FMO DATABASE

FMODB ID: 5JY4Z

Calculation Name: 1PYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PYB

Chain ID: A

ChEMBL ID:

UniProt ID: O66738

Base Structure: X-ray

Registration Date: 2023-09-23

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-744348.187952
FMO2-HF: Nuclear repulsion	704590.503518
FMO2-HF: Total energy	-39757.684434
FMO2-MP2: Total energy	-39876.011223

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:5:ALA)

Summations of interaction energy for fragment #1(A:5:ALA)

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.
-0.809	1.998	-0.023	-1.573	-1.211	0.007

Interaction energy analysis for fragmet #1(A:5:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / 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	7	ILE	0	0.018	0.000	3.794	-1.057	1.750	-0.023	-1.573	-1.211	0.007
4	A	8	GLY	0	0.039	0.034	5.487	0.201	0.201	0.000	0.000	0.000	0.000
5	A	9	ILE	0	-0.027	-0.021	7.227	0.226	0.226	0.000	0.000	0.000	0.000
6	A	10	GLU	-1	-0.849	-0.931	10.627	-0.451	-0.451	0.000	0.000	0.000	0.000
7	A	11	ASP	-1	-0.864	-0.937	8.138	-0.797	-0.797	0.000	0.000	0.000	0.000
8	A	12	PHE	0	-0.002	0.004	10.424	0.116	0.116	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.022	-0.010	11.767	0.051	0.051	0.000	0.000	0.000	0.000
10	A	14	LYS	1	0.786	0.890	11.514	0.563	0.563	0.000	0.000	0.000	0.000
11	A	15	VAL	0	-0.039	-0.005	11.803	0.041	0.041	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.795	-0.875	14.951	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.015	0.005	14.953	0.025	0.025	0.000	0.000	0.000	0.000
14	A	18	ARG	1	0.781	0.855	19.072	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	19	VAL	0	-0.007	0.008	22.709	0.015	0.015	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.002	-0.008	24.769	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	21	LYS	1	0.837	0.903	27.935	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	22	VAL	0	-0.008	0.006	29.593	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	23	LEU	0	0.042	0.031	32.108	0.000	0.000	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.019	-0.013	34.968	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	25	ALA	0	0.035	0.013	34.446	0.004	0.004	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.825	-0.896	35.396	0.057	0.057	0.000	0.000	0.000	0.000
23	A	27	ARG	1	0.852	0.908	35.956	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.012	0.007	35.925	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.896	-0.955	38.696	0.056	0.056	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.004	0.008	40.336	0.001	0.001	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.065	-0.034	35.136	0.004	0.004	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.820	-0.918	33.542	0.118	0.118	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.911	0.964	27.485	-0.166	-0.166	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.016	0.010	31.059	0.000	0.000	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.017	0.013	30.100	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.792	0.877	30.561	-0.058	-0.058	0.000	0.000	0.000	0.000
33	A	37	LEU	0	-0.009	0.001	28.164	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	38	THR	0	0.055	0.018	30.547	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	39	LEU	0	-0.022	-0.002	26.087	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.083	0.008	30.209	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	41	LEU	0	-0.074	-0.046	25.388	0.000	0.000	0.000	0.000	0.000	0.000
38	A	42	GLY	0	-0.024	-0.030	29.383	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.914	-0.948	31.977	0.001	0.001	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.876	-0.923	28.182	0.007	0.007	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.923	-0.963	31.924	0.034	0.034	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.725	0.855	24.176	-0.030	-0.030	0.000	0.000	0.000	0.000
43	A	47	THR	0	0.008	-0.003	30.315	0.004	0.004	0.000	0.000	0.000	0.000
44	A	48	VAL	0	-0.030	-0.022	24.506	0.003	0.003	0.000	0.000	0.000	0.000
45	A	49	VAL	0	-0.044	-0.010	27.710	0.000	0.000	0.000	0.000	0.000	0.000
46	A	50	ALA	0	-0.021	-0.005	26.195	0.014	0.014	0.000	0.000	0.000	0.000
47	A	51	GLY	0	-0.017	-0.033	25.912	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.005	-0.011	25.977	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	53	ALA	0	0.035	0.003	27.770	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	54	LYS	1	0.857	0.927	29.896	-0.112	-0.112	0.000	0.000	0.000	0.000
51	A	55	TYR	0	0.027	0.024	27.464	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	56	TYR	0	0.026	0.004	27.137	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	57	THR	0	0.023	0.021	31.758	0.001	0.001	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.024	-0.013	34.518	0.000	0.000	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.939	-0.975	35.697	0.069	0.069	0.000	0.000	0.000	0.000
56	A	60	GLU	-1	-0.825	-0.872	32.922	0.084	0.084	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.043	-0.039	29.759	0.001	0.001	0.000	0.000	0.000	0.000
58	A	62	VAL	0	-0.024	0.012	32.815	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.016	0.018	34.355	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.734	0.854	28.646	-0.098	-0.098	0.000	0.000	0.000	0.000
61	A	65	LYS	1	0.868	0.918	28.227	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	66	ILE	0	0.037	0.020	23.521	0.007	0.007	0.000	0.000	0.000	0.000
63	A	67	VAL	0	0.014	0.014	19.168	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	68	ILE	0	-0.014	-0.016	20.978	0.024	0.024	0.000	0.000	0.000	0.000
65	A	69	VAL	0	0.001	0.002	16.180	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.043	0.023	19.139	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	ASN	0	-0.063	-0.047	17.382	0.025	0.025	0.000	0.000	0.000	0.000
68	A	72	LEU	0	0.005	0.015	15.372	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	73	LYN	0	0.064	0.047	18.678	0.000	0.000	0.000	0.000	0.000	0.000
70	A	74	PRO	0	0.013	0.018	21.810	0.004	0.004	0.000	0.000	0.000	0.000
71	A	75	ARG	1	1.009	0.976	25.253	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.900	0.948	19.983	-0.173	-0.173	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.019	-0.004	23.330	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	78	PHE	0	-0.029	-0.012	23.373	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	79	GLY	0	0.026	0.024	28.268	0.002	0.002	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.034	-0.022	26.620	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.794	-0.877	28.024	0.064	0.064	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.026	-0.014	23.869	0.010	0.010	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.021	0.017	25.059	0.000	0.000	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.084	0.036	21.782	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	85	MET	0	-0.050	-0.029	18.012	0.004	0.004	0.000	0.000	0.000	0.000
82	A	86	ILE	0	0.045	0.019	19.908	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	87	LEU	0	-0.029	-0.013	15.967	0.026	0.026	0.000	0.000	0.000	0.000
84	A	88	ALA	0	-0.018	-0.013	19.168	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	89	ALA	0	0.007	0.007	18.041	0.042	0.042	0.000	0.000	0.000	0.000
86	A	90	SER	0	-0.050	-0.030	17.380	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	91	ASP	-1	-0.842	-0.898	18.387	0.306	0.306	0.000	0.000	0.000	0.000
88	A	92	GLY	0	-0.045	-0.029	20.600	0.013	0.013	0.000	0.000	0.000	0.000
89	A	93	GLU	-1	-0.959	-0.985	21.800	0.200	0.200	0.000	0.000	0.000	0.000
90	A	94	ASN	0	-0.031	0.003	24.414	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	95	LEU	0	-0.009	-0.008	22.220	0.019	0.019	0.000	0.000	0.000	0.000
92	A	96	SER	0	0.012	-0.011	22.364	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.014	-0.016	22.501	0.015	0.015	0.000	0.000	0.000	0.000
94	A	98	ILE	0	0.007	0.010	17.738	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	99	VAL	0	-0.020	-0.021	22.125	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	100	PRO	0	-0.051	-0.010	24.121	0.004	0.004	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.864	-0.929	24.585	0.092	0.092	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.904	0.942	27.221	-0.059	-0.059	0.000	0.000	0.000	0.000
99	A	103	ASP	-1	-0.872	-0.934	29.126	0.049	0.049	0.000	0.000	0.000	0.000
100	A	104	VAL	0	0.002	0.012	25.957	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.912	0.945	29.325	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.797	-0.854	28.712	0.036	0.036	0.000	0.000	0.000	0.000
103	A	107	GLY	0	0.031	0.021	27.309	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.052	-0.027	25.093	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	109	LYS	1	0.988	0.996	22.548	0.044	0.044	0.000	0.000	0.000	0.000
106	A	110	LEU	0	-0.010	-0.001	18.072	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	111	SER	0	-0.001	0.008	16.509	-0.026	-0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ALA)