FMO DATABASE

FMODB ID: 59K4Z

Calculation Name: 1YE5-A-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1371629.263939
FMO2-HF: Nuclear repulsion	1314470.346737
FMO2-HF: Total energy	-57158.917202
FMO2-MP2: Total energy	-57326.265305

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:1:ACE )

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

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.
3.068	-1.295	14.832	-6.093	-4.375	-0.038

Interaction energy analysis for fragmet #1(A:1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.021

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	3	LEU	0	0.000	0.009	3.731	1.173	2.027	0.013	-0.288	-0.579	0.000
4	A	4	PRO	0	-0.007	0.001	6.022	0.427	0.427	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.036	0.004	9.633	-0.009	-0.009	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.835	-0.904	12.578	-0.322	-0.322	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.023	-0.012	11.252	-0.060	-0.060	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.019	-0.041	14.368	0.080	0.080	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.020	0.012	14.068	-0.037	-0.037	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.753	-0.848	18.130	-0.164	-0.164	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.015	-0.041	21.105	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.005	-0.010	22.289	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.021	0.016	17.423	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.031	0.015	19.256	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.017	-0.020	20.644	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.819	0.899	19.370	0.129	0.129	0.000	0.000	0.000	0.000
17	A	17	MET	0	0.025	0.028	14.469	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	HIS	0	0.002	0.026	18.744	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.044	-0.013	21.382	0.023	0.023	0.000	0.000	0.000	0.000
20	A	20	GLN	0	0.018	-0.014	22.133	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.062	-0.038	21.551	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	MET	0	0.028	0.020	15.702	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.943	0.985	18.059	0.061	0.061	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.959	0.992	15.468	0.127	0.127	0.000	0.000	0.000	0.000
25	A	25	ILE	0	0.091	0.032	12.420	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.006	0.004	14.246	-0.053	-0.053	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.938	-0.977	16.796	-0.194	-0.194	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.024	-0.013	11.569	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.002	-0.009	12.586	-0.069	-0.069	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.004	-0.009	13.600	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.021	0.012	15.509	0.010	0.010	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.831	0.912	11.282	0.336	0.336	0.000	0.000	0.000	0.000
33	A	33	PHE	0	-0.037	-0.005	7.743	-0.066	-0.066	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.006	0.025	13.806	0.071	0.071	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.010	-0.012	15.801	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.002	0.001	17.873	0.070	0.070	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.008	0.021	20.049	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.053	0.037	22.646	0.019	0.019	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.046	0.001	25.443	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.002	-0.009	27.891	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.027	0.015	22.691	0.011	0.011	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.034	0.012	25.816	0.004	0.004	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.018	0.019	27.501	0.009	0.009	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.908	0.987	27.973	0.097	0.097	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.025	0.007	24.183	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.035	-0.023	27.756	0.006	0.006	0.000	0.000	0.000	0.000
47	A	47	THR	0	-0.081	-0.054	30.919	0.009	0.009	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.023	-0.013	28.938	0.006	0.006	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.927	0.969	26.612	0.106	0.106	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.051	0.045	31.145	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.059	-0.027	30.328	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.065	-0.021	29.975	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.866	0.928	30.370	0.083	0.083	0.000	0.000	0.000	0.000
54	A	54	LYS	1	1.036	1.010	34.419	0.044	0.044	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.037	-0.003	36.929	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.063	0.016	34.430	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.909	-0.943	34.639	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.018	-0.001	35.443	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.885	-0.971	30.506	-0.094	-0.094	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.032	-0.014	30.560	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.908	-0.963	30.786	-0.093	-0.093	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.036	-0.006	27.871	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.034	-0.023	25.295	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.894	0.932	26.398	0.093	0.093	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.955	-0.971	28.058	-0.122	-0.122	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.032	0.013	22.192	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.055	-0.058	19.274	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.021	0.032	21.531	0.031	0.031	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.043	-0.022	23.812	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.017	-0.011	24.132	0.009	0.009	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.016	-0.002	27.029	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.016	0.016	29.434	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	73	LEU	0	0.002	-0.015	28.954	0.008	0.008	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.817	-0.909	32.215	-0.077	-0.077	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.909	-0.957	30.696	-0.092	-0.092	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.075	-0.030	27.224	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.024	0.006	29.827	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.013	-0.007	33.017	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.947	0.970	26.050	0.118	0.118	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.019	0.011	29.242	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.024	0.022	30.203	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	GLN	0	-0.062	-0.036	31.413	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.011	-0.004	25.593	0.004	0.004	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.881	-0.945	29.708	-0.067	-0.067	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.010	0.008	31.663	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.082	-0.055	30.136	0.004	0.004	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.003	-0.007	27.073	0.004	0.004	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.073	0.050	31.056	0.005	0.005	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.881	0.958	34.534	0.046	0.046	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.837	0.928	28.620	0.062	0.062	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.947	-0.974	33.327	-0.031	-0.031	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.077	-0.030	27.952	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.026	-0.033	31.378	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.032	0.001	25.342	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.833	-0.902	28.575	-0.091	-0.091	0.000	0.000	0.000	0.000
96	A	96	MET	0	0.067	0.007	29.128	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.802	-0.890	26.151	-0.122	-0.122	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.829	-0.916	24.796	-0.128	-0.128	0.000	0.000	0.000	0.000
99	A	99	ILE	0	0.011	0.005	24.676	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.004	0.009	26.249	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.027	-0.010	21.261	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.001	-0.008	21.232	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	103	THR	0	-0.049	-0.052	22.101	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.021	-0.031	23.315	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.006	0.011	18.420	-0.009	-0.009	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.024	-0.006	19.676	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	107	TYR	0	-0.057	-0.028	21.245	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.046	-0.019	20.426	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	109	ASN	0	-0.031	-0.005	16.526	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	110	SER	0	0.016	0.007	15.747	-0.049	-0.049	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.024	-0.011	9.302	0.026	0.026	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.024	-0.029	13.563	0.004	0.004	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.020	0.000	11.737	0.001	0.001	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.011	-0.047	14.059	0.059	0.059	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.777	-0.897	15.364	-0.161	-0.161	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.953	-0.975	17.627	-0.073	-0.073	0.000	0.000	0.000	0.000
117	A	117	PRO	0	0.015	0.002	14.864	0.004	0.004	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.954	0.964	17.348	0.050	0.050	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.915	0.996	19.934	0.121	0.121	0.000	0.000	0.000	0.000
120	A	120	TYR	0	0.017	-0.010	19.202	0.006	0.006	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.884	-0.934	17.879	-0.122	-0.122	0.000	0.000	0.000	0.000
122	A	122	PRO	0	-0.065	-0.039	20.470	0.001	0.001	0.000	0.000	0.000	0.000
123	A	123	ILE	0	0.013	-0.008	21.960	0.007	0.007	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.947	0.993	14.917	0.178	0.178	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.869	0.952	19.936	0.070	0.070	0.000	0.000	0.000	0.000
126	A	126	PHE	0	-0.064	-0.046	22.600	0.011	0.011	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.013	0.008	19.980	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	LEU	0	-0.033	0.009	17.657	-0.024	-0.024	0.000	0.000	0.000	0.000
129	A	129	ASP	-1	-0.868	-0.940	12.459	-0.384	-0.384	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.041	-0.015	13.721	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	131	MET	0	0.018	0.007	5.524	0.046	0.046	0.000	0.000	0.000	0.000
132	A	132	PRO	0	-0.062	-0.031	10.098	0.034	0.034	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.079	0.039	11.010	-0.074	-0.074	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.891	-0.948	12.008	-0.140	-0.140	0.000	0.000	0.000	0.000
135	A	135	LYS	1	0.864	0.931	7.284	0.147	0.147	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.113	0.046	7.476	-0.051	-0.051	0.000	0.000	0.000	0.000
137	A	137	ILE	0	-0.003	-0.005	8.257	-0.080	-0.080	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.935	0.961	7.933	-0.079	-0.079	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.924	-0.942	2.320	2.494	-2.816	14.819	-5.794	-3.715	-0.038
140	A	140	VAL	0	-0.030	-0.009	5.020	-0.237	-0.220	0.000	-0.002	-0.014	0.000
141	A	141	GLU	-1	-1.005	-0.985	7.704	0.072	0.072	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.038	-0.037	4.303	0.154	0.230	0.000	-0.009	-0.067	0.000
143	A	143	MET	0	-0.076	-0.027	8.289	-0.156	-0.156	0.000	0.000	0.000	0.000
144	A	144	NME	0	0.011	0.016	6.235	0.112	0.112	0.000	0.000	0.000	0.000

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