FMO DATABASE

FMODB ID: 14KNZ

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:

Apendix: None

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	100
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-789662.189413
FMO2-HF: Nuclear repulsion	747632.012606
FMO2-HF: Total energy	-42030.176807
FMO2-MP2: Total energy	-42149.842558

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.
-2.98	2.75	3.814	-2.718	-6.825	-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 : -0.016 / q_NPA : -0.015

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	-0.041	-0.028	2.482	-1.592	1.924	1.024	-1.554	-2.986	-0.004
4	A	4	ALA	0	0.077	0.044	5.830	0.306	0.306	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.012	-0.001	9.271	0.188	0.188	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.878	0.901	12.259	0.281	0.281	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.029	-0.021	13.210	0.020	0.020	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.014	0.009	12.690	0.050	0.050	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.052	0.036	9.350	0.042	0.042	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.046	-0.031	12.557	0.090	0.090	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.899	-0.962	15.930	-0.248	-0.248	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.903	-0.934	12.057	-0.770	-0.770	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.065	-0.034	12.074	0.083	0.083	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.009	-0.006	17.049	0.052	0.052	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.915	-0.946	19.106	-0.278	-0.278	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.076	-0.043	18.680	0.025	0.025	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.040	-0.012	20.987	0.029	0.029	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.874	-0.940	23.189	-0.056	-0.056	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.002	-0.002	23.768	0.014	0.014	0.000	0.000	0.000	0.000
20	A	20	MET	0	-0.036	-0.006	22.609	0.023	0.023	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.025	-0.018	25.086	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.938	-0.956	28.063	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.057	-0.029	27.209	0.008	0.008	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.060	-0.044	25.037	0.010	0.010	0.000	0.000	0.000	0.000
25	A	25	GLY	0	-0.019	0.011	29.935	0.007	0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.076	-0.046	26.852	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.914	-0.954	30.986	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.014	0.010	30.310	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.002	-0.008	24.173	0.014	0.014	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.021	0.020	24.608	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.014	-0.012	18.410	0.019	0.019	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.056	-0.016	17.306	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.717	-0.820	15.967	-0.175	-0.175	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.804	-0.872	15.785	0.200	0.200	0.000	0.000	0.000	0.000
35	A	35	HIS	0	-0.067	-0.025	13.955	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.033	0.011	12.808	0.004	0.004	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.939	-0.970	13.465	0.307	0.307	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.036	-0.027	10.721	0.095	0.095	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.002	-0.002	4.474	-0.014	0.052	-0.001	-0.003	-0.061	0.000
40	A	40	ARG	1	0.952	0.992	7.223	-0.717	-0.717	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.028	-0.042	9.096	-0.219	-0.219	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.008	0.002	10.508	0.170	0.170	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.028	0.015	12.072	-0.093	-0.093	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.022	-0.001	14.369	0.063	0.063	0.000	0.000	0.000	0.000
45	A	45	TYR	0	-0.038	-0.024	17.021	-0.032	-0.032	0.000	0.000	0.000	0.000
46	A	46	THR	0	0.003	0.002	20.742	0.040	0.040	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.010	0.002	23.939	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	48	ASN	0	0.014	0.003	26.943	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.832	0.896	30.474	-0.072	-0.072	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.940	-0.972	32.490	0.041	0.041	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.905	-0.952	34.831	0.029	0.029	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.911	-0.935	30.989	0.092	0.092	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.048	-0.023	28.009	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.028	-0.010	25.037	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.035	-0.019	20.254	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.018	0.002	19.697	0.035	0.035	0.000	0.000	0.000	0.000
57	A	57	HIS	0	-0.050	-0.044	15.235	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	58	MET	0	0.014	0.017	11.289	0.025	0.025	0.000	0.000	0.000	0.000
59	A	59	PRO	0	-0.030	-0.004	8.669	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.047	0.009	6.900	0.274	0.274	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.007	-0.002	2.355	-1.098	-0.265	1.132	-0.305	-1.660	0.000
62	A	62	LYS	1	0.912	0.965	5.228	-0.363	-0.345	-0.001	-0.003	-0.014	0.000
63	A	63	ASN	0	-0.051	-0.028	5.497	0.522	0.522	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.920	-0.981	7.065	-0.258	-0.258	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.854	0.938	9.748	1.208	1.208	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.048	-0.020	10.605	0.036	0.036	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.906	-0.940	8.203	-1.814	-1.814	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.022	-0.026	7.390	0.155	0.155	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.056	0.034	2.200	-0.941	-0.886	1.576	-0.590	-1.041	-0.003
70	A	70	LEU	0	0.014	0.015	4.245	1.265	1.545	-0.001	-0.020	-0.259	0.000
71	A	71	GLU	-1	-1.006	-1.000	3.798	1.921	2.678	0.086	-0.252	-0.591	-0.001
72	A	72	LYS	1	0.850	0.896	4.878	-1.293	-1.088	-0.001	0.009	-0.213	0.000
73	A	73	GLN	0	0.015	0.014	7.975	-0.298	-0.298	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.861	-0.949	10.767	0.825	0.825	0.000	0.000	0.000	0.000
75	A	75	TRP	0	0.058	0.033	13.085	0.042	0.042	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.066	-0.042	15.095	0.043	0.043	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.010	0.002	17.613	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.731	0.805	18.844	-0.211	-0.211	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.891	0.939	22.940	-0.149	-0.149	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.869	-0.927	26.692	0.132	0.132	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.047	-0.019	26.610	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.871	0.931	24.810	-0.173	-0.173	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.772	-0.864	18.425	0.343	0.343	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.790	0.894	21.488	-0.203	-0.203	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.918	0.949	13.187	-0.829	-0.829	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.021	-0.004	17.164	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.010	0.007	18.451	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	88	HIS	1	0.828	0.903	14.424	-0.463	-0.463	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.015	-0.008	15.865	-0.022	-0.022	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.055	0.032	17.815	0.022	0.022	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.067	0.022	19.385	0.018	0.018	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.820	-0.873	19.637	0.273	0.273	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.003	-0.004	19.778	0.005	0.005	0.000	0.000	0.000	0.000
94	A	94	MET	0	0.017	0.008	21.905	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.877	-0.938	24.653	0.076	0.076	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.817	-0.888	24.281	0.188	0.188	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.017	-0.019	24.393	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	98	ILE	0	-0.004	0.001	27.118	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	99	HIS	0	-0.089	-0.015	29.834	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.060	-0.026	29.655	0.007	0.007	0.000	0.000	0.000	0.000

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