FMO DATABASE

FMODB ID: J38J9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-708982.443398
FMO2-HF: Nuclear repulsion	671202.096564
FMO2-HF: Total energy	-37780.346834
FMO2-MP2: Total energy	-37891.802048

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.
-35.961	-27.748	28.284	-13.175	-23.321	-0.086

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 : -0.032 / q_NPA : -0.007

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	ILE	0	-0.005	0.000	2.745	-0.596	1.971	0.120	-0.937	-1.750	0.004
4	A	4	TYR	0	0.028	0.023	4.944	-1.116	-1.035	-0.001	-0.010	-0.070	0.000
5	A	5	LYS	1	0.914	0.943	8.294	-1.348	-1.348	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.044	0.032	8.421	0.326	0.326	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.046	-0.029	10.495	-0.202	-0.202	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.085	0.026	14.127	0.056	0.056	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.910	0.966	16.643	-0.556	-0.556	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.026	-0.022	20.178	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.004	-0.010	16.490	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.905	-0.935	18.844	0.218	0.218	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.062	-0.040	12.395	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.053	0.030	15.437	-0.020	-0.020	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.853	-0.943	13.642	0.098	0.098	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.006	0.011	12.963	-0.048	-0.048	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.012	-0.004	11.837	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.964	0.973	8.772	-0.318	-0.318	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.859	-0.924	8.117	-0.354	-0.354	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.075	-0.043	8.947	-0.274	-0.274	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.003	-0.017	5.632	-0.122	-0.122	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.914	-0.961	4.145	-0.658	-0.409	-0.001	-0.025	-0.223	0.000
23	A	23	LYS	1	0.873	0.947	4.312	-0.138	0.015	-0.001	-0.018	-0.134	0.000
24	A	24	LYS	1	0.859	0.941	6.455	-0.036	-0.036	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.008	-0.017	2.071	-1.541	-3.174	7.932	-2.019	-4.280	0.016
26	A	26	ALA	0	0.051	0.036	2.556	-5.843	-4.037	2.558	-1.295	-3.069	-0.016
27	A	27	ARG	1	0.799	0.877	3.485	0.676	0.702	0.008	0.339	-0.372	0.000
28	A	28	LEU	0	-0.036	-0.019	2.258	0.228	0.878	1.084	-0.408	-1.326	0.001
29	A	29	ASP	-1	-0.790	-0.893	1.911	-25.351	-24.568	11.778	-6.428	-6.133	-0.077
30	A	30	ARG	1	0.878	0.965	4.785	2.889	2.961	-0.001	-0.006	-0.065	0.000
31	A	31	TYR	0	-0.092	-0.064	7.299	0.630	0.630	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.055	-0.039	5.857	0.842	0.842	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.867	-0.928	8.084	-1.399	-1.399	0.000	0.000	0.000	0.000
34	A	34	GLY	0	-0.091	-0.021	8.254	0.204	0.204	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.885	-0.945	5.252	1.427	1.427	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.026	-0.012	2.318	-1.275	-0.851	2.811	-0.725	-2.511	-0.004
37	A	37	MET	0	-0.009	0.008	2.721	0.793	2.691	0.826	-1.134	-1.589	-0.011
38	A	38	ALA	0	0.011	0.007	3.177	-1.046	-0.539	1.103	-0.376	-1.235	0.002
39	A	39	LYS	1	0.909	0.969	4.866	-2.350	-2.327	0.001	-0.005	-0.018	0.000
40	A	40	VAL	0	0.005	-0.012	7.004	-0.060	-0.060	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.059	-0.037	9.643	-0.247	-0.247	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.033	0.026	11.783	-0.043	-0.043	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.060	-0.035	15.053	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.054	0.031	18.826	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.050	-0.016	21.835	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.054	0.020	24.095	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.032	-0.025	27.350	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.028	-0.009	26.352	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.023	-0.013	24.367	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.012	-0.004	28.665	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.876	-0.918	26.777	0.086	0.086	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.851	0.922	24.058	-0.071	-0.071	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.872	0.932	22.856	-0.148	-0.148	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.045	-0.017	18.817	0.017	0.017	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.897	0.949	17.032	-0.408	-0.408	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.001	0.003	12.499	0.039	0.039	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.864	-0.933	13.060	0.617	0.617	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.007	-0.002	6.666	0.203	0.203	0.000	0.000	0.000	0.000
59	A	59	GLN	0	-0.026	-0.024	8.378	-0.540	-0.540	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.019	-0.001	3.043	0.207	0.814	0.067	-0.128	-0.546	-0.001
61	A	61	ASP	-1	-0.906	-0.943	5.756	0.827	0.827	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.008	-0.012	5.902	0.034	0.034	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.001	-0.006	7.635	0.140	0.140	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.015	0.000	10.897	-0.076	-0.076	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.014	-0.028	11.644	-0.083	-0.083	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.005	0.013	9.302	0.106	0.106	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.008	0.003	7.753	-0.159	-0.159	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.808	0.903	8.682	-0.569	-0.569	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.079	-0.022	9.863	-0.197	-0.197	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.874	-0.956	12.332	0.700	0.700	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.843	-0.881	14.254	0.176	0.176	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.818	-0.925	16.565	0.297	0.297	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.848	-0.931	18.724	0.055	0.055	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.027	0.025	20.698	0.018	0.018	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.883	-0.946	18.950	0.070	0.070	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.050	0.005	15.267	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	TYR	0	0.004	-0.010	13.784	0.063	0.063	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.059	0.057	14.677	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.023	-0.009	15.976	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.008	-0.013	9.772	0.069	0.069	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.848	-0.913	11.202	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.924	0.968	12.236	-0.142	-0.142	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.020	-0.023	10.911	-0.022	-0.022	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.001	-0.021	6.413	0.075	0.075	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.877	-0.919	8.635	-0.465	-0.465	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.848	0.895	11.317	-0.319	-0.319	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.011	-0.009	5.308	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.805	-0.885	7.718	-1.224	-1.224	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.075	-0.033	8.556	-0.120	-0.120	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.058	-0.041	9.997	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.047	0.013	5.485	0.028	0.028	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.948	0.991	8.543	0.566	0.566	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.860	0.928	10.950	0.347	0.347	0.000	0.000	0.000	0.000
94	A	94	PHE	0	0.029	0.043	10.345	0.090	0.090	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.929	0.979	11.963	0.578	0.578	0.000	0.000	0.000	0.000

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