FMO DATABASE

FMODB ID: LL5G9

Calculation Name: 4DHX-B-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DHX

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NPA8

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	93
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-576349.191068
FMO2-HF: Nuclear repulsion	539827.76179
FMO2-HF: Total energy	-36521.429278
FMO2-MP2: Total energy	-36628.169742

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(B:8:ACE )

Summations of interaction energy for fragment #1(B:8:ACE )

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.
1.918	2.655	-0.007	-0.333	-0.397	0

Interaction energy analysis for fragmet #1(B:8:ACE )

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 : -0.012

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].
3	B	10	ALA	0	-0.011	-0.012	3.810	1.482	2.219	-0.007	-0.333	-0.397
4	B	11	GLN	0	0.036	0.022	6.861	0.577	0.577	0.000	0.000	0.000
5	B	12	MET	0	0.016	0.010	5.699	0.369	0.369	0.000	0.000	0.000
6	B	13	ARG	1	0.924	0.961	5.415	-0.055	-0.055	0.000	0.000	0.000
7	B	14	ALA	0	-0.011	-0.004	8.498	0.106	0.106	0.000	0.000	0.000
8	B	15	ALA	0	0.037	0.024	10.988	0.066	0.066	0.000	0.000	0.000
9	B	16	ILE	0	0.004	-0.002	9.715	0.060	0.060	0.000	0.000	0.000
10	B	17	ASN	0	-0.038	-0.029	12.317	0.055	0.055	0.000	0.000	0.000
11	B	18	GLN	0	0.007	0.009	14.224	0.013	0.013	0.000	0.000	0.000
12	B	19	LYS	1	0.996	1.016	15.714	0.048	0.048	0.000	0.000	0.000
13	B	20	LEU	0	-0.043	-0.021	14.245	0.015	0.015	0.000	0.000	0.000
14	B	21	ILE	0	-0.059	-0.027	17.850	0.007	0.007	0.000	0.000	0.000
15	B	22	GLU	-1	-0.867	-0.935	20.292	-0.038	-0.038	0.000	0.000	0.000
16	B	23	THR	0	-0.050	-0.033	20.171	0.008	0.008	0.000	0.000	0.000
17	B	24	GLY	0	0.047	0.034	22.745	0.005	0.005	0.000	0.000	0.000
18	B	25	GLU	-1	-0.831	-0.900	19.414	0.089	0.089	0.000	0.000	0.000
19	B	26	ARG	1	0.908	0.941	16.939	-0.043	-0.043	0.000	0.000	0.000
20	B	27	GLU	-1	-0.951	-0.980	20.634	0.026	0.026	0.000	0.000	0.000
21	B	28	ARG	1	0.941	0.968	23.222	-0.066	-0.066	0.000	0.000	0.000
22	B	29	LEU	0	-0.038	-0.026	18.871	0.007	0.007	0.000	0.000	0.000
23	B	30	LYS	1	0.933	0.969	22.807	-0.033	-0.033	0.000	0.000	0.000
24	B	31	GLU	-1	-0.939	-0.964	23.872	0.043	0.043	0.000	0.000	0.000
25	B	32	LEU	0	0.026	0.002	25.572	0.001	0.001	0.000	0.000	0.000
26	B	33	LEU	0	-0.024	-0.011	20.572	0.004	0.004	0.000	0.000	0.000
27	B	34	ARG	1	0.913	0.952	25.280	-0.049	-0.049	0.000	0.000	0.000
28	B	35	ALA	0	0.031	0.018	27.908	-0.002	-0.002	0.000	0.000	0.000
29	B	36	LYS	1	0.977	0.990	27.507	-0.083	-0.083	0.000	0.000	0.000
30	B	37	LEU	0	-0.038	-0.022	24.944	0.000	0.000	0.000	0.000	0.000
31	B	38	ILE	0	-0.056	-0.043	29.166	-0.004	-0.004	0.000	0.000	0.000
32	B	39	GLU	-1	-0.920	-0.949	32.447	0.064	0.064	0.000	0.000	0.000
33	B	40	CYS	0	-0.098	-0.027	29.560	-0.001	-0.001	0.000	0.000	0.000
34	B	41	GLY	0	0.091	0.053	33.021	0.000	0.000	0.000	0.000	0.000
35	B	42	TRP	0	-0.017	-0.021	26.351	-0.005	-0.005	0.000	0.000	0.000
36	B	43	LYS	1	0.950	0.962	31.475	-0.043	-0.043	0.000	0.000	0.000
37	B	44	ASP	-1	-0.879	-0.947	32.755	0.041	0.041	0.000	0.000	0.000
38	B	45	GLN	0	-0.004	-0.007	32.026	0.000	0.000	0.000	0.000	0.000
39	B	46	LEU	0	-0.034	-0.004	29.182	-0.002	-0.002	0.000	0.000	0.000
40	B	47	LYS	1	0.931	0.966	33.348	-0.041	-0.041	0.000	0.000	0.000
41	B	48	ALA	0	0.008	0.010	36.775	-0.003	-0.003	0.000	0.000	0.000
42	B	49	HIS	0	0.027	0.007	32.613	-0.003	-0.003	0.000	0.000	0.000
43	B	50	CYS	0	0.004	0.001	34.736	-0.002	-0.002	0.000	0.000	0.000
44	B	51	LYS	1	0.946	0.981	37.286	-0.029	-0.029	0.000	0.000	0.000
45	B	52	GLU	-1	-0.914	-0.964	39.352	0.030	0.030	0.000	0.000	0.000
46	B	53	VAL	0	0.039	0.024	35.838	-0.002	-0.002	0.000	0.000	0.000
47	B	54	ILE	0	-0.027	-0.016	39.261	-0.002	-0.002	0.000	0.000	0.000
48	B	55	LYS	1	0.878	0.942	41.638	-0.028	-0.028	0.000	0.000	0.000
49	B	56	GLU	-1	-0.961	-0.970	41.343	0.026	0.026	0.000	0.000	0.000
50	B	57	LYS	1	0.909	0.965	38.203	-0.026	-0.026	0.000	0.000	0.000
51	B	58	GLY	0	0.069	0.038	42.662	-0.002	-0.002	0.000	0.000	0.000
52	B	59	LEU	0	-0.026	-0.039	43.320	0.000	0.000	0.000	0.000	0.000
53	B	60	GLU	-1	-0.989	-0.979	44.822	0.009	0.009	0.000	0.000	0.000
54	B	61	HIS	0	-0.031	-0.012	43.006	-0.001	-0.001	0.000	0.000	0.000
55	B	62	VAL	0	-0.071	-0.014	38.268	0.000	0.000	0.000	0.000	0.000
56	B	63	THR	0	0.030	0.006	36.607	-0.001	-0.001	0.000	0.000	0.000
57	B	64	VAL	0	-0.008	-0.034	32.816	0.003	0.003	0.000	0.000	0.000
58	B	65	ASP	-1	-0.882	-0.943	31.725	0.013	0.013	0.000	0.000	0.000
59	B	66	ASP	-1	-0.835	-0.909	31.853	0.020	0.020	0.000	0.000	0.000
60	B	67	LEU	0	-0.029	-0.016	33.446	0.004	0.004	0.000	0.000	0.000
61	B	68	VAL	0	-0.013	-0.007	27.903	0.006	0.006	0.000	0.000	0.000
62	B	69	ALA	0	-0.006	0.009	28.671	0.007	0.007	0.000	0.000	0.000
63	B	70	GLU	-1	-0.924	-0.955	29.416	0.044	0.044	0.000	0.000	0.000
64	B	71	ILE	0	-0.054	-0.036	30.039	0.006	0.006	0.000	0.000	0.000
65	B	72	THR	0	-0.074	-0.045	24.400	0.009	0.009	0.000	0.000	0.000
66	B	73	PRO	0	-0.033	-0.018	25.298	0.012	0.012	0.000	0.000	0.000
67	B	74	LYS	1	1.014	1.007	26.000	-0.053	-0.053	0.000	0.000	0.000
68	B	75	GLY	0	0.055	0.026	27.548	0.004	0.004	0.000	0.000	0.000
69	B	76	ARG	1	0.926	0.949	19.848	-0.100	-0.100	0.000	0.000	0.000
70	B	77	ALA	0	-0.035	-0.018	23.300	0.014	0.014	0.000	0.000	0.000
71	B	78	LEU	0	0.002	0.010	25.147	0.002	0.002	0.000	0.000	0.000
72	B	79	VAL	0	-0.066	-0.013	22.306	-0.002	-0.002	0.000	0.000	0.000
73	B	80	PRO	0	0.066	0.026	24.302	0.011	0.011	0.000	0.000	0.000
74	B	81	ASP	-1	-0.844	-0.953	22.172	0.183	0.183	0.000	0.000	0.000
75	B	82	SER	0	-0.014	-0.003	22.537	0.015	0.015	0.000	0.000	0.000
76	B	83	VAL	0	0.076	0.028	22.743	0.007	0.007	0.000	0.000	0.000
77	B	84	LYS	1	0.907	0.974	18.812	-0.183	-0.183	0.000	0.000	0.000
78	B	85	LYS	1	0.952	0.984	18.846	-0.164	-0.164	0.000	0.000	0.000
79	B	86	GLU	-1	-0.938	-0.971	19.950	0.129	0.129	0.000	0.000	0.000
80	B	87	LEU	0	0.013	0.001	17.546	0.001	0.001	0.000	0.000	0.000
81	B	88	LEU	0	-0.010	-0.005	13.122	0.011	0.011	0.000	0.000	0.000
82	B	89	GLN	0	-0.011	-0.015	15.969	0.020	0.020	0.000	0.000	0.000
83	B	90	ARG	1	0.955	0.985	18.540	-0.120	-0.120	0.000	0.000	0.000
84	B	91	ILE	0	0.012	0.010	12.843	-0.009	-0.009	0.000	0.000	0.000
85	B	92	ARG	1	0.955	0.972	12.443	-0.436	-0.436	0.000	0.000	0.000
86	B	93	THR	0	0.011	0.013	15.071	-0.020	-0.020	0.000	0.000	0.000
87	B	94	PHE	0	0.016	0.003	15.246	-0.015	-0.015	0.000	0.000	0.000
88	B	95	LEU	0	-0.018	-0.030	10.480	-0.012	-0.012	0.000	0.000	0.000
89	B	96	ALA	0	0.007	0.005	14.568	-0.022	-0.022	0.000	0.000	0.000
90	B	97	GLN	0	-0.034	-0.014	16.715	-0.019	-0.019	0.000	0.000	0.000
91	B	98	HIS	0	-0.063	-0.024	16.967	-0.027	-0.027	0.000	0.000	0.000
92	B	99	ALA	0	-0.052	-0.026	13.818	-0.027	-0.027	0.000	0.000	0.000
93	B	100	NME	0	0.009	0.031	15.097	0.019	0.019	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:ACE )