FMO DATABASE

FMODB ID: YVRR2

Calculation Name: 2YYO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YYO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NCJ5

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:

Apendix: None

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1545211.691802
FMO2-HF: Nuclear repulsion	1484187.581118
FMO2-HF: Total energy	-61024.110684
FMO2-MP2: Total energy	-61201.002903

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:6:SER)

Summations of interaction energy for fragment #1(A:6:SER)

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.
-25.296	-19.512	15.919	-10.534	-11.17	-0.039

Interaction energy analysis for fragmet #1(A:6:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : 0.003

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	8	PHE	0	0.014	0.002	3.787	-3.643	0.170	-0.050	-2.313	-1.451	0.003
4	A	9	LYS	1	0.872	0.957	6.717	0.766	0.766	0.000	0.000	0.000	0.000
5	A	10	HIS	0	0.021	0.004	10.351	-0.060	-0.060	0.000	0.000	0.000	0.000
6	A	11	ILE	0	0.000	0.009	9.484	0.048	0.048	0.000	0.000	0.000	0.000
7	A	12	LEU	0	-0.033	-0.014	10.857	-0.105	-0.105	0.000	0.000	0.000	0.000
8	A	13	VAL	0	-0.008	-0.015	7.472	-0.039	-0.039	0.000	0.000	0.000	0.000
9	A	14	ASP	-1	-0.929	-0.943	10.766	-0.224	-0.224	0.000	0.000	0.000	0.000
10	A	15	GLY	0	0.023	0.001	12.109	0.040	0.040	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.946	-0.974	10.814	-0.262	-0.262	0.000	0.000	0.000	0.000
12	A	17	THR	0	-0.045	-0.016	12.540	-0.052	-0.052	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.028	-0.004	8.943	-0.083	-0.083	0.000	0.000	0.000	0.000
14	A	19	SER	0	0.044	0.004	12.547	0.048	0.048	0.000	0.000	0.000	0.000
15	A	20	TYR	0	-0.103	-0.087	14.478	-0.049	-0.049	0.000	0.000	0.000	0.000
16	A	21	HIS	0	-0.040	-0.028	15.211	0.083	0.083	0.000	0.000	0.000	0.000
17	A	22	GLY	0	0.014	0.006	16.635	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	23	ASN	0	-0.062	-0.047	18.346	0.042	0.042	0.000	0.000	0.000	0.000
19	A	24	SER	0	-0.008	-0.025	21.553	0.003	0.003	0.000	0.000	0.000	0.000
20	A	25	GLY	0	-0.004	0.005	21.916	0.005	0.005	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.840	-0.886	17.130	-0.342	-0.342	0.000	0.000	0.000	0.000
22	A	27	VAL	0	-0.020	0.026	13.450	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	28	GLY	0	0.026	0.021	12.436	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	29	CYS	0	-0.085	-0.036	8.426	-0.087	-0.087	0.000	0.000	0.000	0.000
25	A	30	TYR	0	0.054	0.025	5.359	-0.282	-0.282	0.000	0.000	0.000	0.000
26	A	31	VAL	0	0.006	-0.001	2.384	-1.671	0.250	0.943	-1.087	-1.778	0.000
27	A	32	ALA	0	0.044	0.014	2.042	-5.320	-6.748	8.552	-3.851	-3.274	-0.042
28	A	33	SER	0	0.001	-0.017	2.220	-11.350	-9.816	6.452	-3.882	-4.105	-0.002
29	A	34	ARG	1	0.921	0.957	3.134	-1.983	-2.345	0.026	0.619	-0.283	0.002
30	A	35	PRO	0	-0.012	0.014	6.124	-0.486	-0.486	0.000	0.000	0.000	0.000
31	A	36	LEU	0	-0.020	-0.006	8.214	0.153	0.153	0.000	0.000	0.000	0.000
32	A	37	THR	0	0.003	-0.008	11.530	0.053	0.053	0.000	0.000	0.000	0.000
33	A	38	LYS	1	0.986	0.974	14.462	-0.081	-0.081	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.951	-0.968	17.621	0.095	0.095	0.000	0.000	0.000	0.000
35	A	40	SER	0	-0.016	0.002	13.783	-0.028	-0.028	0.000	0.000	0.000	0.000
36	A	41	ASN	0	-0.029	-0.030	13.907	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	42	TYR	0	-0.028	-0.058	15.598	-0.062	-0.062	0.000	0.000	0.000	0.000
38	A	43	PHE	0	0.023	0.028	11.742	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.803	-0.878	14.686	-0.227	-0.227	0.000	0.000	0.000	0.000
40	A	45	VAL	0	-0.004	-0.002	13.032	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	46	SER	0	-0.018	-0.020	15.746	0.043	0.043	0.000	0.000	0.000	0.000
42	A	47	ILE	0	-0.023	-0.006	18.002	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	48	VAL	0	-0.027	-0.008	18.813	0.040	0.040	0.000	0.000	0.000	0.000
44	A	49	ASP	-1	-0.844	-0.926	20.625	-0.221	-0.221	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.068	-0.045	20.871	-0.039	-0.039	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.046	0.024	22.445	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	52	VAL	0	-0.044	-0.023	23.467	0.020	0.020	0.000	0.000	0.000	0.000
48	A	53	ARG	1	0.887	0.926	23.009	0.286	0.286	0.000	0.000	0.000	0.000
49	A	54	GLY	0	0.071	0.044	21.850	0.007	0.007	0.000	0.000	0.000	0.000
50	A	55	THR	0	-0.143	-0.071	19.404	0.006	0.006	0.000	0.000	0.000	0.000
51	A	56	ILE	0	0.028	0.025	15.371	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	57	ALA	0	-0.061	-0.033	14.286	0.064	0.064	0.000	0.000	0.000	0.000
53	A	58	VAL	0	0.048	0.025	12.876	-0.120	-0.120	0.000	0.000	0.000	0.000
54	A	59	GLY	0	-0.006	-0.024	11.850	0.139	0.139	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.008	0.023	9.629	-0.146	-0.146	0.000	0.000	0.000	0.000
56	A	61	VAL	0	-0.034	-0.017	5.628	0.246	0.246	0.000	0.000	0.000	0.000
57	A	62	PRO	0	0.068	0.050	7.273	-0.244	-0.244	0.000	0.000	0.000	0.000
58	A	63	GLN	0	0.032	0.005	4.602	-0.308	-0.243	-0.001	-0.003	-0.060	0.000
59	A	64	TYR	0	-0.024	-0.030	4.461	0.111	0.177	-0.001	-0.002	-0.062	0.000
60	A	65	TYR	0	-0.020	-0.005	5.494	0.043	0.043	0.000	0.000	0.000	0.000
61	A	66	SER	0	0.005	0.019	6.644	0.128	0.128	0.000	0.000	0.000	0.000
62	A	67	LEU	0	0.052	0.005	4.997	-0.248	-0.195	-0.001	-0.008	-0.044	0.000
63	A	68	ASP	-1	-0.835	-0.919	8.806	-0.424	-0.424	0.000	0.000	0.000	0.000
64	A	69	HIS	1	0.819	0.885	11.448	0.455	0.455	0.000	0.000	0.000	0.000
65	A	70	GLN	0	0.120	0.074	11.400	-0.206	-0.206	0.000	0.000	0.000	0.000
66	A	71	PRO	0	0.050	0.054	9.921	0.096	0.096	0.000	0.000	0.000	0.000
67	A	72	GLY	0	0.040	0.003	11.692	0.085	0.085	0.000	0.000	0.000	0.000
68	A	73	TRP	0	-0.054	-0.034	14.445	0.066	0.066	0.000	0.000	0.000	0.000
69	A	74	LEU	0	-0.016	0.003	11.912	0.072	0.072	0.000	0.000	0.000	0.000
70	A	75	PRO	0	0.002	0.001	14.170	-0.049	-0.049	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.877	-0.933	12.774	-0.207	-0.207	0.000	0.000	0.000	0.000
72	A	77	SER	0	-0.019	-0.010	11.250	-0.085	-0.085	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.034	-0.033	12.594	0.097	0.097	0.000	0.000	0.000	0.000
74	A	79	ALA	0	-0.016	-0.011	13.567	-0.084	-0.084	0.000	0.000	0.000	0.000
75	A	80	TYR	0	0.000	0.008	15.492	0.080	0.080	0.000	0.000	0.000	0.000
76	A	81	HIS	1	0.837	0.924	16.049	0.395	0.395	0.000	0.000	0.000	0.000
77	A	82	ALA	0	0.069	0.038	19.280	0.040	0.040	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.849	-0.925	21.212	-0.277	-0.277	0.000	0.000	0.000	0.000
79	A	84	ASP	-1	-0.815	-0.911	23.113	-0.245	-0.245	0.000	0.000	0.000	0.000
80	A	85	GLY	0	-0.013	0.007	23.484	0.020	0.020	0.000	0.000	0.000	0.000
81	A	86	LYS	1	0.852	0.943	23.259	0.204	0.204	0.000	0.000	0.000	0.000
82	A	87	LEU	0	0.002	0.016	18.867	-0.028	-0.028	0.000	0.000	0.000	0.000
83	A	88	TYR	0	-0.165	-0.108	17.569	0.033	0.033	0.000	0.000	0.000	0.000
84	A	89	ASN	0	-0.028	-0.045	16.810	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	90	GLY	0	0.066	0.050	16.735	0.036	0.036	0.000	0.000	0.000	0.000
86	A	91	ARG	1	0.948	0.975	17.676	0.187	0.187	0.000	0.000	0.000	0.000
87	A	92	ALA	0	0.040	0.024	19.542	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	93	LYS	1	0.915	0.962	20.743	0.166	0.166	0.000	0.000	0.000	0.000
89	A	94	GLY	0	0.058	0.034	22.406	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	95	ARG	1	0.879	0.933	23.300	0.173	0.173	0.000	0.000	0.000	0.000
91	A	96	GLN	0	0.018	-0.003	25.015	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	97	PHE	0	-0.017	-0.012	21.856	0.005	0.005	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.054	0.027	25.387	0.013	0.013	0.000	0.000	0.000	0.000
94	A	99	SER	0	-0.039	-0.012	26.545	0.002	0.002	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.985	0.990	25.187	0.176	0.176	0.000	0.000	0.000	0.000
96	A	101	CYS	0	-0.100	-0.040	22.218	0.014	0.014	0.000	0.000	0.000	0.000
97	A	102	ASN	0	0.024	0.025	24.009	-0.020	-0.020	0.000	0.000	0.000	0.000
98	A	103	SER	0	0.076	0.009	23.695	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	104	GLY	0	-0.022	0.005	23.671	0.021	0.021	0.000	0.000	0.000	0.000
100	A	105	ASP	-1	-0.868	-0.911	23.578	-0.193	-0.193	0.000	0.000	0.000	0.000
101	A	106	ARG	1	0.914	0.955	20.104	0.160	0.160	0.000	0.000	0.000	0.000
102	A	107	ILE	0	-0.019	-0.019	17.550	0.031	0.031	0.000	0.000	0.000	0.000
103	A	108	GLY	0	0.056	0.034	17.200	-0.033	-0.033	0.000	0.000	0.000	0.000
104	A	109	CYS	0	-0.094	-0.040	14.539	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.082	0.037	15.556	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	111	ILE	0	-0.019	0.000	13.563	-0.018	-0.018	0.000	0.000	0.000	0.000
107	A	112	GLU	-1	-0.833	-0.903	17.755	-0.081	-0.081	0.000	0.000	0.000	0.000
108	A	113	PRO	0	0.008	-0.002	20.519	0.009	0.009	0.000	0.000	0.000	0.000
109	A	114	VAL	0	0.035	-0.002	21.493	0.012	0.012	0.000	0.000	0.000	0.000
110	A	115	SER	0	-0.017	-0.001	19.918	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	116	PHE	0	-0.081	-0.022	14.825	0.000	0.000	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.928	-0.957	19.751	0.051	0.051	0.000	0.000	0.000	0.000
113	A	118	VAL	0	-0.012	-0.025	18.393	0.001	0.001	0.000	0.000	0.000	0.000
114	A	119	GLN	0	-0.025	-0.011	20.024	0.003	0.003	0.000	0.000	0.000	0.000
115	A	120	THR	0	0.010	-0.012	20.255	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	121	ALA	0	0.031	0.045	16.664	0.007	0.007	0.000	0.000	0.000	0.000
117	A	122	GLN	0	0.001	0.007	18.620	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	123	ILE	0	0.007	0.003	14.969	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	124	PHE	0	-0.056	-0.024	18.696	0.011	0.011	0.000	0.000	0.000	0.000
120	A	125	PHE	0	0.039	0.012	15.767	-0.023	-0.023	0.000	0.000	0.000	0.000
121	A	126	THR	0	-0.042	-0.036	20.256	0.027	0.027	0.000	0.000	0.000	0.000
122	A	127	LYS	1	0.956	0.988	21.183	0.167	0.167	0.000	0.000	0.000	0.000
123	A	128	ASN	0	-0.057	-0.060	23.135	0.011	0.011	0.000	0.000	0.000	0.000
124	A	129	GLY	0	0.027	0.019	23.382	0.018	0.018	0.000	0.000	0.000	0.000
125	A	130	LYS	1	0.938	0.987	24.768	0.128	0.128	0.000	0.000	0.000	0.000
126	A	131	ARG	1	0.874	0.926	24.210	0.115	0.115	0.000	0.000	0.000	0.000
127	A	132	VAL	0	-0.060	-0.012	23.844	0.012	0.012	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.025	0.000	24.045	0.016	0.016	0.000	0.000	0.000	0.000
129	A	134	SER	0	-0.038	-0.034	22.119	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	135	THR	0	-0.052	-0.019	19.362	0.018	0.018	0.000	0.000	0.000	0.000
131	A	136	ILE	0	0.040	0.028	20.688	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	137	MET	0	-0.036	-0.011	16.329	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	138	PRO	0	0.011	-0.002	19.147	0.016	0.016	0.000	0.000	0.000	0.000
134	A	139	MET	0	-0.020	0.018	13.354	0.022	0.022	0.000	0.000	0.000	0.000
135	A	140	SER	0	0.037	0.008	16.156	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	141	PRO	0	-0.007	0.008	14.359	-0.044	-0.044	0.000	0.000	0.000	0.000
137	A	142	ASP	-1	-0.931	-0.965	12.728	0.227	0.227	0.000	0.000	0.000	0.000
138	A	143	GLY	0	-0.009	0.001	9.999	0.086	0.086	0.000	0.000	0.000	0.000
139	A	144	LEU	0	-0.072	-0.049	9.164	-0.143	-0.143	0.000	0.000	0.000	0.000
140	A	145	PHE	0	0.011	-0.014	4.635	0.045	0.167	-0.001	-0.007	-0.113	0.000
141	A	146	PRO	0	0.010	0.020	6.886	-0.164	-0.164	0.000	0.000	0.000	0.000
142	A	147	ALA	0	-0.007	-0.005	6.315	-0.791	-0.791	0.000	0.000	0.000	0.000
143	A	148	VAL	0	0.005	-0.004	7.949	0.398	0.398	0.000	0.000	0.000	0.000
144	A	149	GLY	0	-0.018	-0.024	9.636	-0.177	-0.177	0.000	0.000	0.000	0.000
145	A	150	MET	0	-0.023	-0.008	12.201	0.103	0.103	0.000	0.000	0.000	0.000
146	A	151	HIS	0	-0.113	-0.065	14.990	-0.013	-0.013	0.000	0.000	0.000	0.000
147	A	152	SER	0	-0.069	-0.044	17.902	0.056	0.056	0.000	0.000	0.000	0.000
148	A	153	LEU	0	0.067	0.018	19.971	-0.026	-0.026	0.000	0.000	0.000	0.000
149	A	154	GLY	0	0.030	0.002	21.127	0.021	0.021	0.000	0.000	0.000	0.000
150	A	155	GLU	-1	-0.745	-0.814	17.842	-0.441	-0.441	0.000	0.000	0.000	0.000
151	A	156	GLU	-1	-0.840	-0.924	16.769	-0.376	-0.376	0.000	0.000	0.000	0.000
152	A	157	VAL	0	-0.015	-0.010	13.596	0.037	0.037	0.000	0.000	0.000	0.000
153	A	158	ARG	1	0.967	0.991	14.625	0.210	0.210	0.000	0.000	0.000	0.000
154	A	159	LEU	0	0.000	-0.003	8.382	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	160	HIS	0	-0.009	-0.013	12.680	0.069	0.069	0.000	0.000	0.000	0.000
156	A	161	LEU	0	0.016	-0.019	8.211	-0.006	-0.006	0.000	0.000	0.000	0.000
157	A	162	ASN	0	0.004	0.008	12.880	0.059	0.059	0.000	0.000	0.000	0.000
158	A	163	ALA	0	-0.035	0.001	16.273	0.011	0.011	0.000	0.000	0.000	0.000
159	A	164	GLU	-1	-0.881	-0.938	18.499	-0.076	-0.076	0.000	0.000	0.000	0.000
160	A	165	LEU	0	-0.054	-0.028	21.305	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:SER)