FMO DATABASE

FMODB ID: 824RY

Calculation Name: 1YE5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YE5

Chain ID: A

ChEMBL ID:

UniProt ID: O58236

Base Structure: X-ray

Registration Date: 2023-06-19

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1363892.661204
FMO2-HF: Nuclear repulsion	1306904.623247
FMO2-HF: Total energy	-56988.037957
FMO2-MP2: Total energy	-57154.836993

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:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-6.37	-1.741	0.267	-2.454	-2.441	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.031

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	PRO	0	0.007	0.008	3.806	-0.538	1.465	-0.023	-0.869	-1.111	0.004
4	A	5	PRO	0	0.036	0.004	6.548	0.276	0.276	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.833	-0.904	9.582	-0.358	-0.358	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.024	-0.012	9.521	-0.208	-0.208	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.023	-0.043	12.398	0.157	0.157	0.000	0.000	0.000	0.000
8	A	9	PHE	0	0.027	0.014	13.239	-0.080	-0.080	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.752	-0.846	16.647	-0.317	-0.317	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.019	-0.042	19.751	0.010	0.010	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.003	-0.010	21.500	0.016	0.016	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.019	0.015	16.576	0.019	0.019	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.032	0.015	18.696	0.016	0.016	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.019	-0.021	19.828	0.030	0.030	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.819	0.899	19.168	0.232	0.232	0.000	0.000	0.000	0.000
16	A	17	MET	0	0.026	0.028	14.528	0.022	0.022	0.000	0.000	0.000	0.000
17	A	18	HIS	0	0.001	0.025	18.694	0.014	0.014	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.043	-0.012	21.672	0.018	0.018	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.018	-0.014	22.783	0.004	0.004	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.061	-0.039	22.839	0.019	0.019	0.000	0.000	0.000	0.000
21	A	22	MET	0	0.028	0.021	16.132	0.018	0.018	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.944	0.985	18.884	0.011	0.011	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.959	0.992	17.218	-0.164	-0.164	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.091	0.033	13.291	0.019	0.019	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.006	0.004	14.841	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.940	-0.978	17.025	0.011	0.011	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.021	-0.011	12.295	0.013	0.013	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.001	-0.008	12.553	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.001	-0.010	13.601	-0.036	-0.036	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.022	0.011	15.299	0.005	0.005	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.834	0.912	10.110	-0.262	-0.262	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.039	-0.006	6.829	0.003	0.003	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.007	0.025	12.033	0.087	0.087	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.011	-0.012	14.129	-0.088	-0.088	0.000	0.000	0.000	0.000
35	A	36	ASN	0	0.003	0.001	16.070	0.122	0.122	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.008	0.021	18.502	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.050	0.037	20.801	0.031	0.031	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.051	0.002	23.466	0.007	0.007	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.007	-0.011	26.105	0.014	0.014	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.029	0.016	21.132	0.014	0.014	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.035	0.012	24.275	0.009	0.009	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.015	0.017	26.069	0.015	0.015	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.909	0.987	26.614	0.167	0.167	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.027	0.008	23.633	0.013	0.013	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.036	-0.024	26.706	0.011	0.011	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.081	-0.054	29.960	0.012	0.012	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.018	-0.012	28.139	0.008	0.008	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.926	0.969	26.175	0.107	0.107	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.045	0.042	30.650	0.008	0.008	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.058	-0.027	30.349	0.005	0.005	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.064	-0.021	30.006	0.006	0.006	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.866	0.929	30.383	0.064	0.064	0.000	0.000	0.000	0.000
53	A	54	LYS	1	1.037	1.010	34.158	0.038	0.038	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.038	-0.003	36.476	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.064	0.016	33.432	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.911	-0.944	33.721	-0.063	-0.063	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.017	-0.001	34.522	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.887	-0.972	30.095	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.029	-0.013	29.764	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.909	-0.964	29.723	-0.082	-0.082	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.036	-0.006	27.378	0.000	0.000	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.034	-0.023	24.383	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.896	0.933	25.341	0.094	0.094	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.955	-0.972	26.545	-0.066	-0.066	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.031	0.013	21.463	0.002	0.002	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.055	-0.057	18.396	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.020	0.032	19.120	0.041	0.041	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.044	-0.023	21.896	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.018	-0.011	21.658	0.013	0.013	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.017	-0.001	24.781	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.016	0.016	26.913	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.002	-0.015	25.749	0.012	0.012	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.817	-0.909	29.220	-0.128	-0.128	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.910	-0.958	26.924	-0.160	-0.160	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.074	-0.030	24.242	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.023	0.006	26.704	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.013	-0.007	29.785	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.947	0.971	22.576	0.251	0.251	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.018	0.011	26.572	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.023	0.021	27.486	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.060	-0.036	28.146	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.013	-0.005	22.866	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.878	-0.943	27.005	-0.158	-0.158	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.008	0.007	29.453	0.007	0.007	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.083	-0.055	27.656	0.000	0.000	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.005	-0.005	25.107	0.001	0.001	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.072	0.049	29.146	0.007	0.007	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.881	0.957	32.506	0.126	0.126	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.835	0.927	26.480	0.205	0.205	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.946	-0.973	31.832	-0.114	-0.114	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.076	-0.031	26.482	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.026	-0.033	30.085	0.001	0.001	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.030	0.002	24.091	0.002	0.002	0.000	0.000	0.000	0.000
94	A	95	ASP	-1	-0.833	-0.901	27.277	-0.190	-0.190	0.000	0.000	0.000	0.000
95	A	96	MET	0	0.064	0.006	27.697	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.801	-0.890	24.748	-0.212	-0.212	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.829	-0.916	23.344	-0.273	-0.273	0.000	0.000	0.000	0.000
98	A	99	ILE	0	0.014	0.006	23.058	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.000	0.008	24.197	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.028	-0.010	19.564	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.001	-0.008	19.285	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.053	-0.053	19.570	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	104	THR	0	-0.013	-0.028	20.860	0.010	0.010	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.009	0.010	16.008	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.031	-0.009	16.503	-0.029	-0.029	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.050	-0.025	17.874	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.046	-0.019	17.576	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	109	ASN	0	-0.031	-0.006	12.197	-0.045	-0.045	0.000	0.000	0.000	0.000
109	A	110	SER	0	0.014	0.006	12.844	-0.069	-0.069	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.022	-0.009	7.239	0.018	0.018	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.028	-0.030	11.337	0.085	0.085	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.017	0.000	10.328	-0.059	-0.059	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.013	-0.047	12.777	0.122	0.122	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.775	-0.896	14.799	-0.332	-0.332	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.954	-0.975	17.267	-0.261	-0.261	0.000	0.000	0.000	0.000
116	A	117	PRO	0	0.016	0.003	14.482	0.005	0.005	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.952	0.962	16.635	0.272	0.272	0.000	0.000	0.000	0.000
118	A	119	ARG	1	0.916	0.996	19.274	0.275	0.275	0.000	0.000	0.000	0.000
119	A	120	TYR	0	0.015	-0.011	18.005	0.020	0.020	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.884	-0.935	16.549	-0.495	-0.495	0.000	0.000	0.000	0.000
121	A	122	PRO	0	-0.065	-0.039	19.081	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.013	-0.008	19.736	0.023	0.023	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.948	0.994	12.417	0.680	0.680	0.000	0.000	0.000	0.000
124	A	125	ARG	1	0.867	0.951	17.200	0.258	0.258	0.000	0.000	0.000	0.000
125	A	126	PHE	0	-0.061	-0.045	19.650	0.031	0.031	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.014	0.008	16.245	0.020	0.020	0.000	0.000	0.000	0.000
127	A	128	LEU	0	-0.033	0.009	14.873	-0.053	-0.053	0.000	0.000	0.000	0.000
128	A	129	ASP	-1	-0.870	-0.940	9.751	-1.254	-1.254	0.000	0.000	0.000	0.000
129	A	130	THR	0	-0.041	-0.016	12.046	0.020	0.020	0.000	0.000	0.000	0.000
130	A	131	MET	0	0.017	0.008	4.904	-0.058	-0.058	0.000	0.000	0.000	0.000
131	A	132	PRO	0	-0.055	-0.028	9.899	0.124	0.124	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.074	0.037	10.755	-0.098	-0.098	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.892	-0.948	12.012	-0.262	-0.262	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.864	0.931	7.771	0.894	0.894	0.000	0.000	0.000	0.000
135	A	136	PHE	0	0.112	0.046	7.520	0.061	0.061	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.002	-0.006	8.575	0.147	0.147	0.000	0.000	0.000	0.000
137	A	138	LYS	1	0.935	0.962	9.288	0.205	0.205	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.939	-0.979	2.784	-5.915	-3.289	0.290	-1.585	-1.330	-0.018
139	A	140	VAL	0	-0.026	-0.008	6.540	0.513	0.513	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-1.013	-0.988	9.020	0.217	0.217	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.055	-0.038	7.170	0.110	0.110	0.000	0.000	0.000	0.000
142	A	143	MET	0	-0.038	-0.006	7.865	-0.069	-0.069	0.000	0.000	0.000	0.000

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