FMO DATABASE

FMODB ID: VRYK1

Calculation Name: 3D3R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D3R

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EF93

Base Structure: X-ray

Registration Date: 2023-03-14

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455099.334272
FMO2-HF: Nuclear repulsion	421801.551603
FMO2-HF: Total energy	-33297.782669
FMO2-MP2: Total energy	-33393.061184

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:-6:GLU)

Summations of interaction energy for fragment #1(A:-6:GLU)

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.
42.729	46.998	0.195	-1.761	-2.703	0.003

Interaction energy analysis for fragmet #1(A:-6:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.940 / q_NPA : -0.979

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	-4	LEU	0	-0.003	0.010	2.886	-8.772	-5.676	0.063	-1.355	-1.804	0.002
4	A	-3	TYR	0	-0.055	-0.016	2.918	-6.326	-5.188	0.133	-0.403	-0.868	0.001
5	A	-2	PHE	0	0.013	0.014	5.380	2.092	2.127	-0.001	-0.003	-0.031	0.000
6	A	-1	GLN	0	0.065	0.013	7.833	0.396	0.396	0.000	0.000	0.000	0.000
7	A	0	GLY	0	0.009	0.003	6.990	0.183	0.183	0.000	0.000	0.000	0.000
8	A	1	MET	0	-0.051	-0.026	8.065	-0.289	-0.289	0.000	0.000	0.000	0.000
9	A	2	CYS	0	-0.008	-0.007	9.293	-2.236	-2.236	0.000	0.000	0.000	0.000
10	A	3	LEU	0	0.004	0.009	7.209	1.798	1.798	0.000	0.000	0.000	0.000
11	A	4	SER	0	-0.055	-0.059	8.132	-2.461	-2.461	0.000	0.000	0.000	0.000
12	A	5	ILE	0	-0.007	0.000	9.936	-0.380	-0.380	0.000	0.000	0.000	0.000
13	A	6	PRO	0	0.006	0.001	11.776	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	7	SER	0	-0.044	-0.015	13.591	-1.382	-1.382	0.000	0.000	0.000	0.000
15	A	8	GLN	0	0.023	0.036	16.555	0.353	0.353	0.000	0.000	0.000	0.000
16	A	9	VAL	0	0.044	0.023	18.416	-0.259	-0.259	0.000	0.000	0.000	0.000
17	A	10	VAL	0	-0.061	-0.052	20.928	-0.567	-0.567	0.000	0.000	0.000	0.000
18	A	11	ALA	0	0.003	-0.003	23.912	-0.606	-0.606	0.000	0.000	0.000	0.000
19	A	12	VAL	0	0.005	0.008	22.403	0.584	0.584	0.000	0.000	0.000	0.000
20	A	13	ASP	-1	-0.859	-0.920	24.542	10.379	10.379	0.000	0.000	0.000	0.000
21	A	14	ASN	0	0.040	-0.009	23.454	0.675	0.675	0.000	0.000	0.000	0.000
22	A	15	GLU	-1	-0.979	-0.973	25.571	9.901	9.901	0.000	0.000	0.000	0.000
23	A	16	ARG	1	0.864	0.926	27.116	-10.014	-10.014	0.000	0.000	0.000	0.000
24	A	17	GLN	0	-0.037	-0.001	21.868	0.754	0.754	0.000	0.000	0.000	0.000
25	A	18	SER	0	-0.013	0.002	21.579	0.328	0.328	0.000	0.000	0.000	0.000
26	A	19	VAL	0	0.027	0.011	18.330	-0.179	-0.179	0.000	0.000	0.000	0.000
27	A	20	THR	0	-0.033	-0.031	21.417	0.085	0.085	0.000	0.000	0.000	0.000
28	A	21	VAL	0	-0.010	-0.008	17.389	0.088	0.088	0.000	0.000	0.000	0.000
29	A	22	ASP	-1	-0.836	-0.901	20.587	11.811	11.811	0.000	0.000	0.000	0.000
30	A	23	THR	0	-0.008	-0.024	16.526	0.388	0.388	0.000	0.000	0.000	0.000
31	A	24	LEU	0	-0.025	-0.020	18.007	-0.392	-0.392	0.000	0.000	0.000	0.000
32	A	25	GLY	0	0.042	0.028	20.837	-0.432	-0.432	0.000	0.000	0.000	0.000
33	A	26	VAL	0	-0.072	-0.029	22.242	-0.446	-0.446	0.000	0.000	0.000	0.000
34	A	27	ARG	1	0.840	0.908	22.224	-10.817	-10.817	0.000	0.000	0.000	0.000
35	A	28	ARG	1	0.934	0.958	19.260	-14.626	-14.626	0.000	0.000	0.000	0.000
36	A	29	ASP	-1	-0.816	-0.861	21.688	12.107	12.107	0.000	0.000	0.000	0.000
37	A	30	VAL	0	-0.058	-0.043	17.085	0.149	0.149	0.000	0.000	0.000	0.000
38	A	31	SER	0	0.027	0.012	18.872	-0.175	-0.175	0.000	0.000	0.000	0.000
39	A	32	SER	0	0.030	-0.007	17.542	0.600	0.600	0.000	0.000	0.000	0.000
40	A	33	HIS	0	-0.040	-0.027	17.666	0.131	0.131	0.000	0.000	0.000	0.000
41	A	34	LEU	0	-0.021	-0.002	12.044	0.244	0.244	0.000	0.000	0.000	0.000
42	A	35	MET	0	-0.033	0.002	12.478	1.538	1.538	0.000	0.000	0.000	0.000
43	A	36	THR	0	0.001	-0.008	9.568	-0.152	-0.152	0.000	0.000	0.000	0.000
44	A	37	GLU	-1	-0.965	-0.975	13.016	20.416	20.416	0.000	0.000	0.000	0.000
45	A	38	PRO	0	-0.065	-0.042	16.051	-0.139	-0.139	0.000	0.000	0.000	0.000
46	A	39	LEU	0	0.038	0.030	15.624	0.137	0.137	0.000	0.000	0.000	0.000
47	A	40	ALA	0	-0.025	-0.024	19.694	-0.820	-0.820	0.000	0.000	0.000	0.000
48	A	41	ILE	0	-0.038	-0.033	21.766	0.367	0.367	0.000	0.000	0.000	0.000
49	A	42	GLY	0	-0.038	-0.019	22.960	-0.267	-0.267	0.000	0.000	0.000	0.000
50	A	43	ASP	-1	-0.811	-0.878	17.829	15.281	15.281	0.000	0.000	0.000	0.000
51	A	44	TYR	0	-0.082	-0.060	15.454	-0.263	-0.263	0.000	0.000	0.000	0.000
52	A	45	VAL	0	0.011	0.008	13.252	0.835	0.835	0.000	0.000	0.000	0.000
53	A	46	LEU	0	-0.017	-0.009	7.099	-0.822	-0.822	0.000	0.000	0.000	0.000
54	A	47	ILE	0	0.017	0.010	10.362	0.725	0.725	0.000	0.000	0.000	0.000
55	A	48	HIS	0	0.060	0.045	5.152	-2.369	-2.369	0.000	0.000	0.000	0.000
56	A	49	ILE	0	-0.041	-0.001	8.497	-1.252	-1.252	0.000	0.000	0.000	0.000
57	A	50	GLY	0	0.027	0.003	8.134	3.155	3.155	0.000	0.000	0.000	0.000
58	A	51	PHE	0	-0.060	-0.030	9.056	-2.722	-2.722	0.000	0.000	0.000	0.000
59	A	52	VAL	0	0.051	0.034	10.255	2.401	2.401	0.000	0.000	0.000	0.000
60	A	53	MET	0	-0.029	-0.022	11.403	-1.370	-1.370	0.000	0.000	0.000	0.000
61	A	54	ASN	0	0.025	0.023	15.014	0.195	0.195	0.000	0.000	0.000	0.000
62	A	55	LYS	1	0.927	0.964	18.552	-13.033	-13.033	0.000	0.000	0.000	0.000
63	A	56	ILE	0	0.064	0.026	21.276	-0.292	-0.292	0.000	0.000	0.000	0.000
64	A	57	ASP	-1	-0.865	-0.939	24.437	10.793	10.793	0.000	0.000	0.000	0.000
65	A	58	ARG	1	0.975	0.993	27.483	-11.134	-11.134	0.000	0.000	0.000	0.000
66	A	59	ASN	0	-0.021	-0.031	28.364	-0.171	-0.171	0.000	0.000	0.000	0.000
67	A	60	ASP	-1	-0.854	-0.903	29.363	10.072	10.072	0.000	0.000	0.000	0.000
68	A	61	ALA	0	-0.020	-0.011	26.292	0.018	0.018	0.000	0.000	0.000	0.000
69	A	62	LEU	0	-0.049	-0.039	28.070	-0.051	-0.051	0.000	0.000	0.000	0.000
70	A	63	GLN	0	-0.019	-0.011	30.689	-0.400	-0.400	0.000	0.000	0.000	0.000
71	A	64	SER	0	-0.025	-0.017	29.061	0.007	0.007	0.000	0.000	0.000	0.000
72	A	65	LEU	0	-0.023	-0.022	25.796	0.038	0.038	0.000	0.000	0.000	0.000
73	A	66	GLU	-1	-0.931	-0.957	29.821	9.020	9.020	0.000	0.000	0.000	0.000
74	A	67	LEU	0	0.043	0.022	32.232	-0.081	-0.081	0.000	0.000	0.000	0.000
75	A	68	TYR	0	-0.034	-0.024	25.748	0.140	0.140	0.000	0.000	0.000	0.000
76	A	69	GLN	0	0.026	0.006	29.349	0.173	0.173	0.000	0.000	0.000	0.000
77	A	70	GLU	-1	-0.924	-0.943	30.866	8.588	8.588	0.000	0.000	0.000	0.000
78	A	71	ILE	0	-0.047	-0.023	29.630	-0.162	-0.162	0.000	0.000	0.000	0.000
79	A	72	VAL	0	-0.014	-0.011	27.279	-0.071	-0.071	0.000	0.000	0.000	0.000
80	A	73	SER	0	-0.034	-0.026	30.234	-0.136	-0.136	0.000	0.000	0.000	0.000
81	A	74	LYS	1	0.860	0.935	33.620	-8.672	-8.672	0.000	0.000	0.000	0.000
82	A	75	LEU	0	-0.079	-0.055	30.282	-0.224	-0.224	0.000	0.000	0.000	0.000
83	A	76	GLU	-1	-0.975	-0.945	29.390	10.750	10.750	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-6:GLU)