FMO DATABASE

FMODB ID: J37N9

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	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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1367210.314424
FMO2-HF: Nuclear repulsion	1310221.167573
FMO2-HF: Total energy	-56989.14685
FMO2-MP2: Total energy	-57155.83887

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.
-0.274	1.668	0.01	-0.658	-1.294	0.002

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 : -0.009 / q_NPA : -0.035

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	0.003	0.003	3.868	-0.147	1.272	-0.009	-0.562	-0.848	0.002
4	A	5	PRO	0	0.000	-0.001	6.460	0.323	0.323	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.833	-0.898	9.197	-0.187	-0.187	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.010	-0.010	9.195	-0.193	-0.193	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.029	-0.047	12.167	0.125	0.125	0.000	0.000	0.000	0.000
8	A	9	PHE	0	0.024	0.012	13.254	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.745	-0.828	16.727	-0.227	-0.227	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.015	-0.052	19.933	0.015	0.015	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.019	-0.002	21.443	0.020	0.020	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.022	0.011	16.433	0.019	0.019	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.024	0.020	18.328	0.021	0.021	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.021	-0.029	19.791	0.027	0.027	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.805	0.899	18.939	0.144	0.144	0.000	0.000	0.000	0.000
16	A	17	MET	0	0.024	0.032	14.219	0.024	0.024	0.000	0.000	0.000	0.000
17	A	18	HIS	0	0.008	0.041	18.485	0.019	0.019	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.040	-0.028	21.519	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.016	0.000	22.762	0.021	0.021	0.000	0.000	0.000	0.000
20	A	21	ASN	0	0.011	-0.001	22.778	0.012	0.012	0.000	0.000	0.000	0.000
21	A	22	MET	0	0.032	0.028	15.519	0.023	0.023	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.851	0.923	18.398	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.962	0.990	17.075	-0.296	-0.296	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.086	0.042	12.947	0.033	0.033	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.005	0.017	14.364	0.013	0.013	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.913	-0.957	16.467	0.162	0.162	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.052	-0.034	11.885	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.000	-0.016	12.168	0.027	0.027	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.029	0.007	13.216	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.030	0.004	15.472	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.793	0.883	10.041	-0.399	-0.399	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.005	0.006	6.586	0.009	0.009	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.012	0.025	11.773	0.050	0.050	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.017	-0.012	13.770	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.005	-0.010	15.485	0.086	0.086	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.004	0.030	18.174	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.039	0.021	20.599	0.018	0.018	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.024	-0.005	23.434	0.011	0.011	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.009	-0.002	26.145	0.011	0.011	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.043	0.026	20.818	0.008	0.008	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.042	0.020	24.186	0.010	0.010	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.021	0.018	25.937	0.009	0.009	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.864	0.931	26.435	0.126	0.126	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.031	-0.005	23.181	0.010	0.010	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.041	-0.017	26.433	0.011	0.011	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.051	-0.038	29.706	0.008	0.008	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.027	-0.011	28.083	0.006	0.006	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.824	0.903	26.039	0.042	0.042	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.028	0.024	30.621	0.007	0.007	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.052	-0.028	30.507	0.004	0.004	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.046	-0.010	29.934	0.005	0.005	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.809	0.882	30.869	0.011	0.011	0.000	0.000	0.000	0.000
53	A	54	LYS	1	1.029	1.014	33.879	0.009	0.009	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.033	0.000	36.196	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.060	0.010	33.100	0.001	0.001	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.920	-0.942	33.359	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.024	0.000	34.027	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.774	-0.870	29.630	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.009	-0.002	29.264	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.771	-0.879	29.314	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.020	-0.006	27.132	0.003	0.003	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.042	-0.030	24.044	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.785	0.866	24.914	0.033	0.033	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.978	-0.967	26.804	0.002	0.002	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.039	-0.019	21.348	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.046	-0.051	18.222	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.011	0.009	18.689	0.026	0.026	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.043	-0.018	21.629	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	70	VAL	0	0.011	0.006	21.603	0.010	0.010	0.000	0.000	0.000	0.000
70	A	71	PRO	0	-0.008	-0.016	24.612	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.003	0.005	26.922	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.012	0.003	25.977	0.009	0.009	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.840	-0.923	29.277	-0.105	-0.105	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.859	-0.909	26.567	-0.140	-0.140	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.043	-0.018	24.128	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.023	0.006	26.667	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.013	-0.006	29.907	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.906	0.948	22.789	0.205	0.205	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.044	0.029	26.624	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.031	0.019	27.525	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.045	-0.027	27.547	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.020	-0.008	22.530	0.000	0.000	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.875	-0.945	26.617	-0.134	-0.134	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.015	0.013	29.128	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.036	-0.026	27.559	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.002	0.008	24.557	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.084	0.045	28.696	0.006	0.006	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.864	0.930	32.043	0.112	0.112	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.787	0.887	27.082	0.176	0.176	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.917	-0.953	31.626	-0.104	-0.104	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.046	-0.016	26.262	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.025	-0.021	29.346	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.030	-0.002	24.012	0.002	0.002	0.000	0.000	0.000	0.000
94	A	95	ASP	-1	-0.805	-0.904	27.216	-0.135	-0.135	0.000	0.000	0.000	0.000
95	A	96	MET	0	0.028	0.016	27.770	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.771	-0.854	24.275	-0.151	-0.151	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.794	-0.865	23.190	-0.219	-0.219	0.000	0.000	0.000	0.000
98	A	99	ILE	0	0.006	0.005	23.003	-0.026	-0.026	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.002	0.008	24.160	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.032	-0.011	19.526	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.004	0.001	19.176	-0.027	-0.027	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.035	-0.040	19.503	-0.026	-0.026	0.000	0.000	0.000	0.000
103	A	104	THR	0	-0.003	-0.017	20.722	0.008	0.008	0.000	0.000	0.000	0.000
104	A	105	ALA	0	0.021	0.014	15.956	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.072	-0.024	16.337	-0.039	-0.039	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.080	-0.061	18.008	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.019	-0.024	16.752	0.022	0.022	0.000	0.000	0.000	0.000
108	A	109	ASN	0	-0.050	-0.009	12.091	0.003	0.003	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.011	0.001	12.673	-0.039	-0.039	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.016	-0.003	7.089	0.018	0.018	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.005	0.001	11.129	0.095	0.095	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.003	0.004	10.030	-0.055	-0.055	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.013	-0.048	12.641	0.102	0.102	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.809	-0.898	14.769	-0.198	-0.198	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.894	-0.943	17.285	-0.235	-0.235	0.000	0.000	0.000	0.000
116	A	117	PRO	0	0.045	0.015	14.113	0.006	0.006	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.934	0.964	16.488	0.232	0.232	0.000	0.000	0.000	0.000
118	A	119	ARG	1	0.809	0.877	19.450	0.219	0.219	0.000	0.000	0.000	0.000
119	A	120	TYR	0	0.014	-0.019	17.769	0.013	0.013	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.859	-0.905	15.901	-0.512	-0.512	0.000	0.000	0.000	0.000
121	A	122	PRO	0	-0.052	-0.032	18.684	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.016	0.008	19.584	0.017	0.017	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.830	0.906	11.676	0.697	0.697	0.000	0.000	0.000	0.000
124	A	125	ARG	1	0.824	0.923	17.073	0.245	0.245	0.000	0.000	0.000	0.000
125	A	126	PHE	0	-0.051	-0.036	19.562	0.023	0.023	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.025	0.016	16.343	0.021	0.021	0.000	0.000	0.000	0.000
127	A	128	LEU	0	-0.033	0.007	15.079	-0.041	-0.041	0.000	0.000	0.000	0.000
128	A	129	ASP	-1	-0.805	-0.910	9.419	-1.111	-1.111	0.000	0.000	0.000	0.000
129	A	130	THR	0	-0.038	-0.018	11.282	0.034	0.034	0.000	0.000	0.000	0.000
130	A	131	MET	0	0.000	0.012	5.070	-0.144	-0.144	0.000	0.000	0.000	0.000
131	A	132	PRO	0	-0.020	-0.015	10.005	0.135	0.135	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.041	0.018	10.759	-0.043	-0.043	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.848	-0.911	12.104	-0.085	-0.085	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.964	0.976	7.735	0.813	0.813	0.000	0.000	0.000	0.000
135	A	136	PHE	0	0.069	0.020	7.555	0.127	0.127	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.023	-0.016	8.618	0.192	0.192	0.000	0.000	0.000	0.000
137	A	138	LYS	1	0.844	0.910	9.425	0.140	0.140	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.943	-0.980	3.287	-1.100	-0.577	0.019	-0.096	-0.446	0.000
139	A	140	VAL	0	-0.030	-0.005	6.299	0.655	0.655	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-1.005	-0.997	9.088	0.268	0.268	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.030	-0.013	6.358	-0.068	-0.068	0.000	0.000	0.000	0.000
142	A	143	MET	0	-0.063	-0.026	8.967	0.195	0.195	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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