FMO DATABASE

FMODB ID: GNG11

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1802989.99724
FMO2-HF: Nuclear repulsion	1733178.022691
FMO2-HF: Total energy	-69811.974549
FMO2-MP2: Total energy	-70010.872401

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.
-3.879	0.076	4.377	-4.35	-3.984	-0.029

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 : 0.052 / 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	36	SER	0	0.012	-0.004	3.873	0.280	1.392	-0.012	-0.611	-0.489	0.002
4	A	37	ARG	1	0.777	0.856	6.155	-0.204	-0.204	0.000	0.000	0.000	0.000
5	A	38	ASP	-1	-0.816	-0.900	9.368	-0.318	-0.318	0.000	0.000	0.000	0.000
6	A	39	ALA	0	-0.025	-0.020	11.353	0.022	0.022	0.000	0.000	0.000	0.000
7	A	40	LEU	0	0.030	0.028	7.492	0.063	0.063	0.000	0.000	0.000	0.000
8	A	41	SER	0	-0.057	-0.047	11.330	-0.035	-0.035	0.000	0.000	0.000	0.000
9	A	42	LEU	0	0.044	0.007	13.228	0.003	0.003	0.000	0.000	0.000	0.000
10	A	43	GLU	-1	-0.827	-0.908	14.439	0.337	0.337	0.000	0.000	0.000	0.000
11	A	44	GLU	-1	-0.792	-0.850	9.113	0.568	0.568	0.000	0.000	0.000	0.000
12	A	45	ILE	0	0.002	0.005	10.786	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	46	LEU	0	0.002	0.009	12.736	-0.021	-0.021	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.800	0.886	10.841	-0.468	-0.468	0.000	0.000	0.000	0.000
15	A	48	LEU	0	-0.060	-0.027	6.629	0.024	0.024	0.000	0.000	0.000	0.000
16	A	49	TYR	0	-0.084	-0.065	10.780	-0.056	-0.056	0.000	0.000	0.000	0.000
17	A	50	ASN	0	-0.085	-0.032	14.357	0.005	0.005	0.000	0.000	0.000	0.000
18	A	51	GLN	0	0.018	0.020	16.198	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	52	PRO	0	0.020	0.020	18.431	0.008	0.008	0.000	0.000	0.000	0.000
20	A	53	ILE	0	-0.017	-0.002	18.509	-0.015	-0.015	0.000	0.000	0.000	0.000
21	A	54	ASN	0	0.060	0.024	20.885	0.007	0.007	0.000	0.000	0.000	0.000
22	A	55	GLU	-1	-0.723	-0.855	23.786	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	56	GLU	-1	-0.802	-0.861	25.158	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	57	GLN	0	0.033	-0.002	18.881	0.014	0.014	0.000	0.000	0.000	0.000
25	A	58	ALA	0	0.041	0.033	22.752	0.006	0.006	0.000	0.000	0.000	0.000
26	A	59	TRP	0	0.037	0.013	24.703	0.006	0.006	0.000	0.000	0.000	0.000
27	A	60	ALA	0	-0.017	-0.012	23.280	0.002	0.002	0.000	0.000	0.000	0.000
28	A	61	VAL	0	0.020	0.004	20.349	0.002	0.002	0.000	0.000	0.000	0.000
29	A	62	CYS	0	-0.021	-0.004	23.246	0.008	0.008	0.000	0.000	0.000	0.000
30	A	63	TYR	0	0.013	0.000	26.799	0.005	0.005	0.000	0.000	0.000	0.000
31	A	64	GLN	0	0.007	-0.022	23.390	0.006	0.006	0.000	0.000	0.000	0.000
32	A	65	CYS	0	-0.024	0.009	23.641	0.006	0.006	0.000	0.000	0.000	0.000
33	A	66	CYS	0	-0.020	-0.008	25.062	0.006	0.006	0.000	0.000	0.000	0.000
34	A	67	GLY	0	0.000	-0.018	28.355	0.001	0.001	0.000	0.000	0.000	0.000
35	A	68	SER	0	-0.015	-0.033	24.122	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	69	LEU	0	-0.016	-0.002	26.614	0.003	0.003	0.000	0.000	0.000	0.000
37	A	70	ARG	1	0.939	0.974	28.797	0.003	0.003	0.000	0.000	0.000	0.000
38	A	71	ALA	0	-0.048	-0.024	29.348	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	72	ALA	0	0.032	0.015	28.227	0.000	0.000	0.000	0.000	0.000	0.000
40	A	73	ALA	0	0.038	0.023	30.325	0.001	0.001	0.000	0.000	0.000	0.000
41	A	74	ARG	1	0.882	0.934	33.615	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	75	ARG	1	0.906	0.962	31.977	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	76	ARG	1	0.881	0.930	33.984	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	77	GLN	0	0.043	0.031	28.002	0.007	0.007	0.000	0.000	0.000	0.000
45	A	78	PRO	0	-0.021	-0.005	30.324	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	79	ARG	1	0.813	0.897	30.219	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	80	HIS	0	-0.033	-0.026	23.997	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	81	ARG	1	0.816	0.867	28.350	-0.068	-0.068	0.000	0.000	0.000	0.000
49	A	82	VAL	0	-0.002	0.005	23.102	0.009	0.009	0.000	0.000	0.000	0.000
50	A	83	ARG	1	0.921	0.956	23.584	-0.111	-0.111	0.000	0.000	0.000	0.000
51	A	84	SER	0	0.053	0.023	18.879	0.000	0.000	0.000	0.000	0.000	0.000
52	A	85	ALA	0	0.082	0.033	18.020	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	86	ALA	0	0.037	0.024	15.524	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	87	GLN	0	-0.035	-0.024	16.282	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	88	ILE	0	0.009	0.016	18.911	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	89	ARG	1	0.948	0.984	15.147	-0.157	-0.157	0.000	0.000	0.000	0.000
57	A	90	VAL	0	0.043	0.016	15.241	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	91	TRP	0	-0.026	-0.018	14.453	0.008	0.008	0.000	0.000	0.000	0.000
59	A	92	ARG	1	0.878	0.931	10.903	0.456	0.456	0.000	0.000	0.000	0.000
60	A	93	ASP	-1	-0.871	-0.938	15.737	-0.094	-0.094	0.000	0.000	0.000	0.000
61	A	94	GLY	0	0.027	0.005	18.610	0.006	0.006	0.000	0.000	0.000	0.000
62	A	95	ALA	0	-0.032	-0.003	20.143	0.017	0.017	0.000	0.000	0.000	0.000
63	A	96	VAL	0	0.037	0.000	19.335	0.000	0.000	0.000	0.000	0.000	0.000
64	A	97	THR	0	-0.045	-0.010	19.955	0.004	0.004	0.000	0.000	0.000	0.000
65	A	98	LEU	0	0.032	0.030	20.185	0.011	0.011	0.000	0.000	0.000	0.000
66	A	99	ALA	0	-0.011	-0.008	18.471	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	100	PRO	0	0.022	0.002	20.590	0.002	0.002	0.000	0.000	0.000	0.000
68	A	101	ALA	0	-0.021	0.006	22.435	0.021	0.021	0.000	0.000	0.000	0.000
69	A	114	LYS	1	1.006	0.999	41.459	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	115	LEU	0	0.059	0.038	35.775	0.000	0.000	0.000	0.000	0.000	0.000
71	A	116	GLY	0	-0.045	-0.027	38.882	0.001	0.001	0.000	0.000	0.000	0.000
72	A	117	TYR	0	0.068	0.026	40.854	0.000	0.000	0.000	0.000	0.000	0.000
73	A	118	SER	0	-0.038	-0.027	36.855	0.001	0.001	0.000	0.000	0.000	0.000
74	A	119	GLN	0	0.056	0.027	36.298	0.001	0.001	0.000	0.000	0.000	0.000
75	A	120	CYS	0	-0.028	0.001	32.908	0.006	0.006	0.000	0.000	0.000	0.000
76	A	121	MET	0	-0.012	0.016	35.338	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	122	GLU	-1	-0.802	-0.910	33.902	0.027	0.027	0.000	0.000	0.000	0.000
78	A	123	THR	0	0.049	0.017	33.527	0.002	0.002	0.000	0.000	0.000	0.000
79	A	124	GLU	-1	-0.689	-0.805	33.692	0.056	0.056	0.000	0.000	0.000	0.000
80	A	125	VAL	0	-0.061	-0.021	28.345	0.005	0.005	0.000	0.000	0.000	0.000
81	A	126	ILE	0	-0.022	-0.008	29.266	0.002	0.002	0.000	0.000	0.000	0.000
82	A	127	GLU	-1	-0.834	-0.879	30.698	0.053	0.053	0.000	0.000	0.000	0.000
83	A	128	SER	0	-0.044	-0.042	27.784	0.004	0.004	0.000	0.000	0.000	0.000
84	A	129	LEU	0	-0.041	-0.029	24.702	0.006	0.006	0.000	0.000	0.000	0.000
85	A	130	GLY	0	0.045	0.022	26.393	0.001	0.001	0.000	0.000	0.000	0.000
86	A	131	ILE	0	0.042	0.021	27.392	0.001	0.001	0.000	0.000	0.000	0.000
87	A	132	ILE	0	-0.064	-0.033	21.872	0.006	0.006	0.000	0.000	0.000	0.000
88	A	133	ILE	0	-0.021	-0.020	23.269	0.002	0.002	0.000	0.000	0.000	0.000
89	A	134	TYR	0	-0.013	-0.037	24.891	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	135	LYS	1	0.974	0.975	23.441	-0.092	-0.092	0.000	0.000	0.000	0.000
91	A	136	ALA	0	-0.023	-0.014	20.633	0.006	0.006	0.000	0.000	0.000	0.000
92	A	137	LEU	0	-0.048	-0.019	21.771	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	138	ASP	-1	-0.859	-0.925	24.596	0.057	0.057	0.000	0.000	0.000	0.000
94	A	139	TYR	0	-0.049	-0.029	15.910	0.019	0.019	0.000	0.000	0.000	0.000
95	A	140	GLY	0	0.013	0.003	21.619	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	141	LEU	0	-0.061	-0.009	22.581	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	142	LYS	1	0.804	0.879	26.394	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	143	GLU	-1	-0.907	-0.963	29.005	0.073	0.073	0.000	0.000	0.000	0.000
99	A	144	ASN	0	-0.085	-0.035	31.540	0.000	0.000	0.000	0.000	0.000	0.000
100	A	145	GLU	-1	-0.854	-0.908	29.368	0.029	0.029	0.000	0.000	0.000	0.000
101	A	146	GLU	-1	-0.810	-0.880	31.380	0.038	0.038	0.000	0.000	0.000	0.000
102	A	147	ARG	1	0.759	0.875	24.265	-0.015	-0.015	0.000	0.000	0.000	0.000
103	A	148	GLU	-1	-0.917	-0.949	30.900	0.000	0.000	0.000	0.000	0.000	0.000
104	A	149	LEU	0	-0.016	-0.015	28.988	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	150	SER	0	-0.038	-0.054	32.520	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	151	PRO	0	0.053	0.013	34.663	0.002	0.002	0.000	0.000	0.000	0.000
107	A	152	PRO	0	-0.054	-0.033	35.604	0.002	0.002	0.000	0.000	0.000	0.000
108	A	153	LEU	0	0.018	0.014	28.502	0.002	0.002	0.000	0.000	0.000	0.000
109	A	154	GLU	-1	-0.912	-0.945	32.968	0.018	0.018	0.000	0.000	0.000	0.000
110	A	155	GLN	0	0.019	-0.002	34.469	0.004	0.004	0.000	0.000	0.000	0.000
111	A	156	LEU	0	-0.056	-0.029	31.541	0.002	0.002	0.000	0.000	0.000	0.000
112	A	157	ILE	0	0.021	-0.008	29.077	0.003	0.003	0.000	0.000	0.000	0.000
113	A	158	ASP	-1	-0.807	-0.877	32.726	0.029	0.029	0.000	0.000	0.000	0.000
114	A	159	HIS	0	-0.010	-0.019	36.008	0.001	0.001	0.000	0.000	0.000	0.000
115	A	160	MET	0	-0.126	-0.066	29.166	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	161	ALA	0	-0.033	-0.022	32.288	0.004	0.004	0.000	0.000	0.000	0.000
117	A	162	ASN	0	-0.108	-0.073	33.914	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	163	THR	0	-0.015	-0.025	35.341	0.001	0.001	0.000	0.000	0.000	0.000
119	A	164	VAL	0	-0.055	-0.005	38.158	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	165	GLU	-1	-0.950	-0.966	40.913	0.023	0.023	0.000	0.000	0.000	0.000
121	A	186	GLU	-1	-0.774	-0.877	43.037	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	187	LYS	1	0.809	0.885	43.595	0.006	0.006	0.000	0.000	0.000	0.000
123	A	188	ARG	1	0.876	0.931	45.353	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	189	LYS	1	1.009	1.011	43.290	-0.015	-0.015	0.000	0.000	0.000	0.000
125	A	190	ILE	0	-0.032	0.003	38.567	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	191	SER	0	-0.014	-0.021	43.065	0.001	0.001	0.000	0.000	0.000	0.000
127	A	192	ALA	0	0.023	0.020	41.671	0.001	0.001	0.000	0.000	0.000	0.000
128	A	193	ILE	0	0.025	0.017	35.482	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	194	ARG	1	0.899	0.943	39.126	-0.013	-0.013	0.000	0.000	0.000	0.000
130	A	195	SER	0	-0.066	-0.045	36.943	0.001	0.001	0.000	0.000	0.000	0.000
131	A	196	TYR	0	0.091	0.015	30.740	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	197	ARG	1	0.928	0.964	33.632	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	198	ASP	-1	-0.802	-0.883	36.113	0.009	0.009	0.000	0.000	0.000	0.000
134	A	199	VAL	0	0.083	0.043	30.921	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	200	MET	0	-0.048	0.004	30.053	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	201	LYS	1	0.762	0.855	33.124	0.005	0.005	0.000	0.000	0.000	0.000
137	A	202	LEU	0	0.027	0.015	35.376	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	203	CYS	0	-0.012	0.000	30.758	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	204	ALA	0	-0.029	-0.008	32.770	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	205	ALA	0	0.007	0.009	34.561	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	206	HIS	1	0.801	0.903	30.271	0.025	0.025	0.000	0.000	0.000	0.000
142	A	207	LEU	0	-0.021	-0.006	31.302	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	208	PRO	0	-0.012	-0.011	35.402	0.002	0.002	0.000	0.000	0.000	0.000
144	A	209	THR	0	0.013	-0.009	37.117	0.002	0.002	0.000	0.000	0.000	0.000
145	A	210	GLU	-1	-0.816	-0.888	36.294	-0.015	-0.015	0.000	0.000	0.000	0.000
146	A	211	SER	0	-0.057	-0.051	35.724	0.001	0.001	0.000	0.000	0.000	0.000
147	A	212	ASP	-1	-0.805	-0.874	33.351	-0.043	-0.043	0.000	0.000	0.000	0.000
148	A	213	ALA	0	-0.006	0.000	31.303	-0.005	-0.005	0.000	0.000	0.000	0.000
149	A	214	PRO	0	-0.065	-0.032	29.542	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	215	ASN	0	0.038	0.013	27.871	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	216	HIS	0	-0.017	-0.009	26.997	-0.013	-0.013	0.000	0.000	0.000	0.000
152	A	217	TYR	0	0.008	-0.023	25.769	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	218	GLN	0	-0.037	-0.006	23.104	0.005	0.005	0.000	0.000	0.000	0.000
154	A	219	ALA	0	0.001	-0.010	22.142	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	220	VAL	0	0.009	0.005	21.631	-0.014	-0.014	0.000	0.000	0.000	0.000
156	A	221	CYS	0	-0.057	-0.015	19.541	0.001	0.001	0.000	0.000	0.000	0.000
157	A	222	ARG	1	0.914	0.959	17.768	0.150	0.150	0.000	0.000	0.000	0.000
158	A	223	ALA	0	-0.016	0.005	16.861	-0.031	-0.031	0.000	0.000	0.000	0.000
159	A	224	LEU	0	0.048	0.028	15.891	-0.021	-0.021	0.000	0.000	0.000	0.000
160	A	225	PHE	0	-0.020	0.010	11.174	-0.015	-0.015	0.000	0.000	0.000	0.000
161	A	226	ALA	0	-0.018	-0.021	12.206	-0.043	-0.043	0.000	0.000	0.000	0.000
162	A	227	GLU	-1	-0.807	-0.862	11.597	-0.212	-0.212	0.000	0.000	0.000	0.000
163	A	228	THR	0	0.010	-0.028	10.784	-0.029	-0.029	0.000	0.000	0.000	0.000
164	A	229	MET	0	-0.041	0.003	6.290	0.102	0.102	0.000	0.000	0.000	0.000
165	A	230	GLU	-1	-0.953	-0.965	6.717	-0.802	-0.802	0.000	0.000	0.000	0.000
166	A	231	LEU	0	0.016	0.006	6.395	-0.248	-0.248	0.000	0.000	0.000	0.000
167	A	232	HIS	0	0.013	0.002	4.028	0.310	0.740	0.009	-0.125	-0.314	0.000
168	A	233	THR	0	-0.123	-0.070	2.539	0.133	1.439	2.810	-2.119	-1.998	-0.012
169	A	234	PHE	0	-0.007	-0.012	2.550	-3.212	-2.405	1.571	-1.418	-0.960	-0.019
170	A	235	LEU	0	-0.002	0.019	4.589	0.210	0.231	-0.001	-0.013	-0.007	0.000
171	A	236	THR	0	-0.047	-0.011	3.923	-0.559	-0.280	0.000	-0.064	-0.216	0.000

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