PHE	0	-0.022	-0.008	23.153	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	129	ILE	0	0.016	0.005	19.950	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	130	GLY	0	-0.011	-0.013	20.999	0.009	0.009	0.000	0.000	0.000	0.000
61	A	131	LEU	0	-0.072	-0.031	22.437	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	132	ILE	0	0.026	0.011	25.616	0.008	0.008	0.000	0.000	0.000	0.000
63	A	133	TYR	0	-0.029	-0.017	29.026	0.003	0.003	0.000	0.000	0.000	0.000
64	A	134	HIS	0	-0.043	-0.037	30.629	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	135	ARG	1	0.952	0.959	34.444	0.087	0.087	0.000	0.000	0.000	0.000
66	A	136	GLU	-1	-0.854	-0.917	35.213	-0.101	-0.101	0.000	0.000	0.000	0.000
67	A	137	GLU	-1	-0.805	-0.861	34.307	-0.104	-0.104	0.000	0.000	0.000	0.000
68	A	138	LYS	1	0.886	0.951	37.779	0.060	0.060	0.000	0.000	0.000	0.000
69	A	139	ARG	1	0.899	0.947	32.670	0.093	0.093	0.000	0.000	0.000	0.000
70	A	140	TRP	0	0.022	0.006	29.860	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	141	ARG	1	0.797	0.868	28.409	0.131	0.131	0.000	0.000	0.000	0.000
72	A	142	TRP	0	0.029	0.015	22.289	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	143	ILE	0	-0.002	-0.010	20.846	0.003	0.003	0.000	0.000	0.000	0.000
74	A	144	ASN	0	-0.010	0.008	20.946	0.002	0.002	0.000	0.000	0.000	0.000
75	A	145	ASN	0	-0.010	-0.001	22.889	0.014	0.014	0.000	0.000	0.000	0.000
76	A	146	SER	0	-0.024	-0.013	24.235	0.009	0.009	0.000	0.000	0.000	0.000
77	A	147	VAL	0	0.015	-0.004	26.850	0.000	0.000	0.000	0.000	0.000	0.000
78	A	148	PHE	0	-0.008	0.000	25.808	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	149	ASN	0	-0.030	-0.021	24.273	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	150	GLY	0	0.033	0.029	28.030	0.008	0.008	0.000	0.000	0.000	0.000
81	A	151	ASN	0	-0.028	-0.024	28.852	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	152	VAL	0	0.006	0.017	29.580	0.000	0.000	0.000	0.000	0.000	0.000
83	A	153	THR	0	-0.024	-0.025	31.629	0.003	0.003	0.000	0.000	0.000	0.000
84	A	154	ASN	0	0.008	-0.019	33.964	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	155	GLN	0	0.015	0.015	34.838	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	156	ASN	0	0.034	0.009	37.157	0.004	0.004	0.000	0.000	0.000	0.000
87	A	157	GLN	0	0.003	-0.002	38.908	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	158	ASN	0	-0.018	-0.003	39.663	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	159	PHE	0	-0.038	-0.010	34.405	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	160	ASN	0	0.018	-0.001	33.635	0.000	0.000	0.000	0.000	0.000	0.000
91	A	161	CYS	0	-0.004	-0.002	28.829	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	162	ALA	0	0.052	0.020	27.342	0.011	0.011	0.000	0.000	0.000	0.000
93	A	163	THR	0	-0.032	-0.009	25.274	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	164	ILE	0	0.004	0.001	19.789	0.005	0.005	0.000	0.000	0.000	0.000
95	A	165	GLY	0	0.100	0.048	23.463	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	166	LEU	0	0.015	0.026	24.069	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	167	THR	0	-0.088	-0.064	26.835	0.008	0.008	0.000	0.000	0.000	0.000
98	A	168	LYS	1	0.949	0.963	26.678	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	169	THR	0	-0.051	-0.049	27.281	0.001	0.001	0.000	0.000	0.000	0.000
100	A	170	PHE	0	0.037	0.024	23.135	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	171	ASP	-1	-0.714	-0.795	27.756	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	172	ALA	0	0.007	0.003	29.787	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	173	ALA	0	-0.021	-0.011	30.026	0.006	0.006	0.000	0.000	0.000	0.000
104	A	174	SER	0	0.000	-0.006	32.132	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	176	ASP	-1	-0.884	-0.948	31.198	-0.095	-0.095	0.000	0.000	0.000	0.000
106	A	177	ILE	0	-0.033	-0.004	31.638	0.004	0.004	0.000	0.000	0.000	0.000
107	A	178	SER	0	-0.026	-0.026	29.175	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	179	TYR	0	0.035	0.017	25.919	0.012	0.012	0.000	0.000	0.000	0.000
109	A	180	ARG	1	0.891	0.969	21.364	0.014	0.014	0.000	0.000	0.000	0.000
110	A	181	ARG	1	0.886	0.945	19.246	0.193	0.193	0.000	0.000	0.000	0.000
111	A	182	ILE	0	0.064	0.034	15.403	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	184	GLU	-1	-0.700	-0.839	12.464	-0.476	-0.476	0.000	0.000	0.000	0.000
113	A	185	LYS	1	0.865	0.926	9.340	1.363	1.363	0.000	0.000	0.000	0.000
114	A	186	ASN	0	0.003	0.011	9.439	0.096	0.096	0.000	0.000	0.000	0.000
115	A	187	ALA	0	0.019	0.021	4.059	-0.202	-0.059	0.000	-0.017	-0.125	0.000

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