FMO DATABASE

FMODB ID: N1JKQ

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	OptHSide
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	-1363315.701687
FMO2-HF: Nuclear repulsion	1306326.926176
FMO2-HF: Total energy	-56988.775511
FMO2-MP2: Total energy	-57155.517192

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.
-0.545	1.879	-0.013	-0.964	-1.448	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 : -0.010 / q_NPA : -0.033

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	0.004	0.006	3.806	-0.623	1.176	-0.021	-0.759	-1.020	0.003
4	A	5	PRO	0	0.020	0.002	6.548	0.322	0.322	0.000	0.000	0.000	0.000
5	A	6	ASP	-1	-0.848	-0.905	9.588	-0.293	-0.293	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.019	-0.012	9.457	-0.189	-0.189	0.000	0.000	0.000	0.000
7	A	8	THR	0	-0.024	-0.037	12.417	0.128	0.128	0.000	0.000	0.000	0.000
8	A	9	PHE	0	0.028	0.012	13.254	-0.057	-0.057	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.745	-0.819	16.683	-0.227	-0.227	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.007	-0.057	19.765	0.014	0.014	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.019	-0.007	21.520	0.018	0.018	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.018	0.011	16.651	0.020	0.020	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.025	0.014	18.799	0.023	0.023	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.006	-0.018	19.928	0.027	0.027	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.836	0.918	19.258	0.129	0.129	0.000	0.000	0.000	0.000
16	A	17	MET	0	0.016	0.032	14.502	0.028	0.028	0.000	0.000	0.000	0.000
17	A	18	HIS	0	0.016	0.037	18.855	0.013	0.013	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.045	-0.028	21.861	0.006	0.006	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.026	-0.014	22.986	0.016	0.016	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.052	-0.035	23.088	0.012	0.012	0.000	0.000	0.000	0.000
21	A	22	MET	0	0.025	0.022	16.041	0.023	0.023	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.927	0.981	19.109	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.958	0.991	17.375	-0.248	-0.248	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.090	0.033	13.565	0.015	0.015	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.009	0.012	15.069	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.918	-0.965	17.193	0.088	0.088	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.048	-0.028	12.186	0.002	0.002	0.000	0.000	0.000	0.000
28	A	29	THR	0	-0.003	-0.021	12.536	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.000	-0.006	13.585	-0.038	-0.038	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.022	0.007	15.353	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.842	0.917	10.071	-0.325	-0.325	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.026	-0.003	6.835	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	34	THR	0	0.011	0.027	12.012	0.074	0.074	0.000	0.000	0.000	0.000
34	A	35	VAL	0	-0.015	-0.018	14.129	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	36	ASN	0	0.000	-0.002	16.058	0.092	0.092	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.006	0.021	18.502	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.047	0.028	20.829	0.024	0.024	0.000	0.000	0.000	0.000
38	A	39	ILE	0	0.028	0.000	23.462	0.010	0.010	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.005	-0.006	26.182	0.013	0.013	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.035	0.020	21.108	0.007	0.007	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.031	0.007	24.149	0.011	0.011	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.010	0.019	26.126	0.011	0.011	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.878	0.941	26.682	0.128	0.128	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.021	0.002	23.476	0.011	0.011	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.040	-0.025	26.784	0.011	0.011	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.074	-0.046	30.051	0.009	0.009	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.016	-0.009	28.211	0.007	0.007	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.839	0.917	26.244	0.055	0.055	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.034	0.037	30.768	0.007	0.007	0.000	0.000	0.000	0.000
50	A	51	TYR	0	-0.060	-0.029	30.569	0.004	0.004	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.059	-0.018	30.062	0.005	0.005	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.799	0.879	30.946	0.024	0.024	0.000	0.000	0.000	0.000
53	A	54	LYS	1	1.037	1.009	34.304	0.014	0.014	0.000	0.000	0.000	0.000
54	A	55	ASN	0	-0.030	-0.001	36.741	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.054	0.011	33.553	0.000	0.000	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.908	-0.942	33.828	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	58	ALA	0	0.019	0.001	34.634	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.761	-0.878	30.124	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.033	-0.011	29.876	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.871	-0.953	29.828	-0.056	-0.056	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.029	-0.006	27.621	0.001	0.001	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.028	-0.021	24.496	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.879	0.933	25.344	0.063	0.063	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.960	-0.968	26.525	-0.031	-0.031	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.036	0.000	21.556	0.004	0.004	0.000	0.000	0.000	0.000
66	A	67	TYR	0	-0.054	-0.055	18.459	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.013	0.024	19.002	0.031	0.031	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.031	-0.022	21.896	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.005	-0.004	21.722	0.009	0.009	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.012	-0.005	24.781	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.003	0.013	27.111	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.006	-0.011	25.913	0.010	0.010	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.825	-0.915	29.417	-0.116	-0.116	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.866	-0.926	27.026	-0.155	-0.155	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.060	-0.028	24.302	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.021	0.008	26.901	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.012	-0.010	30.099	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.943	0.971	22.806	0.235	0.235	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.028	0.017	26.766	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.023	0.020	27.680	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.063	-0.034	28.212	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	83	ILE	0	-0.019	-0.012	23.034	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.874	-0.942	27.186	-0.138	-0.138	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.008	0.007	29.636	0.007	0.007	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.060	-0.034	27.998	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.006	-0.002	25.186	0.001	0.001	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.085	0.054	29.312	0.007	0.007	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.890	0.963	32.688	0.114	0.114	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.823	0.911	26.726	0.187	0.187	0.000	0.000	0.000	0.000
90	A	91	GLU	-1	-0.947	-0.974	32.126	-0.100	-0.100	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.073	-0.032	26.713	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.029	-0.034	30.159	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.028	0.004	23.903	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	ASP	-1	-0.844	-0.921	27.785	-0.139	-0.139	0.000	0.000	0.000	0.000
95	A	96	MET	0	0.071	0.018	27.619	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.759	-0.839	24.746	-0.157	-0.157	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.774	-0.833	23.273	-0.220	-0.220	0.000	0.000	0.000	0.000
98	A	99	ILE	0	0.012	0.005	22.975	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.009	0.011	24.307	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.036	-0.016	19.550	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.004	-0.004	19.282	-0.031	-0.031	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.042	-0.049	19.768	-0.027	-0.027	0.000	0.000	0.000	0.000
103	A	104	THR	0	-0.014	-0.029	21.078	0.007	0.007	0.000	0.000	0.000	0.000
104	A	105	ALA	0	0.003	0.018	16.225	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.045	-0.014	16.702	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	107	TYR	0	-0.091	-0.051	18.069	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	108	THR	0	-0.015	-0.029	17.010	0.022	0.022	0.000	0.000	0.000	0.000
108	A	109	ASN	0	-0.044	-0.008	12.239	-0.029	-0.029	0.000	0.000	0.000	0.000
109	A	110	SER	0	-0.026	0.001	13.017	-0.040	-0.040	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.004	0.010	7.112	0.012	0.012	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.017	-0.023	11.343	0.095	0.095	0.000	0.000	0.000	0.000
112	A	113	VAL	0	-0.013	0.001	10.229	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.002	-0.047	12.788	0.097	0.097	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.821	-0.912	14.806	-0.179	-0.179	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.907	-0.951	17.288	-0.196	-0.196	0.000	0.000	0.000	0.000
116	A	117	PRO	0	0.027	0.009	14.234	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.957	0.970	16.552	0.199	0.199	0.000	0.000	0.000	0.000
118	A	119	ARG	1	0.785	0.871	19.284	0.208	0.208	0.000	0.000	0.000	0.000
119	A	120	TYR	0	0.025	-0.025	17.899	0.008	0.008	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.865	-0.921	16.558	-0.472	-0.472	0.000	0.000	0.000	0.000
121	A	122	PRO	0	-0.057	-0.031	19.284	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.026	-0.003	20.079	0.019	0.019	0.000	0.000	0.000	0.000
123	A	124	ARG	1	0.856	0.930	12.087	0.700	0.700	0.000	0.000	0.000	0.000
124	A	125	ARG	1	0.808	0.924	17.355	0.242	0.242	0.000	0.000	0.000	0.000
125	A	126	PHE	0	-0.061	-0.049	19.813	0.026	0.026	0.000	0.000	0.000	0.000
126	A	127	GLY	0	0.017	0.011	16.410	0.019	0.019	0.000	0.000	0.000	0.000
127	A	128	LEU	0	-0.038	0.007	15.053	-0.054	-0.054	0.000	0.000	0.000	0.000
128	A	129	ASP	-1	-0.786	-0.893	9.943	-1.140	-1.140	0.000	0.000	0.000	0.000
129	A	130	THR	0	-0.045	-0.013	12.108	0.030	0.030	0.000	0.000	0.000	0.000
130	A	131	MET	0	0.015	0.012	5.008	-0.194	-0.194	0.000	0.000	0.000	0.000
131	A	132	PRO	0	-0.033	-0.021	9.797	0.119	0.119	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.048	0.022	10.801	-0.032	-0.032	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.857	-0.915	12.130	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.964	0.979	7.768	0.634	0.634	0.000	0.000	0.000	0.000
135	A	136	PHE	0	0.087	0.043	7.649	0.187	0.187	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.009	-0.009	8.711	0.181	0.181	0.000	0.000	0.000	0.000
137	A	138	LYS	1	0.842	0.900	9.678	0.017	0.017	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.952	-0.986	3.719	-0.381	0.244	0.008	-0.205	-0.428	-0.001
139	A	140	VAL	0	-0.036	-0.014	6.779	0.471	0.471	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-1.007	-0.983	9.283	0.320	0.320	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.016	-0.017	7.067	0.039	0.039	0.000	0.000	0.000	0.000
142	A	143	MET	0	-0.081	-0.029	8.534	0.104	0.104	0.000	0.000	0.000	0.000

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