FMO DATABASE

FMODB ID: 43VQN

Calculation Name: 3VC8-A-Xray372

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: 2023-06-19

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554732.437227
FMO2-HF: Nuclear repulsion	521006.635835
FMO2-HF: Total energy	-33725.801393
FMO2-MP2: Total energy	-33820.609083

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:THR)

Summations of interaction energy for fragment #1(A:1:THR)

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.
-46.876	-48.852	32.471	-17.295	-13.2	-0.095

Interaction energy analysis for fragmet #1(A:1:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.059

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	3	GLU	-1	-0.797	-0.899	3.149	-0.663	2.849	0.156	-1.558	-2.110	0.004
4	A	4	GLU	-1	-0.862	-0.891	1.611	-47.136	-54.074	32.279	-15.321	-10.020	-0.099
5	A	5	MET	0	0.004	0.004	2.994	0.137	1.145	0.027	-0.346	-0.688	0.000
6	A	6	ALA	0	0.003	0.011	5.024	0.514	0.611	-0.001	-0.006	-0.090	0.000
7	A	7	LEU	0	-0.009	-0.002	7.132	0.243	0.243	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.053	-0.017	7.266	0.095	0.095	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.002	-0.014	9.687	0.132	0.132	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.029	-0.014	8.887	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.016	0.035	12.463	0.024	0.024	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.005	0.018	12.370	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.042	0.017	14.121	0.019	0.019	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.935	0.946	15.083	-0.061	-0.061	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.822	-0.892	13.360	0.349	0.349	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.025	-0.009	10.373	0.100	0.100	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.000	-0.002	10.198	0.051	0.051	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.005	-0.009	11.073	0.045	0.045	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.823	0.908	7.730	-0.466	-0.466	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.016	0.013	5.692	0.281	0.281	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.887	0.949	7.168	-0.250	-0.250	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.021	-0.017	9.088	-0.033	-0.033	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.080	-0.029	3.417	-0.253	-0.047	0.011	-0.060	-0.158	0.000
24	A	24	VAL	0	-0.024	-0.007	5.145	-0.005	0.134	-0.001	-0.004	-0.134	0.000
25	A	25	SER	0	0.030	0.023	7.219	-0.129	-0.129	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.796	-0.918	10.435	0.288	0.288	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.025	0.011	13.354	-0.030	-0.030	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.004	0.000	9.099	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.014	0.008	10.577	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.018	-0.012	11.601	-0.051	-0.051	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.860	0.935	12.297	-0.336	-0.336	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.036	-0.053	6.901	-0.182	-0.182	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.013	0.012	13.116	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.096	-0.057	15.878	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.022	-0.009	14.622	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.006	0.000	17.090	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.020	-0.009	18.409	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.903	0.973	17.847	-0.106	-0.106	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.011	-0.059	15.798	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.904	0.979	19.802	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.046	-0.032	21.713	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.022	0.029	21.095	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.007	0.000	23.663	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.002	-0.003	26.002	0.003	0.003	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.930	0.953	23.613	0.075	0.075	0.000	0.000	0.000	0.000
46	A	46	MET	0	0.021	0.014	17.503	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.870	-0.917	17.721	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.058	0.004	14.135	0.026	0.026	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.010	0.001	13.046	0.012	0.012	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.048	0.027	13.303	0.064	0.064	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.051	-0.046	13.009	0.017	0.017	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.957	0.970	9.045	0.234	0.234	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.737	-0.830	10.075	0.305	0.305	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.006	-0.002	11.885	0.008	0.008	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.006	-0.017	10.321	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	56	CYS	0	-0.024	0.012	7.857	-0.042	-0.042	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.004	-0.002	10.241	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.014	-0.016	13.704	0.017	0.017	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.005	0.024	8.082	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.037	0.011	11.757	0.016	0.016	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.928	0.967	12.958	-0.055	-0.055	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.008	0.006	14.344	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.028	-0.005	10.103	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.845	-0.897	14.749	0.147	0.147	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.070	-0.043	17.600	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.035	-0.010	16.729	0.005	0.005	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.013	0.010	17.204	0.016	0.016	0.000	0.000	0.000	0.000
68	A	68	HIS	1	0.792	0.867	19.230	-0.141	-0.141	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.021	-0.016	22.095	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.029	-0.018	23.211	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.080	0.056	22.896	0.011	0.011	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.060	-0.026	22.798	0.005	0.005	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.856	-0.943	18.729	0.055	0.055	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.004	-0.001	17.165	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.026	0.010	15.828	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.055	-0.040	10.658	0.083	0.083	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.025	-0.004	13.823	-0.032	-0.032	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.016	0.016	12.042	0.051	0.051	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.004	0.000	13.616	0.028	0.028	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.015	0.008	16.864	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.010	0.023	16.744	0.007	0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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