FMO DATABASE

FMODB ID: K96G3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1267165.802256
FMO2-HF: Nuclear repulsion	1213791.098873
FMO2-HF: Total energy	-53374.703383
FMO2-MP2: Total energy	-53533.746031

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.
-1.653	1.531	0.98	-2.071	-2.093	-0.011

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 : 0.057 / q_NPA : 0.029

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	-0.027	-0.008	2.514	-3.406	-0.338	0.981	-2.058	-1.991	-0.011
4	A	5	VAL	0	0.005	0.002	4.907	0.905	1.021	-0.001	-0.013	-0.102	0.000
5	A	6	LYS	1	0.912	0.946	7.997	0.985	0.985	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.003	0.002	11.304	-0.019	-0.019	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.005	0.000	14.689	0.016	0.016	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.003	0.013	15.696	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.004	0.004	17.475	0.001	0.001	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.012	0.000	19.134	0.026	0.026	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.051	-0.035	22.446	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.745	-0.843	25.707	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.014	-0.027	29.408	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	15	ILE	0	0.008	-0.001	32.473	0.006	0.006	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.002	-0.003	35.265	0.000	0.000	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.814	0.861	37.763	0.048	0.048	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.018	-0.007	41.319	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TRP	0	-0.089	-0.052	43.089	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.831	-0.902	46.368	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.030	0.021	49.137	0.000	0.000	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.929	-0.971	49.038	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.053	-0.036	50.972	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.013	0.006	44.143	0.000	0.000	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.812	0.889	46.741	0.017	0.017	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.002	0.008	45.718	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.023	-0.017	39.330	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.027	-0.009	38.640	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.040	-0.015	37.709	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.016	0.010	33.869	0.006	0.006	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.860	-0.932	36.999	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.805	0.884	29.691	0.038	0.038	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.811	0.896	32.858	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	34	TYR	0	0.005	0.000	29.007	0.006	0.006	0.000	0.000	0.000	0.000
34	A	35	PRO	0	0.019	-0.010	29.050	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	36	PRO	0	-0.002	0.028	28.432	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.002	-0.005	31.609	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.043	0.010	35.101	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.070	-0.027	36.978	0.005	0.005	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.007	0.002	33.237	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	41	LEU	0	0.014	-0.004	32.922	0.006	0.006	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.001	-0.003	32.580	0.000	0.000	0.000	0.000	0.000	0.000
42	A	43	GLY	0	-0.003	-0.015	28.691	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.009	0.012	25.405	0.008	0.008	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.030	-0.025	19.648	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.003	0.006	18.817	0.016	0.016	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.923	-0.958	17.713	0.059	0.059	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.049	-0.042	11.253	-0.034	-0.034	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.016	-0.014	14.689	0.055	0.055	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.816	-0.865	16.507	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.867	0.909	19.483	0.003	0.003	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.027	0.007	21.209	0.009	0.009	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.857	-0.947	23.302	-0.094	-0.094	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.865	-0.913	23.265	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.021	0.028	22.448	0.009	0.009	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.011	0.008	24.497	0.008	0.008	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.017	-0.015	27.746	0.007	0.007	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.748	0.839	22.802	0.010	0.010	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.815	-0.915	25.146	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.061	-0.009	28.604	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.823	0.889	29.504	0.003	0.003	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.839	-0.893	26.941	0.029	0.029	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.811	-0.921	30.530	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.073	-0.077	33.205	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.045	0.041	35.448	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.058	-0.024	36.251	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.796	-0.859	34.466	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.050	-0.024	34.278	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.959	0.993	34.447	0.031	0.031	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.018	0.011	29.693	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.055	-0.015	34.254	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.876	0.914	34.524	0.089	0.089	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.046	0.043	28.457	0.002	0.002	0.000	0.000	0.000	0.000
73	A	74	MET	0	-0.087	-0.020	31.843	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.053	0.007	31.081	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.038	-0.013	24.652	0.000	0.000	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.025	-0.013	27.278	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	78	SER	0	0.039	-0.004	24.281	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.816	-0.895	25.494	-0.165	-0.165	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.028	-0.018	24.390	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.882	-0.948	25.350	-0.165	-0.165	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.719	0.860	25.855	0.149	0.149	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.766	-0.880	25.040	-0.084	-0.084	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.003	-0.003	25.899	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.818	0.895	23.360	0.077	0.077	0.000	0.000	0.000	0.000
85	A	86	ALA	0	-0.019	-0.012	19.967	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.053	0.039	20.225	0.010	0.010	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.017	0.000	20.175	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.002	0.002	20.993	0.015	0.015	0.000	0.000	0.000	0.000
89	A	90	SER	0	-0.060	-0.055	22.530	0.006	0.006	0.000	0.000	0.000	0.000
90	A	91	VAL	0	0.020	0.008	23.387	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.009	0.025	26.133	0.014	0.014	0.000	0.000	0.000	0.000
92	A	93	TRP	0	0.022	-0.001	26.356	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.001	0.009	31.933	0.004	0.004	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.040	0.010	35.298	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.826	-0.846	36.792	-0.039	-0.039	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.043	0.015	38.914	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.000	-0.002	40.806	0.001	0.001	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.020	0.011	42.816	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.830	-0.908	44.068	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	101	PRO	0	-0.002	0.007	40.365	0.002	0.002	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.756	0.847	39.612	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.012	0.005	37.342	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.046	0.023	34.564	0.005	0.005	0.000	0.000	0.000	0.000
104	A	105	SER	0	0.005	-0.027	29.231	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.822	-0.876	27.854	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.039	0.037	30.811	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	108	LYN	0	-0.031	0.000	34.446	0.008	0.008	0.000	0.000	0.000	0.000
108	A	109	LYS	1	0.816	0.885	37.581	0.011	0.011	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.051	0.041	38.238	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.817	0.913	39.955	0.022	0.022	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.028	0.021	41.916	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	113	TYR	0	-0.008	-0.004	42.199	0.002	0.002	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.943	0.954	45.200	0.021	0.021	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.003	-0.004	43.859	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.898	-0.958	46.517	-0.037	-0.037	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.892	-0.928	48.129	-0.024	-0.024	0.000	0.000	0.000	0.000
117	A	118	ILE	0	0.004	0.009	41.841	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.009	0.005	43.881	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.030	-0.014	41.534	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.830	-0.903	41.076	-0.056	-0.056	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.873	0.939	41.523	0.029	0.029	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.083	-0.019	37.147	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	VAL	0	-0.010	0.012	33.380	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.001	-0.010	28.273	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.758	-0.877	30.720	-0.116	-0.116	0.000	0.000	0.000	0.000
126	A	127	HIS	0	0.060	0.020	30.099	0.007	0.007	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.846	0.913	34.583	0.061	0.061	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.802	0.902	31.527	0.131	0.131	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.025	0.021	30.924	0.002	0.002	0.000	0.000	0.000	0.000
130	A	131	ILE	0	0.027	0.009	35.460	0.002	0.002	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.024	-0.015	38.590	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.796	-0.890	36.808	-0.092	-0.092	0.000	0.000	0.000	0.000
133	A	134	PHE	0	-0.013	-0.015	37.976	0.001	0.001	0.000	0.000	0.000	0.000
134	A	135	LEU	0	-0.013	-0.014	39.647	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.827	0.916	40.542	0.080	0.080	0.000	0.000	0.000	0.000
136	A	137	GLY	0	0.015	0.022	41.909	0.001	0.001	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.096	-0.039	38.853	0.001	0.001	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.040	-0.021	36.003	-0.004	-0.004	0.000	0.000	0.000	0.000

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