FMO DATABASE

FMODB ID: ZVR4N

Calculation Name: 2PYT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PYT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZFV5

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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1049683.905889
FMO2-HF: Nuclear repulsion	999577.745348
FMO2-HF: Total energy	-50106.160542
FMO2-MP2: Total energy	-50249.183041

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:100:LEU)

Summations of interaction energy for fragment #1(A:100:LEU)

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.
1.701	0.669	10.691	-2.551	-7.11	-0.024

Interaction energy analysis for fragmet #1(A:100:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / 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

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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	102	LEU	0	-0.008	-0.006	1.633	0.408	-1.174	7.727	-2.672	-3.474	-0.018
4	A	103	GLY	0	-0.024	-0.014	2.280	0.541	0.617	2.821	-0.532	-2.365	-0.002
5	A	104	THR	0	-0.039	-0.031	3.153	0.636	-0.176	0.027	1.172	-0.387	-0.001
6	A	105	MET	0	0.003	0.022	2.945	-2.430	-1.204	0.117	-0.514	-0.830	-0.003
7	A	106	GLN	0	-0.029	-0.012	4.753	0.342	0.402	-0.001	-0.005	-0.054	0.000
8	A	107	PRO	0	0.031	0.031	7.997	0.181	0.181	0.000	0.000	0.000	0.000
9	A	108	SER	0	-0.045	-0.035	10.173	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	109	PHE	0	0.044	0.018	12.183	0.099	0.099	0.000	0.000	0.000	0.000
11	A	110	THR	0	0.020	0.027	14.895	-0.057	-0.057	0.000	0.000	0.000	0.000
12	A	111	SER	0	-0.037	-0.031	17.864	0.011	0.011	0.000	0.000	0.000	0.000
13	A	112	VAL	0	-0.007	0.003	21.317	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	113	THR	0	0.044	0.019	25.029	0.005	0.005	0.000	0.000	0.000	0.000
15	A	114	GLY	0	-0.031	-0.004	27.797	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	115	LYS	1	0.951	0.943	31.450	-0.042	-0.042	0.000	0.000	0.000	0.000
17	A	116	GLY	0	-0.029	-0.021	34.374	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	117	GLY	0	0.050	0.044	31.145	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	118	VAL	0	-0.017	0.005	29.630	0.003	0.003	0.000	0.000	0.000	0.000
20	A	119	LYS	1	0.860	0.922	21.656	-0.096	-0.096	0.000	0.000	0.000	0.000
21	A	120	VAL	0	-0.005	-0.004	23.483	0.004	0.004	0.000	0.000	0.000	0.000
22	A	121	ILE	0	0.038	0.008	18.062	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	122	ASP	-1	-0.861	-0.894	18.092	0.277	0.277	0.000	0.000	0.000	0.000
24	A	123	GLY	0	0.050	0.037	16.662	0.026	0.026	0.000	0.000	0.000	0.000
25	A	124	SER	0	-0.069	-0.059	14.539	0.073	0.073	0.000	0.000	0.000	0.000
26	A	125	SER	0	-0.052	-0.051	13.155	0.046	0.046	0.000	0.000	0.000	0.000
27	A	126	VAL	0	-0.030	-0.016	11.383	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	127	LYS	1	0.874	0.951	7.369	-0.267	-0.267	0.000	0.000	0.000	0.000
29	A	128	PHE	0	0.037	0.019	6.940	-0.220	-0.220	0.000	0.000	0.000	0.000
30	A	129	GLY	0	0.006	0.007	6.363	-0.042	-0.042	0.000	0.000	0.000	0.000
31	A	130	ARG	1	0.922	0.946	4.841	2.211	2.211	0.000	0.000	0.000	0.000
32	A	131	PHE	0	0.001	0.003	9.004	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	132	ASP	-1	-0.867	-0.949	12.636	-0.281	-0.281	0.000	0.000	0.000	0.000
34	A	133	GLY	0	-0.072	-0.035	14.575	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	134	ALA	0	-0.011	0.004	13.803	0.018	0.018	0.000	0.000	0.000	0.000
36	A	135	GLU	-1	-0.918	-0.950	12.007	-0.439	-0.439	0.000	0.000	0.000	0.000
37	A	136	PRO	0	-0.115	-0.070	13.948	0.037	0.037	0.000	0.000	0.000	0.000
38	A	137	HIS	0	-0.026	0.000	12.058	-0.062	-0.062	0.000	0.000	0.000	0.000
39	A	138	CYS	0	0.005	0.019	6.792	-0.279	-0.279	0.000	0.000	0.000	0.000
40	A	139	VAL	0	0.006	0.005	9.339	0.188	0.188	0.000	0.000	0.000	0.000
41	A	140	GLY	0	0.004	0.005	8.759	-0.079	-0.079	0.000	0.000	0.000	0.000
42	A	141	LEU	0	0.004	-0.012	9.389	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	142	THR	0	-0.042	-0.039	10.842	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	143	ASP	-1	-0.841	-0.878	13.192	0.111	0.111	0.000	0.000	0.000	0.000
45	A	144	LEU	0	-0.068	-0.041	15.476	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	145	VAL	0	-0.054	-0.023	18.713	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	146	THR	0	0.029	0.018	20.946	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	147	GLU	-1	-0.830	-0.933	23.793	0.019	0.019	0.000	0.000	0.000	0.000
49	A	148	GLN	0	-0.036	-0.016	24.465	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	149	ASP	-1	-0.840	-0.908	23.906	0.073	0.073	0.000	0.000	0.000	0.000
51	A	150	GLY	0	-0.063	-0.032	27.224	0.001	0.001	0.000	0.000	0.000	0.000
52	A	151	SER	0	-0.073	-0.039	27.041	0.000	0.000	0.000	0.000	0.000	0.000
53	A	152	SER	0	0.012	-0.010	29.032	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	153	MET	0	-0.037	-0.025	27.160	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	154	ALA	0	0.010	0.030	22.422	0.000	0.000	0.000	0.000	0.000	0.000
56	A	155	ALA	0	0.020	0.007	21.650	0.003	0.003	0.000	0.000	0.000	0.000
57	A	156	GLY	0	0.058	0.025	17.472	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	157	PHE	0	-0.062	-0.006	14.058	0.002	0.002	0.000	0.000	0.000	0.000
59	A	158	MET	0	0.041	0.024	13.193	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	159	GLN	0	-0.001	-0.004	8.331	-0.210	-0.210	0.000	0.000	0.000	0.000
61	A	160	TRP	0	-0.086	-0.032	9.329	0.135	0.135	0.000	0.000	0.000	0.000
62	A	161	ASP	-1	-0.811	-0.916	8.639	0.783	0.783	0.000	0.000	0.000	0.000
63	A	162	ASN	0	-0.120	-0.065	11.024	-0.088	-0.088	0.000	0.000	0.000	0.000
64	A	163	ALA	0	0.044	0.025	12.974	-0.046	-0.046	0.000	0.000	0.000	0.000
65	A	164	PHE	0	-0.013	-0.004	14.942	0.037	0.037	0.000	0.000	0.000	0.000
66	A	165	PHE	0	0.019	0.002	15.768	-0.031	-0.031	0.000	0.000	0.000	0.000
67	A	166	PRO	0	0.026	0.028	19.118	0.017	0.017	0.000	0.000	0.000	0.000
68	A	167	TRP	0	-0.015	-0.019	20.339	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	168	THR	0	0.009	0.024	22.913	0.005	0.005	0.000	0.000	0.000	0.000
70	A	169	LEU	0	0.013	0.039	24.261	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	170	ASN	0	-0.024	-0.012	26.437	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	171	TYR	0	-0.059	-0.047	22.088	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	172	ASP	-1	-0.856	-0.912	28.071	0.052	0.052	0.000	0.000	0.000	0.000
74	A	173	GLU	-1	-0.843	-0.950	21.943	0.119	0.119	0.000	0.000	0.000	0.000
75	A	174	ILE	0	-0.062	-0.022	25.677	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	175	ASP	-1	-0.808	-0.914	22.060	0.163	0.163	0.000	0.000	0.000	0.000
77	A	176	MET	0	-0.071	-0.038	22.174	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	177	VAL	0	0.007	-0.002	19.480	0.032	0.032	0.000	0.000	0.000	0.000
79	A	178	LEU	0	-0.071	-0.036	17.335	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	179	GLU	-1	-0.939	-0.988	14.180	0.595	0.595	0.000	0.000	0.000	0.000
81	A	180	GLY	0	0.001	0.012	16.943	0.012	0.012	0.000	0.000	0.000	0.000
82	A	181	GLU	-1	-0.915	-0.959	17.849	0.132	0.132	0.000	0.000	0.000	0.000
83	A	182	LEU	0	0.017	0.021	18.551	0.015	0.015	0.000	0.000	0.000	0.000
84	A	183	HIS	0	-0.092	-0.070	20.293	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	184	VAL	0	0.056	0.025	21.665	0.002	0.002	0.000	0.000	0.000	0.000
86	A	185	ARG	1	0.905	0.963	24.283	-0.037	-0.037	0.000	0.000	0.000	0.000
87	A	186	HIS	0	0.031	-0.004	26.755	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	187	GLU	-1	-0.924	-0.965	29.666	0.030	0.030	0.000	0.000	0.000	0.000
89	A	188	GLY	0	-0.050	-0.021	31.312	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	189	GLU	-1	-0.974	-0.976	31.068	0.046	0.046	0.000	0.000	0.000	0.000
91	A	190	THR	0	-0.017	-0.015	25.363	0.002	0.002	0.000	0.000	0.000	0.000
92	A	191	MET	0	-0.028	-0.007	27.308	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	192	ILE	0	-0.020	-0.021	23.685	0.006	0.006	0.000	0.000	0.000	0.000
94	A	193	ALA	0	-0.008	0.015	23.646	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	194	LYS	1	0.955	0.969	22.564	-0.117	-0.117	0.000	0.000	0.000	0.000
96	A	195	ALA	0	0.011	0.003	20.824	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	196	GLY	0	-0.036	-0.021	22.459	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	197	ASP	-1	-0.883	-0.931	25.005	0.125	0.125	0.000	0.000	0.000	0.000
99	A	198	VAL	0	-0.034	-0.034	25.200	0.014	0.014	0.000	0.000	0.000	0.000
100	A	199	MET	0	-0.037	-0.014	24.337	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	200	PHE	0	-0.027	-0.023	27.271	0.002	0.002	0.000	0.000	0.000	0.000
102	A	201	ILE	0	0.022	0.014	24.391	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	202	PRO	0	-0.003	0.010	28.570	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	203	LYS	1	0.985	0.995	30.105	-0.028	-0.028	0.000	0.000	0.000	0.000
105	A	204	GLY	0	-0.090	-0.048	30.264	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	205	SER	0	-0.029	-0.020	28.740	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	206	SER	0	-0.029	-0.037	27.669	0.000	0.000	0.000	0.000	0.000	0.000
108	A	207	ILE	0	-0.040	-0.031	23.143	0.000	0.000	0.000	0.000	0.000	0.000
109	A	208	GLU	-1	-0.980	-0.984	21.818	0.015	0.015	0.000	0.000	0.000	0.000
110	A	209	PHE	0	0.043	0.018	18.700	0.011	0.011	0.000	0.000	0.000	0.000
111	A	210	GLY	0	0.028	-0.013	17.578	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	211	THR	0	-0.018	-0.006	14.595	0.016	0.016	0.000	0.000	0.000	0.000
113	A	212	PRO	0	-0.003	0.014	16.409	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	213	THR	0	-0.054	-0.029	15.776	0.001	0.001	0.000	0.000	0.000	0.000
115	A	214	SER	0	0.038	0.032	12.304	0.034	0.034	0.000	0.000	0.000	0.000
116	A	215	VAL	0	-0.022	0.003	13.215	-0.063	-0.063	0.000	0.000	0.000	0.000
117	A	216	ARG	1	0.939	0.974	11.706	-0.599	-0.599	0.000	0.000	0.000	0.000
118	A	217	PHE	0	-0.027	-0.014	14.978	-0.048	-0.048	0.000	0.000	0.000	0.000
119	A	218	LEU	0	-0.018	0.001	16.887	0.027	0.027	0.000	0.000	0.000	0.000
120	A	219	TYR	0	0.047	0.019	16.316	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	220	VAL	0	-0.031	-0.037	21.101	0.000	0.000	0.000	0.000	0.000	0.000
122	A	221	ALA	0	0.024	0.010	23.980	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	222	TRP	0	-0.023	0.010	25.620	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	223	PRO	0	-0.005	-0.022	28.997	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	224	ALA	0	0.025	0.002	26.221	0.002	0.002	0.000	0.000	0.000	0.000
126	A	225	ASN	0	-0.035	-0.002	25.475	0.003	0.003	0.000	0.000	0.000	0.000
127	A	226	TRP	0	0.017	0.006	20.693	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	227	GLN	0	-0.043	-0.003	19.991	-0.021	-0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:100:LEU)