FMO DATABASE

FMODB ID: MVGZZ

Calculation Name: 1Y0O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y0O

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SCY2

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-973241.435994
FMO2-HF: Nuclear repulsion	926896.896181
FMO2-HF: Total energy	-46344.539813
FMO2-MP2: Total energy	-46478.960769

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:CYS)

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

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.
-8.794	-6.287	8.716	-3.327	-7.896	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.053

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	PHE	0	-0.062	-0.042	3.166	-0.813	1.943	0.994	-1.142	-2.608	-0.008
4	A	8	SER	0	0.027	0.038	4.643	0.087	0.139	-0.001	-0.009	-0.042	0.000
5	A	9	VAL	0	-0.011	-0.038	8.286	0.224	0.224	0.000	0.000	0.000	0.000
6	A	10	SER	0	-0.014	0.008	10.250	0.078	0.078	0.000	0.000	0.000	0.000
7	A	11	PRO	0	0.058	0.003	13.378	-0.044	-0.044	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.017	0.005	15.493	0.015	0.015	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.021	0.011	13.260	0.033	0.033	0.000	0.000	0.000	0.000
10	A	14	LEU	0	-0.097	-0.035	11.101	-0.067	-0.067	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.034	0.019	6.845	-0.112	-0.112	0.000	0.000	0.000	0.000
12	A	16	PHE	0	-0.017	-0.012	6.525	0.341	0.341	0.000	0.000	0.000	0.000
13	A	17	CYS	0	0.040	0.016	3.078	0.548	-1.069	5.178	-1.188	-2.374	-0.003
14	A	18	ASP	-1	-0.798	-0.905	5.021	1.688	1.845	-0.001	-0.043	-0.112	0.000
15	A	19	LYS	1	0.866	0.935	2.198	-10.033	-9.557	2.255	-0.702	-2.029	0.007
16	A	20	VAL	0	0.009	0.002	6.694	-0.427	-0.427	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.033	0.026	10.441	0.066	0.066	0.000	0.000	0.000	0.000
18	A	22	GLY	0	-0.002	-0.003	12.804	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	23	TYR	0	0.014	0.003	16.035	-0.047	-0.047	0.000	0.000	0.000	0.000
20	A	24	GLY	0	-0.013	-0.008	19.303	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.017	-0.022	20.585	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.876	-0.936	19.294	0.202	0.202	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.031	-0.004	18.924	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.028	0.016	20.651	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	29	LYS	1	1.011	0.979	23.843	-0.090	-0.090	0.000	0.000	0.000	0.000
26	A	30	GLY	0	-0.033	-0.006	24.960	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	31	GLN	0	-0.016	-0.003	24.239	0.006	0.006	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.024	-0.003	24.748	0.012	0.012	0.000	0.000	0.000	0.000
29	A	33	ILE	0	-0.024	-0.008	19.145	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.952	0.969	21.691	-0.315	-0.315	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.019	0.013	16.429	0.025	0.025	0.000	0.000	0.000	0.000
32	A	36	HIS	0	0.060	0.068	16.607	-0.050	-0.050	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.022	-0.051	13.592	0.074	0.074	0.000	0.000	0.000	0.000
34	A	38	VAL	0	0.007	0.004	11.918	-0.143	-0.143	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.012	0.013	11.735	0.197	0.197	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.943	0.955	8.877	-1.728	-1.728	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.029	0.018	12.151	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.847	-0.957	8.838	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	43	ASN	0	0.001	0.015	11.872	0.011	0.011	0.000	0.000	0.000	0.000
40	A	44	GLY	0	-0.004	-0.003	11.701	0.018	0.018	0.000	0.000	0.000	0.000
41	A	45	LYS	1	0.927	0.975	12.644	-0.239	-0.239	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.003	-0.006	14.254	0.032	0.032	0.000	0.000	0.000	0.000
43	A	47	PHE	0	-0.037	-0.023	14.263	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	48	ASP	-1	-0.788	-0.878	17.014	0.396	0.396	0.000	0.000	0.000	0.000
45	A	49	SER	0	0.008	0.009	16.436	0.085	0.085	0.000	0.000	0.000	0.000
46	A	50	SER	0	0.012	0.004	17.545	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.044	-0.071	15.216	-0.110	-0.110	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.035	-0.004	20.161	-0.054	-0.054	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.828	0.904	21.425	-0.415	-0.415	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.013	0.018	23.474	-0.030	-0.030	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.903	0.953	23.408	-0.303	-0.303	0.000	0.000	0.000	0.000
52	A	56	PRO	0	-0.023	-0.008	20.828	0.023	0.023	0.000	0.000	0.000	0.000
53	A	57	LEU	0	0.027	0.021	19.729	-0.041	-0.041	0.000	0.000	0.000	0.000
54	A	58	THR	0	-0.088	-0.066	21.521	0.008	0.008	0.000	0.000	0.000	0.000
55	A	59	PHE	0	0.030	0.013	18.402	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.910	0.955	23.898	-0.172	-0.172	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.000	0.016	18.558	0.000	0.000	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.041	-0.028	21.680	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.105	-0.061	23.041	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	64	GLY	0	-0.003	0.012	24.098	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	65	GLU	-1	-0.866	-0.923	24.235	0.216	0.216	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.031	-0.003	19.398	0.018	0.018	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.037	-0.007	15.691	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	68	LYS	1	1.057	1.009	18.864	-0.033	-0.033	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.040	0.019	15.066	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	70	TRP	0	-0.033	-0.017	14.000	0.058	0.058	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.773	-0.901	15.922	0.261	0.261	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.013	-0.021	16.543	0.006	0.006	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.022	0.030	12.943	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	74	ILE	0	-0.026	-0.004	12.768	0.121	0.121	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.030	-0.001	15.222	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.034	0.030	15.858	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.075	-0.058	16.833	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.828	-0.893	17.574	-0.099	-0.099	0.000	0.000	0.000	0.000
75	A	79	GLY	0	-0.037	-0.036	15.539	-0.025	-0.025	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.099	-0.054	12.216	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.059	0.045	12.634	0.017	0.017	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.047	0.039	14.214	0.092	0.092	0.000	0.000	0.000	0.000
79	A	83	MET	0	-0.049	-0.006	11.607	0.037	0.037	0.000	0.000	0.000	0.000
80	A	84	LEU	0	-0.008	0.016	14.704	-0.069	-0.069	0.000	0.000	0.000	0.000
81	A	85	THR	0	-0.064	-0.050	16.321	0.074	0.074	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.015	-0.003	17.401	-0.031	-0.031	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.006	0.022	13.578	0.021	0.021	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.893	0.946	7.955	-2.099	-2.099	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.781	0.858	7.449	-0.624	-0.624	0.000	0.000	0.000	0.000
86	A	90	THR	0	-0.055	-0.029	3.628	0.049	0.705	0.292	-0.240	-0.708	0.001
87	A	91	LEU	0	-0.035	-0.014	5.757	-0.467	-0.440	-0.001	-0.003	-0.023	0.000
88	A	92	ARG	1	0.984	0.992	6.317	1.000	1.000	0.000	0.000	0.000	0.000
89	A	93	ILE	0	-0.032	-0.024	8.074	-0.162	-0.162	0.000	0.000	0.000	0.000
90	A	94	PRO	0	0.051	0.033	11.846	0.027	0.027	0.000	0.000	0.000	0.000
91	A	95	PRO	0	0.076	0.030	14.268	0.053	0.053	0.000	0.000	0.000	0.000
92	A	96	GLU	-1	-0.911	-0.944	17.540	-0.043	-0.043	0.000	0.000	0.000	0.000
93	A	97	LEU	0	-0.037	-0.006	15.103	0.019	0.019	0.000	0.000	0.000	0.000
94	A	98	ALA	0	0.006	-0.015	16.032	0.062	0.062	0.000	0.000	0.000	0.000
95	A	99	TYR	0	-0.069	-0.041	18.113	-0.020	-0.020	0.000	0.000	0.000	0.000
96	A	100	GLY	0	0.040	0.016	20.192	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.848	-0.925	21.728	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.871	0.958	22.851	-0.127	-0.127	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.049	0.036	22.120	0.002	0.002	0.000	0.000	0.000	0.000
100	A	104	ALA	0	0.009	-0.026	21.888	0.002	0.002	0.000	0.000	0.000	0.000
101	A	105	GLY	0	0.026	0.008	23.625	0.010	0.010	0.000	0.000	0.000	0.000
102	A	106	CYS	0	-0.040	-0.022	25.600	0.006	0.006	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.970	0.995	28.007	-0.164	-0.164	0.000	0.000	0.000	0.000
104	A	108	GLY	0	0.036	0.022	31.153	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	109	GLY	0	0.032	0.006	30.180	0.003	0.003	0.000	0.000	0.000	0.000
106	A	110	SER	0	-0.014	0.005	27.666	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	111	CYS	0	-0.023	-0.023	24.020	0.002	0.002	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.065	-0.017	21.038	0.001	0.001	0.000	0.000	0.000	0.000
109	A	113	ILE	0	-0.039	-0.014	18.111	0.025	0.025	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.027	0.011	19.163	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	115	PRO	0	0.024	0.044	20.528	0.010	0.010	0.000	0.000	0.000	0.000
112	A	116	ALA	0	0.027	-0.002	20.014	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	117	SER	0	-0.051	-0.060	16.465	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.043	-0.003	10.714	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	119	LEU	0	-0.081	-0.044	12.434	0.056	0.056	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.017	0.026	6.114	0.040	0.040	0.000	0.000	0.000	0.000
117	A	121	PHE	0	-0.001	-0.009	8.685	-0.126	-0.126	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.863	-0.908	6.740	4.330	4.330	0.000	0.000	0.000	0.000
119	A	123	ILE	0	-0.010	-0.029	9.015	-0.391	-0.391	0.000	0.000	0.000	0.000
120	A	124	GLU	-1	-0.823	-0.882	11.328	1.124	1.124	0.000	0.000	0.000	0.000
121	A	125	TYR	0	-0.003	0.002	13.843	-0.136	-0.136	0.000	0.000	0.000	0.000
122	A	126	ILE	0	0.004	-0.004	16.208	-0.031	-0.031	0.000	0.000	0.000	0.000
123	A	127	GLY	0	0.079	0.039	19.251	-0.035	-0.035	0.000	0.000	0.000	0.000
124	A	128	LYS	1	0.938	0.977	21.633	-0.193	-0.193	0.000	0.000	0.000	0.000
125	A	129	ALA	0	-0.037	-0.026	24.622	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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