FMO DATABASE

FMODB ID: VRLM1

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	OptH
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	-1795912.909316
FMO2-HF: Nuclear repulsion	1726102.145379
FMO2-HF: Total energy	-69810.763937
FMO2-MP2: Total energy	-70009.734291

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.
-9.055	-4.246	4.546	-4.611	-4.743	-0.034

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 : 0.049 / q_NPA : 0.028

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	0.031	-0.035	3.798	0.494	1.498	-0.013	-0.459	-0.533	0.002
4	A	37	ARG	1	0.804	0.896	6.478	0.118	0.118	0.000	0.000	0.000	0.000
5	A	38	ASP	-1	-0.823	-0.914	9.290	-0.541	-0.541	0.000	0.000	0.000	0.000
6	A	39	ALA	0	-0.025	-0.025	11.263	0.047	0.047	0.000	0.000	0.000	0.000
7	A	40	LEU	0	0.034	0.032	7.214	0.035	0.035	0.000	0.000	0.000	0.000
8	A	41	SER	0	-0.032	-0.007	11.231	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	42	LEU	0	0.048	0.012	13.151	-0.017	-0.017	0.000	0.000	0.000	0.000
10	A	43	GLU	-1	-0.957	-0.987	14.447	0.291	0.291	0.000	0.000	0.000	0.000
11	A	44	GLU	-1	-0.804	-0.899	8.282	0.479	0.479	0.000	0.000	0.000	0.000
12	A	45	ILE	0	0.006	0.006	11.009	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	46	LEU	0	0.001	0.005	12.655	-0.031	-0.031	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.926	0.970	10.479	-0.473	-0.473	0.000	0.000	0.000	0.000
15	A	48	LEU	0	-0.073	-0.036	6.728	0.013	0.013	0.000	0.000	0.000	0.000
16	A	49	TYR	0	-0.081	-0.087	10.789	-0.047	-0.047	0.000	0.000	0.000	0.000
17	A	50	ASN	0	-0.068	-0.023	14.114	0.026	0.026	0.000	0.000	0.000	0.000
18	A	51	GLN	0	0.010	0.010	16.011	0.012	0.012	0.000	0.000	0.000	0.000
19	A	52	PRO	0	0.009	0.017	18.180	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	53	ILE	0	-0.010	0.009	18.453	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	54	ASN	0	0.015	0.001	20.656	0.025	0.025	0.000	0.000	0.000	0.000
22	A	55	GLU	-1	-0.757	-0.908	23.530	-0.057	-0.057	0.000	0.000	0.000	0.000
23	A	56	GLU	-1	-0.791	-0.858	24.909	-0.098	-0.098	0.000	0.000	0.000	0.000
24	A	57	GLN	0	0.047	0.013	18.738	0.020	0.020	0.000	0.000	0.000	0.000
25	A	58	ALA	0	0.024	0.025	22.714	0.006	0.006	0.000	0.000	0.000	0.000
26	A	59	TRP	0	0.048	0.012	24.820	0.009	0.009	0.000	0.000	0.000	0.000
27	A	60	ALA	0	-0.020	-0.013	23.150	0.005	0.005	0.000	0.000	0.000	0.000
28	A	61	VAL	0	0.025	0.013	20.400	0.003	0.003	0.000	0.000	0.000	0.000
29	A	62	CYS	0	-0.007	0.012	23.175	0.013	0.013	0.000	0.000	0.000	0.000
30	A	63	TYR	0	0.006	-0.004	26.676	0.010	0.010	0.000	0.000	0.000	0.000
31	A	64	GLN	0	-0.019	-0.032	23.010	0.015	0.015	0.000	0.000	0.000	0.000
32	A	65	CYS	0	-0.022	0.007	23.547	0.007	0.007	0.000	0.000	0.000	0.000
33	A	66	CYS	0	0.013	0.005	25.037	0.011	0.011	0.000	0.000	0.000	0.000
34	A	67	GLY	0	-0.006	-0.008	28.251	0.005	0.005	0.000	0.000	0.000	0.000
35	A	68	SER	0	-0.026	-0.033	23.989	0.001	0.001	0.000	0.000	0.000	0.000
36	A	69	LEU	0	-0.008	0.001	26.733	0.007	0.007	0.000	0.000	0.000	0.000
37	A	70	ARG	1	0.944	0.971	28.926	0.049	0.049	0.000	0.000	0.000	0.000
38	A	71	ALA	0	-0.054	-0.031	29.464	0.003	0.003	0.000	0.000	0.000	0.000
39	A	72	ALA	0	0.044	0.021	28.217	0.002	0.002	0.000	0.000	0.000	0.000
40	A	73	ALA	0	0.024	0.017	30.318	0.005	0.005	0.000	0.000	0.000	0.000
41	A	74	ARG	1	0.888	0.942	33.585	0.032	0.032	0.000	0.000	0.000	0.000
42	A	75	ARG	1	0.898	0.958	32.181	0.027	0.027	0.000	0.000	0.000	0.000
43	A	76	ARG	1	0.914	0.952	33.950	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	77	GLN	0	0.028	0.027	28.080	0.006	0.006	0.000	0.000	0.000	0.000
45	A	78	PRO	0	-0.026	-0.004	30.337	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	79	ARG	1	0.833	0.905	30.329	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	80	HIS	0	-0.033	-0.034	24.241	0.000	0.000	0.000	0.000	0.000	0.000
48	A	81	ARG	1	0.842	0.891	28.575	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	82	VAL	0	-0.005	0.003	23.124	0.009	0.009	0.000	0.000	0.000	0.000
50	A	83	ARG	1	0.927	0.950	23.697	-0.085	-0.085	0.000	0.000	0.000	0.000
51	A	84	SER	0	0.042	0.018	19.602	0.001	0.001	0.000	0.000	0.000	0.000
52	A	85	ALA	0	0.107	0.042	18.353	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	86	ALA	0	0.036	0.027	15.756	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	87	GLN	0	-0.002	0.001	16.383	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	88	ILE	0	-0.001	0.013	18.682	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	89	ARG	1	0.927	0.968	15.688	-0.065	-0.065	0.000	0.000	0.000	0.000
57	A	90	VAL	0	0.055	0.026	14.898	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	91	TRP	0	-0.038	-0.036	14.274	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	92	ARG	1	0.912	0.952	10.279	0.777	0.777	0.000	0.000	0.000	0.000
60	A	93	ASP	-1	-0.915	-0.961	15.330	-0.209	-0.209	0.000	0.000	0.000	0.000
61	A	94	GLY	0	0.028	0.003	18.140	0.024	0.024	0.000	0.000	0.000	0.000
62	A	95	ALA	0	-0.018	0.016	19.825	0.027	0.027	0.000	0.000	0.000	0.000
63	A	96	VAL	0	0.052	0.015	19.081	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	97	THR	0	-0.025	0.003	19.843	0.011	0.011	0.000	0.000	0.000	0.000
65	A	98	LEU	0	0.035	0.026	20.436	0.005	0.005	0.000	0.000	0.000	0.000
66	A	99	ALA	0	-0.046	-0.026	18.456	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	100	PRO	0	0.005	-0.011	20.559	0.004	0.004	0.000	0.000	0.000	0.000
68	A	101	ALA	0	0.011	0.024	22.299	0.019	0.019	0.000	0.000	0.000	0.000
69	A	114	LYS	1	1.014	0.996	42.119	0.001	0.001	0.000	0.000	0.000	0.000
70	A	115	LEU	0	0.023	0.008	36.030	0.002	0.002	0.000	0.000	0.000	0.000
71	A	116	GLY	0	-0.018	0.005	39.043	0.000	0.000	0.000	0.000	0.000	0.000
72	A	117	TYR	0	0.054	0.024	40.679	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	118	SER	0	-0.008	-0.017	36.497	0.000	0.000	0.000	0.000	0.000	0.000
74	A	119	GLN	0	0.039	0.015	36.611	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	120	CYS	0	-0.015	0.016	32.870	0.006	0.006	0.000	0.000	0.000	0.000
76	A	121	MET	0	0.009	0.015	35.438	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	122	GLU	-1	-0.877	-0.962	34.424	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	123	THR	0	0.036	0.014	34.066	0.000	0.000	0.000	0.000	0.000	0.000
79	A	124	GLU	-1	-0.715	-0.826	33.988	0.034	0.034	0.000	0.000	0.000	0.000
80	A	125	VAL	0	-0.063	-0.028	28.859	0.003	0.003	0.000	0.000	0.000	0.000
81	A	126	ILE	0	0.002	0.001	29.873	0.000	0.000	0.000	0.000	0.000	0.000
82	A	127	GLU	-1	-0.817	-0.868	30.893	0.025	0.025	0.000	0.000	0.000	0.000
83	A	128	SER	0	-0.085	-0.048	28.221	0.003	0.003	0.000	0.000	0.000	0.000
84	A	129	LEU	0	-0.023	-0.029	24.624	0.004	0.004	0.000	0.000	0.000	0.000
85	A	130	GLY	0	0.050	0.020	26.618	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	131	ILE	0	0.050	0.024	27.584	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	132	ILE	0	-0.070	-0.035	21.991	0.005	0.005	0.000	0.000	0.000	0.000
88	A	133	ILE	0	-0.021	-0.021	23.219	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	134	TYR	0	0.069	0.034	24.847	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	135	LYS	1	0.942	0.965	23.628	-0.061	-0.061	0.000	0.000	0.000	0.000
91	A	136	ALA	0	-0.022	-0.006	20.604	0.003	0.003	0.000	0.000	0.000	0.000
92	A	137	LEU	0	-0.053	-0.030	21.793	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	138	ASP	-1	-0.858	-0.933	24.479	0.012	0.012	0.000	0.000	0.000	0.000
94	A	139	TYR	0	-0.038	-0.014	16.908	0.015	0.015	0.000	0.000	0.000	0.000
95	A	140	GLY	0	-0.024	-0.017	21.919	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	141	LEU	0	-0.046	-0.003	22.634	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	142	LYS	1	0.888	0.925	26.291	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	143	GLU	-1	-0.904	-0.960	29.024	0.055	0.055	0.000	0.000	0.000	0.000
99	A	144	ASN	0	-0.084	-0.041	31.408	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	145	GLU	-1	-0.925	-0.947	28.868	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	146	GLU	-1	-0.876	-0.930	31.533	0.004	0.004	0.000	0.000	0.000	0.000
102	A	147	ARG	1	0.822	0.902	24.189	0.048	0.048	0.000	0.000	0.000	0.000
103	A	148	GLU	-1	-0.936	-0.963	30.760	-0.031	-0.031	0.000	0.000	0.000	0.000
104	A	149	LEU	0	-0.038	-0.015	28.963	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	150	SER	0	-0.015	-0.006	32.507	0.003	0.003	0.000	0.000	0.000	0.000
106	A	151	PRO	0	0.072	0.013	34.584	0.002	0.002	0.000	0.000	0.000	0.000
107	A	152	PRO	0	-0.044	-0.026	35.504	0.003	0.003	0.000	0.000	0.000	0.000
108	A	153	LEU	0	0.013	0.010	28.414	0.001	0.001	0.000	0.000	0.000	0.000
109	A	154	GLU	-1	-0.888	-0.940	32.839	-0.012	-0.012	0.000	0.000	0.000	0.000
110	A	155	GLN	0	-0.003	-0.005	34.433	0.007	0.007	0.000	0.000	0.000	0.000
111	A	156	LEU	0	-0.049	-0.030	30.855	0.003	0.003	0.000	0.000	0.000	0.000
112	A	157	ILE	0	0.005	-0.014	28.918	0.004	0.004	0.000	0.000	0.000	0.000
113	A	158	ASP	-1	-0.786	-0.860	32.742	0.003	0.003	0.000	0.000	0.000	0.000
114	A	159	HIS	0	-0.050	-0.033	36.083	0.003	0.003	0.000	0.000	0.000	0.000
115	A	160	MET	0	-0.137	-0.075	29.103	0.000	0.000	0.000	0.000	0.000	0.000
116	A	161	ALA	0	-0.017	-0.015	32.397	0.004	0.004	0.000	0.000	0.000	0.000
117	A	162	ASN	0	-0.123	-0.063	34.065	0.001	0.001	0.000	0.000	0.000	0.000
118	A	163	THR	0	-0.012	-0.038	35.336	0.003	0.003	0.000	0.000	0.000	0.000
119	A	164	VAL	0	-0.023	0.015	38.260	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	165	GLU	-1	-1.002	-1.004	40.983	0.012	0.012	0.000	0.000	0.000	0.000
121	A	186	GLU	-1	-0.787	-0.889	42.839	-0.029	-0.029	0.000	0.000	0.000	0.000
122	A	187	LYS	1	0.818	0.881	43.537	0.032	0.032	0.000	0.000	0.000	0.000
123	A	188	ARG	1	0.878	0.952	44.908	0.018	0.018	0.000	0.000	0.000	0.000
124	A	189	LYS	1	1.076	1.033	43.623	0.007	0.007	0.000	0.000	0.000	0.000
125	A	190	ILE	0	-0.015	0.019	38.557	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	191	SER	0	-0.031	-0.027	43.171	0.002	0.002	0.000	0.000	0.000	0.000
127	A	192	ALA	0	0.021	0.020	41.749	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	193	ILE	0	0.025	0.016	35.550	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	194	ARG	1	0.927	0.954	39.233	0.010	0.010	0.000	0.000	0.000	0.000
130	A	195	SER	0	-0.036	-0.014	37.203	0.001	0.001	0.000	0.000	0.000	0.000
131	A	196	TYR	0	0.109	0.036	31.358	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	197	ARG	1	0.914	0.955	33.853	0.030	0.030	0.000	0.000	0.000	0.000
133	A	198	ASP	-1	-0.841	-0.918	36.114	-0.023	-0.023	0.000	0.000	0.000	0.000
134	A	199	VAL	0	0.079	0.041	31.074	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	200	MET	0	-0.079	-0.032	30.315	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	201	LYS	1	0.895	0.939	33.154	0.035	0.035	0.000	0.000	0.000	0.000
137	A	202	LEU	0	0.062	0.040	35.139	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	203	CYS	0	-0.018	0.008	30.541	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	204	ALA	0	-0.028	-0.001	32.589	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	205	ALA	0	0.035	0.027	34.311	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	206	HIS	1	0.788	0.902	30.219	0.080	0.080	0.000	0.000	0.000	0.000
142	A	207	LEU	0	-0.028	-0.010	30.876	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	208	PRO	0	0.004	0.000	34.911	0.004	0.004	0.000	0.000	0.000	0.000
144	A	209	THR	0	0.017	0.020	36.813	0.006	0.006	0.000	0.000	0.000	0.000
145	A	210	GLU	-1	-0.889	-0.946	36.128	-0.055	-0.055	0.000	0.000	0.000	0.000
146	A	211	SER	0	-0.052	-0.039	35.487	0.000	0.000	0.000	0.000	0.000	0.000
147	A	212	ASP	-1	-0.871	-0.934	32.734	-0.097	-0.097	0.000	0.000	0.000	0.000
148	A	213	ALA	0	-0.051	-0.027	31.280	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	214	PRO	0	-0.079	-0.042	29.514	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	215	ASN	0	0.054	0.018	27.930	-0.005	-0.005	0.000	0.000	0.000	0.000
151	A	216	HIS	0	-0.034	-0.025	26.841	-0.020	-0.020	0.000	0.000	0.000	0.000
152	A	217	TYR	0	0.003	-0.040	25.641	-0.013	-0.013	0.000	0.000	0.000	0.000
153	A	218	GLN	0	-0.041	-0.014	22.804	0.001	0.001	0.000	0.000	0.000	0.000
154	A	219	ALA	0	-0.006	-0.012	21.889	-0.024	-0.024	0.000	0.000	0.000	0.000
155	A	220	VAL	0	-0.003	0.007	21.524	-0.025	-0.025	0.000	0.000	0.000	0.000
156	A	221	CYS	0	-0.033	-0.012	19.129	-0.012	-0.012	0.000	0.000	0.000	0.000
157	A	222	ARG	1	0.954	0.975	17.388	0.265	0.265	0.000	0.000	0.000	0.000
158	A	223	ALA	0	-0.033	-0.003	16.620	-0.054	-0.054	0.000	0.000	0.000	0.000
159	A	224	LEU	0	0.038	0.031	15.454	-0.039	-0.039	0.000	0.000	0.000	0.000
160	A	225	PHE	0	-0.027	0.006	10.669	-0.054	-0.054	0.000	0.000	0.000	0.000
161	A	226	ALA	0	-0.036	-0.030	11.732	-0.102	-0.102	0.000	0.000	0.000	0.000
162	A	227	GLU	-1	-0.803	-0.848	11.748	-0.469	-0.469	0.000	0.000	0.000	0.000
163	A	228	THR	0	0.004	-0.017	10.344	-0.081	-0.081	0.000	0.000	0.000	0.000
164	A	229	MET	0	-0.082	0.018	5.842	-0.043	-0.043	0.000	0.000	0.000	0.000
165	A	230	GLU	-1	-0.945	-0.968	6.351	-1.493	-1.493	0.000	0.000	0.000	0.000
166	A	231	LEU	0	0.038	0.006	6.926	-0.402	-0.402	0.000	0.000	0.000	0.000
167	A	232	HIS	0	-0.038	-0.028	4.035	0.292	0.851	0.017	-0.212	-0.364	-0.001
168	A	233	THR	0	-0.116	-0.065	2.327	-3.231	-1.136	3.525	-3.117	-2.502	-0.023
169	A	234	PHE	0	-0.023	-0.023	2.697	-4.789	-3.855	1.019	-0.792	-1.160	-0.012
170	A	235	LEU	0	0.003	0.030	4.902	0.693	0.728	-0.001	-0.005	-0.028	0.000
171	A	236	THR	0	-0.051	-0.011	4.192	-0.321	-0.139	-0.001	-0.026	-0.156	0.000

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