FMO DATABASE

FMODB ID: 828ZY

Calculation Name: 3VH5-D-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VH5

Chain ID: D

ChEMBL ID:

UniProt ID: E1BSW7

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	76
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-427467.868081
FMO2-HF: Nuclear repulsion	397792.525684
FMO2-HF: Total energy	-29675.342397
FMO2-MP2: Total energy	-29763.632491

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(D:5:ACE )

Summations of interaction energy for fragment #1(D:5: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.
2.145	3.077	-0.006	-0.435	-0.491	-0.001

Interaction energy analysis for fragmet #1(D:5:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / 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

Sort

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	D	7	GLY	0	-0.027	-0.010	3.805	0.859	1.791	-0.006	-0.435	-0.491	-0.001
4	D	8	PHE	0	0.016	0.023	6.594	0.016	0.016	0.000	0.000	0.000	0.000
5	D	9	ARG	1	0.985	0.989	9.267	0.215	0.215	0.000	0.000	0.000	0.000
6	D	10	LYS	1	1.015	0.992	11.495	0.281	0.281	0.000	0.000	0.000	0.000
7	D	11	GLU	-1	-0.860	-0.919	15.185	-0.082	-0.082	0.000	0.000	0.000	0.000
8	D	12	THR	0	-0.027	-0.015	12.194	0.011	0.011	0.000	0.000	0.000	0.000
9	D	13	VAL	0	0.030	0.018	13.331	0.035	0.035	0.000	0.000	0.000	0.000
10	D	14	GLU	-1	-0.884	-0.954	15.774	-0.071	-0.071	0.000	0.000	0.000	0.000
11	D	15	ARG	1	0.896	0.941	18.394	0.074	0.074	0.000	0.000	0.000	0.000
12	D	16	LEU	0	0.013	0.014	15.057	0.013	0.013	0.000	0.000	0.000	0.000
13	D	17	LEU	0	0.002	-0.006	18.755	0.011	0.011	0.000	0.000	0.000	0.000
14	D	18	ARG	1	0.868	0.923	21.198	0.058	0.058	0.000	0.000	0.000	0.000
15	D	19	LEU	0	-0.043	-0.004	21.008	0.004	0.004	0.000	0.000	0.000	0.000
16	D	20	HIS	0	0.001	-0.004	20.543	0.012	0.012	0.000	0.000	0.000	0.000
17	D	21	PHE	0	-0.037	0.004	24.034	0.000	0.000	0.000	0.000	0.000	0.000
18	D	22	ARG	1	1.005	0.995	27.679	-0.002	-0.002	0.000	0.000	0.000	0.000
19	D	23	ASP	-1	-0.838	-0.923	30.813	-0.019	-0.019	0.000	0.000	0.000	0.000
20	D	24	GLY	0	0.055	0.034	31.034	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	25	ARG	1	0.892	0.940	31.351	0.019	0.019	0.000	0.000	0.000	0.000
22	D	26	THR	0	-0.024	0.005	27.649	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	27	ARG	1	0.841	0.906	26.820	0.044	0.044	0.000	0.000	0.000	0.000
24	D	28	VAL	0	0.044	0.027	21.507	0.004	0.004	0.000	0.000	0.000	0.000
25	D	29	ASN	0	0.018	0.023	23.873	-0.013	-0.013	0.000	0.000	0.000	0.000
26	D	30	GLY	0	0.054	-0.003	21.230	-0.005	-0.005	0.000	0.000	0.000	0.000
27	D	31	ASP	-1	-0.842	-0.920	19.977	-0.157	-0.157	0.000	0.000	0.000	0.000
28	D	32	ALA	0	0.018	0.005	20.099	-0.009	-0.009	0.000	0.000	0.000	0.000
29	D	33	LEU	0	-0.013	-0.005	17.887	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	34	LEU	0	-0.024	-0.016	15.229	-0.018	-0.018	0.000	0.000	0.000	0.000
31	D	35	LEU	0	0.019	0.015	15.382	-0.018	-0.018	0.000	0.000	0.000	0.000
32	D	36	MET	0	0.032	0.014	16.402	0.006	0.006	0.000	0.000	0.000	0.000
33	D	37	ALA	0	-0.033	-0.010	12.045	0.019	0.019	0.000	0.000	0.000	0.000
34	D	38	GLU	-1	-0.928	-0.972	11.769	-0.372	-0.372	0.000	0.000	0.000	0.000
35	D	39	LEU	0	0.013	0.017	12.770	0.034	0.034	0.000	0.000	0.000	0.000
36	D	40	LEU	0	0.023	-0.001	12.512	0.037	0.037	0.000	0.000	0.000	0.000
37	D	41	LYS	1	0.912	0.958	6.374	0.777	0.777	0.000	0.000	0.000	0.000
38	D	42	VAL	0	-0.015	-0.008	9.809	0.102	0.102	0.000	0.000	0.000	0.000
39	D	43	PHE	0	0.028	0.031	12.198	0.055	0.055	0.000	0.000	0.000	0.000
40	D	44	VAL	0	0.005	-0.007	8.289	0.049	0.049	0.000	0.000	0.000	0.000
41	D	45	ARG	1	0.888	0.936	6.278	-0.207	-0.207	0.000	0.000	0.000	0.000
42	D	46	GLU	-1	-0.858	-0.918	9.872	0.135	0.135	0.000	0.000	0.000	0.000
43	D	47	ALA	0	0.020	0.004	13.207	0.003	0.003	0.000	0.000	0.000	0.000
44	D	48	ALA	0	-0.016	-0.007	10.173	0.004	0.004	0.000	0.000	0.000	0.000
45	D	49	ALA	0	-0.020	-0.009	12.154	-0.014	-0.014	0.000	0.000	0.000	0.000
46	D	50	ARG	1	0.796	0.895	13.570	-0.139	-0.139	0.000	0.000	0.000	0.000
47	D	51	ALA	0	0.045	0.030	15.369	-0.018	-0.018	0.000	0.000	0.000	0.000
48	D	52	ALA	0	0.020	0.005	13.866	-0.014	-0.014	0.000	0.000	0.000	0.000
49	D	53	ARG	1	0.958	0.972	15.986	-0.179	-0.179	0.000	0.000	0.000	0.000
50	D	54	GLN	0	-0.015	0.001	18.823	-0.022	-0.022	0.000	0.000	0.000	0.000
51	D	55	ALA	0	0.038	0.014	18.685	-0.014	-0.014	0.000	0.000	0.000	0.000
52	D	56	GLN	0	-0.026	-0.014	17.898	-0.013	-0.013	0.000	0.000	0.000	0.000
53	D	57	ALA	0	-0.066	-0.020	21.220	-0.014	-0.014	0.000	0.000	0.000	0.000
54	D	58	GLU	-1	-0.935	-0.977	23.830	0.123	0.123	0.000	0.000	0.000	0.000
55	D	59	ASP	-1	-0.979	-0.983	24.448	0.115	0.115	0.000	0.000	0.000	0.000
56	D	60	LEU	0	-0.045	-0.008	21.941	0.003	0.003	0.000	0.000	0.000	0.000
57	D	61	GLU	-1	-0.962	-0.992	18.575	0.211	0.211	0.000	0.000	0.000	0.000
58	D	62	LYS	1	0.820	0.917	17.266	-0.202	-0.202	0.000	0.000	0.000	0.000
59	D	63	VAL	0	-0.010	-0.005	14.835	-0.017	-0.017	0.000	0.000	0.000	0.000
60	D	64	ASP	-1	-0.865	-0.948	16.990	0.260	0.260	0.000	0.000	0.000	0.000
61	D	65	ILE	0	-0.052	-0.032	19.075	0.006	0.006	0.000	0.000	0.000	0.000
62	D	66	GLU	-1	-0.820	-0.917	20.015	0.157	0.157	0.000	0.000	0.000	0.000
63	D	67	HIS	0	0.036	0.035	19.069	0.009	0.009	0.000	0.000	0.000	0.000
64	D	68	VAL	0	-0.030	-0.022	16.249	-0.004	-0.004	0.000	0.000	0.000	0.000
65	D	69	GLU	-1	-0.923	-0.969	18.953	0.131	0.131	0.000	0.000	0.000	0.000
66	D	70	LYS	1	0.872	0.951	22.367	-0.130	-0.130	0.000	0.000	0.000	0.000
67	D	71	VAL	0	-0.075	-0.052	18.202	-0.015	-0.015	0.000	0.000	0.000	0.000
68	D	72	LEU	0	-0.003	0.011	19.511	-0.009	-0.009	0.000	0.000	0.000	0.000
69	D	73	PRO	0	0.000	0.003	21.283	-0.010	-0.010	0.000	0.000	0.000	0.000
70	D	74	GLN	0	-0.032	-0.033	23.373	-0.008	-0.008	0.000	0.000	0.000	0.000
71	D	75	LEU	0	-0.027	-0.005	16.573	-0.004	-0.004	0.000	0.000	0.000	0.000
72	D	76	LEU	0	-0.041	-0.045	20.263	-0.009	-0.009	0.000	0.000	0.000	0.000
73	D	77	LEU	0	-0.044	-0.008	22.325	-0.010	-0.010	0.000	0.000	0.000	0.000
74	D	78	ASP	-1	-0.830	-0.893	21.955	0.062	0.062	0.000	0.000	0.000	0.000
75	D	79	PHE	0	-0.133	-0.056	16.285	-0.007	-0.007	0.000	0.000	0.000	0.000
76	D	80	VAL	-1	-0.915	-0.961	20.525	0.025	0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:5:ACE )