FMO DATABASE

FMODB ID: G6ZL1

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	OptH
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	-339861.401047
FMO2-HF: Nuclear repulsion	312344.333367
FMO2-HF: Total energy	-27517.06768
FMO2-MP2: Total energy	-27596.097139

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.
-4.868	-0.079	2.765	-2.979	-4.574	-0.001

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 : 0.021 / q_NPA : -0.005

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	-0.923	-0.930	3.016	-3.115	-0.333	0.090	-1.092	-1.779	0.003
4	A	10	GLU	-1	-0.978	-0.971	1.956	-4.320	-2.875	2.674	-1.770	-2.349	-0.004
5	A	11	LEU	0	-0.008	-0.017	3.740	0.643	1.205	0.001	-0.117	-0.446	0.000
6	A	12	THR	0	-0.002	-0.044	5.596	0.546	0.546	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.002	0.022	6.944	0.333	0.333	0.000	0.000	0.000	0.000
8	A	14	ALA	0	0.027	0.013	7.641	0.320	0.320	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.018	-0.011	9.546	0.223	0.223	0.000	0.000	0.000	0.000
10	A	16	ALA	0	0.016	0.005	11.609	0.120	0.120	0.000	0.000	0.000	0.000
11	A	17	GLN	0	-0.045	-0.029	11.995	0.011	0.011	0.000	0.000	0.000	0.000
12	A	18	LEU	0	0.031	0.000	12.979	0.087	0.087	0.000	0.000	0.000	0.000
13	A	19	GLY	0	0.017	0.017	15.371	0.065	0.065	0.000	0.000	0.000	0.000
14	A	20	THR	0	-0.034	-0.026	16.916	0.064	0.064	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.020	-0.004	17.708	0.026	0.026	0.000	0.000	0.000	0.000
16	A	22	GLY	0	0.038	0.026	19.724	0.026	0.026	0.000	0.000	0.000	0.000
17	A	23	ALA	0	0.020	0.019	21.507	0.028	0.028	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.004	0.001	22.866	0.021	0.021	0.000	0.000	0.000	0.000
19	A	25	MET	0	-0.034	-0.014	23.775	0.018	0.018	0.000	0.000	0.000	0.000
20	A	26	ALA	0	0.042	0.009	25.505	0.018	0.018	0.000	0.000	0.000	0.000
21	A	27	ALA	0	-0.061	-0.026	27.134	0.015	0.015	0.000	0.000	0.000	0.000
22	A	28	GLN	0	-0.006	-0.015	28.651	0.006	0.006	0.000	0.000	0.000	0.000
23	A	29	ASN	0	0.042	0.023	29.543	0.006	0.006	0.000	0.000	0.000	0.000
24	A	30	ALA	0	0.025	0.015	31.661	0.010	0.010	0.000	0.000	0.000	0.000
25	A	31	ALA	0	-0.045	-0.009	33.297	0.007	0.007	0.000	0.000	0.000	0.000
26	A	32	ALA	0	-0.001	-0.011	34.620	0.007	0.007	0.000	0.000	0.000	0.000
27	A	33	ALA	0	0.051	0.054	36.520	0.005	0.005	0.000	0.000	0.000	0.000
28	A	34	ALA	0	0.038	0.037	38.065	0.004	0.004	0.000	0.000	0.000	0.000
29	A	35	PRO	0	-0.031	-0.020	39.444	0.004	0.004	0.000	0.000	0.000	0.000
30	A	36	THR	0	-0.064	-0.054	38.300	0.002	0.002	0.000	0.000	0.000	0.000
31	A	37	THR	0	-0.038	-0.042	40.645	0.004	0.004	0.000	0.000	0.000	0.000
32	A	38	ALA	0	-0.023	0.004	43.436	0.004	0.004	0.000	0.000	0.000	0.000
33	A	39	ILE	0	-0.010	-0.006	44.578	0.000	0.000	0.000	0.000	0.000	0.000
34	A	40	ALA	0	-0.015	-0.005	48.141	0.002	0.002	0.000	0.000	0.000	0.000
35	A	41	PRO	0	-0.003	-0.017	51.869	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	42	ALA	0	0.001	0.013	53.637	0.000	0.000	0.000	0.000	0.000	0.000
37	A	43	ALA	0	-0.016	-0.009	55.071	0.001	0.001	0.000	0.000	0.000	0.000
38	A	44	LEU	0	-0.030	-0.030	58.191	0.000	0.000	0.000	0.000	0.000	0.000
39	A	45	ASP	-1	-0.810	-0.886	59.455	-0.039	-0.039	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.865	-0.954	59.127	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	47	VAL	0	-0.037	-0.016	56.105	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	48	SER	0	-0.045	-0.032	55.195	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.010	0.006	54.044	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	50	LEU	0	-0.007	0.000	52.717	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	51	GLN	0	0.018	0.003	49.410	0.000	0.000	0.000	0.000	0.000	0.000
46	A	52	ALA	0	0.007	0.002	49.204	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	53	ALA	0	0.026	0.007	48.441	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	54	LEU	0	-0.011	-0.001	47.111	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	55	PHE	0	-0.005	-0.005	43.443	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	56	THR	0	-0.027	0.011	43.406	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	57	ALA	0	0.026	0.010	43.637	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	58	TYR	0	-0.047	-0.025	37.903	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	59	GLY	0	0.045	0.024	39.101	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	60	THR	0	0.015	0.002	38.586	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	61	PHE	0	-0.036	-0.030	38.820	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	62	TYR	0	-0.050	-0.020	31.104	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.030	-0.015	34.370	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	64	GLN	0	-0.016	-0.004	34.289	0.001	0.001	0.000	0.000	0.000	0.000
59	A	65	VAL	0	0.026	0.025	32.029	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	66	SER	0	-0.040	-0.026	30.028	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	67	ALA	0	-0.009	0.002	29.006	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	68	GLU	-1	-0.950	-0.983	29.111	-0.068	-0.068	0.000	0.000	0.000	0.000
63	A	69	ALA	0	-0.039	-0.021	26.675	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.023	-0.030	24.297	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.053	0.049	24.036	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	72	MET	0	0.006	-0.003	22.248	0.001	0.001	0.000	0.000	0.000	0.000
67	A	73	HIS	0	-0.042	-0.020	18.189	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	74	ASP	-1	-0.883	-0.949	19.308	-0.181	-0.181	0.000	0.000	0.000	0.000
69	A	75	MET	0	-0.082	-0.040	19.478	0.004	0.004	0.000	0.000	0.000	0.000
70	A	76	PHE	0	-0.014	0.000	12.951	0.009	0.009	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.059	0.030	14.660	-0.040	-0.040	0.000	0.000	0.000	0.000
72	A	78	ASN	0	-0.010	-0.004	14.437	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	79	THR	0	-0.030	-0.016	13.651	0.043	0.043	0.000	0.000	0.000	0.000
74	A	80	LEU	0	-0.055	-0.026	9.267	0.056	0.056	0.000	0.000	0.000	0.000
75	A	81	GLY	0	-0.006	-0.013	9.703	-0.050	-0.050	0.000	0.000	0.000	0.000
76	A	82	ILE	0	-0.069	-0.025	11.029	0.089	0.089	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.076	-0.025	7.913	0.188	0.188	0.000	0.000	0.000	0.000
78	A	84	ALA	0	-0.008	0.002	7.004	0.079	0.079	0.000	0.000	0.000	0.000

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