FMO DATABASE

FMODB ID: LJ589

Calculation Name: 2YWQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SIS0

Base Structure: X-ray

Registration Date: 2023-06-21

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-710353.060933
FMO2-HF: Nuclear repulsion	672571.41433
FMO2-HF: Total energy	-37781.646602
FMO2-MP2: Total energy	-37893.058623

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.
-38.472	-26.681	25.921	-12.893	-24.818	-0.094

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 : -0.048 / q_NPA : -0.018

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	3	ILE	0	0.000	-0.005	2.280	-0.533	1.966	1.376	-1.077	-2.797	0.003
4	A	4	TYR	0	-0.052	-0.032	4.646	-1.238	-1.083	0.000	-0.027	-0.128	0.000
5	A	5	LYS	1	0.914	0.949	8.031	-1.300	-1.300	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.048	0.035	7.989	0.378	0.378	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.044	-0.022	9.972	-0.217	-0.217	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.056	0.024	13.700	0.057	0.057	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.821	0.888	16.323	-0.552	-0.552	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.044	-0.040	19.874	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.007	0.001	15.902	-0.018	-0.018	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.882	-0.930	18.415	0.340	0.340	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.034	-0.019	11.794	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.073	0.031	14.911	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.785	-0.890	13.069	0.455	0.455	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.025	0.017	12.594	0.003	0.003	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.052	-0.013	11.643	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.836	0.899	8.608	-0.532	-0.532	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.805	-0.890	7.887	0.280	0.280	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.041	-0.041	8.400	-0.182	-0.182	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.009	-0.012	5.816	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.842	-0.915	3.760	0.411	0.723	0.003	-0.045	-0.270	0.000
23	A	23	LYS	1	0.740	0.852	3.734	-1.671	-1.241	0.008	-0.129	-0.309	-0.001
24	A	24	LYS	1	0.808	0.893	6.268	-0.222	-0.222	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.013	-0.004	2.286	-1.901	-1.618	4.249	-1.238	-3.295	0.008
26	A	26	ALA	0	0.055	0.026	2.248	-6.376	-4.391	3.841	-2.088	-3.738	-0.018
27	A	27	ARG	1	0.745	0.859	3.239	1.644	1.241	0.032	0.733	-0.362	0.000
28	A	28	LEU	0	-0.014	-0.005	2.435	0.350	1.047	1.117	-0.372	-1.443	0.002
29	A	29	ASP	-1	-0.738	-0.880	1.964	-26.576	-22.859	9.396	-6.334	-6.779	-0.082
30	A	30	ARG	1	0.796	0.889	4.913	2.698	2.750	-0.001	-0.007	-0.045	0.000
31	A	31	TYR	0	-0.041	-0.049	7.419	0.701	0.701	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.054	-0.041	5.884	0.829	0.829	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.829	-0.896	8.285	-1.535	-1.535	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.023	-0.011	8.632	0.260	0.260	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.938	-0.973	4.807	-1.905	-1.824	-0.001	-0.005	-0.074	0.000
36	A	36	LEU	0	-0.020	0.009	2.386	-0.026	0.427	2.596	-0.663	-2.386	-0.003
37	A	37	MET	0	-0.012	0.003	3.141	-0.505	0.914	0.173	-0.712	-0.879	-0.005
38	A	38	ALA	0	-0.006	-0.011	2.930	-0.008	-0.567	3.089	-0.778	-1.752	0.003
39	A	39	LYS	1	0.870	0.932	4.759	-2.164	-2.095	0.001	-0.024	-0.046	0.000
40	A	40	VAL	0	-0.010	-0.007	6.703	-0.240	-0.240	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.052	-0.038	9.457	-0.218	-0.218	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.048	0.040	11.327	-0.077	-0.077	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.035	-0.028	14.739	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.034	0.028	18.557	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.044	-0.025	21.575	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.055	0.024	23.855	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.004	-0.014	27.151	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.064	-0.021	26.116	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.004	-0.005	24.585	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.016	0.000	29.064	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.827	-0.900	26.075	0.111	0.111	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.821	0.896	22.641	-0.132	-0.132	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.794	0.911	22.285	-0.143	-0.143	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.024	-0.001	18.542	0.015	0.015	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.829	0.891	16.748	-0.404	-0.404	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.006	0.003	12.140	0.048	0.048	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.772	-0.838	13.159	0.531	0.531	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.010	-0.005	6.835	0.200	0.200	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.038	-0.025	8.708	-0.446	-0.446	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.021	0.001	3.278	0.398	0.999	0.042	-0.127	-0.515	-0.001
61	A	61	ASP	-1	-0.783	-0.863	5.759	0.671	0.671	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.025	0.004	6.054	-0.139	-0.139	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.014	-0.009	7.951	0.177	0.177	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.013	0.010	11.044	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.010	-0.013	11.496	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.036	-0.002	9.579	0.062	0.062	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.012	-0.004	7.828	-0.120	-0.120	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.799	0.880	9.054	-0.469	-0.469	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.042	-0.013	9.650	-0.188	-0.188	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.840	-0.921	12.313	0.633	0.633	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.796	-0.861	14.803	0.079	0.079	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.793	-0.896	16.537	0.308	0.308	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.842	-0.916	18.860	0.066	0.066	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.015	0.009	20.665	0.021	0.021	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.821	-0.928	18.959	0.163	0.163	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.046	0.029	15.017	0.013	0.013	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.014	-0.018	13.382	0.059	0.059	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.017	0.019	14.264	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.009	-0.006	15.574	-0.015	-0.015	0.000	0.000	0.000	0.000
80	A	80	ILE	0	0.001	-0.007	9.382	0.058	0.058	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.775	-0.845	10.865	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.854	0.915	11.867	-0.169	-0.169	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.007	-0.002	11.088	-0.042	-0.042	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.005	-0.010	6.629	0.010	0.010	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.815	-0.898	8.441	-0.580	-0.580	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.825	0.905	11.088	-0.223	-0.223	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.007	0.006	5.278	-0.034	-0.034	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.712	-0.801	7.945	-1.336	-1.336	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.089	-0.052	8.720	-0.079	-0.079	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.011	-0.014	10.382	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.046	0.027	5.707	0.038	0.038	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.849	0.929	8.865	0.766	0.766	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.841	0.916	11.382	0.457	0.457	0.000	0.000	0.000	0.000
94	A	94	PHE	0	0.016	0.022	10.462	0.083	0.083	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.796	0.907	12.297	0.984	0.984	0.000	0.000	0.000	0.000

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