FMO DATABASE

FMODB ID: V24V1

Calculation Name: 3VC8-A-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VC8

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6X9

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	83
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-559297.087135
FMO2-HF: Nuclear repulsion	525401.190832
FMO2-HF: Total energy	-33895.896302
FMO2-MP2: Total energy	-33991.259689

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:0:ACE )

Summations of interaction energy for fragment #1(A:0: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.
-3.697	-0.48	1.379	-2.393	-2.204	-0.023

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.003

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	A	2	PHE	0	0.042	0.017	3.865	1.222	1.852	-0.005	-0.292	-0.333	0.000
4	A	3	GLU	-1	-0.806	-0.922	7.050	-0.801	-0.801	0.000	0.000	0.000	0.000
5	A	4	GLU	-1	-0.907	-0.951	2.522	-4.866	-2.400	1.384	-2.085	-1.766	-0.023
6	A	5	MET	0	0.003	0.001	4.237	0.565	0.686	0.000	-0.016	-0.105	0.000
7	A	6	ALA	0	0.009	0.009	6.355	0.136	0.136	0.000	0.000	0.000	0.000
8	A	7	LEU	0	-0.013	0.025	8.840	0.050	0.050	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.056	-0.014	7.316	0.097	0.097	0.000	0.000	0.000	0.000
10	A	9	THR	0	0.019	-0.008	10.218	-0.079	-0.079	0.000	0.000	0.000	0.000
11	A	10	PHE	0	-0.041	-0.020	9.793	0.066	0.066	0.000	0.000	0.000	0.000
12	A	11	MET	0	0.029	0.043	12.620	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	12	ILE	0	0.000	0.015	13.375	0.016	0.016	0.000	0.000	0.000	0.000
14	A	13	THR	0	0.060	0.022	14.579	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	14	LYS	1	1.027	0.988	15.621	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.864	-0.923	12.757	0.163	0.163	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.013	-0.016	10.815	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	17	TYR	0	0.048	0.026	11.022	-0.063	-0.063	0.000	0.000	0.000	0.000
19	A	18	CYS	0	0.003	-0.013	12.982	-0.060	-0.060	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.846	0.932	8.526	-0.231	-0.231	0.000	0.000	0.000	0.000
21	A	20	LEU	0	0.016	0.017	7.420	-0.156	-0.156	0.000	0.000	0.000	0.000
22	A	21	LYS	1	0.931	0.968	9.632	0.108	0.108	0.000	0.000	0.000	0.000
23	A	22	ASN	0	-0.022	-0.017	11.438	-0.036	-0.036	0.000	0.000	0.000	0.000
24	A	23	SER	0	-0.087	-0.028	7.084	-0.112	-0.112	0.000	0.000	0.000	0.000
25	A	24	VAL	0	-0.010	0.002	9.207	-0.177	-0.177	0.000	0.000	0.000	0.000
26	A	25	SER	0	0.015	0.018	11.581	0.118	0.118	0.000	0.000	0.000	0.000
27	A	26	ASP	-1	-0.844	-0.958	15.082	-0.195	-0.195	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.045	0.026	17.876	0.014	0.014	0.000	0.000	0.000	0.000
29	A	28	ALA	0	-0.022	-0.011	14.465	0.016	0.016	0.000	0.000	0.000	0.000
30	A	29	PHE	0	0.008	0.008	14.343	0.009	0.009	0.000	0.000	0.000	0.000
31	A	30	ASN	0	0.073	0.019	16.200	0.031	0.031	0.000	0.000	0.000	0.000
32	A	31	ARG	1	0.886	0.956	17.538	0.266	0.266	0.000	0.000	0.000	0.000
33	A	32	TYR	0	-0.041	-0.026	11.963	0.073	0.073	0.000	0.000	0.000	0.000
34	A	33	LEU	0	0.024	0.014	17.738	0.027	0.027	0.000	0.000	0.000	0.000
35	A	34	SER	0	-0.111	-0.070	19.904	0.022	0.022	0.000	0.000	0.000	0.000
36	A	35	LEU	0	-0.023	-0.008	19.148	0.014	0.014	0.000	0.000	0.000	0.000
37	A	36	TYR	0	0.020	0.010	20.171	0.013	0.013	0.000	0.000	0.000	0.000
38	A	37	ASN	0	0.017	-0.010	21.905	0.015	0.015	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.960	0.991	23.252	0.125	0.125	0.000	0.000	0.000	0.000
40	A	39	TYR	0	-0.043	-0.065	20.143	0.013	0.013	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.898	0.977	23.165	0.043	0.043	0.000	0.000	0.000	0.000
42	A	41	TYR	0	-0.047	-0.031	24.446	0.012	0.012	0.000	0.000	0.000	0.000
43	A	42	PHE	0	0.007	0.023	24.934	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.005	-0.002	27.001	0.008	0.008	0.000	0.000	0.000	0.000
45	A	44	GLY	0	0.001	-0.002	29.289	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	45	LYS	1	0.933	0.952	26.284	0.031	0.031	0.000	0.000	0.000	0.000
47	A	46	MET	0	0.022	0.014	19.893	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	47	ASP	-1	-0.884	-0.921	21.617	-0.092	-0.092	0.000	0.000	0.000	0.000
49	A	48	THR	0	0.056	0.005	16.426	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	49	ALA	0	-0.010	-0.002	16.383	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.066	0.037	16.982	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	51	TYR	0	-0.059	-0.068	14.600	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	52	ARG	1	0.961	0.971	12.271	0.206	0.206	0.000	0.000	0.000	0.000
54	A	53	GLU	-1	-0.782	-0.862	13.590	-0.249	-0.249	0.000	0.000	0.000	0.000
55	A	54	ALA	0	0.003	-0.001	15.795	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	55	ALA	0	-0.017	-0.018	13.050	0.014	0.014	0.000	0.000	0.000	0.000
57	A	56	CYS	0	-0.015	0.011	12.059	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	57	SER	0	-0.012	-0.002	13.512	0.005	0.005	0.000	0.000	0.000	0.000
59	A	58	GLN	0	-0.034	-0.024	16.100	0.012	0.012	0.000	0.000	0.000	0.000
60	A	59	LEU	0	-0.002	0.023	9.864	0.024	0.024	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.033	0.007	14.197	0.011	0.011	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.934	0.977	15.801	0.093	0.093	0.000	0.000	0.000	0.000
63	A	62	ALA	0	0.003	0.001	15.945	0.014	0.014	0.000	0.000	0.000	0.000
64	A	63	MET	0	-0.039	-0.009	13.082	0.000	0.000	0.000	0.000	0.000	0.000
65	A	64	GLU	-1	-0.860	-0.906	16.723	-0.091	-0.091	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.057	-0.027	20.071	0.011	0.011	0.000	0.000	0.000	0.000
67	A	66	PHE	0	-0.065	-0.027	18.310	0.008	0.008	0.000	0.000	0.000	0.000
68	A	67	ASN	0	-0.019	-0.008	19.433	0.012	0.012	0.000	0.000	0.000	0.000
69	A	68	HIS	0	-0.094	-0.070	21.268	0.006	0.006	0.000	0.000	0.000	0.000
70	A	69	ASN	0	-0.035	-0.022	24.056	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	70	ASN	0	-0.058	-0.048	24.809	0.013	0.013	0.000	0.000	0.000	0.000
72	A	71	GLY	0	0.051	0.046	24.196	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	72	ASN	0	-0.071	-0.032	23.361	0.008	0.008	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.889	-0.950	19.123	0.053	0.053	0.000	0.000	0.000	0.000
75	A	74	VAL	0	-0.007	-0.006	17.988	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	75	LEU	0	0.010	-0.004	15.879	0.008	0.008	0.000	0.000	0.000	0.000
77	A	76	TYR	0	-0.074	-0.077	11.794	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	77	GLN	0	0.017	-0.011	14.571	0.035	0.035	0.000	0.000	0.000	0.000
79	A	78	PRO	0	-0.034	0.007	13.272	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	79	PRO	0	0.005	0.009	15.149	0.007	0.007	0.000	0.000	0.000	0.000
81	A	80	THR	0	0.019	0.010	18.311	0.011	0.011	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.019	0.035	17.695	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	82	NME	0	-0.020	0.001	19.425	0.010	0.010	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )