FMO DATABASE

FMODB ID: YVY82

Calculation Name: 1YOZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOZ

Chain ID: A

ChEMBL ID:

UniProt ID: O29321

Base Structure: X-ray

Registration Date: 2023-09-21

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1021475.872619
FMO2-HF: Nuclear repulsion	973255.148072
FMO2-HF: Total energy	-48220.724547
FMO2-MP2: Total energy	-48361.666818

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:9:GLY)

Summations of interaction energy for fragment #1(A:9:GLY)

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.
-6.294	0.271	3.378	-5.215	-4.726	-0.032

Interaction energy analysis for fragmet #1(A:9:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.010

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	11	MET	0	-0.039	-0.020	3.743	-1.673	1.249	-0.051	-1.508	-1.363	-0.005
4	A	12	LEU	0	-0.010	0.002	5.249	0.208	0.208	0.000	0.000	0.000	0.000
5	A	13	TYR	0	-0.063	-0.060	6.912	0.075	0.075	0.000	0.000	0.000	0.000
6	A	14	ILE	0	0.026	0.036	9.742	-0.041	-0.041	0.000	0.000	0.000	0.000
7	A	15	ASN	0	0.013	-0.024	12.847	0.043	0.043	0.000	0.000	0.000	0.000
8	A	16	SER	0	0.018	-0.004	15.622	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	17	PHE	0	0.005	-0.020	19.146	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.038	-0.020	16.029	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	19	ASP	-1	-0.866	-0.928	17.554	-0.043	-0.043	0.000	0.000	0.000	0.000
12	A	20	ARG	1	0.941	0.968	20.217	-0.025	-0.025	0.000	0.000	0.000	0.000
13	A	21	MET	0	-0.038	-0.007	21.993	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	22	GLY	0	-0.010	-0.014	22.895	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	23	GLU	-1	-0.899	-0.963	23.615	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	24	ILE	0	-0.045	-0.015	25.969	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	25	ILE	0	-0.037	-0.019	26.540	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	26	ARG	1	0.762	0.854	22.436	0.050	0.050	0.000	0.000	0.000	0.000
19	A	27	GLY	0	-0.020	0.004	28.632	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	28	GLU	-1	-0.849	-0.889	26.212	-0.049	-0.049	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.868	0.937	27.448	0.011	0.011	0.000	0.000	0.000	0.000
22	A	30	SER	0	0.026	0.022	31.124	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	31	VAL	0	0.070	0.017	32.917	0.002	0.002	0.000	0.000	0.000	0.000
24	A	32	GLU	-1	-0.935	-0.962	34.290	0.011	0.011	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.949	-0.988	30.613	0.016	0.016	0.000	0.000	0.000	0.000
26	A	34	ALA	0	-0.009	-0.002	30.613	0.004	0.004	0.000	0.000	0.000	0.000
27	A	35	ASP	-1	-0.854	-0.926	31.542	0.030	0.030	0.000	0.000	0.000	0.000
28	A	36	LYS	1	0.923	0.956	31.313	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	37	LEU	0	0.032	0.019	24.899	0.006	0.006	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.038	-0.016	28.068	0.006	0.006	0.000	0.000	0.000	0.000
31	A	39	ASP	-1	-0.834	-0.933	30.235	0.053	0.053	0.000	0.000	0.000	0.000
32	A	40	GLN	0	0.062	0.023	28.428	0.006	0.006	0.000	0.000	0.000	0.000
33	A	41	LYS	1	0.944	0.988	27.780	-0.059	-0.059	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.029	-0.025	27.937	0.009	0.009	0.000	0.000	0.000	0.000
35	A	43	ILE	0	0.001	0.012	23.566	0.006	0.006	0.000	0.000	0.000	0.000
36	A	44	PHE	0	-0.023	-0.020	23.258	0.010	0.010	0.000	0.000	0.000	0.000
37	A	45	GLU	-1	-0.897	-0.955	23.121	0.123	0.123	0.000	0.000	0.000	0.000
38	A	46	MET	0	-0.024	0.001	21.407	0.004	0.004	0.000	0.000	0.000	0.000
39	A	47	PHE	0	0.051	0.013	17.143	0.006	0.006	0.000	0.000	0.000	0.000
40	A	48	ARG	1	0.861	0.950	18.325	-0.099	-0.099	0.000	0.000	0.000	0.000
41	A	49	SER	0	0.071	0.034	19.328	0.016	0.016	0.000	0.000	0.000	0.000
42	A	50	ASP	-1	-0.770	-0.848	15.433	0.139	0.139	0.000	0.000	0.000	0.000
43	A	51	CYS	0	-0.083	-0.046	14.852	0.045	0.045	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.975	-0.983	15.253	0.189	0.189	0.000	0.000	0.000	0.000
45	A	53	GLU	-1	-0.925	-0.970	15.013	0.132	0.132	0.000	0.000	0.000	0.000
46	A	54	ILE	0	-0.010	-0.010	9.841	0.022	0.022	0.000	0.000	0.000	0.000
47	A	55	LEU	0	0.006	-0.008	11.812	0.060	0.060	0.000	0.000	0.000	0.000
48	A	56	ASN	0	-0.002	-0.005	13.867	0.014	0.014	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.018	-0.004	10.679	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	58	TYR	0	0.038	0.019	10.167	0.019	0.019	0.000	0.000	0.000	0.000
51	A	59	LYS	1	0.903	0.958	11.767	-0.283	-0.283	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.097	-0.052	15.163	-0.032	-0.032	0.000	0.000	0.000	0.000
53	A	61	GLY	0	0.010	0.000	12.897	-0.037	-0.037	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.892	0.960	12.605	-0.124	-0.124	0.000	0.000	0.000	0.000
55	A	63	ALA	0	0.004	0.013	7.739	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.888	-0.947	5.866	0.217	0.217	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.945	0.962	6.147	-0.370	-0.370	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.886	-0.949	2.252	-2.346	-1.177	0.959	-0.948	-1.179	-0.003
59	A	67	GLU	-1	-0.729	-0.853	2.529	-1.633	0.748	2.388	-2.839	-1.930	-0.024
60	A	68	VAL	0	-0.016	-0.010	3.326	-0.333	-0.625	0.021	0.224	0.048	0.000
61	A	69	GLN	0	0.001	-0.003	5.569	0.151	0.151	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.921	0.987	3.083	-0.196	0.174	0.062	-0.142	-0.290	0.000
63	A	71	ASN	0	0.018	0.001	5.092	-0.651	-0.636	-0.001	-0.002	-0.012	0.000
64	A	72	PHE	0	0.051	0.029	7.716	-0.203	-0.203	0.000	0.000	0.000	0.000
65	A	73	TYR	0	0.009	0.021	8.260	-0.187	-0.187	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.035	-0.027	8.146	-0.182	-0.182	0.000	0.000	0.000	0.000
67	A	75	LEU	0	-0.005	0.010	10.721	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.863	0.915	13.075	-0.401	-0.401	0.000	0.000	0.000	0.000
69	A	77	THR	0	0.007	0.000	13.143	-0.058	-0.058	0.000	0.000	0.000	0.000
70	A	78	TYR	0	-0.038	-0.074	14.710	-0.047	-0.047	0.000	0.000	0.000	0.000
71	A	79	VAL	0	0.002	-0.001	16.596	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.028	-0.012	18.532	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	81	SER	0	-0.031	-0.023	18.504	-0.021	-0.021	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.081	-0.044	19.232	-0.032	-0.032	0.000	0.000	0.000	0.000
75	A	83	LEU	0	0.025	0.045	20.938	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	84	SER	0	0.012	0.000	22.416	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	85	ILE	0	0.023	0.005	24.217	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	86	HIS	0	0.003	0.052	20.243	0.000	0.000	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.056	0.030	25.144	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	88	GLU	-1	-0.901	-0.944	27.485	0.022	0.022	0.000	0.000	0.000	0.000
81	A	89	ARG	1	0.973	0.994	23.950	0.007	0.007	0.000	0.000	0.000	0.000
82	A	90	LEU	0	-0.005	0.001	27.177	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.911	0.957	29.711	-0.028	-0.028	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-0.886	-0.950	32.670	0.007	0.007	0.000	0.000	0.000	0.000
85	A	93	PHE	0	-0.061	-0.026	31.555	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	94	ALA	0	-0.011	-0.022	33.482	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	95	GLU	-1	-0.807	-0.902	35.095	0.014	0.014	0.000	0.000	0.000	0.000
88	A	96	SER	0	-0.121	-0.059	36.400	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	97	LYS	1	0.831	0.904	35.260	0.007	0.007	0.000	0.000	0.000	0.000
90	A	98	GLY	0	0.008	0.021	39.842	0.000	0.000	0.000	0.000	0.000	0.000
91	A	99	PHE	0	-0.011	-0.030	38.258	0.002	0.002	0.000	0.000	0.000	0.000
92	A	100	LYS	1	0.746	0.870	34.500	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	101	ILE	0	0.018	0.002	39.881	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	102	GLU	-1	-0.835	-0.911	37.008	0.031	0.031	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.868	0.986	33.825	-0.038	-0.038	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.827	0.909	29.378	-0.047	-0.047	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.007	0.010	25.767	0.002	0.002	0.000	0.000	0.000	0.000
98	A	106	ASP	-1	-0.815	-0.928	30.437	0.058	0.058	0.000	0.000	0.000	0.000
99	A	107	PRO	0	0.001	-0.022	28.393	0.007	0.007	0.000	0.000	0.000	0.000
100	A	108	GLU	-1	-0.918	-0.967	27.643	0.085	0.085	0.000	0.000	0.000	0.000
101	A	109	VAL	0	0.011	0.008	26.615	0.009	0.009	0.000	0.000	0.000	0.000
102	A	110	ILE	0	0.003	-0.003	22.986	0.010	0.010	0.000	0.000	0.000	0.000
103	A	111	ASN	0	-0.004	0.000	23.017	0.026	0.026	0.000	0.000	0.000	0.000
104	A	112	GLU	-1	-0.931	-0.963	23.477	0.145	0.145	0.000	0.000	0.000	0.000
105	A	113	ILE	0	-0.048	-0.008	19.717	0.014	0.014	0.000	0.000	0.000	0.000
106	A	114	ALA	0	0.020	0.001	18.970	0.025	0.025	0.000	0.000	0.000	0.000
107	A	115	LEU	0	-0.009	-0.004	19.029	0.034	0.034	0.000	0.000	0.000	0.000
108	A	116	TYR	0	-0.041	-0.021	19.170	0.010	0.010	0.000	0.000	0.000	0.000
109	A	117	ILE	0	0.052	0.011	14.353	0.011	0.011	0.000	0.000	0.000	0.000
110	A	118	ASP	-1	-0.811	-0.887	15.720	0.393	0.393	0.000	0.000	0.000	0.000
111	A	119	ARG	1	0.835	0.909	17.075	-0.180	-0.180	0.000	0.000	0.000	0.000
112	A	120	VAL	0	-0.019	-0.006	15.062	0.012	0.012	0.000	0.000	0.000	0.000
113	A	121	GLU	-1	-0.872	-0.931	10.647	0.877	0.877	0.000	0.000	0.000	0.000
114	A	122	LYS	1	0.871	0.943	13.883	-0.272	-0.272	0.000	0.000	0.000	0.000
115	A	123	GLU	-1	-0.971	-0.979	15.940	0.286	0.286	0.000	0.000	0.000	0.000
116	A	124	VAL	0	-0.089	-0.036	9.389	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLY)