FMO DATABASE

FMODB ID: 8213Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-524769.03484
FMO2-HF: Nuclear repulsion	490303.734869
FMO2-HF: Total energy	-34465.299971
FMO2-MP2: Total energy	-34563.713519

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.
-12.431	-5.052	11.583	-6.282	-12.68	-0.038

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 : -0.036 / q_NPA : -0.014

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	0.882	0.945	3.771	0.143	2.287	-0.026	-0.924	-1.194	0.000
4	A	4	ALA	0	0.010	0.004	5.749	-0.177	-0.177	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.032	-0.043	9.051	0.119	0.119	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.008	-0.009	12.008	-0.061	-0.061	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.032	-0.010	15.044	0.010	0.010	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.014	0.002	18.390	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.882	0.933	21.217	-0.075	-0.075	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.036	0.012	24.847	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.840	0.918	28.069	-0.056	-0.056	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.983	0.988	29.901	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.031	-0.017	31.490	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.023	0.004	32.501	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.022	-0.012	33.435	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.065	0.011	29.196	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	PRO	0	-0.013	-0.021	33.170	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.816	-0.848	27.965	0.093	0.093	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.066	0.040	31.732	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.950	0.957	32.391	-0.046	-0.046	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.009	-0.017	34.828	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.038	0.022	29.998	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.005	0.014	34.311	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.871	0.923	36.424	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.024	0.024	36.788	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.011	0.000	33.165	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.081	-0.058	37.791	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.023	-0.007	41.056	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.010	-0.001	37.999	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.027	0.026	41.802	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.011	0.013	37.546	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.018	-0.022	39.707	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.006	0.001	38.706	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.026	-0.005	34.903	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.919	0.951	36.800	-0.036	-0.036	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.959	-0.975	33.627	0.045	0.045	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.036	-0.009	30.479	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.021	0.014	27.316	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.064	-0.060	26.194	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.015	0.000	22.035	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.964	0.997	19.405	-0.173	-0.173	0.000	0.000	0.000	0.000
42	A	42	MET	0	-0.009	-0.007	13.845	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.015	-0.019	13.193	0.011	0.011	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.780	-0.868	9.517	0.331	0.331	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.025	-0.017	7.975	0.102	0.102	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.009	0.005	2.790	-1.054	-1.029	2.098	-0.520	-1.603	0.004
47	A	47	MET	0	-0.032	-0.002	4.222	-0.322	0.597	0.098	-0.246	-0.772	0.000
48	A	48	GLU	-1	-0.819	-0.906	2.439	-7.954	-5.074	6.314	-3.433	-5.761	-0.037
49	A	49	GLY	0	0.008	-0.010	3.789	-1.345	-1.339	0.007	0.031	-0.043	0.000
50	A	50	GLU	-1	-0.932	-0.964	6.031	-0.451	-0.451	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.015	0.005	6.864	0.115	0.115	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.778	-0.919	7.575	-0.353	-0.353	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.872	-0.919	8.761	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.838	0.899	9.995	0.249	0.249	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.012	0.005	6.032	0.078	0.078	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.817	0.887	9.411	0.171	0.171	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.895	-0.951	12.538	-0.047	-0.047	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.913	-0.956	9.770	0.180	0.180	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.004	-0.026	10.522	0.050	0.050	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.886	-0.933	13.150	0.018	0.018	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.853	-0.925	15.984	0.041	0.041	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.047	-0.013	10.356	0.016	0.016	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.071	-0.034	16.222	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.880	0.948	18.727	-0.047	-0.047	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.836	0.903	19.318	-0.061	-0.061	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.047	-0.008	17.345	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.013	-0.009	14.733	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.017	0.001	19.447	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.044	0.023	22.516	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.057	0.017	25.274	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.030	-0.016	27.320	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.020	-0.017	28.334	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	HIS	0	-0.001	0.004	24.546	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.815	-0.891	25.201	0.048	0.048	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.039	-0.034	18.877	0.010	0.010	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.872	-0.921	18.744	0.061	0.061	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.019	0.000	13.287	0.024	0.024	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.862	0.945	13.662	-0.106	-0.106	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.023	0.017	8.097	0.065	0.065	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.926	-0.949	8.374	0.040	0.040	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.878	0.928	3.873	-3.005	-2.709	0.001	-0.086	-0.211	0.000
82	A	82	ILE	0	-0.067	-0.031	2.083	-0.830	-0.030	3.090	-1.028	-2.862	-0.005
83	A	83	GLU	-1	-0.885	-0.929	4.023	1.925	2.234	0.001	-0.076	-0.234	0.000

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