FMO DATABASE

FMODB ID: 53ZLZ

Calculation Name: 3VP8-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VP8

Chain ID: A

ChEMBL ID:

UniProt ID: P16649

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	77
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-366491.850551
FMO2-HF: Nuclear repulsion	334089.724487
FMO2-HF: Total energy	-32402.126064
FMO2-MP2: Total energy	-32495.556532

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:3:ACE )

Summations of interaction energy for fragment #1(A:3: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.
1.248	3.168	0.036	-0.747	-1.207	-0.001

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.012

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	5	VAL	0	0.084	0.045	3.803	0.597	1.609	-0.007	-0.446	-0.559	0.000
4	A	6	SER	0	0.046	0.014	3.378	-0.281	-0.056	0.015	-0.073	-0.166	0.000
5	A	7	ASN	0	0.012	0.026	3.737	-0.103	0.522	0.028	-0.224	-0.429	-0.001
6	A	8	THR	0	-0.044	-0.041	5.329	0.284	0.342	0.000	-0.004	-0.053	0.000
7	A	9	GLN	0	-0.008	-0.008	7.770	0.088	0.088	0.000	0.000	0.000	0.000
8	A	10	ASN	0	0.015	0.005	7.185	0.111	0.111	0.000	0.000	0.000	0.000
9	A	11	LYS	1	0.994	0.996	9.466	0.650	0.650	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.036	-0.010	11.645	0.041	0.041	0.000	0.000	0.000	0.000
11	A	13	ASN	0	0.030	0.004	12.555	0.008	0.008	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.918	-0.954	13.636	-0.133	-0.133	0.000	0.000	0.000	0.000
13	A	15	LEU	0	-0.019	-0.008	15.461	0.011	0.011	0.000	0.000	0.000	0.000
14	A	16	LEU	0	-0.020	-0.017	16.891	0.013	0.013	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.940	-0.963	18.498	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	18	ALA	0	0.029	0.011	19.702	0.005	0.005	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.038	0.022	21.562	0.007	0.007	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.872	0.938	22.283	0.012	0.012	0.000	0.000	0.000	0.000
19	A	21	GLN	0	-0.003	-0.004	23.482	0.009	0.009	0.000	0.000	0.000	0.000
20	A	22	GLU	-1	-0.911	-0.951	24.541	-0.066	-0.066	0.000	0.000	0.000	0.000
21	A	23	PHE	0	-0.025	-0.024	26.727	0.002	0.002	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.029	-0.015	28.353	0.004	0.004	0.000	0.000	0.000	0.000
23	A	25	GLN	0	0.012	0.014	30.114	0.005	0.005	0.000	0.000	0.000	0.000
24	A	26	VAL	0	0.013	0.013	31.872	0.001	0.001	0.000	0.000	0.000	0.000
25	A	27	SER	0	-0.020	-0.012	33.855	0.002	0.002	0.000	0.000	0.000	0.000
26	A	28	GLN	0	-0.054	-0.027	32.727	0.002	0.002	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.880	-0.957	34.526	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	30	ALA	0	0.003	0.019	37.822	0.000	0.000	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.023	-0.018	39.317	0.000	0.000	0.000	0.000	0.000	0.000
30	A	32	THR	0	-0.003	-0.001	39.737	0.001	0.001	0.000	0.000	0.000	0.000
31	A	33	TYR	0	0.038	0.013	38.932	0.001	0.001	0.000	0.000	0.000	0.000
32	A	34	ARG	1	0.942	0.987	43.587	0.010	0.010	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.025	-0.013	44.689	0.001	0.001	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.043	-0.023	43.720	0.000	0.000	0.000	0.000	0.000	0.000
35	A	37	ASN	0	-0.013	-0.008	47.608	0.001	0.001	0.000	0.000	0.000	0.000
36	A	38	GLN	0	0.017	0.013	49.513	0.000	0.000	0.000	0.000	0.000	0.000
37	A	39	LYS	1	0.975	0.983	50.653	0.009	0.009	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.927	-0.957	51.648	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	41	TYR	0	0.018	0.002	53.522	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.871	-0.950	55.468	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	43	PHE	0	-0.087	-0.030	56.519	0.000	0.000	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.939	0.966	55.370	0.013	0.013	0.000	0.000	0.000	0.000
43	A	45	MET	0	0.022	0.027	59.611	0.000	0.000	0.000	0.000	0.000	0.000
44	A	46	ASN	0	0.003	-0.018	60.142	0.001	0.001	0.000	0.000	0.000	0.000
45	A	47	GLN	0	-0.006	0.009	62.245	0.001	0.001	0.000	0.000	0.000	0.000
46	A	48	GLN	0	0.021	0.004	63.440	0.000	0.000	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.025	-0.010	64.678	0.000	0.000	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.029	-0.010	66.801	0.000	0.000	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.908	-0.958	66.949	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	52	MET	0	-0.010	-0.011	69.498	0.000	0.000	0.000	0.000	0.000	0.000
51	A	53	GLN	0	-0.092	-0.035	70.999	0.001	0.001	0.000	0.000	0.000	0.000
52	A	54	GLN	0	0.025	0.011	72.544	0.000	0.000	0.000	0.000	0.000	0.000
53	A	55	ILE	0	0.020	0.017	73.149	0.000	0.000	0.000	0.000	0.000	0.000
54	A	56	ARG	1	0.963	0.981	73.894	0.005	0.005	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.006	-0.017	76.235	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	THR	0	0.008	0.007	78.154	0.000	0.000	0.000	0.000	0.000	0.000
57	A	59	VAL	0	-0.001	0.007	80.157	0.000	0.000	0.000	0.000	0.000	0.000
58	A	60	TYR	0	-0.001	-0.009	80.872	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.910	-0.946	83.127	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.032	-0.009	83.488	0.000	0.000	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.945	-0.972	86.437	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.022	-0.009	87.802	0.000	0.000	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.067	-0.057	88.134	0.000	0.000	0.000	0.000	0.000	0.000
64	A	66	HIS	0	0.022	0.009	89.237	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.819	0.917	92.436	0.003	0.003	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.984	0.996	91.067	0.004	0.004	0.000	0.000	0.000	0.000
67	A	69	MET	0	-0.003	0.016	93.965	0.000	0.000	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.929	0.959	96.643	0.004	0.004	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.811	-0.913	97.943	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	72	ALA	0	-0.003	-0.001	99.197	0.000	0.000	0.000	0.000	0.000	0.000
71	A	73	TYR	0	-0.003	-0.012	99.240	0.000	0.000	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.972	-0.987	102.260	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	75	GLU	-1	-0.973	-0.995	103.859	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-1.035	-1.005	104.513	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.055	-0.027	106.394	0.000	0.000	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.889	0.965	108.445	0.002	0.002	0.000	0.000	0.000	0.000
77	A	79	NME	0	-0.012	-0.003	109.791	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )