FMO DATABASE

FMODB ID: RY5Y8

Calculation Name: 2YZI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZI

Chain ID: A

ChEMBL ID:

UniProt ID: O57847

Base Structure: X-ray

Registration Date: 2023-09-26

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1139140.522904
FMO2-HF: Nuclear repulsion	1086602.374793
FMO2-HF: Total energy	-52538.148111
FMO2-MP2: Total energy	-52689.136461

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-24.553	-19.616	28.702	-11.799	-21.836	-0.08

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.051 / q_NPA : -0.026

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	6	MET	0	-0.015	-0.007	2.716	-0.971	1.166	1.238	-0.946	-2.429	0.006
4	A	7	LYS	1	0.901	0.936	5.738	0.994	0.994	0.000	0.000	0.000	0.000
5	A	8	ALA	0	0.050	0.032	5.272	0.333	0.333	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.029	-0.011	7.038	0.424	0.424	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.049	0.024	7.231	0.008	0.008	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.924	0.941	8.609	0.094	0.094	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.076	-0.018	5.783	-0.070	-0.070	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.048	-0.057	2.352	-1.359	0.844	1.443	-1.331	-2.316	-0.005
11	A	14	MET	0	-0.060	0.006	6.896	0.299	0.299	0.000	0.000	0.000	0.000
12	A	15	THR	0	0.054	0.035	10.245	-0.250	-0.250	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.999	0.975	13.058	-0.209	-0.209	0.000	0.000	0.000	0.000
14	A	17	LYS	1	0.847	0.951	16.167	-0.358	-0.358	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.022	-0.010	18.096	0.025	0.025	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.022	0.006	19.657	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.029	-0.011	23.285	0.025	0.025	0.000	0.000	0.000	0.000
18	A	21	VAL	0	-0.042	-0.004	26.064	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	22	LYS	1	1.008	1.011	29.658	-0.122	-0.122	0.000	0.000	0.000	0.000
20	A	23	PRO	0	0.067	0.016	32.827	0.003	0.003	0.000	0.000	0.000	0.000
21	A	24	SER	0	0.015	0.000	33.781	0.004	0.004	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.033	-0.009	32.039	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	26	SER	0	0.067	0.050	33.830	0.009	0.009	0.000	0.000	0.000	0.000
24	A	27	VAL	0	0.043	0.010	29.837	0.009	0.009	0.000	0.000	0.000	0.000
25	A	28	GLN	0	0.006	0.017	30.701	0.009	0.009	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.797	-0.868	31.978	0.140	0.140	0.000	0.000	0.000	0.000
27	A	30	ALA	0	0.006	-0.002	28.213	0.007	0.007	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.039	-0.041	27.304	0.019	0.019	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.721	0.814	27.607	-0.126	-0.126	0.000	0.000	0.000	0.000
30	A	33	LEU	0	0.020	0.015	27.874	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	MET	0	-0.047	-0.015	23.510	0.021	0.021	0.000	0.000	0.000	0.000
32	A	35	MET	0	-0.039	-0.009	23.512	0.034	0.034	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.814	-0.878	25.758	0.136	0.136	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.010	-0.011	24.137	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	38	ASP	-1	-0.951	-0.958	19.895	0.339	0.339	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.002	-0.002	19.088	0.033	0.033	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.010	0.000	17.623	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	41	SER	0	-0.014	-0.029	18.672	0.009	0.009	0.000	0.000	0.000	0.000
39	A	42	LEU	0	-0.002	0.011	20.572	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	43	VAL	0	-0.002	0.001	21.842	0.012	0.012	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.038	-0.017	24.346	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.003	-0.010	26.014	0.009	0.009	0.000	0.000	0.000	0.000
43	A	46	ASN	0	-0.020	-0.041	29.636	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.874	-0.946	33.003	0.113	0.113	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.856	-0.891	32.999	0.111	0.111	0.000	0.000	0.000	0.000
46	A	49	GLY	0	-0.011	0.001	30.804	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.063	-0.031	28.673	0.020	0.020	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.020	-0.014	23.903	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.010	-0.010	27.227	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	53	GLY	0	0.010	-0.013	26.817	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	54	PHE	0	-0.004	-0.005	18.176	0.013	0.013	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.012	0.000	23.112	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	56	THR	0	0.020	-0.019	18.247	0.012	0.012	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.920	0.938	20.683	-0.343	-0.343	0.000	0.000	0.000	0.000
55	A	58	SER	0	0.005	0.004	20.108	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	59	ASP	-1	-0.843	-0.897	21.987	0.321	0.321	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.053	0.033	24.363	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	61	ILE	0	0.016	0.003	23.800	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.862	0.918	23.663	-0.292	-0.292	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.845	0.915	25.217	-0.258	-0.258	0.000	0.000	0.000	0.000
61	A	64	VAL	0	-0.001	0.008	29.808	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	65	ILE	0	0.001	0.002	29.589	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.011	-0.007	29.214	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	67	PRO	0	-0.066	-0.017	31.699	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.024	0.020	34.587	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.065	-0.026	34.974	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	70	PRO	0	0.028	0.024	35.980	0.004	0.004	0.000	0.000	0.000	0.000
68	A	71	TYR	0	0.039	-0.004	34.323	0.007	0.007	0.000	0.000	0.000	0.000
69	A	72	ASP	-1	-0.902	-0.962	34.820	0.116	0.116	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.020	-0.001	33.671	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	74	PRO	0	0.028	0.005	34.932	0.007	0.007	0.000	0.000	0.000	0.000
72	A	75	VAL	0	0.019	0.008	29.754	0.004	0.004	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.835	-0.916	30.759	0.153	0.153	0.000	0.000	0.000	0.000
74	A	77	ARG	1	0.912	0.967	32.527	-0.123	-0.123	0.000	0.000	0.000	0.000
75	A	78	ILE	0	-0.006	-0.007	28.009	0.000	0.000	0.000	0.000	0.000	0.000
76	A	79	MET	0	-0.063	0.015	27.126	0.021	0.021	0.000	0.000	0.000	0.000
77	A	80	THR	0	-0.006	-0.008	23.302	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.902	0.940	26.081	-0.166	-0.166	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.014	-0.008	25.678	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	83	LEU	0	-0.006	0.001	22.267	0.025	0.025	0.000	0.000	0.000	0.000
81	A	84	ILE	0	0.012	0.024	17.569	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.006	-0.002	17.555	0.039	0.039	0.000	0.000	0.000	0.000
83	A	86	ALA	0	-0.006	-0.013	13.673	0.007	0.007	0.000	0.000	0.000	0.000
84	A	87	ASN	0	0.082	0.045	15.641	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.017	-0.002	13.593	0.087	0.087	0.000	0.000	0.000	0.000
86	A	89	ASN	0	-0.024	-0.015	12.481	-0.033	-0.033	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.051	-0.026	11.825	-0.093	-0.093	0.000	0.000	0.000	0.000
88	A	91	PRO	0	-0.005	0.019	9.183	0.110	0.110	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.050	0.016	2.620	-0.842	-0.420	1.820	-0.493	-1.749	0.006
90	A	93	GLY	0	0.038	0.004	6.750	0.382	0.382	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.827	-0.878	8.572	0.478	0.478	0.000	0.000	0.000	0.000
92	A	95	VAL	0	0.001	-0.001	9.026	-0.060	-0.060	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.023	0.005	4.336	-0.470	-0.201	0.007	-0.065	-0.210	0.000
94	A	97	ARG	1	0.723	0.822	8.739	-0.692	-0.692	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.899	0.957	11.835	-0.616	-0.616	0.000	0.000	0.000	0.000
96	A	99	MET	0	-0.020	-0.017	9.921	0.016	0.016	0.000	0.000	0.000	0.000
97	A	100	ALA	0	-0.014	0.002	11.248	-0.101	-0.101	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.859	-0.903	12.938	0.309	0.309	0.000	0.000	0.000	0.000
99	A	102	HIS	0	-0.034	-0.033	16.066	-0.065	-0.065	0.000	0.000	0.000	0.000
100	A	103	ARG	1	0.880	0.947	15.091	-0.382	-0.382	0.000	0.000	0.000	0.000
101	A	104	ILE	0	-0.022	-0.001	14.258	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	105	LYS	1	0.943	0.962	12.279	-0.477	-0.477	0.000	0.000	0.000	0.000
103	A	106	HIS	0	0.012	-0.007	12.342	0.094	0.094	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.015	-0.003	12.144	-0.091	-0.091	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.027	0.019	14.386	0.061	0.061	0.000	0.000	0.000	0.000
106	A	109	ILE	0	-0.015	-0.020	12.255	0.022	0.022	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.818	-0.895	15.814	0.212	0.212	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.905	-0.967	17.713	0.173	0.173	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.917	-0.950	20.062	0.081	0.081	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.015	-0.010	22.511	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.859	0.921	23.027	-0.151	-0.151	0.000	0.000	0.000	0.000
112	A	115	ILE	0	-0.018	-0.013	19.444	0.020	0.020	0.000	0.000	0.000	0.000
113	A	116	VAL	0	0.010	0.008	17.230	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	117	GLY	0	-0.009	-0.009	15.730	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.060	-0.015	14.571	-0.018	-0.018	0.000	0.000	0.000	0.000
116	A	119	PHE	0	0.049	0.025	5.262	-0.217	-0.115	-0.001	-0.016	-0.085	0.000
117	A	120	THR	0	-0.008	-0.039	10.303	-0.178	-0.178	0.000	0.000	0.000	0.000
118	A	121	LEU	0	0.014	-0.010	7.708	0.389	0.389	0.000	0.000	0.000	0.000
119	A	122	SER	0	0.026	0.016	7.766	0.085	0.085	0.000	0.000	0.000	0.000
120	A	123	ASP	-1	-0.824	-0.882	8.470	1.234	1.234	0.000	0.000	0.000	0.000
121	A	124	LEU	0	0.007	0.007	2.391	-0.093	-0.071	2.639	-0.598	-2.063	0.001
122	A	125	LEU	0	-0.020	0.020	4.020	1.005	1.604	0.082	-0.256	-0.424	-0.002
123	A	126	GLU	-1	-0.781	-0.892	6.268	0.269	0.269	0.000	0.000	0.000	0.000
124	A	127	ALA	0	-0.048	-0.032	2.499	-1.496	-1.642	2.784	-0.675	-1.963	0.005
125	A	128	SER	0	-0.031	-0.037	2.558	-9.217	-6.316	4.841	-2.712	-5.030	-0.028
126	A	129	ARG	1	0.832	0.908	3.331	-0.700	-1.112	0.051	0.785	-0.423	0.000
127	A	130	ARG	1	0.798	0.918	3.773	0.844	1.147	0.000	-0.033	-0.271	0.000
128	A	131	ARG	1	0.935	0.961	4.369	0.288	0.430	-0.001	-0.012	-0.128	0.000
129	A	132	LEU	0	0.009	0.012	5.863	0.213	0.213	0.000	0.000	0.000	0.000
130	A	133	GLU	-1	-0.731	-0.847	1.855	-14.672	-18.321	13.800	-5.446	-4.704	-0.063
131	A	134	THR	0	-0.045	-0.039	5.353	0.673	0.717	-0.001	-0.001	-0.041	0.000
132	A	135	ALA	0	0.029	0.033	7.872	0.107	0.107	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)