FMO DATABASE

FMODB ID: K3LK3

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	OptH
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	-554277.749347
FMO2-HF: Nuclear repulsion	520552.344462
FMO2-HF: Total energy	-33725.404884
FMO2-MP2: Total energy	-33820.221486

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.
-36.722	-23.344	8.225	-9.895	-11.707	-0.043

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 : 0.027 / q_NPA : -0.006

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	3	GLU	-1	-0.809	-0.925	2.987	-0.440	3.412	0.387	-1.767	-2.472	0.001
4	A	4	GLU	-1	-0.912	-0.950	2.049	-35.555	-27.491	7.807	-7.698	-8.173	-0.044
5	A	5	MET	0	0.007	0.003	3.090	-0.800	0.226	0.023	-0.362	-0.687	0.000
6	A	6	ALA	0	0.009	0.007	5.016	0.144	0.241	-0.001	-0.006	-0.089	0.000
7	A	7	LEU	0	-0.017	0.024	7.203	0.011	0.011	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.050	-0.011	6.850	0.020	0.020	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.019	-0.008	9.666	0.085	0.085	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.037	-0.018	8.720	0.020	0.020	0.000	0.000	0.000	0.000
11	A	11	MET	0	0.030	0.043	12.487	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.003	0.013	12.551	0.055	0.055	0.000	0.000	0.000	0.000
13	A	13	THR	0	0.061	0.023	14.196	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	LYS	1	1.022	0.984	15.147	-0.186	-0.186	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.859	-0.921	13.160	0.555	0.555	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.006	-0.011	10.552	0.109	0.109	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.037	0.021	10.232	0.096	0.096	0.000	0.000	0.000	0.000
18	A	18	CYS	0	0.002	-0.014	11.094	0.039	0.039	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.853	0.936	7.913	-0.820	-0.820	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.018	0.019	5.913	0.311	0.311	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.920	0.961	7.171	-0.380	-0.380	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.019	-0.016	9.011	-0.108	-0.108	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.086	-0.027	3.436	-0.253	-0.048	0.010	-0.058	-0.157	0.000
24	A	24	VAL	0	-0.008	0.004	5.116	-0.211	-0.077	-0.001	-0.004	-0.129	0.000
25	A	25	SER	0	0.020	0.021	7.253	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.851	-0.962	10.463	0.282	0.282	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.048	0.026	13.389	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.017	-0.008	9.074	-0.026	-0.026	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.006	0.007	10.815	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.057	0.012	11.641	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.893	0.960	12.460	-0.176	-0.176	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.039	-0.023	6.760	-0.158	-0.158	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.017	0.008	13.153	-0.035	-0.035	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.112	-0.071	15.919	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.016	-0.004	14.336	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	36	TYR	0	0.019	0.010	17.389	-0.018	-0.018	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.014	-0.010	18.446	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.962	0.991	18.906	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.040	-0.063	15.887	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.897	0.976	19.626	-0.052	-0.052	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.045	-0.030	21.523	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	PHE	0	0.006	0.023	21.330	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.005	-0.002	23.491	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.004	0.000	25.845	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.933	0.953	23.416	0.104	0.104	0.000	0.000	0.000	0.000
46	A	46	MET	0	0.022	0.014	16.435	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.882	-0.919	18.138	-0.132	-0.132	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.057	0.006	13.859	0.017	0.017	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.012	-0.004	12.966	0.010	0.010	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.067	0.038	13.191	0.050	0.050	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.050	-0.065	12.691	0.033	0.033	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.962	0.972	8.924	0.529	0.529	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.787	-0.864	9.907	0.222	0.222	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.006	0.000	11.737	0.036	0.036	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.016	-0.017	10.066	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	CYS	0	-0.016	0.011	7.951	0.105	0.105	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.011	-0.002	10.085	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.029	-0.021	13.741	0.002	0.002	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.004	0.023	8.080	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.036	0.008	11.838	0.011	0.011	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.934	0.975	13.003	-0.135	-0.135	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.006	0.004	14.339	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.030	-0.004	10.244	0.008	0.008	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.847	-0.895	14.760	0.194	0.194	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.054	-0.028	17.603	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.053	-0.018	16.841	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.003	-0.001	17.237	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	HIS	1	0.779	0.854	19.243	-0.200	-0.200	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.006	-0.006	22.102	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.044	-0.038	23.216	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.047	0.044	22.917	0.013	0.013	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.062	-0.026	22.763	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.887	-0.949	18.830	0.206	0.206	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.009	-0.006	16.999	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.013	-0.001	15.554	0.018	0.018	0.000	0.000	0.000	0.000
76	A	76	TYR	0	-0.079	-0.082	10.474	0.028	0.028	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.019	-0.009	13.829	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.031	0.008	11.970	0.034	0.034	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.005	0.005	13.389	0.003	0.003	0.000	0.000	0.000	0.000
80	A	80	THR	0	0.008	0.010	16.664	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.018	0.040	16.743	-0.009	-0.009	0.000	0.000	0.000	0.000

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