FMO DATABASE

FMODB ID: YVGY2

Calculation Name: 1Y6X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y6X

Chain ID: A

ChEMBL ID:

UniProt ID: P9WMM9

Base Structure: X-ray

Registration Date: 2023-09-23

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-545320.443046
FMO2-HF: Nuclear repulsion	511992.984544
FMO2-HF: Total energy	-33327.458501
FMO2-MP2: Total energy	-33426.244873

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:7:VAL)

Summations of interaction energy for fragment #1(A:7:VAL)

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.
-8.101	-0.645	4.643	-4.28	-7.821	-0.015

Interaction energy analysis for fragmet #1(A:7:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.011

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

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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	9	THR	0	0.009	0.006	2.983	-3.118	-0.105	0.178	-1.417	-1.774	0.002
4	A	10	PHE	0	0.056	0.016	2.628	-0.989	-0.219	1.410	-0.656	-1.525	-0.009
5	A	11	GLU	-1	-0.891	-0.968	4.768	-0.095	0.013	-0.001	-0.007	-0.100	0.000
6	A	12	ASP	-1	-0.811	-0.873	2.077	1.077	2.286	2.254	-1.479	-1.984	-0.005
7	A	13	LEU	0	0.034	0.023	2.635	-1.846	0.006	0.786	-0.628	-2.010	-0.003
8	A	14	PHE	0	0.023	0.016	3.968	0.093	0.247	0.014	-0.026	-0.142	0.000
9	A	15	ALA	0	-0.030	-0.022	6.748	0.071	0.071	0.000	0.000	0.000	0.000
10	A	16	GLU	-1	-0.963	-0.972	3.936	-0.882	-0.532	0.002	-0.067	-0.286	0.000
11	A	17	LEU	0	-0.001	-0.008	6.928	0.067	0.067	0.000	0.000	0.000	0.000
12	A	18	GLY	0	0.023	0.010	9.141	0.044	0.044	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.959	-0.989	10.061	0.244	0.244	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.917	0.963	8.310	-0.066	-0.066	0.000	0.000	0.000	0.000
15	A	21	ALA	0	-0.004	0.003	12.403	0.004	0.004	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.886	0.947	13.221	-0.106	-0.106	0.000	0.000	0.000	0.000
17	A	23	THR	0	-0.032	-0.022	14.109	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.772	0.888	16.116	0.062	0.062	0.000	0.000	0.000	0.000
19	A	25	PRO	0	0.006	0.013	13.549	0.004	0.004	0.000	0.000	0.000	0.000
20	A	26	ALA	0	-0.008	-0.035	16.728	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.935	-0.966	12.919	-0.170	-0.170	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.010	0.015	12.518	-0.071	-0.071	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.071	0.027	11.982	0.026	0.026	0.000	0.000	0.000	0.000
24	A	30	THR	0	0.032	0.007	10.388	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	31	VAL	0	-0.023	0.004	13.209	0.024	0.024	0.000	0.000	0.000	0.000
26	A	32	ALA	0	0.041	0.024	16.369	0.012	0.012	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.005	-0.001	15.447	0.011	0.011	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.066	-0.036	14.635	0.010	0.010	0.000	0.000	0.000	0.000
29	A	35	ASP	-1	-0.832	-0.902	18.175	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	36	GLY	0	-0.033	-0.004	20.597	0.012	0.012	0.000	0.000	0.000	0.000
31	A	37	GLY	0	-0.016	0.002	21.697	0.005	0.005	0.000	0.000	0.000	0.000
32	A	38	VAL	0	0.033	-0.004	21.161	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	39	HIS	0	-0.038	-0.023	21.922	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.027	0.006	21.717	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	41	LEU	0	0.043	0.027	16.367	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	42	GLY	0	-0.004	0.002	18.558	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.925	0.957	20.750	0.159	0.159	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.932	0.978	16.216	0.338	0.338	0.000	0.000	0.000	0.000
39	A	45	LEU	0	0.011	0.016	14.831	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	46	LEU	0	-0.056	-0.028	17.346	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.896	-0.956	19.406	-0.291	-0.291	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.836	-0.930	14.352	-0.483	-0.483	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.056	-0.016	17.140	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	50	GLY	0	-0.051	-0.024	18.320	0.009	0.009	0.000	0.000	0.000	0.000
45	A	51	GLU	-1	-0.869	-0.934	17.757	-0.291	-0.291	0.000	0.000	0.000	0.000
46	A	52	VAL	0	-0.019	-0.015	14.769	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	53	TRP	0	-0.167	-0.076	17.573	0.018	0.018	0.000	0.000	0.000	0.000
48	A	54	LEU	0	0.026	0.000	21.033	0.017	0.017	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.049	0.019	18.075	0.014	0.014	0.000	0.000	0.000	0.000
50	A	56	ALA	0	-0.075	-0.039	19.146	0.006	0.006	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.959	-0.970	20.416	-0.180	-0.180	0.000	0.000	0.000	0.000
52	A	58	HIS	0	-0.078	-0.042	23.360	0.013	0.013	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.941	-0.944	20.217	-0.232	-0.232	0.000	0.000	0.000	0.000
54	A	60	SER	0	-0.038	-0.015	18.736	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	61	ASN	0	0.024	-0.015	16.125	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.984	-0.987	13.497	-0.574	-0.574	0.000	0.000	0.000	0.000
57	A	63	ALA	0	0.071	0.042	13.809	-0.070	-0.070	0.000	0.000	0.000	0.000
58	A	64	LEU	0	0.029	0.017	15.069	-0.038	-0.038	0.000	0.000	0.000	0.000
59	A	65	ALA	0	-0.064	-0.040	10.523	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.917	-0.950	10.536	-0.997	-0.997	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.798	-0.892	11.456	-0.575	-0.575	0.000	0.000	0.000	0.000
62	A	68	ILE	0	-0.043	-0.026	9.654	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	69	SER	0	-0.108	-0.065	6.912	-0.111	-0.111	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.069	0.029	8.067	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	71	LEU	0	0.032	0.021	10.641	0.051	0.051	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.071	-0.037	6.867	0.058	0.058	0.000	0.000	0.000	0.000
67	A	73	TYR	0	0.020	0.001	7.013	0.080	0.080	0.000	0.000	0.000	0.000
68	A	74	TRP	0	0.046	0.004	8.640	0.161	0.161	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.048	-0.028	11.007	0.113	0.113	0.000	0.000	0.000	0.000
70	A	76	GLN	0	-0.012	-0.016	5.520	0.126	0.126	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.015	0.014	10.682	0.102	0.102	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.013	-0.001	12.865	0.074	0.074	0.000	0.000	0.000	0.000
73	A	79	MET	0	-0.073	-0.030	12.543	0.023	0.023	0.000	0.000	0.000	0.000
74	A	80	ILE	0	0.014	0.013	11.163	0.050	0.050	0.000	0.000	0.000	0.000
75	A	81	SER	0	-0.053	-0.014	15.457	0.038	0.038	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.885	0.927	18.349	0.164	0.164	0.000	0.000	0.000	0.000
77	A	83	GLY	0	-0.016	0.008	18.609	0.016	0.016	0.000	0.000	0.000	0.000
78	A	84	LEU	0	-0.060	-0.020	16.495	0.016	0.016	0.000	0.000	0.000	0.000
79	A	85	SER	0	0.000	-0.003	14.710	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	86	LEU	0	0.050	0.009	8.670	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.876	-0.933	12.829	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.915	-0.965	15.969	-0.101	-0.101	0.000	0.000	0.000	0.000
83	A	89	VAL	0	-0.025	-0.018	13.985	0.003	0.003	0.000	0.000	0.000	0.000
84	A	90	TYR	0	0.037	-0.003	9.074	0.007	0.007	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.893	0.957	15.693	0.084	0.084	0.000	0.000	0.000	0.000
86	A	92	LYS	1	0.871	0.941	18.754	0.140	0.140	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.015	0.019	14.330	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:VAL)