FMO DATABASE

FMODB ID: YZKZ2

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	OptAll
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	-1060058.716653
FMO2-HF: Nuclear repulsion	1010621.674814
FMO2-HF: Total energy	-49437.041839
FMO2-MP2: Total energy	-49578.166641

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.
-3.765	0.445	0.781	-2.326	-2.664	-0.008

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 : 0.014

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	-0.010	-0.013	2.589	-4.368	-0.718	0.780	-2.235	-2.195	-0.008
4	A	73	LYS	1	0.999	0.990	5.109	-0.350	-0.228	-0.001	-0.009	-0.112	0.000
5	A	74	ASP	-1	-0.896	-0.949	6.996	-0.201	-0.201	0.000	0.000	0.000	0.000
6	A	75	TRP	0	-0.057	-0.030	7.251	-0.179	-0.179	0.000	0.000	0.000	0.000
7	A	76	GLU	-1	-0.870	-0.935	6.364	-0.062	-0.062	0.000	0.000	0.000	0.000
8	A	77	PHE	0	0.008	-0.033	4.013	-0.400	-0.089	0.003	-0.065	-0.249	0.000
9	A	78	TYR	0	0.019	0.006	6.223	0.361	0.361	0.000	0.000	0.000	0.000
10	A	79	GLN	0	-0.001	-0.005	9.048	-0.185	-0.185	0.000	0.000	0.000	0.000
11	A	80	ALA	0	0.004	0.006	7.217	-0.046	-0.046	0.000	0.000	0.000	0.000
12	A	81	ARG	1	0.805	0.887	8.242	0.392	0.392	0.000	0.000	0.000	0.000
13	A	83	PHE	0	0.018	0.001	8.209	0.117	0.117	0.000	0.000	0.000	0.000
14	A	84	PHE	0	-0.002	0.006	10.549	-0.028	-0.028	0.000	0.000	0.000	0.000
15	A	85	LEU	0	0.065	0.040	13.134	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	86	SER	0	-0.053	-0.024	16.244	0.021	0.021	0.000	0.000	0.000	0.000
17	A	87	THR	0	0.056	0.022	18.319	0.010	0.010	0.000	0.000	0.000	0.000
18	A	88	SER	0	-0.009	0.004	20.672	0.001	0.001	0.000	0.000	0.000	0.000
19	A	89	GLU	-1	-0.849	-0.937	22.872	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	90	SER	0	-0.046	-0.027	24.942	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	91	SER	0	0.015	-0.010	27.206	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	92	TRP	0	-0.001	0.005	25.320	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	93	ASN	0	0.020	0.002	26.463	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	94	GLU	-1	-0.782	-0.851	26.540	-0.132	-0.132	0.000	0.000	0.000	0.000
25	A	95	SER	0	-0.050	-0.046	23.222	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	96	ARG	1	0.842	0.887	21.898	0.159	0.159	0.000	0.000	0.000	0.000
27	A	97	ASP	-1	-0.792	-0.865	21.975	-0.250	-0.250	0.000	0.000	0.000	0.000
28	A	98	PHE	0	0.010	-0.001	20.125	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	99	CYS	0	-0.086	-0.015	15.188	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	100	LYS	1	0.912	0.971	17.248	0.182	0.182	0.000	0.000	0.000	0.000
31	A	101	GLY	0	-0.013	-0.002	18.506	-0.039	-0.039	0.000	0.000	0.000	0.000
32	A	102	LYS	1	0.907	0.957	13.663	0.351	0.351	0.000	0.000	0.000	0.000
33	A	103	GLY	0	-0.007	0.008	13.451	-0.159	-0.159	0.000	0.000	0.000	0.000
34	A	104	SER	0	-0.088	-0.055	14.014	-0.117	-0.117	0.000	0.000	0.000	0.000
35	A	105	THR	0	0.012	0.006	15.847	0.063	0.063	0.000	0.000	0.000	0.000
36	A	106	LEU	0	0.026	0.003	17.318	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	107	ALA	0	0.000	-0.004	16.780	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	108	ILE	0	-0.022	-0.002	17.593	0.050	0.050	0.000	0.000	0.000	0.000
39	A	109	VAL	0	-0.004	0.010	18.434	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	110	ASN	0	0.033	-0.003	19.295	0.005	0.005	0.000	0.000	0.000	0.000
41	A	111	THR	0	-0.029	-0.023	19.122	0.001	0.001	0.000	0.000	0.000	0.000
42	A	112	PRO	0	0.058	0.023	20.813	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	113	GLU	-1	-0.828	-0.898	17.468	-0.060	-0.060	0.000	0.000	0.000	0.000
44	A	114	LYS	1	0.814	0.907	14.857	0.344	0.344	0.000	0.000	0.000	0.000
45	A	115	LEU	0	-0.018	-0.007	17.305	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	116	LYS	1	0.797	0.874	19.496	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	117	PHE	0	0.002	-0.001	11.081	0.008	0.008	0.000	0.000	0.000	0.000
48	A	118	LEU	0	0.049	0.013	14.825	0.006	0.006	0.000	0.000	0.000	0.000
49	A	119	GLN	0	-0.037	-0.006	17.372	0.018	0.018	0.000	0.000	0.000	0.000
50	A	120	ASP	-1	-0.819	-0.882	17.678	0.070	0.070	0.000	0.000	0.000	0.000
51	A	121	ILE	0	-0.036	-0.004	13.600	0.019	0.019	0.000	0.000	0.000	0.000
52	A	122	THR	0	-0.102	-0.064	17.255	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	123	ASP	-1	-0.824	-0.908	19.897	0.048	0.048	0.000	0.000	0.000	0.000
54	A	124	ALA	0	-0.047	-0.032	22.577	-0.015	-0.015	0.000	0.000	0.000	0.000
55	A	125	GLU	-1	-0.808	-0.870	23.087	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	126	LYS	1	0.772	0.874	24.561	0.046	0.046	0.000	0.000	0.000	0.000
57	A	127	TYR	0	-0.018	-0.016	19.554	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	128	PHE	0	-0.022	-0.012	23.512	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	129	ILE	0	0.016	0.005	20.415	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	130	GLY	0	-0.004	-0.003	21.382	0.011	0.011	0.000	0.000	0.000	0.000
61	A	131	LEU	0	-0.068	-0.028	22.764	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	132	ILE	0	0.034	0.007	25.976	0.009	0.009	0.000	0.000	0.000	0.000
63	A	133	TYR	0	-0.036	-0.018	29.454	0.002	0.002	0.000	0.000	0.000	0.000
64	A	134	HIS	0	-0.037	-0.027	30.817	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	135	ARG	1	0.889	0.922	34.622	0.092	0.092	0.000	0.000	0.000	0.000
66	A	136	GLU	-1	-0.839	-0.916	35.370	-0.106	-0.106	0.000	0.000	0.000	0.000
67	A	137	GLU	-1	-0.802	-0.858	34.407	-0.109	-0.109	0.000	0.000	0.000	0.000
68	A	138	LYS	1	0.905	0.960	38.109	0.065	0.065	0.000	0.000	0.000	0.000
69	A	139	ARG	1	0.903	0.953	33.259	0.100	0.100	0.000	0.000	0.000	0.000
70	A	140	TRP	0	0.002	-0.006	29.936	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	141	ARG	1	0.779	0.858	28.465	0.139	0.139	0.000	0.000	0.000	0.000
72	A	142	TRP	0	0.023	0.016	22.712	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	143	ILE	0	-0.004	-0.014	21.228	0.001	0.001	0.000	0.000	0.000	0.000
74	A	144	ASN	0	-0.005	0.017	21.073	0.004	0.004	0.000	0.000	0.000	0.000
75	A	145	ASN	0	0.007	0.006	23.036	0.014	0.014	0.000	0.000	0.000	0.000
76	A	146	SER	0	-0.029	-0.019	24.328	0.013	0.013	0.000	0.000	0.000	0.000
77	A	147	VAL	0	0.023	-0.004	26.866	0.001	0.001	0.000	0.000	0.000	0.000
78	A	148	PHE	0	-0.013	0.003	26.272	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	149	ASN	0	-0.040	-0.027	24.309	0.000	0.000	0.000	0.000	0.000	0.000
80	A	150	GLY	0	0.041	0.024	28.267	0.006	0.006	0.000	0.000	0.000	0.000
81	A	151	ASN	0	-0.023	-0.018	29.380	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	152	VAL	0	0.008	0.009	29.762	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	153	THR	0	-0.010	-0.030	31.889	0.004	0.004	0.000	0.000	0.000	0.000
84	A	154	ASN	0	0.020	-0.017	34.180	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	155	GLN	0	0.007	0.019	34.736	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	156	ASN	0	0.011	0.000	37.028	0.004	0.004	0.000	0.000	0.000	0.000
87	A	157	GLN	0	0.025	0.011	38.892	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	158	ASN	0	-0.006	-0.001	39.788	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	159	PHE	0	-0.073	-0.022	34.848	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	160	ASN	0	0.028	0.015	33.966	0.000	0.000	0.000	0.000	0.000	0.000
91	A	161	CYS	0	-0.027	-0.001	28.891	-0.015	-0.015	0.000	0.000	0.000	0.000
92	A	162	ALA	0	0.038	0.014	27.488	0.012	0.012	0.000	0.000	0.000	0.000
93	A	163	THR	0	-0.026	-0.011	25.419	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	164	ILE	0	0.006	-0.001	20.084	0.004	0.004	0.000	0.000	0.000	0.000
95	A	165	GLY	0	0.104	0.058	23.844	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	166	LEU	0	0.002	0.019	24.389	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	167	THR	0	-0.074	-0.061	27.154	0.007	0.007	0.000	0.000	0.000	0.000
98	A	168	LYS	1	0.932	0.952	26.555	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	169	THR	0	-0.045	-0.050	27.691	0.001	0.001	0.000	0.000	0.000	0.000
100	A	170	PHE	0	0.048	0.030	23.194	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	171	ASP	-1	-0.717	-0.784	27.861	-0.042	-0.042	0.000	0.000	0.000	0.000
102	A	172	ALA	0	0.015	0.006	29.812	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	173	ALA	0	-0.003	-0.001	30.647	0.007	0.007	0.000	0.000	0.000	0.000
104	A	174	SER	0	-0.002	-0.037	32.702	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	176	ASP	-1	-0.848	-0.911	31.351	-0.099	-0.099	0.000	0.000	0.000	0.000
106	A	177	ILE	0	0.003	0.002	32.158	0.002	0.002	0.000	0.000	0.000	0.000
107	A	178	SER	0	-0.029	-0.025	29.383	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	179	TYR	0	0.027	0.022	26.407	0.012	0.012	0.000	0.000	0.000	0.000
109	A	180	ARG	1	0.828	0.913	21.822	0.026	0.026	0.000	0.000	0.000	0.000
110	A	181	ARG	1	0.857	0.934	19.713	0.185	0.185	0.000	0.000	0.000	0.000
111	A	182	ILE	0	0.057	0.034	15.953	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	184	GLU	-1	-0.730	-0.845	12.943	-0.479	-0.479	0.000	0.000	0.000	0.000
113	A	185	LYS	1	0.858	0.928	9.390	1.357	1.357	0.000	0.000	0.000	0.000
114	A	186	ASN	0	0.024	0.015	9.301	0.109	0.109	0.000	0.000	0.000	0.000
115	A	187	ALA	0	0.012	0.017	4.135	-0.308	-0.181	-0.001	-0.017	-0.108	0.000

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