FMO DATABASE

FMODB ID: N1R5Q

Calculation Name: 2YX5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-525488.461009
FMO2-HF: Nuclear repulsion	491022.618916
FMO2-HF: Total energy	-34465.842093
FMO2-MP2: Total energy	-34564.213036

3D Structure Molmil

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.
-12.944	-5.094	11.506	-6.423	-12.929	-0.04

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 : -0.024 / 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	3	LYS	1	0.870	0.939	3.867	0.748	2.632	-0.009	-0.801	-1.073	0.000
4	A	4	ALA	0	0.019	0.001	6.050	-0.355	-0.355	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.037	-0.026	9.599	0.096	0.096	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.012	0.007	12.530	-0.081	-0.081	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.035	-0.022	15.510	0.015	0.015	0.000	0.000	0.000	0.000
8	A	8	ILE	0	0.009	0.004	18.831	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.884	0.936	21.964	-0.086	-0.086	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.035	0.009	25.623	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.830	0.912	28.761	-0.051	-0.051	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.949	0.958	30.499	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.016	-0.004	31.999	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.024	0.000	33.120	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.001	-0.009	34.074	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	ASN	0	0.011	-0.007	29.656	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	17	PRO	0	0.013	-0.006	33.577	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.838	-0.854	28.466	0.100	0.100	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.043	0.022	32.068	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.962	0.976	32.837	-0.050	-0.050	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.007	-0.003	35.521	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.032	0.012	30.669	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.003	0.009	34.947	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.851	0.912	36.881	-0.050	-0.050	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.029	0.020	37.146	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.014	0.006	33.655	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.059	-0.043	38.292	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.005	0.001	41.557	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.023	-0.011	38.343	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.055	0.040	42.100	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.003	0.013	38.298	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.036	-0.036	39.874	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.017	-0.002	39.433	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.008	0.004	35.414	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.894	0.941	37.515	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.936	-0.965	33.885	0.056	0.056	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.025	-0.013	31.030	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.024	0.016	27.903	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.065	-0.066	26.964	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.019	0.004	22.570	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.950	0.975	20.255	-0.168	-0.168	0.000	0.000	0.000	0.000
42	A	42	MET	0	0.005	0.013	14.231	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.020	-0.021	13.449	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.763	-0.852	10.238	0.478	0.478	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.036	-0.012	8.167	0.043	0.043	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.003	-0.008	3.004	-0.383	-0.750	2.463	-0.519	-1.577	0.003
47	A	47	MET	0	-0.039	0.005	3.880	-1.213	-0.296	0.166	-0.311	-0.772	-0.001
48	A	48	GLU	-1	-0.878	-0.956	2.349	-8.643	-5.029	6.251	-3.747	-6.117	-0.039
49	A	49	GLY	0	0.012	0.014	3.586	-0.406	-0.402	0.005	0.049	-0.059	0.000
50	A	50	GLU	-1	-0.835	-0.912	5.975	-0.415	-0.415	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.006	0.008	6.219	0.132	0.132	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.768	-0.908	7.157	-0.217	-0.217	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.849	-0.907	8.631	0.022	0.022	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.830	0.900	9.448	0.264	0.264	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.005	0.007	5.827	0.072	0.072	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.816	0.896	9.205	0.153	0.153	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.910	-0.963	12.598	-0.080	-0.080	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.924	-0.961	9.505	-0.068	-0.068	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.018	-0.011	10.758	0.045	0.045	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.881	-0.945	13.450	0.025	0.025	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.846	-0.903	16.184	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.032	-0.011	10.777	0.023	0.023	0.000	0.000	0.000	0.000
63	A	63	CYS	0	-0.068	-0.038	16.621	0.009	0.009	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.856	0.926	19.092	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.776	0.882	19.556	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.025	-0.001	17.255	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.010	-0.010	14.841	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.004	0.001	19.520	0.006	0.006	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.054	0.029	22.722	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	70	PRO	0	0.040	0.013	25.423	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.009	-0.008	27.491	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.028	-0.021	28.888	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	HIS	0	0.012	0.016	25.302	0.005	0.005	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.816	-0.890	25.968	0.048	0.048	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.013	-0.018	19.136	0.010	0.010	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.873	-0.917	19.495	0.087	0.087	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.024	0.000	13.816	0.024	0.024	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.851	0.936	14.130	-0.152	-0.152	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.008	-0.013	8.396	0.063	0.063	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.906	-0.951	8.211	0.225	0.225	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.869	0.923	3.746	-3.767	-3.323	0.005	-0.154	-0.294	0.001
82	A	82	ILE	0	-0.047	-0.016	2.146	-0.805	0.194	2.623	-0.842	-2.779	-0.004
83	A	83	GLU	-1	-0.900	-0.929	3.960	1.530	1.885	0.002	-0.098	-0.258	0.000

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