FMO DATABASE

FMODB ID: VRLQ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-789464.378834
FMO2-HF: Nuclear repulsion	747434.63095
FMO2-HF: Total energy	-42029.747883
FMO2-MP2: Total energy	-42149.428032

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.
-2.901	2.66	3.462	-2.636	-6.387	-0.008

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 : -0.017 / q_NPA : -0.016

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	-0.034	-0.028	2.700	-1.685	1.662	0.442	-1.432	-2.357	-0.004
4	A	4	ALA	0	0.084	0.049	5.841	0.338	0.338	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.015	0.000	9.334	0.176	0.176	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.869	0.892	12.334	0.337	0.337	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.047	-0.030	13.311	0.023	0.023	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.040	0.023	12.485	0.055	0.055	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.049	0.031	9.528	0.047	0.047	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.042	-0.027	12.579	0.094	0.094	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.909	-0.971	15.964	-0.267	-0.267	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.901	-0.926	11.947	-0.790	-0.790	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.080	-0.041	12.109	0.083	0.083	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.020	-0.005	17.023	0.057	0.057	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.909	-0.947	19.036	-0.302	-0.302	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.062	-0.036	18.532	0.028	0.028	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.039	-0.013	20.920	0.030	0.030	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.881	-0.941	23.148	-0.063	-0.063	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.001	-0.002	23.808	0.015	0.015	0.000	0.000	0.000	0.000
20	A	20	MET	0	-0.038	-0.007	22.551	0.024	0.024	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.025	-0.017	25.061	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.925	-0.948	28.054	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.058	-0.033	27.133	0.009	0.009	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.056	-0.044	24.857	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.015	0.010	29.853	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.083	-0.051	26.872	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.912	-0.954	30.939	-0.027	-0.027	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.002	-0.005	30.181	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.000	-0.008	24.162	0.014	0.014	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.016	0.017	24.624	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.009	-0.008	18.433	0.019	0.019	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.048	-0.009	17.195	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.718	-0.837	16.255	-0.225	-0.225	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.795	-0.875	15.560	0.174	0.174	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.076	-0.031	13.772	-0.016	-0.016	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.032	0.010	12.643	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.945	-0.969	13.357	0.247	0.247	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.045	-0.030	10.723	0.090	0.090	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.010	-0.005	4.910	0.059	0.059	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.961	0.991	7.083	-0.746	-0.746	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.028	-0.022	8.953	-0.189	-0.189	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.007	-0.003	10.287	0.164	0.164	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.029	0.020	12.207	-0.090	-0.090	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.019	-0.001	14.407	0.069	0.069	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.044	-0.031	17.023	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.013	-0.025	20.740	0.030	0.030	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.006	-0.008	23.950	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	48	ASN	0	0.015	0.014	26.935	0.015	0.015	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.902	0.946	30.476	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.943	-0.974	32.473	0.036	0.036	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.911	-0.952	34.941	0.024	0.024	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.958	-0.974	30.816	0.090	0.090	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.062	-0.032	28.028	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.024	-0.004	25.027	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.008	0.016	20.224	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.027	0.004	19.634	0.035	0.035	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.043	-0.038	15.454	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.012	0.017	11.209	0.029	0.029	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.043	-0.011	8.656	-0.127	-0.127	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.065	0.019	6.917	0.305	0.305	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.006	0.008	2.357	-1.037	-0.318	1.435	-0.338	-1.816	-0.001
62	A	62	LYS	1	0.943	0.980	5.004	-0.266	-0.244	-0.001	-0.003	-0.018	0.000
63	A	63	ASN	0	-0.043	-0.005	5.541	0.618	0.618	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.920	-0.990	7.021	-0.246	-0.246	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.868	0.938	9.712	1.230	1.230	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.055	-0.026	10.490	0.050	0.050	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.944	-0.966	8.224	-1.969	-1.969	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.016	-0.026	7.050	0.106	0.106	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.052	0.035	2.210	-0.921	-0.773	1.474	-0.571	-1.050	-0.002
70	A	70	LEU	0	0.017	0.016	4.319	1.158	1.433	-0.001	-0.023	-0.252	0.000
71	A	71	GLU	-1	-0.994	-1.000	3.782	2.239	3.080	0.114	-0.285	-0.670	-0.001
72	A	72	LYS	1	0.898	0.936	4.853	-1.378	-1.169	-0.001	0.016	-0.224	0.000
73	A	73	GLN	0	0.000	0.003	7.972	-0.321	-0.321	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.898	-0.992	10.859	0.779	0.779	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.047	0.027	13.056	0.032	0.032	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.063	-0.037	15.166	0.042	0.042	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.010	0.003	17.603	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.730	0.814	18.761	-0.186	-0.186	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.912	0.956	22.945	-0.148	-0.148	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.854	-0.921	26.695	0.128	0.128	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.049	-0.020	26.451	0.002	0.002	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.873	0.929	24.676	-0.171	-0.171	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.780	-0.874	18.455	0.321	0.321	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.852	0.937	21.491	-0.205	-0.205	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.928	0.974	13.636	-0.803	-0.803	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.028	-0.011	17.106	-0.036	-0.036	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.014	0.008	18.392	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	88	HIS	1	0.868	0.920	14.907	-0.461	-0.461	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.042	0.039	15.949	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.066	0.042	17.875	0.020	0.020	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.050	0.012	19.283	0.017	0.017	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.859	-0.929	20.010	0.282	0.282	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.009	0.003	19.733	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	MET	0	0.002	0.003	21.846	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.894	-0.950	24.572	0.081	0.081	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.888	-0.927	24.274	0.183	0.183	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.033	-0.034	24.278	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.024	-0.008	27.095	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	99	HIS	0	-0.072	-0.009	29.820	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.068	-0.037	29.828	0.009	0.009	0.000	0.000	0.000	0.000

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