FMO DATABASE

FMODB ID: GNM91

Calculation Name: 2YX5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YX5

Chain ID: A

ChEMBL ID:

UniProt ID: Q58988

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	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-524224.842137
FMO2-HF: Nuclear repulsion	489760.369564
FMO2-HF: Total energy	-34464.472573
FMO2-MP2: Total energy	-34562.938755

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.
-14.57	-9.137	14.923	-7.115	-13.243	-0.042

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 : -0.040 / q_NPA : -0.009

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	LYS	1	0.942	0.983	3.771	-0.334	1.810	-0.029	-0.960	-1.155	0.001
4	A	4	ALA	0	0.015	0.009	5.841	-0.012	-0.012	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.029	-0.017	9.075	0.076	0.076	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.006	-0.003	12.051	-0.017	-0.017	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.013	-0.001	15.033	0.000	0.000	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.016	0.001	18.402	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.903	0.950	21.188	-0.044	-0.044	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.021	0.008	24.832	0.001	0.001	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.865	0.951	28.205	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.987	0.991	29.878	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.031	-0.017	31.504	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.012	0.009	32.491	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.026	-0.014	33.427	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.083	0.021	29.293	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.023	-0.021	33.151	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.821	-0.875	28.093	0.029	0.029	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.072	0.043	31.751	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.928	0.939	32.405	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.017	-0.031	34.748	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.039	0.024	30.083	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.012	0.014	34.331	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.913	0.953	36.469	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.031	0.030	36.805	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.013	0.002	33.320	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.094	-0.062	37.845	0.000	0.000	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.029	-0.011	41.120	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.013	-0.007	38.108	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.016	0.023	41.856	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.000	0.009	37.232	0.000	0.000	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.023	-0.031	39.796	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.013	-0.002	38.536	0.000	0.000	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.048	-0.018	34.932	0.001	0.001	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.957	0.970	36.930	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.933	-0.954	33.680	0.021	0.021	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.044	-0.013	30.366	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.024	0.004	28.254	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.065	-0.026	26.217	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.018	0.001	22.007	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.952	0.992	19.241	-0.064	-0.064	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.019	-0.013	14.173	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.023	-0.021	12.987	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.844	-0.924	9.450	0.085	0.085	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.021	-0.022	8.039	0.053	0.053	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.011	0.005	2.645	-1.155	-0.482	0.587	-0.236	-1.025	0.001
47	A	47	MET	0	-0.024	-0.003	4.085	-0.040	0.717	0.051	-0.190	-0.618	0.000
48	A	48	GLU	-1	-0.819	-0.912	2.573	-8.101	-5.224	6.898	-3.870	-5.905	-0.040
49	A	49	GLY	0	0.006	-0.003	3.793	-1.472	-1.560	0.013	0.139	-0.064	0.000
50	A	50	GLU	-1	-0.950	-0.990	5.939	-0.124	-0.124	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.022	-0.002	6.899	0.145	0.145	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.848	-0.949	7.613	0.089	0.089	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.932	-0.955	8.815	0.035	0.035	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.888	0.938	9.990	0.013	0.013	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.024	0.007	6.186	0.026	0.026	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.913	0.951	9.391	0.035	0.035	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.868	-0.931	12.519	0.043	0.043	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.938	-0.963	9.977	0.232	0.232	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.016	-0.048	10.461	0.023	0.023	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.903	-0.964	13.136	0.040	0.040	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.918	-0.966	15.992	0.049	0.049	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.063	-0.011	10.281	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.055	-0.029	16.413	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.885	0.953	18.713	-0.054	-0.054	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.888	0.942	19.312	-0.061	-0.061	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.049	-0.011	17.676	-0.002	-0.002	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.010	-0.002	15.065	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.018	-0.002	19.572	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.042	0.019	22.444	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.046	0.019	25.463	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.019	-0.019	27.304	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.012	-0.014	28.026	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.008	0.007	24.474	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.832	-0.917	25.176	0.034	0.034	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.048	-0.041	19.103	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.944	-0.973	19.065	0.037	0.037	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.024	0.012	13.218	0.007	0.007	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.912	0.967	13.560	-0.042	-0.042	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.019	0.018	8.071	0.014	0.014	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.923	-0.946	8.684	0.021	0.021	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.942	0.980	3.693	-6.794	-6.215	0.017	-0.247	-0.350	0.002
82	A	82	ILE	0	-0.082	-0.040	1.966	0.172	-1.653	7.385	-1.674	-3.886	-0.006
83	A	83	GLU	-1	-0.925	-0.967	4.005	2.624	2.940	0.001	-0.077	-0.240	0.000

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