FMO DATABASE

FMODB ID: 14KRZ

Calculation Name: 2YLE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YLE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NZ56

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	171
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1797769.771363
FMO2-HF: Nuclear repulsion	1727958.168183
FMO2-HF: Total energy	-69811.60318
FMO2-MP2: Total energy	-70010.575009

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:34:GLY)

Summations of interaction energy for fragment #1(A:34: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.
-9.511	-4.731	4.87	-4.756	-4.893	-0.037

Interaction energy analysis for fragmet #1(A:34:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.026

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	36	SER	0	0.017	-0.009	3.798	0.231	1.273	-0.013	-0.480	-0.549	0.002
4	A	37	ARG	1	0.776	0.869	6.091	0.145	0.145	0.000	0.000	0.000	0.000
5	A	38	ASP	-1	-0.806	-0.898	9.291	-0.504	-0.504	0.000	0.000	0.000	0.000
6	A	39	ALA	0	-0.027	-0.026	11.269	0.041	0.041	0.000	0.000	0.000	0.000
7	A	40	LEU	0	0.022	0.022	7.239	0.030	0.030	0.000	0.000	0.000	0.000
8	A	41	SER	0	-0.056	-0.046	11.236	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	42	LEU	0	0.040	0.005	13.157	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	43	GLU	-1	-0.847	-0.916	14.515	0.233	0.233	0.000	0.000	0.000	0.000
11	A	44	GLU	-1	-0.775	-0.841	8.633	0.363	0.363	0.000	0.000	0.000	0.000
12	A	45	ILE	0	0.007	0.007	11.015	-0.036	-0.036	0.000	0.000	0.000	0.000
13	A	46	LEU	0	-0.004	0.003	12.660	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.825	0.902	10.910	-0.310	-0.310	0.000	0.000	0.000	0.000
15	A	48	LEU	0	-0.064	-0.031	6.699	0.000	0.000	0.000	0.000	0.000	0.000
16	A	49	TYR	0	-0.075	-0.060	10.793	-0.042	-0.042	0.000	0.000	0.000	0.000
17	A	50	ASN	0	-0.065	-0.028	14.116	0.028	0.028	0.000	0.000	0.000	0.000
18	A	51	GLN	0	0.002	0.007	16.015	0.020	0.020	0.000	0.000	0.000	0.000
19	A	52	PRO	0	0.006	0.017	18.184	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	53	ILE	0	-0.001	0.014	18.390	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	54	ASN	0	0.054	0.015	20.659	0.026	0.026	0.000	0.000	0.000	0.000
22	A	55	GLU	-1	-0.719	-0.860	23.532	-0.064	-0.064	0.000	0.000	0.000	0.000
23	A	56	GLU	-1	-0.806	-0.866	24.877	-0.100	-0.100	0.000	0.000	0.000	0.000
24	A	57	GLN	0	0.037	-0.003	18.530	0.020	0.020	0.000	0.000	0.000	0.000
25	A	58	ALA	0	0.036	0.030	22.716	0.005	0.005	0.000	0.000	0.000	0.000
26	A	59	TRP	0	0.059	0.023	24.823	0.010	0.010	0.000	0.000	0.000	0.000
27	A	60	ALA	0	-0.024	-0.012	23.149	0.006	0.006	0.000	0.000	0.000	0.000
28	A	61	VAL	0	0.018	0.007	20.369	0.004	0.004	0.000	0.000	0.000	0.000
29	A	62	CYS	0	-0.014	0.007	23.179	0.012	0.012	0.000	0.000	0.000	0.000
30	A	63	TYR	0	0.025	0.005	26.680	0.011	0.011	0.000	0.000	0.000	0.000
31	A	64	GLN	0	-0.019	-0.035	22.957	0.015	0.015	0.000	0.000	0.000	0.000
32	A	65	CYS	0	-0.006	0.014	23.601	0.009	0.009	0.000	0.000	0.000	0.000
33	A	66	CYS	0	-0.024	-0.014	25.041	0.012	0.012	0.000	0.000	0.000	0.000
34	A	67	GLY	0	0.004	-0.008	28.255	0.005	0.005	0.000	0.000	0.000	0.000
35	A	68	SER	0	-0.027	-0.039	23.982	0.002	0.002	0.000	0.000	0.000	0.000
36	A	69	LEU	0	-0.012	-0.004	26.776	0.007	0.007	0.000	0.000	0.000	0.000
37	A	70	ARG	1	0.946	0.978	28.931	0.050	0.050	0.000	0.000	0.000	0.000
38	A	71	ALA	0	-0.058	-0.032	29.450	0.003	0.003	0.000	0.000	0.000	0.000
39	A	72	ALA	0	0.035	0.017	28.222	0.003	0.003	0.000	0.000	0.000	0.000
40	A	73	ALA	0	0.030	0.020	30.314	0.005	0.005	0.000	0.000	0.000	0.000
41	A	74	ARG	1	0.900	0.947	33.581	0.030	0.030	0.000	0.000	0.000	0.000
42	A	75	ARG	1	0.892	0.956	32.146	0.025	0.025	0.000	0.000	0.000	0.000
43	A	76	ARG	1	0.915	0.954	33.947	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	77	GLN	0	0.038	0.032	27.917	0.006	0.006	0.000	0.000	0.000	0.000
45	A	78	PRO	0	-0.027	-0.008	30.412	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	79	ARG	1	0.799	0.898	30.325	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	80	HIS	0	-0.021	-0.025	24.140	0.002	0.002	0.000	0.000	0.000	0.000
48	A	81	ARG	1	0.822	0.867	28.570	-0.039	-0.039	0.000	0.000	0.000	0.000
49	A	82	VAL	0	0.001	0.004	23.130	0.008	0.008	0.000	0.000	0.000	0.000
50	A	83	ARG	1	0.942	0.963	23.741	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	84	SER	0	0.045	0.016	19.751	0.000	0.000	0.000	0.000	0.000	0.000
52	A	85	ALA	0	0.101	0.039	18.364	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	86	ALA	0	0.029	0.020	15.835	-0.016	-0.016	0.000	0.000	0.000	0.000
54	A	87	GLN	0	-0.013	-0.004	16.378	0.002	0.002	0.000	0.000	0.000	0.000
55	A	88	ILE	0	-0.004	0.013	18.715	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	89	ARG	1	0.938	0.974	15.382	-0.059	-0.059	0.000	0.000	0.000	0.000
57	A	90	VAL	0	0.049	0.019	14.884	0.000	0.000	0.000	0.000	0.000	0.000
58	A	91	TRP	0	-0.043	-0.039	14.277	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	92	ARG	1	0.895	0.940	10.531	0.679	0.679	0.000	0.000	0.000	0.000
60	A	93	ASP	-1	-0.903	-0.950	15.329	-0.194	-0.194	0.000	0.000	0.000	0.000
61	A	94	GLY	0	0.029	-0.001	18.150	0.022	0.022	0.000	0.000	0.000	0.000
62	A	95	ALA	0	-0.024	0.011	19.825	0.024	0.024	0.000	0.000	0.000	0.000
63	A	96	VAL	0	0.046	0.015	19.084	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	97	THR	0	-0.034	-0.001	19.851	0.012	0.012	0.000	0.000	0.000	0.000
65	A	98	LEU	0	0.032	0.028	20.441	0.003	0.003	0.000	0.000	0.000	0.000
66	A	99	ALA	0	-0.038	-0.017	18.449	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	100	PRO	0	0.035	0.004	20.555	0.004	0.004	0.000	0.000	0.000	0.000
68	A	101	ALA	0	-0.031	-0.003	22.279	0.027	0.027	0.000	0.000	0.000	0.000
69	A	114	LYS	1	0.995	0.985	42.133	0.004	0.004	0.000	0.000	0.000	0.000
70	A	115	LEU	0	0.032	0.014	36.144	0.002	0.002	0.000	0.000	0.000	0.000
71	A	116	GLY	0	-0.031	-0.014	39.039	0.000	0.000	0.000	0.000	0.000	0.000
72	A	117	TYR	0	0.055	0.019	40.674	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	118	SER	0	-0.009	-0.020	36.479	0.000	0.000	0.000	0.000	0.000	0.000
74	A	119	GLN	0	0.042	0.019	36.519	0.000	0.000	0.000	0.000	0.000	0.000
75	A	120	CYS	0	-0.014	0.018	32.875	0.004	0.004	0.000	0.000	0.000	0.000
76	A	121	MET	0	-0.007	0.011	35.433	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	122	GLU	-1	-0.826	-0.927	34.413	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	123	THR	0	0.037	0.012	34.072	0.000	0.000	0.000	0.000	0.000	0.000
79	A	124	GLU	-1	-0.717	-0.817	33.979	0.025	0.025	0.000	0.000	0.000	0.000
80	A	125	VAL	0	-0.057	-0.027	28.864	0.002	0.002	0.000	0.000	0.000	0.000
81	A	126	ILE	0	-0.006	0.002	29.879	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	127	GLU	-1	-0.829	-0.875	30.898	0.013	0.013	0.000	0.000	0.000	0.000
83	A	128	SER	0	-0.080	-0.047	28.245	0.002	0.002	0.000	0.000	0.000	0.000
84	A	129	LEU	0	-0.029	-0.032	24.646	0.003	0.003	0.000	0.000	0.000	0.000
85	A	130	GLY	0	0.044	0.018	26.623	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	131	ILE	0	0.045	0.022	27.627	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	132	ILE	0	-0.067	-0.032	22.130	0.003	0.003	0.000	0.000	0.000	0.000
88	A	133	ILE	0	-0.015	-0.017	23.126	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	134	TYR	0	0.008	-0.006	24.852	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	135	LYS	1	0.954	0.968	23.672	-0.037	-0.037	0.000	0.000	0.000	0.000
91	A	136	ALA	0	-0.022	-0.009	20.624	0.001	0.001	0.000	0.000	0.000	0.000
92	A	137	LEU	0	-0.054	-0.029	21.797	-0.014	-0.014	0.000	0.000	0.000	0.000
93	A	138	ASP	-1	-0.850	-0.923	24.483	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	139	TYR	0	-0.031	-0.009	16.514	0.021	0.021	0.000	0.000	0.000	0.000
95	A	140	GLY	0	-0.015	-0.014	21.922	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	141	LEU	0	-0.056	-0.006	22.639	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	142	LYS	1	0.801	0.877	26.296	0.025	0.025	0.000	0.000	0.000	0.000
98	A	143	GLU	-1	-0.902	-0.959	29.029	0.033	0.033	0.000	0.000	0.000	0.000
99	A	144	ASN	0	-0.078	-0.039	31.414	0.000	0.000	0.000	0.000	0.000	0.000
100	A	145	GLU	-1	-0.871	-0.908	29.251	-0.022	-0.022	0.000	0.000	0.000	0.000
101	A	146	GLU	-1	-0.809	-0.898	31.496	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	147	ARG	1	0.774	0.883	24.066	0.063	0.063	0.000	0.000	0.000	0.000
103	A	148	GLU	-1	-0.935	-0.962	30.763	-0.039	-0.039	0.000	0.000	0.000	0.000
104	A	149	LEU	0	-0.033	-0.014	28.829	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	150	SER	0	-0.033	-0.046	32.449	0.004	0.004	0.000	0.000	0.000	0.000
106	A	151	PRO	0	0.060	0.009	34.587	0.001	0.001	0.000	0.000	0.000	0.000
107	A	152	PRO	0	-0.050	-0.030	35.566	0.003	0.003	0.000	0.000	0.000	0.000
108	A	153	LEU	0	0.017	0.014	28.437	0.001	0.001	0.000	0.000	0.000	0.000
109	A	154	GLU	-1	-0.897	-0.944	32.843	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	155	GLN	0	0.002	-0.012	34.437	0.006	0.006	0.000	0.000	0.000	0.000
111	A	156	LEU	0	-0.051	-0.027	31.076	0.003	0.003	0.000	0.000	0.000	0.000
112	A	157	ILE	0	0.017	-0.009	29.031	0.004	0.004	0.000	0.000	0.000	0.000
113	A	158	ASP	-1	-0.791	-0.869	32.746	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	159	HIS	0	-0.034	-0.028	36.089	0.003	0.003	0.000	0.000	0.000	0.000
115	A	160	MET	0	-0.129	-0.071	29.082	0.000	0.000	0.000	0.000	0.000	0.000
116	A	161	ALA	0	-0.018	-0.012	32.452	0.004	0.004	0.000	0.000	0.000	0.000
117	A	162	ASN	0	-0.120	-0.065	34.071	0.001	0.001	0.000	0.000	0.000	0.000
118	A	163	THR	0	-0.016	-0.034	35.356	0.003	0.003	0.000	0.000	0.000	0.000
119	A	164	VAL	0	-0.046	0.005	38.266	0.000	0.000	0.000	0.000	0.000	0.000
120	A	165	GLU	-1	-0.944	-0.968	40.988	0.002	0.002	0.000	0.000	0.000	0.000
121	A	186	GLU	-1	-0.788	-0.891	42.783	-0.033	-0.033	0.000	0.000	0.000	0.000
122	A	187	LYS	1	0.828	0.892	43.541	0.034	0.034	0.000	0.000	0.000	0.000
123	A	188	ARG	1	0.880	0.950	44.912	0.022	0.022	0.000	0.000	0.000	0.000
124	A	189	LYS	1	1.017	1.003	43.630	0.012	0.012	0.000	0.000	0.000	0.000
125	A	190	ILE	0	-0.025	0.015	38.497	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	191	SER	0	-0.025	-0.025	43.176	0.002	0.002	0.000	0.000	0.000	0.000
127	A	192	ALA	0	0.018	0.018	41.772	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	193	ILE	0	0.026	0.014	35.562	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	194	ARG	1	0.929	0.962	39.238	0.013	0.013	0.000	0.000	0.000	0.000
130	A	195	SER	0	-0.056	-0.040	37.202	0.001	0.001	0.000	0.000	0.000	0.000
131	A	196	TYR	0	0.110	0.033	31.021	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	197	ARG	1	0.918	0.958	33.857	0.030	0.030	0.000	0.000	0.000	0.000
133	A	198	ASP	-1	-0.822	-0.899	36.118	-0.025	-0.025	0.000	0.000	0.000	0.000
134	A	199	VAL	0	0.082	0.044	31.071	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	200	MET	0	-0.078	-0.024	30.059	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	201	LYS	1	0.796	0.880	33.157	0.042	0.042	0.000	0.000	0.000	0.000
137	A	202	LEU	0	0.035	0.022	35.115	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	203	CYS	0	-0.015	0.001	30.517	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	204	ALA	0	-0.029	-0.002	32.592	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	205	ALA	0	0.019	0.015	34.313	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	206	HIS	1	0.795	0.900	29.983	0.084	0.084	0.000	0.000	0.000	0.000
142	A	207	LEU	0	-0.033	-0.012	30.838	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	208	PRO	0	0.005	-0.001	34.912	0.004	0.004	0.000	0.000	0.000	0.000
144	A	209	THR	0	0.012	0.018	36.815	0.006	0.006	0.000	0.000	0.000	0.000
145	A	210	GLU	-1	-0.779	-0.879	36.128	-0.055	-0.055	0.000	0.000	0.000	0.000
146	A	211	SER	0	-0.040	-0.032	35.488	0.000	0.000	0.000	0.000	0.000	0.000
147	A	212	ASP	-1	-0.864	-0.933	32.832	-0.091	-0.091	0.000	0.000	0.000	0.000
148	A	213	ALA	0	-0.035	-0.020	31.282	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	214	PRO	0	-0.072	-0.037	29.515	-0.005	-0.005	0.000	0.000	0.000	0.000
150	A	215	ASN	0	0.037	0.011	27.930	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	216	HIS	0	-0.015	-0.006	26.840	-0.019	-0.019	0.000	0.000	0.000	0.000
152	A	217	TYR	0	0.006	-0.033	25.642	-0.013	-0.013	0.000	0.000	0.000	0.000
153	A	218	GLN	0	-0.039	-0.013	22.803	0.000	0.000	0.000	0.000	0.000	0.000
154	A	219	ALA	0	-0.007	-0.013	21.889	-0.023	-0.023	0.000	0.000	0.000	0.000
155	A	220	VAL	0	0.014	0.012	21.523	-0.024	-0.024	0.000	0.000	0.000	0.000
156	A	221	CYS	0	-0.042	-0.013	19.150	-0.014	-0.014	0.000	0.000	0.000	0.000
157	A	222	ARG	1	0.944	0.974	17.388	0.242	0.242	0.000	0.000	0.000	0.000
158	A	223	ALA	0	-0.028	-0.001	16.618	-0.050	-0.050	0.000	0.000	0.000	0.000
159	A	224	LEU	0	0.033	0.029	15.473	-0.038	-0.038	0.000	0.000	0.000	0.000
160	A	225	PHE	0	-0.014	0.005	10.644	-0.053	-0.053	0.000	0.000	0.000	0.000
161	A	226	ALA	0	-0.028	-0.023	11.732	-0.098	-0.098	0.000	0.000	0.000	0.000
162	A	227	GLU	-1	-0.818	-0.867	11.745	-0.460	-0.460	0.000	0.000	0.000	0.000
163	A	228	THR	0	0.006	-0.020	10.415	-0.082	-0.082	0.000	0.000	0.000	0.000
164	A	229	MET	0	-0.031	0.008	5.661	-0.031	-0.031	0.000	0.000	0.000	0.000
165	A	230	GLU	-1	-0.945	-0.961	6.348	-1.453	-1.453	0.000	0.000	0.000	0.000
166	A	231	LEU	0	0.035	0.014	6.922	-0.380	-0.380	0.000	0.000	0.000	0.000
167	A	232	HIS	0	-0.019	-0.011	3.823	0.321	0.892	0.024	-0.223	-0.372	-0.001
168	A	233	THR	0	-0.129	-0.083	2.319	-2.960	-0.967	3.628	-3.130	-2.491	-0.023
169	A	234	PHE	0	-0.016	-0.019	2.535	-5.220	-4.260	1.233	-0.894	-1.299	-0.015
170	A	235	LEU	0	0.013	0.032	4.969	0.645	0.680	-0.001	-0.005	-0.028	0.000
171	A	236	THR	0	-0.047	-0.010	4.217	-0.392	-0.213	-0.001	-0.024	-0.154	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:GLY)