FMO DATABASE

FMODB ID: GNG51

Calculation Name: 1YLX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YLX

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KZY7

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-790256.015749
FMO2-HF: Nuclear repulsion	748225.670572
FMO2-HF: Total energy	-42030.345178
FMO2-MP2: Total energy	-42150.017975

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-3.089	2.599	3.534	-2.479	-6.741	-0.007

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.014

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	3	PHE	0	-0.032	-0.022	2.527	-1.475	1.898	1.548	-1.536	-3.385	-0.004
4	A	4	ALA	0	0.062	0.035	5.562	0.290	0.290	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.006	-0.010	9.158	0.215	0.215	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.867	0.904	12.134	0.278	0.278	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.014	-0.011	13.014	0.014	0.014	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.005	0.006	12.375	0.051	0.051	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.069	0.040	9.484	0.047	0.047	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.057	-0.026	12.664	0.095	0.095	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.895	-0.959	16.126	-0.262	-0.262	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.888	-0.939	12.281	-0.790	-0.790	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.046	-0.023	12.412	0.076	0.076	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.004	0.004	17.320	0.053	0.053	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.928	-0.960	19.414	-0.289	-0.289	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.078	-0.045	18.277	0.025	0.025	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.032	-0.009	20.827	0.030	0.030	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.875	-0.937	23.048	-0.066	-0.066	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.012	-0.013	23.825	0.015	0.015	0.000	0.000	0.000	0.000
20	A	20	MET	0	-0.041	-0.003	22.860	0.023	0.023	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.021	-0.011	25.150	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.941	-0.965	28.217	-0.061	-0.061	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.062	-0.033	27.205	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.093	-0.073	25.267	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.022	0.003	30.047	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.067	-0.037	26.983	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.912	-0.959	31.062	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.011	0.009	30.741	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.009	-0.014	24.437	0.013	0.013	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.007	0.015	24.747	-0.015	-0.015	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.004	-0.006	18.417	0.018	0.018	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.038	-0.005	17.429	0.013	0.013	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.750	-0.843	15.666	-0.172	-0.172	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.819	-0.873	15.797	0.221	0.221	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.017	-0.013	14.047	0.005	0.005	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.038	0.020	12.856	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.880	-0.929	13.461	0.393	0.393	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.040	-0.024	11.002	0.098	0.098	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.015	0.009	4.443	-0.076	-0.016	-0.001	-0.003	-0.056	0.000
40	A	40	ARG	1	0.867	0.930	7.243	-0.689	-0.689	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.039	-0.056	9.090	-0.250	-0.250	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.004	0.013	10.729	0.192	0.192	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.013	0.008	11.841	-0.090	-0.090	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.014	-0.005	14.242	0.058	0.058	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.033	-0.030	17.115	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.039	-0.039	20.878	0.032	0.032	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.014	0.002	24.166	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.027	-0.015	27.200	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.816	0.897	30.830	-0.066	-0.066	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.928	-0.961	32.720	0.036	0.036	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.869	-0.937	34.481	0.027	0.027	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.908	-0.953	31.132	0.087	0.087	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.047	-0.017	28.541	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.030	0.007	25.264	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.009	0.002	20.701	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.021	0.000	20.140	0.029	0.029	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.033	-0.039	15.440	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.011	0.023	11.536	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.020	-0.001	9.061	-0.103	-0.103	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.029	-0.003	7.082	0.125	0.125	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.027	-0.007	2.534	-1.095	-0.085	0.897	-0.301	-1.606	0.000
62	A	62	LYS	1	0.893	0.964	5.421	-0.464	-0.464	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.040	-0.034	5.477	0.509	0.509	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.930	-0.979	7.324	-0.259	-0.259	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.862	0.941	9.859	1.183	1.183	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.037	-0.012	10.803	0.029	0.029	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.909	-0.944	8.305	-1.760	-1.760	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.013	-0.021	7.529	0.215	0.215	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.051	0.033	2.320	-1.169	-0.846	1.075	-0.476	-0.922	-0.003
70	A	70	LEU	0	0.010	0.012	4.370	1.175	1.411	-0.001	-0.018	-0.216	0.000
71	A	71	GLU	-1	-0.994	-0.996	4.240	1.960	2.466	0.017	-0.139	-0.384	0.000
72	A	72	LYS	1	0.846	0.898	5.334	-1.176	-0.996	-0.001	-0.006	-0.172	0.000
73	A	73	GLN	0	0.042	0.026	8.107	-0.283	-0.283	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.867	-0.930	10.886	0.806	0.806	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.063	0.035	13.324	0.030	0.030	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.067	-0.042	15.338	0.059	0.059	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.005	0.011	17.905	-0.035	-0.035	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.718	0.800	19.076	-0.211	-0.211	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.909	0.946	23.342	-0.138	-0.138	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.875	-0.935	27.173	0.133	0.133	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.042	-0.014	27.560	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.858	0.925	25.176	-0.169	-0.169	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.753	-0.856	18.683	0.329	0.329	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.801	0.899	21.962	-0.183	-0.183	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.908	0.942	13.440	-0.767	-0.767	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.005	-0.002	18.036	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.001	0.012	18.885	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	HIS	1	0.798	0.876	14.286	-0.401	-0.401	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.002	-0.014	15.903	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.064	0.031	18.072	0.027	0.027	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.074	0.035	19.566	0.015	0.015	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.824	-0.883	19.790	0.229	0.229	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.011	-0.005	19.836	0.010	0.010	0.000	0.000	0.000	0.000
94	A	94	MET	0	0.031	0.018	21.979	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.845	-0.909	24.801	0.060	0.060	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.811	-0.880	24.673	0.166	0.166	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.005	-0.007	24.730	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.008	0.009	27.449	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	HIS	0	-0.092	-0.036	29.831	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.072	-0.040	29.257	0.006	0.006	0.000	0.000	0.000	0.000

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