FMO DATABASE

FMODB ID: 8555Y

Calculation Name: 4FD9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FD9

Chain ID: A

ChEMBL ID:

UniProt ID: Q80W49

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	92
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-668032.738419
FMO2-HF: Nuclear repulsion	631554.258348
FMO2-HF: Total energy	-36478.48007
FMO2-MP2: Total energy	-36585.317742

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.
-8.989	-1.57	4.768	-3.246	-8.94	-0.009

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 : 0.003 / q_NPA : 0.001

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	LEU	0	-0.001	0.010	2.364	-1.396	1.989	0.964	-1.270	-3.079	0.005
4	A	4	LYS	1	0.852	0.904	4.958	0.950	0.991	-0.001	-0.006	-0.034	0.000
5	A	5	VAL	0	-0.013	0.018	8.582	0.287	0.287	0.000	0.000	0.000	0.000
6	A	6	ILE	0	-0.017	-0.012	11.327	-0.079	-0.079	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.034	-0.011	14.944	0.080	0.080	0.000	0.000	0.000	0.000
8	A	8	TYR	0	0.051	0.009	17.479	-0.037	-0.037	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.765	-0.878	21.239	-0.136	-0.136	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.814	0.900	24.677	0.157	0.157	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.017	0.007	24.428	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.081	-0.058	24.140	-0.016	-0.016	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.046	-0.028	18.954	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.012	0.013	22.715	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.022	-0.021	25.150	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.014	-0.001	24.854	-0.019	-0.019	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.020	-0.003	19.284	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.757	0.886	18.144	0.373	0.373	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.799	-0.888	14.211	-0.738	-0.738	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.031	-0.018	10.118	0.030	0.030	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.037	-0.002	7.464	-0.165	-0.165	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.949	-0.957	7.437	-1.577	-1.577	0.000	0.000	0.000	0.000
23	A	23	HIS	0	0.006	0.005	5.965	0.310	0.310	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.021	0.025	9.838	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.808	-0.904	13.408	-0.141	-0.141	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.001	-0.029	15.494	0.058	0.058	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.030	0.016	17.284	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.022	0.002	19.218	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.032	-0.027	20.439	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.017	-0.013	15.972	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.046	-0.014	19.626	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.978	1.000	22.551	0.304	0.304	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.074	-0.016	24.871	0.008	0.008	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.843	-0.930	26.702	-0.180	-0.180	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.860	0.931	25.471	0.310	0.310	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.855	-0.925	23.763	-0.331	-0.331	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.008	0.013	21.099	0.018	0.018	0.000	0.000	0.000	0.000
38	A	38	HIS	0	-0.022	-0.029	25.061	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.005	0.007	24.487	0.015	0.015	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.018	-0.019	18.346	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.025	0.016	22.380	0.024	0.024	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.036	-0.019	20.922	0.017	0.017	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.029	-0.019	14.626	-0.041	-0.041	0.000	0.000	0.000	0.000
44	A	44	ARG	1	0.894	0.960	14.774	0.226	0.226	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.041	-0.006	8.951	-0.135	-0.135	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.027	-0.019	9.868	0.084	0.084	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.036	0.025	5.984	0.009	0.009	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.010	-0.007	3.775	-0.603	-0.404	0.006	-0.065	-0.139	0.000
49	A	49	VAL	0	0.005	0.009	4.604	-0.453	-0.285	-0.001	-0.033	-0.134	0.000
50	A	50	TRP	0	-0.043	-0.038	5.860	-0.296	-0.296	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.028	-0.004	8.465	0.100	0.100	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.011	0.013	11.315	-0.140	-0.140	0.000	0.000	0.000	0.000
53	A	53	TYR	0	-0.015	-0.019	11.987	0.061	0.061	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.725	-0.849	16.883	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.800	0.882	19.802	-0.038	-0.038	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.767	-0.848	18.682	-0.164	-0.164	0.000	0.000	0.000	0.000
57	A	57	HIS	1	0.754	0.840	16.814	0.198	0.198	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.012	-0.003	12.537	0.035	0.035	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.880	0.951	15.745	0.069	0.069	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.012	-0.005	19.111	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.014	-0.015	19.519	0.022	0.022	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.023	0.017	14.636	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.020	0.013	15.839	0.021	0.021	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.013	0.000	10.516	-0.031	-0.031	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.004	-0.008	11.839	-0.054	-0.054	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.912	-0.960	9.878	1.168	1.168	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.866	-0.941	6.213	0.466	0.466	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.014	0.006	10.456	0.056	0.056	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.894	-0.925	14.072	-0.188	-0.188	0.000	0.000	0.000	0.000
70	A	70	PHE	0	-0.022	-0.024	13.656	0.025	0.025	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.832	-0.928	18.956	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.735	-0.856	22.327	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	SER	0	0.005	-0.009	23.004	0.011	0.011	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.150	-0.086	24.694	0.021	0.021	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.023	0.033	20.835	0.020	0.020	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.025	-0.016	17.435	0.044	0.044	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.061	0.032	20.630	-0.027	-0.027	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.004	-0.001	18.075	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.021	-0.006	20.139	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.097	-0.047	22.430	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.001	-0.008	23.976	0.001	0.001	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.040	-0.022	23.092	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	ILE	0	0.040	0.040	16.746	0.015	0.015	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.046	-0.028	19.156	-0.036	-0.036	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.052	-0.027	15.003	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.052	0.027	11.245	0.056	0.056	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.883	0.955	8.221	-0.298	-0.298	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.040	0.032	2.423	-0.676	0.068	0.953	-0.336	-1.361	-0.002
89	A	89	LEU	0	-0.051	-0.040	4.654	-0.432	-0.283	-0.001	-0.033	-0.115	0.000
90	A	90	GLN	0	0.034	-0.004	2.309	-5.095	-2.392	2.819	-1.714	-3.808	-0.013
91	A	91	ALA	0	-0.011	0.009	3.441	-1.355	-1.325	0.029	0.211	-0.270	0.001
92	A	92	ASN	0	0.006	0.005	5.940	0.450	0.450	0.000	0.000	0.000	0.000

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