FMO DATABASE

FMODB ID: QY3VY

Calculation Name: 2YYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YYH

Chain ID: A

ChEMBL ID:

UniProt ID: O67435

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:

Apendix: None

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	138
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1264746.999031
FMO2-HF: Nuclear repulsion	1211372.660678
FMO2-HF: Total energy	-53374.338353
FMO2-MP2: Total energy	-53533.382877

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:2:GLY)

Summations of interaction energy for fragment #1(A:2: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.
1.193	2.992	-0.005	-0.92	-0.875	0.004

Interaction energy analysis for fragmet #1(A:2:GLY)

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 : 0.025

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	4	ASN	0	-0.018	-0.012	3.614	-0.396	1.403	-0.005	-0.920	-0.875	0.004
4	A	5	VAL	0	0.012	0.009	5.881	0.744	0.744	0.000	0.000	0.000	0.000
5	A	6	LYS	1	0.920	0.961	8.605	0.876	0.876	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.011	0.007	11.379	-0.003	-0.003	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.021	-0.003	14.481	0.016	0.016	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.004	0.003	15.407	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.012	0.007	17.364	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.016	0.007	19.085	0.025	0.025	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.047	-0.027	22.312	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.759	-0.855	25.440	-0.064	-0.064	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.012	-0.022	29.137	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.011	-0.002	32.252	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.002	-0.012	34.867	0.000	0.000	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.798	0.854	37.627	0.034	0.034	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.008	-0.006	41.181	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TRP	0	-0.088	-0.057	43.018	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.858	-0.912	45.965	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.030	0.006	48.413	0.000	0.000	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.939	-0.972	48.658	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.053	-0.038	50.777	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.012	0.011	43.857	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.845	0.908	46.421	0.008	0.008	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.005	0.017	45.308	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.013	-0.015	39.087	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.030	-0.012	38.243	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.040	-0.010	37.520	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.024	0.000	33.685	0.006	0.006	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.903	-0.960	36.844	-0.017	-0.017	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.863	0.917	28.858	0.030	0.030	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.832	0.912	33.000	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.014	-0.010	28.583	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	PRO	0	-0.015	-0.024	28.492	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.025	0.038	28.484	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.024	0.005	31.522	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.024	0.005	34.896	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.069	-0.019	36.417	0.003	0.003	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.001	-0.002	33.218	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.005	0.003	32.737	0.006	0.006	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.014	0.009	32.296	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.008	-0.015	28.566	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.012	0.025	25.222	0.007	0.007	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.065	-0.040	19.489	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.011	-0.001	18.560	0.016	0.016	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.936	-0.953	17.335	0.093	0.093	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.027	-0.035	11.091	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.040	-0.022	14.468	0.047	0.047	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.771	-0.857	15.884	0.034	0.034	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.839	0.903	19.116	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.035	0.006	21.075	0.007	0.007	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.877	-0.957	22.932	-0.058	-0.058	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.872	-0.921	22.870	0.027	0.027	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.042	0.034	22.212	0.008	0.008	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.002	0.007	24.268	0.004	0.004	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.017	-0.010	27.503	0.004	0.004	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.752	0.834	22.317	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.828	-0.914	25.042	0.012	0.012	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.049	-0.010	28.175	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.817	0.895	29.279	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.900	-0.944	26.702	0.049	0.049	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.864	-0.936	30.183	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.090	-0.075	32.937	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.034	0.031	35.054	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.073	-0.028	36.334	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.814	-0.871	34.189	0.019	0.019	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.048	-0.027	33.898	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.959	0.994	34.086	0.017	0.017	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.008	-0.005	29.322	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.039	-0.011	33.907	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.887	0.926	34.371	0.072	0.072	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.034	0.044	28.241	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	MET	0	-0.096	-0.039	31.656	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.056	0.010	30.955	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.031	-0.007	24.532	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.034	-0.032	27.325	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	78	SER	0	0.050	-0.004	24.041	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.849	-0.909	25.383	-0.150	-0.150	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.010	-0.020	24.742	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.922	-0.956	25.501	-0.157	-0.157	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.761	0.878	25.634	0.133	0.133	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.785	-0.882	24.832	-0.075	-0.075	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.014	-0.006	25.644	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.802	0.885	23.465	0.064	0.064	0.000	0.000	0.000	0.000
85	A	86	ALA	0	-0.013	-0.006	19.730	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.034	0.032	19.889	0.013	0.013	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.001	0.003	19.882	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.013	-0.007	21.030	0.008	0.008	0.000	0.000	0.000	0.000
89	A	90	SER	0	-0.073	-0.063	22.452	0.006	0.006	0.000	0.000	0.000	0.000
90	A	91	VAL	0	0.005	0.004	23.313	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.021	0.018	26.079	0.013	0.013	0.000	0.000	0.000	0.000
92	A	93	TRP	0	0.035	0.007	26.053	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.008	0.029	31.703	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.045	0.009	35.252	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.820	-0.846	36.351	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.033	0.009	38.454	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.018	0.021	40.448	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.016	0.005	42.154	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.850	-0.922	43.883	0.003	0.003	0.000	0.000	0.000	0.000
100	A	101	PRO	0	0.002	0.006	40.188	0.002	0.002	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.758	0.846	39.279	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.019	0.000	37.288	0.000	0.000	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.058	0.028	34.754	0.004	0.004	0.000	0.000	0.000	0.000
104	A	105	SER	0	0.078	0.033	29.496	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.785	-0.871	28.000	0.003	0.003	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.040	0.043	30.932	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	108	LYN	0	-0.041	-0.015	34.382	0.007	0.007	0.000	0.000	0.000	0.000
108	A	109	LYS	1	0.828	0.881	37.408	0.004	0.004	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.054	0.052	38.194	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.822	0.912	39.785	0.014	0.014	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.030	0.024	41.689	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	TYR	0	-0.038	-0.016	41.951	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.958	0.967	45.093	0.014	0.014	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.006	-0.002	43.293	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.912	-0.961	46.244	-0.029	-0.029	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.925	-0.946	48.028	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	118	ILE	0	0.025	0.019	41.779	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.029	-0.009	43.462	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.044	-0.014	41.550	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.862	-0.921	41.128	-0.049	-0.049	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.914	0.965	41.438	0.023	0.023	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.068	-0.014	37.187	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	VAL	0	-0.008	0.013	33.320	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.021	-0.012	28.064	0.000	0.000	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.742	-0.864	30.638	-0.103	-0.103	0.000	0.000	0.000	0.000
126	A	127	HIS	0	0.082	0.024	30.080	0.005	0.005	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.890	0.947	34.618	0.056	0.056	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.828	0.913	31.618	0.117	0.117	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.013	0.018	30.885	0.001	0.001	0.000	0.000	0.000	0.000
130	A	131	ILE	0	0.042	0.015	35.327	0.002	0.002	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.054	-0.029	38.375	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.817	-0.893	36.366	-0.083	-0.083	0.000	0.000	0.000	0.000
133	A	134	PHE	0	-0.022	-0.019	37.748	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	LEU	0	-0.021	-0.022	39.411	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.902	0.957	42.051	0.066	0.066	0.000	0.000	0.000	0.000
136	A	137	GLY	0	-0.006	0.013	41.572	0.000	0.000	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.099	-0.043	39.088	0.001	0.001	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.029	-0.011	35.757	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLY)