FMO DATABASE

FMODB ID: R9J88

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1264478.332451
FMO2-HF: Nuclear repulsion	1211104.87132
FMO2-HF: Total energy	-53373.461131
FMO2-MP2: Total energy	-53532.556998

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.
0.498	2.262	-0.004	-0.977	-0.783	0.003

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 : 0.049 / 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	-0.004	-0.005	3.664	-1.095	0.669	-0.004	-0.977	-0.783	0.003
4	A	5	VAL	0	0.012	0.008	5.864	0.773	0.773	0.000	0.000	0.000	0.000
5	A	6	LYS	1	0.917	0.958	8.944	0.857	0.857	0.000	0.000	0.000	0.000
6	A	7	THR	0	0.002	-0.005	11.376	0.006	0.006	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.030	-0.003	14.479	0.016	0.016	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.015	0.011	15.351	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.016	0.010	17.363	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.008	0.002	19.084	0.025	0.025	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.048	-0.020	22.311	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.768	-0.855	25.440	-0.061	-0.061	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.021	-0.025	29.137	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.009	-0.002	32.252	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.009	-0.009	34.568	0.000	0.000	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.798	0.871	37.627	0.034	0.034	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.013	-0.002	41.181	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	TRP	0	-0.095	-0.056	42.999	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.918	-0.953	45.966	0.000	0.000	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.021	-0.002	48.405	0.000	0.000	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.946	-0.980	48.660	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.052	-0.031	50.776	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.015	0.009	43.932	0.001	0.001	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.909	0.949	46.363	0.009	0.009	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.005	0.016	45.308	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.008	-0.012	39.192	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.024	-0.008	38.120	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.043	-0.010	37.522	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.029	-0.002	34.090	0.005	0.005	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.937	-0.961	36.844	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.864	0.901	28.660	0.035	0.035	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.879	0.934	33.093	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	34	TYR	0	0.006	0.008	29.066	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	PRO	0	-0.002	-0.016	27.973	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	36	PRO	0	0.045	0.045	28.484	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.015	0.024	31.520	0.002	0.002	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.025	0.007	34.895	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.037	-0.003	36.416	0.003	0.003	0.000	0.000	0.000	0.000
39	A	40	ALA	0	-0.014	-0.017	33.205	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.011	-0.006	32.709	0.006	0.006	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.004	0.010	32.289	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.025	-0.015	28.559	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.047	0.046	25.222	0.006	0.006	0.000	0.000	0.000	0.000
44	A	45	PHE	0	-0.088	-0.056	19.491	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.011	-0.002	18.438	0.016	0.016	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.948	-0.961	17.344	0.086	0.086	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.022	-0.031	11.168	-0.026	-0.026	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.048	-0.027	14.470	0.047	0.047	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.759	-0.857	15.887	0.038	0.038	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.865	0.929	19.118	-0.038	-0.038	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.039	0.010	21.222	0.007	0.007	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.884	-0.961	22.933	-0.057	-0.057	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.903	-0.950	22.675	0.033	0.033	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.038	0.029	22.197	0.008	0.008	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.009	0.015	24.270	0.004	0.004	0.000	0.000	0.000	0.000
56	A	57	ALA	0	-0.003	-0.006	27.504	0.004	0.004	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.776	0.857	22.292	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.832	-0.916	25.515	0.010	0.010	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.053	-0.010	28.176	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.877	0.974	28.977	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.917	-0.957	26.817	0.048	0.048	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.874	-0.938	29.207	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.096	-0.078	32.938	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.025	0.025	35.059	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.084	-0.034	36.347	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.892	-0.940	34.430	0.020	0.020	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.041	-0.026	33.881	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.952	0.990	34.087	0.015	0.015	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.008	-0.006	29.335	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.041	-0.022	33.908	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.931	0.953	34.377	0.069	0.069	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.017	0.036	28.238	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	MET	0	-0.101	-0.052	31.657	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.053	0.013	30.954	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.022	0.000	24.637	0.002	0.002	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.060	-0.042	27.331	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	SER	0	0.018	-0.020	24.042	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.889	-0.929	25.380	-0.157	-0.157	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.017	-0.033	24.731	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.930	-0.960	25.498	-0.154	-0.154	0.000	0.000	0.000	0.000
81	A	82	ARG	1	0.788	0.905	25.635	0.133	0.133	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.794	-0.882	24.806	-0.076	-0.076	0.000	0.000	0.000	0.000
83	A	84	PRO	0	0.022	-0.003	25.641	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.792	0.874	23.493	0.064	0.064	0.000	0.000	0.000	0.000
85	A	86	ALA	0	-0.014	-0.006	19.752	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.039	0.037	19.848	0.015	0.015	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.011	0.001	19.880	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	89	VAL	0	-0.010	-0.009	21.063	0.008	0.008	0.000	0.000	0.000	0.000
89	A	90	SER	0	-0.079	-0.062	22.451	0.005	0.005	0.000	0.000	0.000	0.000
90	A	91	VAL	0	0.006	0.002	23.345	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.023	0.012	26.079	0.012	0.012	0.000	0.000	0.000	0.000
92	A	93	TRP	0	0.034	0.010	26.146	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.011	0.027	31.703	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	GLY	0	0.038	0.004	35.253	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.825	-0.862	36.352	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.036	0.010	38.452	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.027	0.030	40.450	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	GLY	0	0.017	0.005	42.155	0.002	0.002	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.944	-0.984	43.881	0.002	0.002	0.000	0.000	0.000	0.000
100	A	101	PRO	0	-0.015	-0.006	40.296	0.002	0.002	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.872	0.922	39.164	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.021	-0.004	37.284	0.000	0.000	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.049	0.025	34.755	0.004	0.004	0.000	0.000	0.000	0.000
104	A	105	SER	0	0.085	0.038	29.548	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.857	-0.942	27.996	0.008	0.008	0.000	0.000	0.000	0.000
106	A	107	ALA	0	0.028	0.028	30.932	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	108	LYN	0	-0.057	-0.018	34.382	0.007	0.007	0.000	0.000	0.000	0.000
108	A	109	LYS	1	0.826	0.885	37.408	0.004	0.004	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.084	0.062	38.220	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.837	0.926	39.785	0.014	0.014	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.049	0.030	41.689	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	TYR	0	-0.033	-0.013	41.932	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.982	1.000	45.093	0.014	0.014	0.000	0.000	0.000	0.000
114	A	115	LEU	0	0.008	-0.004	43.301	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.918	-0.959	46.243	-0.029	-0.029	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.945	-0.980	48.029	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	118	ILE	0	0.017	0.015	41.805	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.036	-0.012	43.256	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	120	LEU	0	0.041	-0.018	41.637	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.897	-0.951	41.126	-0.048	-0.048	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.896	0.951	41.436	0.024	0.024	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.068	-0.010	37.169	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	VAL	0	-0.004	0.018	33.497	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.032	-0.020	28.033	0.000	0.000	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.754	-0.884	30.708	-0.102	-0.102	0.000	0.000	0.000	0.000
126	A	127	HIS	0	0.095	0.035	30.150	0.006	0.006	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.956	0.997	34.617	0.058	0.058	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.913	0.961	32.448	0.112	0.112	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.025	0.025	30.842	0.001	0.001	0.000	0.000	0.000	0.000
130	A	131	ILE	0	0.048	0.016	35.325	0.002	0.002	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.055	-0.030	38.374	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.833	-0.908	36.026	-0.084	-0.084	0.000	0.000	0.000	0.000
133	A	134	PHE	0	-0.031	-0.019	37.823	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	LEU	0	-0.028	-0.026	39.410	0.002	0.002	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.892	0.947	42.331	0.064	0.064	0.000	0.000	0.000	0.000
136	A	137	GLY	0	0.002	0.019	41.570	0.000	0.000	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.053	-0.017	39.068	0.001	0.001	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.046	-0.018	35.779	-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)