FMO DATABASE

FMODB ID: 8548Y

Calculation Name: 5XFS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5XFS

Chain ID: A

ChEMBL ID:

UniProt ID: O53943

Base Structure: X-ray

Registration Date: 2023-06-26

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	OptHSide
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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-339690.725426
FMO2-HF: Nuclear repulsion	312173.310815
FMO2-HF: Total energy	-27517.414611
FMO2-MP2: Total energy	-27596.405272

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:7:VAL)

Summations of interaction energy for fragment #1(A:7:VAL)

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.
-5.056	0.151	1.278	-2.084	-4.4	-0.003

Interaction energy analysis for fragmet #1(A:7:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.000

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	9	GLU	-1	-0.955	-0.964	3.165	-2.813	-0.273	0.018	-1.005	-1.553	0.002
4	A	10	GLU	-1	-0.958	-0.975	2.495	-4.348	-2.593	1.254	-0.871	-2.137	-0.005
5	A	11	LEU	0	-0.038	-0.016	3.531	0.356	1.139	0.007	-0.201	-0.588	0.000
6	A	12	THR	0	0.016	-0.013	5.337	0.370	0.499	-0.001	-0.007	-0.122	0.000
7	A	13	ALA	0	0.020	0.026	7.198	0.280	0.280	0.000	0.000	0.000	0.000
8	A	14	ALA	0	0.019	0.007	7.650	0.286	0.286	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.016	-0.007	9.339	0.200	0.200	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.028	0.011	11.465	0.104	0.104	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.042	-0.025	11.983	0.039	0.039	0.000	0.000	0.000	0.000
12	A	18	LEU	0	0.017	-0.005	12.226	0.078	0.078	0.000	0.000	0.000	0.000
13	A	19	GLY	0	0.031	0.021	15.068	0.061	0.061	0.000	0.000	0.000	0.000
14	A	20	THR	0	-0.034	-0.023	16.996	0.049	0.049	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.027	-0.010	17.372	0.024	0.024	0.000	0.000	0.000	0.000
16	A	22	GLY	0	0.046	0.030	19.457	0.023	0.023	0.000	0.000	0.000	0.000
17	A	23	ALA	0	0.019	0.019	21.294	0.025	0.025	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.001	-0.001	22.783	0.018	0.018	0.000	0.000	0.000	0.000
19	A	25	MET	0	-0.044	-0.007	23.399	0.017	0.017	0.000	0.000	0.000	0.000
20	A	26	ALA	0	0.048	0.002	25.184	0.016	0.016	0.000	0.000	0.000	0.000
21	A	27	ALA	0	-0.058	-0.021	26.945	0.013	0.013	0.000	0.000	0.000	0.000
22	A	28	GLN	0	-0.007	-0.012	28.425	0.006	0.006	0.000	0.000	0.000	0.000
23	A	29	ASN	0	0.046	0.028	28.094	0.010	0.010	0.000	0.000	0.000	0.000
24	A	30	ALA	0	0.033	0.025	31.258	0.009	0.009	0.000	0.000	0.000	0.000
25	A	31	ALA	0	-0.042	-0.007	33.065	0.006	0.006	0.000	0.000	0.000	0.000
26	A	32	ALA	0	-0.001	-0.010	34.301	0.006	0.006	0.000	0.000	0.000	0.000
27	A	33	ALA	0	0.050	0.045	36.157	0.005	0.005	0.000	0.000	0.000	0.000
28	A	34	ALA	0	0.037	0.036	37.663	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	PRO	0	-0.031	-0.019	39.098	0.003	0.003	0.000	0.000	0.000	0.000
30	A	36	THR	0	-0.064	-0.047	37.743	0.002	0.002	0.000	0.000	0.000	0.000
31	A	37	THR	0	-0.029	-0.039	40.137	0.003	0.003	0.000	0.000	0.000	0.000
32	A	38	ALA	0	-0.038	-0.005	42.912	0.004	0.004	0.000	0.000	0.000	0.000
33	A	39	ILE	0	-0.016	-0.006	43.935	0.000	0.000	0.000	0.000	0.000	0.000
34	A	40	ALA	0	-0.011	0.000	47.647	0.002	0.002	0.000	0.000	0.000	0.000
35	A	41	PRO	0	0.004	-0.014	51.395	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	42	ALA	0	-0.005	0.009	53.036	0.000	0.000	0.000	0.000	0.000	0.000
37	A	43	ALA	0	-0.011	-0.009	54.551	0.001	0.001	0.000	0.000	0.000	0.000
38	A	44	LEU	0	-0.022	-0.024	57.608	0.000	0.000	0.000	0.000	0.000	0.000
39	A	45	ASP	-1	-0.791	-0.855	58.811	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.867	-0.951	58.441	-0.029	-0.029	0.000	0.000	0.000	0.000
41	A	47	VAL	0	-0.037	-0.019	55.103	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.067	-0.064	54.481	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.016	0.001	53.378	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	50	LEU	0	-0.001	0.002	51.970	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	51	GLN	0	0.002	-0.001	48.225	0.000	0.000	0.000	0.000	0.000	0.000
46	A	52	ALA	0	0.010	0.003	48.467	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	53	ALA	0	0.031	0.016	47.766	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	54	LEU	0	-0.010	0.003	46.355	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	55	PHE	0	0.000	-0.005	42.955	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	56	THR	0	-0.004	0.013	42.713	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.016	0.016	42.952	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	58	TYR	0	-0.041	-0.021	36.653	0.000	0.000	0.000	0.000	0.000	0.000
53	A	59	GLY	0	0.045	0.024	38.408	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	60	THR	0	-0.019	-0.025	37.925	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	61	PHE	0	-0.034	-0.026	38.101	0.000	0.000	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.043	-0.032	30.484	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.035	-0.021	33.623	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	64	GLN	0	-0.026	-0.003	33.635	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.027	0.021	31.078	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	66	SER	0	-0.019	-0.017	29.239	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	67	ALA	0	-0.013	-0.001	28.289	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.961	-0.986	28.458	-0.048	-0.048	0.000	0.000	0.000	0.000
63	A	69	ALA	0	-0.031	-0.017	25.926	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.025	-0.032	23.549	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.062	0.052	23.372	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	72	MET	0	-0.006	-0.007	21.863	0.003	0.003	0.000	0.000	0.000	0.000
67	A	73	HIS	0	-0.038	-0.017	17.757	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.876	-0.952	18.693	-0.145	-0.145	0.000	0.000	0.000	0.000
69	A	75	MET	0	-0.076	-0.033	19.233	0.010	0.010	0.000	0.000	0.000	0.000
70	A	76	PHE	0	-0.006	0.015	12.311	0.020	0.020	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.047	0.023	14.251	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	78	ASN	0	-0.020	-0.004	14.175	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	79	THR	0	-0.045	-0.042	13.821	0.047	0.047	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.063	-0.026	8.286	0.065	0.065	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.001	-0.013	9.756	-0.019	-0.019	0.000	0.000	0.000	0.000
76	A	82	ILE	0	-0.069	-0.026	11.090	0.087	0.087	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.075	-0.018	7.811	0.186	0.186	0.000	0.000	0.000	0.000
78	A	84	ALA	0	-0.003	0.002	6.989	0.051	0.051	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:VAL)